Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 16 of 127
Found at i:3801101 original size:3 final size:3
Alignment explanation
Indices: 3801093--3801262 Score: 65
Period size: 3 Copynumber: 55.3 Consensus size: 3
3801083 GATAATTAAA
* **
3801093 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- GAT AA- ACCC AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T
*
3801137 ATAT ATT ACA- AA- AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATAT AACT
1 A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AA-T
* * *
3801185 ATAT ACAT -AT AA- ATCT AAT -CT AAT AA- AAA AAT AAAT AAAT ATAT
1 A-AT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT -AAT A-AT
3801229 ACAT AAT AAT AAT AAT AAT AA- AAT ACAT AA- AAT A
1 A-AT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A
3801263 CAAAAAAAGA
Statistics
Matches: 131, Mismatches: 14, Indels: 44
0.69 0.07 0.23
Matches are distributed among these distances:
2 17 0.13
3 79 0.60
4 33 0.25
5 2 0.02
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3801465 original size:1 final size:1
Alignment explanation
Indices: 3801461--3801591 Score: 172
Period size: 1 Copynumber: 131.0 Consensus size: 1
3801451 TTTTCTTAAA
* * * * * * * *
3801461 TTTTTGTTTTTTTGTTTTTGTTTTTTTTTTGTTTTTTGTTTTTTTTTGTTTTTGTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
3801526 TTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3801591 T
1 T
3801592 GCCGAAGCTC
Statistics
Matches: 110, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 110 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (1 bp):
T
Found at i:3801505 original size:34 final size:31
Alignment explanation
Indices: 3801461--3801591 Score: 192
Period size: 31 Copynumber: 4.1 Consensus size: 31
3801451 TTTTCTTAAA
* *
3801461 TTTTTGTTTTTTTGTTTTTGTTTTTTTTTTGT
1 TTTTTGTTTTTTT-TTTTTTTTTTTTTTTTTT
3801493 TTTTTGTTTTTTTTTGTTTTTGTTTTTTTTTGTT
1 TTTTTGTTTTTTTTT-TTTTT-TTTTTTTTT-TT
*
3801527 TTTTT-TGTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTGTTTTTTTTTTTTTTTTTTTTTTTTT
3801557 TTTTTGTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTGTTTTTTTTTTTTTTTTTTTTTTTTT
3801588 TTTT
1 TTTT
3801592 GCCGAAGCTC
Statistics
Matches: 91, Mismatches: 4, Indels: 9
0.88 0.04 0.09
Matches are distributed among these distances:
30 7 0.08
31 39 0.43
32 22 0.24
33 17 0.19
34 6 0.07
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (31 bp):
TTTTTGTTTTTTTTTTTTTTTTTTTTTTTTT
Found at i:3801734 original size:82 final size:82
Alignment explanation
Indices: 3801598--3802414 Score: 1253
Period size: 82 Copynumber: 10.0 Consensus size: 82
3801588 TTTTGCCGAA
* * * * *
3801598 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
3801662 ACTTTGGAAAGTAAATT
66 ACTTTGGAAAGTAAATT
* * *
3801679 GCTCCTCTCAACTGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
* *
3801744 ACTTTGAAAAATAAATT
66 ACTTTGGAAAGTAAATT
* *
3801761 GCTCCTCTCAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTCAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--AC
*
3801825 G-ACTTTGAAAAGTAAATT
64 GAACTTTGGAAAGTAAATT
3801843 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
3801907 ACTTTGGAAAAGTAAATT
66 ACTTTGG-AAAGTAAATT
3801925 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG-
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
3801989 ACTTTGGAAAAGTAAATT
66 ACTTTGG-AAAGTAAATT
*
3802007 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
3802071 ACTTTGGAAAAGTAAATT
66 ACTTTGG-AAAGTAAATT
*
3802089 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
*
3802153 ACTTTGAAAAGTAAATT
66 ACTTTGGAAAGTAAATT
* * * *
3802170 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGTACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGG--CAAC
*
3802235 G-ACTTTGGAAAATAAATT
64 GAACTTTGGAAAGTAAATT
*
3802253 GCTCCTCTAAACAGAGGCA--ACGAACTTT-GAAAAATAAATTGCTCCTCTAAACAGAGGCAACG
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
*
3802315 AACTTTGAAAAAGTAAATT
65 AACTTTG-GAAAGTAAATT
3802334 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
3802398 ACTTTGGAAAAGTAAAT
66 ACTTTGG-AAAGTAAAT
3802415 ACTCCTAGAC
Statistics
Matches: 689, Mismatches: 31, Indels: 31
0.92 0.04 0.04
Matches are distributed among these distances:
79 4 0.01
80 9 0.01
81 190 0.28
82 411 0.60
83 71 0.10
84 4 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
ACTTTGGAAAGTAAATT
Found at i:3801748 original size:41 final size:40
Alignment explanation
Indices: 3801598--3802414 Score: 1136
Period size: 41 Copynumber: 20.0 Consensus size: 40
3801588 TTTTGCCGAA
* *
3801598 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAG--GCAACGACTTTGGAAAAGTAAATT
3801639 GCTCCTCTAAACAGAGGCAACGGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCAAC-GACTTTGGAAAAGTAAATT
* * *
3801679 GCTCCTCTCAACTGAGGCACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
*
3801721 GCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
*
3801761 GCTCCTCTCAACAGAGGCACCACGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
*
3801802 GCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
3801843 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
3801884 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
3801925 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
3801967 GCTCCTCTAAACAGAGGCAACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGGAAAAGTAAATT
*
3802007 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGG--CAACGACTTTGGAAAAGTAAATT
3802048 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
*
3802089 GCTCCTCTAAACAGAGGTACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGG--CAACGACTTTGGAAAAGTAAATT
3802130 GCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
* *
3802170 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGG--CAACGACTTTGGAAAAGTAAATT
* *
3802212 GCTCCTCTCAACAGAGGTACCACGACTTTGGAAAA-TAAATT
1 GCTCCTCTAAACAGAGG--CAACGACTTTGGAAAAGTAAATT
*
3802253 GCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
*
3802293 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
3802334 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
3802375 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAAT
3802415 ACTCCTAGAC
Statistics
Matches: 723, Mismatches: 22, Indels: 62
0.90 0.03 0.08
Matches are distributed among these distances:
39 27 0.04
40 196 0.27
41 352 0.49
42 138 0.19
43 10 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (40 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGGAAAAGTAAATT
Found at i:3803654 original size:19 final size:20
Alignment explanation
Indices: 3803630--3803671 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3803620 TGATCTCTTT
3803630 TTTCATTTT-TCATTTTTTC
1 TTTCATTTTCTCATTTTTTC
3803649 TTTCATTTTCTCATTTTTTC
1 TTTCATTTTCTCATTTTTTC
3803669 TTT
1 TTT
3803672 TTTCTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTCATTTTCTCATTTTTTC
Found at i:3803665 original size:27 final size:27
Alignment explanation
Indices: 3803627--3803696 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
3803617 ATTTGATCTC
*
3803627 TTTTTTCATTTTTCATTTTTTCTTTCA
1 TTTTCTCATTTTTCATTTTTTCTTTCA
*
3803654 TTTTCTCATTTTTTC-TTTTTTCTTTCT
1 TTTTCTCA-TTTTTCATTTTTTCTTTCA
**
3803681 TTTTCTTTTTTTTCAT
1 TTTTCTCATTTTTCAT
3803697 CATCTTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.16
27 25 0.68
28 6 0.16
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (27 bp):
TTTTCTCATTTTTCATTTTTTCTTTCA
Found at i:3803704 original size:20 final size:19
Alignment explanation
Indices: 3803635--3803705 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
3803625 TCTTTTTTCA
*
3803635 TTTT-TCATTTTTTCTTTCA
1 TTTTCTCATTTTTTCTTT-T
3803654 TTTTCTCATTTTTTCTTTT
1 TTTTCTCATTTTTTCTTTT
3803673 TTCTT-TC--TTTTTCTTTT
1 TT-TTCTCATTTTTTCTTTT
3803690 TTTTCATCATCTTTTT
1 TTTTC-TCAT-TTTTT
3803706 TTCATTCTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
16 2 0.05
17 12 0.27
18 2 0.05
19 8 0.18
20 15 0.34
21 5 0.11
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTCATTTTTTCTTTT
Found at i:3803714 original size:37 final size:38
Alignment explanation
Indices: 3803622--3803719 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 38
3803612 TTTCAATTTG
3803622 ATCTCTTTTTTCATT-TTTCATTTTTTCTTTCATTTTCTC
1 ATCT-TTTTTTCATTCTTTCA-TTTTTCTTTCATTTTCTC
** *
3803661 AT-TTTTTCTTTTTTCTTTC-TTTTTCTTT-TTTTTCATC
1 ATCTTTTT-TTCATTCTTTCATTTTTCTTTCATTTTC-TC
*
3803698 ATCTTTTTTTCATTCTTCCATT
1 ATCTTTTTTTCATTCTTTCATT
3803720 ATTGATATCT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
36 5 0.10
37 25 0.52
38 12 0.25
39 6 0.12
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.71
Consensus pattern (38 bp):
ATCTTTTTTTCATTCTTTCATTTTTCTTTCATTTTCTC
Found at i:3807616 original size:152 final size:155
Alignment explanation
Indices: 3807339--3807793 Score: 709
Period size: 152 Copynumber: 2.9 Consensus size: 155
3807329 TTTACCAAGT
* * *
3807339 AATTAGTTGTTGGAAATGATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* *
3807404 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGGGGCTCCGTCGTCGGATTTAT
66 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAAT
*
3807469 TAAAGAAAAAAA-CAAAATCATC-C
131 TAAAGAAAAAAATCAAAATCAGCAC
*
3807492 AATTAATTATTGGAAATTATTCTCAATTAACTCTAATACTTTTAGCAGAAAATTGAG-AAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
*
