Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, 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: 16099665
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 27 of 77
Found at i:5271730 original size:33 final size:35
Alignment explanation
Indices: 5271667--5271733 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 35
5271657 AAAATTACTA
5271667 TTTTTCTTTTTCTCTTCTTTTACTATTTCTTTCTC
1 TTTTTCTTTTTCTCTTCTTTTACTATTTCTTTCTC
* *
5271702 TTTTT-TTTTTC-CTTTTTTTCCT-TCTTCTTTCT
1 TTTTTCTTTTTCTCTTCTTTTACTAT-TTCTTTCT
5271734 TCCTCCATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 1 0.03
33 17 0.59
34 6 0.21
35 5 0.17
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (35 bp):
TTTTTCTTTTTCTCTTCTTTTACTATTTCTTTCTC
Found at i:5274549 original size:4 final size:5
Alignment explanation
Indices: 5274527--5274560 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
5274517 ATATTTTTAA
5274527 ATTTT ATTTT ATTTT -TATTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT AT-TTT ATTTT ATTTT ATTT
5274561 CTACTTGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 25 0.93
6 1 0.04
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:5275879 original size:95 final size:94
Alignment explanation
Indices: 5275745--5275921 Score: 228
Period size: 95 Copynumber: 1.9 Consensus size: 94
5275735 ATAAAAAAAT
* * * * * * * *
5275745 AAAATAAAATTTTCAGCCCTACCAAATTATTGGAGGATTTCAATCTCTTAATTAAATATTACCAG
1 AAAATAAAATTTTCAACCCTACCAAACTATTAGAAGATTTAAATATC-GAATTAAATATTACCAA
*
5275810 ACTATTGGAAGATTTAATGAGTTTTTATGA
65 ACTATTAGAAGATTTAATGAGTTTTTATGA
* * *
5275840 AAAATAAAATTTTCAATCCTACCAAACTATTAGAAGATTTAAATATCGAATTAAATCTTATCAAA
1 AAAATAAAATTTTCAACCCTACCAAACTATTAGAAGATTTAAATATCGAATTAAATATTACCAAA
*
5275905 TTATTAGAAGATTTAAT
66 CTATTAGAAGATTTAAT
5275922 TATTCTTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
94 29 0.42
95 40 0.58
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (94 bp):
AAAATAAAATTTTCAACCCTACCAAACTATTAGAAGATTTAAATATCGAATTAAATATTACCAAA
CTATTAGAAGATTTAATGAGTTTTTATGA
Found at i:5282607 original size:23 final size:24
Alignment explanation
Indices: 5282570--5282614 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
5282560 CCAATTCCAA
5282570 AGAAGCTAAAGAAAA-ACATGATG
1 AGAAGCTAAAGAAAAGACATGATG
5282593 AGAAGCTGAAA-AAAAGACATGA
1 AGAAGCT-AAAGAAAAGACATGA
5282615 AGAAAAGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.58, C:0.09, G:0.22, T:0.11
Consensus pattern (24 bp):
AGAAGCTAAAGAAAAGACATGATG
Found at i:5283534 original size:16 final size:16
Alignment explanation
Indices: 5283512--5283550 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
5283502 AGTTTCAAGC
5283512 CTTTCTTAAGAAAGAG
1 CTTTCTTAAGAAAGAG
*
5283528 TTTTCTTAAGAAAGAG
1 CTTTCTTAAGAAAGAG
5283544 CTTTCTT
1 CTTTCTT
5283551 GGTCATTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (16 bp):
CTTTCTTAAGAAAGAG
Found at i:5283743 original size:37 final size:37
Alignment explanation
Indices: 5283667--5283757 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 37
5283657 AGTAGAGTGA
**
5283667 TACTTTATTTTTTCAAAGTTAAAGCTTGGATAAAAAAG
1 TACTTTA-TTTTTCAAAGTTAAAGCTCAGATAAAAAAG
* *
5283705 TACTTTATTTTTCAAAGTTAAAGCCTCAG-TAGAGAAG
1 TACTTTATTTTTCAAAGTTAAAG-CTCAGATAAAAAAG
*
5283742 TAATTTATTTTTCAAA
1 TACTTTATTTTTCAAA
5283758 AGTTGAAACA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
37 37 0.79
38 10 0.21
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (37 bp):
TACTTTATTTTTCAAAGTTAAAGCTCAGATAAAAAAG
Found at i:5284281 original size:12 final size:12
Alignment explanation
Indices: 5284266--5284295 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5284256 ATTTGAATTT
5284266 TTTTTAGTTTAA
1 TTTTTAGTTTAA
*
5284278 TTTTTTGTTTAA
1 TTTTTAGTTTAA
5284290 TTTTTA
1 TTTTTA
5284296 TTCTTTTAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTTAGTTTAA
Found at i:5286054 original size:24 final size:23
Alignment explanation
Indices: 5286014--5286074 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 23
5286004 TTAATATATT
5286014 TATTATTGTATGATATGATTTTA
1 TATTATTGTATGATATGATTTTA
5286037 TATTTATTGTAGTG-TATGATTTTA
1 TA-TTATTGTA-TGATATGATTTTA
*
5286061 TATTATTGCATGAT
1 TATTATTGTATGAT
5286075 TTATTGTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 2 0.06
23 10 0.29
24 20 0.59
25 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.56
Consensus pattern (23 bp):
TATTATTGTATGATATGATTTTA
Found at i:5286114 original size:35 final size:34
Alignment explanation
Indices: 5286026--5286114 Score: 99
Period size: 35 Copynumber: 2.6 Consensus size: 34
5286016 TTATTGTATG
* *
5286026 ATATGATTTTATATTTATTGTAGTGTATGATTTT
1 ATATTATTGTATATTTATTGTAGTGTATGATTTT
*
5286060 ATATTATTGCATGATTTATTGTA-TGATATGATTTT
1 ATATTATTGTAT-ATTTATTGTAGTG-TATGATTTT
* *
5286095 TTATTTATTGTATAATTATT
1 ATA-TTATTGTATATTTATT
5286115 TTTGCATGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
34 11 0.24
35 27 0.59
36 8 0.17
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.58
Consensus pattern (34 bp):
ATATTATTGTATATTTATTGTAGTGTATGATTTT
Found at i:5289219 original size:22 final size:23
Alignment explanation
Indices: 5289169--5289220 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
5289159 ATACCTTTCA
*
5289169 ATTTATAAATTTAAATTTAAATTT
1 ATTTA-AAATTTAAATTTAAATAT
* *
5289193 TTTTAAAATTT-TATTTAAATAT
1 ATTTAAAATTTAAATTTAAATAT
5289215 ATTTAA
1 ATTTAA
5289221 TAAAAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 14 0.58
23 6 0.25
24 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAAAATTTAAATTTAAATAT
Found at i:5289562 original size:3 final size:3
Alignment explanation
Indices: 5289554--5289584 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5289544 GCGAAGCTTT
5289554 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5289585 AAGAGTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5289676 original size:18 final size:18
Alignment explanation
Indices: 5289653--5289688 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5289643 TTGGATGAGT
5289653 AAATTTTAAAATTTTAAA
1 AAATTTTAAAATTTTAAA
5289671 AAATTTTAAAATTTTAAA
1 AAATTTTAAAATTTTAAA
5289689 TATTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTTTAAAATTTTAAA
Found at i:5289700 original size:10 final size:8
Alignment explanation
Indices: 5289653--5289699 Score: 58
Period size: 8 Copynumber: 5.5 Consensus size: 8
5289643 TTGGATGAGT
5289653 AAATTTTA
1 AAATTTTA
5289661 AAATTTTAAA
1 AAATTTT--A
5289671 AAATTTTA
1 AAATTTTA
5289679 AAATTTTA
1 AAATTTTA
*
5289687 AATATTTTG
1 AA-ATTTTA
5289696 AAAT
1 AAAT
5289700 ACATCAATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
8 20 0.57
9 7 0.20
10 8 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (8 bp):
AAATTTTA
Found at i:5290356 original size:2 final size:2
Alignment explanation
Indices: 5290351--5290381 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5290341 AAAAAAAGTA
5290351 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 A
5290382 AAGTGGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5291736 original size:14 final size:14
Alignment explanation
Indices: 5291717--5291743 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5291707 AAAATTAAAA
5291717 AATATTTTTATATT
1 AATATTTTTATATT
5291731 AATATTTTTATAT
1 AATATTTTTATAT
5291744 GTTAAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:5292046 original size:22 final size:22
Alignment explanation
Indices: 5292012--5292057 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
5292002 TTTGATAGAA
5292012 AATTGATTAGTCAACAAAAAAT
1 AATTGATTAGTCAACAAAAAAT
* * **
5292034 AATTTATTGGTCAATGAAAAAT
1 AATTGATTAGTCAACAAAAAAT
5292056 AA
1 AA
5292058 GATAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (22 bp):
AATTGATTAGTCAACAAAAAAT
Found at i:5292321 original size:22 final size:22
Alignment explanation
Indices: 5292261--5292321 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
5292251 TTTTTTATTT
*
5292261 AATTTT-ACTTTAAA-A-TTAA
1 AATTTTAATTTTAAATATTTAA
*
5292280 AATTTTAATATT-AATCATTTAA
1 AATTTTAATTTTAAAT-ATTTAA
*
5292302 CATTTTAATTTTAAATATTT
1 AATTTTAATTTTAAATATTT
5292322 TTATAGTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 8 0.24
20 3 0.09
21 1 0.03
22 18 0.55
23 3 0.09
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTTAATTTTAAATATTTAA
Found at i:5292399 original size:166 final size:162
Alignment explanation
Indices: 5292192--5292488 Score: 377
Period size: 166 Copynumber: 1.8 Consensus size: 162
5292182 TACATGATTT
* *
5292192 TTTTAAGCTTAAAATTAATTTGATCAGACTAAAAATATTATTATATTAATAAATAATATTTTTTT
1 TTTTAAACTTAAAATTAATTTGATCAGACTAAAAATATTATTATATTAATAAA-AA-A----ATT
* * * *
5292257 ATTTAATTTTACTTTAAAATTAAAATTTTAATATT-AA-TCAT-TTAACATTTTAATTTTAAATA
60 ATTTAATTTTAATTTAAAATTAAAATATCAATATTAAAGTC-TCTTAACATTTCAATTTTAAATA
5292319 TTTTTATAGTTCTACACAAGTAAGACTTTGAATATAGTA
124 TTTTTATAGTTCTACACAAGTAAGACTTTGAATATAGTA
* * * *
5292358 TTTTAAACTTAAACTTGATTTGATTCA-ATTTAAAATATTATTATATTAATAAAAAAATTATTTA
1 TTTTAAACTTAAAATTAATTTGA-TCAGACTAAAAATATTATTATATTAATAAAAAAATTATTTA
* *
5292422 ATTTTAATTTAAAATTAAAATATCAATATTAAAAGTCTCTTGAGATTTCAATTTTAAATATTTTT
65 ATTTTAATTTAAAATTAAAATATCAATATT-AAAGTCTCTTAACATTTCAATTTTAAATATTTTT
5292487 AT
129 AT
5292489 TTTGTATATT
