Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168478.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_77, 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: 119140
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:330 original size:80 final size:80
Alignment explanation
Indices: 219--464 Score: 361
Period size: 80 Copynumber: 3.1 Consensus size: 80
209 TTCAGTGTAG
* * * * *
219 AGTTTTATCCATTTTTTTTGGCCTATCATTTCTAACGTATTCATAGTGCTAATTAAATTATTGGC
1 AGTTGTATTCATTTCTTTTGACCTCTCATTTCTAACGTATTCATAGTGCTAATTAAATTATTGGC
284 TAAAGGATATGTAAT
66 TAAAGGATATGTAAT
*
299 AGTTGTATTCATTTCTTTTGACCTCTCATTTCTAACGTATTCATGGTGCTAATTAAATTATTGGC
1 AGTTGTATTCATTTCTTTTGACCTCTCATTTCTAACGTATTCATAGTGCTAATTAAATTATTGGC
*
364 TAAAGGATATATAAT
66 TAAAGGATATGTAAT
379 AGTTGTA-TCAATTTCTTTTGACCTCTCATTTCTAACGTATTCA-AGGTGCTAATTAAATTATTG
1 AGTTGTATTC-ATTTCTTTTGACCTCTCATTTCTAACGTATTCATA-GTGCTAATTAAATTATTG
* * *
442 GCCAAAGAATATGAAAT
64 GCTAAAGGATATGTAAT
*
459 ACTTGT
1 AGTTGT
465 CAACATTATG
Statistics
Matches: 151, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
79 2 0.01
80 149 0.99
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (80 bp):
AGTTGTATTCATTTCTTTTGACCTCTCATTTCTAACGTATTCATAGTGCTAATTAAATTATTGGC
TAAAGGATATGTAAT
Found at i:927 original size:80 final size:80
Alignment explanation
Indices: 794--953 Score: 248
Period size: 80 Copynumber: 2.0 Consensus size: 80
784 ATTTGGAGTC
* * * *
794 ATCCATTTCTTTTGGCCTCTCATTTTTAACATATTCATGGTGCTAATTAAATTATTGGTCAAAGG
1 ATCCATTTCTTCTGACCTCTCATTTCTAACATATTCATGGTGCTAATTAAATTATTGGCCAAAGG
*
859 AGATGCAATAGTTAT
66 AGATGCAATAATTAT
* *
874 ATCCATTTCTTCTGACCTCTCATTTCTAACGTGTTCATGGTGCTAATTAAATTATTGGCCAAAGG
1 ATCCATTTCTTCTGACCTCTCATTTCTAACATATTCATGGTGCTAATTAAATTATTGGCCAAAGG
*
939 ATATGCAATAATTAT
66 AGATGCAATAATTAT
954 CAACATTACA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (80 bp):
ATCCATTTCTTCTGACCTCTCATTTCTAACATATTCATGGTGCTAATTAAATTATTGGCCAAAGG
AGATGCAATAATTAT
Found at i:1562 original size:21 final size:21
Alignment explanation
Indices: 1536--1584 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1526 ATATTATTAA
*
1536 TAATATTTAAGACTATTAAAT
1 TAATATTTAAGACTACTAAAT
* * *
1557 TAATATTTAATATTACTAATT
1 TAATATTTAAGACTACTAAAT
1578 TAATATT
1 TAATATT
1585 AATTCATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
TAATATTTAAGACTACTAAAT
Found at i:2321 original size:17 final size:18
Alignment explanation
Indices: 2294--2342 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 18
2284 ATCCCTCTTT
2294 ATTTTTT-TATTTAAT-A
1 ATTTTTTATATTTAATAA
2310 ATTTTTTATATTTAATAA
1 ATTTTTTATATTTAATAA
2328 ATTTTTTA-ATTTAAT
1 ATTTTTTATATTTAAT
2343 TTTCTTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.23
17 15 0.48
18 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTTATATTTAATAA
Found at i:2984 original size:18 final size:18
Alignment explanation
Indices: 2957--2991 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2947 TATTTTATAA
*
2957 TAATATATTTATAAAAAT
1 TAATAAATTTATAAAAAT
*
2975 TAATAAATTTTTAAAAA
1 TAATAAATTTATAAAAA
2992 CTCTGTCATC
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATTTATAAAAAT
Found at i:3674 original size:19 final size:20
Alignment explanation
Indices: 3638--3680 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
3628 ATTATTTAGC
*
3638 ATTTATAAAATTAATAAATA
1 ATTTATAAAATCAATAAATA
* *
3658 ATTTA-AAAATCAGTAAATT
1 ATTTATAAAATCAATAAATA
3677 ATTT
1 ATTT
3681 TTATGTCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTATAAAATCAATAAATA
Found at i:3883 original size:17 final size:17
Alignment explanation
Indices: 3840--3883 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3830 TTTAGCTAAT
*
3840 TAATTGTTTATATAATAA
1 TAATT-TTTATAAAATAA
**
3858 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
3875 TAATTTTTA
1 TAATTTTTA
3884 GTTCATAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:7602 original size:19 final size:19
Alignment explanation
Indices: 7578--7616 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
7568 ATTTTGCCTT
* *
7578 TCATTTTTTTTTCCTTCCA
1 TCATTTTTTTGTCATTCCA
7597 TCATTTTTTTGTCATTCCA
1 TCATTTTTTTGTCATTCCA
7616 T
1 T
7617 TTTTGTGTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (19 bp):
TCATTTTTTTGTCATTCCA
Found at i:12222 original size:94 final size:96
Alignment explanation
Indices: 11889--12307 Score: 574
Period size: 94 Copynumber: 4.3 Consensus size: 96
11879 AAATTTGAAA
*
11889 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCTTTTTCGAGAAAAAATTTTAAA
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCTTTTTC-AGAAGAAATTTTAAA
** * * *
11954 GTTGTTGAGCCTCTACTAAGATGAGCTTTTTC
65 GTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCC
* *
11986 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTTAAGAAGAAATTTTAAA
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGC-TTTTTCAGAAGAAATTTTAAA
*
12051 GTTGTTGAGCCTCTGCTGAGAGCAGAGGAGCTTTTCC
65 GTTGTTGAGCCTCTG-T---TG-AGAGGAGCTTTTCC
* * *
12088 AAGATAAGAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCATTTTCAGATGAAATTTTAAAG
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCTTTTTCAGAAGAAATTTTAAAG
*
12153 TTGTGGAGCCTCTGTTGAGAGGAGCTTTTCC
66 TTGTTGAGCCTCTGTTGAGAGGAGCTTTTCC
* * * *
12184 AA-ATGAG-ATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGACCTTTTCCAGATGAAATTTTAAAG
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCTTTTTCAGAAGAAATTTTAAAG
*
12247 TTGTTGAGCCTCTGTTGAGAGGAGCTTTTTC
66 TTGTTGAGCCTCTGTTGAGAGGAGCTTTTCC
* *
12278 -AGATGAGATTTTTAAAGTTGTTGAGCCTCT
1 AAGATGAGAATTTTAAAGTTGTGGAGCCTCT
12308 TTCAGATGAG
Statistics
Matches: 289, Mismatches: 25, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
93 1 0.00
94 86 0.30
95 24 0.08
96 16 0.06
97 71 0.25
98 5 0.02
100 1 0.00
101 32 0.11
102 53 0.18
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (96 bp):
AAGATGAGAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCTTTTTCAGAAGAAATTTTAAAG
TTGTTGAGCCTCTGTTGAGAGGAGCTTTTCC
Found at i:12313 original size:33 final size:33
Alignment explanation
Indices: 12274--12340 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
12264 AGAGGAGCTT
12274 TTTCAGATGAGATTTTTAAAGTTGTTGAGCCTC
1 TTTCAGATGAGATTTTTAAAGTTGTTGAGCCTC
12307 TTTCAGATGAGATTTTTAAAGTTGTTGAGCCTC
1 TTTCAGATGAGATTTTTAAAGTTGTTGAGCCTC
12340 T
1 T
12341 GCTGAGATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (33 bp):
TTTCAGATGAGATTTTTAAAGTTGTTGAGCCTC
Found at i:12323 original size:47 final size:48
Alignment explanation
Indices: 11890--12307 Score: 513
Period size: 47 Copynumber: 8.6 Consensus size: 48
11880 AATTTGAAAA
*
11890 AGATGAGAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCTTTTTC
1 AGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
* * * ** * *
11938 GAGA-AAAAATTTTAAAGTTGTTGAGCCTCTACTAAGATGAGCTTTTTC
1 -AGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
*
11986 AAGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTTA
1 -AGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGC-TTTTTC
* * * *
12036 AGAAGA-AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGCAGAGGAGCTTTTCC
1 AGATGAGAATTTTAAAGTTGTGGAGCCTCTG-T---TG-AGAGGAGCTTTTTC
* * *
12088 AAGATAAGAATTTTAAAGTTGTGGAGCCTCTATTGAGAGGAGCATTTTC
1 -AGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
*
12137 AGATGA-AATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTCC
1 AGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
* * *
12184 AAATGAG-ATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGACCTTTTCC
1 AGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
*
12231 AGATGA-AATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTC
1 AGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
* *
12278 AGATGAGATTTTTAAAGTTGTTGAGCCTCT
1 AGATGAGAATTTTAAAGTTGTGGAGCCTCT
12308 TTCAGATGAG
Statistics
Matches: 319, Mismatches: 38, Indels: 25
0.84 0.10 0.07
Matches are distributed among these distances:
47 130 0.41
48 91 0.29
49 52 0.16
50 6 0.02
52 5 0.02
53 13 0.04
54 22 0.07
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (48 bp):
AGATGAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGCTTTTTC
Found at i:12331 original size:81 final size:79
Alignment explanation
Indices: 12230--12387 Score: 262
Period size: 81 Copynumber: 2.0 Consensus size: 79
12220 GGACCTTTTC
*
12230 CAGATGAAATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTTCAGATGAGATTTTTAAAG
1 CAGATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGA-TTTTAAAG
*
12295 TTGTTGAGCCTCTTT
65 TTATTGAGCCTCTTT
* *
12310 CAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGATGAGCTTTTTCAGATGAGATTTTAAAG
1 CAGATGA-AATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGATTTTAAAG
12375 TTATTGAGCCTCT
65 TTATTGAGCCTCT
12388 GCTGAGAGGA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
80 27 0.37
81 46 0.63
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.39
Consensus pattern (79 bp):
CAGATGAAATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAGATGAGATTTTAAAGT
TATTGAGCCTCTTT
Found at i:12357 original size:34 final size:33
Alignment explanation
Indices: 12276--12357 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
12266 AGGAGCTTTT
*
12276 TCAGATGAGATTTTTAAAGTTGTTGAGCCTCTT
1 TCAGATGAGATTTTTAAAGTTGTTGAGCCTCTC
12309 TCAGATGAGATTTTTAAAGTTGTTGAGCCTCTGC
1 TCAGATGAGATTTTTAAAGTTGTTGAGCCTCT-C
* *
12343 TGAGATGAGCTTTTT
1 TCAGATGAGATTTTT
12358 CAGATGAGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 32 0.71
34 13 0.29
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.41
Consensus pattern (33 bp):
TCAGATGAGATTTTTAAAGTTGTTGAGCCTCTC
Found at i:12406 original size:47 final size:48
Alignment explanation
Indices: 12300--12406 Score: 162
Period size: 47 Copynumber: 2.2 Consensus size: 48
12290 TAAAGTTGTT
* *
12300 GAGCCTCTTTCAGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAT
1 GAGCC-CTTTCAGATGAGATTTTTAAAGTTATTGAGCCTCTGCTGAGAG
**
12349 GAGCTTTTTCAGATGAGA-TTTTAAAGTTATTGAGCCTCTGCTGAGAG
1 GAGCCCTTTCAGATGAGATTTTTAAAGTTATTGAGCCTCTGCTGAGAG
12396 GAGCCCTTTCA
1 GAGCCCTTTCA
12407 AAAATAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 36 0.69
48 12 0.23
49 4 0.08
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (48 bp):
GAGCCCTTTCAGATGAGATTTTTAAAGTTATTGAGCCTCTGCTGAGAG
Found at i:14650 original size:192 final size:192
Alignment explanation
Indices: 14318--14698 Score: 570
Period size: 192 Copynumber: 2.0 Consensus size: 192
14308 GCATTGCATG
* * * * *
14318 CATGATATTTTCTTACAAAAAATAAATTCGAGCTTCCGAGGATGAGATTCTAAGGTATTCTGAGA
1 CATGACATTTTCTTACAAAAAATAAATTCGAGCTTCCAAAGATGAGATTCTAAAGTATTCCGAGA
* * *
14383 AACGATGCCTAAGAAATCTTTAGGTGAGAAAAAGTTCTTCTAATGTTACCAACGTATTGGAACAT
66 AACGATGCCTAAGAAATCTCTAGGTGAGAAAAAGTTATTCTAATGTTACCAACGTACTGGAACAT
* *
14448 TTTAAGAATTATTTCAATAAGAAGGTTTTAATTTATTTTTCTCGAGAAT-AATTTTTTTAAA
131 TTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCAAGAATAAATTTTTTTAAA
* *
14509 CATGACATTTTCTTACGAAAAATAAATTTGAGC-TCCAAAGATGAGATTCTAAAAGTATTCCGAG
1 CATGACATTTTCTTACAAAAAATAAATTCGAGCTTCCAAAGATGAGATTCT-AAAGTATTCCGAG
* * * *
14573 TAGA-GATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTATTTTAATGTTACCAACGTACTGGAA
65 -AAACGATGC-CTAAGAAATCTCTAGGTGAGAAAAAGTTATTCTAATGTTACCAACGTACTGGAA
14637 CATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCAAGAATAAATTTTTTT
128 CATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCAAGAATAAATTTTTTT
14699 TAATAAATAA
Statistics
Matches: 170, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
190 15 0.09
191 46 0.27
192 100 0.59
193 9 0.05
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (192 bp):
CATGACATTTTCTTACAAAAAATAAATTCGAGCTTCCAAAGATGAGATTCTAAAGTATTCCGAGA
AACGATGCCTAAGAAATCTCTAGGTGAGAAAAAGTTATTCTAATGTTACCAACGTACTGGAACAT
TTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCAAGAATAAATTTTTTTAAA
Found at i:15509 original size:17 final size:17
Alignment explanation
Indices: 15482--15531 Score: 75
Period size: 18 Copynumber: 2.9 Consensus size: 17
15472 ATCCCTCTTT
15482 ATTTTTTTATTTAAT-A
1 ATTTTTTTATTTAATAA
15498 ATTTTTTATATTTAATAA
1 ATTTTTT-TATTTAATAA
15516 ATTTTTTTAATTTAAT
1 ATTTTTTT-ATTTAAT
15532 TTTCTTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.23
17 9 0.29
18 15 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTTTTTATTTAATAA
Found at i:16171 original size:18 final size:18
Alignment explanation
Indices: 16144--16178 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16134 TATTTTATAA
*
16144 TAATATATTTATAAAAAT
1 TAATAAATTTATAAAAAT
*
16162 TAATAAATTTTTAAAAA
1 TAATAAATTTATAAAAA
16179 CTCTGTCATC
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATTTATAAAAAT
Found at i:16288 original size:44 final size:44
Alignment explanation
Indices: 16237--16322 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
16227 ATACTAACCC
*
16237 TATAAATCATAAATCAATATTCAAGTCAATTTATAAAATAAACG
1 TATAAATCATAAATCAATAGTCAAGTCAATTTATAAAATAAACG
*
16281 TATAAATCATAAATCGATAGTCAAGTCAATTTATAAAATAAA
1 TATAAATCATAAATCAATAGTCAAGTCAATTTATAAAATAAA
16323 AATTCTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (44 bp):
TATAAATCATAAATCAATAGTCAAGTCAATTTATAAAATAAACG
Found at i:16905 original size:19 final size:20
Alignment explanation
Indices: 16869--16911 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
16859 ATTATTTAGC
*
16869 ATTTATAAAATTAATAAATA
1 ATTTATAAAATCAATAAATA
* *
16889 ATTTA-AAAATCAGTAAATT
1 ATTTATAAAATCAATAAATA
16908 ATTT
1 ATTT
16912 TTATGTCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTATAAAATCAATAAATA
Found at i:23554 original size:19 final size:20
Alignment explanation
Indices: 23512--23553 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
23502 CACAAATTTA
*
23512 TTTAATTTTAATAATTAATT
1 TTTAATTTTAATAAATAATT
23532 TTTAA-TTTAATAAATATATT
1 TTTAATTTTAATAAATA-ATT
23552 TT
1 TT
23554 AGTGGAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAATTTTAATAAATAATT
Found at i:23989 original size:22 final size:23
Alignment explanation
Indices: 23964--24019 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
23954 AACAGAAAAC
23964 TTACTGATCAACT-AAAAATTAT
1 TTACTGATCAACTGAAAAATTAT
23986 TTACT-AGTCAA-TGAAAAATTAT
1 TTACTGA-TCAACTGAAAAATTAT
*
24008 TTACTGGTCAAC
1 TTACTGATCAAC
24020 AGAATTTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (23 bp):
TTACTGATCAACTGAAAAATTAT
Found at i:24625 original size:15 final size:16
Alignment explanation
Indices: 24605--24634 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24595 AAACTTCATA
24605 AAATTA-TTTTAAAAG
1 AAATTAGTTTTAAAAG
24620 AAATTAGTTTTAAAA
1 AAATTAGTTTTAAAA
24635 TATGTGGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
AAATTAGTTTTAAAAG
Found at i:35486 original size:26 final size:26
Alignment explanation