3807556 CTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAAT
66 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAAT
*
3807621 TAAAGAAAAAAAAAATCAAAATCAGCAAAGT
131 TAAAG---AAAAAAATCAAAATCAGC--A-C
*
3807652 AATTAATTATCGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
1 AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
* * *
3807717 CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTCGGATTGA
66 CTCACCTCAGGAGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCGGATTAA
3807782 TTAAAGAAAAAA
130 TTAAAGAAAAAA
3807794 GAAAAAAAAA
Statistics
Matches: 277, Mismatches: 15, Indels: 14
0.91 0.05 0.05
Matches are distributed among these distances:
152 74 0.27
153 53 0.19
155 7 0.03
156 9 0.03
159 6 0.02
160 55 0.20
161 38 0.14
162 35 0.13
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (155 bp):
AATTAATTATTGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCC
CTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAAT
TAAAGAAAAAAATCAAAATCAGCAC
Found at i:3807843 original size:1 final size:1
Alignment explanation
Indices: 3807839--3807863 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3807829 AAAAAAATTC
3807839 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
3807864 CCTGGAGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3808217 original size:20 final size:20
Alignment explanation
Indices: 3808188--3808233 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3808178 GGAAGATTCA
*
3808188 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCG
***
3808208 CCGGAATCTGGGTTTTTTCG
1 CCGGAATCTGGAAATTTTCG
3808228 CCGGAA
1 CCGGAA
3808234 GTTGGCCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCG
Found at i:3808260 original size:62 final size:63
Alignment explanation
Indices: 3808178--3808295 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 63
3808168 GAACTCCGGT
* *
3808178 GGAAGATTCACCGGATTCTGGAAATT-TTCGCCGGAATCTGGGTTTTTTCGCCGGAAGTTGGCC
1 GGAAGATTCACCGGATTCTGG-AATTCTTCGCCGGAATCTGGGATTCTTCGCCGGAAGTTGGCC
* * **
3808241 GGAA-ATTCACCGGTTTCTGGGATTCTTCGCCGGTTTCTGGGATTCTTCGCCGGAA
1 GGAAGATTCACCGGATTCTGGAATTCTTCGCCGGAATCTGGGATTCTTCGCCGGAA
3808296 ACTGGGCAGG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 3 0.06
62 41 0.85
63 4 0.08
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.31
Consensus pattern (63 bp):
GGAAGATTCACCGGATTCTGGAATTCTTCGCCGGAATCTGGGATTCTTCGCCGGAAGTTGGCC
Found at i:3808275 original size:20 final size:20
Alignment explanation
Indices: 3808250--3808293 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3808240 CGGAAATTCA
3808250 CCGGTTTCTGGGATTCTTCG
1 CCGGTTTCTGGGATTCTTCG
3808270 CCGGTTTCTGGGATTCTTCG
1 CCGGTTTCTGGGATTCTTCG
3808290 CCGG
1 CCGG
3808294 AAACTGGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.05, C:0.27, G:0.32, T:0.36
Consensus pattern (20 bp):
CCGGTTTCTGGGATTCTTCG
Found at i:3808300 original size:20 final size:20
Alignment explanation
Indices: 3808257--3808301 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3808247 TCACCGGTTT
***
3808257 CTGGGATTCTTCGCCGGTTT
1 CTGGGATTCTTCGCCGGAAA
3808277 CTGGGATTCTTCGCCGGAAA
1 CTGGGATTCTTCGCCGGAAA
3808297 CTGGG
1 CTGGG
3808302 CAGGTCGTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.24, G:0.33, T:0.31
Consensus pattern (20 bp):
CTGGGATTCTTCGCCGGAAA
Found at i:3808359 original size:18 final size:18
Alignment explanation
Indices: 3808310--3808370 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
3808300 GGCAGGTCGT
3808310 CGGAAACTTCAATGTTGGC
1 CGGAAACTTCAA-GTTGGC
3808329 CGG-AA-TT----TTGGC
1 CGGAAACTTCAAGTTGGC
3808341 CGGAAACTTCAAGTTGGC
1 CGGAAACTTCAAGTTGGC
*
3808359 CGGAAAATTCAA
1 CGGAAACTTCAA
3808371 CCGGAAACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
12 8 0.23
13 2 0.06
14 2 0.06
17 2 0.06
18 18 0.51
19 3 0.09
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (18 bp):
CGGAAACTTCAAGTTGGC
Found at i:3808375 original size:31 final size:31
Alignment explanation
Indices: 3808310--3808379 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
3808300 GGCAGGTCGT
* ***
3808310 CGGAAACTTCAATGTTGGCCGGAATTTTGGC
1 CGGAAACTTCAATGTTGGCCGGAAATTCAAC
3808341 CGGAAACTTCAA-GTTGGCCGGAAAATTCAAC
1 CGGAAACTTCAATGTTGGCCGG-AAATTCAAC
3808372 CGGAAACT
1 CGGAAACT
3808380 GGAATTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 9 0.26
31 25 0.74
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (31 bp):
CGGAAACTTCAATGTTGGCCGGAAATTCAAC
Found at i:3808808 original size:3 final size:3
Alignment explanation
Indices: 3808800--3808961 Score: 63
Period size: 3 Copynumber: 52.3 Consensus size: 3
3808790 GATAATTAAA
* * *
3808800 AAT AAT AAT AAT AAT AAT AAT AA- AAT AA- GAT AACCC AAGT ATAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T AA-T A-AT AAT
* *
3808847 ACAA AAT AAT AAT AAT -AT AAT AAT AAT AAT ATAT ACT ATAT ACAT -AT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT A-AT AAT
* * *
3808894 AA- ATCT AAT -CT AAT AA- AAA AAT AAAT AAAT ATAT ACAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT -AAT -AAT A-AT A-AT AAT AAT
3808938 AAT AAT AAT AA- AAT ACAT AA- AAT A
1 AAT AAT AAT AAT AAT A-AT AAT AAT A
3808962 CAAAAGAAGA
Statistics
Matches: 122, Mismatches: 18, Indels: 38
0.69 0.10 0.21
Matches are distributed among these distances:
2 15 0.12
3 76 0.62
4 28 0.23
5 3 0.02
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3811784 original size:103 final size:102
Alignment explanation
Indices: 3811592--3811791 Score: 242
Period size: 103 Copynumber: 2.0 Consensus size: 102
3811582 TTTGTTATAA
* * * *
3811592 AAAAATTTTTCATTTGTGAAAACAATTTATTTTCAAAAATATTTTTCATTATATTGGTAAGATTT
1 AAAAATTTATCATTTGTGAAAACAATTTATTTTCAAAAATATCTTTCAATATATTGGTAAAATTT
* * * *
3811657 TCTGTCAAATATTGCCCTCTAATATGTTGGTAGGATC
66 TCTATCAAATATTACCCTCCAATATATTGGTAGGATC
* * * *
3811694 AAAAATTTATCTATTTGTGAAAATAATTTATTTTTAGAAATATCTTTCAATATGTTGGTAAAATT
1 AAAAATTTATC-ATTTGTGAAAACAATTTATTTTCAAAAATATCTTTCAATATATTGGTAAAATT
*
3811759 TT-TCATCAAGA-ATTACTCTCCAATATATTGGTA
65 TTCT-ATCAA-ATATTACCCTCCAATATATTGGTA
3811792 AGATTTTAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
102 11 0.13
103 70 0.85
104 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (102 bp):
AAAAATTTATCATTTGTGAAAACAATTTATTTTCAAAAATATCTTTCAATATATTGGTAAAATTT
TCTATCAAATATTACCCTCCAATATATTGGTAGGATC
Found at i:3812007 original size:21 final size:21
Alignment explanation
Indices: 3811983--3812045 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 21
3811973 CTTTATGCAA
*
3811983 ATAATACCATGCAATAATAAT
1 ATAATATCATGCAATAATAAT
3812004 ATAATATATCATGCAATAATAAT
1 AT-A-ATATCATGCAATAATAAT
3812027 A-AACTATCATGCAATAATA
1 ATAA-TATCATGCAATAATA
3812046 TAATATATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
20 1 0.03
21 18 0.47
22 1 0.03
23 18 0.47
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAATATCATGCAATAATAAT
Found at i:3812018 original size:23 final size:23
Alignment explanation
Indices: 3811990--3812083 Score: 92
Period size: 23 Copynumber: 4.2 Consensus size: 23
3811980 CAAATAATAC
3811990 CATGCAATAATAATATAATATAT
1 CATGCAATAATAATATAATATAT
*
3812013 CATGCAATAATAATA-AA-CTAT
1 CATGCAATAATAATATAATATAT
*
3812034 CATGCAATAATATAATATATAAATTAT
1 CATGCAAT-A-ATAATATA-ATA-TAT
3812061 CATGCAAT--TAAT-TAATA-AT
1 CATGCAATAATAATATAATATAT
3812080 CATG
1 CATG
3812084 TAAAAAATAA
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
19 6 0.10
21 13 0.21
22 5 0.08
23 25 0.40
24 1 0.02
25 1 0.02
27 11 0.18
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (23 bp):
CATGCAATAATAATATAATATAT
Found at i:3812061 original size:27 final size:27
Alignment explanation
Indices: 3812019--3812079 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
3812009 ATATCATGCA
3812019 ATAATAATAAACTATCATGCAA-TAAT
1 ATAATAATAAACTATCATGCAATTAAT
*
3812045 ATAATATATAAATTATCATGCAATTAAT
1 ATAATA-ATAAACTATCATGCAATTAAT
3812073 -TAATAAT
1 ATAATAAT
3812080 CATGTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 8 0.25
27 20 0.62
28 4 0.12
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.36
Consensus pattern (27 bp):
ATAATAATAAACTATCATGCAATTAAT
Found at i:3812159 original size:3 final size:3
Alignment explanation
Indices: 3812153--3812185 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3812143 TTTTATTATT
3812153 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3812186 ACACATAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3812690 original size:16 final size:16
Alignment explanation
Indices: 3812653--3812684 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3812643 TGGAAAGTTC
*
3812653 AAAAGAAACCCAAAAA
1 AAAAAAAACCCAAAAA
3812669 AAAAAAAACCCAAAAA
1 AAAAAAAACCCAAAAA
3812685 TTAAAATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.19, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAAACCCAAAAA
Found at i:3813308 original size:6 final size:6
Alignment explanation
Indices: 3813299--3813397 Score: 62
Period size: 6 Copynumber: 16.7 Consensus size: 6
3813289 TTTTTTCAAC
* *
3813299 AAAATT AAAATC AAAACT -AAATT AAAAATCT -AAATCT -AAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT -AAAAT-T AAAAT-T AAAATT AAAATT
* * * * * * *
3813347 AATATT AAAATT GAGATC AAGATT AAAATT -AAATT CAAATT ATAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
3813394 AAAA
1 AAAA
3813398 ATTTTGGGCT
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
5 10 0.14
6 58 0.79