Statistics
Matches: 114, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
160 34 0.30
162 3 0.03
163 27 0.24
164 1 0.01
165 2 0.02
166 44 0.39
167 3 0.03
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (162 bp):
TTTTAAACTTAAAATTAATTTGATCAGACTAAAAATATTATTATATTAATAAAAAAATTATTTAA
TTTTAATTTAAAATTAAAATATCAATATTAAAGTCTCTTAACATTTCAATTTTAAATATTTTTAT
AGTTCTACACAAGTAAGACTTTGAATATAGTA
Found at i:5292435 original size:22 final size:21
Alignment explanation
Indices: 5292384--5292436 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
5292374 GATTTGATTC
5292384 AATTTAAAATATTATTATATT
1 AATTTAAAATATTATTATATT
* * *
5292405 AA-TAAAAAAATTATTTAATTTT
1 AATTTAAAATATTA-TT-ATATT
5292427 AATTTAAAAT
1 AATTTAAAAT
5292437 TAAAATATCA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 9 0.38
21 4 0.17
22 6 0.25
23 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTAAAATATTATTATATT
Found at i:5292592 original size:42 final size:42
Alignment explanation
Indices: 5292545--5292626 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
5292535 TAGTATTAAA
*
5292545 TTATTATTTTAATAATAAATAG-TAACAT-ATATAATAATATGT
1 TTATTATTTAAATAATAAAT-GTTAA-ATAATATAATAATATGT
*
5292587 TTATTATTTAAATAATTAATGTTAAATAATATAATAATAT
1 TTATTATTTAAATAATAAATGTTAAATAATATAATAATAT
5292627 TATTTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 3 0.08
42 33 0.92
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (42 bp):
TTATTATTTAAATAATAAATGTTAAATAATATAATAATATGT
Found at i:5292805 original size:21 final size:22
Alignment explanation
Indices: 5292781--5292847 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
5292771 AGATACTTTC
5292781 AATATA-AAATATAAATATTTT
1 AATATATAAATATAAATATTTT
* *
5292802 AATA-ATAAATATTACTATTTT
1 AATATATAAATATAAATATTTT
*
5292823 AATATTAATAAAAAT-AATATTTT
1 AATA-T-ATAAATATAAATATTTT
5292846 AA
1 AA
5292848 GAATAGTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 1 0.03
21 21 0.55
23 9 0.24
24 7 0.18
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATATAAATATAAATATTTT
Found at i:5292843 original size:44 final size:46
Alignment explanation
Indices: 5292784--5292881 Score: 123
Period size: 44 Copynumber: 2.2 Consensus size: 46
5292774 TACTTTCAAT
* *
5292784 ATAAAATATAAATATTTTAATAATAAATATTACTATTTT-AATATTA
1 ATAAAATATAAATATTTTAAGAAT-AATAATACTATTTTAAATATTA
*
5292830 ATAAAA-AT-AATATTTTAAGAATAGTAATACTATTTTAAATATT-
1 ATAAAATATAAATATTTTAAGAATAATAATACTATTTTAAATATTA
*
5292873 TTAAAATAT
1 ATAAAATAT
5292882 TAAAATAAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
43 17 0.37
44 21 0.46
45 2 0.04
46 6 0.13
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (46 bp):
ATAAAATATAAATATTTTAAGAATAATAATACTATTTTAAATATTA
Found at i:5292981 original size:16 final size:16
Alignment explanation
Indices: 5292927--5292999 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 16
5292917 ATTTTTATAT
5292927 TAATATAA-TATTTTAA
1 TAATATAATTATTTT-A
*
5292943 TATTATATATTATTATTA
1 TAATATA-ATTATT-TTA
* *
5292961 AAATATAATTATTTTT
1 TAATATAATTATTTTA
*
5292977 TAATATTAATAATTTTAA
1 TAATA-TAATTATTTT-A
5292995 TAATA
1 TAATA
5293000 AATAATTTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
16 12 0.27
17 16 0.36
18 15 0.33
19 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAATATAATTATTTTA
Found at i:5293003 original size:16 final size:16
Alignment explanation
Indices: 5292974--5293039 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 16
5292964 TATAATTATT
*
5292974 TTTTAAT-ATTAATAA
1 TTTTAATAATAAATAA
5292989 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
*
5293005 -TTT--CAAT--AT-A
1 TTTTAATAATAAATAA
5293015 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
5293031 TTTTTAATA
1 -TTTTAATA
5293040 TTTTAATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
10 1 0.03
11 5 0.12
13 6 0.15
15 12 0.30
16 8 0.20
17 8 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTAATAATAAATAA
Found at i:5293017 original size:26 final size:26
Alignment explanation
Indices: 5292984--5293047 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
5292974 TTTTAATATT
5292984 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
*
5293009 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
5293035 TA-ATATTTTAATA
1 AATATATTTTAATA
5293048 GTTATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:5293039 original size:10 final size:9
Alignment explanation
Indices: 5292977--5293047 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
5292967 AATTATTTTT
*
5292977 TAATATTAA
1 TAATTTTAA
5292986 TAATTTTAA
1 TAATTTTAA
*
5292995 TAA--TAAA
1 TAATTTTAA
*
5293002 TAATTTCAA
1 TAATTTTAA
5293011 TATATTTTAA
1 TA-ATTTTAA
*
5293021 TAA--TAAA
1 TAATTTTAA
5293028 TAATTTTTAA
1 TAA-TTTTAA
5293038 T-ATTTTAA
1 TAATTTTAA
5293046 TA
1 TA
5293048 GTTATATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
7 12 0.24
8 7 0.14
9 18 0.37
10 12 0.24
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (9 bp):
TAATTTTAA
Found at i:5298597 original size:3 final size:3
Alignment explanation
Indices: 5298589--5298626 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5298579 CATACAAGTG
5298589 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
5298627 GTCTATCAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:5299994 original size:2 final size:2
Alignment explanation
Indices: 5299989--5300026 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5299979 CAAAGACATA
5299989 AT AT AT AT AT 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 AT AT AT AT AT
5300027 GCACATTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5301307 original size:21 final size:22
Alignment explanation
Indices: 5301282--5301323 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5301272 ATTTAAAAGA
5301282 AAATTA-ATAAATAAAT-TAAAT
1 AAATTATA-AAATAAATATAAAT
5301303 AAATTATAAAATAAATATAAA
1 AAATTATAAAATAAATATAAA
5301324 ATTAGACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATTATAAAATAAATATAAAT
Found at i:5312054 original size:3 final size:3
Alignment explanation
Indices: 5312046--5312076 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5312036 CGTCGTTCCT
5312046 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5312077 ACAATGACGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5312929 original size:23 final size:23
Alignment explanation
Indices: 5312862--5312933 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
5312852 AAAAAAATAT
*
5312862 AAAAAT-TAATTTTGAAATATAA
1 AAAAATATAATTTTGAAACATAA
* **
5312884 AAATAATA-AA-CTT-AAATGTTAA
1 AAA-AATATAATTTTGAAA-CATAA
5312906 AAAAATATAATTTTGAAACATAA
1 AAAAATATAATTTTGAAACATAA
5312929 AAAAA
1 AAAAA
5312934 ATGCAAGGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
21 7 0.18
22 13 0.34
23 15 0.39
24 3 0.08
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (23 bp):
AAAAATATAATTTTGAAACATAA
Found at i:5313946 original size:13 final size:13
Alignment explanation
Indices: 5313928--5313975 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
5313918 AATCATCTTA
5313928 TTTTTCTTTTATT
1 TTTTTCTTTTATT
**
5313941 TTTTTCTTTCCTT
1 TTTTTCTTTTATT
*
5313954 TTATT-TTTTATT
1 TTTTTCTTTTATT
*
5313966 TTTTACTTTT
1 TTTTTCTTTT
5313976 TTATGCAAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 8 0.30
13 19 0.70
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTTATT
Found at i:5315577 original size:15 final size:15
Alignment explanation
Indices: 5315553--5315609 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
5315543 TTTAGAAGTT
5315553 TAATTAAAATATTTA
1 TAATTAAAATATTTA
*
5315568 TAATTTAAATA-TTA
1 TAATTAAAATATTTA
* *
5315582 T-ATTAAAAAATTTT
1 TAATTAAAATATTTA
*
5315596 TAAATTTAAATATT
1 T-AATTAAAATATT
5315610 ACAATGATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
13 7 0.21
14 7 0.21
15 10 0.30
16 9 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATTAAAATATTTA
Found at i:5315602 original size:29 final size:28
Alignment explanation
Indices: 5315535--5315610 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 28
5315525 TAAGTTAGAG
*
5315535 TTTTTAAATTTAGAAGT-TTAATTAAAATA
1 TTTTTAAATTTA-AA-TATTAATTAAAAAA
*
5315564 TTTAT-AATTTAAATATTATATTAAAAAA
1 TTTTTAAATTTAAATATTA-ATTAAAAAA
5315592 TTTTTAAATTTAAATATTA
1 TTTTTAAATTTAAATATTA
5315611 CAATGATCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 1 0.02
27 5 0.12
28 18 0.44
29 17 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
TTTTTAAATTTAAATATTAATTAAAAAA
Found at i:5317065 original size:15 final size:13
Alignment explanation
Indices: 5317033--5317057 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5317023 GGAAAAAATT
5317033 AAATTATATTTTG
1 AAATTATATTTTG
5317046 AAATTATATTTT
1 AAATTATATTTT
5317058 TTATAATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
AAATTATATTTTG
Found at i:5317911 original size:28 final size:28
Alignment explanation
Indices: 5317831--5317912 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 28
5317821 AAATATAGTA
*
5317831 TTTGAATTTGTTTTCACTACATTAAGCT
1 TTTGAATTTGTTTTCACTACGTTAAGCT
* * *
5317859 TTTGGAGTTCAGGTTTTCACTACGTTCAGCT
1 TTT-GAATT--TGTTTTCACTACGTTAAGCT
*
5317890 TTTGAATTTGTTTTTACTACGTT
1 TTTGAATTTGTTTTCACTACGTT
5317913 TCTAACATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 16 0.36
