Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 13 of 105
Found at i:2420043 original size:27 final size:27
Alignment explanation
Indices: 2419957--2420050 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 27
2419947 TTAGATTAGA
* *
2419957 TTTATTTAATATTTTTTATCTTTATCTTATT
1 TTTATTT-TTATTTATT-TCTTTAT-TTA-T
*
2419988 TTTATTTTTGTTTTACCTTTCTTTA--TAT
1 TTTATTTTT-ATTTA--TTTCTTTATTTAT
2420016 TTTATTTTTATTTATTTCTTTATTTAT
1 TTTATTTTTATTTATTTCTTTATTTAT
*
2420043 TCTATTTT
1 TTTATTTT
2420051 CTTTAAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
25 8 0.15
27 14 0.26
28 10 0.19
29 2 0.04
30 1 0.02
31 10 0.19
32 6 0.11
33 2 0.04
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.73
Consensus pattern (27 bp):
TTTATTTTTATTTATTTCTTTATTTAT
Found at i:2420229 original size:59 final size:59
Alignment explanation
Indices: 2420058--2420465 Score: 521
Period size: 59 Copynumber: 7.0 Consensus size: 59
2420048 TTTCTTTAAA
*
2420058 TAAAAATCAAAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAATTT-C--AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* *
2420121 TGAAAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAATTT-CAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
**
2420182 TAAAAATAAAATTTCAAAAAAAGGATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* *
2420241 TAAAAATAAAGTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
* ** *** *
2420300 TAAAAATAAATTTTCGGAAAAGGGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAATAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
**
2420359 TAAAAATAAAATTTC-AAAAAAGGATTTTTGGGG---A----AAAGTATCAATTTTCCT
1 TAAAAATAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
** *
2420410 CGAAATTAAAA-TTC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 TAAAAATAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
2420466 CTGAACAAGA
Statistics
Matches: 314, Mismatches: 24, Indels: 20
0.88 0.07 0.06
Matches are distributed among these distances:
50 19 0.06
51 25 0.08
53 1 0.00
55 1 0.00
57 16 0.05
58 15 0.05
59 164 0.52
60 7 0.02
61 50 0.16
63 16 0.05
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (59 bp):
TAAAAATAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCT
Found at i:2420446 original size:50 final size:51
Alignment explanation
Indices: 2420342--2420447 Score: 160
Period size: 50 Copynumber: 2.1 Consensus size: 51
2420332 GGAAAAGTTG
* *
2420342 AAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAGGATTTTTGGGGA
1 AAAGTATCAATTTTCCTCAAAAATAAAATTTCAAAAAAAGATTTTTGGGGA
* * *
2420393 AAAGTATCAATTTTCCTCGAAATTAAAA-TTCAAAAAAATATTTTTGGGGA
1 AAAGTATCAATTTTCCTCAAAAATAAAATTTCAAAAAAAGATTTTTGGGGA
2420443 AAAGT
1 AAAGT
2420448 TGAAAGTATC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 25 0.50
51 25 0.50
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (51 bp):
AAAGTATCAATTTTCCTCAAAAATAAAATTTCAAAAAAAGATTTTTGGGGA
Found at i:2421986 original size:29 final size:28
Alignment explanation
Indices: 2421922--2421976 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2421912 CACGTTGATT
*
2421922 TAATTAAAATTTAATTTGTTTTGTTGTCA
1 TAATT-AAATTTAATTTGTTTTATTGTCA
* *
2421951 TTATTAAATTTAATTTTTTTTATTGT
1 TAATTAAATTTAATTTGTTTTATTGT
2421977 TCTAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (28 bp):
TAATTAAATTTAATTTGTTTTATTGTCA
Found at i:2422449 original size:19 final size:20
Alignment explanation
Indices: 2422425--2422467 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2422415 TATTTTATTA
*
2422425 ATTTATATTTGATTGATA-G
1 ATTTATATTTCATTGATATG
*
2422444 ATTTATATTTCATTTATATG
1 ATTTATATTTCATTGATATG
2422464 ATTT
1 ATTT
2422468 CATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.58
Consensus pattern (20 bp):
ATTTATATTTCATTGATATG
Found at i:2426164 original size:11 final size:11
Alignment explanation
Indices: 2426150--2426199 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
2426140 TTTTTTAAAA
2426150 TTATATAATTT
1 TTATATAATTT
*
2426161 TTATTAAAATTT
1 TTA-TATAATTT
*
2426173 TTA-ATTATTT
1 TTATATAATTT
2426183 TTATATTAA-TT
1 TTATA-TAATTT
2426194 TTATAT
1 TTATAT
2426200 CATGTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
10 9 0.28
11 11 0.34
12 12 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATAATTT
Found at i:2426177 original size:19 final size:19
Alignment explanation
Indices: 2426140--2426185 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2426130 TTTTTTAAAA
2426140 TTTTTTAAAATTATATAAT
1 TTTTTTAAAATTATATAAT
*
2426159 TTTTATTAAAATT-TTTAAT
1 TTTT-TTAAAATTATATAAT
2426178 TATTTTTA
1 T-TTTTTA
2426186 TATTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTAAAATTATATAAT
Found at i:2426561 original size:31 final size:31
Alignment explanation
Indices: 2426500--2426562 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
2426490 TTATTATTTT
*
2426500 ATATAAAAATTATATATAGTAATTTATATTA
1 ATATAAAAATTAAATATAGTAATTTATATTA
*
2426531 ATATAAAAATATAAA-ATA-TATATTTTTATTA
1 ATATAAAAAT-TAAATATAGTA-ATTTATATTA
2426562 A
1 A
2426563 ATTTATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.07
31 23 0.82
32 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (31 bp):
ATATAAAAATTAAATATAGTAATTTATATTA
Found at i:2426602 original size:24 final size:24
Alignment explanation
Indices: 2426523--2426626 Score: 70
Period size: 24 Copynumber: 4.4 Consensus size: 24
2426513 ATATAGTAAT
* * * *
2426523 TTATATTAATATAAAAATATAAAA
1 TTATATTATTATTAAAATTTTAAA
* *
2426547 TATATATTTTTATT-AAA-TTTATA
1 T-TATATTATTATTAAAATTTTAAA
* *
2426570 TAATGTTATTATTAAAATTTTAAA
1 TTATATTATTATTAAAATTTTAAA
* * *
2426594 TTATATTATTTTTATATATTTT-AT
1 TTATATTATTATTA-AAATTTTAAA
2426618 TTATATTAT
1 TTATATTAT
2426627 ATTGGTTTCA
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
22 9 0.15
23 7 0.11
24 30 0.49
25 15 0.25
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (24 bp):
TTATATTATTATTAAAATTTTAAA
Found at i:2426639 original size:29 final size:30
Alignment explanation
Indices: 2426588--2426653 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 30
2426578 TTATTAAAAT
* * * *
2426588 TTTAAATTATATTATTTTTATAT-ATTTTA
1 TTTATATTATATTAGTTTCATATCATTATA
*
2426617 TTTATATTATATTGGTTTCATATCATTATA
1 TTTATATTATATTAGTTTCATATCATTATA
2426647 -TTATATT
1 TTTATATT
2426654 TTTAATTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTATATTATATTAGTTTCATATCATTATA
Found at i:2443468 original size:59 final size:57
Alignment explanation
Indices: 2443246--2443701 Score: 587
Period size: 59 Copynumber: 7.7 Consensus size: 57
2443236 TTTTTTGTAG
* *
2443246 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTT--ATTTCT-AA
* * *
2443305 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCCCTTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-----TATTTTTTGGAAATTTATTTCTAA
2443367 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAATTT--ATTTCT-AA
* *
2443428 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCT-TTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA---TATTTTTTGGAAATTTATTTCTAA
* *
2443487 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAGTTTTTGGAATTTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
* * *
2443544 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATGTTTTTTTTTGAAATTTATTTCTGAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTTGGAAATTTATTTCT-AA
2443604 -GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
*
2443660 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTT
2443702 TTTGGAATTT
Statistics
Matches: 355, Mismatches: 21, Indels: 43
0.85 0.05 0.10
Matches are distributed among these distances:
56 3 0.01
57 106 0.30
58 5 0.01
59 131 0.37
60 4 0.01
61 51 0.14
62 38 0.11
63 1 0.00
64 16 0.05
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:2443701 original size:116 final size:117
Alignment explanation
Indices: 2443246--2443705 Score: 655
Period size: 116 Copynumber: 3.9 Consensus size: 117
2443236 TTTTTTGTAG
* *
2443246 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTCGATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTC-ATTTTCAAGGAAAA
*
2443311 TTGATACTTTCAACTTTTCCTCAAAAACCCCCTTTTTTTTGAAAATTTATTTCTAA
65 TTGATACTTTCAACTTTTCCTCAAAAA---TCTTTTTTTTGAAAATTTATTTCTAA
2443367 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTCGATTTTCAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAATTTC-ATTTTCAAGGAA
* *
2443432 AATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAA
63 AATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTCTAA
* *
2443487 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAGTTTTTGG-AATTTTA-TTTCTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCATTTTC-AAGGAAAA
*
2443550 TTGATACTTTCAACTTTTCC-CTAAAAATGTTTTTTTTTG-AAATTTATTTCTGAA
65 TTGATACTTTCAACTTTTCCTC-AAAAAT-CTTTTTTTTGAAAATTTATTTCT-AA
2443604 -GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTT-A-TTTCTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCATTTTC-AAGGAAAA
* *
2443666 TTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTTG
65 TTGATACTTTCAACTTTT-CCTCAAAA-ATCTTTTTTTTG
2443706 GAATTTTTTT
Statistics
Matches: 318, Mismatches: 11, Indels: 24
0.90 0.03 0.07
Matches are distributed among these distances:
115 5 0.02
116 119 0.37
117 35 0.11
118 9 0.03
120 60 0.19
121 34 0.11
123 56 0.18
