Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 77 of 91
Found at i:12755482 original size:31 final size:31
Alignment explanation
Indices: 12755441--12755505 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
12755431 CACTCCTTCG
*
12755441 TTCTTTAATCCTTCAGTCGATTCATACCCAA
1 TTCTTCAATCCTTCAGTCGATTCATACCCAA
* *
12755472 TTCTTCAATCCTTCAGTCGATTCCTATCCAA
1 TTCTTCAATCCTTCAGTCGATTCATACCCAA
12755503 TTC
1 TTC
12755506 CAATTCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.31, G:0.06, T:0.40
Consensus pattern (31 bp):
TTCTTCAATCCTTCAGTCGATTCATACCCAA
Found at i:12756044 original size:21 final size:20
Alignment explanation
Indices: 12756016--12756058 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
12756006 CAGTAGCCAG
*
12756016 GAAAAGAACCTCAGCAATCT
1 GAAAAGAACCTCAACAATCT
12756036 GAAACAGAACCTCAACAATCT
1 GAAA-AGAACCTCAACAATCT
12756057 GA
1 GA
12756059 GCAAGGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.47, C:0.26, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAAAGAACCTCAACAATCT
Found at i:12759402 original size:19 final size:19
Alignment explanation
Indices: 12759378--12759414 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12759368 CATTGATTTC
*
12759378 GTTAATGTAATTCTTGGTT
1 GTTAATGTAATTCCTGGTT
12759397 GTTAATGTAATTCCTGGT
1 GTTAATGTAATTCCTGGT
12759415 CTGGTAGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.49
Consensus pattern (19 bp):
GTTAATGTAATTCCTGGTT
Found at i:12764988 original size:13 final size:14
Alignment explanation
Indices: 12764968--12764999 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12764958 GAATAATATA
12764968 TTAT-TTTAA-TTT
1 TTATATTTAATTTT
12764980 TTATATTTAATTTT
1 TTATATTTAATTTT
12764994 TTATAT
1 TTATAT
12765000 ATATTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 5 0.28
14 9 0.50
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATATTTAATTTT
Found at i:12765628 original size:101 final size:99
Alignment explanation
Indices: 12765452--12765638 Score: 293
Period size: 101 Copynumber: 1.9 Consensus size: 99
12765442 GGATGCTTTT
***
12765452 GGTTTTTATTTTTTTAATAAATGAATTGAAAATTTAAAAAAATAGTAAAGGAAAAAAAATACAAA
1 GGTTTTTATTTTTTTAATAAATGAATTGAAAACAAAAAAAAATAGTAAAGGAAAAAAAATACAAA
12765517 CCAAACGAAATCTAAATTATATTTTTCAGTTTAG
66 CCAAACGAAATCTAAATTATATTTTTCAGTTTAG
* *
12765551 GGTTTTTATTTTTTTTAATAAATGAATTGAAAGCAAAAAATAAATAGTAAAGGAAAAAAAATCCA
1 GGTTTTTA-TTTTTTTAATAAATGAATTGAAAACAAAAAA-AAATAGTAAAGGAAAAAAAATACA
* *
12765616 AACCAAATGAAATCTATATTATA
64 AACCAAACGAAATCTAAATTATA
12765639 ATTAATCATC
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 8 0.10
100 27 0.34
101 44 0.56
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (99 bp):
GGTTTTTATTTTTTTAATAAATGAATTGAAAACAAAAAAAAATAGTAAAGGAAAAAAAATACAAA
CCAAACGAAATCTAAATTATATTTTTCAGTTTAG
Found at i:12765788 original size:32 final size:32
Alignment explanation
Indices: 12765752--12765814 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
12765742 ATCAGATACT
12765752 TAAATTTTTAATTATTAAAAAATAATAGGATC
1 TAAATTTTTAATTATTAAAAAATAATAGGATC
* **
12765784 TAAATTTTTGATTATTTGAAAATAATAGGAT
1 TAAATTTTTAATTATTAAAAAATAATAGGAT
12765815 GAAAGAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.43
Consensus pattern (32 bp):
TAAATTTTTAATTATTAAAAAATAATAGGATC
Found at i:12766112 original size:2 final size:2
Alignment explanation
Indices: 12766100--12766140 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
12766090 TCACATAATG
* * *
12766100 TA TA GA TA TA TA TA TA TA TA TA CA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12766141 TATTAGTAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12768153 original size:3 final size:3
Alignment explanation
Indices: 12768145--12768201 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
12768135 TTTATATTTG
12768145 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12768193 TAT TAT TAT
1 TAT TAT TAT
12768202 ATTTTAGTCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12768827 original size:2 final size:2
Alignment explanation
Indices: 12768820--12768853 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12768810 CAAGATAACT
12768820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12768854 AAACAATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12772100 original size:9 final size:9
Alignment explanation
Indices: 12772074--12772107 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
12772064 ATACCCTTAA
12772074 AAATTATAT
1 AAATTATAT
* *
12772083 CAATAATAT
1 AAATTATAT
12772092 AAATTATAT
1 AAATTATAT
12772101 AAATTAT
1 AAATTAT
12772108 GAAAAAAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (9 bp):
AAATTATAT
Found at i:12772319 original size:20 final size:17
Alignment explanation
Indices: 12772270--12772321 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 17
12772260 AAAATAATAG
12772270 ATATAAAATTATTAATT
1 ATATAAAATTATTAATT
*
12772287 ATATATCAATTATTACATTT
1 ATATA-AAATTATTA-A-TT
12772307 AATATAAAATTATTA
1 -ATATAAAATTATTA
12772322 TGATAAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 5 0.17
18 8 0.28
19 1 0.03
20 10 0.34
21 5 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAAAATTATTAATT
Found at i:12780130 original size:21 final size:20
Alignment explanation
Indices: 12780106--12780149 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
12780096 TTTTACCTTG
* *
12780106 TTCAGATTGTTGAGGTTCTGT
1 TTCAAATTGCTGAGGTTCT-T
12780127 TTCAAATTGCTGAGGTTCTT
1 TTCAAATTGCTGAGGTTCTT
12780147 TTC
1 TTC
12780150 CTGGATACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.16, C:0.14, G:0.23, T:0.48
Consensus pattern (20 bp):
TTCAAATTGCTGAGGTTCTT
Found at i:12782483 original size:19 final size:18
Alignment explanation
Indices: 12782439--12782483 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
12782429 CAGATCGATG
12782439 ATTAAATATTTTTATTCA
1 ATTAAATATTTTTATTCA
12782457 ATTCAAATGATTTTTGATTC-
1 ATT-AAAT-ATTTTT-ATTCA
12782477 ATTAAAT
1 ATTAAAT
12782484 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.12
19 8 0.33
20 9 0.38
21 4 0.17
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (18 bp):
ATTAAATATTTTTATTCA
Found at i:12782540 original size:21 final size:18
Alignment explanation
Indices: 12782514--12782553 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
12782504 TAAATTATAT
12782514 TTTTATTAATTTTTATATAAA
1 TTTTATT-A-TTTTATA-AAA
12782535 TTTTATTATTTTATAAAA
1 TTTTATTATTTTATAAAA
12782553 T
1 T
12782554 AAAAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 1 0.05
21 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATTATTTTATAAAA
Found at i:12783372 original size:29 final size:27
Alignment explanation
Indices: 12783331--12783394 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 27
12783321 TAATAAAATA
*
12783331 TTTAATATTATATTTAAATTTTAAAATTT
1 TTTAAT-TTATATTTAAATTAT-AAATTT
12783360 TTTAATTTGATATTTAAATTATAAATTT
1 TTTAATTT-ATATTTAAATTATAAATTT
*
12783388 ATTAATT
1 TTTAATT
12783395 AATTTGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTAATTTATATTTAAATTATAAATTT
Found at i:12783394 original size:28 final size:28
Alignment explanation
Indices: 12783323--12783394 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
12783313 TTAAATCATA
*
12783323 ATAAAATAT-TTAATATTATATTTAAATT
1 ATAAAATTTATTAAT-TTATATTTAAATT
* *
12783351 TTAAAATTTTTTAATTTGATATTTAAATT
1 ATAAAATTTATTAATTT-ATATTTAAATT
12783380 AT-AAATTTATTAATT
1 ATAAAATTTATTAATT
12783395 AATTTGATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 21 0.55
29 17 0.45
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
ATAAAATTTATTAATTTATATTTAAATT
Found at i:12785781 original size:2 final size:2
Alignment explanation
Indices: 12785774--12785804 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12785764 GTTTATAATT
*
12785774 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12785805 TACAAGTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12786546 original size:27 final size:27
Alignment explanation
Indices: 12786512--12786568 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
12786502 GGAGTGACAC
*
12786512 ATAAATTTATTAATT-TAAAATAT-TAA
1 ATAAATTT-TTAATTAAAAAATATATAA
*
12786538 ATAATATTTTTTATTAAAAAATATATAA
1 ATAA-ATTTTTAATTAAAAAATATATAA
12786566 ATA
1 ATA
12786569 TAGAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 9 0.35
27 11 0.42
28 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAAATTTTTAATTAAAAAATATATAA
Found at i:12787092 original size:18 final size:18
Alignment explanation
Indices: 12787071--12787115 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
12787061 AAAAAAATTC
* *
12787071 AAAAACTAAATAA-AAAG
1 AAAAAATAAAAAATAAAG
12787088 AAAAAATAAAAAATAAAG
1 AAAAAATAAAAAATAAAG
12787106 AAAAAATAAA
1 AAAAAATAAA
12787116 GCTTTGGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.11
Consensus pattern (18 bp):
AAAAAATAAAAAATAAAG
Found at i:12806660 original size:32 final size:32
Alignment explanation
Indices: 12806619--12806682 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
12806609 TTTTTCTTTC
12806619 ATCCTATTATTTTCAAATAATTAAAAATTTAG
1 ATCCTATTATTTTCAAATAATTAAAAATTTAG
* *
12806651 ATCCTATTATTTTCAAATAATTGAATATTTAG
1 ATCCTATTATTTTCAAATAATTAAAAATTTAG
12806683 GTATCTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (32 bp):
ATCCTATTATTTTCAAATAATTAAAAATTTAG
Found at i:12807475 original size:21 final size:21
Alignment explanation
Indices: 12807434--12807475 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
12807424 AAGATTGAAG
*
12807434 TTGAACAATTAATATTTAATT
1 TTGAACAATTAATATTAAATT
*
12807455 TTGAATAATTTAA-ATTAAATT
1 TTGAACAA-TTAATATTAAATT
12807476 CCCTTTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (21 bp):
TTGAACAATTAATATTAAATT
Found at i:12808307 original size:15 final size:14
Alignment explanation
Indices: 12808286--12808319 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
12808276 GTTTTGTCAC
12808286 TTTCATATTTCTAA
1 TTTCATATTTCTAA
*
12808300 TGTTCATATTTGTAA
1 T-TTCATATTTCTAA
12808315 TTTCA
1 TTTCA
12808320 CTCATTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTCATATTTCTAA
Found at i:12808783 original size:49 final size:48
Alignment explanation