29 4 0.09
30 4 0.09
31 20 0.45
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.50
Consensus pattern (28 bp):
TTTGAATTTGTTTTCACTACGTTAAGCT
Found at i:5319392 original size:21 final size:21
Alignment explanation
Indices: 5319369--5319410 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5319359 TAATGCAAAA
*
5319369 TTTGATTTTATTTGTTTTAAAT
1 TTTGATTTT-TTTGTTATAAAT
*
5319391 TTTTATTTTTTTGTTATAAA
1 TTTGATTTTTTTGTTATAAA
5319411 AGACTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (21 bp):
TTTGATTTTTTTGTTATAAAT
Found at i:5319454 original size:161 final size:163
Alignment explanation
Indices: 5319287--5319746 Score: 424
Period size: 162 Copynumber: 2.8 Consensus size: 163
5319277 AATAACATAG
* ** *
5319287 TATTTGATTGTATATTTTTTAAAAATAT-AATAGTTCTT-TATAATGCACTAAATTACTGTGTTG
1 TATTTGATTGTATATTTTTTAAAAATATCAATAGTT-TTGTATAAGGCACTAAATTACTAAGTTA
* ** * * *
5319350 TAA-ACAAATTAATGCA-A-AATTTGATT-TTATTTGTTTTAAATTTTTATTTTTTTGTTATAAA
65 TAATAAAAATTAA--CATAGAATTTGATTAAAATTTATTTTAAATTTTAAATTTTTTGTTATAAA
*
5319411 AGACTTAATTACTGCATTATAACAAAAAGTAATGCAA
128 A-ACTTAATTACTACATTATAACAAAAAGTAATGCAA
** * * * *
5319448 TATTTGATTG-A-ATTTTTTTTAAATGTCAATTGTTTTGTATAAGGCTCTCAATTACTAAGTTAT
1 TATTTGATTGTATATTTTTTAAAAATATCAATAGTTTTGTATAAGGCACTAAATTACTAAGTTAT
*
5319511 AATAAAAATTAACATAGTATTTGATTAAAATTTATTTTAAATTTTAAATTTTTTGTTATAAAAAC
66 AATAAAAATTAACATAGAATTTGATTAAAATTTATTTTAAATTTTAAATTTTTTGTTATAAAAAC
* * * *
5319576 TTAATTACTACGTTATAATAAAAAGTAATGTAG
131 TTAATTACTACATTATAACAAAAAGTAATGCAA
* * * * * *
5319609 TATTTGATTGTAT-TTTTTTTAAAATGTCAATTGCTTTGTATAA--CACTTATAATTATTGCA-T
1 TATTTGATTGTATATTTTTTAAAAATATCAATAGTTTTGTATAAGGCAC-TA-AATTACT-AAGT
* * * * * *
5319670 TACAATAAAAATTAACACA-ATATTTGATTAAATTTTGTTTTAAATTTTTAATTTTTTTGGTATA
63 TATAATAAAAATTAACATAGA-ATTTGATTAAAATTTATTTTAAA-TTTTAAATTTTTTGTTATA
*
5319734 AAGAACTCAATTA
126 AA-AACTTAATTA
5319747 TTGTGTTATA
Statistics
Matches: 249, Mismatches: 36, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
159 16 0.06
160 32 0.13
161 67 0.27
162 105 0.42
163 20 0.08
164 9 0.04
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (163 bp):
TATTTGATTGTATATTTTTTAAAAATATCAATAGTTTTGTATAAGGCACTAAATTACTAAGTTAT
AATAAAAATTAACATAGAATTTGATTAAAATTTATTTTAAATTTTAAATTTTTTGTTATAAAAAC
TTAATTACTACATTATAACAAAAAGTAATGCAA
Found at i:5319468 original size:81 final size:81
Alignment explanation
Indices: 5319359--5319735 Score: 288
Period size: 81 Copynumber: 4.6 Consensus size: 81
5319349 GTAAACAAAT
* ** * *
5319359 TAATGCAAAATTTGATTTTATTTGTTTTAAATTTTTATTTTTTTGTTATAAAAGACT-TAATTAC
1 TAATGCAATATTTGATTAAATTTTTTTTAAATTTTAATTTTTTTG-TATAAAAGACTATAATTAC
*
5319423 TGCATTATAACAAAAAG
65 TGCATTATAATAAAAAG
* * * * * *
5319440 TAATGCAATATTTGATTGAATTTTTTTTAAATGTCAATTGTTTTGTAT--AAGGCTCTCAATTAC
1 TAATGCAATATTTGATTAAATTTTTTTTAAATTTTAATTTTTTTGTATAAAAGACTAT-AATTAC
* *
5319503 T-AAGTTATAATAAAAAT
65 TGCA-TTATAATAAAAAG
* *
5319520 TAA--CATAGTATTTGATTAAAATTTATTTTAAATTTTAAATTTTTTGTTATAAAA-ACT-TAAT
1 TAATGCA-A-TATTTGATT-AAATTTTTTTTAAATTTTAATTTTTTTG-TATAAAAGACTATAAT
* *
5319581 TACTACGTTATAATAAAAAG
62 TACTGCATTATAATAAAAAG
* * ** * * ** *
5319601 TAATGTAGTATTTGATTGTATTTTTTTTAAAATGTCAATTGCTTTGTAT--AACACTTATAATTA
1 TAATGCAATATTTGATTAAATTTTTTTT-AAATTTTAATTTTTTTGTATAAAAGAC-TATAATTA
* * *
5319664 TTGCATTACAATAAAAAT
64 CTGCATTATAATAAAAAG
**
5319682 TAACACAATATTTGATTAAATTTTGTTTTAAATTTTTAATTTTTTTGGTATAAA
1 TAATGCAATATTTGATTAAATTTT-TTTTAAA-TTTTAATTTTTTT-GTATAAA
5319736 GAACTCAATT
Statistics
Matches: 228, Mismatches: 47, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
78 9 0.04
79 5 0.02
80 45 0.20
81 142 0.62
82 17 0.07
83 7 0.03
84 2 0.01
85 1 0.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (81 bp):
TAATGCAATATTTGATTAAATTTTTTTTAAATTTTAATTTTTTTGTATAAAAGACTATAATTACT
GCATTATAATAAAAAG
Found at i:5319650 original size:162 final size:161
Alignment explanation
Indices: 5319378--5319775 Score: 503
Period size: 162 Copynumber: 2.4 Consensus size: 161
5319368 ATTTGATTTT
* * *
5319378 ATTTGTTTTAAATTTTTATTTTTTTGTTATAAAAGACTTAATTACTGCATTATAACAAAAAGTAA
1 ATTTGTTTTAAATTTTAATTTTTTTGTTATAAAA-ACTTAATTACTGCGTTATAATAAAAAGTAA
* * * **
5319443 TGCAATATTTGATTGAATTTTTTTTAAATGTCAATTGTTTTGTATAAGGCTCT-CAATTACT-AA
65 TGTAGTATTTGATTGAATTTTTTTTAAATGTCAATTGCTTTGTATAACACT-TACAATTACTGAA
* * *
5319506 GTTATAATAAAAATTAACATAGTATTTGATTAAA
129 -TTACAATAAAAATTAACACAATATTTGATTAAA
* * *
5319540 ATTTATTTTAAATTTTAAATTTTTTGTTATAAAAACTTAATTACTACGTTATAATAAAAAGTAAT
1 ATTTGTTTTAAATTTTAATTTTTTTGTTATAAAAACTTAATTACTGCGTTATAATAAAAAGTAAT
* * * *
5319605 GTAGTATTTGATTGTATTTTTTTTAAAATGTCAATTGCTTTGTATAACACTTATAATTATTGCAT
66 GTAGTATTTGATTGAATTTTTTTT-AAATGTCAATTGCTTTGTATAACACTTACAATTACTGAAT
5319670 TACAATAAAAATTAACACAATATTTGATTAAA
130 TACAATAAAAATTAACACAATATTTGATTAAA
* * * * * *
5319702 TTTTGTTTTAAATTTTTAATTTTTTTGGTATAAAGAACTCAATTATTGTGTTATAATGAAAAGTA
1 ATTTGTTTTAAA-TTTTAATTTTTTTGTTATAAA-AACTTAATTACTGCGTTATAATAAAAAGT-
5319767 AATGTAGTA
63 AATGTAGTA
5319776 ATTGTCAAGT
Statistics
Matches: 203, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
161 50 0.25
162 100 0.49
163 20 0.10
164 24 0.12
165 9 0.04
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (161 bp):
ATTTGTTTTAAATTTTAATTTTTTTGTTATAAAAACTTAATTACTGCGTTATAATAAAAAGTAAT
GTAGTATTTGATTGAATTTTTTTTAAATGTCAATTGCTTTGTATAACACTTACAATTACTGAATT
ACAATAAAAATTAACACAATATTTGATTAAA
Found at i:5322009 original size:19 final size:19
Alignment explanation
Indices: 5321971--5322009 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5321961 TTAAATCAAA
*
5321971 TGATTTTAATTTCTATTTT
1 TGATTTTAATTTCTACTTT
*
5321990 TGATTTTAATTTTTACTTT
1 TGATTTTAATTTCTACTTT
5322009 T
1 T
5322010 TTTAAAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (19 bp):
TGATTTTAATTTCTACTTT
Found at i:5322026 original size:16 final size:16
Alignment explanation
Indices: 5322006--5322038 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5321996 TAATTTTTAC
5322006 TTTTTTTAAAATGCTAA
1 TTTTTTTAAAATG-TAA
5322023 TTTTTTTAAAATGTAA
1 TTTTTTTAAAATGTAA
5322039 AATTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTTTTTAAAATGTAA
Found at i:5322044 original size:17 final size:17
Alignment explanation
Indices: 5322007--5322048 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
5321997 AATTTTTACT
*
5322007 TTTTTTAAAATGCTAAT
1 TTTTTTAAAATGCTAAA
5322024 TTTTTTAAAATG-TAAA
1 TTTTTTAAAATGCTAAA
*
5322040 -ATTTTAAAA
1 TTTTTTAAAA
5322049 GGATATCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 8 0.35
16 3 0.13
17 12 0.52
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTTTTAAAATGCTAAA
Found at i:5326154 original size:18 final size:18
Alignment explanation
Indices: 5326133--5326167 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5326123 ATGAATAAAT
*
5326133 AATAAAAGCTGAAAATAA
1 AATAAAAACTGAAAATAA
*
5326151 AATAAAAACTTAAAATA
1 AATAAAAACTGAAAATA
5326168 TAAAATAATA
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:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (18 bp):
AATAAAAACTGAAAATAA
Found at i:5326188 original size:7 final size:7
Alignment explanation
Indices: 5326149--5326216 Score: 50
Period size: 7 Copynumber: 9.3 Consensus size: 7
5326139 AGCTGAAAAT
5326149 AAAATAA
1 AAAATAA
*
5326156 AAACTTAA
1 AAA-ATAA
*
5326164 AATATAA
1 AAAATAA
5326171 AATAATAAA
1 AA-AAT-AA
5326180 AAAATAA
1 AAAATAA
*
5326187 AAACAT-C
1 AAA-ATAA
5326194 AAAATCAA
1 AAAAT-AA
5326202 AAAAT-A
1 AAAATAA
5326208 AAAATAA
1 AAAATAA
5326215 AA
1 AA
5326217 TGGTAAAAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
6 8 0.17
7 19 0.40
8 17 0.35
9 4 0.08
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAATAA
Found at i:5326203 original size:14 final size:13
Alignment explanation
Indices: 5326144--5326216 Score: 58
Period size: 14 Copynumber: 5.2 Consensus size: 13
5326134 ATAAAAGCTG
5326144 AAAAT-AAAATAA
1 AAAATAAAAATAA
*
5326156 AAACTTAAAATATAA
1 AAA-ATAAAA-ATAA
5326171 AATAATAAAAAAATAA
1 AA-AAT--AAAAATAA
*
5326187 AAACATCAAAATCAA
1 AAA-ATAAAAAT-AA
5326202 AAAATAAAAATAA
1 AAAATAAAAATAA
5326215 AA
1 AA
5326217 TGGTAAAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 3 0.06
13 5 0.10
14 15 0.31
15 13 0.27
16 9 0.18
17 4 0.08
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:5326217 original size:5 final size:6
Alignment explanation
Indices: 5326144--5326216 Score: 51
Period size: 6 Copynumber: 11.5 Consensus size: 6
5326134 ATAAAAGCTG
* * *
5326144 AAAAT- AAAATA AAAACTT AAAATA TAAAATA ATAA-A AAAATAA AAACATC
1 AAAATA AAAATA AAAA-TA AAAATA -AAAATA AAAATA AAAAT-A AAA-ATA
5326194 AAAATCAA AAAATA AAAATA AAA
1 AAAAT--A AAAATA AAAATA AAA
5326217 TGGTAAAAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
5 9 0.17
6 20 0.37
7 18 0.33
8 7 0.13
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:5326585 original size:11 final size:10
Alignment explanation
Indices: 5326541--5326587 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
5326531 CTTAAAACCC
5326541 AAAATTTTCAA
1 AAAATTTTC-A
5326552 AAAATTTT-A
1 AAAATTTTCA
* *
5326561 AAAAATTTCT
1 AAAATTTTCA
*
5326571 AAATTTTTCA
1 AAAATTTTCA
5326581 AAAATTT
1 AAAATTT
5326588 CTAGATTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
