Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 72 of 144
Found at i:21724110 original size:7 final size:7
Alignment explanation
Indices: 21724098--21724122 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21724088 AGTCGATTAA
21724098 TATTTAG
1 TATTTAG
21724105 TATTTAG
1 TATTTAG
21724112 TATTTAG
1 TATTTAG
21724119 TATT
1 TATT
21724123 ATTATGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:21724804 original size:18 final size:18
Alignment explanation
Indices: 21724781--21724816 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21724771 CCGTTTCCTA
21724781 ACCCTTATATGTACCCTT
1 ACCCTTATATGTACCCTT
*
21724799 ACCCTTATATGTATCCTT
1 ACCCTTATATGTACCCTT
21724817 TTCCGAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.31, G:0.06, T:0.42
Consensus pattern (18 bp):
ACCCTTATATGTACCCTT
Found at i:21725274 original size:44 final size:44
Alignment explanation
Indices: 21725221--21725310 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 44
21725211 TTATTTGTAC
*
21725221 AAATATTTTGA-ATATTTTGATATTATTTTTATGTAAAAAAATAG
1 AAATATTTTGAGATATTTTGATATTA-TTTCATGTAAAAAAATAG
* * *
21725265 AAATTTTTTGAGTTATTTTGATATTATTTCATGTAATAAAATAG
1 AAATATTTTGAGATATTTTGATATTATTTCATGTAAAAAAATAG
21725309 AA
1 AA
21725311 GTTTATTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 28 0.68
45 13 0.32
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (44 bp):
AAATATTTTGAGATATTTTGATATTATTTCATGTAAAAAAATAG
Found at i:21725364 original size:29 final size:29
Alignment explanation
Indices: 21725318--21726427 Score: 1227
Period size: 29 Copynumber: 37.7 Consensus size: 29
21725308 GAAGTTTATT
*
21725318 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
21725347 CCTAACCCTAACCTAATTCAATTAAAACC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21725376 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21725405 CCTAACCCTAA-CTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * *
21725433 CCTAACCTTAACCCAATTCAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21725462 CCTTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAAC
1 CC-----T---AACCCTAA-CCT-----AATTTAATTAAAAAC
* *
21725505 CCTAACCCTAACCTAACTT-A-TCAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
21725532 CCTAACCCTAACCAAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * *
21725561 CCTAACACTAACCCAATTCAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * * *
21725590 CCTAACCCAAACCCAATTTAAATAAAACC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21725619 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21725648 CCTAACCCTAA-CTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * *
21725676 CCTAACCTTAACCCAATTCAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
** *
21725705 ATTTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAAC
1 -----CCT---AACCCTAA-CCT-----AATTTAATTAAAAAC
* * *
21725748 CCTAACCCTAGCATAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21725777 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
21725806 CCTAGCCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
21725835 CCCAACCCTAACC-CATTTCAATTAAAAAC
1 CCTAACCCTAACCTAATTT-AATTAAAAAC
* *
21725864 CCTAACTCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21725893 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21725922 CCTAA--C---CC-AATTAAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
21725945 CCTAATCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21725974 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21726003 CCTAATCCTAACCTAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
21726032 CCTAACCCTAA-CTCGATTCAATTAAAAAC
1 CCTAACCCTAACCT-AATTTAATTAAAAAC
* * *
21726061 CCTAACCCTTACATAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21726090 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
21726119 CCTAGCCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * *
21726148 CCCAACCCTAACCCAATTCAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21726177 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21726206 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21726235 CCTAACCCTAACCCAATTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * *
21726264 CCTAACCTTAACTTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21726293 CCTAACCCTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* *
21726322 CCTAACCTTAACCTAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * *
21726351 CCTAACCCTAACCCAATTCAATTAAAAAT
1 CCTAACCCTAACCTAATTTAATTAAAAAC
* * *
21726380 CCTAACCCTATCCAAACTTAATTAAAAAC
1 CCTAACCCTAACCTAATTTAATTAAAAAC
*
21726409 CCTAACCCTAACCCAATTT
1 CCTAACCCTAACCTAATTT
21726428 TATATAATTT
Statistics
Matches: 931, Mismatches: 108, Indels: 84
0.83 0.10 0.07
Matches are distributed among these distances:
23 19 0.02
24 2 0.00
25 1 0.00
27 25 0.03
28 64 0.07
29 742 0.80
30 4 0.00
34 7 0.01
35 15 0.02
37 14 0.02
38 6 0.01
43 32 0.03
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (29 bp):
CCTAACCCTAACCTAATTTAATTAAAAAC
Found at i:21725468 original size:43 final size:43
Alignment explanation
Indices: 21725420--21725507 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
21725410 CCCTAACTAA
*
21725420 CTTAATTAAAAACCCTAACCTTAACCCAATTCAATTAAAAACC
1 CTTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAACC
21725463 CTTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAACC
1 CTTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAACC
21725506 CT
1 CT
21725508 AACCCTAACC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (43 bp):
CTTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAACC
Found at i:21725469 original size:14 final size:14
Alignment explanation
Indices: 21725452--21725478 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21725442 AACCCAATTC
21725452 AATTAAAAACCCTT
1 AATTAAAAACCCTT
21725466 AATTAAAAACCCT
1 AATTAAAAACCCT
21725479 AACCCTAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (14 bp):
AATTAAAAACCCTT
Found at i:21725648 original size:23 final size:23
Alignment explanation
Indices: 21725622--21725683 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 23
21725612 TAAAACCCCT
21725622 AACCCTAACCTAACTTAATTAAA
1 AACCCTAACCTAACTTAATTAAA
21725645 AACCCTAACCCTAACTAACTTAATTAAA
1 AACCCTAA--C---CTAACTTAATTAAA
21725673 AACCCTAACCT
1 AACCCTAACCT
21725684 TAACCCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
23 10 0.29
25 1 0.03
26 1 0.03
28 22 0.65
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (23 bp):
AACCCTAACCTAACTTAATTAAA
Found at i:21725712 original size:43 final size:43
Alignment explanation
Indices: 21725664--21725747 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
21725654 CCTAACTAAC
*
21725664 TTAATTAAAAACCCTAACCTTAACCCAATTCAATTAAAAACAT
1 TTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAACAT
21725707 TTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAAC
1 TTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAAC
21725748 CCTAACCCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (43 bp):
TTAATTAAAAACCCTAACCCTAACCCAATTCAATTAAAAACAT
Found at i:21725773 original size:72 final size:71
Alignment explanation
Indices: 21725636--21725776 Score: 196
Period size: 72 Copynumber: 2.0 Consensus size: 71
21725626 CTAACCTAAC
* * *
21725636 TTAATTAAAAACCCTAACCCTAACTAACTTAATTAAAAACCCTAACCTTAACCCAATTCAATTAA
1 TTAATTAAAAACCCTAACCCTAACCAACTTAATTAAAAACCCTAACCCTAACACAATTCAATTAA
21725701 AAACAT
66 AAACAT
* *
21725707 TTAATTAAAAACCCTAACCCTAACCCAA-TTCAATTAAAAACCCTAACCCTAGCATAACTT-AAT
1 TTAATTAAAAACCCTAACCCTAA-CCAACTT-AATTAAAAACCCTAACCCTAACACAA-TTCAAT
21725770 TAAAAAC
63 TAAAAAC
21725777 CCTAACCCTA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
71 25 0.40
72 35 0.56
73 2 0.03
ACGTcount: A:0.48, C:0.26, G:0.01, T:0.26
Consensus pattern (71 bp):
TTAATTAAAAACCCTAACCCTAACCAACTTAATTAAAAACCCTAACCCTAACACAATTCAATTAA
AAACAT
Found at i:21726463 original size:19 final size:19
Alignment explanation
Indices: 21726436--21726565 Score: 116
Period size: 19 Copynumber: 7.0 Consensus size: 19
21726426 TTTATATAAT
21726436 TTGATAATTTTACTAACCA
1 TTGATAATTTTACTAACCA
*
21726455 TTAATAATTTTA-TATA--A
1 TTGATAATTTTACTA-ACCA
21726472 TTTGATAATTTTACTAACCA
1 -TTGATAATTTTACTAACCA
*
21726492 TTAATAATTTTA-TATA--A
1 TTGATAATTTTACTA-ACCA
21726509 TTTGATAATTTTACTAACCA
1 -TTGATAATTTTACTAACCA
*
21726529 TTTATAATTTTA-TATA--A
1 TTGATAATTTTACTA-ACCA
21726546 TATGATAATTTTACTAACCA
1 T-TGATAATTTTACTAACCA
21726566 CACTACACCA
Statistics
Matches: 90, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
17 4 0.04
18 41 0.46
19 42 0.47
20 3 0.03
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (19 bp):
TTGATAATTTTACTAACCA
Found at i:21726465 original size:37 final size:37
Alignment explanation
Indices: 21726423--21726565 Score: 268
Period size: 37 Copynumber: 3.9 Consensus size: 37
21726413 ACCCTAACCC
21726423 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
21726460 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
*
21726497 AATTTTATATAATTTGATAATTTTACTAACCATTTAT
1 AATTTTATATAATTTGATAATTTTACTAACCATTAAT
*
21726534 AATTTTATATAATATGATAATTTTACTAACCA
1 AATTTTATATAATTTGATAATTTTACTAACCA
21726566 CACTACACCA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (37 bp):
AATTTTATATAATTTGATAATTTTACTAACCATTAAT
Found at i:21726701 original size:16 final size:16
Alignment explanation
Indices: 21726680--21726711 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21726670 AAAAATGAGA
21726680 ATTAGCGGCGATTTTC
1 ATTAGCGGCGATTTTC
*
21726696 ATTAGCGGCGTTTTTC
1 ATTAGCGGCGATTTTC
21726712 GAAAAACGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.41
Consensus pattern (16 bp):
ATTAGCGGCGATTTTC
Found at i:21726909 original size:82 final size:83
Alignment explanation
Indices: 21726814--21727001 Score: 215
Period size: 82 Copynumber: 2.3 Consensus size: 83
21726804 GGTTTTAGAA
* *
21726814 GCGTTTTTGAAAAAGCGCT-GCTGAAT-CTCAGGTCTTTAGCGGC-ATTTTGGAAAAAGCGCCGC
1 GCGTTTTTAAAAAAGCGCTCGCT-AATGCTCAGGGCTTTAGCGGCGATTTTGG-AAAAGCGCCGC
** *
21726876 TAAATCTCAATTCTTTAGTG
64 TAAATCTCAAGGCTTTAGCG
* * * *
21726896 GCGTTTTTAAAAAAGCG-TCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGGAAAGGCGTCGCTA
1 GCGTTTTTAAAAAAGCGCTCGCTAATGCTCAGGGCTTTAGCGGCGATTTTGGAAAAGCGCCGCTA
*
21726960 AATCTCAGGGCTTTAGCG
66 AATCTCAAGGCTTTAGCG
**
21726978 GCGTTTTTATTAAAGCGC-CGCTAA
1 GCGTTTTTAAAAAAGCGCTCGCTAA
21727002 AAACATTAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
81 4 0.04
82 80 0.89
83 6 0.07
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (83 bp):
GCGTTTTTAAAAAAGCGCTCGCTAATGCTCAGGGCTTTAGCGGCGATTTTGGAAAAGCGCCGCTA
AATCTCAAGGCTTTAGCG
Found at i:21726985 original size:41 final size:41
Alignment explanation
Indices: 21726814--21727002 Score: 195
Period size: 41 Copynumber: 4.6 Consensus size: 41
21726804 GGTTTTAGAA
* *