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.43
Consensus pattern (117 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTTGAAAATTTATTTCTAA
Found at i:2443805 original size:13 final size:12
Alignment explanation
Indices: 2443780--2443817 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
2443770 CTAATCTAAT
2443780 AAATAAAAAATA
1 AAATAAAAAATA
2443792 AAATAAACAAATA
1 AAATAAA-AAATA
2443805 AAA-AAAAAA-A
1 AAATAAAAAATA
2443815 AAA
1 AAA
2443818 ACCTGGAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 3 0.12
12 10 0.40
13 8 0.32
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.11
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:2443805 original size:20 final size:20
Alignment explanation
Indices: 2443780--2443819 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2443770 CTAATCTAAT
* *
2443780 AAATAAAAAATAAAATAAAC
1 AAATAAAAAAAAAAAAAAAC
2443800 AAATAAAAAAAAAAAAAAAC
1 AAATAAAAAAAAAAAAAAAC
2443820 CTGGAGCGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (20 bp):
AAATAAAAAAAAAAAAAAAC
Found at i:2444174 original size:19 final size:20
Alignment explanation
Indices: 2444133--2444176 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2444123 ACACCGGTGT
* *
2444133 CGGATTCTGGAAATTTTCGC
1 CGGAATCTGGAAATTTTCAC
2444153 CGGAATCTGGAAA-TTTCAC
1 CGGAATCTGGAAATTTTCAC
2444172 CGGAA
1 CGGAA
2444177 GTTGGCCGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (20 bp):
CGGAATCTGGAAATTTTCAC
Found at i:2444275 original size:31 final size:31
Alignment explanation
Indices: 2444229--2444299 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
2444219 ACTGGGCAGA
* ** *
2444229 TCGCCGGAAACTTCAATGTTGGCCGGAATTT
1 TCGCCGGAAAATTCAAACTTCGCCGGAATTT
*
2444260 TCGTCGGAAAATTCAAACTTCGCCGGAATTT
1 TCGCCGGAAAATTCAAACTTCGCCGGAATTT
2444291 TCGCCGGAA
1 TCGCCGGAA
2444300 TCTGGAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (31 bp):
TCGCCGGAAAATTCAAACTTCGCCGGAATTT
Found at i:2444347 original size:26 final size:24
Alignment explanation
Indices: 2444308--2444361 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
2444298 AATCTGGAAA
*
2444308 TTTCCCAGAAATTTCCAGAAAAAAT
1 TTTCCCAAAAATTTCCA-AAAAAAT
* *
2444333 TTTCGCCAAAAATTTCTAAAAAATT
1 TTTC-CCAAAAATTTCCAAAAAAAT
2444358 TTTC
1 TTTC
2444362 TCACTCCCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.35
Consensus pattern (24 bp):
TTTCCCAAAAATTTCCAAAAAAAT
Found at i:2444785 original size:15 final size:15
Alignment explanation
Indices: 2444765--2444832 Score: 59
Period size: 15 Copynumber: 4.3 Consensus size: 15
2444755 AATCTAATCT
*
2444765 AATAAAAAATAAATA
1 AATAAAAAATACATA
*
2444780 AATAAATATATACAT-
1 AATAAA-AAATACATA
2444795 AATAATAAAATACATAA
1 AATAA-AAAATACAT-A
2444812 AATACATAAAATACA-A
1 AATA-A-AAAATACATA
2444828 AATAA
1 AATAA
2444833 TACAGGACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
15 19 0.42
16 12 0.27
17 4 0.09
18 10 0.22
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAAAAATACATA
Found at i:2444813 original size:9 final size:9
Alignment explanation
Indices: 2444795--2444836 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
2444785 ATATATACAT
2444795 AATA-ATAA
1 AATACATAA
2444803 AATACATAA
1 AATACATAA
2444812 AATACATAA
1 AATACATAA
*
2444821 AATACAAAA
1 AATACATAA
2444830 TAATACA
1 -AATACA
2444837 GGACAAATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 4 0.13
9 21 0.68
10 6 0.19
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (9 bp):
AATACATAA
Found at i:2444820 original size:18 final size:19
Alignment explanation
Indices: 2444793--2444836 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
2444783 AAATATATAC
*
2444793 ATAATA-ATAAAATACATA
1 ATAATACATAAAATACAAA
2444811 A-AATACATAAAATACAAA
1 ATAATACATAAAATACAAA
2444829 ATAATACA
1 ATAATACA
2444837 GGACAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (19 bp):
ATAATACATAAAATACAAA
Found at i:2444826 original size:33 final size:31
Alignment explanation
Indices: 2444764--2444834 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 31
2444754 AAATCTAATC
*
2444764 TAATAA-AAAATAAATAAATAAATATATACA
1 TAATAATAAAATAAATAAATAAATAAATACA
* *
2444794 TAATAATAAAATACATAAAATACATAAAATACA
1 TAATAATAAAATAAAT-AAATAAAT-AAATACA
*
2444827 AAATAATA
1 TAATAATA
2444835 CAGGACAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.18
31 8 0.24
32 7 0.21
33 13 0.38
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (31 bp):
TAATAATAAAATAAATAAATAAATAAATACA
Found at i:2445085 original size:42 final size:42
Alignment explanation
Indices: 2445021--2445164 Score: 245
Period size: 42 Copynumber: 3.5 Consensus size: 42
2445011 TTTTACCAAA
2445021 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
* *
2445063 GCTCCTCTAAACAGAGGTACCACGAC-TTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
* *
2445104 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
2445146 GCTCCTCTAAACAGAGGCA
1 GCTCCTCTAAACAGAGGCA
2445165 ACGGAACTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
41 39 0.41
42 56 0.59
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
Found at i:2445174 original size:42 final size:41
Alignment explanation
Indices: 2445021--2445182 Score: 222
Period size: 42 Copynumber: 3.9 Consensus size: 41
2445011 TTTTACCAAA
* *
2445021 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAAATAAATT
* *
2445063 GCTCCTCTAAACAGAGGTACCACGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAAATAAATT
2445104 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAAATAAATT
2445146 GCTCCTCTAAACAGAGGCA-ACGGAACTTT-GAAAAATA
1 GCTCCTCTAAACAGAGGCACAC-G-ACTTTGGAAAAATA
2445183 GAACTTTGAA
Statistics
Matches: 113, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
40 2 0.02
41 49 0.43
42 62 0.55
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACACGACTTTGGAAAAATAAATT
Found at i:2445188 original size:15 final size:15
Alignment explanation
Indices: 2445168--2445197 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2445158 AGAGGCAACG
2445168 GAACTTTGAAAAATA
1 GAACTTTGAAAAATA
2445183 GAACTTTGAAAAATA
1 GAACTTTGAAAAATA
2445198 AATTGCTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
GAACTTTGAAAAATA
Found at i:2445215 original size:56 final size:57
Alignment explanation
Indices: 2445128--2445236 Score: 211
Period size: 56 Copynumber: 1.9 Consensus size: 57
2445118 AGGCACCACG
2445128 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAGA
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAGA
2445185 ACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAA
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAA
2445237 ATAAATTGCT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 47 0.90
57 5 0.10
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (57 bp):
ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAGA
Found at i:2445245 original size:42 final size:40
Alignment explanation
Indices: 2445185--2445401 Score: 301
Period size: 42 Copynumber: 5.2 Consensus size: 40
2445175 GAAAAATAGA
2445185 ACTTTG-AAAAATAAATTGCTCCTCTAAACAGAGGCAACGG
1 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCAAC-G
2445225 AACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
1 -ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCA--ACG
* * *
2445268 ACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGTACCACG
1 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGG--CAACG
2445310 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACG
1 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCA--ACG
*
2445352 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACG
1 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCAACG
*
2445392 AACTTGGAAA
1 -ACTTTGAAA
2445402 GTAAATACTC
Statistics
Matches: 159, Mismatches: 9, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
40 4 0.03
41 13 0.08
42 138 0.87
43 1 0.01
44 3 0.02
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (40 bp):
ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCAACG
Found at i:2445272 original size:98 final size:98
Alignment explanation
Indices: 2445087--2445281 Score: 290
Period size: 98 Copynumber: 2.0 Consensus size: 98
2445077 AGGTACCACG
* * *
2445087 ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCT
1 ACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA-CACGACTTTGAAAAAATAAATTGCTCCT
2445152 CTAAACAGAGGCAACGGAACTTT-GAAAAATAGA
65 CTAAACAGAGGCAACGGAACTTTGGAAAAATAGA
2445185 ACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA-ACGGAACTTTGAAAAAATAAATTGCTCC
1 ACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACAC-G-ACTTTGAAAAAATAAATTGCTCC
2445249 TCTAAACAGAGGCACCAC-G-ACTTTGGAAAAATA
64 TCTAAACAGAGGCA--ACGGAACTTTGGAAAAATA
2445282 AATTGCTCCT
Statistics
Matches: 89, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
96 2 0.02
97 1 0.01
98 75 0.84
99 9 0.10
100 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (98 bp):
ACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCACACGACTTTGAAAAAATAAATTGCTCCTC
TAAACAGAGGCAACGGAACTTTGGAAAAATAGA
Found at i:2445299 original size:140 final size:138
Alignment explanation
Indices: 2445048--2445388 Score: 435
Period size: 140 Copynumber: 2.5 Consensus size: 138
2445038 CACCACGACT
* * * *
2445048 TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAGTAAATTGCTCCTCTA
1 TTTGAAAAATAAATTGCTCCTCTAAACAGAGG-ACAACGACTTTGAAAAATAAATTGCTCCTCTA
2445113 AACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAA
65 AACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAA
2445178 AAATAGAAC
130 AAATAGAAC
2445187 TTTGAAAAATAAATTGCTCCTCTAAACAGAGG-CAACGGAACTTTGAAAAAATAAATTGCTCCTC
1 TTTGAAAAATAAATTGCTCCTCTAAACAGAGGACAAC-G-ACTTTG-AAAAATAAATTGCTCCTC
* *
2445251 TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGG-TAC----C----
63 TAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTG
*
2445307 ----A-CG-AC
128 AAAAATAGAAC
*
2445312 TTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTC
1 TTTG-AAAAATAAATTGCTCCTCTAAACAGAGG-ACAACGACTTT-GAAAAATAAATTGCTCCTC
2445377 TAAACAGAGGCA
63 TAAACAGAGGCA
2445389 ACGAACTTGG
Statistics
Matches: 187, Mismatches: 8, Indels: 27
0.84 0.04 0.12
Matches are distributed among these distances:
125 6 0.03
126 64 0.34
127 3 0.02
128 3 0.02
135 1 0.01
137 3 0.02
138 1 0.01
139 39 0.21
140 67 0.36
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (138 bp):
TTTGAAAAATAAATTGCTCCTCTAAACAGAGGACAACGACTTTGAAAAATAAATTGCTCCTCTAA
ACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAA
AATAGAAC
Found at i:2445325 original size:84 final size:84
Alignment explanation
Indices: 2445185--2445401 Score: 361
Period size: 84 Copynumber: 2.6 Consensus size: 84
2445175 GAAAAATAGA
2445185 ACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAAATAAATTGCTCC
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAAATAAATTGCTCC
2445249 TCTAAACAGAGGCACCACG
66 TCTAAACAGAGGCACCACG
* *
2445268 ACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGTACCAC-G-ACTTTGAAAAAATAAATTGCT
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGG--CAACGGAACTTTGAAAAAATAAATTGCT
2445331 CCTCTAAACAGAGGCACCACG
64 CCTCTAAACAGAGGCACCACG
*
2445352 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAAC-GAACTTGGAAA
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAA
2445402 GTAAATACTC
Statistics
Matches: 125, Mismatches: 5, Indels: 8
0.91 0.04 0.06
Matches are distributed among these distances:
82 4 0.03
83 13 0.10
84 104 0.83
85 1 0.01
86 3 0.02
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (84 bp):
ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAAATAAATTGCTCC
TCTAAACAGAGGCACCACG
Found at i:2446422 original size:8 final size:8
Alignment explanation
Indices: 2446394--2446539 Score: 157
Period size: 8 Copynumber: 19.2 Consensus size: 8
2446384 GTCCTCCTTG
*
2446394 TTCACTTT
1 TTCATTTT
2446402 TTC-TTTT
1 TTCATTTT
2446409 TT--TTTT
1 TTCATTTT
*
2446415 TCCATTTT
1 TTCATTTT
2446423 TTC-TTTT
1 TTCATTTT
2446430 TTCATTTT
1 TTCATTTT
2446438 TTCA-TTT
1 TTCATTTT
2446445 TT-ATTTT
1 TTCATTTT
*
2446452 TCCATTTT
1 TTCATTTT
2446460 TTCATTTT
1 TTCATTTT
2446468 TTCA-TTT
1 TTCATTTT
*
2446475 TTCATATT
1 TTCATTTT
*
2446483 TCCA-TTT
1 TTCATTTT
2446490 TTCATTTT
1 TTCATTTT
2446498 TTCA-TTT
1 TTCATTTT
2446505 TTCATTTT
1 TTCATTTT
*
2446513 TCCATTTT
1 TTCATTTT
*
2446521 TCCATTTT
1 TTCATTTT
2446529 TGTCATTTT
1 T-TCATTTT
2446538 TT
1 TT
2446540 TTCAAGCATA
Statistics
Matches: 118, Mismatches: 11, Indels: 18
0.80 0.07 0.12
Matches are distributed among these distances:
6 6 0.05
7 40 0.34
8 65 0.55
9 7 0.06
ACGTcount: A:0.12, C:0.16, G:0.01, T:0.72
Consensus pattern (8 bp):
TTCATTTT
Found at i:2446429 original size:15 final size:15
Alignment explanation
Indices: 2446394--2446538 Score: 172
Period size: 15 Copynumber: 9.6 Consensus size: 15
2446384 GTCCTCCTTG
2446394 TTCACTTTTTC-TTTT
1 TTCA-TTTTTCATTTT
2446409 TT--TTTTTCCATTTT
1 TTCATTTTT-CATTTT
*
2446423 TTCTTTTTTCATTTT
1 TTCATTTTTCATTTT
2446438 TTCATTTTT-ATTTT
1 TTCATTTTTCATTTT
*
2446452 TCCATTTTTTCATTTT
1 TTCA-TTTTTCATTTT
*
2446468 TTCATTTTTCATATT
1 TTCATTTTTCATTTT
*
2446483 TCCATTTTTCATTTT
1 TTCATTTTTCATTTT
2446498 TTCATTTTTCATTTT
1 TTCATTTTTCATTTT
*
2446513 TCCATTTTTCCATTTT
1 TTCATTTTT-CATTTT
2446529 TGTCATTTTT
1 T-TCATTTTT
2446539 TTTCAAGCAT
Statistics
Matches: 113, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.04
13 1 0.01
14 14 0.12
15 66 0.58
16 20 0.18
17 7 0.06
ACGTcount: A:0.12, C:0.16, G:0.01, T:0.72
Consensus pattern (15 bp):
TTCATTTTTCATTTT
Found at i:2446460 original size:30 final size:31
Alignment explanation
Indices: 2446399--2446538 Score: 193
Period size: 30 Copynumber: 4.6 Consensus size: 31
2446389 CCTTGTTCAC
*
2446399 TTTTTC-TTTTTT--TTTTTCCATTTTTTC-T
1 TTTTTCATTTTTTCATTTTT-CATTTTTCCAT
2446427 TTTTTCATTTTTTCATTTTT-ATTTTTCCAT
1 TTTTTCATTTTTTCATTTTTCATTTTTCCAT
*
2446457 TTTTTCATTTTTTCATTTTTCATATTTCCA-
1 TTTTTCATTTTTTCATTTTTCATTTTTCCAT
2446487 TTTTTCATTTTTTCATTTTTCATTTTTCCAT
1 TTTTTCATTTTTTCATTTTTCATTTTTCCAT
*
2446518 TTTTCCATTTTTGTCATTTTT
1 TTTTTCATTTTT-TCATTTTT
2446539 TTTCAAGCAT
Statistics
Matches: 101, Mismatches: 4, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
28 6 0.06
29 13 0.13
30 50 0.50
31 24 0.24
32 8 0.08
ACGTcount: A:0.11, C:0.15, G:0.01, T:0.73
Consensus pattern (31 bp):
TTTTTCATTTTTTCATTTTTCATTTTTCCAT
Found at i:2450075 original size:18 final size:18
Alignment explanation
Indices: 2450039--2450076 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2450029 TTTATATAAA
*
2450039 ATTATATATAGTAATTAT
1 ATTATATATAGTAAATAT
2450057 ATTATATAATA-TAAATAT
1 ATTATAT-ATAGTAAATAT
2450075 AT
1 AT
2450077 ATGTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTATATATAGTAAATAT
Found at i:2450152 original size:11 final size:11
Alignment explanation
Indices: 2450119--2450152 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2450109 AAATTTTAAA
*
2450119 TTATATTATTT
1 TTATATTATAT
*
2450130 TTATATTTTAT
1 TTATATTATAT
2450141 TTATATTATAT
1 TTATATTATAT
2450152 T
1 T
2450153 GGTTTCATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATATTATAT
Found at i:2450162 original size:27 final size:28
Alignment explanation
Indices: 2450113--2450176 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
2450103 TTATTAAAAT
* * * *
2450113 TTTAAATTATATTATTTTTATAT-TTTA
1 TTTATATTATATTAGTTTCATATCATTA
*
2450140 TTTATATTATATTGGTTTCATATCATTA
1 TTTATATTATATTAGTTTCATATCATTA
2450168 TATTATATT
1 T-TTATATT
2450177 TTTAATTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 19 0.63
28 4 0.13
29 7 0.23
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTATATTATATTAGTTTCATATCATTA
Found at i:2454668 original size:3 final size:3
Alignment explanation
Indices: 2454660--2454689 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2454650 TAACTAATTA
2454660 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2454690 CAACATGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:2461058 original size:102 final size:102
Alignment explanation
Indices: 2460882--2461084 Score: 406
Period size: 102 Copynumber: 2.0 Consensus size: 102
2460872 CATACACTAA
2460882 TTTCTAAATCATTCAAGTGAAAAGGAAGTGATACAAGTCAAGGCTAATGATAAAAGTTAAATATA
1 TTTCTAAATCATTCAAGTGAAAAGGAAGTGATACAAGTCAAGGCTAATGATAAAAGTTAAATATA
2460947 TAAAATAGATTGCATCTTGAAAATAAAGAAATAGGTG
66 TAAAATAGATTGCATCTTGAAAATAAAGAAATAGGTG
2460984 TTTCTAAATCATTCAAGTGAAAAGGAAGTGATACAAGTCAAGGCTAATGATAAAAGTTAAATATA
1 TTTCTAAATCATTCAAGTGAAAAGGAAGTGATACAAGTCAAGGCTAATGATAAAAGTTAAATATA
2461049 TAAAATAGATTGCATCTTGAAAATAAAGAAATAGGT
66 TAAAATAGATTGCATCTTGAAAATAAAGAAATAGGT
2461085 TGTATATATT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (102 bp):
TTTCTAAATCATTCAAGTGAAAAGGAAGTGATACAAGTCAAGGCTAATGATAAAAGTTAAATATA
TAAAATAGATTGCATCTTGAAAATAAAGAAATAGGTG
Found at i:2469248 original size:23 final size:25
Alignment explanation
Indices: 2469218--2469263 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2469208 TGTTGCGCCT
*
2469218 GAAGCAATA-ATCACAAT-AATACA
1 GAAGCAATAGATAACAATCAATACA
2469241 GAAGCAATAGATAACAATCAATA
1 GAAGCAATAGATAACAATCAATA
2469264 ATCAAATACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.57, C:0.15, G:0.11, T:0.17
Consensus pattern (25 bp):
GAAGCAATAGATAACAATCAATACA
Found at i:2474702 original size:25 final size:23
Alignment explanation
Indices: 2474662--2474717 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 23
2474652 ATATGTCAAT
*
2474662 TAAAAAAATTTAAAAATA-AAAAA
1 TAAAAATATTTAAAAA-ACAAAAA
2474685 TAAAAATATTTATCAAAAACAAAAA
1 TAAAAATATTTA--AAAAACAAAAA
2474710 TAAAAATA
1 TAAAAATA
2474718 AAATAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.38
24 1 0.03
25 17 0.59
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (23 bp):
TAAAAATATTTAAAAAACAAAAA
Found at i:2488926 original size:23 final size:24
Alignment explanation
Indices: 2488898--2488944 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
2488888 AAATTCATTC
*
2488898 AATAAACATTATATTT-GTTTTTT
1 AATAAACATGATATTTGGTTTTTT
*
2488921 AATAAACATGATCTTTGGTTTTTT
1 AATAAACATGATATTTGGTTTTTT
2488945 TTTATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (24 bp):
AATAAACATGATATTTGGTTTTTT
Found at i:2500724 original size:14 final size:15
Alignment explanation
Indices: 2500698--2500729 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
2500688 CATTTTCTAT
2500698 ATATATAAAAAATGC
1 ATATATAAAAAATGC
2500713 ATATAT-AAAAATGC
1 ATATATAAAAAATGC
2500727 ATA
1 ATA
2500730 CATGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (15 bp):
ATATATAAAAAATGC
Found at i:2505767 original size:39 final size:39