9 8 0.28
10 13 0.45
11 8 0.28
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (10 bp):
AAAATTTTCA
Found at i:5326598 original size:19 final size:19
Alignment explanation
Indices: 5326556--5326598 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
5326546 TTTCAAAAAA
*
5326556 TTTTAAAAAATTTCTAAAT
1 TTTTCAAAAATTTCTAAAT
*
5326575 TTTTCAAAAATTTCTAGAT
1 TTTTCAAAAATTTCTAAAT
5326594 TTTTC
1 TTTTC
5326599 TTAGAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTCAAAAATTTCTAAAT
Found at i:5327120 original size:3 final size:3
Alignment explanation
Indices: 5327112--5327195 Score: 71
Period size: 3 Copynumber: 28.0 Consensus size: 3
5327102 ACTATACTAG
* * * *
5327112 TAA TAA TAA CAA TAA TAA -AA TAA TAA CAAA TAA TAC TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* * * * *
5327157 TAA CAA GAA TAA TAA TAG TAA TAG TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5327196 AAATCAACCT
Statistics
Matches: 62, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
2 2 0.03
3 58 0.94
4 2 0.03
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:5327135 original size:17 final size:18
Alignment explanation
Indices: 5327113--5327146 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5327103 CTATACTAGT
5327113 AATAATAAC-AATAATAA
1 AATAATAACAAATAATAA
5327130 AATAATAACAAATAATA
1 AATAATAACAAATAATA
5327147 CTAATACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
AATAATAACAAATAATAA
Found at i:5330113 original size:89 final size:89
Alignment explanation
Indices: 5329962--5330137 Score: 298
Period size: 89 Copynumber: 2.0 Consensus size: 89
5329952 CAATAATATC
* * *
5329962 CAGCTCTCATAATCTATCTTGCCATCATATGTCCATTGGCATGTGCTCTATATATGCTATCATGG
1 CAGCTCTCATAATCAATCTTGCCATCATATGTCCATTGACATGTGCTCCATATATGCTATCATGG
5330027 ACTTCCCAATAATCTTTTTGGCTT
66 ACTTCCCAATAATCTTTTTGGCTT
*
5330051 CAGCTCTCATAATCAATCTTGCCATCATATGTCCATTTACATGTGCTCCATATATGCTATCATGG
1 CAGCTCTCATAATCAATCTTGCCATCATATGTCCATTGACATGTGCTCCATATATGCTATCATGG
* *
5330116 ACTTCTCAATGATCTTTTTGGC
66 ACTTCCCAATAATCTTTTTGGC
5330138 CTTAGAGGCA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (89 bp):
CAGCTCTCATAATCAATCTTGCCATCATATGTCCATTGACATGTGCTCCATATATGCTATCATGG
ACTTCCCAATAATCTTTTTGGCTT
Found at i:5337898 original size:52 final size:53
Alignment explanation
Indices: 5337833--5337936 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 53
5337823 TTCCACAATT
* *
5337833 TGGGCTAAATTAAAAATATTTTCTCTTTT-AAATTTTTAAATTTTTCACCATC
1 TGGGCCAAATTAAAAATATTTTCTCTTTTGAAATTTCTAAATTTTTCACCATC
* *
5337885 TGGGCCAATTTAAAAATATTTTCTTTTTTGAAATTTCTAAATTTTTCACCAT
1 TGGGCCAAATTAAAAATATTTTCTCTTTTGAAATTTCTAAATTTTTCACCAT
5337937 TTAGGCTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 26 0.55
53 21 0.45
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (53 bp):
TGGGCCAAATTAAAAATATTTTCTCTTTTGAAATTTCTAAATTTTTCACCATC
Found at i:5337949 original size:53 final size:52
Alignment explanation
Indices: 5337842--5337942 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 52
5337832 TTGGGCTAAA
* *
5337842 TTAAAAATATTTTCTCTTTTAAATTTTTAAATTTTTCACCATCTGGGCCAAT
1 TTAAAAATATTTTCTCTTTTAAATTTCTAAATTTTTCACCATCTAGGCCAAT
* *
5337894 TTAAAAATATTTTCTTTTTTGAAATTTCTAAATTTTTCACCATTTAGGC
1 TTAAAAATATTTTCTCTTTT-AAATTTCTAAATTTTTCACCATCTAGGC
5337943 TTATTTAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 19 0.43
53 25 0.57
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (52 bp):
TTAAAAATATTTTCTCTTTTAAATTTCTAAATTTTTCACCATCTAGGCCAAT
Found at i:5338483 original size:24 final size:25
Alignment explanation
Indices: 5338436--5338483 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
5338426 TTTTCACCTA
*
5338436 GAAATTTTATAAAAATTTACCATTT
1 GAAATTTTATAAAAATTCACCATTT
* *
5338461 GAAATTTT-TATAAATTCATCATT
1 GAAATTTTATAAAAATTCACCATT
5338484 GGATAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (25 bp):
GAAATTTTATAAAAATTCACCATTT
Found at i:5338574 original size:9 final size:9
Alignment explanation
Indices: 5338562--5338586 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5338552 AAAAATACTT
5338562 AAAAAATTA
1 AAAAAATTA
5338571 AAAAAATTA
1 AAAAAATTA
5338580 AAAAAAT
1 AAAAAAT
5338587 ACCAAAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTA
Found at i:5338877 original size:17 final size:15
Alignment explanation
Indices: 5338839--5338888 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
5338829 TCCCTTCAAA
5338839 TTTCTCCTTCCCCTTC
1 TTTCT-CTTCCCCTTC
5338855 TTTCTCTTCCACCTTC
1 TTTCTCTTCC-CCTTC
*
5338871 TTT-TC-TCTCCTTC
1 TTTCTCTTCCCCTTC
5338884 TTTCT
1 TTTCT
5338889 TTAACCCTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 8 0.26
14 3 0.10
15 7 0.23
16 13 0.42
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTCTCTTCCCCTTC
Found at i:5339505 original size:18 final size:18
Alignment explanation
Indices: 5339482--5339527 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
5339472 TGAAAACCAA
5339482 AAAAATAAATAAATAAAT
1 AAAAATAAATAAATAAAT
* *
5339500 AAAAATATATAACTAAAT
1 AAAAATAAATAAATAAAT
5339518 AAAATATAAA
1 AAAA-ATAAA
5339528 ATACAATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATAAATAAATAAAT
Found at i:5339511 original size:22 final size:24
Alignment explanation
Indices: 5339486--5339530 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
5339476 AACCAAAAAA
5339486 ATAAATAAAT-AAATA-AAAATAT
1 ATAAATAAATAAAATATAAAATAT
*
5339508 ATAACTAAATAAAATATAAAATA
1 ATAAATAAATAAAATATAAAATA
5339531 CAATGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (24 bp):
ATAAATAAATAAAATATAAAATAT
Found at i:5339921 original size:80 final size:79
Alignment explanation
Indices: 5339658--5340393 Score: 442
Period size: 80 Copynumber: 9.1 Consensus size: 79
5339648 AATAACGCTT
* ** *
5339658 TCAATTATTGCATTATAATAAAAATTAACATAGTAGTTGATTAAAATTT-TTTTAAAATTTTTAA
1 TCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTT-AAA-TTTT-A
*
5339722 ATTTTTTGCTACAACAAAC
63 ATTTTTTG-TATAA-AAAC
** * * * ** * * *
5339741 TCAATTACTATATTATAATAAAAAGTAACGTAGTATTGGATT-GTATTTTTTTTAAAATGTCAAT
1 TCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTT-AAATTTTAAT
***
5339805 TATTTTGTAT-AGCGC
65 T-TTTTGTATAAAAAC
* *
5339820 TACCAATTACTGTATTATAATAAAAATTAA-GTAGTATTTTATTAAAATTTGTTTTAAATTTTAA
1 T--CAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAAATTTTAA
5339884 TTTTTTGTTATAAAGAAC
64 TTTTTTG-TATAAA-AAC
* ** * * * * * *
5339902 TCAATCACTGTGTTATAATAAAAAGTAATGCAGTATTTG-TT---TTTTTTTTTAAATGTCAATT
1 TCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAAATTTTAATT
**
5339963 GTTTTGTATAACACTC
66 -TTTTGTATAA-AAAC
* * *
5339979 TCAATTACTGTATTATAATAAAAATTAATGCAGTATTTGATTAAATTTTGTTTTAAATTTTCAAT
1 TCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAAATTTT-AAT
5340044 TTTTTGTTATGAAAAAC
65 TTTTTG-TAT-AAAAAC
* * * * ** * * *
5340061 TTAATTACTGCATTATAAT--AAAGTAATGCAGTATGTGATT-GTATTTTTTTTAAATGTCAATT
1 TCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAAATTTTAATT
**
5340123 GTTTTGTAT-AACGC
66 -TTTTGTATAAAAAC
* * * ** * * * * *
5340137 TCCCAATTGCTGCGTTATAATCAAAATTAATCCAATAATTGATTAAAATCTATTTTCAATTTTCA
1 T--CAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAAATTTT-A
*
5340202 ATTTTTTGTTATAAAAAAA
63 ATTTTTTG-TAT-AAAAAC
* * *** * * ** *
5340221 TCAATTACTACATTACAATAGAAAA-TAACACAATATTTAATT-GTATTT-TTTTAAAATGTTAA
1 TCAATTACTGCATTATAATA-AAAATTAATGTAGTATTTGATTAAAATTTGTTTT-AAATTTTAA
**
5340283 TTGTTTTGTATAACACTC
64 TT-TTTTGTATAA-AAAC
* * *
5340301 TCAATTACTACATTATAATAAAAATTAATGTAGTATTTAATTAAAATTTGTTTTAAATTTTTTAT
1 TCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAAA-TTTTAAT
5340366 TTTTAAT-TATAAAGAAC
65 TTTT--TGTATAAA-AAC
*
5340383 TTAATTACTGC
1 TCAATTACTGC
5340394 GTTTATATTG
Statistics
Matches: 508, Mismatches: 106, Indels: 79
0.73 0.15 0.11
Matches are distributed among these distances:
76 4 0.01
77 58 0.11
78 30 0.06
79 30 0.06
80 129 0.25
81 106 0.21
82 98 0.19
83 50 0.10
84 3 0.01
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (79 bp):
TCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAAATTTTAATT
TTTTGTATAAAAAC
Found at i:5340309 original size:322 final size:318
Alignment explanation
Indices: 5339649--5340393 Score: 872
Period size: 322 Copynumber: 2.3 Consensus size: 318
5339639 AGTGTCTACA
* * * ** * *
5339649 ATAACGCTTTCAATTATTGCATTATAATAAAAATTAACATAGTAGTTGATTAAAATTTT-TTTAA
1 ATAACACTCTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATT-AAATTTTGTTTTA
* * * ** *
5339713 AATTTTTAAATTTTTTGCTACAACAAACTCAATTACTATATTATAATAAAAAGTAACGTAGTATT
65 AA-TTTTAAATTTTTTGTTATAA-AAACTTAATTACTGCATTATAAT-AAAAGTAACGCAGTATT
* *
5339778 GGATTGTATTTTTTTTAAAATGTCAATTATTTTGTATAGCGCTACCAATTACTGTATTATAATAA
127 GGATTGTATTTTTTTTAAAATGTCAATTATTTTGTATAACGCTACCAATTACTGCATTATAATAA
* * * * * * *
5339843 AAATTAAGTAGTATTTTATTAAAATTTGTTTTAAATTTTAATTTTTTGTTATAAAGAACTCAATC
192 AAATTAAGTAATAATTGATTAAAATCTATTTTAAATTTTAATTTTTTGTTATAAAAAAATCAATC
*** * ** * * *
5339908 ACTGTGTTATAATAAAAAGTAATGCAGTATTTGTTTTTTTTTTTAAATGTCAATTGTTTTGT
257 ACTACATTACAATAAAAAGTAACACAATATTTATTTTTTTTTTAAAATGTCAATTGTTTTGT
* *
5339970 ATAACACTCTCAATTACTGTATTATAATAAAAATTAATGCAGTATTTGATTAAATTTTGTTTTAA
1 ATAACACTCTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAATTTTGTTTTAA
* *
5340035 ATTTTCAATTTTTTGTTATGAAAAACTTAATTACTGCATTATAAT-AAAGTAATGCAGTA-TGTG
66 ATTTTAAATTTTTTGTTAT-AAAAACTTAATTACTGCATTATAATAAAAGTAACGCAGTATTG-G
* * * * *
5340098 ATTGTATTTTTTTT-AAATGTCAATTGTTTTGTATAACGCTCCCAATTGCTGCGTTATAATCAAA
129 ATTGTATTTTTTTTAAAATGTCAATTATTTTGTATAACGCTACCAATTACTGCATTATAATAAAA
*
5340162 ATTAA-TCCAATAATTGATTAAAATCTATTTTCAATTTTCAATTTTTTGTTATAAAAAAATCAAT
194 ATTAAGT--AATAATTGATTAAAATCTATTTTAAATTTT-AATTTTTTGTTATAAAAAAATCAAT
* *
5340226 TACTACATTACAATAGAAAA-TAACACAATATTTAATTGTATTTTTTTAAAATGTTAATTGTTTT
256 CACTACATTACAATA-AAAAGTAACACAATATTT-ATT-T-TTTTTTTAAAATGTCAATTGTTTT
5340290 GT
317 GT
* * *
5340292 ATAACACTCTCAATTACTACATTATAATAAAAATTAATGTAGTATTTAATTAAAATTTGTTTTAA
1 ATAACACTCTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAATTTTGTTTTAA
** **
5340357 ATTTTTTATTTTTAATTATAAAGAACTTAATTACTGC
66 ATTTTAAATTTTTTGTTATAAA-AACTTAATTACTGC
5340394 GTTTATATTG
Statistics
Matches: 361, Mismatches: 52, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
316 1 0.00
317 50 0.14
318 51 0.14
319 43 0.12
320 48 0.13
321 55 0.15
322 113 0.31
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (318 bp):
ATAACACTCTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAATTTTGTTTTAA
ATTTTAAATTTTTTGTTATAAAAACTTAATTACTGCATTATAATAAAAGTAACGCAGTATTGGAT
TGTATTTTTTTTAAAATGTCAATTATTTTGTATAACGCTACCAATTACTGCATTATAATAAAAAT
TAAGTAATAATTGATTAAAATCTATTTTAAATTTTAATTTTTTGTTATAAAAAAATCAATCACTA
CATTACAATAAAAAGTAACACAATATTTATTTTTTTTTTAAAATGTCAATTGTTTTGT
Found at i:5340346 original size:162 final size:162
Alignment explanation
Indices: 5339649--5340391 Score: 840
Period size: 162 Copynumber: 4.6 Consensus size: 162
5339639 AGTGTCTACA
* * ** *
5339649 ATAACGCTTTCAATTATTGCATTATAATAAAAATTAACATAGTAGTTGATTAAAATTT-TTTTAA
1 ATAACGCTCTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTT-A
* * * * * *
5339713 AATTTTTAAATTTTTTGCTACAACAAACTCAATTACTATATTATAATAAAAAGTAACGTAGTATT
65 AA-TTTTCAATTTTTTGTTATAAAAAACTCAATTACTACATTATAATAAAAAGTAACGCAGTATT
* *
5339778 GGATTGTATTTTTTTTAAAATGTCAATTATTTTGT
129 TGATTGTA-TTTTTTTAAAATGTCAATTGTTTTGT
* * *
5339813 ATAGCGCTAC-CAATTACTGTATTATAATAAAAATTAA-GTAGTATTTTATTAAAATTTGTTTTA
1 ATAACGCT-CTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTA
* * *** *
5339876 AATTTT-AATTTTTTGTTATAAAGAACTCAATCACTGTGTTATAATAAAAAGTAATGCAGTATTT
65 AATTTTCAATTTTTTGTTATAAAAAACTCAATTACTACATTATAATAAAAAGTAACGCAGTATTT
*
5339940 G-TT-T-TTTTTTTTAAATGTCAATTGTTTTGT
130 GATTGTATTTTTTTAAAATGTCAATTGTTTTGT
* * * *
5339970 ATAACACTCTCAATTACTGTATTATAATAAAAATTAATGCAGTATTTGATTAAATTTTGTTTTAA
1 ATAACGCTCTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAA
* * * * *
5340035 ATTTTCAATTTTTTGTTATGAAAAACTTAATTACTGCATTATAAT--AAAGTAATGCAGTATGTG
66 ATTTTCAATTTTTTGTTATAAAAAACTCAATTACTACATTATAATAAAAAGTAACGCAGTATTTG
*
5340098 ATTGTATTTTTTTTAAATGTCAATTGTTTTGT
131 ATTGTATTTTTTTAAAATGTCAATTGTTTTGT
* * * * ** * * * * *
5340130 ATAACGCTCCCAATTGCTGCGTTATAATCAAAATTAATCCAATAATTGATTAAAATCTATTTTCA
1 ATAACGCTCTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAA
* * * *
5340195 ATTTTCAATTTTTTGTTATAAAAAAATCAATTACTACATTACAATAGAAAA-TAACACAATATTT
66 ATTTTCAATTTTTTGTTATAAAAAACTCAATTACTACATTATAATA-AAAAGTAACGCAGTATTT
* *
5340259 AATTGTATTTTTTTAAAATGTTAATTGTTTTGT
130 GATTGTATTTTTTTAAAATGTCAATTGTTTTGT
* * *
5340292 ATAACACTCTCAATTACTACATTATAATAAAAATTAATGTAGTATTTAATTAAAATTTGTTTTAA
1 ATAACGCTCTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAA
** ** * *
5340357 ATTTTTTATTTTTAATTATAAAGAACTTAATTACT
66 ATTTTCAATTTTTTGTTATAAAAAACTCAATTACT
5340392 GCGTTTATAT
Statistics
Matches: 491, Mismatches: 77, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
156 1 0.00
157 74 0.15
158 31 0.06
159 35 0.07
160 120 0.24
161 49 0.10
162 122 0.25
163 23 0.05
164 36 0.07
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (162 bp):
ATAACGCTCTCAATTACTGCATTATAATAAAAATTAATGTAGTATTTGATTAAAATTTGTTTTAA
ATTTTCAATTTTTTGTTATAAAAAACTCAATTACTACATTATAATAAAAAGTAACGCAGTATTTG
ATTGTATTTTTTTAAAATGTCAATTGTTTTGT
Found at i:5344294 original size:128 final size:128
Alignment explanation
Indices: 5344144--5344397 Score: 293
Period size: 128 Copynumber: 2.0 Consensus size: 128
5344134 AATTAGTAAT
* * * *
5344144 TGTATATTCGTTTAAAACAATCAAAT-ATTGCATTACTCTAG-TGTATAACGCAATAATTGAT-C
1 TGTATATGCGTTTAAAACAATCAAATAATTG--TTACT-TAGAAGTATAACACAATAATTGATAA
* * *
5344206 A-TTAT-ATATGCTTTTAAAGCAATCAAATACTACGTTACTCTGGTGTATAACTCAATAATTGAT
63 ACTT-TCATATACTTTTAAAG-AATAAAATACTACGTTACTCTGGTGTATAACGCAATAATTGAT
5344269 CAA
126 CAA
* * * *
5344272 TGTATATGCTTTTAAAATAATCAAATACATTGTTACTTTGAAGTATAACACAGTAATTGATAAAC
1 TGTATATGCGTTTAAAACAATCAAATA-ATTGTTACTTAGAAGTATAACACAATAATTGATAAAC
* * *
5344337 TTTCATATACTTTTAAAGAATAAAATATTACGTTACTTTGGTGTATAACGCAGTAATTGAT
65 TTTCATATACTTTTAAAGAATAAAATACTACGTTACTCTGGTGTATAACGCAATAATTGAT
5344398 ACTTGTATTT
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
127 2 0.02
128 45 0.42
129 40 0.38
130 19 0.18
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (128 bp):
TGTATATGCGTTTAAAACAATCAAATAATTGTTACTTAGAAGTATAACACAATAATTGATAAACT
TTCATATACTTTTAAAGAATAAAATACTACGTTACTCTGGTGTATAACGCAATAATTGATCAA
Found at i:5344307 original size:64 final size:64
Alignment explanation
Indices: 5344144--5344397 Score: 214
Period size: 64 Copynumber: 4.0 Consensus size: 64
5344134 AATTAGTAAT
* * *
5344144 TGTATATTCGTTTAAAACAATCAAAT--ATTGCATTACTCTAGTGTATAACGCAATAATTGATCA
1 TGTATATGCTTTTAAAACAATCAAATACATTG--TTACTCTGGTGTATAACGCAATAATTGATCA
*
5344207 T
64 A
* * * *
5344208 TATATATGCTTTTAAAGCAATCAAATAC-TACGTTACTCTGGTGTATAACTCAATAATTGATCAA
1 TGTATATGCTTTTAAAACAATCAAATACAT-TGTTACTCTGGTGTATAACGCAATAATTGATCAA
* * ** * * *
5344272 TGTATATGCTTTTAAAATAATCAAATACATTGTTACTTTGAAGTATAACACAGTAATTGATAAA
1 TGTATATGCTTTTAAAACAATCAAATACATTGTTACTCTGGTGTATAACGCAATAATTGATCAA
* * * * * *
5344336 CTTTCATATACTTTT-AAAGAAT-AAA-ATATTACGTTACTTTGGTGTATAACGCAGTAATTGAT
1 -TGT-ATATGCTTTTAAAACAATCAAATACATT--GTTACTCTGGTGTATAACGCAATAATTGAT
5344398 ACTTGTATTT
Statistics
Matches: 157, Mismatches: 25, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
63 4 0.03
64 106 0.68
65 37 0.24
66 10 0.06
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (64 bp):
TGTATATGCTTTTAAAACAATCAAATACATTGTTACTCTGGTGTATAACGCAATAATTGATCAA
Found at i:5344518 original size:15 final size:15
Alignment explanation
Indices: 5344490--5344529 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5344480 CTGAATGTTG
5344490 TACAATAGTA-TAAGA
1 TACAAT-GTATTAAGA
*
5344505 TACATTGTATTAAGA
1 TACAATGTATTAAGA
5344520 TACAATGTAT
1 TACAATGTAT
5344530 GTTATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (15 bp):
TACAATGTATTAAGA
Found at i:5354265 original size:18 final size:20
Alignment explanation
Indices: 5354242--5354284 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5354232 ATTTTTATTT
*
5354242 TATAAAA-TTAA-AAATATA
1 TATAAAAGTTAATAAAAATA
5354260 TATAAAAGTTAATAAAAATA
1 TATAAAAGTTAATAAAAATA
5354280 TATAA
1 TATAA
5354285 TTCAGTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 4 0.18
20 11 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
TATAAAAGTTAATAAAAATA
Found at i:5357508 original size:2 final size:2
Alignment explanation
Indices: 5357501--5357526 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5357491 TGTAAAAGTT
5357501 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
5357527 AGGAAGTATT
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):
TA
Found at i:5359054 original size:34 final size:34
Alignment explanation
Indices: 5359016--5359084 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
5359006 TTTTTAACAA
5359016 TGATTCAATTAATGAAAATAAATATTTAAAAATT
1 TGATTCAATTAATGAAAATAAATATTTAAAAATT
*
5359050 TGATTCAATTGATGAAAATAAATATTTAAAAATT
1 TGATTCAATTAATGAAAATAAATATTTAAAAATT
5359084 T
1 T
5359085 TATTGATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (34 bp):
TGATTCAATTAATGAAAATAAATATTTAAAAATT
Found at i:5360291 original size:2 final size:2
Alignment explanation
Indices: 5360284--5360316 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5360274 AACAGTCTTG
5360284 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 A
5360317 AAGCCAGATA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5362224 original size:18 final size:19
Alignment explanation
Indices: 5362187--5362224 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
5362177 AAATCAAATA
*
5362187 AAAATAATTTTTATTAACT
1 AAAATAATTGTTATTAACT
*
5362206 AAAATAA-TGTTATTGACT
1 AAAATAATTGTTATTAACT
5362224 A
1 A
5362225 GGCAAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
AAAATAATTGTTATTAACT
Found at i:5367723 original size:18 final size:19
Alignment explanation
Indices: 5367689--5367727 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5367679 AATCTAAAAA
5367689 ATCTAATGCTAAATTTGGC
1 ATCTAATGCTAAATTTGGC
*
5367708 ATCTAATGGT-AATTTGGC
1 ATCTAATGCTAAATTTGGC
5367726 AT
1 AT
5367728 TGGGGACCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (19 bp):
ATCTAATGCTAAATTTGGC
Found at i:5369047 original size:2 final size:2
Alignment explanation
Indices: 5369040--5369064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5369030 ACAAAGAATA