Indices: 12808675--12808788 Score: 137
Period size: 49 Copynumber: 2.4 Consensus size: 48
12808665 AAGATTAAAT
* *
12808675 TATTACAATAAATAGTATATTAACTAATTTTAAAGAGTGGATAAATAAG
1 TATTACAATAAATAATATATTAACTAATTTTAAAGAG-GCATAAATAAG
* *
12808724 TATTACAATAAGTAATATATTAACTAATTTTAAATA-GCATAAAT-AG
1 TATTACAATAAATAATATATTAACTAATTTTAAAGAGGCATAAATAAG
*
12808770 TA-TA-TATCAAATAATATAT
1 TATTACAAT-AAATAATATAT
12808789 CAAATATTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
44 2 0.03
45 12 0.21
46 4 0.07
47 7 0.12
49 33 0.57
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (48 bp):
TATTACAATAAATAATATATTAACTAATTTTAAAGAGGCATAAATAAG
Found at i:12813579 original size:2 final size:2
Alignment explanation
Indices: 12813572--12813606 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12813562 TATAAGTGTG
12813572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12813607 CTCATTTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12819300 original size:2 final size:2
Alignment explanation
Indices: 12819293--12819324 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12819283 CCCTTTTCAT
12819293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12819325 AAACTTACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12829600 original size:167 final size:166
Alignment explanation
Indices: 12829252--12829788 Score: 744
Period size: 167 Copynumber: 3.2 Consensus size: 166
12829242 AAGATGAAAG
*
12829252 TGTGTCAGTCTTTTTGCCCCCCATCTTTACTTCACAAAAATAAGTATAAAGCAAAGACTAAAACT
1 TGTGTCAGTCTTTTTG-CCCCCATCTTTACTTCACAAAAATAAATATAAAGCAAAGACTAAAACT
* * *
12829317 TATCATAGAAATTAAGGAAAGCTTTTAAAAAGAAAAAAA-AATAATGAAAGAAAGATAAGTCTTA
65 TATCATAGAAATTAAGGGAAG-TTTTAAAAAGAAAAAAACCA-AA-GAAAGAATGATAAGTCTTA
* * *
12829381 GTCTTTGCTTTGTACTTAGTCTTGACATGAAACATGTAAA
127 GTCTTTGCTTTATACTTAGTCTTGACATGAAGCATGCAAA
* * * **
12829421 TGTATCAGTCTTTTTG-CCCCACCTTTACTTCACCAAAATAAATATAAAGCAAAGGTTAAAACTT
1 TGTGTCAGTCTTTTTGCCCCCATCTTTACTTCACAAAAATAAATATAAAGCAAAGACTAAAACTT
* *
12829485 GTCACAGAAATTAAGGGAAGTTTTAAAAAGAAAAGAAACCAAAGAAAGAATGATAAGTCTTAGTC
66 ATCATAGAAATTAAGGGAAGTTTTAAAAAGAAAA-AAACCAAAGAAAGAATGATAAGTCTTAGTC
* * *
12829550 TTCGCTTTATACTTAGTCTTAACATGATGCATGCAAA
130 TTTGCTTTATACTTAGTCTTGACATGAAGCATGCAAA
* * *
12829587 TGTGTCAAGTCTTTTTGCCCCCATCTTTACTTCAAAAAAATCACA-ATAAAGCAAAGACTAAGAC
1 TGTGTC-AGTCTTTTTGCCCCCATCTTTACTTCACAAAAAT-AAATATAAAGCAAAGACTAAAAC
*
12829651 TTATCATAGAAATTAAGGGAAGTTTTAAAAAG---AAAACGAAAGAAAGAATGATAAGTCTTAGT
64 TTATCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAAAACCAAAGAAAGAATGATAAGTCTTAGT
* *
12829713 CTTTGCTTTATACTTAGTATTGGCATGAAGCATGCAAA
129 CTTTGCTTTATACTTAGTCTTGACATGAAGCATGCAAA
* *
12829751 TGTGTCAATCTTTTTGCCCCTATCTTTACTTCACAAAA
1 TGTGTCAGTCTTTTTGCCCCCATCTTTACTTCACAAAA
12829789 TTAATAATAT
Statistics
Matches: 327, Mismatches: 36, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
163 29 0.09
164 67 0.20
165 1 0.00
166 71 0.22
167 75 0.23
168 67 0.20
169 17 0.05
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (166 bp):
TGTGTCAGTCTTTTTGCCCCCATCTTTACTTCACAAAAATAAATATAAAGCAAAGACTAAAACTT
ATCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAAAACCAAAGAAAGAATGATAAGTCTTAGTCT
TTGCTTTATACTTAGTCTTGACATGAAGCATGCAAA
Found at i:12830323 original size:35 final size:37
Alignment explanation
Indices: 12830255--12830330 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 37
12830245 TTAATATGTA
* *
12830255 TATAATATATATTTTTAAAATTTTATTATATATTATT
1 TATAATATATATTTTAAAAATTATATTATATATTATT
12830292 TATAAT-TA-ATTTTAAAAATTAT-TTAT-TA-TATT
1 TATAATATATATTTTAAAAATTATATTATATATTATT
*
12830324 TACAATA
1 TATAATA
12830331 CAATATGGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
32 9 0.26
33 2 0.06
34 4 0.11
35 12 0.34
36 2 0.06
37 6 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (37 bp):
TATAATATATATTTTAAAAATTATATTATATATTATT
Found at i:12832032 original size:22 final size:23
Alignment explanation
Indices: 12831990--12832033 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12831980 AATACATATG
*
12831990 AGGAAGTTGATCGAGAGAAGAAA
1 AGGAAATTGATCGAGAGAAGAAA
12832013 AGGAAATTGATCG-GAGAAGAA
1 AGGAAATTGATCGAGAGAAGAA
12832034 TAAGAAGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.48, C:0.05, G:0.34, T:0.14
Consensus pattern (23 bp):
AGGAAATTGATCGAGAGAAGAAA
Found at i:12837175 original size:26 final size:24
Alignment explanation
Indices: 12837135--12837187 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
12837125 TATTTGCATG
*
12837135 TATTAAAATATTCAATTAATATTAAT
1 TATTAAAATATTCAAAT-A-ATTAAT
12837161 TATTAAAATCA-TCAAATAATTAAT
1 TATTAAAAT-ATTCAAATAATTAAT
12837185 TAT
1 TAT
12837188 CTCACATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
25 1 0.04
26 14 0.56
27 1 0.04
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
TATTAAAATATTCAAATAATTAAT
Found at i:12838152 original size:168 final size:163
Alignment explanation
Indices: 12837622--12838223 Score: 592
Period size: 168 Copynumber: 3.6 Consensus size: 163
12837612 AACTTAAGAA
* * * * *
12837622 AATGATAAGTCTTTA-TCTTTGCTTTGTACTTAGTCTTGGTATGAAGCATGCCAATGTGTCAGTC
1 AATGATAAGTC-TTAGTCTTTGCTTTATACTTAGTCTTGGCATGAAACATGCAAATGTGTCAATC
* *
12837686 TTTTTGCCTCCATCTTTACTTTTATAAAAATAAGTATAAAGCAAAGATTAAGACTTATCATAGAA
65 TTTTTGCCTCCATCTTTAC-TTCACAAAAATAAGTATAAAGCAAAGATTAAGACTTATCATAGAA
* * *
12837751 ATTAAGAAAAATTTTTTAAAAG--AAAAAAAATGAATG
129 ATTAAG--AAA-GTTTTAAAAGAAAAAAAAAAAGAAAG
* * * * *
12837787 AATGACAAGTCCTAGTCTTTGCCTTATACTTAGTGTTGGCATGAAGCACATGCAAATGTGGT-AG
1 AATGATAAGTCTTAGTCTTTGCTTTATACTTAGTCTTGGCATGAA--ACATGCAAATGT-GTCAA
* * ** * *
12837851 TCTTTTTG-CTCCGATCTTTACTTCACAAAAAAAAAAGCATAAAATAAAGA--ATGACTTATCGT
63 TCTTTTTGCCTCC-ATCTTTACTTCAC--AAAAATAAGTATAAAGCAAAGATTAAGACTTATCAT
*
12837913 AGAAAGTAACGAAAGTTTTTAAAAAGAAAAAAAAAAAGAAAG
125 AGAAATTAA-GAAAG-TTTT-AAAAGAAAAAAAAAAAGAAAG
* * * * *
12837955 AATAAATTATAACTCTTAGTCTTTGCTTTATTCTTAGTTTTGGCATGAAACATACAAATGTGTCA
1 ----AATGATAAGTCTTAGTCTTTGCTTTATACTTAGTCTTGGCATGAAACATGCAAATGTGTCA
* *
12838020 ATCATTTTGCCT-CATCTTTACTTCACAAAAATAAGTATAAAGCAAAGATTAAGAGTTATCATAG
62 ATCTTTTTGCCTCCATCTTTACTTCACAAAAATAAGTATAAAGCAAAGATTAAGACTTATCATAG
*
12838084 AAATTAATGGAAGTTTTAAAAGGAAAAGTAAAACCAAAGAAAG
127 AAATTAA-GAAAGTTTTAAAA-GAAAA--AAAA--AAAGAAAG
* * * *
12838127 AATGATAAGTCTTAGTCTTTGCTTTACACTTAGCCTGGGCATGAAGCATGCAAATGTGTCAGAT-
1 AATGATAAGTCTTAGTCTTTGCTTTATACTTAGTCTTGGCATGAAACATGCAAATGTGTCA-ATC
* *
12838191 TTTTTGCCCCCATCTTTACTTAACAAAAATAAG
65 TTTTTGCCTCCATCTTTACTTCACAAAAATAAG
12838224 AATATTAGTG
Statistics
Matches: 358, Mismatches: 52, Indels: 50
0.78 0.11 0.11
Matches are distributed among these distances:
164 2 0.01
165 43 0.12
166 30 0.08
167 51 0.14
168 100 0.28
169 60 0.17
170 24 0.07
171 2 0.01
172 46 0.13
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (163 bp):
AATGATAAGTCTTAGTCTTTGCTTTATACTTAGTCTTGGCATGAAACATGCAAATGTGTCAATCT
TTTTGCCTCCATCTTTACTTCACAAAAATAAGTATAAAGCAAAGATTAAGACTTATCATAGAAAT
TAAGAAAGTTTTAAAAGAAAAAAAAAAAGAAAG
Found at i:12847254 original size:35 final size:36
Alignment explanation
Indices: 12847202--12847272 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
12847192 GGAGCCCATT
* *
12847202 TTTTTTTAACTTGAAACTATTAAAAATTAAATTTTA
1 TTTTTTTAACTTAAAACTATTAAAAATTAAAATTTA
*
12847238 TTTTTTT-ACTTAAAACTGTTAAAAATTAAAATTTA
1 TTTTTTTAACTTAAAACTATTAAAAATTAAAATTTA
12847273 ATATTTAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 25 0.78
36 7 0.22
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTTTTTAACTTAAAACTATTAAAAATTAAAATTTA
Found at i:12848123 original size:12 final size:12
Alignment explanation
Indices: 12848101--12848133 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
12848091 TAGTGTAGAG
12848101 ATATAATATATGT
1 ATAT-ATATATGT
12848114 ATATATATATGT
1 ATATATATATGT
12848126 ATATATAT
1 ATATATAT
12848134 CACACTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (12 bp):
ATATATATATGT
Found at i:12852555 original size:29 final size:31
Alignment explanation
Indices: 12852506--12852565 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
12852496 TGACTTGCAC
12852506 AAATTATAATAAAATATTTAATAT-GATATTT
1 AAATTATAATAAAATATTTAAT-TCGATATTT
*
12852537 AAATTTTAA-AAAAT-TTTAATTCGATATTT
1 AAATTATAATAAAATATTTAATTCGATATTT
12852566 GAACTAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 1 0.04
29 13 0.48
30 5 0.19
31 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (31 bp):
AAATTATAATAAAATATTTAATTCGATATTT
Found at i:12852636 original size:28 final size:28
Alignment explanation
Indices: 12852598--12852661 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
12852588 GAATCAAATT
*
12852598 AATTAATAAA-TTTATAA-TTTAAATATCA
1 AATTAAAAAATTTTA-AATTTTAAATAT-A
12852626 AATTAAAAAATTTTAAATTTTAAATATA
1 AATTAAAAAATTTTAAATTTTAAATATA
12852654 ATATTAAA
1 A-ATTAAA
12852662 TATTTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
AATTAAAAAATTTTAAATTTTAAATATA
Found at i:12852650 original size:29 final size:27
Alignment explanation
Indices: 12852598--12852661 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
12852588 GAATCAAATT
*
12852598 AATTAATAAATTTATAATTTAAATATCA
1 AATTAAAAAATTTATAATTTAAATAT-A
12852626 AATTAAAAAATTT-TAAATTTTAAATATA
1 AATTAAAAAATTTAT-AA-TTTAAATATA
12852654 ATATTAAA
1 A-ATTAAA
12852662 TATTTTATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 1 0.03
28 16 0.50
29 15 0.47
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTAAAAAATTTATAATTTAAATATA
Found at i:12852662 original size:19 final size:19
Alignment explanation
Indices: 12852637--12852680 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12852627 ATTAAAAAAT
12852637 TTTAAAT-TTTAAATATAA
1 TTTAAATATTTAAATATAA
* *
12852655 TATTAAATATTTTATTATAA
1 T-TTAAATATTTAAATATAA
12852675 TTTAAA
1 TTTAAA
12852681 ATTATTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAAATATTTAAATATAA
Found at i:12852675 original size:20 final size:17
Alignment explanation
Indices: 12852650--12852697 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 17
12852640 AAATTTTAAA
12852650 TATAATATTAAATATTTTAT
1 TATAATATTAAA-A--TTAT
12852670 TATAAT-TTAAAATTAT
1 TATAATATTAAAATTAT
12852686 TCATAATATTAA
1 T-ATAATATTAA