Alignment explanation
Indices: 2505709--2505783 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
2505699 ATACTAAAGT
* **
2505709 TGTTCAAAGGTTCGTCAAAACCCACCAAATGCATTTTAG
1 TGTTCAAAAGTTCACCAAAACCCACCAAATGCATTTTAG
*
2505748 TGTTCAAAAGTTCACCAAAACCCTCCAAATGCATTT
1 TGTTCAAAAGTTCACCAAAACCCACCAAATGCATTT
2505784 ATTTAGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.28
Consensus pattern (39 bp):
TGTTCAAAAGTTCACCAAAACCCACCAAATGCATTTTAG
Found at i:2507690 original size:19 final size:23
Alignment explanation
Indices: 2507666--2507717 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 23
2507656 TATACTATTT
2507666 TTTTTAAATAAA-AA-T-TTTA-
1 TTTTTAAATAAATAATTCTTTAC
2507685 TTTTT-AATAAATAATTCTTTAC
1 TTTTTAAATAAATAATTCTTTAC
2507707 TTTTTAAATAA
1 TTTTTAAATAA
2507718 TAGTGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 6 0.21
19 7 0.25
20 1 0.04
21 4 0.14
22 5 0.18
23 5 0.18
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTTAAATAAATAATTCTTTAC
Found at i:2507713 original size:22 final size:18
Alignment explanation
Indices: 2507662--2507700 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2507652 TAAATATACT
*
2507662 ATTTT-TTTTAAATAAAA
1 ATTTTATTTTTAATAAAA
2507679 ATTTTATTTTTAATAAATA
1 ATTTTATTTTTAATAAA-A
2507698 ATT
1 ATT
2507701 CTTTACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTATTTTTAATAAAA
Found at i:2507719 original size:22 final size:20
Alignment explanation
Indices: 2507666--2507719 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
2507656 TATACTATTT
2507666 TTTTTAAATAA-AAATTTTA
1 TTTTTAAATAATAAATTTTA
*
2507685 TTTTT-AATAAATAATTCTTTA
1 TTTTTAAAT-AATAAAT-TTTA
2507706 CTTTTTAAATAATA
1 -TTTTTAAATAATA
2507720 GTGTATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 3 0.10
19 7 0.24
20 3 0.10
21 4 0.14
22 9 0.31
23 3 0.10
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTAAATAATAAATTTTA
Found at i:2507850 original size:18 final size:18
Alignment explanation
Indices: 2507824--2507874 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
2507814 TGCAATTAAG
*
2507824 AGTTGGGAAATTAAAGGT
1 AGTTTGGAAATTAAAGGT
2507842 AGTTTGGAAATTAAAGGT
1 AGTTTGGAAATTAAAGGT
*
2507860 AGTTTAGAAATTAAA
1 AGTTTGGAAATTAAA
2507875 AAAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.25, T:0.31
Consensus pattern (18 bp):
AGTTTGGAAATTAAAGGT
Found at i:2511526 original size:26 final size:27
Alignment explanation
Indices: 2511489--2511541 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2511479 ATATTTATTA
*
2511489 GATATTAGAT-AATATCAATTTTAAAT
1 GATATTAGATAAATATAAATTTTAAAT
*
2511515 GATATTTA-ATAAATTTAAATTTTAAAT
1 GATA-TTAGATAAATATAAATTTTAAAT
2511542 TTTAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (27 bp):
GATATTAGATAAATATAAATTTTAAAT
Found at i:2529444 original size:21 final size:21
Alignment explanation
Indices: 2529418--2529457 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2529408 CAAGGATTTC
* *
2529418 ATCATTTATCTTTGTCCTTGG
1 ATCATTGATCTTTATCCTTGG
2529439 ATCATTGATCTTTATCCTT
1 ATCATTGATCTTTATCCTT
2529458 TATGGCTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.10, T:0.53
Consensus pattern (21 bp):
ATCATTGATCTTTATCCTTGG
Found at i:2533427 original size:2 final size:2
Alignment explanation
Indices: 2533420--2533459 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2533410 TTTTATTCTT
2533420 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2533460 ACTTCTAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2536228 original size:17 final size:18
Alignment explanation
Indices: 2536195--2536232 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
2536185 AATTAAATAA
2536195 AAAATTATAAACATAAAT
1 AAAATTATAAACATAAAT
*
2536213 AAAATT-TAACCATAAAT
1 AAAATTATAAACATAAAT
2536230 AAA
1 AAA
2536233 TAAAACGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTATAAACATAAAT
Found at i:2554023 original size:16 final size:16
Alignment explanation
Indices: 2554002--2554050 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
2553992 TTGTGTGTCA
2554002 TAGCTCAAATAACACT
1 TAGCTCAAATAACACT
2554018 TAGCTCAAATAACACT
1 TAGCTCAAATAACACT
2554034 TAGCTCAAATAACACT
1 TAGCTCAAATAACACT
2554050 T
1 T
2554051 TCCTACCTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.43, C:0.24, G:0.06, T:0.27
Consensus pattern (16 bp):
TAGCTCAAATAACACT
Found at i:2554730 original size:78 final size:78
Alignment explanation
Indices: 2554638--2554790 Score: 261
Period size: 78 Copynumber: 2.0 Consensus size: 78
2554628 TTTAAAAATA
* *
2554638 AAACCCATAAGACTTTGACTTTATTATATCTGTCTACACAAATTTTTTTAATAGATTGTCAAAGT
1 AAACCCATAAGACTTTGACTTTATTATATCTGTCAACACAAATTTTTTTAATAGATTATCAAAGT
2554703 ATTGAAATTCTTC
66 ATTGAAATTCTTC
** *
2554716 AAACCCATAAGACTTTGACTTTATTATATCTGTCAACATGAATTTTTTTAATAGATTATCAATGT
1 AAACCCATAAGACTTTGACTTTATTATATCTGTCAACACAAATTTTTTTAATAGATTATCAAAGT
2554781 ATTGAAATTC
66 ATTGAAATTC
2554791 CTTAAATGGA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (78 bp):
AAACCCATAAGACTTTGACTTTATTATATCTGTCAACACAAATTTTTTTAATAGATTATCAAAGT
ATTGAAATTCTTC
Found at i:2556434 original size:64 final size:64
Alignment explanation
Indices: 2556360--2556547 Score: 322
Period size: 64 Copynumber: 2.9 Consensus size: 64
2556350 TATAACTAAT
* *
2556360 ACAAAGATAAGATAAACGTTCCAGATTGTGTCACATAGCCATAACAATTACTGAGGATGATAAC
1 ACAAAGATAAGATAAACGCTCCAGATTGTGTCACATAGCCATAACGATTACTGAGGATGATAAC
**
2556424 ACAAAGATAAGATAAACGCTCCAGATTGTGTCATGTAGCCATAACGATTACTGAGGATGATAAC
1 ACAAAGATAAGATAAACGCTCCAGATTGTGTCACATAGCCATAACGATTACTGAGGATGATAAC
* *
2556488 ACAAAGATAAGATAAACGCTCTAGATTGTGTCACATAGCCATAACGGTTACTGAGGATGA
1 ACAAAGATAAGATAAACGCTCCAGATTGTGTCACATAGCCATAACGATTACTGAGGATGA
2556548 CCTTCAACAT
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 116 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (64 bp):
ACAAAGATAAGATAAACGCTCCAGATTGTGTCACATAGCCATAACGATTACTGAGGATGATAAC
Found at i:2557724 original size:20 final size:20
Alignment explanation
Indices: 2557701--2557738 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2557691 AATAAAGCTG
2557701 AAAAATA-ATTATAAAAAATA
1 AAAAATATATTA-AAAAAATA
2557721 AAAAATATATTAAAAAAA
1 AAAAATATATTAAAAAAA
2557739 CTTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATATATTAAAAAAATA
Found at i:2558801 original size:2 final size:2
Alignment explanation
Indices: 2558796--2558820 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2558786 GTTTTTTAAA
2558796 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2558821 GTTTTTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2565956 original size:21 final size:21
Alignment explanation
Indices: 2565938--2566002 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2565928 TATAAATTTT
*
2565938 AATTTTTATAATTAAAATTAA
1 AATTTTAATAATTAAAATTAA
*
2565959 AATTTTAATAATT--TATTAA
1 AATTTTAATAATTAAAATTAA
* *
2565978 AATTTT-TTAATTAAATTTAA
1 AATTTTAATAATTAAAATTAA
2565998 TAATT
1 -AATT
2566003 CGTATATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
20 4 0.11
21 16 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTAATAATTAAAATTAA
Found at i:2567990 original size:31 final size:31
Alignment explanation
Indices: 2567952--2568015 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
2567942 ATATATATAC
*
2567952 AAATTATTTTGAACTTATTAGAATGAATATT
1 AAATTATTTTGAACTTATAAGAATGAATATT
2567983 AAATTATTTTGAACTTATAAGAATGAATATT
1 AAATTATTTTGAACTTATAAGAATGAATATT
2568014 AA
1 AA
2568016 TTTGAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (31 bp):
AAATTATTTTGAACTTATAAGAATGAATATT
Found at i:2573254 original size:52 final size:51
Alignment explanation
Indices: 2573166--2573310 Score: 166
Period size: 52 Copynumber: 2.8 Consensus size: 51
2573156 GGACAAGAAA
* * * *
2573166 ACTTGCAAAAAAAAAATTTTAAGAGAAAAAGAATTCTTAATA-AGTAAATTTG
1 ACTTGCAAGAAAAGAATTTTAAAAGAAAAAG-ATTCTTAATAGA-CAAATTTG
*
2573218 ACTTGCAAGATAAGAATTTTAAAAGGAAAAAGATTCTTAATAGACAAATTTG
1 ACTTGCAAGAAAAGAATTTTAAAA-GAAAAAGATTCTTAATAGACAAATTTG
* * * *
2573270 ACTTACAAGAGAAGAATTCTAAGAAGAAAGAGATTCTTAAT
1 ACTTGCAAGAAAAGAATTTTAA-AAGAAAAAGATTCTTAAT
2573311 GGATAAGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
52 71 0.88
53 10 0.12
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (51 bp):
ACTTGCAAGAAAAGAATTTTAAAAGAAAAAGATTCTTAATAGACAAATTTG
Found at i:2576401 original size:24 final size:24
Alignment explanation
Indices: 2576343--2576404 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
2576333 ATATCCATCA
* *
2576343 TTTGT-TGGAATATGAAATTTTTC
1 TTTGTATGGATTATGAAATTTTAC
* *
2576366 TTTGAAAT-GATTATGGAATTTTAC
1 TTTG-TATGGATTATGAAATTTTAC
2576390 TTTGTATGGATTATG
1 TTTGTATGGATTATG
2576405 TTTTATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.19
24 24 0.77
25 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.50
Consensus pattern (24 bp):
TTTGTATGGATTATGAAATTTTAC
Found at i:2578224 original size:51 final size:52
Alignment explanation
Indices: 2578149--2578250 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 52
2578139 CAATTAATGA
* * *
2578149 TGAACACATTGTTCATGTACACGTTTTCTTCACTTCAGAAGACGAAGAAAAG
1 TGAACACATTGTCCATGTAAACGTTTTCTTCACTTCAAAAGACGAAGAAAAG
2578201 TGAACACATT-TCCATGTAAACGTTTTCTTCACTTCAAAAGACGAAGAAAA
1 TGAACACATTGTCCATGTAAACGTTTTCTTCACTTCAAAAGACGAAGAAAA
