Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, 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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 21 of 74
Found at i:5178983 original size:7 final size:7
Alignment explanation
Indices: 5178889--5178975 Score: 80
Period size: 7 Copynumber: 13.0 Consensus size: 7
5178879 TAAAAATTCC
5178889 ATTTTTA
1 ATTTTTA
5178896 ATTTTTA
1 ATTTTTA
5178903 A-TTTTA
1 ATTTTTA
5178909 A-TTTT-
1 ATTTTTA
5178914 ATTTATT-
1 ATTT-TTA
5178921 -TTTTTA
1 ATTTTTA
5178927 ATTTTT-
1 ATTTTTA
*
5178933 ATTTATAAA
1 ATTT-T-TA
5178942 ATTTTTA
1 ATTTTTA
5178949 ATTTTTA
1 ATTTTTA
5178956 ATTTTTA
1 ATTTTTA
*
5178963 A-TTTAA
1 ATTTTTA
5178969 ATTTTTA
1 ATTTTTA
5178976 TAATTTATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
5 3 0.04
6 24 0.35
7 36 0.53
8 1 0.01
9 4 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTTTTA
Found at i:5188720 original size:18 final size:17
Alignment explanation
Indices: 5188677--5188722 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
5188667 TAGTATTTAG
5188677 TTTCCTTAAAA-AAATA
1 TTTCCTTAAAACAAATA
5188693 TTT-C--AAAACAAATAA
1 TTTCCTTAAAACAAAT-A
5188708 TTTCCTTAAAACAAA
1 TTTCCTTAAAACAAA
5188723 GGCTCCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 4 0.16
14 4 0.16
15 5 0.20
16 4 0.16
18 8 0.32
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (17 bp):
TTTCCTTAAAACAAATA
Found at i:5194193 original size:27 final size:28
Alignment explanation
Indices: 5194163--5194217 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
5194153 GTTTGATTTG
*
5194163 AGAAAATATTTTTTATTTTC-ATTTTTT
1 AGAAAATAGTTTTTATTTTCTATTTTTT
5194190 AGAAAATAGTTTTTATTTTCTATTTTTT
1 AGAAAATAGTTTTTATTTTCTATTTTTT
5194218 TGTTTTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (28 bp):
AGAAAATAGTTTTTATTTTCTATTTTTT
Found at i:5199811 original size:18 final size:18
Alignment explanation
Indices: 5199784--5199820 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5199774 GGCAAAGGGA
*
5199784 CTGTATATCAGAAGTTTT
1 CTGTAAATCAGAAGTTTT
5199802 CTGTAAATCAGAAGTTTT
1 CTGTAAATCAGAAGTTTT
5199820 C
1 C
5199821 ATATATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (18 bp):
CTGTAAATCAGAAGTTTT
Found at i:5208776 original size:19 final size:19
Alignment explanation
Indices: 5208725--5208776 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
5208715 TAATCGTGTC
*
5208725 TATTCGTATATATTCATAT
1 TATTTGTATATATTCATAT
* * *
5208744 TAGTTATATCTATTCATAT
1 TATTTGTATATATTCATAT
5208763 ATATTTGTAT-TATT
1 -TATTTGTATATATT
5208777 AGTGTTTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.56
Consensus pattern (19 bp):
TATTTGTATATATTCATAT
Found at i:5208786 original size:29 final size:29
Alignment explanation
Indices: 5208701--5208787 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
5208691 TTGTGTTCTT
* * *
5208701 ATATATATTTATGTTAATCGTGTCTATTC
1 ATATATATTTATATTATTAGTGTCTATTC
* * *
5208730 GTATATATTCATATTAGTTA-TATCTATTC