Indices: 35447--35498 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
35437 AACTTATGCT
* *
35447 TAAATTCAGGGGGAGTTTGTTTTTCA
1 TAAATTCAGAGGGAGCTTGTTTTTCA
*
35473 TAAATTTAGAGGGAGCTTGTTTTTCA
1 TAAATTCAGAGGGAGCTTGTTTTTCA
35499 AAAGGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (26 bp):
TAAATTCAGAGGGAGCTTGTTTTTCA
Found at i:35926 original size:21 final size:21
Alignment explanation
Indices: 35900--35957 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
35890 GCCTGAACCA
*
35900 ATCGATCCCCTAAAGGAGGGG
1 ATCGATCCCCTAAAGGAAGGG
*
35921 ATCGATCCCATAAAGGAAGGG
1 ATCGATCCCCTAAAGGAAGGG
*
35942 ATCGATCCCCTGAAGG
1 ATCGATCCCCTAAAGG
35958 CCAAAAACTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.29, T:0.16
Consensus pattern (21 bp):
ATCGATCCCCTAAAGGAAGGG
Found at i:39912 original size:85 final size:88
Alignment explanation
Indices: 39786--39963 Score: 236
Period size: 85 Copynumber: 2.0 Consensus size: 88
39776 TATTGACAAA
* * * * *
39786 TTAAGTGTTAAACTTCAAAGATTAAATAGACATTTGATACTTGATTTAGA-CAAATTCTTTGATG
1 TTAAATGTTAAACTTCAAAGATTAAATACACATTTGATACTTGAATTAGAGAAAATTCTTTGATA
39850 CTT-AAATTGAAAAGTTACAATC
66 CTTGAAATTGAAAAGTTACAATC
* * *
39872 TTAAATGTTAAACTTCAAA-ATTTATTACACATTTGATACTTGAATTAGAGTAAAATTCTTTGGT
1 TTAAATGTTAAACTTCAAAGATTAAATACACATTTGATACTTGAATTAGAG-AAAATTCTTTGAT
**
39936 ACTTGAGTTTGAAAAGTTACAATC
65 ACTTGAAATTGAAAAGTTACAATC
39960 TTAA
1 TTAA
39964 TGCTACTTGA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
85 26 0.33
86 18 0.23
87 14 0.18
88 21 0.27
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (88 bp):
TTAAATGTTAAACTTCAAAGATTAAATACACATTTGATACTTGAATTAGAGAAAATTCTTTGATA
CTTGAAATTGAAAAGTTACAATC
Found at i:42106 original size:144 final size:144
Alignment explanation
Indices: 41840--42587 Score: 1040
Period size: 144 Copynumber: 5.2 Consensus size: 144
41830 GCTTTGACAT
* *
41840 GTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAAATCAAAGTCAGTGAGAG
1 GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAG
* *
41905 ATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGA-CAGAGGTAGAGAGT
66 ATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGA-AGGTAGAGAAT
41969 GGATAAGCTAGTCAA
130 GGATAAGCTAGTCAA
*
41984 GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTTTCAC-CTAACTCAAAGTCAGTGAGA
1 GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTC-AACTCAAAGTCAGTGAGA
* * *
42048 GATTTAAGGATCCCTATCTCTTTAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAGT
65 GATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAAT
*
42113 GGATAAGCTTGTCAA
130 GGATAAGCTAGTCAA
* *
42128 GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTTTCACCCAACTCAAAGTCAGTGAGAG
1 GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAG
* * *
42193 ATTTAAGCATCCCTATCTCTTGAGGTATTGACCCAGAAAACATATTATGATGAAGGTAGAAAATG
66 ATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAATG
* *
42258 GATAAACTGGTCAA
131 GATAAGCTAGTCAA
* *
42272 GTTTCTTA-TGAAAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACTCAAAGTCAGTGAGA
1 GTTTCCTATTG-AAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGA
* * * * * *
42336 GATTTAAGCAGCCTTATCTCTTGAGATATTGACCCAGAAAACATATTATGATGAAGGTTGAGAAT
65 GATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAAT
* * *
42401 GGATAAACTGGTTAA
130 GGATAAGCTAGTCAA
* * * *
42416 GTTTCTTA-TGAAAGCAGGGATTGAACCAGAGAAATTATTATGACTCAACACAAAGTCAGTGAGT
1 GTTTCCTATTG-AAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGA
* * * *
42480 GATTTAAGCATCCCTATTTCTTGAGGTATCGATCCACAAAACATATTTTGAT-AGAGGTGGAGAA
65 GATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGA-AGGTAGAGAA
**
42544 CAGATAAG-TAGGTCAA
129 TGGATAAGCTA-GTCAA
* * *
42560 GTTTCCTATGGAAGCGGGGATAGAACCA
1 GTTTCCTATTGAAGCAGGGATTGAACCA
42588 CGTAGATAGT
Statistics
Matches: 552, Mismatches: 45, Indels: 14
0.90 0.07 0.02
Matches are distributed among these distances:
143 5 0.01
144 544 0.99
145 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (144 bp):
GTTTCCTATTGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAG
ATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGAATG
GATAAGCTAGTCAA
Found at i:42223 original size:72 final size:71
Alignment explanation
Indices: 41859--42229 Score: 170
Period size: 72 Copynumber: 5.2 Consensus size: 71
41849 GGAAGCAGGG
* *
41859 ATTGAACCAGAGAAATTATTTTGACTCAAATCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTC
1 ATTGAACCAGAGAAATTATTTTGACCCAACTCAAAGTCAGTGAGAGATTTAAG-ATCCCTATCTC
41924 TTGAGGT
65 TTGAGGT
* * * ** ** * * * * * *
41931 ATCGACCCAGA-AAACATATTTTGACAGAGGT-AGAG--AGTGGATAAGCTAGTCAAGTTTCCTA
1 ATTGAACCAGAGAAA-TTATTTTGACCCAACTCAAAGTCAGT-GA-GAG--ATTTAAGATCCCTA
*** *
41992 T-TGAAGCAGGG
61 TCTCTTG-AGGT
* *
42003 ATTGAACCAGAGAAATTATTTTCACCTAACTCAAAGTCAGTGAGAGATTTAAGGATCCCTATCTC
1 ATTGAACCAGAGAAATTATTTTGACCCAACTCAAAGTCAGTGAGAGATTTAA-GATCCCTATCTC
*
42068 TTTAGGT
65 TTGAGGT
* * * ** * * * * * *
42075 ATCGACCCAGA-AAACATATTTTGA-TGAAGGT-AGAG--AGTGGATAAGCTTGTCAAGTTTCCT
1 ATTGAACCAGAGAAA-TTATTTTGACCCAA-CTCAAAGTCAGT-GA-GAGATT-T-AAGATCCCT
*** *
42135 AT-TGAAGCAGGG
60 ATCTCTTG-AGGT
*
42147 ATTGAACCAGAGAAATTATTTTCACCCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTC
1 ATTGAACCAGAGAAATTATTTTGACCCAACTCAAAGTCAGTGAGAGATTTAAG-ATCCCTATCTC
42212 TTGAGGT
65 TTGAGGT
*
42219 ATTGACCCAGA
1 ATTGAACCAGA
42230 AAACATATTA
Statistics
Matches: 203, Mismatches: 70, Indels: 52
0.62 0.22 0.16
Matches are distributed among these distances:
69 6 0.03
70 4 0.02
71 30 0.15
72 123 0.61
73 30 0.15
74 4 0.02
75 6 0.03
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (71 bp):
ATTGAACCAGAGAAATTATTTTGACCCAACTCAAAGTCAGTGAGAGATTTAAGATCCCTATCTCT
TGAGGT
Found at i:45068 original size:17 final size:17
Alignment explanation
Indices: 45026--45068 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
45016 ATTTAGTTAT
*
45026 TAATTTTTATATAATAA
1 TAATTTTTATAAAATAA
**
45043 TAAAATTTATAAAATAA
1 TAATTTTTATAAAATAA
45060 TAATTTTTA
1 TAATTTTTA
45069 ATTCATAACA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTTTTATAAAATAA
Found at i:47010 original size:21 final size:20
Alignment explanation
Indices: 46985--47033 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
46975 TCTCTTTTTA
* *
46985 TTTATTTTTTATTTAATATTT
1 TTTATTTTTTAATAAATA-TT
*
47006 TTTATATATTTAATAAATATT
1 TTTAT-TTTTTAATAAATATT
47027 TTTATTT
1 TTTATTT
47034 AATATTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTTTTTAATAAATATT
Found at i:47582 original size:19 final size:19
Alignment explanation
Indices: 47560--47596 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
47550 TTTATTTCTA
*
47560 ATAGTTTAGTATGAAAAAT
1 ATAGTTTAATATGAAAAAT
*
47579 ATAGTTTAATATTAAAAA
1 ATAGTTTAATATGAAAAA
47597 GAATACAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
ATAGTTTAATATGAAAAAT
Found at i:47648 original size:40 final size:41
Alignment explanation
Indices: 47585--47676 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 41
47575 AAATATAGTT
*
47585 TAATAT-TAAAAAGAATACAA-TTTTCAAAAAATTATAATC
1 TAATATATAAAAAGAATACAATTTTTCAAAAAATCATAATC
* * * * *
47624 TAATATATAAAAGGACTACGATTTTTTAAAAAATCATAGTC
1 TAATATATAAAAAGAATACAATTTTTCAAAAAATCATAATC
*
47665 TATATAGATAAA
1 TA-ATATATAAA
47677 TTTGTAGTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
39 6 0.14
40 11 0.26
41 18 0.42
42 8 0.19
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.34
Consensus pattern (41 bp):