21726814 GCGTTTTTGAAAAAGCG-CTGCTGAATCTCAGGTCTTTAGCG
1 GCGTTTTTGAAAAAGCGTC-GCTAAATCTCAGGGCTTTAGCG
* * * *** *
21726855 GCATTTTGGAAAAAGCGCCGCTAAATCTCAATTCTTTAGTG
1 GCGTTTTTGAAAAAGCGTCGCTAAATCTCAGGGCTTTAGCG
* *
21726896 GCGTTTTTAAAAAAGCGTCGCT-AATGCTCGGGGCTTTAGCG
1 GCGTTTTTGAAAAAGCGTCGCTAAAT-CTCAGGGCTTTAGCG
* *
21726937 GCGTTTTTGGAAAGGCGTCGCTAAATCTCAGGGCTTTAGCG
1 GCGTTTTTGAAAAAGCGTCGCTAAATCTCAGGGCTTTAGCG
* *
21726978 GCGTTTTT-ATTAAAGCGCCGCTAAA
1 GCGTTTTTGA-AAAAGCGTCGCTAAA
21727003 AACATTAATT
Statistics
Matches: 121, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
40 3 0.02
41 114 0.94
42 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (41 bp):
GCGTTTTTGAAAAAGCGTCGCTAAATCTCAGGGCTTTAGCG
Found at i:21726993 original size:123 final size:121
Alignment explanation
Indices: 21726765--21727002 Score: 300
Period size: 123 Copynumber: 2.0 Consensus size: 121
21726755 GACCTTTCAG
* * *
21726765 TTCTTTAGTGGCGATTTCGAAAAAGCGCCTAATGCTTGGGGTTTTAGAAGCGTTTTTGAAAAAGC
1 TTCTTTAGTGGCGATTTCAAAAAAGCGCCTAATGCTCGGGGCTTTAGAAGCGTTTTTGAAAAAGC
* *
21726830 GCTGCTGAATCTCAGGTCTTTAGCGGCATTTTGGAAAAAGCGCCGCTAAATCTCAA
66 GCTGCTAAATCTCAGGGCTTTAGCGGCATTTTGGAAAAAGCGCCGCTAAATCTCAA
* * ** * *
21726886 TTCTTTAGTGGCGTTTTTAAAAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGGAAAG
1 TTCTTTAGTGGCGATTTCAAAAAAGCG-C-CTAATGCTCGGGGCTTTAGAAGCGTTTTTGAAAAA
* * *
21726951 GCG-TCGCTAAATCTCAGGGCTTTAGCGGCGTTTT-TATTAAAGCGCCGCTAAA
64 GCGCT-GCTAAATCTCAGGGCTTTAGCGGCATTTTGGA-AAAAGCGCCGCTAAA
21727003 AACATTAATT
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
121 24 0.24
122 3 0.03
123 72 0.73
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (121 bp):
TTCTTTAGTGGCGATTTCAAAAAAGCGCCTAATGCTCGGGGCTTTAGAAGCGTTTTTGAAAAAGC
GCTGCTAAATCTCAGGGCTTTAGCGGCATTTTGGAAAAAGCGCCGCTAAATCTCAA
Found at i:21727078 original size:15 final size:15
Alignment explanation
Indices: 21727058--21727098 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
21727048 ATGAAAATCT
*
21727058 TTCTTTTTTTCCCTC
1 TTCTTTTTTTCCCCC
21727073 TTC--TTTTTCCCCC
1 TTCTTTTTTTCCCCC
*
21727086 TTTTTTTTTTCCC
1 TTCTTTTTTTCCC
21727099 AAAATCGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 11 0.50
15 11 0.50
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
TTCTTTTTTTCCCCC
Found at i:21728444 original size:3 final size:3
Alignment explanation
Indices: 21728436--21728467 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
21728426 ATGATTTTTC
21728436 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21728468 AAAATCGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:21730268 original size:686 final size:683
Alignment explanation
Indices: 21729130--21730494 Score: 2660
Period size: 686 Copynumber: 2.0 Consensus size: 683
21729120 TAGGCGACTG
21729130 TTTAAAGGTAAAATTTTAATTTACCCCTGTTCAAGAAAATTATGTTAGCTAAAACAATAACCTCG
1 TTTAAAGGTAAAATTTTAATTTACCCCTGTTCAAGAAAATTATGTTAGCTAAAACAATAACCTCG
21729195 TTGATTTTCTGACTTGCTTAATATAGATTAGTTGTTTCATGTTTGGAAACTTTTGATGCTCTTGG
66 TTGATTTTCTGACTTGCTTAATATAGATTAGTTGTTTCATGTTTGGAAACTTTTGATGCTCTTGG
* *
21729260 TCTTATGTCCTGCAGTCATTGACAAAAATTTGGTTCTCATTCTTCACTTAACAAGTCCAGTGGCA
131 TCTTATGTCCTGCAGTCATTGACAAAAATTTGATTCTCATTCTTCACGTAACAAGTCCAGTGGCA
21729325 CATACATATGTAAACTAGGAAATTGAAACAAGAAAGAAACGCAAAGCCAAAGCACATTGATACTC
196 CATACATATGTAAACTAGGAAATTGAAACAAGAAAGAAACGCAAAGCCAAAGCACATTGATACTC
21729390 TTGAATGATAGTTATAAATGAATAATATGCCTGACTTGGCATTTATAAAACTCACATGCTTGAAG
261 TTGAATGATAGTTATAAATGAATAATATGCCTGACTTGGCATTTATAAAACTCACATGCTTGAAG
21729455 GATAGAACAGAAATTGCTGTTAGAATTGGATTGTCAGCTTTAAGTGTCTATGACGTGTTTGATAT
326 GATAGAACAGAAATTGCTGTTAGAATTGGATTGTCAGCTTTAAGTGTCTATGACGTGTTTGATAT
21729520 TGGTTTCATTGGAAGAATTCATTGGTTTCATTGGTTTCTCTGCTGATATCAATTAATTTGTAAAA
391 TGGTTTCATTGGAAGAATTCATTGGTTTCATTGGTTTCTCTGCTGATATCAATTAATTTGTAAAA
21729585 GCTTCCTGAAAATTAAGCATGTGCTTTGCTGAAGGAATTTGTATTTTTAAAATTTCATAATTCTA
456 GCTTCCTGAAAATTAAGCATGTGCTTTGCTGAAGGAATTTGTATTTTTAAAATTTCATAATTCTA
21729650 TTTTGTAAACCATGGTAATAAACTTTAAGGTTCATGGATATAGATATATATATAGAGAGAGAGAG
521 TTTTGTAAACCATGGTAATAAACTTTAAGGTTCATGGATATAG--ATATATAT--AGAGAGAGAG
*
21729715 AGAGAGAAGTGCAATAGGGACTGTAATTCTTTCTTAATTATTAGCTACT-TTTGAGACCATCCAA
582 AGAGAGAAGTGAAATAGGGACTGTAATTCTTTCTTAATTATTAGCTACTATTTGAGACCATCCAA
21729779 GGTTAAGCTTATTCCATGTTTCTTATCTTGTGCTTTA
647 GGTTAAGCTTATTCCATGTTTCTTATCTTGTGCTTTA
21729816 TTTAAAGGTAAAATTTTAATTTACCCCTGTTCAAGAAAATTATGTTAGCTAAAACAATAACCTCG
1 TTTAAAGGTAAAATTTTAATTTACCCCTGTTCAAGAAAATTATGTTAGCTAAAACAATAACCTCG
21729881 TTGATTTTCTGACTTGCTTAATATAGATTAGTTGTTTCATGTTTGGAAACTTTTGATGCTCTTGG
66 TTGATTTTCTGACTTGCTTAATATAGATTAGTTGTTTCATGTTTGGAAACTTTTGATGCTCTTGG
21729946 TCTTATGTCCTGCAGTCATTGACAAAAATTTGATTCTCATTCTTCACGTAACAAGTCCAGTGGCA
131 TCTTATGTCCTGCAGTCATTGACAAAAATTTGATTCTCATTCTTCACGTAACAAGTCCAGTGGCA
21730011 CATACATATGTAAACTAGGAAATTGAAACAAGAAAGAAACGCAAAGCCAAAGCACATTGATACTC
196 CATACATATGTAAACTAGGAAATTGAAACAAGAAAGAAACGCAAAGCCAAAGCACATTGATACTC
21730076 TTGAATGATAGTTATAAATGAATAATATGCCTGACTTGGCATTTATAAAACTCACATGCTTGAAG
261 TTGAATGATAGTTATAAATGAATAATATGCCTGACTTGGCATTTATAAAACTCACATGCTTGAAG
21730141 GATAGAACAGAAATTGCTGTTAGAATTGGATTGTCAGCTTTAAGTGTCTATGACGTGTTTGATAT
326 GATAGAACAGAAATTGCTGTTAGAATTGGATTGTCAGCTTTAAGTGTCTATGACGTGTTTGATAT
21730206 TGGTTTCATTGGAAGAATTCATTGGTTTCATTGGTTTCTCTGCTGATATCAATTAATTTGTAAAA
391 TGGTTTCATTGGAAGAATTCATTGGTTTCATTGGTTTCTCTGCTGATATCAATTAATTTGTAAAA
21730271 GCTTCCTGAAAATTAAGCATGTGCTTTGCTGAAGGAATTTGTATTTTTAAAATTTCATAATTCTA
456 GCTTCCTGAAAATTAAGCATGTGCTTTGCTGAAGGAATTTGTATTTTTAAAATTTCATAATTCTA
21730336 TTTTGTAAACCATGGTAATAAACTTTAAGGTTCATGGATATAGATATATATAGAGAGAGAGAGAG
521 TTTTGTAAACCATGGTAATAAACTTTAAGGTTCATGGATATAGATATATATAGAGAGAGAGAGAG
21730401 AGAAGTGAAATAGGGACTGTAATTCTTTCTTAATTATTAGCTACTATTTGAGACCATCCAAGGTT
586 AGAAGTGAAATAGGGACTGTAATTCTTTCTTAATTATTAGCTACTATTTGAGACCATCCAAGGTT
21730466 AAGCTTATTCCATGTTTCTTATCTTGTGC
651 AAGCTTATTCCATGTTTCTTATCTTGTGC
21730495 ATTCTTTTTT
Statistics
Matches: 675, Mismatches: 3, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
682 58 0.09
683 48 0.07
684 8 0.01
686 561 0.83
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (683 bp):
TTTAAAGGTAAAATTTTAATTTACCCCTGTTCAAGAAAATTATGTTAGCTAAAACAATAACCTCG
TTGATTTTCTGACTTGCTTAATATAGATTAGTTGTTTCATGTTTGGAAACTTTTGATGCTCTTGG
TCTTATGTCCTGCAGTCATTGACAAAAATTTGATTCTCATTCTTCACGTAACAAGTCCAGTGGCA
CATACATATGTAAACTAGGAAATTGAAACAAGAAAGAAACGCAAAGCCAAAGCACATTGATACTC
TTGAATGATAGTTATAAATGAATAATATGCCTGACTTGGCATTTATAAAACTCACATGCTTGAAG
GATAGAACAGAAATTGCTGTTAGAATTGGATTGTCAGCTTTAAGTGTCTATGACGTGTTTGATAT
TGGTTTCATTGGAAGAATTCATTGGTTTCATTGGTTTCTCTGCTGATATCAATTAATTTGTAAAA
GCTTCCTGAAAATTAAGCATGTGCTTTGCTGAAGGAATTTGTATTTTTAAAATTTCATAATTCTA
TTTTGTAAACCATGGTAATAAACTTTAAGGTTCATGGATATAGATATATATAGAGAGAGAGAGAG
AGAAGTGAAATAGGGACTGTAATTCTTTCTTAATTATTAGCTACTATTTGAGACCATCCAAGGTT
AAGCTTATTCCATGTTTCTTATCTTGTGCTTTA
Found at i:21731943 original size:18 final size:18
Alignment explanation
Indices: 21731920--21731977 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
21731910 AACAGAACTT
21731920 ATGTAATTCTAATATAGA
1 ATGTAATTCTAATATAGA
* * ***
21731938 ATGTAA-AC-AATTTCTT
1 ATGTAATTCTAATATAGA
21731954 ATGTAATTCTAATATAGA
1 ATGTAATTCTAATATAGA
21731972 ATGTAA
1 ATGTAA
21731978 CTTGTTTTAA
Statistics
Matches: 28, Mismatches: 10, Indels: 4
0.67 0.24 0.10
Matches are distributed among these distances:
16 10 0.36
17 2 0.07
18 16 0.57
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (18 bp):
ATGTAATTCTAATATAGA
Found at i:21732289 original size:43 final size:43
Alignment explanation
Indices: 21732223--21732334 Score: 170
Period size: 43 Copynumber: 2.6 Consensus size: 43
21732213 AAGTCATGTT
*
21732223 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGTTCCTGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGTTCCTGGTC
* * *
21732266 TTTAACGGCGTTTGTGGAAAAAGCGCCGCTAAAGTTCTTGGTT
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGTTCCTGGTC
* *
21732309 TTTAGCAGCGTTTGCGGAAAAAGCGC
1 TTTAGCGGCGTTTGTGGAAAAAGCGC
21732335 TAAAGTTAGC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGTTCCTGGTC
Found at i:21732465 original size:37 final size:37
Alignment explanation
Indices: 21732415--21732550 Score: 245
Period size: 37 Copynumber: 3.7 Consensus size: 37
21732405 TGGAGTAGTG
*
21732415 CCATTTATAATTTTATATAATTTGATAATTTTACTAA
1 CCATTAATAATTTTATATAATTTGATAATTTTACTAA
* *
21732452 CCATTTATAATTTTATATAATTTGATAATTTTACTGA
1 CCATTAATAATTTTATATAATTTGATAATTTTACTAA
21732489 CCATTAATAATTTTATATAATTTGATAATTTTACTAA
1 CCATTAATAATTTTATATAATTTGATAATTTTACTAA
21732526 CCATTAATAATTTTATATAATTTGA
1 CCATTAATAATTTTATATAATTTGA
21732551 GTTAATACAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 96 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (37 bp):
CCATTAATAATTTTATATAATTTGATAATTTTACTAA
Found at i:21736555 original size:17 final size:17
Alignment explanation
Indices: 21736533--21736567 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21736523 TAATTAGTAC
21736533 ATATATGATTAAA-TTAT
1 ATATAT-ATTAAAGTTAT
21736550 ATATATATTAAAGTTAT
1 ATATATATTAAAGTTAT
21736567 A
1 A
21736568 ATTAAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
ATATATATTAAAGTTAT
Found at i:21736555 original size:19 final size:20
Alignment explanation
Indices: 21736510--21736557 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
21736500 CACTTCGTGA
*
21736510 ATATACTATAATTTAATTAGT
1 ATATA-TATAATTAAATTAGT
* *
21736531 ACATATATGATTAAATTA-T
1 ATATATATAATTAAATTAGT
21736550 ATATATAT
1 ATATATAT
21736558 TAAAGTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 8 0.35
20 11 0.48
21 4 0.17
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (20 bp):
ATATATATAATTAAATTAGT
Found at i:21749338 original size:19 final size:18
Alignment explanation
Indices: 21749296--21749337 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
21749286 AAATTTTGAA
*
21749296 AATTTTATAAATATTTTG
1 AATTTTAAAAATATTTTG
21749314 AATTTTAAAAATTATTTT-
1 AATTTTAAAAA-TATTTTG
21749332 AATTTT
1 AATTTT
21749338 TTTGTTGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTTTAAAAATATTTTG
Found at i:21750921 original size:62 final size:61
Alignment explanation
Indices: 21750855--21750987 Score: 160
Period size: 62 Copynumber: 2.2 Consensus size: 61
21750845 CAAATAGTGA
*
21750855 GTCACACGGCTTGGACACACACCCATGCCCCTGG-CTCGTGTGGTCTCTAATAACAATAATGT
1 GTCACACGACTTGGACACACACCCATGCCCCTGGTC-CGTGTGGTC-CTAATAACAATAATGT
** * * * * *
21750917 GTCACACGACTTGGACACACGTCTATGTCTCTGGTCCGTGTGGTCCTAATAACAATAGTGA
1 GTCACACGACTTGGACACACACCCATGCCCCTGGTCCGTGTGGTCCTAATAACAATAATGT
*
21750978 GTCAAACGAC
1 GTCACACGAC
21750988 CTGCCACACG
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
61 23 0.38
62 37 0.61
63 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (61 bp):
GTCACACGACTTGGACACACACCCATGCCCCTGGTCCGTGTGGTCCTAATAACAATAATGT