1 ATATATATTTATATTA-TTAGTGTCTATTC
* *
5208759 ATATATATTTGTATTATTAGTGTTTATTC
1 ATATATATTTATATTATTAGTGTCTATTC
5208788 GTGCATATTT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
28 3 0.07
29 41 0.91
30 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (29 bp):
ATATATATTTATATTATTAGTGTCTATTC
Found at i:5221232 original size:36 final size:36
Alignment explanation
Indices: 5221182--5221252 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
5221172 GATCTTCTTA
*
5221182 AAAGGATACCAACCCCTTAGATTTAAAATACCAACT
1 AAAGGACACCAACCCCTTAGATTTAAAATACCAACT
* * *
5221218 AAAGGACACTAACCCTTTAGTTTTAAAATACCAAC
1 AAAGGACACCAACCCCTTAGATTTAAAATACCAAC
5221253 CTTCACCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (36 bp):
AAAGGACACCAACCCCTTAGATTTAAAATACCAACT
Found at i:5222923 original size:231 final size:233
Alignment explanation
Indices: 5222631--5223095 Score: 702
Period size: 233 Copynumber: 2.0 Consensus size: 233
5222621 TCGCTATATC
* * * * *
5222631 TCTTATATAAATATATAAAAGTTAAAACCTCTAATAAAAAAAAAATAATTTGATGTGGATAATTT
1 TCTTATATAAATATATAAAAATCAAAACCTCTAATAAAAAAAAAATAATCTGATATGGATAATCT
* * * **
5222696 AT-ATTTTTGACATATGTACAATCT-AAAAAATTGACATATATTTTTTAATAAATGTATTTCAAT
66 ATAATTTTTGACATATGGACAATCTAAAAAAATTGACATATATTCTCTAATAAATACATTTCAAT
5222759 AATTCAAAAAAACTAAATT-AATAAATTTATTTTTATTTGTCTTAAATCATTCTCAATTAAATTG
131 AATT-AAAAAAACTAAATTAAATAAATTTATTTTTATTTGTCTTAAATCATTCTCAATTAAATTG
* * *
5222823 ACAAAGAAGGTAATAAAAGTTTAATTGCCATCGTTAATA
195 ACAAAGAAGGAAATAAAAGTTTAATTGACATCATTAATA
*
5222862 TCTTATATAAATATATAAAAATCAAAACCTCTAATAAAAAGAAAATAATCTGATATGGATAATCT
1 TCTTATATAAATATATAAAAATCAAAACCTCTAATAAAAAAAAAATAATCTGATATGGATAATCT
* ** * * *
5222927 ATAATTTTTGACATGTGGACAATCTAAAAAAATTGTTATATGTTCTCTATTAAATACATTTTAAT
66 ATAATTTTTGACATATGGACAATCTAAAAAAATTGACATATATTCTCTAATAAATACATTTCAAT
*
5222992 AATTAAAAAAACTAAATTAAATAAATTTATTTTTATTTGTCTTAAATCATTTTCAATTAAATTGA
131 AATTAAAAAAACTAAATTAAATAAATTTATTTTTATTTGTCTTAAATCATTCTCAATTAAATTGA
*
5223057 TAAAGAAGGAAATAAAAGTTTAATTGACATCATTAATA
196 CAAAGAAGGAAATAAAAGTTTAATTGACATCATTAATA
5223095 T
1 T
5223096 ATTGAGTAAT
Statistics
Matches: 209, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
231 61 0.29
232 34 0.16
233 114 0.55
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.38
Consensus pattern (233 bp):
TCTTATATAAATATATAAAAATCAAAACCTCTAATAAAAAAAAAATAATCTGATATGGATAATCT
ATAATTTTTGACATATGGACAATCTAAAAAAATTGACATATATTCTCTAATAAATACATTTCAAT
AATTAAAAAAACTAAATTAAATAAATTTATTTTTATTTGTCTTAAATCATTCTCAATTAAATTGA
CAAAGAAGGAAATAAAAGTTTAATTGACATCATTAATA
Found at i:5225620 original size:23 final size:27
Alignment explanation
Indices: 5225546--5225605 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
5225536 ATTATTTATT
* *
5225546 ATTATAAAAATATAATTTTTTAATCAAA
1 ATTATAAATATATTATTTTTTAAT-AAA
5225574 ATTATAAATATATTATTTTTTAAAATAAA
1 ATTATAAATATATTATTTTTT--AATAAA
5225603 ATT
1 ATT
5225606 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 19 0.68