TAATATATAAAAAGAATACAATTTTTCAAAAAATCATAATC
Found at i:48686 original size:19 final size:19
Alignment explanation
Indices: 48662--48708 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
48652 TAAAAAATTT
48662 AAATTATTTAA-TATTTATA
1 AAATTATTTAATTATTT-TA
**
48681 AAATTATAAAATTATTTTA
1 AAATTATTTAATTATTTTA
48700 AAATTATTT
1 AAATTATTT
48709 TATGTCAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTATTTAATTATTTTA
Found at i:50397 original size:47 final size:46
Alignment explanation
Indices: 50300--50400 Score: 123
Period size: 47 Copynumber: 2.2 Consensus size: 46
50290 GCATTTAGGA
* * *
50300 GTTTTTATTTTAAGGAAAATTAATACTTTCAACTTTTCCTTAAACC
1 GTTTTTCTTTTAAGGAAAATTAATACTTTCAACTTTTCCTCAAAAC
** *
50346 GTTTTTCTTTTAAAGGAAAATTGGTACTTTCAACTTTTTCC-CAAAAT
1 GTTTTTCTTTT-AAGGAAAATTAATACTTTCAAC-TTTTCCTCAAAAC
50393 GTTTTTCT
1 GTTTTTCT
50401 GAAACTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 10 0.21
47 31 0.66
48 6 0.13
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.48
Consensus pattern (46 bp):
GTTTTTCTTTTAAGGAAAATTAATACTTTCAACTTTTCCTCAAAAC
Found at i:50423 original size:57 final size:60
Alignment explanation
Indices: 50358--50505 Score: 187
Period size: 60 Copynumber: 2.5 Consensus size: 60
50348 TTTTCTTTTA
* * * *
50358 AAGGAAAATTGGTACTTTCAACTTTTTC-CCAAAAT-GTTTTTCT-GAAACTTTAATTTC
1 AAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATAGTTTTTCTAAAAAATTTAATTTC
* * * * *
50415 GAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTAAAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATAGTTTTTCTAAAAAATTTAATTTC
50475 AAGGAAAATTGATACTTTCAACTTTTT-TCAA
1 AAGGAAAATTGATACTTTCAACTTTTTCTCAA
50506 CTTTTCCTCA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
57 26 0.33
58 6 0.08
59 10 0.13
60 36 0.46
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (60 bp):
AAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATAGTTTTTCTAAAAAATTTAATTTC
Found at i:50518 original size:127 final size:126
Alignment explanation
Indices: 50373--50628 Score: 320
Period size: 128 Copynumber: 2.0 Consensus size: 126
50363 AAATTGGTAC
** ** * * *
50373 TTTCAACTTTTTCCC-AAAATGTTTTTCTGAAACTTTAATTTCGAGGAAAATTGATACTTTCAAC
1 TTTCAACTTTTTCCCAAAAAAATTTTT-AAAAACTTTAATTTCAAGGAAAATTAATACTCTCAAC
* * * *
50437 TTTTTCTCAAAAATATTTTTTTTAAAAAATTTATTTTTAAGG-AAAATTGATACTTTCAACTTT
65 TTTTCCTCAAAAATATTTTTTTT--AAAATTTAATTTCAAGGAAAAATTAATACTTTCAACTTT
* *
50500 TTTCAAC-TTTTCCTCAAAAAAAATTTTTAAAAATTTTATTTTCAAGGAAAATTAATACTCTCAA
1 TTTCAACTTTTTCC-C-AAAAAAATTTTTAAAAACTTTAATTTCAAGGAAAATTAATACTCTCAA
*
50564 CTTTTCCTCAAAAATATTTTTTTTAGAATTTAATTTCAAGGAAAAATTAATACTTTCAACTTT
64 CTTTTCCTCAAAAATATTTTTTTTAAAATTTAATTTCAAGGAAAAATTAATACTTTCAACTTT
50627 TT
1 TT
50629 CTTAAAAAAT
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
126 20 0.18
127 30 0.27
128 52 0.47
129 9 0.08
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.45
Consensus pattern (126 bp):
TTTCAACTTTTTCCCAAAAAAATTTTTAAAAACTTTAATTTCAAGGAAAATTAATACTCTCAACT
TTTCCTCAAAAATATTTTTTTTAAAATTTAATTTCAAGGAAAAATTAATACTTTCAACTTT
Found at i:50548 original size:68 final size:70
Alignment explanation
Indices: 50430--50568 Score: 201
Period size: 68 Copynumber: 2.0 Consensus size: 70
50420 AAATTGATAC
* ** * * *
50430 TTTCAACTTTTTCTCAAAAATATTTTTTTTAAAAAATTTATTTTTAAGGAAAATTGATACTTTCA
1 TTTCAACTTTTCCTCAAAAATATAATTTTTAAAAAATTTATTTTCAAGGAAAATTAATACTCTCA
50495 ACTTT
66 ACTTT
*
50500 TTTCAACTTTTCCTCAAAAA-A-AATTTTTAAAAATTTTATTTTCAAGGAAAATTAATACTCTCA
1 TTTCAACTTTTCCTCAAAAATATAATTTTTAAAAAATTTATTTTCAAGGAAAATTAATACTCTCA
50563 ACTTT
66 ACTTT
50568 T
1 T
50569 CCTCAAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 42 0.68
69 1 0.02
70 19 0.31
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (70 bp):
TTTCAACTTTTCCTCAAAAATATAATTTTTAAAAAATTTATTTTCAAGGAAAATTAATACTCTCA
ACTTT
Found at i:50645 original size:58 final size:58
Alignment explanation
Indices: 50500--50648 Score: 201
Period size: 58 Copynumber: 2.6 Consensus size: 58
50490 TTTCAACTTT
* * *
50500 TTTCAACTTTTCCTCAAAAAAAATTTTTAAAAATTTTATTTTCAAGGAAAATTAATAC
1 TTTCAACTTTTCCTCAAAAAATATTTTTTAAAATTTTAATTTCAAGGAAAATTAATAC
* * *
50558 TCTCAACTTTTCCTCAAAAATATTTTTTTTAGAA-TTTAATTTCAAGGAAAAATTAATAC
1 TTTCAACTTTTCCTCAAAAA-ATATTTTTTAAAATTTTAATTTCAAGG-AAAATTAATAC
* *
50617 TTTCAACTTTTTCTTAAAAAATATTTTTTAAA
1 TTTCAACTTTTCCTCAAAAAATATTTTTTAAA
50649 TCTTTTTATC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
58 41 0.53
59 37 0.47
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.44
Consensus pattern (58 bp):
TTTCAACTTTTCCTCAAAAAATATTTTTTAAAATTTTAATTTCAAGGAAAATTAATAC
Found at i:53182 original size:17 final size:16
Alignment explanation
Indices: 53152--53198 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
53142 ACTCAACATT
* *
53152 TTTTTTCTTTTTTTGCT
1 TTTTTT-TTCTTTTGCC
53169 TTTCTTTTTCTTTTGCC
1 TTT-TTTTTCTTTTGCC
53186 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
53199 TTTTTTGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 10 0.37
17 14 0.52
18 3 0.11
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCTTTTGCC
Found at i:53378 original size:43 final size:43
Alignment explanation
Indices: 53261--53499 Score: 164
Period size: 45 Copynumber: 5.4 Consensus size: 43
53251 TTGAGAAACT
* * * * * *
53261 TAAACAAAGCTCCTCTAAACAGAGGCGCCACAACTTCAAGAAGAA
1 TAAATAAAGCTCCTCTAAACAAAGGCTCAACCACTTTAA-AA-AA
* * *
53306 -AAAAACAAGGCTCCTCTAAACAAATGCTCAACCACTTTGAAAAA
1 TAAATA-AA-GCTCCTCTAAACAAAGGCTCAACCACTTTAAAAAA
* * * *
53350 TAAATAAAGCTCGTCTAATCAAAGGCTCAACGACTTAAAAAAAAA
1 TAAATAAAGCTCCTCTAAACAAAGGCTCAACCACTT--TAAAAAA
* * * * *
53395 TAAAAAAAACTCCTCTAAACAGAGG-T-AACCATGACTTTGAAAGA
1 TAAATAAAGCTCCTCTAAACAAAGGCTCAACC---ACTTTAAAAAA
* * *
53439 T-AA-AATGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAA
1 TAAATAAAGCTCCTCTAAACAAAGGCTCAACCAC-TTTAAAAAA
53481 TAAATAAAGCTCCTCTAAA
1 TAAATAAAGCTCCTCTAAA
53500 TAGAGGCAAC
Statistics
Matches: 151, Mismatches: 30, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
41 2 0.01
42 26 0.17
43 32 0.21
44 30 0.20
45 33 0.22
46 28 0.19
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.20
Consensus pattern (43 bp):
TAAATAAAGCTCCTCTAAACAAAGGCTCAACCACTTTAAAAAA
Found at i:53443 original size:44 final size:44
Alignment explanation
Indices: 53394--53528 Score: 145
Period size: 44 Copynumber: 3.1 Consensus size: 44
53384 TTAAAAAAAA
*
53394 ATAAAAAAAACTCCTCTAAACAGAGGTAACCATGACTTTGAAAG
1 ATAAAAAAAGCTCCTCTAAACAGAGGTAACCATGACTTTGAAAG
* * *
53438 AT--AAAATGCTCCTCTAAACAGAGGCTCAA-CA--ACTTTTAAAAA
1 ATAAAAAAAGCTCCTCTAAACAGAGG-T-AACCATGAC-TTTGAAAG
* * *
53480 ATAAATAAAGCTCCTCTAAATAGAGGCAACCATGACTTTGAAAG
1 ATAAAAAAAGCTCCTCTAAACAGAGGTAACCATGACTTTGAAAG
53524 ATAAA
1 ATAAA
53529 GTGTTTCTCT
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
41 2 0.03
42 30 0.41
43 5 0.07
44 34 0.47
45 2 0.03
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (44 bp):
ATAAAAAAAGCTCCTCTAAACAGAGGTAACCATGACTTTGAAAG
Found at i:53496 original size:86 final size:85
Alignment explanation
Indices: 53269--53655 Score: 341
Period size: 86 Copynumber: 4.5 Consensus size: 85
53259 CTTAAACAAA
* * ** * * * * *
53269 GCTCCTCTAAACAGAGGCGCCACAACTTCAAGAAGAAAAAAACAAGGCTCCTCTAAACAAATGCT
1 GCTCCTCTAAACAGAGGCTCAACAACTTTTA-AA-AAATAAATAAAGCTCCTCTAAACAGA-G-G
* *
53334 CAACC--ACTTTGAAAAATAAATAAA
62 CAACCAGACTTTGAAAGAT-AA-AAT
* * * * ** * * *