Found at i:21751564 original size:21 final size:21
Alignment explanation
Indices: 21751540--21751579 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
21751530 ACAACAACCC
*
21751540 AAAAGAAAAAAAAGGAAAGGA
1 AAAAGAAAAAAAAGAAAAGGA
* *
21751561 AAAAGGAAAAGAAGAAAAG
1 AAAAGAAAAAAAAGAAAAG
21751580 AGAAGAAGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAAAGAAAAGGA
Found at i:21756124 original size:31 final size:31
Alignment explanation
Indices: 21756089--21756154 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
21756079 GAAAGCATCA
*
21756089 TATTCTGATGGATCTGGTGCCCTAAGTGTAG
1 TATTCTGATGGATCTGGTGCCCTAAGTATAG
*
21756120 TATTCTGATGGATCTGGTGCTCTAAGTATAG
1 TATTCTGATGGATCTGGTGCCCTAAGTATAG
21756151 TATT
1 TATT
21756155 TTCATCTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.39
Consensus pattern (31 bp):
TATTCTGATGGATCTGGTGCCCTAAGTATAG
Found at i:21756571 original size:20 final size:21
Alignment explanation
Indices: 21756541--21756579 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
21756531 CAATTATTCA
21756541 AGGAGCTAGAGTCGCGACATC
1 AGGAGCTAGAGTCGCGACATC
21756562 AGGA-CTAGAGTCGCGACA
1 AGGAGCTAGAGTCGCGACA
21756580 CCAATGCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.31, C:0.23, G:0.33, T:0.13
Consensus pattern (21 bp):
AGGAGCTAGAGTCGCGACATC
Found at i:21757593 original size:23 final size:23
Alignment explanation
Indices: 21757551--21757598 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
21757541 AAATTTTATA
* *
21757551 TAATCTTAATTATATTAAATACTT
1 TAATATTAATTATATGAAATA-TT
21757575 TAATATTAA-TATATGAAATATT
1 TAATATTAATTATATGAAATATT
21757597 TA
1 TA
21757599 TATGTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 10 0.45
24 8 0.36
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATATTAATTATATGAAATATT
Found at i:21777421 original size:3 final size:3
Alignment explanation
Indices: 21777413--21777451 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
21777403 TATTTAAAAT
21777413 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21777452 GGGTAGACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:21779874 original size:17 final size:17
Alignment explanation
Indices: 21779852--21779905 Score: 81
Period size: 17 Copynumber: 3.1 Consensus size: 17
21779842 TAGAAAAGTC
*
21779852 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAA
*
21779869 AAAGATATGGGTATAAAA
1 AAAGATATGGGTAT-CAA
21779887 AAAGATATGGGTATCAA
1 AAAGATATGGGTATCAA
21779904 AA
1 AA
21779906 TCTGGGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.50, C:0.04, G:0.24, T:0.22
Consensus pattern (17 bp):
AAAGATATGGGTATCAA
Found at i:21779892 original size:18 final size:18
Alignment explanation
Indices: 21779852--21779905 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
21779842 TAGAAAAGTC
* *
21779852 AAAGATATGGGTAT-CAG
1 AAAGATATGGGTATAAAA
21779869 AAAGATATGGGTATAAAA
1 AAAGATATGGGTATAAAA
21779887 AAAGATATGGGTATCAAAA
1 AAAGATATGGGTAT-AAAA
21779906 TCTGGGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 14 0.42
18 15 0.45
19 4 0.12
ACGTcount: A:0.50, C:0.04, G:0.24, T:0.22
Consensus pattern (18 bp):
AAAGATATGGGTATAAAA
Found at i:21787363 original size:81 final size:80
Alignment explanation
Indices: 21787226--21787507 Score: 386
Period size: 81 Copynumber: 3.5 Consensus size: 80
21787216 ACCCTAAAAT
* *
21787226 AGGTAAAATGACCAAAATACCCTCATAGGGTAGAAA-GACCGAAATACCTCTATAGGGTAAAATG
1 AGGTAAAATGACCAAAATACCCTTATAGGGTA-AAATGACCGAAATACC-CAATAGGGTAAAATG
*
21787290 ACCAAAATACCCCAATA
64 ACCGAAATACCCCAATA
* * *
21787307 AAGTAAAATGACTAAAATACCCTTATAGGGTAAAATGACCAAAATACCCAAATAGGGTAAAATGA
1 AGGTAAAATGACCAAAATACCCTTATAGGGTAAAATGACCGAAATACCC-AATAGGGTAAAATGA
* *
21787372 TCGAAATACCCCCATA
65 CCGAAATACCCCAATA
* * *
21787388 AGGTAAAATGACCAAAATACCCTTATAGGGTAAAATGACTGAAATACCCCCATAGGGTAGAATGA
1 AGGTAAAATGACCAAAATACCCTTATAGGGTAAAATGACCGAAATA-CCCAATAGGGTAAAATGA
**
21787453 CCGAAATACCCTTATA
65 CCGAAATACCCCAATA
* *
21787469 GGGTAAAATGACCAAAATACCCCTATAGGGTAAAATGAC
1 AGGTAAAATGACCAAAATACCCTTATAGGGTAAAATGAC
21787508 TATTATACCC
Statistics
Matches: 179, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
80 4 0.02
81 172 0.96
82 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.19
Consensus pattern (80 bp):
AGGTAAAATGACCAAAATACCCTTATAGGGTAAAATGACCGAAATACCCAATAGGGTAAAATGAC
CGAAATACCCCAATA
Found at i:21787517 original size:27 final size:27
Alignment explanation
Indices: 21787227--21787507 Score: 350
Period size: 27 Copynumber: 10.4 Consensus size: 27
21787217 CCCTAAAATA
21787227 GGTAAAATGACCAAAATA-CCCTCATAG
1 GGTAAAATGACCAAAATACCCCT-ATAG
* *
21787254 GGTAGAAA-GACCGAAATACCTCTATAG
1 GGTA-AAATGACCAAAATACCCCTATAG
* *
21787281 GGTAAAATGACCAAAATACCCCAATAA
1 GGTAAAATGACCAAAATACCCCTATAG
* * *
21787308 AGTAAAATGACTAAAATACCCTTATAG
1 GGTAAAATGACCAAAATACCCCTATAG
**
21787335 GGTAAAATGACCAAAATACCCAAATAG
1 GGTAAAATGACCAAAATACCCCTATAG
* * * *
21787362 GGTAAAATGATCGAAATACCCCCATAA
1 GGTAAAATGACCAAAATACCCCTATAG
*
21787389 GGTAAAATGACCAAAATACCCTTATAG
1 GGTAAAATGACCAAAATACCCCTATAG
** *
21787416 GGTAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCTATAG
* * *
21787443 GGTAGAATGACCGAAATACCCTTATAG
1 GGTAAAATGACCAAAATACCCCTATAG
21787470 GGTAAAATGACCAAAATACCCCTATAG
1 GGTAAAATGACCAAAATACCCCTATAG
21787497 GGTAAAATGAC
1 GGTAAAATGAC
21787508 TATTATACCC
Statistics
Matches: 215, Mismatches: 36, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
26 3 0.01
27 206 0.96
28 6 0.03
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.19
Consensus pattern (27 bp):
GGTAAAATGACCAAAATACCCCTATAG
Found at i:21793782 original size:17 final size:18
Alignment explanation
Indices: 21793756--21793790 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
21793746 TTCTTTTTCT
21793756 TTCTTATTC-TCAGCAAC
1 TTCTTATTCTTCAGCAAC
*
21793773 TTCTTTTTCTTCAGCAAC
1 TTCTTATTCTTCAGCAAC
21793791 AACTTCCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.46
Consensus pattern (18 bp):
TTCTTATTCTTCAGCAAC
Found at i:21810323 original size:18 final size:18
Alignment explanation
Indices: 21810300--21810338 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
21810290 GAGATAATTC
21810300 TGATTGCATCGACACCTT
1 TGATTGCATCGACACCTT
*
21810318 TGATTGCGTCGACACCTT
1 TGATTGCATCGACACCTT
21810336 TGA
1 TGA
21810339 GGGTCAGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (18 bp):
TGATTGCATCGACACCTT
Found at i:21811591 original size:17 final size:16
Alignment explanation
Indices: 21811560--21811593 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
21811550 AAATATTATG
21811560 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
21811576 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
21811593 A
1 A
21811594 CGTCATTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:21822411 original size:18 final size:18
Alignment explanation
Indices: 21822378--21822412 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21822368 CAAAGGAAGC
* *
21822378 AAATCAAAGAATCAAAAA
1 AAATCAAAAAAACAAAAA
21822396 AAATCAAAAAAACAAAA
1 AAATCAAAAAAACAAAA
21822413 TGGGTGTCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.11, G:0.03, T:0.09
Consensus pattern (18 bp):
AAATCAAAAAAACAAAAA
Found at i:21823573 original size:14 final size:16
Alignment explanation
Indices: 21823554--21823585 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
21823544 ACCACTGAGC
21823554 CAAAAA-TCCCTA-TA
1 CAAAAATTCCCTAGTA
21823568 CAAAAATTCCCTAGTA
1 CAAAAATTCCCTAGTA
21823584 CA
1 CA
21823586 TAATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.22
Consensus pattern (16 bp):
CAAAAATTCCCTAGTA
Found at i:21835050 original size:40 final size:40
Alignment explanation
Indices: 21834994--21835108 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
21834984 GCTTGGATAA
* * *
21834994 AAAATGCCGCTAAAGATCAAGCATTAGCGGCGTTTTTAGG
1 AAAACGCCGCTAAAGATCAAGCATTAGCGGCATTTTAAGG
* * * *
21835034 AAAACGCTGCTAAAGATCGAGCATTTGCGGCACTTTAAGG
1 AAAACGCCGCTAAAGATCAAGCATTAGCGGCATTTTAAGG
*
21835074 AAAACGCCGCTAAAAAT-AAGCATTAGCGGCATTTT
1 AAAACGCCGCTAAAGATCAAGCATTAGCGGCATTTT
21835109 CCAGAAAGCG
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
39 15 0.24
40 48 0.76
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCAAGCATTAGCGGCATTTTAAGG
Found at i:21835229 original size:41 final size:41
Alignment explanation
Indices: 21835164--21835416 Score: 273
Period size: 41 Copynumber: 6.2 Consensus size: 41
21835154 GAGCTTTCGA
* *
21835164 GGCTTTAGCT-GCGTTTTTGGGAAAGCGCCACTAATGCTCAG
1 GGCTTTAG-TGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAG
* * * *
21835205 GGATTTAGTGACGTTTCTGTGAAAGCGCCACTAATGCTCAG
1 GGCTTTAGTGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAG
* *
21835246 GGCTTTAGTGGCGTTTTTGGGAAAGTGCCGCTAATGCTCA-
1 GGCTTTAGTGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAG
* * **
21835286 AGCTTTTAGCGGCGTTTTT-TGGAAAGCGCCGCTAATGCTCCT
1 GGC-TTTAGTGGCGTTTTTGT-GAAAGCGCCGCTAATGCTCAG
* * *
21835328 GGCTTTAGCGGAGTTTTTG-GAAAAGCGCCGCTAATGCTCGG
1 GGCTTTAGTGGCGTTTTTGTG-AAAGCGCCGCTAATGCTCAG
*
21835369 GGCTTTAGCGGCGTTTTTGAT-AAAGCGCCGCTAATGCTCAG
1 GGCTTTAGTGGCGTTTTTG-TGAAAGCGCCGCTAATGCTCAG
*
21835410 GGATTTA
1 GGCTTTA
21835417 AAATAATTTA
Statistics
Matches: 182, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
40 4 0.02
41 176 0.97
42 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (41 bp):
GGCTTTAGTGGCGTTTTTGTGAAAGCGCCGCTAATGCTCAG
Found at i:21835386 original size:123 final size:123
Alignment explanation
Indices: 21835167--21835408 Score: 326
Period size: 123 Copynumber: 2.0 Consensus size: 123
21835157 CTTTCGAGGC
* *
21835167 TTTAGCTGCGTTTTTGGGAAAGCGCCACTAATGCTCAGGGATTTAGTGACGTTTCTGTGAAAGCG
1 TTTAGCGGCGTTTTTGGGAAAGCGCCACTAATGCTCAGGGATTTAGGGACGTTTCTGTGAAAGCG
* * *
21835232 CCACTAATGCTCAGGGCTTTAGTGGCGTTTTTGGGAAAGTGCCGCTAATGCTCAAGCT
66 CCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAAGCT
* * ** * *
21835290 TTTAGCGGCGTTTTTTGGAAAGCGCCGCTAATGCTCCTGGCTTTAGCGGA-GTTTTTG-GAAAAG
1 TTTAGCGGCGTTTTTGGGAAAGCGCCACTAATGCTCAGGGATTTAG-GGACGTTTCTGTG-AAAG
* * *
21835353 CGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTCA
64 CGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
21835409 GGGATTTAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
122 1 0.01
123 100 0.97
124 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (123 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCACTAATGCTCAGGGATTTAGGGACGTTTCTGTGAAAGCG
CCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCAAGCT
Found at i:21836116 original size:22 final size:23
Alignment explanation
Indices: 21836089--21836142 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
21836079 TTTAAGTGTT
21836089 GGGGTTTAA-GATTCAGGGG-TTA
1 GGGGTTTAAGGATT-AGGGGTTTA
*
21836111 GGGG-TTAAGGGTTAGGGGTTTA
1 GGGGTTTAAGGATTAGGGGTTTA
21836133 GGGG-TTAAGG
1 GGGGTTTAAGG