29 6 0.21
30 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTATAAATATATTATTTTTTAATAAA
Found at i:5225623 original size:22 final size:21
Alignment explanation
Indices: 5225577--5225616 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5225567 AATCAAAATT
5225577 ATAAATATATTATTTTTTAAA
1 ATAAATATATTATTTTTTAAA
*
5225598 ATAAA-ATTTTATTTTTTAA
1 ATAAATATATTATTTTTTAA
5225617 TAAATAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAAATATATTATTTTTTAAA
Found at i:5233241 original size:46 final size:47
Alignment explanation
Indices: 5233165--5233260 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 47
5233155 ACATATATAA
* * *
5233165 AAATATATATATATATATATACATATATTATCAAATTGTCAACTATT
1 AAATACATACATATATATATACATATATTATCAAATTGGCAACTATT
**
5233212 AAATACATACATATATATAT-GTTATATTATCAAATTGGCAACTATT
1 AAATACATACATATATATATACATATATTATCAAATTGGCAACTATT
5233258 AAA
1 AAA
5233261 CTAAATAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 26 0.59
47 18 0.41
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (47 bp):
AAATACATACATATATATATACATATATTATCAAATTGGCAACTATT
Found at i:5235046 original size:85 final size:85
Alignment explanation
Indices: 5234903--5235072 Score: 295
Period size: 85 Copynumber: 2.0 Consensus size: 85
5234893 GTGAAAAAGG
* *
5234903 ACTAGGAGAGATTATATTCTTGTTGTTCTGGCAAGCCCAGAACAAGTTTCTCAATATCCCAATTT
1 ACTAGGAGAGATTATATTCTTGTTGTTCTGGCAAACCCAGAACAAGTTTCTCAATATCCCAAGTT
*
5234968 ACTGATTGGCATGTAATGCT
66 ACCGATTGGCATGTAATGCT
*
5234988 ACTAGGAGAGATTATATTCTTGTTGTTGTGGCAAACCCAGAACAAGTTTCTCAATATCCCAAGTT
1 ACTAGGAGAGATTATATTCTTGTTGTTCTGGCAAACCCAGAACAAGTTTCTCAATATCCCAAGTT
*
5235053 ACCGATTGGCATTTAATGCT
66 ACCGATTGGCATGTAATGCT
5235073 TGTTTAAATT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (85 bp):
ACTAGGAGAGATTATATTCTTGTTGTTCTGGCAAACCCAGAACAAGTTTCTCAATATCCCAAGTT
ACCGATTGGCATGTAATGCT
Found at i:5235108 original size:38 final size:38
Alignment explanation
Indices: 5235057--5235136 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
5235047 CAAGTTACCG
* * * *
5235057 ATTGGCATTTAATGCTTGTTTAAATTAGAAATAATTCC
1 ATTGGCATGTAATGCTCGTTCAAATTAGAAATAACTCC
5235095 ATTGGCATGTAATGCTCGTTCAAATTAGAAATAACTCC
1 ATTGGCATGTAATGCTCGTTCAAATTAGAAATAACTCC
5235133 ATTG
1 ATTG
5235137 CGATTACTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (38 bp):
ATTGGCATGTAATGCTCGTTCAAATTAGAAATAACTCC
Found at i:5239592 original size:36 final size:36
Alignment explanation
Indices: 5239552--5239625 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
5239542 TTTCGGTTTG
* *
5239552 AGAATTTAT-TTATTGCCTTGTAATAAATGCAATTCT
1 AGAATTTATCTT-TTGCCTTGTAACAAAAGCAATTCT
5239588 AGAATTTATCTTTTGCCTTGTAACAAAAGCAATTCT
1 AGAATTTATCTTTTGCCTTGTAACAAAAGCAATTCT
5239624 AG
1 AG
5239626 TGTTTTCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (36 bp):
AGAATTTATCTTTTGCCTTGTAACAAAAGCAATTCT
Found at i:5239980 original size:17 final size:17
Alignment explanation