5369040 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5369065 AGAATGCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5372018 original size:12 final size:12
Alignment explanation
Indices: 5372003--5372049 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
5371993 AAGTAATTAA
5372003 TTGAATTTAAAT
1 TTGAATTTAAAT
* *
5372015 TTGAGTTTAAAA
1 TTGAATTTAAAT
5372027 TTG-ATTTAAAT
1 TTGAATTTAAAT
5372038 TT-AA-TTAAAT
1 TTGAATTTAAAT
5372048 TT
1 TT
5372050 TATTATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 8 0.27
11 9 0.30
12 13 0.43
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (12 bp):
TTGAATTTAAAT
Found at i:5372045 original size:10 final size:10
Alignment explanation
Indices: 5372032--5372073 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
5372022 TAAAATTGAT
5372032 TTAAATTTAA
1 TTAAATTTAA
*
5372042 TTAAATTTTA
1 TTAAATTTAA
*
5372052 TT-ATTTTAA
1 TTAAATTTAA
5372061 TTAATATTTAA
1 TTAA-ATTTAA
5372072 TT
1 TT
5372074 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 7 0.27
10 12 0.46
11 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTAAATTTAA
Found at i:5373841 original size:22 final size:22
Alignment explanation
Indices: 5373816--5373867 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
5373806 CAAATGATTT
5373816 TTTATAAAAATATAAAAAT-ATA
1 TTTATAAAAAT-TAAAAATAATA
* * *
5373838 TTTACATAAATTAATAATAATA
1 TTTATAAAAATTAAAAATAATA
5373860 TTT-TAAAA
1 TTTATAAAA
5373868 TAATAATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTATAAAAATTAAAAATAATA
Found at i:5373887 original size:22 final size:20
Alignment explanation
Indices: 5373850--5373910 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
5373840 TACATAAATT
5373850 AATAATAA-TA-TTTTA--A
1 AATAATAATTATTTTTATTA
5373866 AATAATAATTATTTTATATTA
1 AATAATAATTATTTT-TATTA
5373887 AATAATAATTATTTTTATTTA
1 AATAATAATTATTTTTA-TTA
5373908 AAT
1 AAT
5373911 TAAAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.21
17 2 0.05
18 3 0.08
19 2 0.05
20 2 0.05
21 22 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATAATTATTTTTATTA
Found at i:5374147 original size:21 final size:21
Alignment explanation
Indices: 5374110--5374149 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5374100 AATAATAAAA
*
5374110 ATAAAATTAATTATTATAACT
1 ATAAAATTAAATATTATAACT
5374131 ATAAAATTAAA-ATTTATAA
1 ATAAAATTAAATA-TTATAA
5374150 TAAGATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAAATTAAATATTATAACT
Found at i:5374307 original size:19 final size:18
Alignment explanation
Indices: 5374270--5374330 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
5374260 TTAAATTTTA
* *
5374270 AAATTTTTTAAAATTAAT
1 AAATTATTTAAAATAAAT
5374288 AAATTATTTAAAATCAAAT
1 AAATTATTTAAAAT-AAAT
* *
5374307 AATAGT-TTTATTAATAAAT
1 AA-ATTATTTA-AAATAAAT
5374326 AAATT
1 AAATT
5374331 TAAATGATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 15 0.43
19 15 0.43
20 5 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AAATTATTTAAAATAAAT
Found at i:5375333 original size:9 final size:9
Alignment explanation
Indices: 5375319--5375385 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
5375309 TATTAAAAAA
5375319 AAAATTTTT
1 AAAATTTTT
5375328 AAAATTTTT
1 AAAATTTTT
*
5375337 --AA-TTAT
1 AAAATTTTT
5375343 AAAATTTTTTT
1 AAAA--TTTTT
*
5375354 AAAATTTTA
1 AAAATTTTT
*
5375363 AAAATTCTT
1 AAAATTTTT
*
5375372 AAAA-ATTT
1 AAAATTTTT
5375380 AAAATT
1 AAAATT
5375386 GGAAGATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
6 3 0.07
7 2 0.05
8 8 0.18
9 24 0.55
11 7 0.16
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (9 bp):
AAAATTTTT
Found at i:5376660 original size:11 final size:11
Alignment explanation
Indices: 5376644--5376684 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5376634 AATCCCATAA
5376644 GAGATTTGTTT
1 GAGATTTGTTT
*
5376655 GAGATTTGTTA
1 GAGATTTGTTT
5376666 GAGATTTGTTT
1 GAGATTTGTTT
5376677 G-GATTTGT
1 GAGATTTGT
5376685 CAGATATTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 7 0.25
11 21 0.75
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:5376683 original size:21 final size:22
Alignment explanation
Indices: 5376643--5376684 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5376633 AAATCCCATA
5376643 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTGAGATTTGTT
5376665 AGAGATTTGTTTG-GATTTGT
1 AGAGATTTGTTTGAGATTTGT
5376685 CAGATATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:5376796 original size:52 final size:52
Alignment explanation
Indices: 5376709--5376865 Score: 217
Period size: 52 Copynumber: 3.0 Consensus size: 52
5376699 TGGACAAGAA
* *
5376709 GACTTGCAAAAGAAGAATTCCAAAA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAG-GGATTCTTAATAGGTAAGTTT
*
5376761 GACTTGCAAGAGAAGAATTTTAAAAGGAAAGGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGTAAGTTT
* * * * * *
5376813 GACTTACAGGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGTAAGTTT
5376865 G
1 G
5376866 TATGGTTATA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
52 89 0.95
53 5 0.05
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGTAAGTTT
Found at i:5377366 original size:30 final size:32
Alignment explanation
Indices: 5377332--5377416 Score: 129
Period size: 30 Copynumber: 2.7 Consensus size: 32
5377322 AGGCTTTTAG
*
5377332 CCCAACAAATGGTATCGGAGCTGTGGTG-AT-
1 CCCAACAAATGGTATCAGAGCTGTGGTGTATC
*
5377362 CCCAACAAATGGTATCAGAGCTGTGGTGTTTC
1 CCCAACAAATGGTATCAGAGCTGTGGTGTATC
*
5377394 CCCAACAAGTGGTATCAGAGCTG
1 CCCAACAAATGGTATCAGAGCTG
5377417 AAGGTTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
30 27 0.54
31 1 0.02
32 22 0.44
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (32 bp):
CCCAACAAATGGTATCAGAGCTGTGGTGTATC
Found at i:5377462 original size:25 final size:24
Alignment explanation
Indices: 5377434--5377514 Score: 83
Period size: 25 Copynumber: 3.3 Consensus size: 24
5377424 GAAATGAGAG
*
5377434 AAGAGTTGAAGATTCAAGATGTGAA
1 AAGAGCTGAAGATTCAAGATGTG-A
* *
5377459 AAGAGCCGAAGGTTCAAGATGTGA
1 AAGAGCTGAAGATTCAAGATGTGA
* *
5377483 AAGAGCTGAA-AGTTCGAGATGTGGG
1 AAGAGCTGAAGA-TTCAAGATGT-GA
5377508 AAGAGCT
1 AAGAGCT
5377515 AAAGGTTTGG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 19 0.40
25 28 0.60
ACGTcount: A:0.38, C:0.09, G:0.33, T:0.20
Consensus pattern (24 bp):
AAGAGCTGAAGATTCAAGATGTGA
Found at i:5377497 original size:24 final size:24
Alignment explanation
Indices: 5377446--5377518 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
5377436 GAGTTGAAGA
* *
5377446 TTCAAGATGTGAAAAGAGCCGAAGG
1 TTCAAGATGTG-AAAGAGCTGAAAG
5377471 TTCAAGATGTGAAAGAGCTGAAAG
1 TTCAAGATGTGAAAGAGCTGAAAG
* *
5377495 TTCGAGATGTGGGAAGAGCT-AAAG
1 TTCAAGATGT-GAAAGAGCTGAAAG
5377519 GTTTGGGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
24 24 0.56
25 19 0.44
ACGTcount: A:0.38, C:0.10, G:0.33, T:0.19
Consensus pattern (24 bp):
TTCAAGATGTGAAAGAGCTGAAAG
Found at i:5377585 original size:18 final size:19
Alignment explanation
Indices: 5377562--5377598 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5377552 AAGCAAGTTC
5377562 AGAAGAGCTCGA-TTCGAG
1 AGAAGAGCTCGAGTTCGAG
*
5377580 AGAAGAGTTCGAGTTCGAG
1 AGAAGAGCTCGAGTTCGAG
5377599 TTTTGAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.14, G:0.35, T:0.19
Consensus pattern (19 bp):
AGAAGAGCTCGAGTTCGAG
Found at i:5377786 original size:11 final size:11
Alignment explanation
Indices: 5377770--5377810 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
5377760 AATCCCATAA
5377770 GAGATTTGTTT
1 GAGATTTGTTT
*
5377781 GAGATTTGTTA
1 GAGATTTGTTT
5377792 GAGATTTGTTT
1 GAGATTTGTTT
5377803 G-GATTTGT
1 GAGATTTGT
5377811 CAGATATTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 7 0.25
11 21 0.75
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:5377809 original size:21 final size:22
Alignment explanation
Indices: 5377769--5377810 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5377759 AAATCCCATA
5377769 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTGAGATTTGTT
5377791 AGAGATTTGTTTG-GATTTGT
1 AGAGATTTGTTTGAGATTTGT
5377811 CAGATATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:5377922 original size:52 final size:52
Alignment explanation
Indices: 5377835--5377990 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
5377825 TGGACAAGAA
* *
5377835 GACTTGCAAAAGAAGAATTCCAAAA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAG-GGATTCTTAATAGGTAAGTTT
*
5377887 GACTTGCAAGAGAAGAATTTTAAAAGGAAAGGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGTAAGTTT
* * * * * *
5377939 GACTTACAGGAGAAGAATTCTAAGAGGAGAGGGA-TCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGTAAGTTT
5377990 G
1 G
5377991 TATGGTTATA
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
51 16 0.17
52 72 0.77
53 5 0.05
ACGTcount: A:0.40, C:0.08, G:0.26, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGTAAGTTT
Found at i:5378494 original size:31 final size:31
Alignment explanation
Indices: 5378456--5378524 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
5378446 AGGCTTTTAG
5378456 CCCAACAAATGGTATCAGAGCTGTGGTGATC
1 CCCAACAAATGGTATCAGAGCTGTGGTGATC
* *
5378487 CCCAACAAATGGTATCAGAGCTGTGGTGTTT
1 CCCAACAAATGGTATCAGAGCTGTGGTGATC
5378518 CCCAACA
1 CCCAACA
5378525 GAAAGTGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (31 bp):