7 4 0.05
8 1 0.01
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:3813339 original size:19 final size:18
Alignment explanation
Indices: 3813300--3813344 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
3813290 TTTTTCAACA
3813300 AAATT-AAAATCAAAACT
1 AAATTAAAAATCAAAACT
*
3813317 AAATTAAAAATCTAAATCT
1 AAATTAAAAATC-AAAACT
3813336 AAATTAAAA
1 AAATTAAAA
3813345 TTAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 5 0.20
18 6 0.24
19 14 0.56
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATTAAAAATCAAAACT
Found at i:3816346 original size:17 final size:16
Alignment explanation
Indices: 3816311--3816351 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
3816301 TATGATTTTT
3816311 ATATT-AATAATGTAC
1 ATATTAAATAATGTAC
*
3816326 ATATTAAATATATGTAG
1 ATATTAAATA-ATGTAC
3816343 ATATTAAAT
1 ATATTAAAT
3816352 GTATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.22
16 4 0.17
17 14 0.61
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (16 bp):
ATATTAAATAATGTAC
Found at i:3818501 original size:18 final size:19
Alignment explanation
Indices: 3818466--3818510 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3818456 ATTAATTTAG
*
3818466 TTATGTTATTCATGTATAT
1 TTATGTTATTCATATATAT
*
3818485 TTGTGTTA-TCATATATAT
1 TTATGTTATTCATATATAT
3818503 TTATGTTA
1 TTATGTTA
3818511 CTTATATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.27, C:0.04, G:0.11, T:0.58
Consensus pattern (19 bp):
TTATGTTATTCATATATAT
Found at i:3821210 original size:1 final size:1
Alignment explanation
Indices: 3821204--3821273 Score: 59
Period size: 1 Copynumber: 70.0 Consensus size: 1
3821194 GTAAACACTA
* * * * * * * * *
3821204 TTTTTTTTTTTATTATTATTTTTTCTTTTTTCTTTTTTTCTTTTTTTTCTTTTTTTCTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3821269 TTTTT
1 TTTTT
3821274 CGTTTCTGTG
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:3821240 original size:8 final size:8
Alignment explanation
Indices: 3821222--3821273 Score: 72
Period size: 8 Copynumber: 6.6 Consensus size: 8
3821212 TTTATTATTA
3821222 TTTTTTC-
1 TTTTTTCT
3821229 TTTTTTCT
1 TTTTTTCT
3821237 TTTTTTCTT
1 TTTTTTC-T
3821246 TTTTTTCT
1 TTTTTTCT
3821254 TTTTTTCT
1 TTTTTTCT
*
3821262 CTTTTT-T
1 TTTTTTCT
3821269 TTTTT
1 TTTTT
3821274 CGTTTCTGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 12 0.29
8 21 0.51
9 8 0.20
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTCT
Found at i:3821242 original size:17 final size:16
Alignment explanation
Indices: 3821204--3821273 Score: 72
Period size: 15 Copynumber: 4.4 Consensus size: 16
3821194 GTAAACACTA
* *
3821204 TTTTTTTTT-TTATTA
1 TTTTTTTTTCTTTTTT
*
3821219 TTATTTTTTC-TTTTT
1 TTTTTTTTTCTTTTTT
*
3821234 TCTTTTTTTCTTTTTT
1 TTTTTTTTTCTTTTTT
3821250 TTCTTTTTTTCTCTTTTT
1 TT-TTTTTTTCT-TTTTT
3821268 TTTTTT
1 TTTTTT
3821274 CGTTTCTGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 19 0.42
16 6 0.13
17 13 0.29
18 7 0.16
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTTTCTTTTTT
Found at i:3821259 original size:25 final size:24
Alignment explanation
Indices: 3821204--3821273 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
3821194 GTAAACACTA
*
3821204 TTTTTTT-TTTTATTATTATTTTTTC
1 TTTTTTTCTTTT-TT-TTTTTTTTTC
3821229 -TTTTTTCTTTTTTTCTTTTTTTTC
1 TTTTTTTCTTTTTTT-TTTTTTTTC
*
3821253 TTTTTTTCTCTTTTTTTTTTT
1 TTTTTTTCTTTTTTTTTTTTT
3821274 CGTTTCTGTG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 1 0.03
24 22 0.55
25 17 0.43
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (24 bp):
TTTTTTTCTTTTTTTTTTTTTTTC
Found at i:3821291 original size:27 final size:27
Alignment explanation
Indices: 3821234--3821291 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
3821224 TTTTCTTTTT
* * *
3821234 TCTTTTTTTCTTTTTTTTCTTTTTTTC
1 TCTTTTTTTCTTTTGTTTCTGTGTTTC
*
3821261 TCTTTTTTT-TTTTCGTTTCTGTGTTTG
1 TCTTTTTTTCTTTT-GTTTCTGTGTTTC
3821288 TCTT
1 TCTT
3821292 CTTCTTCCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (27 bp):
TCTTTTTTTCTTTTGTTTCTGTGTTTC
Found at i:3822882 original size:12 final size:12
Alignment explanation
Indices: 3822865--3822897 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3822855 AATTTTAATT
3822865 TTAATAAAAAAA
1 TTAATAAAAAAA
*
3822877 TTAATAAAACAA
1 TTAATAAAAAAA
3822889 TTAATAAAA
1 TTAATAAAA
3822898 TTTTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
TTAATAAAAAAA
Found at i:3823332 original size:196 final size:197
Alignment explanation
Indices: 3822945--3823334 Score: 653
Period size: 196 Copynumber: 2.0 Consensus size: 197
3822935 TGCATTGCAT
* * *
3822945 ACATGACATAATTTTTACGAAAAGTAAATTTAGACCTCCCAAAGATGAGATTCTAAAAGTATTTC
1 ACATGACAT-ATTTTTACGAAAAATAAATTGAGACCTCCCAAAGATGAGATTCTAAAAGTATTCC
3823010 GAGTAGAGATGCTTTAAGAAATCTCTAAGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGG
65 GAGTAGAGATGCTTTAAGAAATCTCTAAGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGG
3823075 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTT
130 AACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTT
3823140 TTA
195 TTA
3823143 ACATGACAT-TTTCTTACGAAAAATAAATTCGAG-CCT-CCAAAGATGAGATTCTAAAAGTATTC
1 ACATGACATATTT-TTACGAAAAATAAATT-GAGACCTCCCAAAGATGAGATTCTAAAAGTATTC
* * *
3823205 CGAGTAGAGATGCTTTAAGAAATCTTTAGGTGAGAAAGAGTTTTTTTAATGTTACCAACGTACTG
64 CGAGTAGAGATGCTTTAAGAAATCTCTAAGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTG
*
3823270 GAACATTTTAAGAATTATTTCAATAAAAAAGGTTTTGATTTATTTTTCTCGAGAAT-AATTTTTT
129 GAACATTTTAAGAATTATTTCAAT-AAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTT
3823334 T
193 T
3823335 AATAAATAAA
Statistics
Matches: 182, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
196 123 0.68
197 48 0.26
198 11 0.06
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (197 bp):
ACATGACATATTTTTACGAAAAATAAATTGAGACCTCCCAAAGATGAGATTCTAAAAGTATTCCG
AGTAGAGATGCTTTAAGAAATCTCTAAGTGAGAAAGAGTTCTTTTAATGTTACCAACGTACTGGA
ACATTTTAAGAATTATTTCAATAAAAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTTTTT
TA
Found at i:3825849 original size:145 final size:145
Alignment explanation
Indices: 3825581--3825870 Score: 571
Period size: 145 Copynumber: 2.0 Consensus size: 145
3825571 TATAGGGAAT
3825581 CGAATCCATCAAGAACCTCGGAGCAGTTGATCCAAGCATGGAAAAGAACACAAAGAATGAGGTTA
1 CGAATCCATCAAGAACCTCGGAGCAGTTGATCCAAGCATGGAAAAGAACACAAAGAATGAGGTTA
*
3825646 GGGCCTCTCATTGACAAAGTCACTTTTGATTATCAGATTTGGAAAGCAATGCGGCCTAGAGACAT
66 GGGCCTCTCATTGACAAAGTCACTTTTGATTATCAGATTTGGAAAGCAATGCGACCTAGAGACAT
3825711 AGTACTCCTTCCTGA
131 AGTACTCCTTCCTGA
3825726 CGAATCCATCAAGAACCTCGGAGCAGTTGATCCAAGCATGGAAAAGAACACAAAGAATGAGGTTA
1 CGAATCCATCAAGAACCTCGGAGCAGTTGATCCAAGCATGGAAAAGAACACAAAGAATGAGGTTA
3825791 GGGCCTCTCATTGACAAAGTCACTTTTGATTATCAGATTTGGAAAGCAATGCGACCTAGAGACAT
66 GGGCCTCTCATTGACAAAGTCACTTTTGATTATCAGATTTGGAAAGCAATGCGACCTAGAGACAT
3825856 AGTACTCCTTCCTGA
131 AGTACTCCTTCCTGA
3825871 TGATAGCTCA
Statistics
Matches: 144, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 144 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (145 bp):
CGAATCCATCAAGAACCTCGGAGCAGTTGATCCAAGCATGGAAAAGAACACAAAGAATGAGGTTA
GGGCCTCTCATTGACAAAGTCACTTTTGATTATCAGATTTGGAAAGCAATGCGACCTAGAGACAT
AGTACTCCTTCCTGA
Found at i:3827782 original size:18 final size:17
Alignment explanation
Indices: 3827759--3827818 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
3827749 GGGCATCTCC
*
3827759 TTTTTTAAATTTCTTTGT
1 TTTTTTAAATTT-TTTCT
*** *
3827777 TTTTTTTTCTTTTTTTT
1 TTTTTTAAATTTTTTCT
*
3827794 TTTTTTAAATATTTTCT
1 TTTTTTAAATTTTTTCT
3827811 TTTTTTAA
1 TTTTTTAA
3827819 TTAAAATGGA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 24 0.73
18 9 0.27
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTTAAATTTTTTCT
Found at i:3827798 original size:14 final size:14
Alignment explanation
Indices: 3827768--3827797 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3827758 CTTTTTTAAA
3827768 TTTCTTTGTTTTTT
1 TTTCTTTGTTTTTT
3827782 TTTCTTT-TTTTTT
1 TTTCTTTGTTTTTT
3827795 TTT
1 TTT
3827798 TTAAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (14 bp):
TTTCTTTGTTTTTT
Found at i:3829343 original size:18 final size:19
Alignment explanation
Indices: 3829279--3829334 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
3829269 TTGTAAATTG
*
3829279 ATAGTTGT-TTATTGAT-T
1 ATAGTTGTGTTATTCATAT
* *
3829296 -TAGTTATGTTATTCATGT
1 ATAGTTGTGTTATTCATAT
3829314 ATAGTTGTGTTA-TCATAT
1 ATAGTTGTGTTATTCATAT
3829332 ATA
1 ATA
3829335 TTTTTGTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
16 6 0.19
17 7 0.22
18 9 0.28
19 10 0.31
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.54
Consensus pattern (19 bp):
ATAGTTGTGTTATTCATAT
Found at i:3832071 original size:2 final size:2
Alignment explanation
Indices: 3832064--3832091 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3832054 TTTTCACTTT
3832064 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
3832092 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3832096 original size:2 final size:2
Alignment explanation
Indices: 3832091--3832123 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3832081 ATATATATAT
3832091 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3832124 CTTGGCGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3832254 original size:16 final size:16
Alignment explanation
Indices: 3832197--3832254 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