Indices: 5239961--5239994 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5239951 ATTTTTTATA
5239961 TTTCATAGTTTTTAACAT
1 TTTC-TAGTTTTTAACAT
*
5239979 TTTCTATTTTTTAACA
1 TTTCTAGTTTTTAACA
5239995 ATAAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.26, C:0.12, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTCTAGTTTTTAACAT
Found at i:5242480 original size:18 final size:20
Alignment explanation
Indices: 5242457--5242494 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5242447 TCAGGGTAAA
*
5242457 TCTTG-ATTTTTA-AATATT
1 TCTTGAATTATTAGAATATT
5242475 TCTTGAATTATTAGAATATT
1 TCTTGAATTATTAGAATATT
5242495 AAAAGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (20 bp):
TCTTGAATTATTAGAATATT
Found at i:5242937 original size:979 final size:983
Alignment explanation
Indices: 5241273--5243071 Score: 2620
Period size: 979 Copynumber: 1.8 Consensus size: 983
5241263 TTGTAATAAT
* *
5241273 ATTTTTTTATGTTTTAATACTTAATTTTACATTTATACTCAATTTTTGGTATTTTGCTGGATTAA
1 ATTTTTTTATGTTTTAATACTTAATTTTACATTTATACTCAATTTTTGATATTTTGCTAGATTAA
* * * * * * **
5241338 AAAAATATTTTATATATTGAAAGAATATACTTCCAAATAATTTTGAATTGTTGAAAAGTTTGCCA
66 AAAAATATCTTATATACTAAAAGAAAATACTTCCAAATAACTTTGAATTATCAAAAAGTTTGCCA
* * * *
5241403 TATAACCCAATTTTCTTAGAATAACCCATGAAAGGTTTGTCTTGTTGAATTTATGTTTTAGGGGT
131 CACAACCCAATTTTCTTAGAATAACCCATGAAAGGTTTGCCTTGTTAAATTTATGTTTTAGGGGT
* *
5241468 AAATTTTGATTTTTAAATATTTCTTAAATTATTAAAATATTAAGAGAATTGAGTGATTTACTACT
196 AAATCTTGATTTTTAAATATTTCTTAAATTATTAAAATATTAAAAGAATTGAGTGATTTACTACT
* * * *
5241533 TAAGTTTCAATTTAGCGCATTAGATAAGTAACTTAATATCCCTTTGATTTTTATATCTCTAAAAA
261 TAAGTTTCAATTTAACACATTAGATAAGTAACTTAATATCCCTTTAATTTTTATATCCCTAAAAA
* *
5241598 TCAGCCTCAATATGTTAAAGAATTGATATATATATATATATATATAATATTATTTGTCAATTTGT
326 TCAGCCTCAATATATTAAAGAACTGATATATATATATATATATATAATATTATTTGTCAATTTGT
*
5241663 TTTGTAAATAGGGTTGAGCATTCAAAATGTATATATATGATTTTTTTGCTATAATAAGTTTGGAT
391 TTTGTAAATAGGGTTGAGCATGCAAAATGTATATATATGATTTTTTTGCTATAATAAGTTTGGAT
* * *
5241728 ATGATTTTGTTATTTCATTGATCTCTAAATATGATTTCATAATAATATATTGGTATATCTGTTGA
456 ATGATTTTGTTATTTCATTGATCTCTAAATATGATTTCATAATAATAAATTGGTATATCTATCGA
* *
5241793 TTTTTGAATATAAAATTTTGCTTTGAAATAACATACAAAATTTATTATGTATCAAATATGTTTTG
521 TTTCTAAATATAAAATTTTGCTTTGAAATAACATACAAAATTTATTATGTATCAAATATGTTTTG
* *
5241858 AGAAAGCATATGAATATTGATTTTGTTTATATTAGGTAATCGAAAAATATATTTTGATTTTTGGT
586 AGAAAGCATATAAATATTGATTTTGTCTATATTAGGTAATCGAAAAATATATTTTGATTTTTGGT
** * * *
5241923 CTCTTAGTATGACTATGTTCTAACCCTGCCAATGGGGGTTAATTATTGGTCATGTTGATATGTAC
651 CTCTTAGTATGACTATGTTCTAACCCTGCCAATGGGGGTTAATTATTGACCATATCGACATGTAC
* * *
5241988 TTTATAATATCAATATTGGTTAAGAAATAGTGAATTTTGTTTATCGTACCATCAATGCTTTTGTT
716 TTTATAATATCAATATTAGTTAAG-AATAGTGAATTTTGTTTACCATACCATCAATGCTTTTGTT
* * *
5242053 CCATTACACTAAAAATGTTATTTTTGTCCTATTGCACTAAAGGGGTTACTTCTATCCCATTTTAC
780 CCATTACACTAAAAAGGTTACTTCTGTCCTATTGCACTAAAGGGGTTACTTCTATCCCATTTTAC
5242118 TAGTTATTATGATACTAGTTTTGTTCCATTGCATAAACAAGGTTAATTATAATTGTCAGTGCAAT