12852698 TTTTTGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
18 5 0.19
19 5 0.19
20 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAATATTAAAATTAT
Found at i:12857629 original size:12 final size:11
Alignment explanation
Indices: 12857598--12857642 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
12857588 CCTCCAAAAC
*
12857598 TTTAATTTTTA
1 TTTATTTTTTA
*
12857609 TTTACTTTTTA
1 TTTATTTTTTA
12857620 TTTAGTTTTTTAA
1 TTTA-TTTTTT-A
12857633 TTTATTTTTT
1 TTTATTTTTT
12857643 TAAATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 14 0.47
12 11 0.37
13 5 0.17
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTATTTTTTA
Found at i:12858207 original size:14 final size:14
Alignment explanation
Indices: 12858164--12858207 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
12858154 CTATATATGT
*
12858164 ATTTTATTTAAAAA
1 ATTTTATTTAATAA
*
12858178 ATATTATTTAAT--
1 ATTTTATTTAATAA
12858190 ATTTTATTTAATAA
1 ATTTTATTTAATAA
12858204 ATTT
1 ATTT
12858208 ATGTGTCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 11 0.44
14 14 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTATTTAATAA
Found at i:12858493 original size:21 final size:21
Alignment explanation
Indices: 12858452--12858494 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12858442 ATATATAAAA
*
12858452 AAATATATTTTATTATTTATT
1 AAATATATTTTATTATATATT
*
12858473 AAATTTATGTTTA-TATATATT
1 AAATATAT-TTTATTATATATT
12858494 A
1 A
12858495 TATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
AAATATATTTTATTATATATT
Found at i:12858890 original size:2 final size:2
Alignment explanation
Indices: 12858879--12858917 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
12858869 AGCATGCACT
* *
12858879 TA TA -A TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12858918 AATTATAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:12860280 original size:28 final size:29
Alignment explanation
Indices: 12860217--12860280 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 29
12860207 ATTCGATATT
12860217 TTAATATTTAATATTATAAATTTTAAAAAA
1 TTAA-ATTTAATATTATAAATTTTAAAAAA
*
12860247 TT-AATTTAA-ATT-TAAATATTTTAAAAA
1 TTAAATTTAATATTATAAAT-TTTAAAAAA
12860274 TTAAATT
1 TTAAATT
12860281 GATGCGAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 5 0.16
27 13 0.42
28 10 0.32
29 1 0.03
30 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TTAAATTTAATATTATAAATTTTAAAAAA
Found at i:12861312 original size:3 final size:3
Alignment explanation
Indices: 12861304--12861340 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12861294 TCTTACCCTT
12861304 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
12861341 GCTGCTGCTG
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:12865625 original size:44 final size:46
Alignment explanation
Indices: 12865549--12865635 Score: 124
Period size: 44 Copynumber: 1.9 Consensus size: 46
12865539 GACAAAAAAT
*
12865549 TTTTAGCATGACCTTTTGTTTCCTTTTTTCCCTCTAAATTTTTCTG
1 TTTTAGCATGACCTTTTGTTTCCTTTTTTCCCTCTAAAATTTTCTG
* * *
12865595 TTTTAGCATGA-GTTTT-TTTTCTTTTTTCCCTGTAAAATTTT
1 TTTTAGCATGACCTTTTGTTTCCTTTTTTCCCTCTAAAATTTT
12865636 AAAACGGCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 22 0.59
45 4 0.11
46 11 0.30
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.59
Consensus pattern (46 bp):
TTTTAGCATGACCTTTTGTTTCCTTTTTTCCCTCTAAAATTTTCTG
Found at i:12866326 original size:22 final size:22
Alignment explanation
Indices: 12866301--12866344 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12866291 TGTATATTTA
* *
12866301 TATTTGTATCTCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
*
12866323 TATTTATATCCCTATAATTAAG
1 TATTTATATCCCTAGAATTAAG
12866345 GACAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (22 bp):
TATTTATATCCCTAGAATTAAG
Found at i:12874980 original size:2 final size:2
Alignment explanation
Indices: 12874973--12875000 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12874963 GAAATCACTC
12874973 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
12875001 GAAAGGGAGA
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:12875206 original size:76 final size:76
Alignment explanation
Indices: 12875116--12875262 Score: 231
Period size: 76 Copynumber: 1.9 Consensus size: 76
12875106 CGTCGTACAC
* * *
12875116 ATATGTTTCTTGCTTTGCTTTACGTGTCTCATGATTCATGAAACCACTCAAGTCTCAGCGAAGGC
1 ATATGTTTCTTGCTTTGCTTCACGTGTCTCATGATTCATGAAACCACTCAAGTCTCAGAGAAGAC
12875181 TTGACTCTTCA
66 TTGACTCTTCA
* * * *
12875192 ATATGTTTCTTGCTTTGCTTCATGTGTTTCATGATTCTTGAAACCACTCAAGTCTCATAGAAGAC
1 ATATGTTTCTTGCTTTGCTTCACGTGTCTCATGATTCATGAAACCACTCAAGTCTCAGAGAAGAC
12875257 TTGACT
66 TTGACT
12875263 TCATCAAAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (76 bp):
ATATGTTTCTTGCTTTGCTTCACGTGTCTCATGATTCATGAAACCACTCAAGTCTCAGAGAAGAC
TTGACTCTTCA
Found at i:12879081 original size:15 final size:15
Alignment explanation
Indices: 12879043--12879081 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
12879033 TCTTGCTTTA
*
12879043 CTTTGTCTAATGTTG
1 CTTTGTCTAAAGTTG
*
12879058 -TTGGTCTAAAGTTG
1 CTTTGTCTAAAGTTG
12879072 CTTTGTCTAA
1 CTTTGTCTAA
12879082 GGTCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.49
Consensus pattern (15 bp):
CTTTGTCTAAAGTTG
Found at i:12879751 original size:19 final size:19
Alignment explanation
Indices: 12879711--12879752 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12879701 ACTTCTAAGT
* *
12879711 TTTTTTTTTTTGTCATTTA
1 TTTTTTTATTTGTCATTCA
12879730 TTTTTTTATTT-TCAGTTCA
1 TTTTTTTATTTGTCA-TTCA
12879749 TTTT
1 TTTT
12879753 CTAATTCGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTTTTATTTGTCATTCA
Found at i:12879956 original size:20 final size:19
Alignment explanation
Indices: 12879928--12879965 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12879918 TAAAACCTCA
12879928 AAATATAAGTTTTATATAAT
1 AAATATAAGTTTTA-ATAAT
*
12879948 AAATTTAAGTTTTAATAA
1 AAATATAAGTTTTAATAA
12879966 AATACACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
AAATATAAGTTTTAATAAT
Found at i:12880891 original size:12 final size:12
Alignment explanation
Indices: 12880874--12880898 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12880864 GTAAAAAAGA
12880874 ATATATATAAAT
1 ATATATATAAAT
12880886 ATATATATAAAT
1 ATATATATAAAT
12880898 A
1 A
12880899 ATAAAAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:12881069 original size:2 final size:2
Alignment explanation
Indices: 12881062--12881112 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
12881052 TAGATCTTTC
*
12881062 AT AT AT AT AT AT AT AT TT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
12881103 AC AT AT AT AT
1 AT AT AT AT AT
12881113 GGAAGGTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12881952 original size:26 final size:23
Alignment explanation
Indices: 12881895--12881968 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 23
12881885 CGTTTTGTAA
12881895 ATATAATAAATAATTTTAAAAAT
1 ATATAATAAATAATTTTAAAAAT
* *
12881918 -TAATTATAAATAATATATATATAAAT
1 AT-ATAATAAATAAT-T-T-TAAAAAT
*
12881944 ATATAATAAA-ATTTTTAAAAA-
1 ATATAATAAATAATTTTAAAAAT
12881965 ATAT
1 ATAT
12881969 TATACATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
21 4 0.10
22 6 0.15
23 12 0.29
24 2 0.05
25 3 0.07
26 13 0.32
27 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAATAAATAATTTTAAAAAT
Found at i:12882805 original size:42 final size:42
Alignment explanation
Indices: 12882759--12882846 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
12882749 TCTTTTTAAA
*
12882759 ACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTGCGTTAT
1 ACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTGCATTAT
12882801 ACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTGCATTAT
1 ACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTGCATTAT
12882843 ACTT
1 ACTT
12882847 ATTTTTGTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.23, C:0.19, G:0.10, T:0.48
Consensus pattern (42 bp):
ACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTGCATTAT
Found at i:12882995 original size:211 final size:212
Alignment explanation
Indices: 12882608--12883015 Score: 728
Period size: 211 Copynumber: 1.9 Consensus size: 212
12882598 AAAACTAAGT
* *
12882608 ATAAGTCTTAGTCTTTGTCGTTATACTTATTTTTGTGAAGTAAAGATGGGAACAAAAACACTGAC
1 ATAAGTCTTAGTCTTTGTCATTATACTTATTTTTGTGAAGCAAAGATGGGAACAAAAACACTGAC
* * *
12882673 ACATTTGCATGCTTCATGCCAAGACTGAGCATAAAGCAAAGACTAAGACTTATCATTCTTTCTTT
66 ACATTTGCATGCTTCATGCCAAGACTAAGCATAAAGCAAAGACTAAAACTTATCATTCTTTCTGT
*
12882738 GGTTTTACTTTTCTTTTTAAAACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTGCGTTATAC
131 GGTTTTACTTTTCTTTTTAAAACTTCCCTTAATTTCTATAATAAGTCTTAGTCTTTGCGTTATAC
12882803 TTCCCTTAATTTCTATG
196 TTCCCTTAATTTCTATG
**
12882820 ATAAGTCTTAGTCTTTG-CATTATACTTATTTTTGTGAAGCAAAGATGGGGGCAAAAACACTGAC
1 ATAAGTCTTAGTCTTTGTCATTATACTTATTTTTGTGAAGCAAAGATGGGAACAAAAACACTGAC
12882884 ACATTTGCATGCTTCATGCCAAGACTAAGCATAAAGCAAAGACTAAAACTTATCATTCTTTCTGT
66 ACATTTGCATGCTTCATGCCAAGACTAAGCATAAAGCAAAGACTAAAACTTATCATTCTTTCTGT
*
12882949 GGTTTTACTTTTCTTTTTAAAACTTCCCTTAATTTCTATAATAAGTCTTAGTCTTTGCTTTATAC
131 GGTTTTACTTTTCTTTTTAAAACTTCCCTTAATTTCTATAATAAGTCTTAGTCTTTGCGTTATAC
12883014 TT
196 TT
12883016 ATTTTTGTGA
Statistics
Matches: 187, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
211 170 0.91
212 17 0.09
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (212 bp):
ATAAGTCTTAGTCTTTGTCATTATACTTATTTTTGTGAAGCAAAGATGGGAACAAAAACACTGAC
ACATTTGCATGCTTCATGCCAAGACTAAGCATAAAGCAAAGACTAAAACTTATCATTCTTTCTGT
GGTTTTACTTTTCTTTTTAAAACTTCCCTTAATTTCTATAATAAGTCTTAGTCTTTGCGTTATAC
TTCCCTTAATTTCTATG
Found at i:12883080 original size:169 final size:169
Alignment explanation
Indices: 12882801--12883108 Score: 553
Period size: 169 Copynumber: 1.8 Consensus size: 169
12882791 TTTGCGTTAT
*
12882801 ACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTGCATTATACTTATTTTTGTGAAGCAAAGAT
1 ACTTCCCTTAATTTCTATAATAAGTCTTAGTCTTTGCATTATACTTATTTTTGTGAAGCAAAGAT
12882866 GGGGGCAAAAACACTGACACATTTGCATGCTTCATGCCAAGACTAAGCATAAAGCAAAGACTAAA
66 GGGGGCAAAAACACTGACACATTTGCATGCTTCATGCCAAGACTAAGCATAAAGCAAAGACTAAA
12882931 ACTTATCATTCTTTCTGTGGTTTTACTTTTCTTTTTAAA