53358 GCTCGTCTAATCAAAGGCTCAACGACTTAAAAAAAAATAAAAAAAACTCCTCTAAACAGAGGTAA
1 GCTCCTCTAAACAGAGGCTCAACAACTT-TTAAAAAATAAATAAAGCTCCTCTAAACAGAGGCAA
53423 CCATGACTTTGAAAGATAAAAT
65 CCA-GACTTTGAAAGATAAAAT
*
53445 GCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAATAAAGCTCCTCTAAATAGAGGCAAC
1 GCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGGCAAC
*
53510 CATGACTTTGAAAGATAAAGT
66 CA-GACTTTGAAAGATAAAAT
* * * * * *
53531 GTTTCTCTAAACAGAGGCTCAACAACTTTTGAAAAATAAATAAAGCTCATTTAAATAGAGGCAA-
1 GCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGGCAAC
*
53595 CAGAACTTTGAAA-ATAAATT
66 CAG-ACTTTGAAAGATAAAAT
* * * * * *
53615 ACTCCACTAAACAGAGGCACCATAACTTTTGAAAAATAAAT
1 GCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAAT
53656 TGCTCCTTGA
Statistics
Matches: 253, Mismatches: 40, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
84 41 0.16
85 11 0.04
86 114 0.45
87 27 0.11
88 23 0.09
89 35 0.14
90 2 0.01
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (85 bp):
GCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAATAAAGCTCCTCTAAACAGAGGCAAC
CAGACTTTGAAAGATAAAAT
Found at i:53592 original size:44 final size:43
Alignment explanation
Indices: 53261--53655 Score: 187
Period size: 42 Copynumber: 9.1 Consensus size: 43
53251 TTGAGAAACT
* * * **
53261 TAAACAAAGCTCCTCTAAACAGAGGCGCCACAACTTCAAGAAGAAA
1 TAAATAAAGCT-CTCTAAACAGAGGCTCAACAACTT-TTGAA-AAA
* * * * * *
53307 AAAACAAGGCTCCTCTAAACAAATGCTCAACCAC-TTTGAAAAA
1 TAAATAAAGCT-CTCTAAACAGAGGCTCAACAACTTTTGAAAAA
* * * ***
53350 TAAATAAAGCTCGTCTAATCAAAGGCTCAACGACTTAAAAAAAAA
1 TAAATAAAGCTC-TCTAAACAGAGGCTCAACAACTT-TTGAAAAA
* * *
53395 TAAAAAAAACTCCTCTAAACAGAGG-T-AACCATGAC-TTTGAAAGA
1 TAAATAAAGCT-CTCTAAACAGAGGCTCAA-CA--ACTTTTGAAAAA
* *
53439 T-AA-AATGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAA
1 TAAATAAAGCT-CTCTAAACAGAGGCTCAACAACTTTTGAAAAA
* *
53481 TAAATAAAGCTCCTCTAAATAGAGG--CAACCATGAC-TTTGAAAGA
1 TAAATAAAGCT-CTCTAAACAGAGGCTCAA-CA--ACTTTTGAAAAA
*
53525 TAAAGT---GTTTCTCTAAACAGAGGCTCAACAACTTTTGAAAAA
1 TAAA-TAAAG-CTCTCTAAACAGAGGCTCAACAACTTTTGAAAAA
* *
53567 TAAATAAAGCTCATTTAAATAGAGG--CAACAGAAC-TTTG-AAAA
1 TAAATAAAGCTC-TCTAAACAGAGGCTCAAC--AACTTTTGAAAAA
* * * * *
53609 TAAAT-TA-CTCCACTAAACAGAGGCACCATAACTTTTGAAAAA
1 TAAATAAAGCT-CTCTAAACAGAGGCTCAACAACTTTTGAAAAA
53651 TAAAT
1 TAAAT
53656 TGCTCCTTGA
Statistics
Matches: 271, Mismatches: 47, Indels: 66
0.71 0.12 0.17
Matches are distributed among these distances:
40 14 0.05
41 11 0.04
42 79 0.29
43 49 0.18
44 59 0.22
45 29 0.11
46 30 0.11
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (43 bp):
TAAATAAAGCTCTCTAAACAGAGGCTCAACAACTTTTGAAAAA
Found at i:58225 original size:13 final size:13
Alignment explanation
Indices: 58204--58239 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
58194 CGATCAATGT
*
58204 ACGGCTCGGTTCA
1 ACGGTTCGGTTCA
*
58217 ACGGTTCGGTTCG
1 ACGGTTCGGTTCA
58230 ACGGTTCGGT
1 ACGGTTCGGT
58240 CCGGTCTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.11, C:0.25, G:0.36, T:0.28
Consensus pattern (13 bp):
ACGGTTCGGTTCA
Found at i:59138 original size:13 final size:13
Alignment explanation
Indices: 59116--59146 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
59106 TGTCTTATTC
59116 TGTTTCTTTTGTT
1 TGTTTCTTTTGTT
*
59129 TGTTTTTTTTGTT
1 TGTTTCTTTTGTT
59142 TGTTT
1 TGTTT
59147 ATTAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (13 bp):
TGTTTCTTTTGTT
Found at i:59168 original size:18 final size:18
Alignment explanation
Indices: 59145--59186 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
59135 TTTTGTTTGT
* * *
59145 TTATTAATAATTTTTTTA
1 TTATTAAAAATATTATTA
59163 TTATTAAAAATATTATTA
1 TTATTAAAAATATTATTA
59181 TTATTA
1 TTATTA
59187 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTAAAAATATTATTA
Found at i:59174 original size:21 final size:21
Alignment explanation
Indices: 59145--59192 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
59135 TTTTGTTTGT
*
59145 TTATTAATAAT-TT-TT-TTA
1 TTATTAAAAATATTATTATTA
59163 TTATTAAAAATATTATTATTA
1 TTATTAAAAATATTATTATTA
59184 TTATTAAAA
1 TTATTAAAA
59193 TTAAAATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 10 0.38
19 2 0.08
20 2 0.08
21 12 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTAAAAATATTATTATTA
Found at i:59195 original size:18 final size:18
Alignment explanation
Indices: 59145--59191 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
59135 TTTTGTTTGT
* *
59145 TTATTAATAATTTTTTTA
1 TTATTAATAAATTTATTA
59163 TTATTAA-AAATATTATTA
1 TTATTAATAAAT-TTATTA
*
59181 TTATTATTAAA
1 TTATTAATAAA
59192 ATTAAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTAATAAATTTATTA
Found at i:59953 original size:54 final size:52
Alignment explanation
Indices: 59593--60724 Score: 1211
Period size: 45 Copynumber: 22.9 Consensus size: 52
59583 TTGAAAGTTT
* * *
59593 AAAAGGCTCATCTTAGTAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
* *
59645 AAAA-GTTCCTCTCAACAGAGGCTCAACAACTTTAAAAATCTC--A---T-G
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
* *
59690 AAAAGGCTCCTCTTAGCAAAGGCTCAACAACTTTAAAAATCTCATATCTT-G
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
*
59741 AAAAGGGCTCATCTCAGCAGAGGCTCAACAACTTT-AAAA--T--T-TCTT-G
1 AAAA-GGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
* * * *
59787 AAAAAGCTCCTCTCAACAGAGGATCAAAAACTTT-AAAA--TC---TCTT-G
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
* *
59832 AAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTT-AAAA--TC---TCTT-G
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
*
59877 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAAATCTCATATCTTGG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT--AAAAATCTCATATCTTGG
*
59931 AAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAA--TC---TCTT-G
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
*
59976 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTTAAAAAATCTCATATCTT-G
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAAC-TTT-AAAAATCTCATATCTTGG
*
60029 AAAAGGCTCCTCTCAGCAAAGGCTCAACAACTTTAAAAAAATCTCATATCTTGG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT--AAAAATCTCATATCTTGG
* * * * *
60083 AAAAGGCTCCTATCAGTAAAGGCTTAATAACTTTAAAAATCTCATATCTT-G
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
** *
60134 AAAAGGGCTCCTCTCAATAAAGGCTCAACAACTTTTAAAAAATCTCATATCTTGG
1 AAAA-GGCTCCTCTCAGCAGAGGCTCAACAAC-TTT-AAAAATCTCATATCTTGG
*
60189 -AAAGGATTCCTCTCAGCAGAGGCTCAACAACTTTAAAAAAGTCTCATATCTTGG
1 AAAAGG-CTCCTCTCAGCAGAGGCTCAACAACTTT-AAAAA-TCTCATATCTTGG
*
60243 AAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAA--TC---TCTT-G
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
* * *
60288 AAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAAAATCTCATATCTTAG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT--AAAAATCTCATATCTTGG
* *
60342 AAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTAG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
*
60394 AAAA-GTTCCTCTCAGCAGAGGCTCAACAACTTT--AAA----ATATCTTGG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
* *
60439 AAAA-GCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATCTCATATCTTAG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
* * *
60490 AAAA-GCTCCTCTCAGCAGAAGCTTAACAACTTT-AAAAT-TC---TCTT-A
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
*