21836143 TTTATGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.31
22 20 0.69
ACGTcount: A:0.20, C:0.02, G:0.48, T:0.30
Consensus pattern (23 bp):
GGGGTTTAAGGATTAGGGGTTTA
Found at i:21836133 original size:8 final size:7
Alignment explanation
Indices: 21836103--21836139 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
21836093 TTTAAGATTC
21836103 AGGGGTT
1 AGGGGTT
21836110 AGGGGTT
1 AGGGGTT
*
21836117 AAGGGTT
1 AGGGGTT
21836124 AGGGGTTT
1 AGGGG-TT
21836132 AGGGGTT
1 AGGGGTT
21836139 A
1 A
21836140 AGGTTTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.19, C:0.00, G:0.51, T:0.30
Consensus pattern (7 bp):
AGGGGTT
Found at i:21836144 original size:14 final size:14
Alignment explanation
Indices: 21836052--21836146 Score: 59
Period size: 14 Copynumber: 6.7 Consensus size: 14
21836042 TATCCAAATT
*
21836052 TTAAGGTTTAGGGA
1 TTAAGGTTTAGGGG
* * *
21836066 TTATGGTTTATGGT
1 TTAAGGTTTAGGGG
21836080 TTAA-GTGTT-GGGG
1 TTAAGGT-TTAGGGG
* *
21836093 TTTAAGATTCAGGGG
1 -TTAAGGTTTAGGGG
* * *
21836108 TTAGGGGTTAAGGG
1 TTAAGGTTTAGGGG
*
21836122 TTAGGGGTTTAGGGG
1 TTA-AGGTTTAGGGG
21836137 TTAAGGTTTA
1 TTAAGGTTTA
21836147 TGTTTTATGA
Statistics
Matches: 60, Mismatches: 16, Indels: 10
0.70 0.19 0.12
Matches are distributed among these distances:
13 4 0.07
14 39 0.65
15 17 0.28
ACGTcount: A:0.21, C:0.01, G:0.39, T:0.39
Consensus pattern (14 bp):
TTAAGGTTTAGGGG
Found at i:21836178 original size:71 final size:71
Alignment explanation
Indices: 21836056--21836194 Score: 176
Period size: 71 Copynumber: 2.0 Consensus size: 71
21836046 CAAATTTTAA
* *
21836056 GGTTTAGGGATTATGGTTTATGGTTTAAGTGTTGGGGTTTAAGATTCAGGGGTTAGGGGTTAAGG
1 GGTTTAGGGATTAAGGTTTATGGTTTAAGTGTTAGGGTTTAAGATTCAGGGGTTAGGGGTTAAGG
21836121 GTTAGG
66 GTTAGG
* * * *
21836127 GGTTTAGGGGTTAAGGTTTATGTTTTATGAT-TTAGGGTTTAAAAGA-T-AGGGGTTAGGGGTTT
1 GGTTTAGGGATTAAGGTTTATGGTTTAAG-TGTTAGGGTTT--AAGATTCAGGGGTTAGGGGTTA
21836189 AGGGTT
63 AGGGTT
21836195 TAGATTAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
71 53 0.90
72 2 0.03
73 4 0.07
ACGTcount: A:0.21, C:0.01, G:0.39, T:0.40
Consensus pattern (71 bp):
GGTTTAGGGATTAAGGTTTATGGTTTAAGTGTTAGGGTTTAAGATTCAGGGGTTAGGGGTTAAGG
GTTAGG
Found at i:21837540 original size:74 final size:73
Alignment explanation
Indices: 21837393--21837613 Score: 218
Period size: 74 Copynumber: 3.0 Consensus size: 73
21837383 AAAAGTGCCT
* * * ***
21837393 AAAAAACGTAAGCCCAACGACGCCG-TTTCTGAGC-TTTCGGAGATTTAGCGGCGTTTACGGTAA
1 AAAAAACATAAGCCCAACAACGCCGTTTTTTGAGCTTTTCGGAGATTTAGCGGCGTTTTTAGTAA
*
21837456 AGCGCCGC
66 AGCACCGC
* *
21837464 AAAGAAACATAAGCCGAACAACACCGTTTTTTGAGCTTTTCGCG-GATTTAGCGGCGTTTTTAGT
1 AAA-AAACATAAGCCCAACAACGCCGTTTTTTGAGCTTTTCG-GAGATTTAGCGGCGTTTTTAGT
* *
21837528 TAAGCACTGC
64 AAAGCACCGC
* * * * *
21837538 AAAAATACCTAAGCCTAATAATGCCGTTTTTTGAGCTTTT-GGAGATTTAGTGGCGTTTTTATGT
1 AAAAA-ACATAAGCCCAACAACGCCGTTTTTTGAGCTTTTCGGAGATTTAGCGGCGTTTTTA-GT
*
21837602 -AAGCGCCGC
64 AAAGCACCGC
21837611 AAA
1 AAA
21837614 TGCCAAGGGC
Statistics
Matches: 124, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
71 3 0.02
72 19 0.15
73 38 0.31
74 63 0.51
75 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (73 bp):
AAAAAACATAAGCCCAACAACGCCGTTTTTTGAGCTTTTCGGAGATTTAGCGGCGTTTTTAGTAA
AGCACCGC
Found at i:21837743 original size:73 final size:74
Alignment explanation
Indices: 21837624--21837783 Score: 232
Period size: 73 Copynumber: 2.2 Consensus size: 74
21837614 TGCCAAGGGC
* * * * *
21837624 TTTAGTGGCATTTTTGAGAAAGCGCCGCAAAAATACCTAAGCCCAACGATGTCGTTTTCAAAGCT
1 TTTAGTGGCGTTTTTGAAAAAGCGCCGCAAAAATACCTAACCCCAACGATGCCATTTTCAAAGCT
21837689 TTC-GGGGA
66 TTCGGGGGA
* **
21837697 TTTAGTGGCGTTTTTGAAAAAGTGCCGCAAAAATACCTAACCCCAACGATGCCATTTTCTGAGCT
1 TTTAGTGGCGTTTTTGAAAAAGCGCCGCAAAAATACCTAACCCCAACGATGCCATTTTCAAAGCT
21837762 TTCGGGGGA
66 TTCGGGGGA
*
21837771 TTTAGTAGCGTTT
1 TTTAGTGGCGTTT
21837784 ATGGGTAAGT
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 60 0.78
74 17 0.22
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (74 bp):
TTTAGTGGCGTTTTTGAAAAAGCGCCGCAAAAATACCTAACCCCAACGATGCCATTTTCAAAGCT
TTCGGGGGA
Found at i:21838469 original size:14 final size:14
Alignment explanation
Indices: 21838450--21838500 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
21838440 ACACTTGTAT
21838450 GGATTTAGGGTTTG
1 GGATTTAGGGTTTG
*
21838464 GGATTTAAGGTTTAG
1 GGATTTAGGGTTT-G
* *
21838479 GG-GTTAGGGTTAG
1 GGATTTAGGGTTTG
21838492 GGA-TTAGGG
1 GGATTTAGGG
21838501 GTTAGAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 9 0.29
14 19 0.61
15 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (14 bp):
GGATTTAGGGTTTG
Found at i:21839784 original size:337 final size:333
Alignment explanation
Indices: 21839315--21840297 Score: 978
Period size: 336 Copynumber: 2.9 Consensus size: 333
21839305 TCTAATGCTT
* * * * * * * *
21839315 AAGCAATAGCGGCATTTGTACAAAAACGCCGCAAAAGTGACTTAAAATTTTGGTTGAACAACGCC
1 AAGCAATAGCGGCGTTTGTTCAAAAACGCCGCAAAAGTGTCTTAAAATTTTTGCTAAACGACGTC
* * * *
21839380 GTTTCTGTCCACGATTTTTAACTTAGCATTTTCTCTATATTAACAAAACGGCGCCGTTTATGTTA
66 GTTTCTGTACACG-TTTTTAACTTAGCATTTTCTCTATATTAATACAACGGCGCCGTTTCTGTTA
** ** * * * *
21839445 ATTTTTCGTGGCGTTTGTT-CAGGAAACGCCATAAAAGTGACTTGAAATATTGGCTAAACGTCGA
130 ATTTTT-GTGGCGTTT-TTACACAAAACGCCGCAAAAGTGACTTAAAATATTGCCTAAACGACCA
* * ** *
21839509 CGTCTAACTTAAGCAAATTAATTTTTTGTGGTGCTTTAAC-GTAAAACGCCAGAAATGTGCATTA
193 CGTATAGCTTAAGCAAATTAATTTTTACTGGCG-TTTAACAG-AAAACGCCAGAAATGTGCATTA
* ** * *
21839573 AATCTTAACAAAACGACGTCGTTTCGGATTAGAACCTT-CATTCTTTGTGGCG-CTGGTCTAG-A
256 AAGCTTAACAAAACGACACCGTTTCGGATTAGAACCTTAAATT-TTAGTGGCGCCT--TCTAGAA
*
21839635 AACGCCACAAATACAC
318 AACGCCACAAACACAC
* * * *
21839651 AAGCTATAGCGGTGTTTGTTCAATAAACGCCGCGAAAGTGTCTTAAAATTTTTGCTAAACGGCGT
1 AAGCAATAGCGGCGTTTGTTCAA-AAACGCCGCAAAAGTGTCTTAAAATTTTTGCTAAACGACGT
* * *
21839716 CGTCTT-TGTACACGCTTTTATACTTAGCATTTTCTCTATATTAATTCAACGGCGTCGTTTCTGT
65 CGT-TTCTGTACACGTTTTTA-ACTTAGCATTTTCTCTATATTAATACAACGGCGCCGTTTCTGT
* * * * **
21839780 TAATTTTTGTGGCGTTTTTAAACCAAACGCCGCAAAAGTGACATAAAATATTGCCTAAACGGCTT
128 TAATTTTTGTGGCGTTTTTACACAAAACGCCGCAAAAGTGACTTAAAATATTGCCTAAACGACCA
* * * * *
21839845 CGTTTAGCTTAAGCAACTTAATTTTTACTGACGTTTAATCAGAAAACGCCAAAAATGTGCATTAC
193 CGTATAGCTTAAGCAAATTAATTTTTACTGGCGTTTAA-CAGAAAACGCCAGAAATGTGCATTAA
* * * * * *
21839910 AGCTTAATAAAACGGCACCGTTTTGGATTAGAACTTTAAATTTTAGTGGTGCCTTTTAGAAAACG
257 AGCTTAACAAAACGACACCGTTTCGGATTAGAACCTTAAATTTTAGTGGCGCCTTCTAGAAAACG
* **
21839975 CCATAAACGTAC
322 CCACAAACACAC
* ** *
21839987 AAGCAATAGCGGCGTTTGTTCAGGATGCGCCGCAAAATTGTCTTAAAA-TTTTGTCTAAACGACG
1 AAGCAATAGCGGCGTTTGTTCA-AAAACGCCGCAAAAGTGTCTTAAAATTTTTG-CTAAACGACG
* * * *
21840051 TCGTTTCTGTACTA-GTTTTTTAACTTAGCATTTTCTCTAAATTAATCCAAAGGCGCCGTTTCTC
64 TCGTTTCTGTAC-ACG-TTTTTAACTTAGCATTTTCTCTATATTAATACAACGGCGCCGTTTCTG
* * * *
21840115 TTAATTTATAGTGGTGTTTTTGCACAAAACGCCGCAAAA-TGACTTAAAATATTGTCTAAACGAC
127 TTAATTT-TTGTGGCGTTTTTACACAAAACGCCGCAAAAGTGACTTAAAATATTGCCTAAACGAC
* * * * *
21840179 CCCATATAGCTTAAGCAAATTAATTTTTACTGGCATTTTTACAGAAAACGCCAGAACTGTGCATT
191 CACGTATAGCTTAAGCAAATTAATTTTTACTGGC-GTTTAACAGAAAACGCCAGAAATGTGCATT
** * * * * *
21840244 AAAGCTTAATTAAACGGGGCGCCGTTTCGG-TTTGAACTTTAATTTTTAGTGGCG
255 AAAGCTTAACAAAAC--GACACCGTTTCGGATTAGAACCTTAAATTTTAGTGGCG
21840298 TTTTTCAAAA
Statistics
Matches: 536, Mismatches: 93, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
335 18 0.03
336 353 0.66
337 152 0.28
338 13 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (333 bp):
AAGCAATAGCGGCGTTTGTTCAAAAACGCCGCAAAAGTGTCTTAAAATTTTTGCTAAACGACGTC
GTTTCTGTACACGTTTTTAACTTAGCATTTTCTCTATATTAATACAACGGCGCCGTTTCTGTTAA
TTTTTGTGGCGTTTTTACACAAAACGCCGCAAAAGTGACTTAAAATATTGCCTAAACGACCACGT
ATAGCTTAAGCAAATTAATTTTTACTGGCGTTTAACAGAAAACGCCAGAAATGTGCATTAAAGCT
TAACAAAACGACACCGTTTCGGATTAGAACCTTAAATTTTAGTGGCGCCTTCTAGAAAACGCCAC
AAACACAC
Found at i:21841129 original size:11 final size:12
Alignment explanation
Indices: 21841096--21841129 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21841086 ATTTTCCAGC
21841096 ACTCTGTAATTA
1 ACTCTGTAATTA
*
21841108 GCTCTGTAATTA
1 ACTCTGTAATTA
21841120 ACTC-GTAATT
1 ACTCTGTAATT
21841130 TTTTATAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (12 bp):
ACTCTGTAATTA
Found at i:21841830 original size:20 final size:20
Alignment explanation
Indices: 21841802--21841858 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
21841792 CCTAAATCTT
21841802 AAACC-TGAACCCTAAACCC
1 AAACCTTGAACCCTAAACCC
* *
21841821 AAACCTTGAA-CTTGAACCCC
1 AAACCTTGAACCCT-AAACCC
* *
21841841 GAACCTTGAACACTAAAC
1 AAACCTTGAACCCTAAAC
21841859 TTGGATTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 7 0.24
20 21 0.72
21 1 0.03
ACGTcount: A:0.40, C:0.35, G:0.09, T:0.16
Consensus pattern (20 bp):
AAACCTTGAACCCTAAACCC
Found at i:21841845 original size:26 final size:26
Alignment explanation
Indices: 21841769--21841839 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
21841759 CTAAATCCTG
* *
21841769 AACCTTGAACTTTAAACCCAAAACCTA
1 AACCTTGAAC-TTGAACCCAAAACCCA
* * * *
21841796 AATCTTAAACCTGAACCCTAAACCCA
1 AACCTTGAACTTGAACCCAAAACCCA
21841822 AACCTTGAACTTGAACCC
1 AACCTTGAACTTGAACCC
21841840 CGAACCTTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 27 0.77
27 8 0.23
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (26 bp):
AACCTTGAACTTGAACCCAAAACCCA
Found at i:21841924 original size:20 final size:20
Alignment explanation
Indices: 21841878--21841926 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
21841868 AGATTTAGAG
* *
21841878 TTCGAGTTTGGGGTCTAAGG
1 TTCGAGTTCGGGGTCTAAGA
* * *
21841898 TTAGAGTTCGGGGTTTAATA
1 TTCGAGTTCGGGGTCTAAGA
21841918 TTCGAGTTC
1 TTCGAGTTC
21841927 AGGTTTAAGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.10, G:0.33, T:0.39
Consensus pattern (20 bp):
TTCGAGTTCGGGGTCTAAGA
Found at i:21842448 original size:17 final size:18
Alignment explanation
Indices: 21842428--21842461 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21842418 ATTTTTAATG
21842428 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
21842445 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
21842462 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:21842609 original size:9 final size:9
Alignment explanation
Indices: 21842595--21842700 Score: 167
Period size: 9 Copynumber: 11.8 Consensus size: 9
21842585 ACTAACATCA
*
21842595 TACATAACC
1 TACATAACT
21842604 TACATAACT
1 TACATAACT
21842613 TACATAACT
1 TACATAACT
*
21842622 TACATAAAT
1 TACATAACT
*
21842631 TAAATAACT
1 TACATAACT
21842640 TACATAACT
1 TACATAACT
*
21842649 TACATAAAT
1 TACATAACT
*
21842658 TAAATAACT
1 TACATAACT
21842667 TACATAACT
1 TACATAACT
21842676 TACATAACT
1 TACATAACT
21842685 TACATAACT
1 TACATAACT
21842694 TACATAA
1 TACATAA
21842701 TAACTGGCGT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 88 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:21847746 original size:21 final size:21