2578251 TTCAATACAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 37 0.79
52 10 0.21
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (52 bp):
TGAACACATTGTCCATGTAAACGTTTTCTTCACTTCAAAAGACGAAGAAAAG
Found at i:2589020 original size:39 final size:39
Alignment explanation
Indices: 2588966--2589044 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
2588956 AGAATTTTGG
* * *
2588966 TTACTTAAGACTATAAAATATTAATCTACTATGTATATA
1 TTACTTAAGACTATAAAACAATAATCTACTACGTATATA
*
2589005 TTACTTAAGAGTATAAAACAATAATCTACTACGTATATA
1 TTACTTAAGACTATAAAACAATAATCTACTACGTATATA
2589044 T
1 T
2589045 ATTAAGCCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.38
Consensus pattern (39 bp):
TTACTTAAGACTATAAAACAATAATCTACTACGTATATA
Found at i:2589830 original size:31 final size:32
Alignment explanation
Indices: 2589787--2589846 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
2589777 AACTTTACCA
*
2589787 ATTTGATTTTATTTA-ATGATTTTTTTAATTTT
1 ATTTGATTTTATTTATAT-ATTATTTTAATTTT
2589819 ATTT-ATTTTATTTATATATTATTTTAAT
1 ATTTGATTTTATTTATATATTATTTTAAT
2589847 GTAAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (32 bp):
ATTTGATTTTATTTATATATTATTTTAATTTT
Found at i:2591642 original size:2 final size:2
Alignment explanation
Indices: 2591635--2591671 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2591625 CTGCTGCTTC
2591635 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2591672 ATGGGTTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2593767 original size:23 final size:23
Alignment explanation
Indices: 2593734--2593792 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
2593724 TTTGGTTGTA
* * * *
2593734 ATATATATTTATTATTTATAAAT
1 ATATTTATTTAATATTCACAAAT
*
2593757 ATATTTGTTTAATATTCACAAAT
1 ATATTTATTTAATATTCACAAAT
*
2593780 ATGTTTATTTAAT
1 ATATTTATTTAAT
2593793 TTAATTGAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (23 bp):
ATATTTATTTAATATTCACAAAT
Found at i:2600478 original size:19 final size:20
Alignment explanation
Indices: 2600433--2600470 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2600423 GAACACCGGT
*
2600433 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
2600453 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
2600471 CGTCGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:2601086 original size:17 final size:18
Alignment explanation
Indices: 2601050--2601090 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2601040 AAAAAGATAA
* *
2601050 AAATATATATATATACAT
1 AAATATATAAATACACAT
2601068 AAATA-ATAAATACACAT
1 AAATATATAAATACACAT
2601085 AAATAT
1 AAATAT
2601091 TAACAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATATAAATACACAT
Found at i:2601162 original size:16 final size:15
Alignment explanation
Indices: 2601062--2601163 Score: 75
Period size: 16 Copynumber: 6.6 Consensus size: 15
2601052 ATATATATAT
2601062 ATACATAAATAATAA
1 ATACATAAATAATAA
*
2601077 ATACACATAAATATTAA
1 AT--ACATAAATAATAA
* *
2601094 CAAAAATAAATAAATAA
1 -ATACATAAAT-AATAA
* * *
2601111 ATATATACATATATTA
1 ATACATAAATA-ATAA
2601127 ATACAT-AATAAT-A
1 ATACATAAATAATAA
2601140 ATA-ATAAATAATACA
1 ATACATAAATAATA-A
2601155 ATACATAAA
1 ATACATAAA
2601164 ATACAAAAGA
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
12 2 0.03
13 10 0.15
14 2 0.03
15 10 0.15
16 27 0.40
17 16 0.24
18 1 0.01
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (15 bp):
ATACATAAATAATAA
Found at i:2601366 original size:1 final size:1
Alignment explanation
Indices: 2601362--2601387 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2601352 CATTTTTTGG
2601362 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
2601388 ACCAAAGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2601519 original size:42 final size:41
Alignment explanation
Indices: 2601394--2601886 Score: 720
Period size: 42 Copynumber: 12.0 Consensus size: 41
2601384 TTTTACCAAA
*
2601394 GCTCCTCTAAACAGAGGTACCACGACTTTGG-ATAGTAAATT
1 GCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAAATT
*
2601435 GCTCCTCTAAACAGAGG-CAACGAAC-TTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGACCACG-ACTTTGGAAAAGTAAATT
2601475 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAAATT
2601517 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAAATT
* *
2601558 GCTCCCTCTAAACAGAGGGCAACGAACTTT-GAAAAGTAAATT
1 GCT-CCTCTAAACAGAGGACCACG-ACTTTGGAAAAGTAAATT
2601600 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAAATT
2601642 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAAATT
*
2601683 GCTCCTCTAAACAGAGG-CGACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGACCACG-ACTTTGGAAAAGTAAATT
2601723 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAAATT
2601765 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGG-ACCACGACTTTGGAAAAGTAAATT
*
2601807 GCTCCTCTAAACAGAGG-CAACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGACCACG-ACTTTGGAAAAGTAAATT
* *
2601847 GCTCCTCTAAACAGAGG-CAACGAACTTTGAAAAAGTAAAT
1 GCTCCTCTAAACAGAGGACCACG-ACTTTGGAAAAGTAAAT
2601887 ACTCCTAGAC
Statistics
Matches: 422, Mismatches: 13, Indels: 34
0.90 0.03 0.07
Matches are distributed among these distances:
39 13 0.03
40 104 0.25
41 103 0.24
42 202 0.48
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGACCACGACTTTGGAAAAGTAAATT
Found at i:2601719 original size:165 final size:163
Alignment explanation
Indices: 2601394--2601886 Score: 773
Period size: 165 Copynumber: 3.0 Consensus size: 163
2601384 TTTTACCAAA
* *
2601394 GCTCCTCTAAACAGAGGTACCACGACTTTGGATAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
1 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
2601457 AAC-TTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATTGCTC
66 -ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTC
* *
2601521 CTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
129 CTCTAAACAGAGGCACGA--ACTTTGAAAAGTAAATT
* *
2601558 GCTCCCTCTAAACAGAGG-GCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 GCT-CCTCTAAACAGAGGTACCACG-ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
2601622 CGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTC
64 CGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTC
2601687 CTCTAAACAGAGGCGACGAACTTTGAAAAGTAAATT
129 CTCTAAACAGAGGC-ACGAACTTTGAAAAGTAAATT
2601723 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
2601788 GACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAATTGCTC
65 GACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAGTAAATTGCTC
2601851 CTCTAAACAGAGGCAACGAACTTTGAAAAAGTAAAT
129 CTCTAAACAGAGGC-ACGAACTTTG-AAAAGTAAAT
2601887 ACTCCTAGAC
Statistics
Matches: 308, Mismatches: 11, Indels: 19
0.91 0.03 0.06
Matches are distributed among these distances:
163 3 0.01
164 70 0.23
165 154 0.50
166 30 0.10
167 51 0.17
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (163 bp):
GCTCCTCTAAACAGAGGTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCT
CTAAACAGAGGCACGAACTTTGAAAAGTAAATT
Found at i:2601772 original size:123 final size:123
Alignment explanation
Indices: 2601394--2601886 Score: 873
Period size: 123 Copynumber: 4.0 Consensus size: 123
2601384 TTTTACCAAA
* *
2601394 GCTCCTCTAAACAGAGGTACCACGACTTTGGATAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
*
2601459 CTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
66 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
2601517 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCCTCTAAACAGAGGGCAACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCT-CCTCTAAACAGA-GGCAACG
*
2601582 AACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
64 AACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
*
2601642 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCGACGAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
2601707 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
66 CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
2601765 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
* *
2601830 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG--CAACGAACTTTGAAAAAGTAAAT
65 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACG-ACTTTGGAAAAGTAAAT
2601887 ACTCCTAGAC
Statistics
Matches: 357, Mismatches: 9, Indels: 8
0.95 0.02 0.02
Matches are distributed among these distances:
122 4 0.01
123 154 0.43
124 90 0.25
125 109 0.31
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (123 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
CTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAGTAAATT
Found at i:2603136 original size:21 final size:20
Alignment explanation
Indices: 2603112--2603187 Score: 79
Period size: 23 Copynumber: 3.8 Consensus size: 20
2603102 TCTTTTTTCA
2603112 TTTTCTCATTTTTCCTTCTTTTT
1 TTTTCTCATTTTT--TTC-TTTT
2603135 TTTTCTCATTTTTTTC-TTT
1 TTTTCTCATTTTTTTCTTTT
2603154 TTTT-T--TTTTTTTCTTTT
1 TTTTCTCATTTTTTTCTTTT
2603171 TTTTCATCATCTTTTTT
1 TTTTC-TCAT-TTTTTT
2603188 TTTCATCCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
16 8 0.17
17 7 0.15
18 1 0.02
19 8 0.17
21 4 0.09
22 6 0.13
23 13 0.28
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTCTCATTTTTTTCTTTT
Found at i:2603147 original size:24 final size:23
Alignment explanation
Indices: 2603112--2603159 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
2603102 TCTTTTTTCA