60535 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTC--AT-TTGG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
60583 AAAA-GCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTC--ATC-TGG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
* * * * *
60630 ACAA-GCTCCTCTCAGCAAAAGCTCAACAACTTTAAAAATCTCATTTCTTGA
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
*
60681 AAAAGGCTCCTCTCAACAGAGGCTCAACAACTTT-AAAATCTCAT
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCAT
60725 CTGTTTTCAA
Statistics
Matches: 951, Mismatches: 70, Indels: 119
0.83 0.06 0.10
Matches are distributed among these distances:
45 219 0.23
46 91 0.10
47 80 0.08
48 26 0.03
49 11 0.01
50 13 0.01
51 133 0.14
52 124 0.13
53 73 0.08
54 176 0.19
55 5 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (52 bp):
AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTGG
Found at i:60467 original size:96 final size:96
Alignment explanation
Indices: 60333--60719 Score: 541
Period size: 96 Copynumber: 4.0 Consensus size: 96
60323 AAAAAATCTC
*
60333 ATATCTTAGAAAGGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTAGAAAA
1 ATATCTTAGAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTAGAAAA
*
60398 GTTCCTCTCAGCAGAGGCTCAACAACTTTAAA
65 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAA
* *
60430 ATATCTTGGAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATCTCATATCTTAGAAAAG
1 ATATCTTAGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTAGAAAAG
* *
60495 CTCCTCTCAGCAGAAGCTTAACAACTTTAAA
66 CTCCTCTCAGCAGAGGCTCAACAACTTTAAA
* * *
60526 ATTCTCTTAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTC--AT-TTGGAAAA
1 A-TATCTTAGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTAGAAAA
60587 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAA
65 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAA
* * * * * *
60619 ATCTCATCTGGACAAGCTCCTCTCAGCAAAAGCTCAACAACTTTAAAAATCTCATTTCTT-GAAA
1 ATATC-T-TAGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTAG-AA
*
60683 AAGGCTCCTCTCAACAGAGGCTCAACAACTTTAAA
63 AA-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAA
60718 AT
1 AT
60720 CTCATCTGTT
Statistics
Matches: 261, Mismatches: 20, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
92 4 0.02
93 39 0.15
94 33 0.13
95 8 0.03
96 88 0.34
97 50 0.19
98 6 0.02
99 33 0.13
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (96 bp):
ATATCTTAGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATATCTTAGAAAAG
CTCCTCTCAGCAGAGGCTCAACAACTTTAAA
Found at i:60719 original size:99 final size:100
Alignment explanation
Indices: 59610--60727 Score: 1173
Period size: 99 Copynumber: 11.3 Consensus size: 100
59600 TCATCTTAGT
* *
59610 AGAGGCTCAACAACTTTAAAAATCTCATATCTTGGAAAA-GTTCCTCTCAACAGAGGCTCAACAA
1 AGAGGCTCAACAACTTTAAAAATCTCA-ATC-TGGAAAAGGCTCCTCTCAGCAGAGGCTCAACAA
* *
59674 CTTTAAAAATCTCA----TGAAAAGGCTCCTCTTAGC
64 CTTTAAAAATCTCATTCTTGAAAAAGCTCCTCTCAGC
* * *
59707 AAAGGCTCAACAACTTTAAAAATCTCATATCTTGAAAAGGGCTCATCTCAGCAGAGGCTCAACAA
1 AGAGGCTCAACAACTTTAAAAATCTCA-ATCTGGAAAA-GGCTCCTCTCAGCAGAGGCTCAACAA
*
59772 CTTT-AAAA--T--TTCTTGAAAAAGCTCCTCTCAAC
64 CTTTAAAAATCTCATTCTTGAAAAAGCTCCTCTCAGC
* * * *
59804 AGAGGATCAAAAACTTT-AAAATCTC--T-T-GAAAAAGCTCCTCTCAGTAGAGGCTCAACAACT
1 AGAGGCTCAACAACTTTAAAAATCTCAATCTGGAAAAGGCTCCTCTCAGCAGAGGCTCAACAACT
59864 TT-AAAA--TC--TCTTGAAAAAGCTCCTCTCAGC
66 TTAAAAATCTCATTCTTGAAAAAGCTCCTCTCAGC
*
59894 AGAGGCTCAACAACTTTAAAAAAATCTCATATCTTGGAAAGGGCTCCTCTCAGCAGAGGCTCAAC
1 AGAGGCTCAACAACTTT--AAAAATCTCA-ATC-TGGAAAAGGCTCCTCTCAGCAGAGGCTCAAC
59959 AACTTT-AAAA--TC--TCTTGAAAAAGCTCCTCTCAGC
62 AACTTTAAAAATCTCATTCTTGAAAAAGCTCCTCTCAGC
* *
59993 AGAGGCTCAACAACTTTTAAAAAATCTCATATCTTGAAAAGGCTCCTCTCAGCAAAGGCTCAACA
1 AGAGGCTCAACAAC-TTT-AAAAATCTCA-ATCTGGAAAAGGCTCCTCTCAGCAGAGGCTCAACA
* * *
60058 ACTTTAAAAAAATCTCATATCTTGGAAAAGGCTCCTATCAGT
63 ACTTT--AAAAATCTCAT-TCTT-GAAAAAGCTCCTCTCAGC
* * * * ** *
60100 AAAGGCTTAATAACTTTAAAAATCTCATATCTTGAAAAGGGCTCCTCTCAATAAAGGCTCAACAA
1 AGAGGCTCAACAACTTTAAAAATCTCA-ATCTGGAAAA-GGCTCCTCTCAGCAGAGGCTCAACAA
* * *
60165 CTTTTAAAAAATCTCATATCTTGGAAAGGATTCCTCTCAGC
64 C-TTT-AAAAATCTCAT-TCTTGAAAAAG-CTCCTCTCAGC
*
60206 AGAGGCTCAACAACTTTAAAAAAGTCTCATATCTTGGAAAGGGCTCCTCTCAGCAGAGGCTCAAC
1 AGAGGCTCAACAACTTT-AAAAA-TCTCA-ATC-TGGAAAAGGCTCCTCTCAGCAGAGGCTCAAC
*
60271 AACTTT-AAAA--TC--TCTTGAAAAAGCTCCTCTCAAC
62 AACTTTAAAAATCTCATTCTTGAAAAAGCTCCTCTCAGC
* *
60305 AGAGGCTCAACAACTTTAAAAAAATCTCATATCTTAGAAAGGGCTCCTCTCAGCAGAGGCTCAAC
1 AGAGGCTCAACAACTTT--AAAAATCTCA-ATC-TGGAAAAGGCTCCTCTCAGCAGAGGCTCAAC
*
60370 AACTTTAAAAATCTCATATCTT-AGAAAAGTTCCTCTCAGC
62 AACTTTAAAAATCTCAT-TCTTGA-AAAAGCTCCTCTCAGC
* *
60410 AGAGGCTCAACAACTTT-AAAATATC--T-TGGAAAA-GCTCCTCTCAACAGAGGCTCAACAACT
1 AGAGGCTCAACAACTTTAAAAATCTCAATCTGGAAAAGGCTCCTCTCAGCAGAGGCTCAACAACT
60470 TTAAAAATCTCATATCTT-AGAAAAGCTCCTCTCAGC
66 TTAAAAATCTCAT-TCTTGA-AAAAGCTCCTCTCAGC
* * ** *
60506 AGAAGCTTAACAACTTT-AAAAT-TC--TCTTAAAAAAGCTCCTCTCAGCAGAGGCTCAACAACT
1 AGAGGCTCAACAACTTTAAAAATCTCAATCTGGAAAAGGCTCCTCTCAGCAGAGGCTCAACAACT
*
60567 TT-AAAATCTCA-T-TTGGAAAAGCTCCTCTCAGC
66 TTAAAAATCTCATTCTTGAAAAAGCTCCTCTCAGC
* * *
60599 AGAGGCTCAACAACTTT-AAAATCTC-ATCTGGACAA-GCTCCTCTCAGCAAAAGCTCAACAACT
1 AGAGGCTCAACAACTTTAAAAATCTCAATCTGGAAAAGGCTCCTCTCAGCAGAGGCTCAACAACT
*
60661 TTAAAAATCTCATTTCTTGAAAAAGGCTCCTCTCAAC
66 TTAAAAATCTCA-TTCTTGAAAAA-GCTCCTCTCAGC
60698 AGAGGCTCAACAACTTT-AAAATCTC-ATCTG
1 AGAGGCTCAACAACTTTAAAAATCTCAATCTG
60728 TTTTCAAATT
Statistics
Matches: 901, Mismatches: 70, Indels: 98
0.84 0.07 0.09
Matches are distributed among these distances:
90 68 0.08
91 5 0.01
92 1 0.00
93 47 0.05
94 30 0.03
95 19 0.02
96 110 0.12
97 98 0.11
98 68 0.08
99 203 0.23
100 22 0.02
101 4 0.00
102 9 0.01
103 4 0.00
104 1 0.00
105 66 0.07
106 71 0.08
107 37 0.04
108 33 0.04
109 5 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (100 bp):
AGAGGCTCAACAACTTTAAAAATCTCAATCTGGAAAAGGCTCCTCTCAGCAGAGGCTCAACAACT
TTAAAAATCTCATTCTTGAAAAAGCTCCTCTCAGC
Found at i:62448 original size:122 final size:122
Alignment explanation
Indices: 62301--62544 Score: 389
Period size: 122 Copynumber: 2.0 Consensus size: 122
62291 CTACCCATTT
* * *
62301 GGTGAAGTAATCAATCATTACAAAAATGAATCTATGCCCATTCAAAGCTTTTGGAGTGATGAGAC
1 GGTGAAGTAATCAATCATAAAAAAAATAAATCTATGCCCATTCAAAGCTTTTGGAGTGATGAGAC
* ** * *
62366 CAATGACATCCATGCCTCACATAGAGAATGGCCATGGAAGAGCCAGAACGTGTAATG
66 CAATGACATCCATGCCCCACATAGAGAATGGCCACAGAAGAGCCAAAACATGTAATG
* *
62423 GGTGAAGTAATCAATCATAAAAAAAATAAATCTATGCCCATTCGAAGCTTTTGGAGTGATGGGAC
1 GGTGAAGTAATCAATCATAAAAAAAATAAATCTATGCCCATTCAAAGCTTTTGGAGTGATGAGAC
*
62488 CAATGACATCCATGCCCCACATAGAGAATGGCCACAGAGGAGCCAAAACATGTAATG
66 CAATGACATCCATGCCCCACATAGAGAATGGCCACAGAAGAGCCAAAACATGTAATG
62545 TTGATGGCGA
Statistics
Matches: 111, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
122 111 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (122 bp):
GGTGAAGTAATCAATCATAAAAAAAATAAATCTATGCCCATTCAAAGCTTTTGGAGTGATGAGAC
CAATGACATCCATGCCCCACATAGAGAATGGCCACAGAAGAGCCAAAACATGTAATG
Found at i:70277 original size:23 final size:22
Alignment explanation
Indices: 70247--70300 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
70237 ATGTGTGTGA
70247 ATTTTTTTGCTTTTTATTTTTG
1 ATTTTTTTGCTTTTTATTTTTG
* *
70269 ATTTGTTTTGTTTTTTGTTTTTTG
1 ATTT-TTTTGCTTTTT-ATTTTTG
*
70293 TTTTTTTT
1 ATTTTTTT
70301 TACCTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 14 0.52