Alignment explanation
Indices: 21847722--21847770 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
21847712 AGTGAGGGAG
*
21847722 GCAGAGGCTGCAGCGAGAGAA
1 GCAGAGGCTGCAGCAAGAGAA
21847743 GCAGAGGCTGCAGCAAGAGAA
1 GCAGAGGCTGCAGCAAGAGAA
*
21847764 GTAGAGG
1 GCAGAGG
21847771 TTCAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.43, T:0.06
Consensus pattern (21 bp):
GCAGAGGCTGCAGCAAGAGAA
Found at i:21847854 original size:21 final size:21
Alignment explanation
Indices: 21847830--21847878 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
21847820 AGTGAGGGAG
*
21847830 GCAGAGGCTGCAGCGAGAGAA
1 GCAGAGGCTGCAGCAAGAGAA
21847851 GCAGAGGCTGCAGCAAGAGAA
1 GCAGAGGCTGCAGCAAGAGAA
*
21847872 GTAGAGG
1 GCAGAGG
21847879 TTCAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.43, T:0.06
Consensus pattern (21 bp):
GCAGAGGCTGCAGCAAGAGAA
Found at i:21847943 original size:108 final size:108
Alignment explanation
Indices: 21847659--21847928 Score: 531
Period size: 108 Copynumber: 2.5 Consensus size: 108
21847649 GACCACATTT
*
21847659 GAGGTTCAAACGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGACAGTGAGGGAGGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGACAGTGAGGGAGGC
21847724 AGAGGCTGCAGCGAGAGAAGCAGAGGCTGCAGCAAGAGAAGTA
66 AGAGGCTGCAGCGAGAGAAGCAGAGGCTGCAGCAAGAGAAGTA
21847767 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGACAGTGAGGGAGGC
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGACAGTGAGGGAGGC
21847832 AGAGGCTGCAGCGAGAGAAGCAGAGGCTGCAGCAAGAGAAGTA
66 AGAGGCTGCAGCGAGAGAAGCAGAGGCTGCAGCAAGAGAAGTA
21847875 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGACA
1 GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGACA
21847929 TCGAAAGAAG
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 161 1.00
ACGTcount: A:0.40, C:0.17, G:0.30, T:0.13
Consensus pattern (108 bp):
GAGGTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGATGCGACAGTGAGGGAGGC
AGAGGCTGCAGCGAGAGAAGCAGAGGCTGCAGCAAGAGAAGTA
Found at i:21848341 original size:43 final size:43
Alignment explanation
Indices: 21848248--21848516 Score: 233
Period size: 42 Copynumber: 6.3 Consensus size: 43
21848238 ATCCCAAAAA
* * * *
21848248 TTAGTGGCGTTTTTTAAGAAAGCGCCGCTAAAGAACAT-TTCTT
1 TTAGCGGCGTTTTTGAACAAAGCGCCGCTAAAGAACATGATC-T
* * * *
21848291 TTCGCGGCGTTTGTGAAGAAAGCGCCACTAAAGAACATGATCT
1 TTAGCGGCGTTTTTGAACAAAGCGCCGCTAAAGAACATGATCT
* * * * *
21848334 ATAGCGGCGTTTTT-TACCAAGCGCCGCTAAAGAATATGATTT
1 TTAGCGGCGTTTTTGAACAAAGCGCCGCTAAAGAACATGATCT
* *
21848376 TTAGCGGCGTTTTTG-TCTAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTGAACAAAGCGCCGCTAAAGAACATGATCT
* ** * * *
21848418 TTAGCGGCATTTTT-CTCCATGCGCCGCTAAAGAACAAGATCT
1 TTAGCGGCGTTTTTGAACAAAGCGCCGCTAAAGAACATGATCT
** **** *
21848460 TTAGCGTTGTCTTTT-TTTTAAGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCGT-TTTTGAACAAAGCGCCGCTAAAGAACATGATCT
21848503 TTAGCGGCGTTTTT
1 TTAGCGGCGTTTTT
21848517 TTCTGTAAAC
Statistics
Matches: 187, Mismatches: 35, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
42 106 0.57
43 79 0.42
44 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTTTGAACAAAGCGCCGCTAAAGAACATGATCT
Found at i:21848373 original size:42 final size:41
Alignment explanation
Indices: 21848310--21848517 Score: 256
Period size: 42 Copynumber: 5.0 Consensus size: 41
21848300 TTTGTGAAGA
* *
21848310 AAGCGCCACTAAAGAACATGATCTATAGCGGCGTTTTTTACC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-CC
* * *
21848352 AAGCGCCGCTAAAGAATATGATTTTTAGCGGCGTTTTTGTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TCC
*
21848394 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTCTCC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TCC
* * **
21848436 ATGCGCCGCTAAAGAACAAGATCTTTAGCGTTGTC-TTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCG--G-CGTTTTTTCC
*
21848479 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
21848518 TCTGTAAACG
Statistics
Matches: 144, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
40 1 0.01
41 7 0.05
42 100 0.69
43 29 0.20
44 6 0.04
45 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
Found at i:21848509 original size:85 final size:84
Alignment explanation
Indices: 21848248--21848517 Score: 283
Period size: 85 Copynumber: 3.2 Consensus size: 84
21848238 ATCCCAAAAA
* ** ** * * ***
21848248 TTAGTGGCGTTTTTTAAGAAAGCGCCGCTAAAGAAC-ATTTCTTTTCGCGGCGTTTGTGAAGAAA
1 TTAGCGGCGTTTTTT-ACCAAGCGCCGCTAAAGAACAAGATC-TTTAGCGGCGTTTTTG-TCTAA
*
21848312 GCGCCACTAAAGAACATGATCT
63 GCGCCGCTAAAGAACATGATCT
* * * *
21848334 ATAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAATATGATTTTTAGCGGCGTTTTTGTCTAAGCG
1 TTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACAAGATCTTTAGCGGCGTTTTTGTCTAAGCG
21848399 CCGCTAAAGAACATGATCT
66 CCGCTAAAGAACATGATCT
* * ** * *
21848418 TTAGCGGCATTTTTCT-CCATGCGCCGCTAAAGAACAAGATCTTTAGCGTTGTCTTTTTTTTAAG
1 TTAGCGGCGTTTTT-TACCAAGCGCCGCTAAAGAACAAGATCTTTAGCGGCGT-TTTTGTCTAAG
*
21848482 CGCCGCTAAAGAACATGACCT
64 CGCCGCTAAAGAACATGATCT
21848503 TTAGCGGCGTTTTTT
1 TTAGCGGCGTTTTTT
21848518 TCTGTAAACG
Statistics
Matches: 154, Mismatches: 27, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
84 66 0.43
85 74 0.48
86 14 0.09
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (84 bp):
TTAGCGGCGTTTTTTACCAAGCGCCGCTAAAGAACAAGATCTTTAGCGGCGTTTTTGTCTAAGCG
CCGCTAAAGAACATGATCT
Found at i:21849145 original size:13 final size:12
Alignment explanation
Indices: 21849133--21849187 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
21849123 TTAAATTTAT
21849133 TATTAATTATTA
1 TATTAATTATTA
21849145 TATTTAA--ATGTA
1 TA-TTAATTAT-TA
21849157 TTATTAATTATTA
1 -TATTAATTATTA
21849170 TATTTAATTATTAA
1 TA-TTAATTATT-A
21849184 TATT
1 TATT
21849188 TATATGTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
11 2 0.06
12 10 0.28
13 19 0.53
14 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TATTAATTATTA
Found at i:21849147 original size:25 final size:25
Alignment explanation
Indices: 21849119--21849176 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
21849109 TTTTTTAGAC
*
21849119 ATATTTAAATTTATTATTAATTATT
1 ATATTTAAATGTATTATTAATTATT
21849144 ATATTTAAATGTATTATTAATTATT
1 ATATTTAAATGTATTATTAATTATT
21849169 ATATTTAA
1 ATATTTAA
21849177 TTATTAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
ATATTTAAATGTATTATTAATTATT
Found at i:21850921 original size:136 final size:133
Alignment explanation
Indices: 21850676--21851074 Score: 586
Period size: 136 Copynumber: 3.0 Consensus size: 133
21850666 CTAAAAATAT
* * * *
21850676 AATTAAGTTCACAACCAACACAGTAGTTTACAAATACATAATTCATTTCACTGCCTTATTGAAGT
1 AATTAAGTTTACAAGCAACACAATAG-TT-CAAATACATAATTTATTTCACTGCCTTATTGAAGT
* *
21850741 AAAGTTTTGGACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGACGGAAATAAACTTAAAAG
64 AAAGTCTTGGACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGATGGAAATAAACTT-AAAG
21850806 TAATTC
128 TAATTC
* * * * *
21850812 GATTAAGTTTACAAGCAACATAATAGCTTGCAAATACATGATTTATTTCACTGTCTTATTGAAAT
1 AATTAAGTTTACAAGCAACACAATAG-TT-CAAATACATAATTTATTTCACTGCCTTATTGAAGT
* *
21850877 AAAGTCTTGGACTCAAATAGTTTCAAAATGATTTGGCACTTGAAAAATGGAAATAAACTT-AAGT
64 AAAGTCTTGGACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGATGGAAATAAACTTAAAGT
*
21850941 AGTTC
129 AATTC
21850946 AATTAAGTTTACAAGCAACACAATAG-TCAAATACATAATTTATTTCACTGCCTTATTGAAGTAA
1 AATTAAGTTTACAAGCAACACAATAGTTCAAATACATAATTTATTTCACTGCCTTATTGAAGTAA
* *
21851010 AGTCTTTGACTCAAATAGTTCCAAAATGATTTGGCACTTAAAAGATGGAAATAAACTTGAAAGTA
66 AGTCTTGGACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGATGGAAATAAACTT-AAAGTA
21851075 GTTTGACTAA
Statistics
Matches: 236, Mismatches: 25, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
131 88 0.37
132 1 0.00
133 5 0.02
134 32 0.14
136 110 0.47
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (133 bp):
AATTAAGTTTACAAGCAACACAATAGTTCAAATACATAATTTATTTCACTGCCTTATTGAAGTAA
AGTCTTGGACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGATGGAAATAAACTTAAAGTAA
TTC
Found at i:21852201 original size:154 final size:152
Alignment explanation
Indices: 21852043--21852469 Score: 586
Period size: 154 Copynumber: 2.8 Consensus size: 152
21852033 TGGGTTGTAA
* * * *
21852043 GTGTGCTTTATAAAATTATTATTTAAATAATGATATGTTAAATAAAATTATTGATTAAA-AATAT
1 GTGTGTTTTATAAAATTATTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATAT
*
21852107 TTAAAAGATATAATCAAAATTTAAAATATACTTAAGTTTTTGAAATATAATATACTAGTTTTTTT
66 TTAAAAGATATAA-C-AAATTAAAAATATACTTAAGTTTTTGAAATATAATATACTAG-TTTTTT
* * * *
21852172 ATCTCGTGTGATGCACGGGTTACTT
128 ATCCCATGTGATGCACGGATTACTC
*
21852197 GTGTGTTTTATAAAATCATTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATAT
1 GTGTGTTTTATAAAATTATTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATAT
* *
21852262 TTAAAAGATATAAACAAATTAAAAAATATACTTAAGTTTTCGAGATATAATATACTAGTTTTTTA
66 TTAAAAGATAT-AACAAATT-AAAAATATACTTAAGTTTTTGAAATATAATATACTAGTTTTTTA
* * *
21852327 TCCCATGTGATGTATGGATTGCTC
129 TCCCATGTGATGCACGGATTACTC
* * * * *
21852351 GTATGTTTTATAAAATTGTTATTTAAATAACGATATATTAAATAAAATTATTAATAAAATAATAT
1 GTGTGTTTTATAAAATTATTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATAT
* *
21852416 TTAAAACATATAACCAAATTAAAAATTATACTTAAGTTTTTAAAATATAATATA
66 TTAAAAGATATAA-CAAATTAAAAA-TATACTTAAGTTTTTGAAATATAATATA
21852470 TTTGTAATGT
Statistics
Matches: 243, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
153 7 0.03
154 183 0.75
155 51 0.21
156 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (152 bp):
GTGTGTTTTATAAAATTATTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATAT
TTAAAAGATATAACAAATTAAAAATATACTTAAGTTTTTGAAATATAATATACTAGTTTTTTATC
CCATGTGATGCACGGATTACTC
Found at i:21852276 original size:20 final size:18
Alignment explanation
Indices: 21852249--21852291 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
21852239 TAAAATTATT
21852249 GATA-AAACAATATTTAAAA
1 GATATAAACAA-A-TTAAAA
21852268 GATATAAACAAATTAAAA
1 GATATAAACAAATTAAAA
*
21852286 AATATA
1 GATATA
21852292 CTTAAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 5 0.23
20 6 0.27
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
GATATAAACAAATTAAAA
Found at i:21852286 original size:19 final size:20
Alignment explanation
Indices: 21852249--21852291 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
21852239 TAAAATTATT
*
21852249 GATA-AAACAATATTTAAAA
1 GATATAAACAATATTAAAAA
21852268 GATATAAACAA-ATTAAAAA
1 GATATAAACAATATTAAAAA
21852287 -ATATA
1 GATATA
21852292 CTTAAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (20 bp):
GATATAAACAATATTAAAAA
Found at i:21853665 original size:24 final size:25
Alignment explanation
Indices: 21853638--21853686 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
21853628 TAGTTTATAT
* *
21853638 TTTTATAATTTTTAA-AAGATTAAA
1 TTTTATAATTTATAAGAAAATTAAA
*