2603112 TTTTCTCATTTTTCCTTCTTTTT
1 TTTTCTCATTTTTCCTTCTTTTT
2603135 TTTTCTCATTTTT--TTCTTTTT
1 TTTTCTCATTTTTCCTTCTTTTT
2603156 TTTT
1 TTTT
2603160 TTTTTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTCTCATTTTTCCTTCTTTTT
Found at i:2603158 original size:25 final size:25
Alignment explanation
Indices: 2603112--2603191 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
2603102 TCTTTTTTCA
2603112 TTTTCTCA--TTTTTCCTTCTTTTT
1 TTTTCTCATTTTTTTCCTTCTTTTT
* *
2603135 TTTTCTCATTTTTTTCTTTTTTTTT
1 TTTTCTCATTTTTTTCCTTCTTTTT
* * *
2603160 TTTTTTCTTTTTTTTCATCATCTTTTT
1 TTTTCTCATTTTTTTC--CTTCTTTTT
2603187 TTTTC
1 TTTTC
2603192 ATCCATGTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
23 8 0.18
25 27 0.60
27 10 0.22
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTCTCATTTTTTTCCTTCTTTTT
Found at i:2603171 original size:16 final size:16
Alignment explanation
Indices: 2603143--2603174 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2603133 TTTTTTCTCA
2603143 TTTTTTTCTTTTTTTT
1 TTTTTTTCTTTTTTTT
2603159 TTTTTTTCTTTTTTTT
1 TTTTTTTCTTTTTTTT
2603175 CATCATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (16 bp):
TTTTTTTCTTTTTTTT
Found at i:2607161 original size:61 final size:61
Alignment explanation
Indices: 2607031--2607277 Score: 356
Period size: 61 Copynumber: 4.0 Consensus size: 61
2607021 TTTTTTGTAG
*
2607031 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTCGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTTGATTTTCAA
2607091 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTTTGG-AATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTTGGAAATTTTGATTTTCAA
* *
2607152 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTTTTTTGAAAATTT-ATTTTTCTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA---TTTTTTTTGGAAATTTTGA-TTTTC--
2607216 TTAA
60 --AA
*
2607220 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTTGATTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTTGATTTT
2607278 TCTTTAAAGA
Statistics
Matches: 169, Mismatches: 7, Indels: 17
0.88 0.04 0.09
Matches are distributed among these distances:
60 35 0.21
61 49 0.29
62 9 0.05
63 10 0.06
64 10 0.06
65 19 0.11
66 1 0.01
68 36 0.21
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (61 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTTGATTTTCAA
Found at i:2607331 original size:16 final size:16
Alignment explanation
Indices: 2607297--2607424 Score: 50
Period size: 16 Copynumber: 7.8 Consensus size: 16
2607287 AAAATAAAAT
* *
2607297 AATAAAAAAAAAGTGAA
1 AATAAATAAAAA-TTAA
2607314 AATAAATAAAAATTAA
1 AATAAATAAAAATTAA
*
2607330 AA-AAATTAAAGAAAAGTAA
1 AATAAA-T--A-AAAATTAA
*
2607349 AAAAAATAAAAA-TAA
1 AATAAATAAAAATTAA
* * *
2607364 GATAAAGAAAAAATATTA
1 AATAAA-TAAAAAT-TAA
**
2607382 AATAAAT-CTAATCTAA
1 AATAAATAAAAAT-TAA
*
2607398 AATAAA-AAAAATAATA
1 AATAAATAAAAATTA-A
2607414 AATAAA-AAAAA
1 AATAAATAAAAA
2607425 AAAAAAAACC
Statistics
Matches: 85, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
15 11 0.13
16 41 0.48
17 12 0.14
18 8 0.09
19 10 0.12
20 3 0.04
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.19
Consensus pattern (16 bp):
AATAAATAAAAATTAA
Found at i:2607332 original size:8 final size:9
Alignment explanation
Indices: 2607321--2607360 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
2607311 GAAAATAAAT
2607321 AAAAATTAA
1 AAAAATTAA
2607330 AAAAATTAA
1 AAAAATTAA
*
2607339 AGAAAAGTAA
1 A-AAAATTAA
*
2607349 AAAAAATAA
1 AAAAATTAA
2607358 AAA
1 AAA
2607361 TAAGATAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (9 bp):
AAAAATTAA
Found at i:2607334 original size:19 final size:19
Alignment explanation
Indices: 2607312--2607358 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2607302 AAAAAAAGTG
*
2607312 AAAATAAATAAAAATTAAAA
1 AAAATAAAGAAAAA-TAAAA
* *
2607332 AAATTAAAGAAAAGTAAAA
1 AAAATAAAGAAAAATAAAA
2607351 AAAATAAA
1 AAAATAAA
2607359 AATAAGATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (19 bp):
AAAATAAAGAAAAATAAAA
Found at i:2607356 original size:35 final size:36
Alignment explanation
Indices: 2607287--2607361 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
2607277 TTCTTTAAAG
* *
2607287 AAAA-TAAAATAATAAAAAAAAAGTGAAAATAAATA
1 AAAATTAAAAAAATAAAAAAAAAGTGAAAAAAAATA
* *
2607322 AAAATTAAAAAAATTAAAGAAAAGT-AAAAAAAATA
1 AAAATTAAAAAAATAAAAAAAAAGTGAAAAAAAATA
2607357 AAAAT
1 AAAAT
2607362 AAGATAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 18 0.51
36 17 0.49
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.17
Consensus pattern (36 bp):
AAAATTAAAAAAATAAAAAAAAAGTGAAAAAAAATA
Found at i:2607793 original size:19 final size:20
Alignment explanation
Indices: 2607748--2607785 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2607738 GAACACCGGT
*
2607748 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
2607768 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
2607786 CGTCGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:2608396 original size:51 final size:50
Alignment explanation
Indices: 2608341--2608466 Score: 112
Period size: 55 Copynumber: 2.3 Consensus size: 50
2608331 TAAAAATACA
*
2608341 AAAATGAATAAAATAAAAAAGATAAA-AAATATATATATATACATA-AATAAT
1 AAAAT-AATAAAATAAAAAAAATAAATAAATA-A-ATATATACATATAATAAT
*
2608392 AAAATACACATAAATATTAACAAAAAATAAATAAATAAATATATACATATATTAAT
1 AAAAT--A-ATAAA-A-TAA-AAAAAATAAATAAATAAATATATACATATAATAAT
2608448 ACATAATAATAATAATAAA
1 A-A-AATAATAA-AATAAA
2608467 TAATACAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 18
0.75 0.04 0.22
Matches are distributed among these distances:
51 5 0.08
52 1 0.02
53 6 0.10
54 4 0.06
55 19 0.31
56 18 0.29
57 6 0.10
58 3 0.05
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (50 bp):
AAAATAATAAAATAAAAAAAATAAATAAATAAATATATACATATAATAAT
Found at i:2608773 original size:2 final size:2
Alignment explanation
Indices: 2608766--2608801 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2608756 TTAGGTCCTT
* *
2608766 CA CA CA CA CA GA CA CA CA CA CA CA CA GA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2608802 TATATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.44, G:0.06, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2608787 original size:16 final size:16
Alignment explanation
Indices: 2608766--2608801 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2608756 TTAGGTCCTT
2608766 CACACACACAGACACA
1 CACACACACAGACACA
2608782 CACACACACAGACACA
1 CACACACACAGACACA
2608798 CACA
1 CACA
2608802 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.44, G:0.06, T:0.00
Consensus pattern (16 bp):
CACACACACAGACACA
Found at i:2612423 original size:23 final size:22
Alignment explanation
Indices: 2612396--2612441 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2612386 TATCACAAAA
2612396 ATTTTTT-TTA-AAAAGTATTATT
1 ATTTTTTATTATAAAA-TATT-TT
2612418 ATTTTTTATTATAAAATATTTT
1 ATTTTTTATTATAAAATATTTT
2612440 AT
1 AT
2612442 CACCAAGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 11 0.50
23 7 0.32
24 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTTTTATTATAAAATATTTT
Found at i:2613105 original size:31 final size:31
Alignment explanation
Indices: 2612973--2613239 Score: 181
Period size: 30 Copynumber: 8.5 Consensus size: 31
2612963 TAAGGGTTTG
* *
2612973 GATTTTAGGGATTTTGGATTTT-GGGG-TTTG
1 GATTTTAGGG-GTTTGGATTTTAGGGGTTTTA
* * * *
2613003 GATTTAAGGGATTTTAGATTTTTAGGGGTTCT-
1 GATTTTAGGG-GTTTGGA-TTTTAGGGGTTTTA
* * *
2613035 GAATTTTAAGGGTTTAGA-TTTAGGGGTTTCA
1 G-ATTTTAGGGGTTTGGATTTTAGGGGTTTTA
*
2613066 AATTTTAGGGGTTTGGA-TTTAGGGGATTTTA
1 GATTTTAGGGGTTTGGATTTTAGGGG-TTTTA
* *
2613097 GATTTTAGGGGTTTCGGATTTTA-GGATTTTG
1 GATTTTAGGGGTTT-GGATTTTAGGGGTTTTA
* *
2613128 GATTTTAAGGGGATTTTGGATTTTAGGGGGTTTG
1 GATTTT-AGGGG--TTTGGATTTTAGGGGTTTTA
* ** * *
2613162 GATTTAAGGAATTTTAGATTTTTAGGGG-TTTC
1 GATTTTAGG-GGTTTGGA-TTTTAGGGGTTTTA
*
2613194 GAATTTTAGAGGTTTGGA-TTTAGGGGATTTTA
1 G-ATTTTAGGGGTTTGGATTTTAGGGG-TTTTA
2613226 GATTTTAGGGGTTT
1 GATTTTAGGGGTTT
2613240 TAGAAACCTA
Statistics
Matches: 191, Mismatches: 29, Indels: 33
0.75 0.11 0.13
Matches are distributed among these distances:
30 56 0.29
31 43 0.23
32 39 0.20
33 39 0.20
34 14 0.07
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (31 bp):
GATTTTAGGGGTTTGGATTTTAGGGGTTTTA
Found at i:2613243 original size:16 final size:16
Alignment explanation
Indices: 2612953--2613240 Score: 222
Period size: 16 Copynumber: 18.4 Consensus size: 16
2612943 TGTAGTTTGA
*
2612953 GGTTTT-GA-TTTAAG
1 GGTTTTGGATTTTAGG
2612967 GG-TTTGGATTTTAGG
1 GGTTTTGGATTTTAGG
*
2612982 GATTTTGGATTTT-GG
1 GGTTTTGGATTTTAGG
*
2612997 GG-TTTGGATTTAAGG
1 GGTTTTGGATTTTAGG
* *
2613012 GATTTTAGATTTTTAGG
1 GGTTTTGGA-TTTTAGG
* * *
2613029 GGTTCTGAATTTTAAG
1 GGTTTTGGATTTTAGG
*
2613045 GG-TTTAGA-TTTAGG
1 GGTTTTGGATTTTAGG
***
2613059 GGTTTCAAATTTTAGG
1 GGTTTTGGATTTTAGG
2613075 GG-TTTGGA-TTTAGG
1 GGTTTTGGATTTTAGG
*
2613089 GGATTTTAGATTTTAGG
1 GG-TTTTGGATTTTAGG
*
2613106 GGTTTCGGATTTTA-G
1 GGTTTTGGATTTTAGG
*
2613121 GATTTTGGATTTTAAGG
1 GGTTTTGGATTTT-AGG
2613138 GGATTTTGGATTTTAGG
1 GG-TTTTGGATTTTAGG
* *
2613155 GGGTTTGGATTTAAGG
1 GGTTTTGGATTTTAGG
** *
2613171 AATTTTAGATTTTTAGG
1 GGTTTTGGA-TTTTAGG
* * *
2613188 GGTTTCGAATTTTAGA
1 GGTTTTGGATTTTAGG
2613204 GG-TTTGGA-TTTAGG
1 GGTTTTGGATTTTAGG