24 9 0.33
ACGTcount: A:0.06, C:0.02, G:0.11, T:0.81
Consensus pattern (22 bp):
ATTTTTTTGCTTTTTATTTTTG
Found at i:70308 original size:18 final size:17
Alignment explanation
Indices: 70287--70320 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
70277 TGTTTTTTGT
70287 TTTTTGTTTTTTTTTACC
1 TTTTT-TTTTTTTTTACC
70305 TTTTTTTTTTTTTTAC
1 TTTTTTTTTTTTTTAC
70321 TAAAAGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTTTTACC
Found at i:70318 original size:7 final size:7
Alignment explanation
Indices: 70274--70298 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
70264 TTTTGATTTG
70274 TTTTGTT
1 TTTTGTT
70281 TTTTGTT
1 TTTTGTT
70288 TTTTGTT
1 TTTTGTT
70295 TTTT
1 TTTT
70299 TTTACCTTTT
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:72631 original size:21 final size:18
Alignment explanation
Indices: 72608--72642 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
72598 TTAATAATAA
* *
72608 TAATATATTTATAAAAAT
1 TAATAAATTTTTAAAAAT
72626 TAATAAATTTTTAAAAA
1 TAATAAATTTTTAAAAA
72643 CTCTATCGTC
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATTTTTAAAAAT
Found at i:72664 original size:3 final size:3
Alignment explanation
Indices: 72656--72696 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
72646 TATCGTCTAT
72656 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
72697 TTAATTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:72871 original size:13 final size:13
Alignment explanation
Indices: 72853--72882 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
72843 TTATCCAATT
*
72853 ATTTTGGCCTCTC
1 ATTTTGACCTCTC
72866 ATTTTGACCTCTC
1 ATTTTGACCTCTC
72879 ATTT
1 ATTT
72883 CTAACATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.27, G:0.10, T:0.50
Consensus pattern (13 bp):
ATTTTGACCTCTC
Found at i:73347 original size:19 final size:20
Alignment explanation
Indices: 73319--73361 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
73309 ATTATTTAAC
*
73319 ATTTATAAAATTAATAAATA
1 ATTTATAAAATCAATAAATA
*
73339 ATTTA-AAAATCAATAAATT
1 ATTTATAAAATCAATAAATA
73358 ATTT
1 ATTT
73362 TTATGTCAAA
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:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTATAAAATCAATAAATA
Found at i:73937 original size:14 final size:14
Alignment explanation
Indices: 73919--73955 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
73909 TATTAAACTA
73919 AAATTAAAATTAAT
1 AAATTAAAATTAAT
* *
73933 TAATTTAAATTAAT
1 AAATTAAAATTAAT
73947 AAATTAAAA
1 AAATTAAAA
73956 AAATGGTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTAAAATTAAT
Found at i:75017 original size:18 final size:18
Alignment explanation
Indices: 74990--75024 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
74980 AATTTAATAA
*
74990 TAATATATTTATAAAAAT
1 TAATAAATTTATAAAAAT
*
75008 TAATAAATTTTTAAAAA
1 TAATAAATTTATAAAAA
75025 CTCTATCGTT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATTTATAAAAAT
Found at i:82884 original size:13 final size:14
Alignment explanation
Indices: 82866--82894 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
82856 CTAAATCAAT
82866 AAAATT-ATAAATA
1 AAAATTAATAAATA
82879 AAAATTAATAAATA
1 AAAATTAATAAATA
82893 AA
1 AA
82895 CAAACTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTAATAAATA
Found at i:83900 original size:2 final size:2
Alignment explanation
Indices: 83895--83928 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
83885 AAAATCGGCT
* *
83895 TA TA TA CA TA CA 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
83929 AGATTAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:88425 original size:87 final size:88
Alignment explanation
Indices: 88315--88495 Score: 247
Period size: 87 Copynumber: 2.1 Consensus size: 88
88305 TATTGAAAAA
* * * * **
88315 TTAAGTGTTAAACTTCAAAGATTAAATATACATTTGATACTTGAATT-AGACTAATTCTTTGATA
1 TTAATTGTTAAACGTCAAAGATTAAATACACATTTGATACGTGAATTAAGAAAAATTCTTTGATA
* *
88379 CTTAAATTTGAAAAGTTATAATT
66 CTTAAATTTGAAAAGTTACAATC
* *
88402 TTAATTGTTAAACGTCAAAGATTAATTACACATTTGATACGTGAATTAGAGAAAAATTCTTTGGT
1 TTAATTGTTAAACGTCAAAGATTAAATACACATTTGATACGTGAATTA-AGAAAAATTCTTTGAT
*
88467 ATTTAAATTTGAAAAGTTACAATC
65 ACTTAAATTTGAAAAGTTACAATC
88491 TTAAT
1 TTAAT
88496 ACTACTCGAA
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
87 42 0.52
89 39 0.48
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (88 bp):
TTAATTGTTAAACGTCAAAGATTAAATACACATTTGATACGTGAATTAAGAAAAATTCTTTGATA
CTTAAATTTGAAAAGTTACAATC
Found at i:89452 original size:3 final size:3
Alignment explanation
Indices: 89444--89480 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
89434 TTATTGGCTA
89444 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
89481 GTTGTTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:93561 original size:144 final size:144
Alignment explanation
Indices: 93326--93641 Score: 461
Period size: 144 Copynumber: 2.2 Consensus size: 144
93316 GTTTCGACAT
* ** * *
93326 GTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGATTCAACAAAAATTTAGTGAGAG
1 GTTTCCTATGGAAGCAGGGATTGAACCAAAGAAATTATTTTGAGCCAACAAAAAGTCAGTGAGAG
* *
93391 ATTTAAGCATCCCAATCTCTTTAGGTATCGACCCAAAAAACATATTTTGATGAAGGTAAAGAATG
66 ATTTAAGCATCCCAATCTCTTGAGGTATCAACCCAAAAAACATATTTTGATGAAGGTAAAGAATG
*
93456 GATAAGTTGGTCAA
131 GATAAGCTGGTCAA
* * * **
93470 GTTTCCTATAGAAGCAGGGATTGAACCAAAGAAATTGTTTTGGGCCAACTCAAAGTCAGTGAGAG
1 GTTTCCTATGGAAGCAGGGATTGAACCAAAGAAATTATTTTGAGCCAACAAAAAGTCAGTGAGAG
* * **
93535 ATTTAAGCATCCCTATCTCTTGAGGTATCAATCCAAAAAACATATTTTGATGAAGGTGGAGAATG
66 ATTTAAGCATCCCAATCTCTTGAGGTATCAACCCAAAAAACATATTTTGATGAAGGTAAAGAATG
93600 GATAAGCTGGTCAA
131 GATAAGCTGGTCAA
* *
93614 GTTTCCTATGGAAGCGGGGATAGAACCA
1 GTTTCCTATGGAAGCAGGGATTGAACCA
93642 CGCAGATAGT
Statistics
Matches: 152, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
144 152 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (144 bp):
GTTTCCTATGGAAGCAGGGATTGAACCAAAGAAATTATTTTGAGCCAACAAAAAGTCAGTGAGAG
ATTTAAGCATCCCAATCTCTTGAGGTATCAACCCAAAAAACATATTTTGATGAAGGTAAAGAATG
GATAAGCTGGTCAA
Found at i:95272 original size:18 final size:18
Alignment explanation
Indices: 95251--95305 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 18
95241 AAAACATACC
95251 CTTTGAACTAATCATATT
1 CTTTGAACTAATCATATT
95269 CTTTGAACTTATTCTATCATATT
1 CTTTGAAC-TA----ATCATATT
95292 CTTTGAACTAATCA
1 CTTTGAACTAATCA
95306 AATATATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
18 12 0.38
19 2 0.06
22 2 0.06
23 16 0.50
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.45
Consensus pattern (18 bp):
CTTTGAACTAATCATATT
Found at i:95915 original size:18 final size:17
Alignment explanation
Indices: 95888--95942 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
95878 TATTTTTTTC
95888 TTTTTTTATTTAATAAT
1 TTTTTTTATTTAATAAT
*
95905 TTTTTTATATTTAATAAA
1 TTTTTT-TATTTAATAAT
* *
95923 TATTTTTATTTAATTAT
1 TTTTTTTATTTAATAAT
95940 TTT
1 TTT
95943 GTGTGTGGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTTTATTTAATAAT
Found at i:95928 original size:19 final size:18
Alignment explanation
Indices: 95888--95931 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
95878 TATTTTTTTC
* *
95888 TTTTTTTATTTAATAATT
1 TTTTTATATTTAATAATA
95906 TTTTTATATTTAATAAATA
1 TTTTTATATTTAAT-AATA
95925 TTTTTAT
1 TTTTTAT
95932 TTAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTATATTTAATAATA
Found at i:96596 original size:18 final size:18