3832187 CTAATTAAAG
3832197 TAAAA-GATTTAAATT
1 TAAAATGATTTAAATT
* * *
3832212 TGAAATGATTGAAACT
1 TAAAATGATTTAAATT
*
3832228 TAAAATTATTTAAATT
1 TAAAATGATTTAAATT
3832244 TAAAATGATTT
1 TAAAATGATTT
3832255 GGAACTCATT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
15 4 0.12
16 30 0.88
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (16 bp):
TAAAATGATTTAAATT
Found at i:3835595 original size:45 final size:45
Alignment explanation
Indices: 3835511--3835596 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
3835501 AAACAATAGC
* * * *
3835511 CCAATGCTTACGGAAATTCATATGCTGTAGAGGAAAGCAGGTAGT
1 CCAACGCTTACGGAAATTCATATACCGTAGAAGAAAGCAGGTAGT
* * *
3835556 CCAACGCTTACGGAACTTCATATACCGTGGAAGAGAGCAGG
1 CCAACGCTTACGGAAATTCATATACCGTAGAAGAAAGCAGG
3835597 AGGAAGAAGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.21
Consensus pattern (45 bp):
CCAACGCTTACGGAAATTCATATACCGTAGAAGAAAGCAGGTAGT
Found at i:3836110 original size:21 final size:21
Alignment explanation
Indices: 3836085--3836129 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3836075 AAGGAGGAAC
*
3836085 AAATGGAAGGGAAAATTGAAG
1 AAATGGAAGGCAAAATTGAAG
*
3836106 AAATGGAAGGCAAAATTGATG
1 AAATGGAAGGCAAAATTGAAG
3836127 AAA
1 AAA
3836130 GATTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.02, G:0.29, T:0.16
Consensus pattern (21 bp):
AAATGGAAGGCAAAATTGAAG
Found at i:3837205 original size:22 final size:22
Alignment explanation
Indices: 3837173--3837223 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 22
3837163 ACATTATTGA
3837173 TAAATTTTTTTTAAAAAAAA-T
1 TAAATTTTTTTTAAAAAAAATT
3837194 TAAATTTTTTTTAAAAAAAATT
1 TAAATTTTTTTTAAAAAAAATT
3837216 TAAATTTT
1 TAAATTTT
3837224 ATATATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAATTTTTTTTAAAAAAAATT
Found at i:3845857 original size:2 final size:2
Alignment explanation
Indices: 3845852--3845877 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3845842 ATATCTGGCA
3845852 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
3845878 TATGTACTTC
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:3851116 original size:19 final size:19
Alignment explanation
Indices: 3851092--3851128 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3851082 ATATATATTA
3851092 TTGTGATAACTTTTAGAAT
1 TTGTGATAACTTTTAGAAT
3851111 TTGTGATAACTTTTAGAA
1 TTGTGATAACTTTTAGAA
3851129 ATAATACACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGTGATAACTTTTAGAAT
Found at i:3851450 original size:18 final size:19
Alignment explanation
Indices: 3851427--3851474 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
3851417 ATACTAAAAT
3851427 TTAAATATTATTATAT-GA
1 TTAAATATTATTATATAGA
3851445 TTAAATATTATT-TATAGA
1 TTAAATATTATTATATAGA
3851463 -TAAAT-TTATTAT
1 TTAAATATTATTAT
3851475 TTAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (19 bp):
TTAAATATTATTATATAGA
Found at i:3852082 original size:19 final size:20
Alignment explanation
Indices: 3852056--3852110 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
3852046 AATTTTTTAG
*
3852056 TTTT-ATTATGAT-TTGATA
1 TTTTAATTATAATATTGATA
*
3852074 TTTTAATTATAATATTTATA
1 TTTTAATTATAATATTGATA
3852094 TTTT-A-TATATATATTGA
1 TTTTAATTATA-ATATTGA
3852111 ACATGCTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 8 0.26
19 14 0.45
20 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTAATTATAATATTGATA
Found at i:3852104 original size:20 final size:20
Alignment explanation
Indices: 3852066--3852108 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
3852056 TTTTATTATG
3852066 ATTTGATATTTTAATTATAAT
1 ATTTGATATTTTAATTAT-AT
3852087 ATTT-ATATTTT-ATATATAT
1 ATTTGATATTTTAAT-TATAT
3852106 ATT
1 ATT
3852109 GAACATGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTGATATTTTAATTATAT
Found at i:3857283 original size:47 final size:45
Alignment explanation
Indices: 3857232--3857319 Score: 131
Period size: 47 Copynumber: 1.9 Consensus size: 45
3857222 AAAAAATTGG
* *
3857232 TTTTTTAACATGTGAGATACACAAAATTTTTTATTATATTTTTACAA
1 TTTTTTAACATATGAGATACAC--AATTTTTTACTATATTTTTACAA
*
3857279 TTTTTTAATATATGAGATACACAATTTTTTACTATATTTTT
1 TTTTTTAACATATGAGATACACAATTTTTTACTATATTTTT
3857320 TATAATATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 18 0.47
47 20 0.53
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (45 bp):
TTTTTTAACATATGAGATACACAATTTTTTACTATATTTTTACAA
Found at i:3859908 original size:14 final size:15
Alignment explanation
Indices: 3859882--3859910 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3859872 TAGAGATAAA
3859882 AAAATTGTAAATATT
1 AAAATTGTAAATATT
3859897 AAAATT-TAAATATT
1 AAAATTGTAAATATT
3859911 CAATTTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAATTGTAAATATT
Found at i:3860727 original size:2 final size:2
Alignment explanation
Indices: 3860722--3860749 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3860712 ATATCTGGCA
3860722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3860750 CTCTTAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3871872 original size:15 final size:15
Alignment explanation
Indices: 3871847--3871879 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3871837 TTTTTAATAA
3871847 TTTAAATATATATCAT
1 TTTAAATATATAT-AT
3871863 TTTAAA-ATATATAT
1 TTTAAATATATATAT
3871877 TTT
1 TTT
3871880 TAGAGATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAAATATATATAT
Found at i:3877251 original size:3 final size:3
Alignment explanation
Indices: 3877243--3877288 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3877233 TAAAATTTAT
3877243 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3877289 TGTAGACACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3877398 original size:7 final size:7
Alignment explanation
Indices: 3877386--3877417 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
3877376 CCAATTTTAG
3877386 TTTTAAT
1 TTTTAAT
3877393 TTTTAAT
1 TTTTAAT
3877400 TTTTAAT
1 TTTTAAT
3877407 TTTTAAT
1 TTTTAAT
3877414 TTTT
1 TTTT
3877418 TTATCATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTAAT
Found at i:3877510 original size:18 final size:18
Alignment explanation
Indices: 3877444--3877516 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 18
3877434 TATTATTATC
* *
3877444 TTATTTTTAATTTTG-TAA
1 TTATTTTTTATTTTGAT-T
3877462 TTATTTTATTATTTTCGTCATT
1 TTATTTT-TTATTTT-G--ATT
3877484 TTGATTTTTTATTTTGATT
1 TT-ATTTTTTATTTTGATT
3877503 TTA-TTTTTATTTTG
1 TTATTTTTTATTTTG
3877517 GTGTCTTGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.23
18 8 0.17
19 11 0.23
20 1 0.02
21 1 0.02
22 9 0.19
23 6 0.13
ACGTcount: A:0.19, C:0.03, G:0.07, T:0.71
Consensus pattern (18 bp):
TTATTTTTTATTTTGATT
Found at i:3880696 original size:65 final size:64
Alignment explanation
Indices: 3880418--3880724 Score: 429
Period size: 65 Copynumber: 4.8 Consensus size: 64
3880408 TTTTTTGAAA
* *
3880418 TTTTATTTCTAAGGAAAATTGATACTTTCAACTTTTTCCC-AAAAATACTTTTTTTGGAAATTTA
1 TTTTCTTT-TAAGGAAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTTGGAAATTTA
3880482 T
64 T
3880483 TTTTCTTTTAAGGAAAATTGATACTTATCAACCTTTTCCCTAAAAATATTTTTTTTGGAAATTTA
1 TTTTCTTTTAAGGAAAATTGATACTT-TCAA-CTTTTCCCTAAAAATATTTTTTTTGGAAATTTA
3880548 -
64 T
*
3880548 -TTTC--TAAAGG-AAATTGATACTTTCAACCTTTT-CCTAAAAATA--TTTTTTGGAAATTT-T
1 TTTTCTTTTAAGGAAAATTGATACTTTCAA-CTTTTCCCTAAAAATATTTTTTTTGGAAATTTAT
*
3880605 TTTAT-TTCTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTATTTTGGAAATTTA
1 TTT-TCTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTT-TTTTGGAAATTTA
3880669 T
64 T
3880670 TTTTCTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTT
1 TTTTCTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTT
3880725 AGAATTTTTT
Statistics
Matches: 220, Mismatches: 6, Indels: 32
0.85 0.02 0.12
Matches are distributed among these distances:
57 14 0.06
58 2 0.01
59 11 0.05
60 19 0.09
61 38 0.17
62 5 0.02
63 2 0.01
64 35 0.16
65 67 0.30
66 27 0.12
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (64 bp):
TTTTCTTTTAAGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTAT
Found at i:3880816 original size:8 final size:8
Alignment explanation
Indices: 3880796--3880834 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
3880786 CTAATCTAAT
3880796 AAATAAA-
1 AAATAAAC
3880803 AAATAAAC
1 AAATAAAC
3880811 AAAT--A-
1 AAATAAAC
3880816 AAATAAAC
1 AAATAAAC
3880824 AAATAAAC
1 AAATAAAC
3880832 AAA
1 AAA
3880835 GAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
5 4 0.14
6 1 0.04
7 8 0.29
8 15 0.54
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATAAAC
Found at i:3880820 original size:13 final size:13
Alignment explanation
Indices: 3880802--3880843 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
3880792 TAATAAATAA
3880802 AAAATAAACAAAT
1 AAAATAAACAAAT
3880815 AAAATAAACAAAT
1 AAAATAAACAAAT
* *
3880828 -AAACAAAGAAAT
1 AAAATAAACAAAT
3880840 AAAA
1 AAAA
3880844 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (13 bp):
AAAATAAACAAAT
Found at i:3881309 original size:31 final size:31
Alignment explanation
Indices: 3881271--3881329 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3881261 TGGGCTGGTC
* **
3881271 GCCGGAAACTTCAATGTTCGCCGGAATTGTT
1 GCCGGAAAATTCAAAATTCGCCGGAATTGTT
3881302 GCCGGAAAATTCAAAATTCGCCGGAATT
1 GCCGGAAAATTCAAAATTCGCCGGAATT
3881330 TTCGTCGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (31 bp):
GCCGGAAAATTCAAAATTCGCCGGAATTGTT