21853662 TTTTATTATTTATAAGAAAATTAAA
1 TTTTATAATTTATAAGAAAATTAAA
21853687 GTACAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
TTTTATAATTTATAAGAAAATTAAA
Found at i:21857700 original size:43 final size:43
Alignment explanation
Indices: 21857638--21857912 Score: 270
Period size: 43 Copynumber: 6.4 Consensus size: 43
21857628 ACATTTGCGA
* *
21857638 CGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGTGG
1 CGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGG
* ** * *
21857681 TGCTTTTTTCACAAACGCCGCTATAGAT-AGGGACCTTTAGCAG
1 CGCTTTTCCCACAAACGCCGCTATAGATCA-AGACCTTTAGCGG
* * ** *
21857724 CACTTCT-ATACAAACTCCGCTATAGATCAAGACCTTTAGCGG
1 CGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGG
* * * *
21857766 TGCTTTTCCCAAAAACGCCGCTATAGATCAAGACCATTAGTGG
1 CGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGG
* * * **
21857809 CACTTTTTCCACAAACGCCACTATATCTCAAGACCTTTAGCGG
1 CGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGG
* *
21857852 CGCTTTTCCCACAAACGCTGCTATAG-TACAA-ACCTTTAGCGA
1 CGCTTTTCCCACAAACGCCGCTATAGAT-CAAGACCTTTAGCGG
* * *
21857894 CGCTTCTCGCAAAAACGCC
1 CGCTTTTCCCACAAACGCC
21857913 ACAAAAACAT
Statistics
Matches: 187, Mismatches: 41, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
42 59 0.32
43 128 0.68
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (43 bp):
CGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGG
Found at i:21857791 original size:85 final size:85
Alignment explanation
Indices: 21857647--21857877 Score: 277
Period size: 85 Copynumber: 2.7 Consensus size: 85
21857637 ACGCTTTTCC
* * **
21857647 CACAAACGCCGCTATAGATCAGGACCTTTAGTGGTGCTTTTTTCACAAACGCCGCTATAGAT-AG
1 CACAAACGCCGCTATAGATCAAGACCTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGATCA-
* *
21857711 GGACCTTTAGCAGCACTTCTAT
65 AGACCATTAGCAGCACTT-TAT
* *
21857733 -ACAAACTCCGCTATAGATCAAGACCTTTAGCGGTGCTTTTCCCAAAAACGCCGCTATAGATCAA
1 CACAAACGCCGCTATAGATCAAGACCTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGATCAA
** *
21857797 GACCATTAGTGGCACTTTTT
66 GACCATTAGCAGCACTTTAT
* ** * *
21857817 CCACAAACGCCACTATATCTCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTATAG
1 -CACAAACGCCGCTATAGATCAAGACCTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAG
21857878 TACAAACCTT
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
84 2 0.02
85 69 0.56
86 53 0.43
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (85 bp):
CACAAACGCCGCTATAGATCAAGACCTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGATCAA
GACCATTAGCAGCACTTTAT
Found at i:21857887 original size:128 final size:128
Alignment explanation
Indices: 21857634--21857912 Score: 321
Period size: 128 Copynumber: 2.2 Consensus size: 128
21857624 GCAAACATTT
* * * ** *
21857634 GCGACGCTTTTCCCACAAACGCCGCTATAGATCAGGACCTTTAGTGGTGCTTTTTTCACAAACGC
1 GCGACGCTTTTCCCAAAAACGCCGCTATAGATCAAGACCATTAGTGGCACTTTTTCCACAAACGC
* * * *
21857699 CGCTATAGATAGGGACCTTTAGCAGCACTTCTATACAAACTCCGCTATAGATCAAGACCTTTA
66 CACTATAGATAGAGACCTTTAGCAGCACTTCTACACAAACGCCGCTATAGATCAAGACCTTTA
**
21857762 GCGGTGCTTTTCCCAAAAACGCCGCTATAGATCAAGACCATTAGTGGCACTTTTTCCACAAACGC
1 GCGACGCTTTTCCCAAAAACGCCGCTATAGATCAAGACCATTAGTGGCACTTTTTCCACAAACGC
** * * * * *
21857827 CACTATATCTCA-AGACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTATAG-TACAA-ACCTTT
66 CACTATAGAT-AGAGACCTTTAGCAGCACTTCT-ACACAAACGCCGCTATAGAT-CAAGACCTTT
21857889 A
128 A
* *
21857890 GCGACGCTTCTCGCAAAAACGCC
1 GCGACGCTTTTCCCAAAAACGCC
21857913 ACAAAAACAT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
128 107 0.86
129 18 0.14
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (128 bp):
GCGACGCTTTTCCCAAAAACGCCGCTATAGATCAAGACCATTAGTGGCACTTTTTCCACAAACGC
CACTATAGATAGAGACCTTTAGCAGCACTTCTACACAAACGCCGCTATAGATCAAGACCTTTA
Found at i:21859123 original size:5 final size:5
Alignment explanation
Indices: 21859113--21859139 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
21859103 CTTTCTTGCC
21859113 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
21859140 AACAAGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:21860875 original size:31 final size:31
Alignment explanation
Indices: 21860837--21860916 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
21860827 CATGGTTGAT
*
21860837 TTAGTAGCAAAAATCAATAGAAGGTACCATC
1 TTAGTAGCAAAAACCAATAGAAGGTACCATC
21860868 TTAGTAGCAAAAACCAATAGAAGGTACCATC
1 TTAGTAGCAAAAACCAATAGAAGGTACCATC
21860899 TTAGCT-GCAAAAACCAAT
1 TTAG-TAGCAAAAACCAAT
21860917 TAAAATCCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 46 0.98
32 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (31 bp):
TTAGTAGCAAAAACCAATAGAAGGTACCATC
Found at i:21862465 original size:21 final size:21
Alignment explanation
Indices: 21862439--21862479 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21862429 ACCATGCATT
* * *
21862439 TAAACCTTAAATCATTAACAC
1 TAAACCGTAAACCATAAACAC
21862460 TAAACCGTAAACCATAAACA
1 TAAACCGTAAACCATAAACA
21862480 TCAACCCCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAACCGTAAACCATAAACAC
Found at i:21862561 original size:7 final size:7
Alignment explanation
Indices: 21862551--21862610 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
21862541 CATTAAAACG
21862551 TAAACCC
1 TAAACCC
*
21862558 TAAACCT
1 TAAACCC
21862565 TAAACCC
1 TAAACCC
*
21862572 CAAATCCC
1 TAAA-CCC
*
21862580 -AACCCC
1 TAAACCC
21862586 TAAA-CC
1 TAAACCC
* *
21862592 TACACCA
1 TAAACCC
21862599 TAAACCC
1 TAAACCC
21862606 TAAAC
1 TAAAC
21862611 TCAAAACTCT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
6 8 0.20
7 30 0.73
8 3 0.07
ACGTcount: A:0.43, C:0.42, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:21862846 original size:41 final size:41
Alignment explanation
Indices: 21862724--21863000 Score: 265
Period size: 41 Copynumber: 6.8 Consensus size: 41
21862714 GCCCTCGAGT
* * * *
21862724 ATTAGCGACGCTT-TTTAAAAACGCTGCTAAAGCCTAGAGC
1 ATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGCCCACAGC
* * * * * *
21862764 AATAGCGGCGCTT-TCCCTAAAAACGCCGCTAAATCCAAGAGC
1 ATTAGCGACGCTTCT-TC-AAAAACGCCGCTAAAGCCCACAGC
* * * *
21862806 ATTAGCGATGCTTCTTCAAAAACGTCGCTAAAACCCAGAGC
1 ATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGCCCACAGC
* * *
21862847 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCCAAC
1 ATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGCCCACAGC
* * *
21862888 ATTAGCGACGCTTCTTAAAAAAAGCCGCTAAATCCCACAGC
1 ATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGCCCACAGC
*
21862929 ATTAGCTG-CGCTTCTTCAAAAACGCTGCTAAAGCCC-CAGC
1 ATTAGC-GACGCTTCTTCAAAAACGCCGCTAAAGCCCACAGC
* * * * *
21862969 ATTAGTGGCACTTTTTGAAAAACGCCGCTAAA
1 ATTAGCGACGCTTCTTCAAAAACGCCGCTAAA
21863001 TTCCCCAAAG
Statistics
Matches: 196, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.01
40 41 0.21
41 120 0.61
42 33 0.17
43 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (41 bp):
ATTAGCGACGCTTCTTCAAAAACGCCGCTAAAGCCCACAGC
Found at i:21863113 original size:40 final size:40
Alignment explanation
Indices: 21863069--21863175 Score: 103
Period size: 39 Copynumber: 2.7 Consensus size: 40
21863059 ATAAACGCCG
* *
21863069 CTAATGCTCTATTTTTAGTGGCGTTTTTCAAAAAGTGCCC
1 CTAATGCTCTATTTTTAGTGGCGTTTTTCAAAAAGCGCAC
* * *
21863109 CTAATGCT-TCA-TTTTAGCT-GCGTTTTTCTAAATGCGCAG
1 CTAATGCTCT-ATTTTTAG-TGGCGTTTTTCAAAAAGCGCAC
** *
21863148 CTAATGCTCGCTTTTTAGCGGCGTTTTT
1 CTAATGCTCTATTTTTAGTGGCGTTTTT
21863176 TTGTCCAAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
39 30 0.56
40 24 0.44
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (40 bp):
CTAATGCTCTATTTTTAGTGGCGTTTTTCAAAAAGCGCAC
Found at i:21864257 original size:21 final size:23
Alignment explanation
Indices: 21864224--21864267 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
21864214 AAATAGGATA
**
21864224 AAAATAAATAATTAGTTAATAAT
1 AAAATAAATAATTAAATAATAAT
21864247 AAAA-AAA-AATTAAATAATAAT
1 AAAATAAATAATTAAATAATAAT
21864268 GGTATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAATAAATAATTAAATAATAAT
Found at i:21864599 original size:32 final size:32
Alignment explanation
Indices: 21864559--21864669 Score: 109
Period size: 34 Copynumber: 3.3 Consensus size: 32
21864549 TATTTTCTCT
*
21864559 ATAATATATTTACATACATGGGTGTTATATGA
1 ATAATATATTTACATGCATGGGTGTTATATGA
* * *
21864591 ATAATATATATATGCGTGCATGGGTGGTATAT-A
1 ATAATATAT-T-TACATGCATGGGTGTTATATGA
*
21864624 TATAATATATATTTA-AGTGCATGGGTGTTATATGT
1 -AT-A-ATATATTTACA-TGCATGGGTGTTATATGA
21864659 ATAATATATTT
1 ATAATATATTT
21864670 GTATGAGTCT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
32 17 0.27
33 3 0.05
34 36 0.56
35 2 0.03
36 6 0.09
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (32 bp):
ATAATATATTTACATGCATGGGTGTTATATGA
Found at i:21864613 original size:34 final size:34
Alignment explanation
Indices: 21864575--21864667 Score: 125
Period size: 34 Copynumber: 2.7 Consensus size: 34
21864565 TATTTACATA
**
21864575 CATGGGTGTTATATGAATAATATATATATGCGTG
1 CATGGGTGTTATATGAATAATATATATATAAGTG
* *
21864609 CATGGGTGGTATAT-ATATAATATATATTTAAGTG
1 CATGGGTGTTATATGA-ATAATATATATATAAGTG
*
21864643 CATGGGTGTTATATGTATAATATAT
1 CATGGGTGTTATATGAATAATATAT
21864668 TTGTATGAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
33 1 0.02
34 50 0.98
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (34 bp):
CATGGGTGTTATATGAATAATATATATATAAGTG
Found at i:21864760 original size:29 final size:28
Alignment explanation
Indices: 21864696--21864761 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
21864686 TACATAGTAC
*
21864696 ATATATATGTGTGGTTCTGCCATATATA
1 ATATATATGTGTGGTTCTACCATATATA
**
21864724 ATGA-ATATGTGTGGGTTCTATTATATATA
1 AT-ATATATGTGT-GGTTCTACCATATATA
21864753 ATATATATG
1 ATATATATG
21864762 CAGTTATAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (28 bp):
ATATATATGTGTGGTTCTACCATATATA
Found at i:21868342 original size:20 final size:20
Alignment explanation
Indices: 21868317--21868357 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
21868307 CGATTGAGTC
*
21868317 TAACCAGTGATGGTGGTTTG
1 TAACCAATGATGGTGGTTTG
21868337 TAACCAATGATGGTGGTTTG
1 TAACCAATGATGGTGGTTTG
21868357 T
1 T
21868358 TGGCCGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.10, G:0.32, T:0.37
Consensus pattern (20 bp):
TAACCAATGATGGTGGTTTG
Found at i:21873836 original size:30 final size:32
Alignment explanation
Indices: 21873795--21873879 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
21873785 TATGGGTTTT
* *
21873795 GGTGTTATATATAATTTATATTTACGTGCATG
1 GGTGTTATATATAATATATATTCACGTGCATG
**
21873827 GGTGTTATATATAATATATATTCGGGTGCATG
1 GGTGTTATATATAATATATATTCACGTGCATG
21873859 GGTGTTATATAGATAATATAT
1 GGTGTTATAT--ATAATATAT
21873880 TTGCGTGGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
32 38 0.81
34 9 0.19
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (32 bp):
GGTGTTATATATAATATATATTCACGTGCATG
Found at i:21879458 original size:3 final size:3