*
2613218 GGATTTTAGATTTTAGG
1 GG-TTTTGGATTTTAGG
2613235 GGTTTT
1 GGTTTT
2613241 AGAAACCTAG
Statistics
Matches: 212, Mismatches: 44, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
13 3 0.01
14 35 0.17
15 38 0.18
16 81 0.38
17 44 0.21
18 11 0.05
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.47
Consensus pattern (16 bp):
GGTTTTGGATTTTAGG
Found at i:2613513 original size:3 final size:3
Alignment explanation
Indices: 2613507--2613555 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2613497 ATAAAAATTG
2613507 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2613555 T
1 T
2613556 CTTAAGCATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2616242 original size:51 final size:52
Alignment explanation
Indices: 2616166--2616268 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 52
2616156 CCAATTAATG
* ** * *
2616166 GTGAAGACATTGTTCATGTTCACGTTTTCTTCACTTCAGAAGACAAAGAAAA
1 GTGAACACATTGTTCATGTAAACGTTTTCTTCACTTCAAAACACAAAGAAAA
*
2616218 GTGAACACATT-TTCATGTAAACGTTTTCTTCACTTCAAAACACGAAGAAAA
1 GTGAACACATTGTTCATGTAAACGTTTTCTTCACTTCAAAACACAAAGAAAA
2616269 TTCAATACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
51 35 0.78
52 10 0.22
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (52 bp):
GTGAACACATTGTTCATGTAAACGTTTTCTTCACTTCAAAACACAAAGAAAA
Found at i:2617257 original size:144 final size:144
Alignment explanation
Indices: 2617039--2617621 Score: 1058
Period size: 144 Copynumber: 4.0 Consensus size: 144
2617029 TGTTGGTCCA
*
2617039 ATCCCTTCTTCTGTTAGCAATTTAACCAATCTGACAATGTTGTACCTTCAAAATAACCAACTCAA
1 ATCCCTTCTTCTGTTAGCAATTTAACCAACCTGACAATGTTGTACCTTCAAAATAACCAACTCAA
* *
2617104 TGGATCCATTCCAAAAGAAATAGGAAGACTAACCAAGTTGGTTACTCTAGATCTCTCCTCCAATA
66 TGGATCCATTCCAAAAGAAATAGGGAGACTAACCAATTTGGTTACTCTAGATCTCTCCTCCAATA
2617169 TGCTTTTGGGTCTC
131 TGCTTTTGGGTCTC
* *
2617183 ATCCCTTCTTCTGTTAGCAATTTAACCGACCTGACAATGTTGTACCTTCAAAATAACCAACTCGA
1 ATCCCTTCTTCTGTTAGCAATTTAACCAACCTGACAATGTTGTACCTTCAAAATAACCAACTCAA
*
2617248 TGGATCCATTCCAAAGGAAATAGGGAGACTAACCAATTTGGTTACTCTAGATCTCTCCTCCAATA
66 TGGATCCATTCCAAAAGAAATAGGGAGACTAACCAATTTGGTTACTCTAGATCTCTCCTCCAATA
2617313 TGCTTTTGGGTCTC
131 TGCTTTTGGGTCTC
*
2617327 ATCCCGTCTTCTGTTAGCAATTTAACCAACCTGACAATGTTGTACCTTCAAAATAACCAACTCAA
1 ATCCCTTCTTCTGTTAGCAATTTAACCAACCTGACAATGTTGTACCTTCAAAATAACCAACTCAA
2617392 TGGATCCATTCCAAAAGAAATAGGGAGACTAACCAATTTGGTTACTCTAGATCTCTCCTCCAATA
66 TGGATCCATTCCAAAAGAAATAGGGAGACTAACCAATTTGGTTACTCTAGATCTCTCCTCCAATA
2617457 TGCTTTTGGGTCTC
131 TGCTTTTGGGTCTC
*
2617471 ATCCCGTCTTCTGTTAGCAATTTAACCAACCTGACAATGTTGTACCTTCAAAATAACCAACTCAA
1 ATCCCTTCTTCTGTTAGCAATTTAACCAACCTGACAATGTTGTACCTTCAAAATAACCAACTCAA
* * *
2617536 TGGATTCATTCCAACAGAAATAGGGAGACTAACCAATTTGGTTACTCTAGATCTCTCCTTCAATA
66 TGGATCCATTCCAAAAGAAATAGGGAGACTAACCAATTTGGTTACTCTAGATCTCTCCTCCAATA
*
2617601 TGCTTTTGGGTCCC
131 TGCTTTTGGGTCTC
2617615 ATCCCTT
1 ATCCCTT
2617622 TCTATTTGTG
Statistics
Matches: 424, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 424 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (144 bp):
ATCCCTTCTTCTGTTAGCAATTTAACCAACCTGACAATGTTGTACCTTCAAAATAACCAACTCAA
TGGATCCATTCCAAAAGAAATAGGGAGACTAACCAATTTGGTTACTCTAGATCTCTCCTCCAATA
TGCTTTTGGGTCTC
Found at i:2624750 original size:2 final size:2
Alignment explanation
Indices: 2624743--2624768 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2624733 TGATAACATG
2624743 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2624769 CTGACCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2627837 original size:9 final size:9
Alignment explanation
Indices: 2627823--2627848 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2627813 ATTTTATTTA
2627823 TTATTATTG
1 TTATTATTG
2627832 TTATTATTG
1 TTATTATTG
2627841 TTATTATT
1 TTATTATT
2627849 ATGTAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (9 bp):
TTATTATTG
Found at i:2630701 original size:72 final size:72
Alignment explanation
Indices: 2630604--2630755 Score: 259
Period size: 72 Copynumber: 2.1 Consensus size: 72
2630594 GCTCAGTGGC
* *
2630604 CCTATCCCACTAAATATTGCCAAGCTAAAGAGTTTGGTTACTCTTGATCTTTCAAGCAACATGCT
1 CCTATCCCACAAAATATTGCAAAGCTAAAGAGTTTGGTTACTCTTGATCTTTCAAGCAACATGCT
2630669 TGTTGGT
66 TGTTGGT
* *
2630676 CCTATCCCACAAAATATTGCAAAGCTAAAGAGTTTGGTTACTGTTGATCTTTCAAGCAACATGTT
1 CCTATCCCACAAAATATTGCAAAGCTAAAGAGTTTGGTTACTCTTGATCTTTCAAGCAACATGCT
2630741 TGTTGGT
66 TGTTGGT
*
2630748 CCAATCCC
1 CCTATCCC
2630756 TTCTCCTGTT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (72 bp):
CCTATCCCACAAAATATTGCAAAGCTAAAGAGTTTGGTTACTCTTGATCTTTCAAGCAACATGCT
TGTTGGT
Found at i:2630968 original size:144 final size:144
Alignment explanation
Indices: 2630745--2631046 Score: 514
Period size: 144 Copynumber: 2.1 Consensus size: 144
2630735 CATGTTTGTT
* *
2630745 GGTCCAATCCCTTCTCCTGTTAACAATTTAACCAATCTGACAACGTTGTACCTTCAAGATAACCA
1 GGTCCAATCCCTTCTCCTGTTAACAATTTAACCAATCTGACAACGTTGGACCTTCAAAATAACCA
*
2630810 ACTCAATGGATCCATTCCGAAAGAAATTGGGAGACTAACCAATTTGGTTGCTCTAGATCTCTCCT
66 ACTCAATGGATCCATTCCAAAAGAAATTGGGAGACTAACCAATTTGGTTGCTCTAGATCTCTCCT
*
2630875 TCAATATGCTTTTG
131 CCAATATGCTTTTG
* * *
2630889 GGTCCTATCCCTTCTTCTGTTAGCAATTTAACCAATCTGACAACGTTGGACCTTCAAAATAACCA
1 GGTCCAATCCCTTCTCCTGTTAACAATTTAACCAATCTGACAACGTTGGACCTTCAAAATAACCA
2630954 ACTCAATGGATCCATTCCAAAAGAAATTGGGAGACTAACCAATTTGGTTGCTCTAGATCTCTCCT
66 ACTCAATGGATCCATTCCAAAAGAAATTGGGAGACTAACCAATTTGGTTGCTCTAGATCTCTCCT
*
2631019 CCAATATGTTTTTG
131 CCAATATGCTTTTG
* *
2631033 GATCCCATCCCTTC
1 GGTCCAATCCCTTC
2631047 CTCTTTGGGT
Statistics
Matches: 148, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
144 148 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (144 bp):
GGTCCAATCCCTTCTCCTGTTAACAATTTAACCAATCTGACAACGTTGGACCTTCAAAATAACCA
ACTCAATGGATCCATTCCAAAAGAAATTGGGAGACTAACCAATTTGGTTGCTCTAGATCTCTCCT
CCAATATGCTTTTG
Found at i:2641119 original size:39 final size:39
Alignment explanation
Indices: 2641065--2641143 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
2641055 AGAATTTTGG
* * *
2641065 TTACTTAAGACTATAAAATATTAATCTACTATGTATATA
1 TTACTTAAGACTATAAAACAATAATCTACTACGTATATA
*
2641104 TTACTTAAGAGTATAAAACAATAATCTACTACGTATATA
1 TTACTTAAGACTATAAAACAATAATCTACTACGTATATA
2641143 T
1 T
2641144 ATTAAGCCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.38
Consensus pattern (39 bp):
TTACTTAAGACTATAAAACAATAATCTACTACGTATATA
Found at i:2643741 original size:2 final size:2
Alignment explanation
Indices: 2643734--2643772 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2643724 CTGCTGCTTC
2643734 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2643773 ATGGGTTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2645800 original size:20 final size:20
Alignment explanation
Indices: 2645764--2645801 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2645754 TAATTTAAGA
*
2645764 TTTGTTTATATTTATTTACG
1 TTTGTTTATATTCATTTACG
*
2645784 TTTGTTTATGTTCATTTA
1 TTTGTTTATATTCATTTA
2645802 GGATTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (20 bp):
TTTGTTTATATTCATTTACG
Found at i:2645835 original size:15 final size:15
Alignment explanation
Indices: 2645804--2645845 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
2645794 TTCATTTAGG
*
2645804 ATTTATTTGTTTA-A
1 ATTTATTTGATTATA
2645818 ATTTATTTGATTATA
1 ATTTATTTGATTATA
2645833 ATTTATTT-ATTAT
1 ATTTATTTGATTAT
2645846 TTATAAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
ATTTATTTGATTATA
Found at i:2652688 original size:57 final size:58
Alignment explanation
Indices: 2652600--2652715 Score: 198
Period size: 57 Copynumber: 2.0 Consensus size: 58
2652590 ATGAGAAAAG
*
2652600 ATAGTTTTTATTATTGAGAAAGGCTTTTACTATTACAAGG-TAAATACCCTTCGAATT
1 ATAGTTTTTATTATTGAGAAAGGCCTTTACTATTACAAGGATAAATACCCTTCGAATT
*
2652657 ATAGTTTTTATTATTGAGAAAGGCCTTTACTATTACAAGGAATAAATACCCTTTGAATT
1 ATAGTTTTTATTATTGAGAAAGGCCTTTACTATTACAAGG-ATAAATACCCTTCGAATT
2652716 GAAAGAATAC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
57 39 0.71
59 16 0.29
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (58 bp):
ATAGTTTTTATTATTGAGAAAGGCCTTTACTATTACAAGGATAAATACCCTTCGAATT
Found at i:2677175 original size:3 final size:3
Alignment explanation
Indices: 2677167--2677217 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
2677157 GAGAAAAGGA
* *
2677167 AAG AAG AAGG AAG AAG AAG AAG AAG TAG AAG AAAG AAG TAG AAG AAG
1 AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG
2677214 AAG A
1 AAG A
2677218 GGGAGAAGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:2677202 original size:22 final size:22
Alignment explanation
Indices: 2677171--2677213 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2677161 AAAGGAAAGA
*
2677171 AGAAGGAAGAAGAAGAAGAAGT
1 AGAAGAAAGAAGAAGAAGAAGT
*
2677193 AGAAGAAAGAAGTAGAAGAAG
1 AGAAGAAAGAAGAAGAAGAAG
2677214 AAGAGGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.35, T:0.05
Consensus pattern (22 bp):
AGAAGAAAGAAGAAGAAGAAGT
Found at i:2677204 original size:25 final size:25
Alignment explanation
Indices: 2677168--2677216 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2677158 AGAAAAGGAA
*
2677168 AGAAGAAGGAAGAAGAAGAAGAAGT
1 AGAAGAAAGAAGAAGAAGAAGAAGT
*
2677193 AGAAGAAAGAAGTAGAAGAAGAAG
1 AGAAGAAAGAAGAAGAAGAAGAAG