Found at i:3882127 original size:8 final size:8
Alignment explanation
Indices: 3882105--3882142 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
3882095 CAACTCAACA
*
3882105 TTTTTTGG
1 TTTTTTTG
3882113 TTTTTTTG
1 TTTTTTTG
3882121 TTTTTTTTG
1 -TTTTTTTG
3882130 TTTTTTT-
1 TTTTTTTG
3882137 TTTTTT
1 TTTTTT
3882143 ACCAAAGCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 6 0.21
8 14 0.50
9 8 0.29
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTTTG
Found at i:3882264 original size:41 final size:41
Alignment explanation
Indices: 3882173--3882662 Score: 842
Period size: 41 Copynumber: 12.1 Consensus size: 41
3882163 AGGGACTTTG
3882173 GTAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTG-AAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
*
3882211 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
3882252 GTAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAA
3882292 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
3882333 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
3882374 GTAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
3882413 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAA
*
3882455 GTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
3882496 GTAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
3882535 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
3882576 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAA
3882618 GTAAATTGCTCCTCTAAACAGAGGCA--ACGAAC-TTGAAAA
1 GTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAA
3882657 GTAAAT
1 GTAAAT
3882663 ACTCCTAGAC
Statistics
Matches: 436, Mismatches: 3, Indels: 25
0.94 0.01 0.05
Matches are distributed among these distances:
38 26 0.06
39 97 0.22
40 44 0.10
41 190 0.44
42 79 0.18
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (41 bp):
GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
Found at i:3882387 original size:122 final size:121
Alignment explanation
Indices: 3882173--3882662 Score: 898
Period size: 122 Copynumber: 4.0 Consensus size: 121
3882163 AGGGACTTTG
3882173 GTAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTG-AAAGTAAATTGCTCCTCTAAACAGAGG
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
*
3882235 CACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGGAAAA
66 CACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTT-GAAAA
3882292 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
3882357 CACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAA
66 CACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAA
3882413 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAG
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAG
*
3882478 GTACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAA
65 GCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAA
3882535 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
1 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
3882600 CACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAAC-TTGAAAA
66 CACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG-ACTTTGAAAA
3882657 GTAAAT
1 GTAAAT
3882663 ACTCCTAGAC
Statistics
Matches: 362, Mismatches: 3, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
119 26 0.07
121 90 0.25
122 244 0.67
123 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (121 bp):
GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
CACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAA
Found at i:3882449 original size:163 final size:162
Alignment explanation
Indices: 3882173--3882662 Score: 868
Period size: 163 Copynumber: 3.0 Consensus size: 162
3882163 AGGGACTTTG
3882173 GTAAATTGCTCCTCTAAACAGAGGCAACGACTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCA
1 GTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
*
3882237 CCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATTG
66 -CACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTG
3882300 CTCCTCTAAACAGAGGCACCACGACTTTGAAAA
130 CTCCTCTAAACAGAGGCACCACGACTTTGAAAA
3882333 GTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
1 GTAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGG
3882398 CA-ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
64 CACACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
*
3882462 GCTCCTCTAAACAGAGGTACCACGACTTTGAAAA
129 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAA
3882496 GTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
1 GTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
3882561 CCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTG
66 -CACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTG
3882626 CTCCTCTAAACAGAGGCA--ACGAAC-TTGAAAA
130 CTCCTCTAAACAGAGGCACCACG-ACTTTGAAAA
3882657 GTAAAT
1 GTAAAT
3882663 ACTCCTAGAC
Statistics
Matches: 319, Mismatches: 3, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
160 26 0.08
161 93 0.29
162 11 0.03
163 189 0.59
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (162 bp):
GTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
CACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGC
TCCTCTAAACAGAGGCACCACGACTTTGAAAA
Found at i:3883209 original size:12 final size:12
Alignment explanation
Indices: 3883192--3883224 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3883182 TCAGCACTAG
3883192 CAAATTTCAAAA
1 CAAATTTCAAAA
3883204 CAAATTTCAAAA
1 CAAATTTCAAAA
3883216 CAAATTTCA
1 CAAATTTCA
3883225 TCCACCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (12 bp):
CAAATTTCAAAA
Found at i:3883926 original size:19 final size:18
Alignment explanation
Indices: 3883902--3883949 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
3883892 TCTTTTTTTA
3883902 TTTTTTCATTTTCTCATTT
1 TTTTTTCATTTTCTC-TTT
* *
3883921 TTTTTTCTTTTTTTCTTT
1 TTTTTTCATTTTCTCTTT
3883939 TTTTTT-ATTTT
1 TTTTTTCATTTT
3883950 TTTCTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 4 0.15
18 9 0.35
19 13 0.50
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTCATTTTCTCTTT
Found at i:3883931 original size:9 final size:9
Alignment explanation
Indices: 3883919--3883959 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
3883909 ATTTTCTCAT
3883919 TTTTTTTTC
1 TTTTTTTTC
3883928 -TTTTTTTC
1 TTTTTTTTC
3883936 TTTTTTTT-
1 TTTTTTTTC
3883944 TATTTTTTTC
1 T-TTTTTTTC
3883954 TCTTTT
1 T-TTTT
3883960 CTCATTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
8 9 0.32
9 14 0.50
10 5 0.18
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:3883950 original size:18 final size:18
Alignment explanation
Indices: 3883918--3883959 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3883908 CATTTTCTCA
*
3883918 TTTTTTTTTCTTTTTTTC
1 TTTTTTTTTATTTTTTTC
3883936 TTTTTTTTTATTTTTTTC
1 TTTTTTTTTATTTTTTTC
3883954 TCTTTT
1 T-TTTT
3883960 CTCATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTATTTTTTTC
Found at i:3883966 original size:18 final size:18
Alignment explanation
Indices: 3883928--3883968 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3883918 TTTTTTTTTC
* * *
3883928 TTTTTTTCTTTTTTTTTA
1 TTTTTTTCTCTTTTCTCA
3883946 TTTTTTTCTCTTTTCTCA
1 TTTTTTTCTCTTTTCTCA
3883964 TTTTT
1 TTTTT
3883969 CATCCATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTCTCTTTTCTCA
Found at i:3887897 original size:60 final size:56
Alignment explanation
Indices: 3887768--3888231 Score: 572
Period size: 60 Copynumber: 7.7 Consensus size: 56
3887758 TTTTTTTTAG
*
3887768 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATTTTTTTTGGAAATTT--ATTTCT-AA
*
3887827 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAA---TTTTTTTTGGAAATTTATTTCTAA
*
3887887 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAAT-TTTTTTTGGAAA-TTT-ATTTCT-AA
3887947 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAAT--TTTTTTTGGAAATTTA--TTTC---TAA
3888011 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCC--AAAA-ATTTTTTTTGGAAATTTATTTCTAA
*
3888070 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTTTTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATTTTTTTTGGAAA----TTTATTTCTAA
3888131 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAAT-TTTTTTTGGAAATTTATTTCTAA
3888189 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAAT-T-TTTTTT
3888232 TAGAATTTTT
Statistics
Matches: 370, Mismatches: 9, Indels: 52
0.86 0.02 0.12
Matches are distributed among these distances:
57 14 0.04
58 63 0.17
59 71 0.19
60 79 0.21
61 62 0.17
62 29 0.08
63 3 0.01
64 42 0.11
65 5 0.01
66 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (56 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATTTTTTTTGGAAATTTATTTCTAA
Found at i:3888241 original size:120 final size:121
Alignment explanation
Indices: 3887768--3888247 Score: 667
Period size: 119 Copynumber: 4.0 Consensus size: 121
3887758 TTTTTTTTAG
3887768 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTCGATTTTCAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTT-GATTTTCAAGGAAA
** **
3887832 ATTGATACTTTCAACTTTT-CCTCAAAAACCCTTTTTTTT-GAA--AATTTATTTCTAA
65 ATTGATACTTTCAACTTTTCCCT-AAAAA-TATTTTTTTTAGAATTTTTTTATTTCTAA
*
3887887 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTTTCAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAA-TTTGATTTTCAAGGAAA
* * * *
3887952 ATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTTGGAAATTTATTTT-TCTTTTAA