131 ACTTATCATTCTTTCTGTGGTTTTACTTTTCTTTTTAAA
* *
12882970 ACTTCCCTTAATTTCTATAATAAGTCTTAGTCTTTGCTTTATACTTATTTTTGTGAAGTAAAGAT
1 ACTTCCCTTAATTTCTATAATAAGTCTTAGTCTTTGCATTATACTTATTTTTGTGAAGCAAAGAT
* * * *
12883035 GGGGGCAAAAACACTGACATATTTGCATGCTTCATGCCAAGACTAAGTATAGAGCAAAGACTAAG
66 GGGGGCAAAAACACTGACACATTTGCATGCTTCATGCCAAGACTAAGCATAAAGCAAAGACTAAA
12883100 ACTTATCAT
131 ACTTATCAT
12883109 GTTTGTGAAG
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
169 132 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (169 bp):
ACTTCCCTTAATTTCTATAATAAGTCTTAGTCTTTGCATTATACTTATTTTTGTGAAGCAAAGAT
GGGGGCAAAAACACTGACACATTTGCATGCTTCATGCCAAGACTAAGCATAAAGCAAAGACTAAA
ACTTATCATTCTTTCTGTGGTTTTACTTTTCTTTTTAAA
Found at i:12883663 original size:3 final size:3
Alignment explanation
Indices: 12883655--12883689 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12883645 ATTTTAAGTA
12883655 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12883690 ATTTTAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:12893681 original size:150 final size:149
Alignment explanation
Indices: 12893455--12893753 Score: 469
Period size: 150 Copynumber: 2.0 Consensus size: 149
12893445 ACACATTTGC
* * * *
12893455 ATGCTTTATGCCAAAGACTAAATCTAAAGCAAATACTAAGACTTGTCATTCTTTCTTTGGTTTTA
1 ATGCTTCATGCCAAAGACTAAATATAAAGCAAAGACTAAGACTTATCATTCTTTCTTTGGTTTTA
12893520 CTATTCCTTTTAAAACTTCCCTTAATTTCTATTAAGATAAGTCTTAGTCTTTCCTTTATACTTAT
66 CTATTCCTTTTAAAACTTCCCTTAATTTCTA-T--GATAAGTCTTAGTCTTTCCTTTATACTTAT
12893585 TTTTGT-GAAGTAAAGAT-AGGG
128 TTTTGTAG-AGTAAAGATGAGGG
*
12893606 ATGCTTCATGCC-AAGACTAAATATAAAGCAAAGACTAAGACTTATCATTTTTTCTTTGGTTTTA
1 ATGCTTCATGCCAAAGACTAAATATAAAGCAAAGACTAAGACTTATCATTCTTTCTTTGGTTTTA
* * *
12893670 CTTTTCTTTTTAAAACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTGCTTTATACTTATTTT
66 CTATTCCTTTTAAAACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTCCTTTATACTTATTTT
12893735 TGTAGAGTAAAGATGAGGG
131 TGTAGAGTAAAGATGAGGG
12893754 CAAAAAGATT
Statistics
Matches: 138, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
147 44 0.32
148 5 0.04
149 1 0.01
150 77 0.56
151 11 0.08
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (149 bp):
ATGCTTCATGCCAAAGACTAAATATAAAGCAAAGACTAAGACTTATCATTCTTTCTTTGGTTTTA
CTATTCCTTTTAAAACTTCCCTTAATTTCTATGATAAGTCTTAGTCTTTCCTTTATACTTATTTT
TGTAGAGTAAAGATGAGGG
Found at i:12911635 original size:60 final size:58
Alignment explanation
Indices: 12911492--12911844 Score: 311
Period size: 60 Copynumber: 6.0 Consensus size: 58
12911482 TGCTTTTATA
* * ** ***
12911492 CAAGAAAAATTGATACTTTCAACTTTTCCTTAATG--CATTTTAAG-GTTTTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTTAA-GAATATTTTTTGAAAATTTTATTTT
* *
12911548 CAAGGAAAATTGATACTTTCAATTTTTCCTTAAGAATATTTTTTCGTCAAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAGAATATTTTTT-G-AAAATTTTATTTT
* * * * *
12911608 TAAGAAAAATTGGTA-TTTCCAACTTTTCCTCAAGAAATGTTTTTTTGAAAATTTTATTTT
1 CAAGGAAAATTGATACTTT-CAACTTTTCCTTAAG-AAT-ATTTTTTGAAAATTTTATTTT
* *
12911668 CAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAGAATATTTTTTG-AAAATTTTATTTT
* * * * * * * ** *
12911727 TAAGGGAAGTTGATACTTTTAACTTTCCCTCAAAAATATTTTTAAAACAATTTTTATGTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTTAAGAATATTTTTTGAA-AA-TTTTATTTT
* * * *
12911787 CAAAGAAAATTGATACATTCAAC-TTTCCTTCAAAAATATTTTTTCAAAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTCCTT-AAGAATATTTTTTGAAAATTTTATTTT
12911845 AAAGAGATTA
Statistics
Matches: 241, Mismatches: 43, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
55 1 0.00
56 31 0.13
57 5 0.02
58 18 0.07
59 64 0.27
60 109 0.45
61 7 0.03
62 6 0.02
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (58 bp):
CAAGGAAAATTGATACTTTCAACTTTTCCTTAAGAATATTTTTTGAAAATTTTATTTT
Found at i:12911740 original size:59 final size:59
Alignment explanation
Indices: 12911539--12911844 Score: 325
Period size: 60 Copynumber: 5.2 Consensus size: 59
12911529 TTTTAAGGTT
* * **
12911539 TTTTATTTTCAAGGAAAATTGATACTTTCAATTTTTCCTTAAGAATATTTTTTCGTCAAA
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTT-GAAAAA
* * * * *
12911599 TTTTATTTTTAAGAAAAATTGGTA-TTTCCAACTTTTCCTCAAGAAATGTTTTTTTG-AAAA
1 TTTTATTTTCAAGGAAAATTGATACTTT-CAACTTTTCCTTAA-AAAT-ATTTTTTGAAAAA
*
12911659 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAAA
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTGAAAAA
* * * * * * *
12911718 TTTTATTTTTAAGGGAAGTTGATACTTTTAACTTTCCCTCAAAAATA-TTTTTAAAACAA
1 TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTGAAA-AA
* * * *
12911777 TTTTTATGTTCAAAGAAAATTGATACATTCAAC-TTTCCTTCAAAAATATTTTTT-CAAAA
1 -TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTT-AAAAATATTTTTTGAAAAA
12911836 TTTTATTTT
1 TTTTATTTT
12911845 AAAGAGATTA
Statistics
Matches: 204, Mismatches: 33, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
58 23 0.11
59 60 0.29
60 103 0.50
61 12 0.06
62 6 0.03
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.47
Consensus pattern (59 bp):
TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTGAAAAA
Found at i:12911795 original size:119 final size:120
Alignment explanation
Indices: 12911538--12911849 Score: 368
Period size: 119 Copynumber: 2.6 Consensus size: 120
12911528 ATTTTAAGGT
* **
12911538 TTTTTATTTTCAAGGAAAATTGATACTTTCAA-TTTTTCCTTAAGAATATTTTTTCGTCAAATTT
1 TTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTT-CTTAAAAATATTTTTT-GAAAAATTT
* * * **
12911602 TATTTTTAAGAAAAATTGGTATTTCCAACTTTTCCTCAAGAAATGTTTTTTTGAAAA
64 TATTTTTAAGAAAAATTGATATTTCCAACTTTCCCTCAAGAAATGATTTTTAAAAAA
12911659 -TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAAATTTTA
1 TTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAAATTTTA
** * *
12911723 TTTTTAAGGGAAGTTGATACTTT-TAACTTTCCCTCAA-AAAT-ATTTTTAAAACAA
66 TTTTTAAGAAAAATTGATA-TTTCCAACTTTCCCTCAAGAAATGATTTTTAAAA-AA
* * * * *
12911777 TTTTTATGTTCAAAGAAAATTGATACATTCAAC-TTTCCTTCAAAAATATTTTTT-CAAAATTTT
1 TTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTT-AAAAATATTTTTTGAAAAATTTT
*
12911840 ATTTTAAAGA
65 ATTTTTAAGA
12911850 GATTATTTAA
Statistics
Matches: 167, Mismatches: 19, Indels: 13
0.84 0.10 0.07
Matches are distributed among these distances:
117 7 0.04
118 28 0.17
119 78 0.47
120 49 0.29
121 5 0.03
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (120 bp):
TTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATATTTTTTGAAAAATTTTA
TTTTTAAGAAAAATTGATATTTCCAACTTTCCCTCAAGAAATGATTTTTAAAAAA
Found at i:12917477 original size:3 final size:3
Alignment explanation
Indices: 12917471--12917525 Score: 92
Period size: 3 Copynumber: 18.0 Consensus size: 3
12917461 AAATATTATT
*
12917471 ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12917519 ATTA ATA
1 A-TA ATA
12917526 TACTTAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:12918088 original size:34 final size:34
Alignment explanation
Indices: 12918049--12918152 Score: 97
Period size: 34 Copynumber: 3.1 Consensus size: 34
12918039 CAAAATTTTT
*
12918049 AAGCTTCCAGATATGCAAATTTAGAAACTTTTAA
1 AAGCTTCTAGATATGCAAATTTAGAAACTTTTAA
* * *
12918083 AAGCTTTTGGATATGC--ATTCTAGAGACTTTTAA
1 AAGCTTCTAGATATGCAAATT-TAGAAACTTTTAA
** * *
12918116 GTGCTTCTAGATTTACAAATTT-GAAAACTTTTAA
1 AAGCTTCTAGATATGCAAATTTAG-AAACTTTTAA
12918150 AAG
1 AAG
12918153 TTTTCAAATT
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
32 3 0.06
33 23 0.43
34 24 0.45
35 3 0.06
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (34 bp):
AAGCTTCTAGATATGCAAATTTAGAAACTTTTAA
Found at i:12918938 original size:24 final size:23
Alignment explanation
Indices: 12918907--12918963 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
12918897 ACTTTTTGAC
*
12918907 ATTAAAAATCATGAAATTTTAAT
1 ATTAAAAATAATGAAATTTTAAT
* * *
12918930 CTTATAAAAAAATTAAATTTTAAT
1 ATTA-AAAATAATGAAATTTTAAT
12918954 ATTAAAAATA
1 ATTAAAAATA
12918964 TTAAAGTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (23 bp):
ATTAAAAATAATGAAATTTTAAT
Found at i:12919504 original size:16 final size:16
Alignment explanation
Indices: 12919483--12919517 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12919473 TATATTAATA
12919483 ATATATACAAATATAT
1 ATATATACAAATATAT
* *
12919499 ATATATATAAATATCT
1 ATATATACAAATATAT
12919515 ATA
1 ATA
12919518 AATTATGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATACAAATATAT
Found at i:12919867 original size:93 final size:92
Alignment explanation
Indices: 12919762--12919947 Score: 363
Period size: 92 Copynumber: 2.0 Consensus size: 92
12919752 ATTCAAGGAC
12919762 TTTGAAAAAAAAATAAAGACAATCTTCAAATTCTAAAGTTTTTCTTTCATCCTATTATTTTCAAA
1 TTTGAAAAAAAAATAAAGACAATCTTCAAATTCTAAA-TTTTTCTTTCATCCTATTATTTTCAAA
12919827 TAATTGGAAATTTGAGTATTTGATTGAA
65 TAATTGGAAATTTGAGTATTTGATTGAA
12919855 TTTGAAAAAAAAATAAAGACAATCTTCAAATTCTAAATTTTTCTTTCATCCTATTATTTTCAAAT
1 TTTGAAAAAAAAATAAAGACAATCTTCAAATTCTAAATTTTTCTTTCATCCTATTATTTTCAAAT
12919920 AATTGGAAATTTGAGTATTTGATTGAA
66 AATTGGAAATTTGAGTATTTGATTGAA
12919947 T
1 T
12919948 ACTACCATCA
Statistics
Matches: 93, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
92 56 0.60
93 37 0.40
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (92 bp):
TTTGAAAAAAAAATAAAGACAATCTTCAAATTCTAAATTTTTCTTTCATCCTATTATTTTCAAAT
AATTGGAAATTTGAGTATTTGATTGAA
Found at i:12920163 original size:100 final size:98
Alignment explanation
Indices: 12920047--12920231 Score: 309
Period size: 100 Copynumber: 1.9 Consensus size: 98
12920037 GATGATTAAT
*
12920047 TATAATTAGATTTCATTTGGTTTGTA-TTTTTTTCGTTTACTATTTGTTTTTTGTTTTCAATTCA
1 TATAATTAGATTTCATTTGGTTTGTATTTTTTTTCGTTTACTATTTG-TTTTTGTTCTCAATTCA
12920111 TTTATTAAAAAAAATAAAAACCCTAAACTGAAAAA
65 TTTATT-AAAAAAATAAAAACCCTAAACTGAAAAA
* *
12920146 TATAATTTAGATTTCATTTGGTTTGTATTTTTTTTCTTTTACTATTTGTTTTTGTTCTCAGTTCA
1 TATAA-TTAGATTTCATTTGGTTTGTATTTTTTTTCGTTTACTATTTGTTTTTGTTCTCAATTCA
12920211 TTTATTAAAAAAATAAAAACC
65 TTTATTAAAAAAATAAAAACC
12920232 AAAAGCATCC
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
99 20 0.25
100 42 0.52
101 19 0.23
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.51
Consensus pattern (98 bp):
TATAATTAGATTTCATTTGGTTTGTATTTTTTTTCGTTTACTATTTGTTTTTGTTCTCAATTCAT
TTATTAAAAAAATAAAAACCCTAAACTGAAAAA