CCCAACAAATGGTATCAGAGCTGTGGTGATC
Found at i:5380750 original size:27 final size:26
Alignment explanation
Indices: 5380718--5380775 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
5380708 ATAAGACAGA
5380718 ATAATATTATTTAATCTAATCTTATTT
1 ATAATATTATTTAATCTAATCTTA-TT
* * *
5380745 ATAATATTATTTTATCTTATTTTATT
1 ATAATATTATTTAATCTAATCTTATT
5380771 ATAAT
1 ATAAT
5380776 TTTGTGTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (26 bp):
ATAATATTATTTAATCTAATCTTATT
Found at i:5381002 original size:21 final size:22
Alignment explanation
Indices: 5380967--5381009 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
5380957 ACTGTTAAAA
*
5380967 GTTAAAATTAAAATAATATATG
1 GTTAAAATGAAAATAATATATG
5380989 GTTAAAA-GAAAATAATATATG
1 GTTAAAATGAAAATAATATATG
5381010 ATTTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (22 bp):
GTTAAAATGAAAATAATATATG
Found at i:5384473 original size:3 final size:3
Alignment explanation
Indices: 5384467--5384499 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5384457 ATTATTATTA
5384467 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
5384500 GTACAGGCCA
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:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:5389267 original size:18 final size:17
Alignment explanation
Indices: 5389246--5389280 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5389236 TTTTATTCAA
*
5389246 ATAATTATAATATTTTAT
1 ATAATCATAAT-TTTTAT
5389264 ATAATCATAATTTTTAT
1 ATAATCATAATTTTTAT
5389281 TATTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAATCATAATTTTTAT
Found at i:5390960 original size:23 final size:23
Alignment explanation
Indices: 5390930--5390981 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
5390920 AAGTTTCGTA
* * *
5390930 TTTTTATAAGATTAGCAGTATTT
1 TTTTTATAAAATTAACAATATTT
5390953 TTTTTATAAAATTAACAATATTT
1 TTTTTATAAAATTAACAATATTT
5390976 TTTTTA
1 TTTTTA
5390982 AAACATTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTTTATAAAATTAACAATATTT
Found at i:5391661 original size:61 final size:60
Alignment explanation
Indices: 5391556--5391752 Score: 182
Period size: 61 Copynumber: 3.2 Consensus size: 60
5391546 ATTTTTTAAA
* * * * * * * * *
5391556 GAGATTATTCAATGCGTTTTCTAATTAAAAACACCTTGAATAATCCCTCAAAAAAATGAAAG
1 GAGATTATTCAAGGCATTTT-TTATCACAAACGCCTTGAATAAT-CTTAAAAAAAATAAAAG
* * *
5391618 GAGATTATTCAAGGCATTTTTTGTCATAAACGCCTTGAATAATCTTAAAAAAAAATTAGAA-
1 GAGATTATTCAAGGCATTTTTTATCACAAACGCCTTGAATAATCTT-AAAAAAAA-TAAAAG
* * * *
5391679 GAGATTACTAAAGGCATTTTTTATCACAAATGCCTTGAATAATTTTTAAAAAAAATCAAAAG
1 GAGATTATTCAAGGCATTTTTTATCACAAACGCCTTGAATAA-TCTTAAAAAAAAT-AAAAG
5391741 G-GATTATTCAAG
1 GAGATTATTCAAG
5391753 ATGTTTTTGA
Statistics
Matches: 110, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
60 3 0.03
61 82 0.75
62 25 0.23
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (60 bp):
GAGATTATTCAAGGCATTTTTTATCACAAACGCCTTGAATAATCTTAAAAAAAATAAAAG
Found at i:5391681 original size:123 final size:125
Alignment explanation
Indices: 5391371--5391708 Score: 293
Period size: 123 Copynumber: 2.7 Consensus size: 125
5391361 TTTTGTAAGC
* *
5391371 GATTATTC-AAGATGTTTCTAGTCAAAAACGCCTTGAATAATC-TAAAAAAAAA-TGGCAAGAGA
1 GATTATTCAAAG-TGTTT-TTGTCAAAAACGCCTTGAATAATCTTAAAAAAAAATTAG-AAGAGA
**
5391433 TTATTCAAGGCATTTTTTTTTATCAAAAACGCTTAAAATAATCCCCTCACAAAAAATGAAAAAA
63 TTATTCAAGGCATTTTTAATTA-CAAAAACGCTTAAAATAATCCCCTCACAAAAAATGAAAAAA
* * ** ****
5391497 GATTATTCAAAGTGTTTTTGACCAAAAACACCTTGAATAAT-TTCATTCAATTTTTTA-AAGAGA
1 GATTATTCAAAGTGTTTTTG-TCAAAAACGCCTTGAATAATCTT-A-AAAAAAAATTAGAAGAGA
* * * **
5391560 TTATTCAATGCGTTTTCTAATTA-AAAACAC-CTT-GAATAAT-CCCTCA-AAAAAATGAAAGGA
63 TTATTCAAGGCATTTT-TAATTACAAAA-ACGCTTAAAATAATCCCCTCACAAAAAATGAAAAAA
* *
5391620 GATTATTCAAGGCAT-TTTTTGTCATAAACGCCTTGAATAATCTTAAAAAAAAATTAGAAGAGAT
1 GATTATTCAAAG--TGTTTTTGTCAAAAACGCCTTGAATAATCTTAAAAAAAAATTAGAAGAGAT
* * * *
5391684 TACTAAAGGCATTTTTTATCACAAA
64 TATTCAAGGCATTTTTAATTACAAA
5391709 TGCCTTGAAT
Statistics
Matches: 166, Mismatches: 33, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
122 9 0.05
123 62 0.37
124 14 0.08
125 9 0.05
126 39 0.23
127 26 0.16
128 6 0.04
129 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (125 bp):
GATTATTCAAAGTGTTTTTGTCAAAAACGCCTTGAATAATCTTAAAAAAAAATTAGAAGAGATTA
TTCAAGGCATTTTTAATTACAAAAACGCTTAAAATAATCCCCTCACAAAAAATGAAAAAA
Found at i:5391760 original size:61 final size:60
Alignment explanation
Indices: 5391605--5391969 Score: 188
Period size: 61 Copynumber: 6.0 Consensus size: 60
5391595 ATAATCCCTC
* * * *
5391605 AAAAAAATGAAAGGAGATTATTCAAGGCATTTTTTGTCATAAACGCCTTGAATAATCTTAA
1 AAAAAAATAAAAGG-GATTATTCAAGGCATTTTTTATCACAAATGCCTTGAATAATCTTAA
* * * * * *
5391666 AAAAAAATTAGAAGAGATTACTAAAGGCATTTTTTATCACAAATGCCTTGAATAATTTTTA
1 AAAAAAA-TAAAAGGGATTATTCAAGGCATTTTTTATCACAAATGCCTTGAATAATCTTAA
* *
5391727 AAAAAAATCAAAAGGGATTATTCAA-G-ATGTTTTTGATCAGAAATG-CTTTAGATAATCCAATT
1 AAAAAAAT-AAAAGGGATTATTCAAGGCAT-TTTTT-ATCACAAATGCCTTGA-ATAAT-C--TT
*
5391789 -C
59 AA
***** ** * * * * *
5391790 AATTTTTTGTAAGGGCTTATTCAAGGCATTTTCTAGTAAAAAAATGCCTTGAATAATCTCAA
1 AAAAAAATAAAAGGGATTATTCAAGGCATTTTTTA-T-CACAAATGCCTTGAATAATCTTAA
*** * * * * * *
5391852 AAAAAAA-AAGAAAAAATTATTAAAGACGTTTTTTTGTAAAAAAATGCCTTGAATAATCTT--
1 AAAAAAATAA-AAGGGATTATTCAAGGC-ATTTTTTAT-CACAAATGCCTTGAATAATCTTAA
* * * * * *
5391912 -AAAAAATAAAAAGAATTATTCGAGGCATTTTTTATCATAAATGTCTTGAATAACCTTA
1 AAAAAAATAAAAGGGATTATTCAAGGCATTTTTTATCACAAATGCCTTGAATAATCTTA
5391970 TTCAATTTTT
Statistics
Matches: 227, Mismatches: 59, Indels: 39
0.70 0.18 0.12
Matches are distributed among these distances:
57 18 0.08
58 7 0.03
59 21 0.09
60 13 0.06
61 80 0.35
62 54 0.24
63 15 0.07
64 15 0.07
65 4 0.02
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (60 bp):
AAAAAAATAAAAGGGATTATTCAAGGCATTTTTTATCACAAATGCCTTGAATAATCTTAA
Found at i:5391872 original size:62 final size:63
Alignment explanation
Indices: 5391806--5391926 Score: 181
Period size: 62 Copynumber: 1.9 Consensus size: 63
5391796 TTGTAAGGGC
* *
5391806 TTATTCAAGGCATTTTCTAGTAAAAAAATGCCTTGAATAATCTCAAAAAA-AAAAAGAAAAAA
1 TTATTAAAGACATTTTCTAGTAAAAAAATGCCTTGAATAATCTCAAAAAATAAAAAGAAAAAA
* * * *
5391868 TTATTAAAGACGTTTTTTTGTAAAAAAATGCCTTGAATAATCTTAAAAAATAAAAAGAA
1 TTATTAAAGACATTTTCTAGTAAAAAAATGCCTTGAATAATCTCAAAAAATAAAAAGAA
5391927 TTATTCGAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
62 44 0.85
63 8 0.15
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (63 bp):
TTATTAAAGACATTTTCTAGTAAAAAAATGCCTTGAATAATCTCAAAAAATAAAAAGAAAAAA
Found at i:5391995 original size:183 final size:183
Alignment explanation
Indices: 5391621--5392038 Score: 415
Period size: 183 Copynumber: 2.3 Consensus size: 183
5391611 ATGAAAGGAG
* * * * * * * *
5391621 ATTATTCAAGGCATTTTTTGTCATAAACGCCTTGAATAATCTTAAAAAAAAATTAGAAGAGATTA
1 ATTATTCAAGGCATTTTTAGTAAAAAAAGCCTTGAATAATCTCAAAAAAAAATAAGAAAAAATTA
* * * * * *
5391686 CTAAAGGCATTTTTTATCACAAATGCCTTGAATAATTTTTAAAAAAAATCAAAAGGGATTATTCA
66 CTAAAGACATTTTTTATAAAAAATGCCTTGAATAATTCTT-AAAAAAATCAAAAAGAATTATTCA
* **
5391751 AGATGTTTTTGATCAGAAATGCTTTAGATAATCCAATTCAATTTTTTGTAAGGG
130 AGATGTTTTTGATCAGAAATGCTTGAGATAATCCAATTCAATTTTTTGTAAGAA
*
5391805 CTTATTCAAGGCATTTTCTAGTAAAAAAATGCCTTGAATAATCTCAAAAAAAAA-AAGAAAAAAT
1 ATTATTCAAGGCATTTT-TAGTAAAAAAA-GCCTTGAATAATCTCAAAAAAAAATAAGAAAAAAT
* * *
5391869 TATTAAAGACGTTTTTTTGTAAAAAAATGCCTTGAATAA-TCTT-AAAAAAT-AAAAAGAATTAT
64 TACTAAAGAC-ATTTTTTAT-AAAAAATGCCTTGAATAATTCTTAAAAAAATCAAAAAGAATTAT
* * *
5391931 TCGAGGCAT-TTTTT-ATCATAAATGTCTTGA-ATAA-CCTTATTCAATTTTTTGTAAGAA
127 TC-AAG-ATGTTTTTGATCAGAAATG-CTTGAGATAATCC-AATTCAATTTTTTGTAAGAA
* * * *
5391988 ATTATTCAAGACGTTTTTTGGTAAAAAACA-CCTTGATTAATC-CAAAAAAAA
1 ATTATTCAAGGC-ATTTTTAGTAAAAAA-AGCCTTGAATAATCTCAAAAAAAA
5392039 TGAAAGTGAA
Statistics
Matches: 195, Mismatches: 29, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
181 9 0.05
182 13 0.07
183 61 0.31
184 39 0.20
185 24 0.12
186 33 0.17
187 16 0.08
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (183 bp):
ATTATTCAAGGCATTTTTAGTAAAAAAAGCCTTGAATAATCTCAAAAAAAAATAAGAAAAAATTA
CTAAAGACATTTTTTATAAAAAATGCCTTGAATAATTCTTAAAAAAATCAAAAAGAATTATTCAA
GATGTTTTTGATCAGAAATGCTTGAGATAATCCAATTCAATTTTTTGTAAGAA
Found at i:5392076 original size:59 final size:59
Alignment explanation
Indices: 5392002--5392203 Score: 191
Period size: 62 Copynumber: 3.5 Consensus size: 59
5391992 TTCAAGACGT
* * * *
5392002 TTTTTGGTAAAAAACACCTTGATTAATCCAAAAAAAATGAAAGTGAATTATTTAAGGTG
1 TTTTTGGTAAAAAACACCTTGAATAATCCAAAAAAAATGAAAGGGAATTATTAAAGGTA
* * * * * *
5392061 TTTTTGGTTAGAAACACGTTGAATAATCTTTAAAAAAAAATTAAAGGGGATTATTAAAGGTA
1 TTTTTGGTAAAAAACACCTTGAATAATC---CAAAAAAAATGAAAGGGAATTATTAAAGGTA
*** *
5392123 TTTTTGACCAAAAATACCTTGAATAATCC-AAAAAAA--AAA--G-ATTATTAAAGGTA
1 TTTTTGGTAAAAAACACCTTGAATAATCCAAAAAAAATGAAAGGGAATTATTAAAGGTA
* *
5392176 TTTTTGGTAAAAAACACATTAAATAATC
1 TTTTTGGTAAAAAACACCTTGAATAATC
5392204 TCTTTCAATT
Statistics
Matches: 117, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
53 35 0.30
54 1 0.01
56 3 0.03
58 7 0.06
59 24 0.21
62 47 0.40
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.32
Consensus pattern (59 bp):
TTTTTGGTAAAAAACACCTTGAATAATCCAAAAAAAATGAAAGGGAATTATTAAAGGTA