65 ATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTAG-AATTT-TTTTAT-TTCTAA
*
3888011 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTT-A-TTTCTAAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTTGATTTTC-AAGGAA
**
3888074 AATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGA-AATTTTTTTATTTCTAA
64 AATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTAGAATTTTTTTATTTCTAA
*
3888131 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTT-A-TTTCTAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTGATTTTC-AAGGAAA
3888194 ATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTAGAATTTTTTTATTT
65 ATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTTAGAATTTTTTTATTT
3888248 TTATTTAAAG
Statistics
Matches: 329, Mismatches: 18, Indels: 26
0.88 0.05 0.07
Matches are distributed among these distances:
119 101 0.31
120 99 0.30
121 26 0.08
122 4 0.01
123 43 0.13
124 45 0.14
125 11 0.03
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (121 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTGATTTTCAAGGAAAA
TTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTAGAATTTTTTTATTTCTAA
Found at i:3888326 original size:13 final size:13
Alignment explanation
Indices: 3888304--3888335 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3888294 CTAATCTAAT
3888304 AAAT-AAATAAAC
1 AAATAAAATAAAC
3888316 AAATAAAATAAAC
1 AAATAAAATAAAC
3888329 AAATAAA
1 AAATAAA
3888336 CAAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAATAAAC
Found at i:3888327 original size:21 final size:21
Alignment explanation
Indices: 3888301--3888344 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3888291 AACCTAATCT
* *
3888301 AATAAATAAATAAACAAATAA
1 AATAAACAAATAAACAAAGAA
3888322 AATAAACAAATAAACAAAGAA
1 AATAAACAAATAAACAAAGAA
3888343 AA
1 AA
3888345 AAAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (21 bp):
AATAAACAAATAAACAAAGAA
Found at i:3888807 original size:31 final size:31
Alignment explanation
Indices: 3888769--3888827 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3888759 TGGGCTGGTC
* *
3888769 GCCGGAAACTTC-AATGTTCGCCGGAATTGTT
1 GCCGGAAAATTCAAAT-TTCGCCAGAATTGTT
3888800 GCCGGAAAATTCAAATTTCGCCAGAATT
1 GCCGGAAAATTCAAATTTCGCCAGAATT
3888828 TTCGCCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (31 bp):
GCCGGAAAATTCAAATTTCGCCAGAATTGTT
Found at i:3889203 original size:39 final size:39
Alignment explanation
Indices: 3889160--3889235 Score: 91
Period size: 38 Copynumber: 1.9 Consensus size: 39
3889150 GAGAAGATAA
* *
3889160 ATCAGCAGATATTATAAGATAAATAATAATA-AAAAATAT
1 ATCAG-AGATATAATAAGATAAATAAAAATACAAAAATAT
* * *
3889199 ATCAGATATATAATTAGATAAGTAAAAATACAAAAAT
1 ATCAGAGATATAATAAGATAAATAAAAATACAAAAAT
3889236 GAATAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 20 0.65
39 11 0.35
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (39 bp):
ATCAGAGATATAATAAGATAAATAAAAATACAAAAATAT
Found at i:3893754 original size:20 final size:23
Alignment explanation
Indices: 3893716--3893757 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
3893706 TTTTGTCATT
3893716 TTAGGATTTCTTTTAAAGTAATG
1 TTAGGATTTCTTTTAAAGTAATG
3893739 TTAGG-TTT-TTTT-AAGTAAT
1 TTAGGATTTCTTTTAAAGTAAT
3893758 AGAATTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 3 0.16
23 5 0.26
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (23 bp):
TTAGGATTTCTTTTAAAGTAATG
Found at i:3894684 original size:31 final size:32
Alignment explanation
Indices: 3894642--3894708 Score: 111
Period size: 31 Copynumber: 2.1 Consensus size: 32
3894632 GAGAGATATT
3894642 AAAAATGGATGAAAGATGAGAAAAA-AAAGAAA
1 AAAAATGGATGAAAGATG-GAAAAAGAAAGAAA
3894674 AAAAAT-GATGAAAGATGGAAAAAGAAAGAAA
1 AAAAATGGATGAAAGATGGAAAAAGAAAGAAA
3894705 AAAA
1 AAAA
3894709 GGGAAAATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 6 0.18
31 22 0.65
32 6 0.18
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (32 bp):
AAAAATGGATGAAAGATGGAAAAAGAAAGAAA
Found at i:3894713 original size:20 final size:20
Alignment explanation
Indices: 3894690--3894735 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3894680 GATGAAAGAT
3894690 GGAAAAAGAAAGAAAAAAAG
1 GGAAAAAGAAAGAAAAAAAG
* * *
3894710 GGAAAATGGATGAAAAAAAG
1 GGAAAAAGAAAGAAAAAAAG
*
3894730 AGAAAA
1 GGAAAA
3894736 GTGAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (20 bp):
GGAAAAAGAAAGAAAAAAAG
Found at i:3894740 original size:17 final size:19
Alignment explanation
Indices: 3894701--3894752 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
3894691 GAAAAAGAAA
*
3894701 GAAAAAAAGGGAAAATGGAT
1 GAAAAAAAGAGAAAA-GGAT
3894721 GAAAAAAAGAGAAAA-G-T
1 GAAAAAAAGAGAAAAGGAT
*
3894738 GAAAAAAAAAGAAAA
1 GAAAAAAAGAGAAAA
3894753 AAAAAAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 15 0.50
18 1 0.03
20 14 0.47
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.06
Consensus pattern (19 bp):
GAAAAAAAGAGAAAAGGAT
Found at i:3894753 original size:11 final size:12
Alignment explanation
Indices: 3894732--3894771 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
3894722 AAAAAAAGAG
*
3894732 AAAAGTGAAAAA
1 AAAAGAGAAAAA
3894744 AAAAGA-AAAAA
1 AAAAGAGAAAAA
3894755 AAAAGAGAAAATA
1 AAAAGAGAAAA-A
3894768 AAAA
1 AAAA
3894772 AAATATATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 11 0.44
12 9 0.36
13 5 0.20
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (12 bp):
AAAAGAGAAAAA
Found at i:3894757 original size:13 final size:13
Alignment explanation
Indices: 3894739--3894774 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
3894729 GAGAAAAGTG
3894739 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
*
3894752 AAAAAAAGAGAAA
1 AAAAAAAAAGAAA
3894765 ATAAAAAAAA
1 A-AAAAAAAA
3894775 TATATGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.89, C:0.00, G:0.08, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:3894770 original size:17 final size:17
Alignment explanation
Indices: 3894722--3894774 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
3894712 AAAATGGATG
*
3894722 AAAAAAAGAGAAAAGTGA
1 AAAAAAAGAGAAAA-TAA
3894740 AAAAAAA-AG---A-AA
1 AAAAAAAGAGAAAATAA
3894752 AAAAAAAGAGAAAATAA
1 AAAAAAAGAGAAAATAA
3894769 AAAAAA
1 AAAAAA
3894775 TATATGAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
12 8 0.28
13 2 0.07
14 1 0.03
16 1 0.03
17 10 0.34
18 7 0.24
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (17 bp):
AAAAAAAGAGAAAATAA
Found at i:3896052 original size:43 final size:40
Alignment explanation
Indices: 3895988--3896078 Score: 112
Period size: 43 Copynumber: 2.2 Consensus size: 40
3895978 AGTTCGTTGA
**
3895988 ATGTGAAT-TTTAAACAAATGAAAAGTTTTAAACTTTTGG
1 ATGTGAATCTTTAAACAAATGAAAAACTTTAAACTTTTGG
* *
3896027 ATGTGAATCTTTAAAATTCAAATGAAAAACTTTAGATTTTTGG
1 ATGTGAATCTTT-AAA--CAAATGAAAAACTTTAAACTTTTGG
3896070 ATGTGAATC
1 ATGTGAATC
3896079 CGAAGTTTGC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
39 8 0.18
40 3 0.07
41 3 0.07
43 30 0.68
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (40 bp):
ATGTGAATCTTTAAACAAATGAAAAACTTTAAACTTTTGG
Found at i:3896446 original size:41 final size:41
Alignment explanation
Indices: 3896378--3896648 Score: 323
Period size: 41 Copynumber: 6.6 Consensus size: 41
3896368 GGACATGATT
*
3896378 TTCA-ATGAGCAATTTATTTTCTCAAAGTTCATTGCCTCTA
1 TTCAGATGAGCCATTTATTTTCTCAAAGTTCATTGCCTCTA
* * *
3896418 TTCAGA-GAAGCCATTTATTTTTTCAAAGTTCGTTGTCTCTA
1 TTCAGATG-AGCCATTTATTTTCTCAAAGTTCATTGCCTCTA
* *
3896459 TTCAGATGAGCTATTTTATTTTCTCAAAG-TCTGTTGCCTCTA
1 TTCAGATGAGCCA-TTTATTTTCTCAAAGTTC-ATTGCCTCTA
** * *
3896501 TTCAGATGAGTTATTTATTTTTTTTCAAAGTACATTGCCTCTA
1 TTCAGATGAGCCATTTA--TTTTCTCAAAGTTCATTGCCTCTA
* * * **
3896544 TTCAGAGGAGCCATTTATTTTTTCAAAGTTCGTCACCTCTA
1 TTCAGATGAGCCATTTATTTTCTCAAAGTTCATTGCCTCTA
*
3896585 TTCAGATGAGCCATTTATTTTCTCTAAGTTCATTGCCTCTA
1 TTCAGATGAGCCATTTATTTTCTCAAAGTTCATTGCCTCTA
*
3896626 TTCAGATGAGCTATTTATTTTCT
1 TTCAGATGAGCCATTTATTTTCT
3896649 ATTCAGATGA
Statistics
Matches: 198, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
40 5 0.03
41 123 0.62
42 36 0.18
43 33 0.17
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (41 bp):
TTCAGATGAGCCATTTATTTTCTCAAAGTTCATTGCCTCTA
Found at i:3896649 original size:24 final size:24
Alignment explanation
Indices: 3896622--3896672 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3896612 GTTCATTGCC
3896622 TCTATTCAGATGAGCTATTTATTT
1 TCTATTCAGATGAGCTATTTATTT
3896646 TCTATTCAGATGAGCTATTTATTT
1 TCTATTCAGATGAGCTATTTATTT
3896670 TCT
1 TCT
3896673 CAAAGTTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (24 bp):
TCTATTCAGATGAGCTATTTATTT
Found at i:3896686 original size:65 final size:65
Alignment explanation
Indices: 3896581--3896713 Score: 230
Period size: 65 Copynumber: 2.0 Consensus size: 65
3896571 GTTCGTCACC
* *
3896581 TCTATTCAGATGAGCCATTTATTTTCTCTAAGTTCATTGCCTCTATTCAGATGAGCTATTTATTT
1 TCTATTCAGATGAGCCATTTATTTTCTCAAAGTTCATTGCCTCTATTCAGATGAGCCATTTATTT
* *
3896646 TCTATTCAGATGAGCTATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAGATGAGCCATTTATTT
1 TCTATTCAGATGAGCCATTTATTTTCTCAAAGTTCATTGCCTCTATTCAGATGAGCCATTTATTT
3896711 TCT
1 TCT
3896714 CTAAGTTCGT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.46
Consensus pattern (65 bp):
TCTATTCAGATGAGCCATTTATTTTCTCAAAGTTCATTGCCTCTATTCAGATGAGCCATTTATTT
Found at i:3896727 original size:106 final size:106
Alignment explanation
Indices: 3896540--3896754 Score: 367