Alignment explanation
Indices: 21879450--21879508 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
21879440 CAATGATCTA
21879450 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21879498 AAT AAT AAT AA
1 AAT AAT AAT AA
21879509 AACTAGCTTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:21881146 original size:18 final size:18
Alignment explanation
Indices: 21881123--21881158 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
21881113 TTTTCTCTTG
21881123 GTTTT-CTTCTTCTATTTT
1 GTTTTCCTTC-TCTATTTT
21881141 GTTTTCCTTCTCTATTTT
1 GTTTTCCTTCTCTATTTT
21881159 CAATCTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.06, C:0.19, G:0.06, T:0.69
Consensus pattern (18 bp):
GTTTTCCTTCTCTATTTT
Found at i:21891577 original size:25 final size:25
Alignment explanation
Indices: 21891515--21891578 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
21891505 ACCGAGTCTC
** *
21891515 TTTTCCTAGTTAAGTTTTGCTATCT
1 TTTTCCTAGTTAAACTCTGCTATCT
* *
21891540 TTTTCCCAATTAAACTCTGCTATCT
1 TTTTCCTAGTTAAACTCTGCTATCT
21891565 TTTTCCTAGTTAAA
1 TTTTCCTAGTTAAA
21891579 GCTTGGTTAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.50
Consensus pattern (25 bp):
TTTTCCTAGTTAAACTCTGCTATCT
Found at i:21894815 original size:20 final size:19
Alignment explanation
Indices: 21894792--21894835 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
21894782 AAAAATTTAG
21894792 AAAATTAAAAAAAGTATTTT
1 AAAATT-AAAAAAGTATTTT
*
21894812 AAAAATAAAAAAGTATTTT
1 AAAATTAAAAAAGTATTTT
*
21894831 TAAAT
1 AAAAT
21894836 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAAATTAAAAAAGTATTTT
Found at i:21897427 original size:25 final size:25
Alignment explanation
Indices: 21897386--21897455 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
21897376 CACCGAGTCT
* * *
21897386 TTTTTCCTAGTTGAACTCTGCTATC
1 TTTTTCCGAGTTAAACTCTGCTATA
*
21897411 TTTTTCCCG-GTTAAACTTTGCTATA
1 TTTTT-CCGAGTTAAACTCTGCTATA
*
21897436 TTTTTCTGAGTTAAACTCTG
1 TTTTTCCGAGTTAAACTCTG
21897456 GTTACTCTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
24 2 0.05
25 33 0.89
26 2 0.05
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.49
Consensus pattern (25 bp):
TTTTTCCGAGTTAAACTCTGCTATA
Found at i:21905139 original size:26 final size:26
Alignment explanation
Indices: 21905110--21905292 Score: 181
Period size: 26 Copynumber: 7.0 Consensus size: 26
21905100 ACAGTCATTC
*
21905110 TACCCTTCGAGGGTATTTCGATAATT
1 TACCCATCGAGGGTATTTCGATAATT
* *
21905136 TACCCATCGAGCGTATTT-TAGTAATT
1 TACCCATCGAGGGTATTTCGA-TAATT
21905162 TACCCATCGAGGGTATTTC-AGTAATT
1 TACCCATCGAGGGTATTTCGA-TAATT
* * ** * **
21905188 TATCTATTAAAGGTATTTTAATAATT
1 TACCCATCGAGGGTATTTCGATAATT
* *
21905214 TACCCATCGATGGAATTTCGATAATT
1 TACCCATCGAGGGTATTTCGATAATT
* * *
21905240 TACCCATCGAAGGTGTTTCGTTAATT
1 TACCCATCGAGGGTATTTCGATAATT
* *
21905266 TACCCATCGAGGGTATTTTGGTAATT
1 TACCCATCGAGGGTATTTCGATAATT
21905292 T
1 T
21905293 TAGCCCATTA
Statistics
Matches: 128, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
25 1 0.01
26 126 0.98
27 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.39
Consensus pattern (26 bp):
TACCCATCGAGGGTATTTCGATAATT
Found at i:21905291 original size:78 final size:78
Alignment explanation
Indices: 21905101--21905292 Score: 201
Period size: 78 Copynumber: 2.4 Consensus size: 78
21905091 AGGAGTATAA
* * * * *
21905101 CAGTCATTCTACCCTTCGAGGGTATTTCGATAATTTACCCATCGAGCGTATTTTAGTAATTTACC
1 CAGTAATT-TACCCATCGAGGGTATTTTGATAATTTACCCATCGAGCGAATTTGAGTAATTTACC
*
21905166 CATCGAGGGTATTT
65 CATCGAAGGTATTT
* * ** * *
21905180 CAGTAATTTATCTATTAAAGGTATTTTAATAATTTACCCATCGATG-GAATTTCGA-TAATTTAC
1 CAGTAATTTACCCATCGAGGGTATTTTGATAATTTACCCATCGA-GCGAATTT-GAGTAATTTAC
*
21905243 CCATCGAAGGTGTTT
64 CCATCGAAGGTATTT
*
21905258 C-GTTAATTTACCCATCGAGGGTATTTTGGTAATTT
1 CAG-TAATTTACCCATCGAGGGTATTTTGATAATTT
21905293 TAGCCCATTA
Statistics
Matches: 90, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
77 1 0.01
78 80 0.89
79 9 0.10
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (78 bp):
CAGTAATTTACCCATCGAGGGTATTTTGATAATTTACCCATCGAGCGAATTTGAGTAATTTACCC
ATCGAAGGTATTT
Found at i:21905563 original size:9 final size:9
Alignment explanation
Indices: 21905549--21905598 Score: 100
Period size: 9 Copynumber: 5.6 Consensus size: 9
21905539 AAGATTTAGA
21905549 TCATTCCTT
1 TCATTCCTT
21905558 TCATTCCTT
1 TCATTCCTT
21905567 TCATTCCTT
1 TCATTCCTT
21905576 TCATTCCTT
1 TCATTCCTT
21905585 TCATTCCTT
1 TCATTCCTT
21905594 TCATT
1 TCATT
21905599 TCGAATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (9 bp):
TCATTCCTT
Found at i:21912137 original size:26 final size:26
Alignment explanation
Indices: 21912102--21912151 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
21912092 CCCACACACC
* *
21912102 AATATTGCAGCATAGCTGCCAGTAAT
1 AATATCGCAGCAGAGCTGCCAGTAAT
21912128 AATATCGCAGCAGAGCTGCCAGTA
1 AATATCGCAGCAGAGCTGCCAGTA
21912152 GAGTATATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (26 bp):
AATATCGCAGCAGAGCTGCCAGTAAT
Found at i:21912412 original size:26 final size:26
Alignment explanation
Indices: 21912383--21912503 Score: 125
Period size: 26 Copynumber: 4.7 Consensus size: 26
21912373 CGGTCATTCG
* *
21912383 ACCCTTCGAGGGTATTTCGATAATTT
1 ACCCATCGAGGGTATTTTGATAATTT
* * * *
21912409 ACCCATTGAAGTTATTTTGGTAATTT
1 ACCCATCGAGGGTATTTTGATAATTT
* *
21912435 TCCCATCGAGGGTATTTTAATAATTT
1 ACCCATCGAGGGTATTTTGATAATTT
* * *
21912461 ACCCATCGAAGGTATTTTGGTATTTT
1 ACCCATCGAGGGTATTTTGATAATTT
* *
21912487 ACTCATCGAGAGTATTT
1 ACCCATCGAGGGTATTT
21912504 CATTATTTTT
Statistics
Matches: 75, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (26 bp):
ACCCATCGAGGGTATTTTGATAATTT
Found at i:21912466 original size:52 final size:52
Alignment explanation
Indices: 21912383--21912505 Score: 167
Period size: 52 Copynumber: 2.4 Consensus size: 52
21912373 CGGTCATTCG
* * * *
21912383 ACCCTTCGAGGGTATTTCGATAATTTACCCATTGAAGTTATTTTGGTAATTTT
1 ACCCATCGAGGGTATTTCAATAATTTACCCATCGAAGGTATTTTGGT-ATTTT
*
21912436 -CCCATCGAGGGTATTTTAATAATTTACCCATCGAAGGTATTTTGGTATTTT
1 ACCCATCGAGGGTATTTCAATAATTTACCCATCGAAGGTATTTTGGTATTTT
* *
21912487 ACTCATCGAGAGTATTTCA
1 ACCCATCGAGGGTATTTCA
21912506 TTATTTTTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
51 5 0.08
52 56 0.92
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (52 bp):
ACCCATCGAGGGTATTTCAATAATTTACCCATCGAAGGTATTTTGGTATTTT
Found at i:21916652 original size:19 final size:19
Alignment explanation
Indices: 21916638--21916674 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21916628 ACTTTTTGTC
21916638 TTTAATTTTAATTTTAATA
1 TTTAATTTTAATTTTAATA
*
21916657 TTTATTTTTAATTTTAAT
1 TTTAATTTTAATTTTAAT
21916675 GCTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTTTAATTTTAATA
Found at i:21916680 original size:18 final size:19
Alignment explanation
Indices: 21916643--21916684 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
21916633 TTGTCTTTAA
**
21916643 TTTTAATTTTAATATTTAT
1 TTTTAATTTTAATAGCTAT
21916662 TTTTAATTTTAAT-GCTAT
1 TTTTAATTTTAATAGCTAT
21916680 TTTTA
1 TTTTA
21916685 TTTATACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTAATTTTAATAGCTAT
Found at i:21928901 original size:23 final size:23
Alignment explanation
Indices: 21928848--21928933 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
21928838 TCATTAACAT
*
21928848 TGTTCATGAATATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
* *
21928872 TGTTCATGAACATGTTTATTTAA
1 TGTTCATGAACATGTTCAATTAA
*
21928895 TGTTCATGAACATATTCAATTAA
1 TGTTCATGAACATGTTCAATTAA
*
21928918 -GTTAAATGAACATGTT
1 TGTT-CATGAACATGTT
21928934 TGTAAACATT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.58
24 19 0.36
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:21930703 original size:14 final size:16
Alignment explanation
Indices: 21930684--21930716 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
21930674 TTAAATTAAT
21930684 TTTTAA-TATTTT-TA
1 TTTTAATTATTTTATA
21930698 TTTTAATTATTTTATA
1 TTTTAATTATTTTATA
21930714 TTT
1 TTT
21930717 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 6 0.35
16 5 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTAATTATTTTATA
Found at i:21930708 original size:15 final size:15
Alignment explanation
Indices: 21930684--21930724 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21930674 TTAAATTAAT
21930684 TTTTAATATTTT-TA
1 TTTTAATATTTTATA
21930698 TTTTAATTATTTTATA
1 TTTTAA-TATTTTATA
21930714 -TTT-ATATTTTA
1 TTTTAATATTTTA
21930725 AAATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
14 7 0.28
15 9 0.36
16 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAATATTTTATA
Found at i:21930721 original size:22 final size:21
Alignment explanation
Indices: 21930679--21930725 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
21930669 ATATTTTAAA
*
21930679 TTAATTTTTAATATTTTTATT
1 TTAATTTTTAATATTTATATT
*
21930700 TTAATTATTTTATATTTATATT
1 TTAATT-TTTAATATTTATATT
21930722 TTAA
1 TTAA
21930726 AATAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTAATTTTTAATATTTATATT
Found at i:21931182 original size:11 final size:11
Alignment explanation
Indices: 21931121--21931175 Score: 92
Period size: 11 Copynumber: 5.0 Consensus size: 11
21931111 GTTTCTTTTT
21931121 CTATTTTCTTG
1 CTATTTTCTTG
21931132 CTATTTTCTTG
1 CTATTTTCTTG
21931143 CTATTTTCTTG
1 CTATTTTCTTG
* *
21931154 TTATTTTGTTG
1 CTATTTTCTTG
21931165 CTATTTTCTTG
1 CTATTTTCTTG
21931176 TTGTTTTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.09, C:0.15, G:0.11, T:0.65
Consensus pattern (11 bp):
CTATTTTCTTG
Found at i:21931191 original size:22 final size:22
Alignment explanation
Indices: 21931121--21931182 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
21931111 GTTTCTTTTT
*
21931121 CTATTTTCTTGCTATTTTCTTG
1 CTATTTTCTTGTTATTTTCTTG
*
21931143 CTATTTTCTTGTTATTTTGTTG
1 CTATTTTCTTGTTATTTTCTTG
*
21931165 CTATTTTCTTGTTGTTTT
1 CTATTTTCTTGTTATTTT
21931183 TTCACTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.08, C:0.13, G:0.11, T:0.68
Consensus pattern (22 bp):
CTATTTTCTTGTTATTTTCTTG
Found at i:21931197 original size:33 final size:33
Alignment explanation
Indices: 21931129--21931200 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
21931119 TTCTATTTTC
** *
21931129 TTGCTATTTTCTTGCTATTTTCTTGTTATTTTG
1 TTGCTATTTTCTTGCTATTTTCTTACTATTATG
* *
21931162 TTGCTATTTTCTTGTTGTTTT-TTCACTATTATG
1 TTGCTATTTTCTTGCTATTTTCTT-ACTATTATG
21931195 TTGCTA
1 TTGCTA
21931201 CTATTTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.11, C:0.12, G:0.12, T:0.64
Consensus pattern (33 bp):
TTGCTATTTTCTTGCTATTTTCTTACTATTATG
Found at i:21933471 original size:27 final size:27
Alignment explanation
Indices: 21933435--21933486 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
21933425 AGCTTATGAG
21933435 AAAGGTTCTTAGATCATTATGTCACGA
1 AAAGGTTCTTAGATCATTATGTCACGA