Found at i:5395530 original size:45 final size:45
Alignment explanation
Indices: 5395480--5395566 Score: 106
Period size: 46 Copynumber: 1.9 Consensus size: 45
5395470 AATAAAAATA
* *
5395480 TTATTTT-CTATTCAT-AAAATATATTTTTTAAAATATTAAATATCT
1 TTATTTTCCT-TTCATAAAAATATATTTTATAAAA-AATAAATATCT
**
5395525 TTATTTTCCTTTTTTAAAAATATATTTTATAAAAAATAAATA
1 TTATTTTCCTTTCATAAAAATATATTTTATAAAAAATAAATA
5395567 AAGGAAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 17 0.47
46 19 0.53
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (45 bp):
TTATTTTCCTTTCATAAAAATATATTTTATAAAAAATAAATATCT
Found at i:5395804 original size:32 final size:31
Alignment explanation
Indices: 5395768--5395827 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
5395758 TTACATATCA
* *
5395768 TTTAAAAAATTAAGTAAAAATTTTTATATTGG
1 TTTAAAAAATTAAATAAAAA-CTTTATATTGG
*
5395800 TTTAAGAAATTAAATAAAAACTTTATAT
1 TTTAAAAAATTAAATAAAAACTTTATAT
5395828 CATGTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.42
Consensus pattern (31 bp):
TTTAAAAAATTAAATAAAAACTTTATATTGG
Found at i:5395993 original size:14 final size:14
Alignment explanation
Indices: 5395956--5395995 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
5395946 TAAATTATTT
*
5395956 TTTTATAAAACATA
1 TTTTATAAAATATA
5395970 TTTTATAAAATATA
1 TTTTATAAAATATA
*
5395984 TTTTAAAAAATA
1 TTTTATAAAATA
5395996 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTTATAAAATATA
Found at i:5397264 original size:16 final size:16
Alignment explanation
Indices: 5397227--5397270 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5397217 GGATACAATG
5397227 AATTCATAAAT-GTTT
1 AATTCATAAATAGTTT
5397242 AAGTTCATAAATAG-TT
1 AA-TTCATAAATAGTTT
5397258 AGATTCATAAATA
1 A-ATTCATAAATA
5397271 ATTAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (16 bp):
AATTCATAAATAGTTT
Found at i:5399225 original size:22 final size:20
Alignment explanation
Indices: 5399197--5399270 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 20
5399187 ATTGTAGGTT
5399197 TTTTATTTTTCATTTTTATTTA
1 TTTTATTTTT-ATTTTT-TTTA
5399219 TTTTATTTTTAGATTTTCTTTTA
1 TTTTATTTTT--ATTTT-TTTTA
*
5399242 TTTTACTTATTATTTTTTTTA
1 TTTTA-TTTTTATTTTTTTTA
5399263 TTTTATTT
1 TTTTATTT
5399271 CAAATTGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 2 0.04
21 10 0.22
22 15 0.33
23 14 0.30
24 5 0.11
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (20 bp):
TTTTATTTTTATTTTTTTTA
Found at i:5399289 original size:5 final size:5
Alignment explanation
Indices: 5399210--5399270 Score: 54
Period size: 5 Copynumber: 11.6 Consensus size: 5
5399200 TATTTTTCAT
*
5399210 TTTTA -TTTA TTTTA TTTTTAGA TTTTC TTTTA TTTTA CTTATTA TTTT-
1 TTTTA TTTTA TTTTA -TTTT--A TTTTA TTTTA TTTTA -TT-TTA TTTTA
5399258 TTTTA TTTTA TTT
1 TTTTA TTTTA TTT
5399271 CAAATTGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
4 8 0.17
5 23 0.49
6 8 0.17
7 7 0.15
8 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:5400634 original size:21 final size:21
Alignment explanation
Indices: 5400605--5400654 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
5400595 TACTAATCCT
* * *
5400605 TTATGTTATTTTTTATAGATA
1 TTATATTATTCTTTATACATA
*
5400626 TTATATTATTCTTTGTACATA
1 TTATATTATTCTTTATACATA
5400647 TATATATT
1 T-TATATT
5400655 TACTAACCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATATTATTCTTTATACATA
Found at i:5405836 original size:24 final size:25
Alignment explanation
Indices: 5405792--5405842 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
5405782 TAATAAGTAT
5405792 TATGAAAAAAACTAAGAAATAAAAC
1 TATGAAAAAAACTAAGAAATAAAAC
* *
5405817 TATGTAAAAAATTAAG-AATAAAAC
1 TATGAAAAAAACTAAGAAATAAAAC
5405841 TA
1 TA
5405843 AATGTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.22
Consensus pattern (25 bp):
TATGAAAAAAACTAAGAAATAAAAC
Found at i:5410040 original size:22 final size:22
Alignment explanation
Indices: 5410012--5410055 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5410002 ATTTTATGTC
*
5410012 CTTAATTTTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
*
5410034 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
5410056 TAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:5411844 original size:14 final size:14
Alignment explanation
Indices: 5411810--5411855 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
5411800 ATTCATGAAT
*
5411810 AATAAACAAATTATA
1 AATAAATAAATT-TA
*
5411825 ACTAAATAAATTTA
1 AATAAATAAATTTA
5411839 AATAAATAAATCTTA
1 AATAAATAAAT-TTA
5411854 AA
1 AA
5411856 CGAATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAAATAAATTTA
Found at i:5411897 original size:20 final size:20
Alignment explanation
Indices: 5411840--5411897 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
5411830 ATAAATTTAA
* * *
5411840 ATAAATAAATCTTAAACGAAT
1 ATAAACAAATCTTAAA-AAAC
**
5411861 ATAAACAAATCCAAAAAAAC
1 ATAAACAAATCTTAAAAAAC
5411881 ATAAACAAATCTTAAAA
1 ATAAACAAATCTTAAAA
5411898 TAGGATTAGG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.64, C:0.14, G:0.02, T:0.21
Consensus pattern (20 bp):
ATAAACAAATCTTAAAAAAC
Found at i:5416017 original size:23 final size:23
Alignment explanation
Indices: 5415977--5416020 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5415967 AAGTTATATA
*
5415977 TATTAAATTTTAAATTTTAAATT
1 TATTAAATGTTAAATTTTAAATT
**
5416000 TATTAAATGTTATTTTTTAAA
1 TATTAAATGTTAAATTTTAAA
5416021 AATAATTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTAAATGTTAAATTTTAAATT
Found at i:5416178 original size:25 final size:25
Alignment explanation
Indices: 5416147--5416198 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
5416137 AAATAATTAT
*
5416147 ATAAATT-AATTGAATTAAAATTTGA
1 ATAAATTAAATTAAATT-AAATTTGA
5416172 ATAAATTAAATTAAATTAAATTTGA
1 ATAAATTAAATTAAATTAAATTTGA
5416197 AT
1 AT
5416199 TTAATAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
ATAAATTAAATTAAATTAAATTTGA
Found at i:5416681 original size:18 final size:18
Alignment explanation
Indices: 5416650--5416695 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5416640 TTATTTTTTT
*
5416650 TTTA-TTATTATTATTAA
1 TTTATTTATTTTTATTAA
*
5416667 TATT-TTTATTTTTATTTA
1 T-TTATTTATTTTTATTAA
5416685 TTTATTTATTT
1 TTTATTTATTT
5416696 ATTTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTATTTTTATTAA
Found at i:5416686 original size:4 final size:4
Alignment explanation
Indices: 5416677--5416703 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5416667 TATTTTTATT
5416677 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
5416704 TGTGGAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:5427742 original size:2 final size:2
Alignment explanation
Indices: 5427735--5427772 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5427725 ACCCAAAAGT
5427735 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5427773 AGTGTTACCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5430413 original size:18 final size:18
Alignment explanation
Indices: 5430371--5430414 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5430361 AACTACTCAA
* *
5430371 ATATATATGTACATGTAT
1 ATATACATGTACATGTAC
* *
5430389 GTTTACATGTACATGTAC
1 ATATACATGTACATGTAC
5430407 ATATACAT
1 ATATACAT
5430415 ATATATATGT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
ATATACATGTACATGTAC
Found at i:5433816 original size:145 final size:143
Alignment explanation
Indices: 5433476--5433816 Score: 323
Period size: 145 Copynumber: 2.4 Consensus size: 143
5433466 AGTTTTTCGT
* * ** *
5433476 GAAAAATTTTAAATCATGTTTAAATATTATTTTATGAATTTCGATAC-ATTCAAATCCTAATTGT
1 GAAAAATTTTAAATCATATTTAAATATTATTTTATGAATTTTGATACAATAAAAATCCTAATTGC
* * ** *
5433540 ACCTAAAAAAGGTGAAATTATCAAAATGTTTTTTAGAGATATTTTCGTAAGTTAATCTTTTTTGG
66 ACCTAAAAAAGGTAAAATTATCAAAATGTATTGAAGAGATATTTTCATAAGTTAATCTTTTTTGG
**
5433605 GTCGAATTCTTGT
131 GTCGAATTCTTAC
* * * * ** * ** *
5433618 GAAAAACTCTAAATCA-AGTTTAAATATTATTTTATAAATTTTAATTTATTAAAAATTTTGATTG
1 GAAAAATTTTAAATCATA-TTTAAATATTATTTTATGAATTTTGATACAATAAAAATCCTAATTG
* * * * *
5433682 CACCT-CAAAAGGAATAAAATTATCAAAATGTCATTGAAG-GGTATTTTTTATAATTTAGTCTTT
65 CACCTAAAAAAGG--TAAAATTATCAAAATGT-ATTGAAGAGATA-TTTTCATAAGTTAATCTTT
* *
5433745 TTTGGGTTG-ATTTTTCAC
126 TTTGGGTCGAATTCTT-AC
*
5433763 GAAAAATTTTAAATCATAATTAAATATTATTTTATGAATTTTGATACAATAAAA
1 GAAAAATTTTAAATCATATTTAAATATTATTTTATGAATTTTGATACAATAAAA
5433817 TCTTGAAAAT
Statistics
Matches: 154, Mismatches: 37, Indels: 13
0.75 0.18 0.06
Matches are distributed among these distances:
142 44 0.29
143 14 0.09
144 24 0.16
145 71 0.46
146 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (143 bp):
GAAAAATTTTAAATCATATTTAAATATTATTTTATGAATTTTGATACAATAAAAATCCTAATTGC
ACCTAAAAAAGGTAAAATTATCAAAATGTATTGAAGAGATATTTTCATAAGTTAATCTTTTTTGG
GTCGAATTCTTAC
Found at i:5435323 original size:25 final size:25
Alignment explanation
Indices: 5435295--5435359 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
5435285 AACCAAAGTC
5435295 TAATCCTAACCCTAAAACCTCACCT
1 TAATCCTAACCCTAAAACCTCACCT
* *
5435320 TAATTCTAACCCTAAAATCTCACCT
1 TAATCCTAACCCTAAAACCTCACCT
* *
5435345 TAGTCCTAACTCTAA
1 TAATCCTAACCCTAA
5435360 TCCAAACTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.35, C:0.34, G:0.02, T:0.29
Consensus pattern (25 bp):
TAATCCTAACCCTAAAACCTCACCT
Done.