2677217 AGGGAGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (25 bp):
AGAAGAAAGAAGAAGAAGAAGAAGT
Found at i:2682594 original size:20 final size:21
Alignment explanation
Indices: 2682564--2682605 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2682554 TTTATTATAT
2682564 AATAAATATATTAAATTATTA
1 AATAAATATATTAAATTATTA
* *
2682585 AATAAA-ATATTTATTTATTA
1 AATAAATATATTAAATTATTA
2682605 A
1 A
2682606 GTCAACTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAAATATATTAAATTATTA
Found at i:2689538 original size:17 final size:17
Alignment explanation
Indices: 2689516--2689548 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2689506 TCACTATTTA
2689516 TAGAGCA-TGTGCCAACT
1 TAGAGCACTGT-CCAACT
2689533 TAGAGCACTGTCCAAC
1 TAGAGCACTGTCCAAC
2689549 ACATACAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (17 bp):
TAGAGCACTGTCCAACT
Found at i:2695516 original size:22 final size:24
Alignment explanation
Indices: 2695491--2695544 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
2695481 TTTTTAAAAA
2695491 ATTTTTAATATTTA-ATA-TTTTT
1 ATTTTTAATATTTATATATTTTTT
*
2695513 ATTTTTAATATTTATTTATTTTTT
1 ATTTTTAATATTTATATATTTTTT
*
2695537 ATTATTAA
1 ATTTTTAA
2695545 AAATCATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 14 0.50
23 2 0.07
24 12 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
ATTTTTAATATTTATATATTTTTT
Found at i:2695537 original size:18 final size:16
Alignment explanation
Indices: 2695491--2695535 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
2695481 TTTTTAAAAA
* *
2695491 ATTTTTAATATTTAAT
1 ATTTTTTATTTTTAAT
2695507 A-TTTTTATTTTTAAT
1 ATTTTTTATTTTTAAT
2695522 ATTTATTTATTTTT
1 ATTT-TTTATTTTT
2695536 TATTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.52
16 3 0.12
17 9 0.36
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTATTTTTAAT
Found at i:2698745 original size:19 final size:19
Alignment explanation
Indices: 2698702--2698742 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2698692 TCTTTTAAAA
* *
2698702 AATTAATTTTTATTATATG
1 AATTAATTTTAATGATATG
2698721 AATTAATTTTAATGA-ATG
1 AATTAATTTTAATGATATG
2698739 AATT
1 AATT
2698743 TAAAATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (19 bp):
AATTAATTTTAATGATATG
Found at i:2724352 original size:16 final size:16
Alignment explanation
Indices: 2724331--2724366 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2724321 CTATAGAAAT
2724331 TATAAAAAATATAAAA
1 TATAAAAAATATAAAA
2724347 TAT-AAAAATATAAAA
1 TATAAAAAATATAAAA
2724362 -ATAAA
1 TATAAA
2724367 TAAACAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.11
15 14 0.74
16 3 0.16
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
TATAAAAAATATAAAA
Found at i:2724354 original size:8 final size:8
Alignment explanation
Indices: 2724335--2724364 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2724325 AGAAATTATA
2724335 AAAAATAT
1 AAAAATAT
2724343 -AAAATAT
1 AAAAATAT
2724350 AAAAATAT
1 AAAAATAT
2724358 AAAAATA
1 AAAAATA
2724365 AATAAACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAATAT
Found at i:2726004 original size:54 final size:54
Alignment explanation
Indices: 2725946--2726054 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
2725936 AAGATATTTT
* *
2725946 TGTTAATTATAATAATAAATAAATAAATTTAGTACAAAAATGAACAAAATAAAA
1 TGTTAATTATAATAAAAAATAAATAAATTTAGTACAAAAATGAACAAAACAAAA
2726000 TGTTAATTATAATAAAAAATAAATAAATTTAGTACAAAAATGAACAAAACAAAA
1 TGTTAATTATAATAAAAAATAAATAAATTTAGTACAAAAATGAACAAAACAAAA
2726054 T
1 T
2726055 AATGTGAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (54 bp):
TGTTAATTATAATAAAAAATAAATAAATTTAGTACAAAAATGAACAAAACAAAA
Found at i:2726751 original size:15 final size:15
Alignment explanation
Indices: 2726731--2726761 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2726721 AGGTTTGTGT
2726731 AAAAGAGAAAAAGAG
1 AAAAGAGAAAAAGAG
*
2726746 AAAAGAGAGAAAGAG
1 AAAAGAGAAAAAGAG
2726761 A
1 A
2726762 GAGAGAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAAAAGAG
Found at i:2727073 original size:16 final size:16
Alignment explanation
Indices: 2727052--2727084 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2727042 TTTAAATTTA
2727052 TTTTTATGT-TTTTTTT
1 TTTTTA-GTATTTTTTT
2727068 TTTTTAGTATTTTTTT
1 TTTTTAGTATTTTTTT
2727084 T
1 T
2727085 GCATGATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (16 bp):
TTTTTAGTATTTTTTT
Found at i:2727080 original size:15 final size:16
Alignment explanation
Indices: 2727052--2727084 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2727042 TTTAAATTTA
*
2727052 TTTTTATGTTTTTTTT
1 TTTTTATGTATTTTTT
2727068 TTTTTA-GTATTTTTT
1 TTTTTATGTATTTTTT
2727083 TT
1 TT
2727085 GCATGATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (16 bp):
TTTTTATGTATTTTTT
Found at i:2727499 original size:197 final size:197
Alignment explanation
Indices: 2727147--2727508 Score: 459
Period size: 197 Copynumber: 1.8 Consensus size: 197
2727137 GAATAAATAT
*
2727147 TAATTATCCAATGATGAAATTTATAGAAATTTCAAATGGTAAATTTCTATAAAATTCCTAGGTGA
1 TAATTATCCAATGATGAAATTTATAGAAATTTCAAATGGTAAATTTCTATAAAATTCCTAGATGA
* * * * * *
2727212 GAAATTTTGTCTAAATTTATTCCAAATGGTGGAATAATTTAGATAAAATTTCAACAACAATAATT
66 AAAATTTTCTCTAAATTTATTCCAAATAGTGGAATAATTTAAATAAAATTACAACAAAAATAATT
* *
2727277 AATATTTATTTTCAATCCAAAAAAAATAA-AAAAATAAAAAATAAAAATTTGGGTTGAAAATATT
131 AATATTTATTTGC-ATCCAAAAAAAAAAATAAAAATAAAAAATAAAAATTTGGGTTGAAAATATT
2727341 TGA
195 TGA
*
2727344 TAATTATCCAATGATGAGATTCT-TA-AAATTTTCAAATGGTAAATTTCTA-AGAAATCTCC-AG
1 TAATTATCCAATGATGAAATT-TATAGAAA-TTTCAAATGGTAAATTTCTATA-AAAT-TCCTAG
* * *
2727405 ATGAAAAATTTTCTTTAAATTTATTCCAAATAGTGGAATAATTTAAATGAAATTACAATAAAAAT
62 ATGAAAAATTTTCTCTAAATTTATTCCAAATAGTGGAATAATTTAAATAAAATTACAACAAAAAT
* **
2727470 AATT-GTCATATTATTTGC-TTTAGAAAAAAAAAATAAAAA
127 AATTAAT-AT-TTATTTGCATCCA-AAAAAAAAAATAAAAA
2727509 GAATTTTTAA
Statistics
Matches: 141, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
196 7 0.05
197 118 0.84
198 16 0.11
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (197 bp):
TAATTATCCAATGATGAAATTTATAGAAATTTCAAATGGTAAATTTCTATAAAATTCCTAGATGA
AAAATTTTCTCTAAATTTATTCCAAATAGTGGAATAATTTAAATAAAATTACAACAAAAATAATT
AATATTTATTTGCATCCAAAAAAAAAAATAAAAATAAAAAATAAAAATTTGGGTTGAAAATATTT
GA
Found at i:2731951 original size:72 final size:72
Alignment explanation
Indices: 2731811--2731956 Score: 177
Period size: 72 Copynumber: 2.0 Consensus size: 72
2731801 TTTGCCGATC
* * * *
2731811 TGAGGAGGGATGTACCCCTCTAAATGATTGCTGCTTAGGTCCAAATAGGATAAACTTAAGCAACT
1 TGAGAAGGGATGTACCCCTCTAAATGATTGCTGCTTAGGTCCAAATAGCACAAACTTAAACAACT
2731876 CCCAATT
66 CCCAATT
* * * * * * *
2731883 TGAGAAGGGATGTATCTCTCTAAATTATTGTTGCTTAGGTCC-AATTGCCACAAATTTAAACAAT
1 TGAGAAGGGATGTACCCCTCTAAATGATTGCTGCTTAGGTCCAAATAG-CACAAACTTAAACAAC
2731947 TCCCAATT
65 TCCCAATT
2731955 TG
1 TG
2731957 TGAGGGTATG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
71 4 0.06
72 58 0.94
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (72 bp):
TGAGAAGGGATGTACCCCTCTAAATGATTGCTGCTTAGGTCCAAATAGCACAAACTTAAACAACT
CCCAATT
Found at i:2736207 original size:25 final size:25
Alignment explanation
Indices: 2736168--2736228 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
2736158 TTTGATTTTG
* *
2736168 ATTTATTTTATGTTGATTTTTATGTT
1 ATTTATTTTATGTTG-TTTCTATGAT
2736194 ATTT-TTTTATGTTGTTTCTATGAT
1 ATTTATTTTATGTTGTTTCTATGAT
2736218 A-TTATTATTAT
1 ATTTATT-TTAT
2736229 TATTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 2 0.06
24 11 0.35
25 14 0.45
26 4 0.13
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (25 bp):
ATTTATTTTATGTTGTTTCTATGAT
Found at i:2736223 original size:3 final size:3
Alignment explanation
Indices: 2736217--2736260 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2736207 GTTTCTATGA
2736217 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2736261 CTACTACTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2736696 original size:13 final size:14
Alignment explanation
Indices: 2736663--2736705 Score: 63
Period size: 13 Copynumber: 3.2 Consensus size: 14
2736653 TGATTTAGGC
2736663 AATG-AAAAATAAT
1 AATGAAAAAATAAT
*
2736676 AATAAAAAAATAA-
1 AATGAAAAAATAAT
2736689 AATGAAAAAATAAT
1 AATGAAAAAATAAT
2736703 AAT
1 AAT
2736706 AATTGATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (14 bp):
AATGAAAAAATAAT
Found at i:2745896 original size:31 final size:31
Alignment explanation
Indices: 2745826--2745896 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
2745816 TTTTAAATTT
* * *
2745826 TTTATAAAATTAAAATTTCATGATTTTTAATA
1 TTTA-AAAATTAAAAATTCAAGAGTTTTAATA
**
2745858 TCAAAAAATTAAAAATT-AAGAGTTTTAGATA
1 TTTAAAAATTAAAAATTCAAGAGTTTTA-ATA
2745889 TTTAAAAA
1 TTTAAAAA
2745897 AAATAAAACA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
30 8 0.26
31 21 0.68
32 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.41
Consensus pattern (31 bp):
TTTAAAAATTAAAAATTCAAGAGTTTTAATA
Found at i:2749623 original size:3 final size:3
Alignment explanation
Indices: 2749615--2749671 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
2749605 TGGAAAAGGA
* *
2749615 AAG AAG AAG AAG AAG AAG AAG AAG TAG AAG AAG AAG TAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
2749663 AGG AAG AAG
1 AAG AAG AAG
2749672 GAGTAGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (3 bp):
AAG
Done.