Found at i:12933640 original size:4 final size:4
Alignment explanation
Indices: 12933626--12933656 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
12933616 TTTTAGTGTA
*
12933626 TATG GATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
12933657 ATGTATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:12942239 original size:169 final size:168
Alignment explanation
Indices: 12941960--12942339 Score: 609
Period size: 169 Copynumber: 2.2 Consensus size: 168
12941950 AAGATGAAAG
*
12941960 TGTGTCAATCTTTTTGCCCTCATCTTTAC-TCTACAAAAATAAGTATAAAGCAAAGACTAAGACT
1 TGTGTCAGTCTTTTTGCCC-CATCTTTACTTC-ACAAAAATAAGTATAAAGCAAAGACTAAGACT
* *
12942024 TATCATAGAAATTAAGGGAGGTTTTAAAAAGAAAAGTAAAACCAAAGAAAAAATGATAAGTCTTA
64 TATCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAGTAAAACCAAAGAAAAAATGACAAGTCTTA
* * *
12942089 GTCTTTGCTTTATACTTAGTCTTGGCATGAAGCATGCAAA
129 GTATTTGCTTTAGACTTAGTCTTGGCATAAAGCATGCAAA
*
12942129 TGTGTCAGTCTTTTTGTCCCCATCTTTACTTCACAAAAATAAGTATAAAGGAAAGACTAAGACTT
1 TGTGTCAGTCTTTTTG-CCCCATCTTTACTTCACAAAAATAAGTATAAAGCAAAGACTAAGACTT
* * *
12942194 ATCATAGAAATTAAGGGAAGTTTTAAAAGGAATAGTAAAACCAAAGAAAGAATGACAAGTCTTAG
65 ATCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAGTAAAACCAAAGAAAAAATGACAAGTCTTAG
*
12942259 TATTTGCTTTAGATTTAGTCTTGGCATAAAGCATGCAAA
130 TATTTGCTTTAGACTTAGTCTTGGCATAAAGCATGCAAA
*
12942298 TGTGTTAAGTCTTTTTGCCCCATCTTTACTTCACAAAAATAA
1 TGTG-TCAGTCTTTTTGCCCCATCTTTACTTCACAAAAATAA
12942340 TAATATTAGC
Statistics
Matches: 196, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
169 180 0.92
170 16 0.08
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (168 bp):
TGTGTCAGTCTTTTTGCCCCATCTTTACTTCACAAAAATAAGTATAAAGCAAAGACTAAGACTTA
TCATAGAAATTAAGGGAAGTTTTAAAAAGAAAAGTAAAACCAAAGAAAAAATGACAAGTCTTAGT
ATTTGCTTTAGACTTAGTCTTGGCATAAAGCATGCAAA
Found at i:12951871 original size:3 final size:3
Alignment explanation
Indices: 12951863--12951904 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
12951853 AGACTAAAGT
12951863 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12951905 TAAATATACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12952451 original size:34 final size:34
Alignment explanation
Indices: 12952412--12952497 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
12952402 AGAAAATTTT
* *
12952412 AAGCTTCTAGATATGCAAATCCGGAAACTTTTAA
1 AAGCTTCTAGATATACAAATCCAGAAACTTTTAA
* * * **
12952446 AAGCTTTTGGATATACAAATCTAGAGGCTTTTAA
1 AAGCTTCTAGATATACAAATCCAGAAACTTTTAA
* *
12952480 GAGCTTCTAGATTTACAA
1 AAGCTTCTAGATATACAA
12952498 CTATGAAAAC
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (34 bp):
AAGCTTCTAGATATACAAATCCAGAAACTTTTAA
Found at i:12954239 original size:32 final size:32
Alignment explanation
Indices: 12954198--12954260 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
12954188 TTTTTCTTTC
12954198 ATCCTATTATTTTCAAATAATCAAAAATTTAG
1 ATCCTATTATTTTCAAATAATCAAAAATTTAG
** *
12954230 ATCCTATTATTTTTGAATAATTAAAAATTTA
1 ATCCTATTATTTTCAAATAATCAAAAATTTA
12954261 AGTATCTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (32 bp):
ATCCTATTATTTTCAAATAATCAAAAATTTAG
Found at i:12954549 original size:100 final size:99
Alignment explanation
Indices: 12954374--12954559 Score: 259
Period size: 99 Copynumber: 1.9 Consensus size: 99
12954364 GATGATTAAT
****
12954374 TATAATATAGATTTCATTTGGTTTGTATTTTTTTCCTTTACTATTTGTTTTTTGTTTTCAATTCA
1 TATAATATAGATTTCATTTGGTTTGTATTTTTTTCCTTTACTATTTGTTTTAAAATTTCAATTCA
12954439 TTTATTAAAAAAAATAAAAACCCTAAACTGAAAAA
66 TTTATT-AAAAAAATAAAAACCCTAAACTGAAAAA
* * *
12954474 TATAATTTAGATTTCGTTTGGTTTGTATTTTTTTTCTTTTACTA-TT-TTTTAAAATTTCAATTC
1 TATAATATAGATTTCATTTGGTTTGTA-TTTTTTTCCTTTACTATTTGTTTTAAAATTTCAATTC
*
12954537 ATTTATTGAAAAATATAAAAACC
65 ATTTATT-AAAAAAATAAAAACC
12954560 AAAGGCATCC
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
99 34 0.45
100 27 0.36
101 15 0.20
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (99 bp):
TATAATATAGATTTCATTTGGTTTGTATTTTTTTCCTTTACTATTTGTTTTAAAATTTCAATTCA
TTTATTAAAAAAATAAAAACCCTAAACTGAAAAA
Found at i:12960574 original size:19 final size:19
Alignment explanation
Indices: 12960547--12960583 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12960537 CGACTACCAG
*
12960547 ACCAGGAATTACATTAACA
1 ACCAAGAATTACATTAACA
12960566 ACCAAGAATTACATTAAC
1 ACCAAGAATTACATTAAC
12960584 GAAATCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.22
Consensus pattern (19 bp):
ACCAAGAATTACATTAACA
Found at i:12963930 original size:21 final size:20
Alignment explanation
Indices: 12963904--12963946 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
12963894 TTTACCTTGC
*
12963904 TCAGATTGTTGAGGTTCTGTT
1 TCAGATTGCTGAGGTTCT-TT
12963925 TCAGATTGCTGAGGTTCTTT
1 TCAGATTGCTGAGGTTCTTT
12963945 TC
1 TC
12963947 CTGGCTACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.14, C:0.14, G:0.26, T:0.47
Consensus pattern (20 bp):
TCAGATTGCTGAGGTTCTTT
Found at i:12964492 original size:31 final size:31
Alignment explanation
Indices: 12964457--12964521 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
12964447 ATCAGAATTG
*
12964457 GAATTGGATAGGAATCGACTGAAGGATTGAA
1 GAATTGGATAGGAATCGACTGAAGGATTAAA
*
12964488 GAATTGGATATGAATCGACTGAAGGATTAAA
1 GAATTGGATAGGAATCGACTGAAGGATTAAA
12964519 GAA
1 GAA
12964522 CGAAGGAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (31 bp):
GAATTGGATAGGAATCGACTGAAGGATTAAA
Found at i:12977287 original size:12 final size:12
Alignment explanation
Indices: 12977242--12977274 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
12977232 AATACTGTGC
12977242 TTAAAAAAATAT
1 TTAAAAAAATAT
12977254 TTAAAAAAATAT
1 TTAAAAAAATAT
12977266 TTAAAAAAA
1 TTAAAAAAA
12977275 AATATATTTA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TTAAAAAAATAT
Found at i:12979861 original size:239 final size:238
Alignment explanation
Indices: 12979430--12979889 Score: 705
Period size: 239 Copynumber: 1.9 Consensus size: 238
12979420 GCAAAATATA
*
12979430 AAAAAAAAATTCACAATCATAAATAACATTTTTTTCAATCAAATATTTTTTCTTATTATATGTTA
1 AAAAAAAAATTCACAATCATAAATAACATTTTTTTCAACCAAATATTTTTTCTTATTATATGTTA
*
12979495 CATGTTTTTAATATAACATTTTTCGTATTATAATTTTGAATTTTATTTTTATATATTGCACGTAA
66 CATGTTCTTAATATAACATTTTTCGTATTATAATTTTGAATTTTATTTTTATATATTGCACGTAA
12979560 AAATCTTTTTATATATTATTAACATATTTTATATATTTCAAGAAAAATTATTATTATAAATAATT
131 AAATCTTTTTATATATTATTAACATATTTTATATATTT-AAGAAAAATTATTATTATAAATAATT
12979625 ATTTTATGTGAGTATTAACTTATTATATTTACATGCTCTTACATG
195 -TTTTATGTGAGTATTAACTTATTATATTTACATGCTCTTACATG
* *
12979670 AAAACAAAATTCACAATTATAAATAACATTTTTTTCAACCAAATATTTTTT-TTATTATATGTTA
1 AAAAAAAAATTCACAATCATAAATAACATTTTTTTCAACCAAATATTTTTTCTTATTATATGTTA
** *
12979734 CATGTTCTTGTTATAACAATTTTTTTCTTATTATAATTTTGAATTTTATTTTTATATATTGCAC-
66 CATGTTCTTAATATAAC-A--TTTTTCGTATTATAATTTTGAATTTTATTTTTATATATTGCACG
* * **
12979798 TTAAAAT-TTTTTATATATTATT-ATATATTTTATATATAATT-TTAAAAATTATTATTATAAAT
128 TAAAAATCTTTTTATATATTATTAACATATTTTATATAT--TTAAGAAAAATTATTATTATAAAT
**
12979860 AATTTTTTATGTGAGTATTTGCTTATTATA
191 AATTTTTTATGTGAGTATTAACTTATTATA
12979890 AATAACATTT
Statistics
Matches: 202, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
238 24 0.12
239 64 0.32
240 64 0.32
241 8 0.04
242 42 0.21
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (238 bp):
AAAAAAAAATTCACAATCATAAATAACATTTTTTTCAACCAAATATTTTTTCTTATTATATGTTA
CATGTTCTTAATATAACATTTTTCGTATTATAATTTTGAATTTTATTTTTATATATTGCACGTAA
AAATCTTTTTATATATTATTAACATATTTTATATATTTAAGAAAAATTATTATTATAAATAATTT
TTTATGTGAGTATTAACTTATTATATTTACATGCTCTTACATG
Found at i:12979990 original size:195 final size:202
Alignment explanation
Indices: 12979685--12980090 Score: 616
Period size: 195 Copynumber: 2.0 Consensus size: 202
12979675 AAAATTCACA
*
12979685 ATTATAAATAACATTTTTTTCAACCAAATATTTTTTTTATTATATGTTACATGTTCTTGTTATAA
1 ATTATAAATAACATTTTTTTCAACCAAATATTTTTTTTATTATATGTTACATGTTCTTATTATAA
* * *
12979750 CAATTTTTTTCTTATTATAATTTTGAATTTTATTTTTATATATTGCA-CTTAAA-ATTTTTTATA
66 CAATTTTTTTCTTACTATAATTTTGAATTTTATTCTTATATATTGCACCTAAAATATTTTTTATA
** *
12979813 TATTATTATATATTTTATATATAATTTT-A-AAAATTATTATT-ATAAATAATT-TTTTATGTGA
131 TATTATTA-ATAAATTAT-TAT-ATTTTAAGAAAATTATTATTAAAAAATAATTATTTTATGTGA
12979874 GTATTTGCTT
193 GTATTTGCTT
12979884 ATTATAAATAACATTTTTTTCAA-CAAAT-TTTTTTTTATTATATGTTACATGTTCTTATTATAA
1 ATTATAAATAACATTTTTTTCAACCAAATATTTTTTTTATTATATGTTACATGTTCTTATTATAA
*
12979947 C-A-TTTTTTCTTACTATAATTTTGAATTTTGTTCTTATATATTGCACCTAAAATTATTTTTTAT
66 CAATTTTTTTCTTACTATAATTTTGAATTTTATTCTTATATATTGCACCTAAAA-TATTTTTTAT
12980010 ATATTATTAATAAATTATTATATTTTAAGAGAAAATTATTATTAAAAAATAATTATTTTATGTGA
130 ATATTATTAATAAATTATTATATTTT-A-AGAAAATTATTATTAAAAAATAATTATTTTATGTGA
12980075 GTATTTGCTT
193 GTATTTGCTT
12980085 ATTATA
1 ATTATA
12980091 TGTTACACAG
Statistics
Matches: 190, Mismatches: 8, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
195 45 0.24
196 9 0.05
197 42 0.22
198 24 0.13
199 35 0.18
200 9 0.05
201 26 0.14
ACGTcount: A:0.35, C:0.06, G:0.05, T:0.54
Consensus pattern (202 bp):
ATTATAAATAACATTTTTTTCAACCAAATATTTTTTTTATTATATGTTACATGTTCTTATTATAA
CAATTTTTTTCTTACTATAATTTTGAATTTTATTCTTATATATTGCACCTAAAATATTTTTTATA
TATTATTAATAAATTATTATATTTTAAGAAAATTATTATTAAAAAATAATTATTTTATGTGAGTA
TTTGCTT
Found at i:12980091 original size:165 final size:167
Alignment explanation
Indices: 12979918--12980247 Score: 426
Period size: 167 Copynumber: 2.0 Consensus size: 167
12979908 AAATTTTTTT
* * *
12979918 TTATTATATGTTACA-TG-TTCTTATTATAACATTTTTTCTTACTATAATTTTGAATTTTGTTCT
1 TTATTATATGTTACACAGTTTCTTATTATAACA-TTTTTCTTACTATAA-TGTGAAGTTTGTTCT
12979981 TATATATTGCACCTAAAAT-TATTTTT-T-ATATATTATTAATAAA--T-TATTATATTTTAAGA
64 TATATATTGCACCTAAAATCT-TTTTTATAATATATTATTAATAAATTTATATTAT-TTTTAA-A
* *
12980040 GAAAATTATT-ATTAAAAAATAATTATTTTATGTGAGTATTTGC
126 -AAAATTATTAATT-AAAAATAATTATTTTATATGAATATTTGC
* *
12980083 TTATTATATGTTACACAGTTTCTTATTATAACATTTTTCTTATTATAATGTGAAGTTTGTTTTTA
1 TTATTATATGTTACACAGTTTCTTATTATAACATTTTTCTTACTATAATGTGAAGTTTGTTCTTA
* * * *
12980148 TATGTTGCACCTAAAATCTTTTTTATAATATATTATTAATATATTTATATTATTTTTTAAAAATT
66 TATATTGCACCTAAAATCTTTTTTATAATATATTATTAATAAATTTATATTATTTTTAAAAAAAT
*
12980213 TATTAATTATAAATAATTATTTTATATGAATATTT