Period size: 106 Copynumber: 2.0 Consensus size: 106
3896530 GTACATTGCC
*
3896540 TCTATTCAGAGGAGCCATTTATTTTTTCAAAGTTCGTCACCTCTATTCAGATGAGCCATTTATTT
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTCGTCACCTCTATTCAGATGAGCCATTTATTT
*
3896605 TCTCTAAGTTCATTGCCTCTATTCAGATGAGCTATTTATTT
66 TCTCTAAGTTCATTGCCTCTATTCAGATAAGCTATTTATTT
* * **
3896646 TCTATTCAGATGAGCTATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAGATGAGCCATTTATTT
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTCGTCACCTCTATTCAGATGAGCCATTTATTT
*
3896711 TCTCTAAGTTCGTTGCCTCTATTCAGATAAGCTATTTATTT
66 TCTCTAAGTTCATTGCCTCTATTCAGATAAGCTATTTATTT
3896752 TCT
1 TCT
3896755 CAAAGTTTAT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.45
Consensus pattern (106 bp):
TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTCGTCACCTCTATTCAGATGAGCCATTTATTT
TCTCTAAGTTCATTGCCTCTATTCAGATAAGCTATTTATTT
Found at i:3896767 original size:147 final size:148
Alignment explanation
Indices: 3896497--3896793 Score: 434
Period size: 147 Copynumber: 2.0 Consensus size: 148
3896487 GTCTGTTGCC
* *
3896497 TCTATTCAGATGAGTTATTTATTTTTTTTCAAAGTACATTGCCTCTATTCAGAGGAGCCATTTAT
1 TCTATTCAGATGAGCTATTTA-TTTTTCTCAAAGTACATTGCCTCTATTCAGAGGAGCCATTTAT
* * *
3896562 TTTTTCAAAGTTCGTCACCTCTATTCAGATGAGCCATTTATTTTCTCTAAGTTCATTGCCTCTAT
65 TTTCTCAAAGTTCGTCACCTCTATTCAGATAAGCCATTTATTTTCTCAAAGTTCATTGCCTCTAT
* *
3896627 TCAGATGAGCTATTTATTT
130 TCAGAGGAGCCATTTATTT
* * *
3896646 TCTATTCAGATGAGCTATTTA-TTTTCTCAAAGTTCGTTGCCTCTATTCAGATGAGCCATTTATT
1 TCTATTCAGATGAGCTATTTATTTTTCTCAAAGTACATTGCCTCTATTCAGAGGAGCCATTTATT
* ** * * *
3896710 TTCTCTAAGTTCGTTGCCTCTATTCAGATAAGCTATTTATTTTCTCAAAGTTTATTGCCTTTATT
66 TTCTCAAAGTTCGTCACCTCTATTCAGATAAGCCATTTATTTTCTCAAAGTTCATTGCCTCTATT
3896775 CAGAGGAGCCATTTATTT
131 CAGAGGAGCCATTTATTT
3896793 T
1 T
3896794 TTCAAAAGTT
Statistics
Matches: 132, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
147 112 0.85
149 20 0.15
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (148 bp):
TCTATTCAGATGAGCTATTTATTTTTCTCAAAGTACATTGCCTCTATTCAGAGGAGCCATTTATT
TTCTCAAAGTTCGTCACCTCTATTCAGATAAGCCATTTATTTTCTCAAAGTTCATTGCCTCTATT
CAGAGGAGCCATTTATTT
Found at i:3896826 original size:124 final size:124
Alignment explanation
Indices: 3896646--3896928 Score: 406
Period size: 124 Copynumber: 2.3 Consensus size: 124
3896636 CTATTTATTT
* * * * *
3896646 TCTATTCAGATGAGCTATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAGATGAGCCATTTATTT
1 TCTATTCAGAGGAGCCATTTATTTTTTCAAAGTTCATTGCCTCTATTCAGAGGAGCCATTTATTT
* * * * *
3896711 TCTCTAAGTTCGTTGCCTCTATTCAGATAAGCTATTTA-TTTTCTCAAAGTTTATTGCC
66 TCTCAAAGTTCGTTACCTCTATTCAGAGAAGCTATTTATTTTTCTAAAAGTTCATTGCC
*
3896769 TTTATTCAGAGGAGCCATTTATTTTTTCAAAAGTTCATTGCCTCTATTCAGAGGAGCCATTTATT
1 TCTATTCAGAGGAGCCATTTATTTTTTC-AAAGTTCATTGCCTCTATTCAGAGGAGCCATTTATT
* * * *
3896834 TTCTCAAAGTTTGTTACCTCTATTCAGAGGAGCTATTTATTTTTTTAAAAGTTCGTTGCC
65 TTCTCAAAGTTCGTTACCTCTATTCAGAGAAGCTATTTATTTTTCTAAAAGTTCATTGCC
*
3896894 TCTATTTAGAGGAGCCATTTATTTTTTCAAAGTTC
1 TCTATTCAGAGGAGCCATTTATTTTTTCAAAGTTC
3896929 TGTTGACTCA
Statistics
Matches: 141, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
123 24 0.17
124 75 0.53
125 42 0.30
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (124 bp):
TCTATTCAGAGGAGCCATTTATTTTTTCAAAGTTCATTGCCTCTATTCAGAGGAGCCATTTATTT
TCTCAAAGTTCGTTACCTCTATTCAGAGAAGCTATTTATTTTTCTAAAAGTTCATTGCC
Found at i:3896843 original size:83 final size:83
Alignment explanation
Indices: 3896646--3896950 Score: 414
Period size: 83 Copynumber: 3.7 Consensus size: 83
3896636 CTATTTATTT
* * * *
3896646 TCTATTCAGATGAGCTATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAGATGAGCCATTTATTT
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTTGTTGCCTCTATTCAGAGGAGCCATTTATTT
* *
3896711 TCTC-TAAGTTCGTTGCC
66 TTTCAAAAGTTCGTTGCC
** * * *
3896728 TCTATTCAGATAAGCTATTTATTTTCTCAAAGTTTATTGCCTTTATTCAGAGGAGCCATTTATTT
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTTGTTGCCTCTATTCAGAGGAGCCATTTATTT
*
3896793 TTTCAAAAGTTCATTGCC
66 TTTCAAAAGTTCGTTGCC
* *
3896811 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTTGTTACCTCTATTCAGAGGAGCTATTTATTT
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTTGTTGCCTCTATTCAGAGGAGCCATTTATTT
*
3896876 TTTTAAAAGTTCGTTGCC
66 TTTCAAAAGTTCGTTGCC
* * * * *
3896894 TCTATTTAGAGGAGCCATTTATTTTTTCAAAGTTCTGTTGACTCAATTTAGAGGAGC
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTT-TGTTGCCTCTATTCAGAGGAGC
3896951 TTTGTTTACT
Statistics
Matches: 198, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
82 63 0.32
83 117 0.59
84 18 0.09
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.43
Consensus pattern (83 bp):
TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTTGTTGCCTCTATTCAGAGGAGCCATTTATTT
TTTCAAAAGTTCGTTGCC
Found at i:3896943 original size:42 final size:41
Alignment explanation
Indices: 3896646--3896950 Score: 385
Period size: 41 Copynumber: 7.4 Consensus size: 41
3896636 CTATTTATTT
* *
3896646 TCTATTCAGATGAGCTATTTATTTTCTCAAAGTTCGTTGCC
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTCGTTGCC
* *
3896687 TCTATTCAGATGAGCCATTTATTTTCTCTAAGTTCGTTGCC
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTCGTTGCC
** * **
3896728 TCTATTCAGATAAGCTATTTATTTTCTCAAAGTTTATTGCC
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTCGTTGCC
* * *
3896769 TTTATTCAGAGGAGCCATTTATTTTTTCAAAAGTTCATTGCC
1 TCTATTCAGAGGAGCCATTTATTTTCTC-AAAGTTCGTTGCC
* *
3896811 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTTGTTACC
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTCGTTGCC
* * *
3896852 TCTATTCAGAGGAGCTATTTATTTTTTTAAAAGTTCGTTGCC
1 TCTATTCAGAGGAGCCATTTA-TTTTCTCAAAGTTCGTTGCC
* * *
3896894 TCTATTTAGAGGAGCCATTTATTTTTTCAAAGTTCTGTTGAC
1 TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTC-GTTGCC
* *
3896936 TCAATTTAGAGGAGC
1 TCTATTCAGAGGAGC
3896951 TTTGTTTACT
Statistics
Matches: 233, Mismatches: 28, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
41 141 0.61
42 92 0.39
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.43
Consensus pattern (41 bp):
TCTATTCAGAGGAGCCATTTATTTTCTCAAAGTTCGTTGCC
Found at i:3897195 original size:3 final size:3
Alignment explanation
Indices: 3897184--3897248 Score: 66
Period size: 3 Copynumber: 22.7 Consensus size: 3
3897174 TTAATTTTTT
* * *
3897184 TTA TCA TTA TTA TTA TTA TTA TTA -TC TTA TTT TTAA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
3897228 TTA TT- TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
3897249 TTCATCATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 7 0.14
3 42 0.82
4 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3897230 original size:8 final size:8
Alignment explanation
Indices: 3897182--3897250 Score: 86
Period size: 8 Copynumber: 8.5 Consensus size: 8
3897172 TTTTAATTTT
*
3897182 TTTTATCA
1 TTTTATTA
3897190 TTATTATTA
1 TT-TTATTA
3897199 TTATTATTA
1 TT-TTATTA
*
3897208 TCTTATT-
1 TTTTATTA
*
3897215 TTTAATTA
1 TTTTATTA
3897223 TTTTATTA
1 TTTTATTA
3897231 TTTTATTA
1 TTTTATTA
3897239 TTTTATTA
1 TTTTATTA
3897247 TTTT
1 TTTT
3897251 CATCATTTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
7 5 0.09
8 34 0.63
9 15 0.28
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTATTA
Found at i:3897279 original size:11 final size:11
Alignment explanation
Indices: 3897255--3897289 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3897245 TATTTTCATC
3897255 ATTTTGATTTTT
1 ATTTTGA-TTTT
3897267 ATTTTGATTTT
1 ATTTTGATTTT
*
3897278 ATTTTTATTTT
1 ATTTTGATTTT
3897289 A
1 A
3897290 GTGTTTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (11 bp):
ATTTTGATTTT
Found at i:3897283 original size:17 final size:18
Alignment explanation
Indices: 3897255--3897288 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3897245 TATTTTCATC
3897255 ATTTTGATTTTTATTTTG
1 ATTTTGATTTTTATTTTG
3897273 ATTTT-ATTTTTATTTT
1 ATTTTGATTTTTATTTT
3897289 AGTGTTTTGA
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:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (18 bp):
ATTTTGATTTTTATTTTG
Found at i:3897653 original size:19 final size:20
Alignment explanation
Indices: 3897631--3897675 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3897621 AACTTGAATT
*
3897631 TTTCGACATG-TTTTCTAGA
1 TTTCGACATGATTTTCCAGA
*
3897650 TTTCGACGTGATTTTCCAGA
1 TTTCGACATGATTTTCCAGA
*
3897670 ATTCGA
1 TTTCGA
3897676 TGAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (20 bp):
TTTCGACATGATTTTCCAGA
Found at i:3898028 original size:11 final size:10
Alignment explanation
Indices: 3898012--3898060 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
3898002 CATTTTTTGG
3898012 TATTTTTATT
1 TATTTTTATT
* *
3898022 TGTTTTTAAT
1 TATTTTTATT
3898032 TATTTTTTATT
1 TA-TTTTTATT
3898043 TATGTGTTTATT
1 TAT-T-TTTATT
3898055 TATTTT
1 TATTTT
3898061 AGGAGTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 12 0.38
11 11 0.34
12 9 0.28
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (10 bp):
TATTTTTATT
Found at i:3898057 original size:23 final size:21
Alignment explanation
Indices: 3898014--3898060 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
3898004 TTTTTTGGTA
*
3898014 TTTTTATTTGTTTTTAATTAT
1 TTTTTATTTGTGTTTAATTAT
*
3898035 TTTTTATTTATGTGTTTATTTAT
1 TTTTTA-TT-TGTGTTTAATTAT
3898058 TTT
1 TTT
3898061 AGGAGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 2 0.09