Alignment explanation
Indices: 96565--96604 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
96555 GACATGTTTT
*
96565 AAAATAATATA-TTTTAA
1 AAAATAATAAATTTTTAA
96582 AAAATTAATAAATTTTTAA
1 AAAA-TAATAAATTTTTAA
96601 AAAA
1 AAAA
96605 CTCTATCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAATAAATTTTTAA
Found at i:97479 original size:17 final size:19
Alignment explanation
Indices: 97446--97480 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
97436 TTAGTTAATT
97446 AATTTTTATATAATAATAA
1 AATTTTTATATAATAATAA
97465 AATTTTTA-A-AATAATA
1 AATTTTTATATAATAATA
97481 GTTTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTTTTATATAATAATAA
Found at i:97981 original size:16 final size:17
Alignment explanation
Indices: 97960--97991 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
97950 ATTTTTTTAT
97960 AAAAAATTG-CAATATA
1 AAAAAATTGTCAATATA
97976 AAAAAATTGTCAATAT
1 AAAAAATTGTCAATAT
97992 TGATATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (17 bp):
AAAAAATTGTCAATATA
Found at i:99032 original size:19 final size:20
Alignment explanation
Indices: 99010--99047 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
99000 AAAATTCTAT
*
99010 AAAATTAATAAA-TATTTTA
1 AAAATCAATAAATTATTTTA
*
99029 AAAATCAGTAAATTATTTT
1 AAAATCAATAAATTATTTT
99048 TATGTCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AAAATCAATAAATTATTTTA
Found at i:99255 original size:22 final size:24
Alignment explanation
Indices: 99221--99270 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
99211 TGATAATAGA
*
99221 ATTT-ATAAAATAA-TA-ATTTTT
1 ATTTCATAAAATAATTATAATTTT
*
99242 ATTTCATAATATAATTATAATTTT
1 ATTTCATAAAATAATTATAATTTT
99266 ATTTC
1 ATTTC
99271 TTTATAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 8 0.33
23 2 0.08
24 10 0.42
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTCATAAAATAATTATAATTTT
Found at i:100334 original size:3 final size:3
Alignment explanation
Indices: 100326--100359 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
100316 TCTCTATCAT
100326 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
100360 CAATGTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:100371 original size:3 final size:3
Alignment explanation
Indices: 100365--100400 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
100355 AATAACAATG
100365 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
100401 AGTGAAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:105944 original size:19 final size:19
Alignment explanation
Indices: 105907--105944 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
105897 ATCAAAAACT
105907 AAAATTTCCAAAAGCAAAAA
1 AAAATTTCCAAAAG-AAAAA
*
105927 AAACTTTCCAAAA-AAAAA
1 AAAATTTCCAAAAGAAAAA
105945 TCCTCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
20 12 0.71
ACGTcount: A:0.66, C:0.16, G:0.03, T:0.16
Consensus pattern (19 bp):
AAAATTTCCAAAAGAAAAA
Found at i:107376 original size:161 final size:162
Alignment explanation
Indices: 107109--107437 Score: 588
Period size: 161 Copynumber: 2.0 Consensus size: 162
107099 TGAAATGGAA
*
107109 AATAAAGCAAGTTAGTATGATGAAAATGAATAAAAAATCATATTCATTATAGAATATACATTTAC
1 AATAAAGCAAGTTAGTATGATGAAAATGAATAAAAAATCATATTCATTATAGAATATACATTCAC
*
107174 CTAAATCCACTTTCATAACATACATTCACAAATAGATTATGAAAAAGAAGAATAAAATAGAACAA
66 CTAAATCCACTTTCATAACATACAATCACAAATAGATTATGAAAAAGAAGAATAAAATAGAACAA
*
107239 TTTAATTTACTTATATTAAGTTTTATCAATAC
131 TTTAATTTACTTATATTAAGTTTGATCAATAC
107271 AATAAAGCAAGTTAGTATGATGAAAATGAATAAAAAATCATATTCATTA-AGAATATACATTCAC
1 AATAAAGCAAGTTAGTATGATGAAAATGAATAAAAAATCATATTCATTATAGAATATACATTCAC
*** *
107335 CTAAATCCACTTTCATAACATACAATCATGGATAGATTATGAAAAAGAATAATAAAATAGAACAA
66 CTAAATCCACTTTCATAACATACAATCACAAATAGATTATGAAAAAGAAGAATAAAATAGAACAA
107400 TTTAATTTACTTATATTAAGTTTGATCAATAC
131 TTTAATTTACTTATATTAAGTTTGATCAATAC
107432 AATAAA
1 AATAAA
107438 ATCACAATAT
Statistics
Matches: 160, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
161 111 0.69
162 49 0.31
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (162 bp):
AATAAAGCAAGTTAGTATGATGAAAATGAATAAAAAATCATATTCATTATAGAATATACATTCAC
CTAAATCCACTTTCATAACATACAATCACAAATAGATTATGAAAAAGAAGAATAAAATAGAACAA
TTTAATTTACTTATATTAAGTTTGATCAATAC
Found at i:108315 original size:64 final size:63
Alignment explanation
Indices: 108247--108366 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
108237 TACAGAATTT
* *
108247 CCATCAATAATATCAAAAAGAATTTTTTGAA-TTTTTTTAGCAAT-AGATTTTTTCGTTAGTAAA
1 CCATCAATAATATCAAAAA-AA-ATTTTAAATTTTTTTTAGCAATGA-ATTTTTTCGTTAGTAAA
108310 A
63 A
* *
108311 CCATCAGTAATATTAAAAAAAATTTTAAATTTTTTTTAGCAATGAATTTTTTCGTT
1 CCATCAATAATATCAAAAAAAATTTTAAATTTTTTTTAGCAATGAATTTTTTCGTT
108367 CATAAAATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
62 6 0.12
63 26 0.52
64 18 0.36
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.44
Consensus pattern (63 bp):
CCATCAATAATATCAAAAAAAATTTTAAATTTTTTTTAGCAATGAATTTTTTCGTTAGTAAAA
Found at i:110410 original size:17 final size:18
Alignment explanation
Indices: 110388--110422 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
110378 GTCAAGTGCC
110388 ATTAATTAAAT-ATTAAT
1 ATTAATTAAATAATTAAT
*
110405 ATTAATTATATAATTAAT
1 ATTAATTAAATAATTAAT
110423 CTAAGACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAATTAAATAATTAAT
Found at i:115948 original size:72 final size:72
Alignment explanation
Indices: 115858--116001 Score: 200
Period size: 72 Copynumber: 2.0 Consensus size: 72
115848 GCTTCCTCAT
* * *** *
115858 GTTTCCAATTGAAGCAGGGATTGAACCAGAGAACATA-TTTTGTAAAAGGTCGAGAGTAGATAAG
1 GTTTCCAATGGAAGCAGGGATTGAACCAGAAAACATAGTTACAT-AAAGGTAGAGAGTAGATAAG
115922 CTGGTCAA
65 CTGGTCAA
* *
115930 GTTTCCTATGGAAGCAGGGATTGAACCAGAAAACATAGTTACATGAAGGTAGAGAGTAGATAAGC
1 GTTTCCAATGGAAGCAGGGATTGAACCAGAAAACATAGTTACATAAAGGTAGAGAGTAGATAAGC
115995 TGGTCAA
66 TGGTCAA
116002 CCTTCCGATT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 60 0.95
73 3 0.05
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (72 bp):
GTTTCCAATGGAAGCAGGGATTGAACCAGAAAACATAGTTACATAAAGGTAGAGAGTAGATAAGC
TGGTCAA
Found at i:117798 original size:22 final size:24
Alignment explanation
Indices: 117772--117824 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
117762 TTAATTTTAT
117772 TTAATATTTAAA-ATAT-TAAAAA
1 TTAATATTTAAAGATATATAAAAA
117794 TTAATTATTTAAAGATATAATAAAAA
1 TTAA-TATTTAAAGATAT-ATAAAAA
117820 -TAATA
1 TTAATA
117825 ATGTGAGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 4 0.15
23 8 0.30
24 6 0.22
25 3 0.11
26 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TTAATATTTAAAGATATATAAAAA
Found at i:118693 original size:24 final size:24
Alignment explanation
Indices: 118658--118711 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
118648 GTTATTAATT
*
118658 TTTTATATAATAATAAAATAATAA
1 TTTTATATAATAAGAAAATAATAA
*
118682 TTTTA-ATCAATAAGATAATAATAA
1 TTTTATAT-AATAAGAAAATAATAA
118706 TTTTAT
1 TTTTAT
118712 TTATTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TTTTATATAATAAGAAAATAATAA
Found at i:118699 original size:21 final size:20
Alignment explanation
Indices: 118665--118703 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
118655 ATTTTTTATA
118665 TAATAATAAAATAATAATTT
1 TAATAATAAAATAATAATTT
*
118685 TAATCAATAAGATAATAAT
1 TAAT-AATAAAATAATAAT
118704 AATTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
TAATAATAAAATAATAATTT
Done.