131 TATTAATTAAAAATAATTATTTTATATGAATATTT
12980248 AAGGATATTG
Statistics
Matches: 144, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
165 50 0.35
166 17 0.12
167 61 0.42
168 4 0.03
169 6 0.04
170 6 0.04
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (167 bp):
TTATTATATGTTACACAGTTTCTTATTATAACATTTTTCTTACTATAATGTGAAGTTTGTTCTTA
TATATTGCACCTAAAATCTTTTTTATAATATATTATTAATAAATTTATATTATTTTTAAAAAAAT
TATTAATTAAAAATAATTATTTTATATGAATATTTGC
Found at i:12983269 original size:31 final size:31
Alignment explanation
Indices: 12983228--12983292 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
12983218 TACTCCTTCG
*
12983228 TTCTTTAATCCTTCAGTCGATTCATACCCAA
1 TTCTTCAATCCTTCAGTCGATTCATACCCAA
* *
12983259 TTCTTCAATCCTTCAGTCGATTCCTATCCAA
1 TTCTTCAATCCTTCAGTCGATTCATACCCAA
12983290 TTC
1 TTC
12983293 CAATTCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.31, G:0.06, T:0.40
Consensus pattern (31 bp):
TTCTTCAATCCTTCAGTCGATTCATACCCAA
Found at i:12983830 original size:21 final size:20
Alignment explanation
Indices: 12983802--12983844 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
12983792 CAGTAGCCAG
*
12983802 GAAAAGAACCTCAGCAATCT
1 GAAAAGAACCTCAACAATCT
12983822 GAAACAGAACCTCAACAATCT
1 GAAA-AGAACCTCAACAATCT
12983843 GA
1 GA
12983845 GCAAGGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.47, C:0.26, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAAAGAACCTCAACAATCT
Found at i:12987159 original size:19 final size:19
Alignment explanation
Indices: 12987135--12987171 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12987125 CATTGATTTC
*
12987135 GTTAATGTAATTCTTGGTT
1 GTTAATGTAATTCCTGGTT
12987154 GTTAATGTAATTCCTGGT
1 GTTAATGTAATTCCTGGT
12987172 CTGGTAGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.49
Consensus pattern (19 bp):
GTTAATGTAATTCCTGGTT
Found at i:12992741 original size:15 final size:13
Alignment explanation
Indices: 12992707--12992737 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12992697 GAATAATATA
12992707 TTAT-TTTAATTT
1 TTATATTTAATTT
12992719 TTATATTTAATTT
1 TTATATTTAATTT
12992732 TTATAT
1 TTATAT
12992738 ATTTTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATATTTAATTT
Found at i:12993310 original size:98 final size:99
Alignment explanation
Indices: 12993192--12993376 Score: 257
Period size: 99 Copynumber: 1.9 Consensus size: 99
12993182 GGATGCCTTT
****
12993192 GGTTTTTATATTTTTCAATAAATGAATTGAAA-TTTTAAA-AAATAGTAAAAGAAAAAAAATACA
1 GGTTTTTATATTTTTCAATAAATGAATTGAAAGCAAAAAATAAATAGT-AAAGAAAAAAAATACA
12993255 AACCAAACGAAATCTAAATTATATTTTTCAGTTAG
65 AACCAAACGAAATCTAAATTATATTTTTCAGTTAG
* * * *
12993290 GGTTTTTATTTTTTTTAATAAATGAATTGAAAGCAAAAAATAAATAGTAAAGGAAAAAAATCCAA
1 GGTTTTTATATTTTTCAATAAATGAATTGAAAGCAAAAAATAAATAGTAAAGAAAAAAAATACAA
* *
12993355 ACCAAATGAAATCTATATTATA
66 ACCAAACGAAATCTAAATTATA
12993377 ATTAATCATC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
98 30 0.40
99 38 0.51
100 7 0.09
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.34
Consensus pattern (99 bp):
GGTTTTTATATTTTTCAATAAATGAATTGAAAGCAAAAAATAAATAGTAAAGAAAAAAAATACAA
ACCAAACGAAATCTAAATTATATTTTTCAGTTAG
Found at i:12993528 original size:32 final size:32
Alignment explanation
Indices: 12993490--12993552 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
12993480 ATCAGATACT
*
12993490 TAAATTTTTAATTATTCAAAAATAATAGGATC
1 TAAATTTTTAATTATTCAAAAATAAGAGGATC
* **
12993522 TAAATTTTTGATTATTTGAAAATAAGAGGAT
1 TAAATTTTTAATTATTCAAAAATAAGAGGAT
12993553 GAAAGATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.41
Consensus pattern (32 bp):
TAAATTTTTAATTATTCAAAAATAAGAGGATC
Found at i:12993853 original size:10 final size:10
Alignment explanation
Indices: 12993840--12993872 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
12993830 ATTTCACATA
*
12993840 ATTTATAGAT
1 ATTTATATAT
12993850 ATTTATATAT
1 ATTTATATAT
12993860 ATTTATATAT
1 ATTTATATAT
12993870 ATT
1 ATT
12993873 ATTAGTAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (10 bp):
ATTTATATAT
Found at i:12994485 original size:24 final size:23
Alignment explanation
Indices: 12994428--12994488 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
12994418 AAACTTTGAT
12994428 TTTAAT-ATTTTTAAGATTAAAA
1 TTTAATGATTTTTAAGATTAAAA
** *
12994450 TTTAATTTTTTTATAAGATTAAAG
1 TTTAATGATTTT-TAAGATTAAAA
*
12994474 TTTCATGATTTTTAA
1 TTTAATGATTTTTAA
12994489 TGTCAAAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 6 0.19
23 7 0.22
24 19 0.59
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.54
Consensus pattern (23 bp):
TTTAATGATTTTTAAGATTAAAA
Found at i:12995868 original size:3 final size:3
Alignment explanation
Indices: 12995860--12995896 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12995850 TTAAGTATAT
12995860 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12995897 ACTTTAGTCT
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):
TTA
Found at i:12997205 original size:21 final size:21
Alignment explanation
Indices: 12997180--12997220 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
12997170 TAAGATTATT
*
12997180 ATTTTTTTGAAGTAAAGATGA
1 ATTTTTGTGAAGTAAAGATGA
12997201 ATTTTTGTGAAGTAAAGATG
1 ATTTTTGTGAAGTAAAGATG
12997221 GGGGCAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (21 bp):
ATTTTTGTGAAGTAAAGATGA
Found at i:13001366 original size:23 final size:24
Alignment explanation
Indices: 13001338--13001392 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 24
13001328 TTGTTATCTG
13001338 TTAATTTTATCTGAT-TT-TTTTT
1 TTAATTTTATCTGATATTATTTTT
13001360 TTGAA--TTATCTGATATTATTTTT
1 TT-AATTTTATCTGATATTATTTTT
*
13001383 TTATTTTTAT
1 TTAATTTTAT
13001393 ACTATCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
21 9 0.33
22 5 0.19
23 9 0.33
24 4 0.15
ACGTcount: A:0.22, C:0.04, G:0.05, T:0.69
Consensus pattern (24 bp):
TTAATTTTATCTGATATTATTTTT
Found at i:13001919 original size:19 final size:20
Alignment explanation
Indices: 13001895--13001940 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13001885 TCCGGTCAAC
13001895 TTCCGGCGA-AATTTCCAGA
1 TTCCGGCGACAATTTCCAGA
* *
13001914 TTCCGGCGACATTTTCTAGA
1 TTCCGGCGACAATTTCCAGA
13001934 TTCCGGC
1 TTCCGGC
13001941 ACCGGTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (20 bp):
TTCCGGCGACAATTTCCAGA
Found at i:13004090 original size:61 final size:59
Alignment explanation
Indices: 13003941--13004283 Score: 437
Period size: 61 Copynumber: 5.7 Consensus size: 59
13003931 TGGCTTCCTT
* *
13003941 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC-AAAA
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTCCAAAAA
** *
13003999 AAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTT-CTTCGAAAATCAAGGTTTCCAAAAA
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT-AA-ATTTCCAAAAA
*
13004060 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTCAAAAAA
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAA-TTTCCAAAAA
*
13004122 AAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTTCAAAAA
1 AAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATAAATTTCCAAAAA
* * *
13004181 AAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTT-C-AAGA
1 AAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTCCAAAAA
* *
13004241 AAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTGAA
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAA
13004284 CAAAAAAATC
Statistics
Matches: 253, Mismatches: 18, Indels: 28
0.85 0.06 0.09
Matches are distributed among these distances:
57 3 0.01
58 75 0.30
59 14 0.06
60 14 0.06
61 83 0.33
62 64 0.25
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (59 bp):
AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTCCAAAAA
Found at i:13004180 original size:119 final size:122
Alignment explanation
Indices: 13003941--13004278 Score: 462
Period size: 119 Copynumber: 2.8 Consensus size: 122
13003931 TGGCTTCCTT
* **
13003941 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTCAAAAAAAGGT
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTCAAAAAAAAAT
* * *
13004005 -TTTTGA-GGAAAAGTTGAAAGTATCAATTTT-CTTCGAAAATCAAGGTTTCCAAAAA
66 ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATCAAGATTTCC-AAAA
13004060 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTCAAAAAAAAA
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAATTTTCAAAAAAAAA
*
13004125 TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT-AA-ATTTTCAAAAA
65 TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATCAAGA-TTTCCAAAA
* * *
13004181 AAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAA-TTTC--AAGAAA
1 AAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTCAAAAAAAA
*
13004243 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
64 ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
13004279 CTGAACAAAA
Statistics
Matches: 200, Mismatches: 11, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
119 85 0.43
121 28 0.14
122 15 0.08
123 68 0.34
124 4 0.02
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (122 bp):
AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTCAAAAAAAAAT
ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATCAAGATTTCCAAAA
Found at i:13004246 original size:181 final size:181
Alignment explanation
Indices: 13003941--13004283 Score: 532
Period size: 181 Copynumber: 1.9 Consensus size: 181
13003931 TGGCTTCCTT
**
13003941 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTT
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAATT
* **
13004006 TTTGAGGAAAAGTTGAAAGTATCAATTTTCTTCGAAAATCAAGGTTTCCAAAAAAAATATTTTTG
66 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAATTTCCAAAAAAAATATTTTTG
*
13004071 AGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTCAAAAAA
131 AGGAAAAGTTGAAAGTATCAATTTTCCCTGAAAATCAAAATTTTCAAAAAA
*
13004122 AAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAAAAATA
1 AAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC--AAAAAA-A
* *
13004186 AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCG-AAATTAAAATTT-C-AAGAAAATATT
62 AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAATTTCCAAAAAAAATATT
*
13004248 TTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTGAA
127 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCCTGAA
13004284 CAAAAAAATC
Statistics
Matches: 148, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
180 1 0.01
181 95 0.64
182 1 0.01
183 15 0.10
184 36 0.24
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (181 bp):
AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAATT
TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAATTTCCAAAAAAAATATTTTTG
AGGAAAAGTTGAAAGTATCAATTTTCCCTGAAAATCAAAATTTTCAAAAAA
Found at i:13008177 original size:8 final size:8
Alignment explanation
Indices: 13008166--13008205 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
13008156 GAAGATGATG
13008166 AAAAGAAAA
1 AAAAG-AAA
13008175 AAAAGAAA
1 AAAAGAAA
*
13008183 AAAGGAAA
1 AAAAGAAA
13008191 AAAAGAAA
1 AAAAGAAA
13008199 AAAAGAA
1 AAAAGAA
13008206 GGAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 24 0.83
9 5 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:13008180 original size:9 final size:9
Alignment explanation
Indices: 13008166--13008202 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
13008156 GAAGATGATG
13008166 AAAAGAAAA
1 AAAAGAAAA
13008175 AAAAG--AA
1 AAAAGAAAA
*
13008182 AAAAGGAAA
1 AAAAGAAAA
13008191 AAAAGAAAA
1 AAAAGAAAA
13008200 AAA
1 AAA
13008203 GAAGGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
7 7 0.28
9 18 0.72
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:13008222 original size:20 final size:18
Alignment explanation
Indices: 13008166--13008222 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
13008156 GAAGATGATG
13008166 AAAA-GAAAAAAA-AGAA
1 AAAAGGAAAAAAAGAGAA
*
13008182 AAAAGGAAAAAAAGAAAAA
1 AAAAGGAAAAAAAG-AGAA
13008201 AAGAAGGAAAAAAATGAGAA
1 AA-AAGGAAAAAAA-GAGAA
13008221 AA
1 AA
13008223 TGAAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 4 0.12
17 8 0.24
19 5 0.15
20 16 0.47
21 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAGGAAAAAAAGAGAA
Found at i:13009450 original size:42 final size:41
Alignment explanation
Indices: 13009404--13009735 Score: 428
Period size: 42 Copynumber: 8.1 Consensus size: 41
13009394 ATGATTGTCA
* * *
13009404 AGGAGCAATTTACTTTTTCAAAGT-TTCGCTGCCTCTGTTTAG
1 AGGAGCAATTTAC-TTTTCAAAGTCGT-GGTGCCTCTGTTGAG
*
13009446 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
*
13009487 AGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTGAG
*
13009529 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTC---TCA-
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
13009566 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
* *
13009607 AGGACCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAG
1 AGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTGAG
* *
13009649 AGGAGCAATTTACTTTCCAAAGTCCGT--TGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGT-CGTGGTGCCTCTGTTGAG
* * * *
13009689 AGGAGCAATTTAC-TTTCAAAAGTCGTTGAGTCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTCGTGGTGCCTCTGTTGAG
13009730 AGGAGC
1 AGGAGC
13009736 TTCGGCAAAA
Statistics
Matches: 261, Mismatches: 18, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
37 34 0.13
38 2 0.01
39 6 0.02
40 32 0.12
41 92 0.35
42 95 0.36
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (41 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAG
Found at i:13009520 original size:83 final size:82
Alignment explanation
Indices: 13009404--13009735 Score: 426
Period size: 83 Copynumber: 4.1 Consensus size: 82
13009394 ATGATTGTCA
* * *
13009404 AGGAGCAATTTACTTTTTCAAAGT-TTCGCTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG
1 AGGAGCAATTTAC-TTTTCAAAGTCGT-GGTGCCTCTGTTGAGAGGAGCAATTTACTTTCCAAAG
13009468 TCGTGGTGCCTCTGTTGAG
64 TCGTGGTGCCTCTGTTGAG
* *
13009487 AGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGT
1 AGGAGCAATTTA-CTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGT
*
13009552 CGTGGTGCCTC---TCA-
65 CGTGGTGCCTCTGTTGAG
* * *
13009566 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGACCAATTTATTTTTTCAAAGT
1 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTA-CTTTCCAAAGT
13009631 CGTGGTGCCTCTGTTGAG
65 CGTGGTGCCTCTGTTGAG
* * *
13009649 AGGAGCAATTTACTTTCCAAAGTCCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGT
1 AGGAGCAATTTACTTTTCAAAGT-CGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGT
* * * *
13009712 CGTTGAGTCTCTGTTTAG
65 CGTGGTGCCTCTGTTGAG
13009730 AGGAGC
1 AGGAGC
13009736 TTCGGCAAAA
Statistics
Matches: 221, Mismatches: 20, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
78 39 0.18
79 33 0.15
80 2 0.01
81 28 0.13
82 25 0.11
83 90 0.41
84 4 0.02
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (82 bp):
AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTC
GTGGTGCCTCTGTTGAG
Found at i:13009595 original size:120 final size:121
Alignment explanation
Indices: 13009404--13009735 Score: 447
Period size: 120 Copynumber: 2.7 Consensus size: 121
13009394 ATGATTGTCA
* * * * *
13009404 AGGAGCAATTTACTTTTTCAAAGTTTCGCTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
1 AGGAGCAATTTAC-TTTCCAAAG-TCCGTTGCCTC--TTCAGAGGAGCAATTTACTTTTCAAAGT
13009469 CGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAG
62 CGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAG
*
13009529 AGGAGCAATTTACTTTTCAAAGT-CGTGGTGCCTC-TCA-AGGAGCAATTTACTTTTCAAAGTCG
1 AGGAGCAATTTACTTTCCAAAGTCCGT--TGCCTCTTCAGAGGAGCAATTTACTTTTCAAAGTCG
*
13009591 TGGTGCCTCTGTTGAGAGGACCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAG
64 TGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAG
*
13009649 AGGAGCAATTTACTTTCCAAAGTCCGTTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAAAGTC
1 AGGAGCAATTTACTTTCCAAAGTCCGTTGCCTC--TTCAGAGGAGCAATTTACTTTTC-AAAGTC
* * * *
13009713 GTTGAGTCTCTGTTTAGAGGAGC
63 GTGGTGCCTCTGTTGAGAGGAGC
13009736 TTCGGCAAAA
Statistics
Matches: 188, Mismatches: 11, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
119 6 0.03
120 103 0.55
121 5 0.03
122 8 0.04
123 38 0.20
124 15 0.08
125 13 0.07
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (121 bp):
AGGAGCAATTTACTTTCCAAAGTCCGTTGCCTCTTCAGAGGAGCAATTTACTTTTCAAAGTCGTG
GTGCCTCTGTTGAGAGGAGCAATTTATTTTTTCAAAGTCGTGGTGCCTCTGTTGAG
Found at i:13009748 original size:1 final size:1
Alignment explanation
Indices: 13009742--13009891 Score: 93
Period size: 1 Copynumber: 150.0 Consensus size: 1
13009732 GAGCTTCGGC
* * * * * * *
13009742 AAAAAAACAAAAAAACAAAAAAAACAAAAAAAAAACAAAAAACAAAAAAACAAAAAAATAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** * * ** * * ** **
13009807 AATAAAAACAAATCAAAAAATAAAAACAAATCAAAAAATAAAAACAAAAAAATCAAAAATCAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
13009872 AAATAAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
13009892 TGTTGAGTTG
Statistics
Matches: 107, Mismatches: 42, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 107 1.00
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.07
Consensus pattern (1 bp):
A
Found at i:13009754 original size:8 final size:8
Alignment explanation
Indices: 13009741--13009882 Score: 121
Period size: 8 Copynumber: 17.0 Consensus size: 8
13009731 GGAGCTTCGG
13009741 CAAAAAAA
1 CAAAAAAA
13009749 CAAAAAAA
1 CAAAAAAA
13009757 CAAAAAAAA
1 C-AAAAAAA
13009766 CAAAAAAAA
1 C-AAAAAAA
*
13009775 AACAAAAAA
1 CA-AAAAAA
13009784 CAAAAAAA
1 CAAAAAAA
13009792 CAAAAAAA
1 CAAAAAAA
*
13009800 TAAAAAAA
1 CAAAAAAA
*
13009808 -ATAAAAA
1 CAAAAAAA
13009815 CAAATCAAAA
1 CAAA--AAAA
13009825 -AATAAAAA
1 CAA-AAAAA
13009833 CAAATCAAAA
1 CAAA--AAAA
13009843 -AATAAAAA
1 CAA-AAAAA
13009851 CAAAAAAA
1 CAAAAAAA
*
13009859 TC-AAAAAT
1 -CAAAAAAA
13009867 CAAAAAAA
1 CAAAAAAA
*
13009875 TAAAAAAA
1 CAAAAAAA
13009883 ATAAAAAAAT
Statistics
Matches: 113, Mismatches: 8, Indels: 26
0.77 0.05 0.18
Matches are distributed among these distances:
7 7 0.06
8 64 0.57
9 32 0.28
10 10 0.09
ACGTcount: A:0.84, C:0.10, G:0.00, T:0.06
Consensus pattern (8 bp):
CAAAAAAA
Found at i:13009756 original size:9 final size:9
Alignment explanation
Indices: 13009742--13009891 Score: 109
Period size: 9 Copynumber: 16.7 Consensus size: 9
13009732 GAGCTTCGGC
13009742 AAAAAAAC-
1 AAAAAAACA
13009750 AAAAAAACA
1 AAAAAAACA
13009759 AAAAAAACA
1 AAAAAAACA
13009768 AAAAAAA-A
1 AAAAAAACA
13009776 ACAAAAAAC-
1 A-AAAAAACA
13009785 AAAAAAAC-
1 AAAAAAACA
*
13009793 AAAAAAATA
1 AAAAAAACA
*
13009802 AAAAAAATA
1 AAAAAAACA
13009811 AAAACAAATCA
1 AAAA-AAA-CA
13009822 AAAAATAA-A
1 AAAAA-AACA
* *
13009831 AACAAATCA
1 AAAAAAACA
13009840 AAAAATAA-A
1 AAAAA-AACA
13009849 AACAAAAA-A
1 AA-AAAAACA
*
13009858 ATCAAAAATC-
1 A--AAAAAACA
*
13009868 AAAAAAATA
1 AAAAAAACA
*
13009877 AAAAAAATA
1 AAAAAAACA
13009886 AAAAAA
1 AAAAAA
13009892 TGTTGAGTTG
Statistics
Matches: 119, Mismatches: 9, Indels: 27
0.77 0.06 0.17
Matches are distributed among these distances:
8 30 0.25
9 68 0.57
10 13 0.11
11 8 0.07
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.07
Consensus pattern (9 bp):
AAAAAAACA
Found at i:13009765 original size:18 final size:17
Alignment explanation
Indices: 13009742--13009891 Score: 128
Period size: 17 Copynumber: 8.9 Consensus size: 17
13009732 GAGCTTCGGC
*
13009742 AAAAAAACAAAAAAACA
1 AAAAAAACAAAAAAAAA
13009759 AAAAAAACAAAAAAAAA
1 AAAAAAACAAAAAAAAA
13009776 ACAAAAAAC--AAAAAAA
1 A-AAAAAACAAAAAAAAA
* *
13009792 CAAAAAA-ATAAAAAAA
1 AAAAAAACAAAAAAAAA
* *
13009808 ATAAAAACAAATCAAAAA
1 AAAAAAACAAA-AAAAAA
* *
13009826 ATAAAAACAAATCAAAAA
1 AAAAAAACAAA-AAAAAA
* *
13009844 ATAAAAAC-AAAAAAAT
1 AAAAAAACAAAAAAAAA
* * *
13009860 CAAAAATCAAAAAAATA
1 AAAAAAACAAAAAAAAA
*
13009877 AAAAAAATAAAAAAA
1 AAAAAAACAAAAAAA
13009892 TGTTGAGTTG
Statistics
Matches: 111, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
15 6 0.05
16 28 0.25
17 39 0.35
18 38 0.34
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.07
Consensus pattern (17 bp):
AAAAAAACAAAAAAAAA
Found at i:13010275 original size:22 final size:24
Alignment explanation
Indices: 13010250--13010301 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 24
13010240 GTTATCTGTT
13010250 AATTTTATCTGAT-TT-TTTTTTG
1 AATTTTATCTGATATTATTTTTTG
*
13010272 AA--TTATCTGATATTATTTTTTT
1 AATTTTATCTGATATTATTTTTTG
*
13010294 ATTTTTAT
1 AATTTTAT