23 14 0.64
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTTTATTTGTGTTTAATTAT
Found at i:3898751 original size:50 final size:48
Alignment explanation
Indices: 3898658--3898751 Score: 109
Period size: 50 Copynumber: 1.9 Consensus size: 48
3898648 AAAAAAATAG
*
3898658 AAAAAGAAAATTTCTAAATAGACCCAGATGGTGGAAATTTTAGAAATT
1 AAAAAGAAAATTTCTAAATAGACCCAGATGGTGGAAATATTAGAAATT
* * * *
3898706 AAAAAGAGAATATTTCTAATTTGGCCCATATGGTGG-AATAATTAGA
1 AAAAAGA-AA-ATTTCTAAATAGACCCAGATGGTGGAAAT-ATTAGA
3898752 TTTATTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 7 0.18
49 5 0.13
50 26 0.68
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.29
Consensus pattern (48 bp):
AAAAAGAAAATTTCTAAATAGACCCAGATGGTGGAAATATTAGAAATT
Found at i:3899715 original size:16 final size:17
Alignment explanation
Indices: 3899679--3899718 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3899669 GTTGTGGAAG
3899679 TGTT-TTTTTACAAGAT
1 TGTTGTTTTTACAAGAT
*
3899695 T-TTGTTTTTAC-ATAT
1 TGTTGTTTTTACAAGAT
3899710 TGTTGTTTT
1 TGTTGTTTT
3899719 GAATGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.65
Consensus pattern (17 bp):
TGTTGTTTTTACAAGAT
Found at i:3901806 original size:3 final size:3
Alignment explanation
Indices: 3901798--3901837 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3901788 TGGGTTATCT
3901798 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3901838 CAATGGGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3902654 original size:18 final size:18
Alignment explanation
Indices: 3902620--3902654 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3902610 ATCTATTTAG
*
3902620 TTATAGATTTATGAATTT
1 TTATAGATATATGAATTT
*
3902638 TTATAGATATATTAATT
1 TTATAGATATATGAATT
3902655 AATTAAATTA
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:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (18 bp):
TTATAGATATATGAATTT
Found at i:3908444 original size:22 final size:23
Alignment explanation
Indices: 3908402--3908449 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
3908392 ACTTTTTTAC
*
3908402 TTTTTATATATTATTTTAATAGGA
1 TTTTTATATATTATTTAAATA-GA
3908426 TTTTTA-ATA-TATTTAAATAGA
1 TTTTTATATATTATTTAAATAGA
3908447 TTT
1 TTT
3908450 ACATATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 9 0.39
23 3 0.13
24 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (23 bp):
TTTTTATATATTATTTAAATAGA
Found at i:3916636 original size:2 final size:2
Alignment explanation
Indices: 3916631--3916663 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3916621 TATATATATA
3916631 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3916664 AATATGTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3919111 original size:16 final size:16
Alignment explanation
Indices: 3919087--3919127 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
3919077 ATTGAAAATT
* *
3919087 AAAACCCCAAGTTGAA
1 AAAATCCCAAATTGAA
3919103 AAAATCCCAAATTGAA
1 AAAATCCCAAATTGAA
3919119 AAAATCCCA
1 AAAATCCCA
3919128 GTATGATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.54, C:0.24, G:0.07, T:0.15
Consensus pattern (16 bp):
AAAATCCCAAATTGAA
Found at i:3919429 original size:13 final size:13
Alignment explanation
Indices: 3919395--3919440 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
3919385 ATTCAATAAC
3919395 AAAAAT-TTTA-T
1 AAAAATATTTATT
* *
3919406 CAAAATTTTTATT
1 AAAAATATTTATT
3919419 AAAAATATTTATCT
1 AAAAATATTTAT-T
3919433 AAAAATAT
1 AAAAATAT
3919441 GTCAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 5 0.17
12 4 0.14
13 11 0.38
14 9 0.31
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAAATATTTATT
Found at i:3919520 original size:6 final size:6
Alignment explanation
Indices: 3919509--3919543 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
3919499 CTAATCTATC
3919509 AATTTT AATTTT AATTTT AATTTATT AATTTT AAT
1 AATTTT AATTTT AATTTT AA-TT-TT AATTTT AAT
3919544 AAAAATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
AATTTT
Found at i:3919550 original size:20 final size:20
Alignment explanation
Indices: 3919513--3919551 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3919503 TCTATCAATT
***
3919513 TTAATTTTAATTTTAATTTA
1 TTAATTTTAATAAAAATTTA
3919533 TTAATTTTAATAAAAATTT
1 TTAATTTTAATAAAAATTT
3919552 TCAAATTTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATTTTAATAAAAATTTA
Found at i:3923443 original size:11 final size:11
Alignment explanation
Indices: 3923427--3923453 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3923417 GAAAAATCTC
3923427 ACGTGCCAAAT
1 ACGTGCCAAAT
3923438 ACGTGCCAAAT
1 ACGTGCCAAAT
3923449 ACGTG
1 ACGTG
3923454 AATTGGAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (11 bp):
ACGTGCCAAAT
Found at i:3924146 original size:27 final size:27
Alignment explanation
Indices: 3924116--3924175 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
3924106 ATACTTTGGT
3924116 TTTAATAAAATTAATTGGTTAAATCGA
1 TTTAATAAAATTAATTGGTTAAATCGA
***
3924143 TTTAATTTGATTAATTGGTTAAATCGA
1 TTTAATAAAATTAATTGGTTAAATCGA
3924170 TTTAAT
1 TTTAAT
3924176 TCAATTAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (27 bp):
TTTAATAAAATTAATTGGTTAAATCGA
Found at i:3924176 original size:27 final size:27
Alignment explanation
Indices: 3924125--3924176 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
3924115 TTTTAATAAA
3924125 ATTAATTGGTTAAATCGATTTAATTTG
1 ATTAATTGGTTAAATCGATTTAATTTG
3924152 ATTAATTGGTTAAATCGATTTAATT
1 ATTAATTGGTTAAATCGATTTAATT
3924177 CAATTAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (27 bp):
ATTAATTGGTTAAATCGATTTAATTTG
Found at i:3924182 original size:27 final size:27
Alignment explanation
Indices: 3924124--3924183 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
3924114 GTTTTAATAA
*
3924124 AATTAATTGGTTAAATCGATTTAATTT
1 AATTAATTGGTTAAATCGATTTAATTC
*
3924151 GATTAATTGGTTAAATCGATTTAATTC
1 AATTAATTGGTTAAATCGATTTAATTC
3924178 AATTAA
1 AATTAA
3924184 ACAGTCAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (27 bp):
AATTAATTGGTTAAATCGATTTAATTC
Found at i:3929781 original size:2 final size:2
Alignment explanation
Indices: 3929774--3929799 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3929764 ATACATTTGG
3929774 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
3929800 TTTACAACCC
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:3932532 original size:31 final size:32
Alignment explanation
Indices: 3932497--3932568 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 32
3932487 TTTTATAAAA
* * *
3932497 TAAATATAAATCTTTGATCTTTTATTATA-TG
1 TAAATATAAATCTATAATATTTTATTATATTG
*
3932528 T-AA-ATAAATCTATAATATTTTATTTTATTG
1 TAAATATAAATCTATAATATTTTATTATATTG
3932558 TAAATA-AAATC
1 TAAATATAAATC
3932569 ACAAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 20 0.59
30 5 0.15
31 8 0.24
32 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (32 bp):
TAAATATAAATCTATAATATTTTATTATATTG
Found at i:3932534 original size:29 final size:30
Alignment explanation
Indices: 3932502--3932565 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
3932492 TAAAATAAAT
* * *
3932502 ATAAATCTTTGATCTTTTATTATA-TGTAA
1 ATAAATCTATAATATTTTATTATATTGTAA
*
3932531 ATAAATCTATAATATTTTATTTTATTGTAA
1 ATAAATCTATAATATTTTATTATATTGTAA
3932561 ATAAA
1 ATAAA
3932566 ATCACAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (30 bp):
ATAAATCTATAATATTTTATTATATTGTAA
Found at i:3932578 original size:30 final size:30
Alignment explanation
Indices: 3932516--3932598 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
3932506 ATCTTTGATC
* * *
3932516 TTTTATTATATGTAAAT-AAATCTATAATA
1 TTTTATTTTATGTAAATAAAATCTACAAAA
3932545 TTTTATTTTATTGTAAATAAAATC-ACAAAA
1 TTTTATTTTA-TGTAAATAAAATCTACAAAA
**
3932575 TTTTAAATTATGTAAA-AAAATCTA
1 TTTTATTTTATGTAAATAAAATCTA
3932599 ATTTAATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 6 0.13
29 16 0.35
30 19 0.41
31 5 0.11
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (30 bp):
TTTTATTTTATGTAAATAAAATCTACAAAA
Found at i:3936664 original size:19 final size:18
Alignment explanation
Indices: 3936640--3936676 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
3936630 TATGCATTTA
*
3936640 AGTTAATATATATTTATAT
1 AGTTAATAT-TATCTATAT
3936659 AGTTAATATTATCTATAT
1 AGTTAATATTATCTATAT
3936677 TAATTGCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
AGTTAATATTATCTATAT
Found at i:3941391 original size:17 final size:17
Alignment explanation
Indices: 3941369--3941403 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3941359 ATTACGAGTT
3941369 TAAGATCA-TCTTGGTAA
1 TAAGATCATTC-TGGTAA
3941386 TAAGATCATTCTGGTAA
1 TAAGATCATTCTGGTAA
3941403 T
1 T
3941404 TACATTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (17 bp):
TAAGATCATTCTGGTAA
Found at i:3949363 original size:29 final size:29
Alignment explanation
Indices: 3949295--3949388 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 29
3949285 GCAAGTGATC
* *
3949295 AAATTATATCCTAACAATAAAAAATAAAAAATT
1 AAATTATAT--TAA-AATAATAAAT-AAAAATA
*
3949328 ATATTATATTAAAATAATAAATAAAAATA
1 AAATTATATTAAAATAATAAATAAAAATA
*
3949357 AAATTATATTCAAATAATGAAA-AAATAATA
1 AAATTATATTAAAATAAT-AAATAAA-AATA
3949387 AA
1 AA
3949389 GTAATATTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
29 25 0.46
30 18 0.33
31 3 0.06
33 8 0.15
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (29 bp):
AAATTATATTAAAATAATAAATAAAAATA
Done.