21933462 AAAGGTTCTTAGATCATTATGTCAC
1 AAAGGTTCTTAGATCATTATGTCAC
21933487 ACCCGAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (27 bp):
AAAGGTTCTTAGATCATTATGTCACGA
Found at i:21937441 original size:29 final size:30
Alignment explanation
Indices: 21937384--21937441 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
21937374 AATCATTTAA
* **
21937384 ATAAAAAATTTTAAATAATTCAATGATTTG
1 ATAAAAAATTTCAAATAATTCAAAAATTTG
*
21937414 ATAAAAACTTTCAAATAA-TCAAAAATTT
1 ATAAAAAATTTCAAATAATTCAAAAATTT
21937442 ATTTTATAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.36
Consensus pattern (30 bp):
ATAAAAAATTTCAAATAATTCAAAAATTTG
Found at i:21942741 original size:25 final size:22
Alignment explanation
Indices: 21942716--21942851 Score: 87
Period size: 25 Copynumber: 5.7 Consensus size: 22
21942706 TGCAATGTAT
21942716 TTATTTATTTTAAAC-TTTATA
1 TTATTTATTTTAAACTTTTATA
*
21942737 TTATTTATTTTAAATCGTTCTATTA
1 TTATTTATTTTAAA-C-TTTTA-TA
**
21942762 TTATTTATTTTAAGTTTTTAATATA
1 TTATTTATTTTAA-ACTTT--TATA
21942787 TTATTTATTTTAAACTATGTTAATCAA
1 TTATTTATTTTAAACT-T-TT-AT--A
** *
21942814 TTATCCATTTTAAA-TATATATA
1 TTATTTATTTTAAACT-TTTATA
*
21942836 TTATTTATGTTAAACT
1 TTATTTATTTTAAACT
21942852 ACATATGTAT
Statistics
Matches: 90, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
21 14 0.16
22 13 0.14
23 1 0.01
24 9 0.10
25 34 0.38
26 6 0.07
27 13 0.14
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (22 bp):
TTATTTATTTTAAACTTTTATA
Found at i:21949079 original size:91 final size:91
Alignment explanation
Indices: 21948810--21949086 Score: 326
Period size: 91 Copynumber: 3.1 Consensus size: 91
21948800 CGAAGATTTG
* * **
21948810 ACGTGTTATT-AGTTTGAAAGCTCTTATGAGCAAATTGACGCGTTATTGGGGGAGAATATTTAGC
1 ACGTGTTATTGA-TTGGAAAGCTCTTATGAGCAAATTGACGTGTTATCAGGGGAGAATATTTAGC
* *
21948874 CTACGGG-TTGTACACTATGTGCATCTA
65 CTACGGGCTT-TGCACTATGTGCATCTT
* * * * * * *
21948901 ACATGTTATTGTTTGGAAAACTTTTATGAGCAAATTGACGTGTTATCA-AGGAGAATATTTATCA
1 ACGTGTTATTGATTGGAAAGCTCTTATGAGCAAATTGACGTGTTATCAGGGGAGAATATTTAGCC
* *
21948965 TATGGGCTTTGCATTATGTGCATCTT
66 TACGGGCTTTGCACTATGTGCATCTT
* * * * *
21948991 GCGTGTTATTGATTGGAGAGCTCTTATAAGCAAACTGACATGTTATCAGGGGAGAATATTTAGCC
1 ACGTGTTATTGATTGGAAAGCTCTTATGAGCAAATTGACGTGTTATCAGGGGAGAATATTTAGCC
21949056 TACGGGCTTTGCACTATGTGCATCTT
66 TACGGGCTTTGCACTATGTGCATCTT
*
21949082 TCGTG
1 ACGTG
21949087 CAAAAACCAT
Statistics
Matches: 153, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
90 71 0.46
91 82 0.54
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (91 bp):
ACGTGTTATTGATTGGAAAGCTCTTATGAGCAAATTGACGTGTTATCAGGGGAGAATATTTAGCC
TACGGGCTTTGCACTATGTGCATCTT
Found at i:21955336 original size:126 final size:126
Alignment explanation
Indices: 21955105--21955481 Score: 638
Period size: 126 Copynumber: 3.0 Consensus size: 126
21955095 TAAGGGTTTT
21955105 TAGGTC-CTGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA
1 TAGGTCAC-GGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTA
21955169 GCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
65 GCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
21955231 TAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
1 TAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* *
21955296 CAGGATGTTATTTGAGAAGAATTTGTGAAATCGCAG-CCTCGT-CAGCGCGCTTTTGCTACAG
66 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGC-GCCCTCGTGGA-CGCGCTTTTGCTACAG
* * *
21955357 TAGGTCATGTAAGAAATAA--ATTTTTTTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAG
1 TAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
*
21955420 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAG
66 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
21955481 T
1 T
21955482 GGCGTGTTTG
Statistics
Matches: 238, Mismatches: 8, Indels: 12
0.92 0.03 0.05
Matches are distributed among these distances:
123 1 0.00
124 98 0.41
125 2 0.01
126 135 0.57
127 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (126 bp):
TAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:21960227 original size:116 final size:116
Alignment explanation
Indices: 21959945--21960204 Score: 486
Period size: 116 Copynumber: 2.2 Consensus size: 116
21959935 CGAACCAATG
21959945 GTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATT
1 GTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATT
21960010 AATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCA
66 AATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCA
*
21960061 GTCAAAACATTTTTCTAAATCTAACATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATT
1 GTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATT
* *
21960126 AATGGTTAGTAAAATTATCAAATTATGT-AAATTATTATTTGTTAGTACCA
66 AATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCA
21960176 GTCAAAACATTTTTCCAAATCTAACATTA
1 GTCAAAACATTTTTCCAAATCTAACATTA
21960205 CGTTAAGGTT
Statistics
Matches: 140, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
115 49 0.35
116 91 0.65
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (116 bp):
GTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTAAGTCAAAAAATTGTATT
AATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTACCA
Found at i:21960270 original size:29 final size:29
Alignment explanation
Indices: 21960226--21960323 Score: 151
Period size: 29 Copynumber: 3.3 Consensus size: 29
21960216 GGGCTTTTAA
21960226 GTTAAGGGTTTAGGGTTTTAAATTAAATTAG
1 GTTAA-GG-TTAGGGTTTTAAATTAAATTAG
*
21960257 GTTAAGGTTAGGGTTTTTAATTAAATTAG
1 GTTAAGGTTAGGGTTTTAAATTAAATTAG
*
21960286 GTTAGGGTTAGGGTTTTAAATTAAATTAG
1 GTTAAGGTTAGGGTTTTAAATTAAATTAG
*
21960315 GTTAGGGTT
1 GTTAAGGTT
21960324 TTTAATTTTA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
29 57 0.89
30 2 0.03
31 5 0.08
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.43
Consensus pattern (29 bp):
GTTAAGGTTAGGGTTTTAAATTAAATTAG
Found at i:21960287 original size:23 final size:23
Alignment explanation
Indices: 21960261--21960452 Score: 127
Period size: 23 Copynumber: 7.7 Consensus size: 23
21960251 AATTAGGTTA
21960261 AGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
21960284 AGGTTAGGGTTAGGGTTTTAAATTAAATT
1 AGGTTAGGG-T----TTTT-AATTAAATT
*
21960313 AGGTTAGGGTTTTTAATTTTAAGTT
1 AGGTTAGGGTTTTTAA--TTAAATT
*
21960338 AAGAGTTTAGAGTTTTTAAGTTAAA--
1 -AG-G-TTAGGGTTTTTAA-TTAAATT
*
21960363 GGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGTTAGGGTTTTTAATT-AA--A--TT
*
21960391 AGGGTTAGGGTTTTTAATTAATTT
1 A-GGTTAGGGTTTTTAATTAAATT
****
21960415 AGGTTAGGGTTTAGGGTTAAATT
1 AGGTTAGGGTTTTTAATTAAATT
*
21960438 AGGTTAGAGTTTTTA
1 AGGTTAGGGTTTTTA
21960453 TTATATCAAA
Statistics
Matches: 133, Mismatches: 17, Indels: 38
0.71 0.09 0.20
Matches are distributed among these distances:
21 2 0.02
22 14 0.11
23 40 0.30
24 10 0.08
25 6 0.05
26 2 0.02
27 5 0.04
28 19 0.14
29 35 0.26
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (23 bp):
AGGTTAGGGTTTTTAATTAAATT
Found at i:21960357 original size:22 final size:22
Alignment explanation
Indices: 21960329--21960383 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
21960319 GGGTTTTTAA
*
21960329 TTTTAAGTT-AAGAGTTTAGAGT
1 TTTTAAGTTAAAG-GGTTAGAGT
*
21960351 TTTTAAGTTAAAGGGTTAGGGT
1 TTTTAAGTTAAAGGGTTAGAGT
21960373 TTTTAA-TTAAA
1 TTTTAAGTTAAA
21960384 TTAGGTTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 22 0.73
23 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.45
Consensus pattern (22 bp):
TTTTAAGTTAAAGGGTTAGAGT
Found at i:21960395 original size:29 final size:29
Alignment explanation
Indices: 21960362--21960432 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
21960352 TTTAAGTTAA
21960362 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
21960391 AGGGTTAGGGTTTTTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
21960420 AGGGTTTAGGGTT
1 AGGG-TTAGGGTT
21960433 AAATTAGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 32 0.80
30 8 0.20
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:21960566 original size:35 final size:35
Alignment explanation
Indices: 21960455--21960567 Score: 106
Period size: 35 Copynumber: 3.2 Consensus size: 35
21960445 AGTTTTTATT
21960455 ATATCAAATAAACTTCTATTTTATTACATCAAATA
1 ATATCAAATAAACTTCTATTTTATTACATCAAATA
* ** *** *
21960490 ATATCAAA-ATAAC-TCGAAATTTT-TTTTATTTTATT
1 ATATCAAATA-AACTTC--TATTTTATTACATCAAATA
*
21960525 ACATCAAATAAACTTCTATTTTATTACATCAAATA
1 ATATCAAATAAACTTCTATTTTATTACATCAAATA
21960560 ATATCAAA
1 ATATCAAA
21960568 ATAACTCAAA
Statistics
Matches: 56, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
34 8 0.14
35 40 0.71
36 8 0.14
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (35 bp):
ATATCAAATAAACTTCTATTTTATTACATCAAATA
Found at i:21960602 original size:43 final size:45
Alignment explanation
Indices: 21960528--21960613 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
21960518 TTTTATTACA
*
21960528 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
*
21960573 TCAAA-AAATTTCTATTTT-TTACATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATA
21960614 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:21963200 original size:29 final size:29
Alignment explanation
Indices: 21963134--21963200 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 29
21963124 GCGATTTCGC
21963134 AAAAAAGGA-CCATTCCGGTAAATAATTA
1 AAAAAAGGACCCATTCCGGTAAATAATTA
* * * **
21963162 AATAATGGACCCATTTCGGT-AATTTTTGA
1 AAAAAAGGACCCATTCCGGTAAATAATT-A
21963191 AAAAAAGGAC
1 AAAAAAGGAC
21963201 TTTTATTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
28 12 0.40
29 18 0.60
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (29 bp):
AAAAAAGGACCCATTCCGGTAAATAATTA
Found at i:21963959 original size:22 final size:23
Alignment explanation
Indices: 21963922--21963969 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
21963912 ATTTCATTAA
* * *
21963922 TTTTTTATTTAGTTTAATAAAGT
1 TTTTTTATATAGTTTAAAAAAAT
21963945 TTTTTTATATA-TTTAAAAAAAT
1 TTTTTTATATAGTTTAAAAAAAT
21963967 TTT
1 TTT
21963970 AAAATTCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTTATATAGTTTAAAAAAAT
Found at i:21964006 original size:16 final size:16
Alignment explanation
Indices: 21963963--21964007 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
21963953 ATATTTAAAA
21963963 AAAT-TTTAA-AATTC
1 AAATATTTAATAATTC
*
21963977 AAATTTTTAATAATT-
1 AAATATTTAATAATTC
21963992 AAATATTTAATTAATT
1 AAATATTTAA-TAATT
21964008 TGATGTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATATTTAATAATTC
Found at i:21965162 original size:19 final size:19
Alignment explanation
Indices: 21965138--21965177 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
21965128 ATTAATTTTG
21965138 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
21965157 ATCAAATCAATTAAAATTA
1 ATCAAATAAATTAAAATTA
21965176 AT
1 AT
21965178 ATACTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Done.