13010302 ACTATCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 9 0.38
21 2 0.08
22 9 0.38
24 4 0.17
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (24 bp):
AATTTTATCTGATATTATTTTTTG
Found at i:13010844 original size:19 final size:20
Alignment explanation
Indices: 13010820--13010865 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
13010810 TCCGGTCAAC
13010820 TTCCGGCGA-AATTTCCAGA
1 TTCCGGCGACAATTTCCAGA
* *
13010839 TTCCGGTGACATTTTCCAGA
1 TTCCGGCGACAATTTCCAGA
13010859 TTCCGGC
1 TTCCGGC
13010866 ACCGGTGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (20 bp):
TTCCGGCGACAATTTCCAGA
Found at i:13013015 original size:61 final size:59
Alignment explanation
Indices: 13012866--13013209 Score: 430
Period size: 61 Copynumber: 5.7 Consensus size: 59
13012856 TGGCTTCCTT
* *
13012866 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC-AAAA
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTCCAAAAA
** *
13012924 AAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTT-CTTCGAAAATCAAGGTTTCCAAAAA
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT-AA-ATTTCCAAAAA
*
13012985 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTCAAAAAAA
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAA-TTTC-CAAAAA
*
13013048 AAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTTCAAAAA
1 AAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATAAATTTCCAAAAA
* * *
13013107 AAATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTT-C-AAGA
1 AAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTCCAAAAA
* *
13013167 AAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTGAA
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAA
13013210 CAAAAAAAAT
Statistics
Matches: 253, Mismatches: 18, Indels: 30
0.84 0.06 0.10
Matches are distributed among these distances:
57 3 0.01
58 75 0.30
59 11 0.04
60 14 0.06
61 84 0.33
62 19 0.08
63 47 0.19
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (59 bp):
AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTCCAAAAA
Found at i:13013173 original size:182 final size:182
Alignment explanation
Indices: 13012866--13013209 Score: 534
Period size: 182 Copynumber: 1.9 Consensus size: 182
13012856 TGGCTTCCTT
**
13012866 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTT
1 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAATT
* **
13012931 TTTGAGGAAAAGTTGAAAGTATCAATTTTCTTCGAAAATCAAGGTTTCCAAAAAAAATATTTTTG
66 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAATTTCCAAAAAAAATATTTTTG
*
13012996 AGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTCAAAAAAA
131 AGGAAAAGTTGAAAGTATCAATTTTCCCTGAAAATCAAAATTTTCAAAAAAA
*
13013048 AAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAAAAATA
1 AAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTC--AAAAAA-A
* *
13013112 AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCG-AAATTAAAATTT-C-AAGAAAATATT
62 AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAATTTCCAAAAAAAATATT
*
13013174 TTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTGAA
127 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCCTGAA
13013210 CAAAAAAAAT
Statistics
Matches: 148, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
181 1 0.01
182 95 0.64
183 1 0.01
184 15 0.10
185 36 0.24
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (182 bp):
AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAATT
TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAATCAAAATTTCCAAAAAAAATATTTTTG
AGGAAAAGTTGAAAGTATCAATTTTCCCTGAAAATCAAAATTTTCAAAAAAA
Found at i:13018600 original size:170 final size:181
Alignment explanation
Indices: 13018269--13018623 Score: 470
Period size: 170 Copynumber: 2.0 Consensus size: 181
13018259 GCTAATATTA
* *
13018269 TTTTGTGGAAAGTAAAGATGGGGGCAAAAAAGACTTAACCACATTTGCATGCTTTTATTGCCAAG
1 TTTTGTGGAAAGTAAAGATGGGGACAAAAAAGACTTAACCACATTTGCATGCTTTCATTGCCAAG
* *
13018334 ACTAAATCTAAAGCAATACTAAGACTTGTCCATTTCCTTTCTTTGGGTTTTACTATTCCTTTTTA
66 ACTAAATATAAAGCAAGACTAAGACTTGTCCATTT-CTTTCTTTGGGTTTTACTATTCCTTTTTA
13018399 AAAACTTCCCTTAATTTCTATGATAAAGTCTTGAGTCTTTCCTTTATAC-TAT
130 AAAACTTCCCTTAATTTCTATGATAAAGTCTT-AGTCTTTCCTTTATACTTAT
* *
13018451 TTTTGT-G-AAGTAAAGATGGGGAC-AAAAAGTC-TGA-CACATTTGCATGC-TTCA-TGCCAAG
1 TTTTGTGGAAAGTAAAGATGGGGACAAAAAAGACTTAACCACATTTGCATGCTTTCATTGCCAAG
* *
13018509 ACTAAGTATAAAGCAAAGACTAAGACTT-TATCATTT-TTTCTTT-GGTTTTACT-TT-CTTTTT
66 ACTAAATATAAAGC-AAGACTAAGACTTGT-CCATTTCTTTCTTTGGGTTTTACTATTCCTTTTT
* *
13018569 -AAAACTTCCCTTAATTTCTATTGAT-AAGTCTTAGTTTTTGCTTTATACTTAT
129 AAAAACTTCCCTTAATTTCTA-TGATAAAGTCTTAGTCTTTCCTTTATACTTAT
13018621 TTT
1 TTT
13018624 GTAGAGTAAC
Statistics
Matches: 159, Mismatches: 10, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
169 14 0.09
170 33 0.21
171 10 0.06
172 2 0.01
173 9 0.06
174 7 0.04
175 20 0.13
176 20 0.13
177 13 0.08
178 2 0.01
179 7 0.04
180 15 0.09
181 1 0.01
182 6 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (181 bp):
TTTTGTGGAAAGTAAAGATGGGGACAAAAAAGACTTAACCACATTTGCATGCTTTCATTGCCAAG
ACTAAATATAAAGCAAGACTAAGACTTGTCCATTTCTTTCTTTGGGTTTTACTATTCCTTTTTAA
AAACTTCCCTTAATTTCTATGATAAAGTCTTAGTCTTTCCTTTATACTTAT
Found at i:13020747 original size:8 final size:8
Alignment explanation
Indices: 13020734--13020763 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
13020724 ATACCATATA
13020734 CATACATC
1 CATACATC
13020742 CATACATC
1 CATACATC
13020750 CATACATC
1 CATACATC
13020758 CATACA
1 CATACA
13020764 CACTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (8 bp):
CATACATC
Found at i:13028581 original size:21 final size:20
Alignment explanation
Indices: 13028545--13028609 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
13028535 TGAAATTAAA
*
13028545 AATAGCAATAAAAATAAAATT
1 AATA-CAATAATAATAAAATT
**
13028566 AATTATTATAATAATAAAATT
1 AA-TACAATAATAATAAAATT
13028587 GAATACAATAATAATAAAATT
1 -AATACAATAATAATAAAATT
13028608 AA
1 AA
13028610 AATCAATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.05
21 31 0.84
22 4 0.11
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (20 bp):
AATACAATAATAATAAAATT
Found at i:13028616 original size:21 final size:21
Alignment explanation
Indices: 13028550--13028616 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
13028540 TTAAAAATAG
* *
13028550 CAATAAAAATAAAATTAATTAT
1 CAATAATAATAAAATTAA-AAT
* *
13028572 -TATAATAATAAAATT-GAAT
1 CAATAATAATAAAATTAAAAT
13028591 ACAATAATAATAAAATTAAAAT
1 -CAATAATAATAAAATTAAAAT
13028613 CAAT
1 CAAT
13028617 TATTAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 2 0.06
21 31 0.86
22 3 0.08
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.31
Consensus pattern (21 bp):
CAATAATAATAAAATTAAAAT
Found at i:13029325 original size:14 final size:14
Alignment explanation
Indices: 13029306--13029340 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
13029296 AATCTGTAAT
13029306 CAATGCACATGCAC
1 CAATGCACATGCAC
13029320 CAATGCACATGCAC
1 CAATGCACATGCAC
13029334 CAA-GCAC
1 CAATGCAC
13029341 TAAGTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.37, C:0.37, G:0.14, T:0.11
Consensus pattern (14 bp):
CAATGCACATGCAC
Found at i:13032422 original size:29 final size:29
Alignment explanation
Indices: 13032390--13032468 Score: 79
Period size: 32 Copynumber: 2.6 Consensus size: 29
13032380 TATTATTTAT
* *
13032390 TAAATTTATATTTATATAT-ATTGTATTAA
1 TAAAATTATATTTATATATAATT-TAATAA
*
13032419 TAAAAATATTATTTAATATCATAATTTAATAA
1 TAAAATTA-TATTT-ATAT-ATAATTTAATAA
*
13032451 AAAAATTATATTTATATA
1 TAAAATTATATTTATATA
13032469 ATTAAGTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
29 7 0.17
30 9 0.22
31 9 0.22
32 13 0.32
33 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TAAAATTATATTTATATATAATTTAATAA
Found at i:13032892 original size:20 final size:20
Alignment explanation
Indices: 13032863--13032901 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
13032853 AAGTGTTTAC
13032863 TTATAATAT-ATTTTAAAAA
1 TTATAATATAATTTTAAAAA
13032882 TTATAAATATAATTTTAAAA
1 TTAT-AATATAATTTTAAAA
13032902 TAATATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATAATATAATTTTAAAAA
Found at i:13033589 original size:28 final size:28
Alignment explanation
Indices: 13033538--13033614 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
13033528 ATGTTAAAAA
* *
13033538 TAAAAATTAAAT-T-AATTAATAAA-TT
1 TAAAATTTAAATATAAATTAAAAAATTT
*
13033563 TATAATTTAAATATCAAATTAAAAAATTT
1 TAAAATTTAAATAT-AAATTAAAAAATTT
13033592 TAAAATTTAAATATAATATTAAA
1 TAAAATTTAAATATAA-ATTAAA
13033615 TATTTTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
25 10 0.23
26 1 0.02
28 11 0.26
29 21 0.49
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAAATTTAAATATAAATTAAAAAATTT
Found at i:13033626 original size:20 final size:18
Alignment explanation
Indices: 13033603--13033664 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 18
13033593 AAAATTTAAA
13033603 TATAATATTAAATATTTTAT
1 TATAATATTAAATA--TTAT
13033623 TATAAT-TTAAA-ATTAT
1 TATAATATTAAATATTAT
13033639 TCATAATATTAAAT-TT-T
1 T-ATAATATTAAATATTAT
*
13033656 CATAATATT
1 TATAATATT
13033665 TTTATGGGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
16 13 0.34
17 6 0.16
18 8 0.21
19 5 0.13
20 6 0.16
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (18 bp):
TATAATATTAAATATTAT
Found at i:13036162 original size:8 final size:8
Alignment explanation
Indices: 13036143--13036186 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
13036133 TCTCTCTATA
13036143 ATTTTATTT
1 ATTTT-TTT
13036152 ATTTTTTT
1 ATTTTTTT
*
13036160 ATTTTACTT
1 ATTTT-TTT
*
13036169 ATTATTTT
1 ATTTTTTT
13036177 ATTTTTTT
1 ATTTTTTT
13036185 AT
1 AT
13036187 GAAATAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 19 0.63
9 11 0.37
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTTTTTT
Found at i:13036165 original size:17 final size:17
Alignment explanation
Indices: 13036143--13036186 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
13036133 TCTCTCTATA
*
13036143 ATTTTATTTATTTTTTT
1 ATTTTATTTATTATTTT
*
13036160 ATTTTACTTATTATTTT
1 ATTTTATTTATTATTTT
13036177 ATTTT-TTTAT
1 ATTTTATTTAT
13036187 GAAATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTTATTTATTATTTT
Done.