845 TAGTTATTATGATACTAGTTTTGTTCCATTGCATAAACAAGGTTAATTATAATTGTCAGTGCAAT
5242183 GATCTAGTTATTTATGATATACTTCTGTTCCATTGTACTATATGGGTAATTCTGATTCTGACTTA
910 GATCTAGTTATTTATGATATACTTCTGTTCCATTGTACTATATGGGTAATTCTGATTCTGACTTA
5242248 TTACTATTG
975 TTACTATTG
*
5242257 ATTTTTTTATGTTTTAATACTTAATTTTACATTTATACTCAATTTTTGATATTTTGCTATATTAA
1 ATTTTTTTATGTTTTAATACTTAATTTTACATTTATACTCAATTTTTGATATTTTGCTAGATTAA
* *
5242322 AAAAATGTATCTTATATGCTAAAAGAAAATACTTCCAAATAGCTTTGAATTATCAAAAACG-TTG
66 AAAAA--TATCTTATATACTAAAAGAAAATACTTCCAAATAACTTTGAATTATCAAAAA-GTTTG
** * * *
5242386 CCACACAACTTAATTTTCTTA-AGATGACCCATGGAGGGTTTGCCTTGTTAAATTTATGTTTTCA
128 CCACACAACCCAATTTTCTTAGA-ATAACCCATGAAAGGTTTGCCTTGTTAAATTTATGTTTT-A
* * *
5242450 -GGGTAAATCTTGATTTTTAAATATTTCTTGAATTATTAGAATATTAAAAGAATTGAGTGATTTG
191 GGGGTAAATCTTGATTTTTAAATATTTCTTAAATTATTAAAATATTAAAAGAATTGAGTGATTTA
** * * * *
5242514 CTGA-TTAAGTTTTGATTTAACACATTAGGTAAGTGACTTGATAT-CCTTTCAATTTTTATGTCC
256 CT-ACTTAAGTTTCAATTTAACACATTAGATAAGTAACTTAATATCCCTTT-AATTTTTATATCC
* * * * *
5242577 CTAAAAATCAGTCTCAGTATATT-AAGAACTGATATATATATATA-A-A-A-CATGTTTTTTGTC
319 CTAAAAATCAGCCTCAATATATTAAAGAACTGATATATATATATATATATATAATATTATTTGTC
* *
5242637 CATTTGTTTTGTAAATCA-GGTTGAGCATGCAAAATGTGTATATATGATTTTTTTTG-T-T-ATA
384 AATTTGTTTTGTAAAT-AGGGTTGAGCATGCAAAATGTATATATATGA-TTTTTTTGCTATAATA
* *
5242698 AGTTTGGATATGATTTTGTTATTTCTTTGATCTCTGAATATGATTTCATAATAATAAATTGGTAT
447 AGTTTGGATATGATTTTGTTATTTCATTGATCTCTAAATATGATTTCATAATAATAAATTGGTAT
* * * * *
5242763 ATCTATCGATTTCTAAATATGAAATTTTGCTTTGGAATGACATACAAAATTTGTTATGTATGAAA
512 ATCTATCGATTTCTAAATATAAAATTTTGCTTTGAAATAACATACAAAATTTATTATGTATCAAA
*
5242828 TATGTTTTGAGAAAGCATATAAATATTGATTTTGTCTATGTT-GGATAATCGAAAAATATATTTT
577 TATGTTTTGAGAAAGCATATAAATATTGATTTTGTCTATATTAGG-TAATCGAAAAATATATTTT
* *
5242892 GGTTTTTGGTCTCTTAGTATGACTATGTTCTAACCCTGCCAATGGGGGTTAATTGTTGACCATAT
641 GATTTTTGGTCTCTTAGTATGACTATGTTCTAACCCTGCCAATGGGGGTTAATTATTGACCATAT
* * * * * * **
5242957 CGACATGTATTTTATGATATCGATATTAGTTGAGAATAGTTATTTTTGTTTACCATACCATTGAT
706 CGACATGTACTTTATAATATCAATATTAGTTAAGAATAGTGAATTTTGTTTACCATACCATCAAT
* * *
5243022 GCTTTTGTTCCATTATACTAAAGAGGTTACTTCTGTCTTATTGCACTAAA
771 GCTTTTGTTCCATTACACTAAAAAGGTTACTTCTGTCCTATTGCACTAAA
5243072 AGGATTATTA
Statistics
Matches: 719, Mismatches: 86, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
978 71 0.10
979 266 0.37
980 1 0.00
981 53 0.07
982 10 0.01
983 1 0.00
984 68 0.09
985 26 0.04
986 220 0.31
987 3 0.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (983 bp):
ATTTTTTTATGTTTTAATACTTAATTTTACATTTATACTCAATTTTTGATATTTTGCTAGATTAA
AAAAATATCTTATATACTAAAAGAAAATACTTCCAAATAACTTTGAATTATCAAAAAGTTTGCCA
CACAACCCAATTTTCTTAGAATAACCCATGAAAGGTTTGCCTTGTTAAATTTATGTTTTAGGGGT
AAATCTTGATTTTTAAATATTTCTTAAATTATTAAAATATTAAAAGAATTGAGTGATTTACTACT
TAAGTTTCAATTTAACACATTAGATAAGTAACTTAATATCCCTTTAATTTTTATATCCCTAAAAA
TCAGCCTCAATATATTAAAGAACTGATATATATATATATATATATAATATTATTTGTCAATTTGT
TTTGTAAATAGGGTTGAGCATGCAAAATGTATATATATGATTTTTTTGCTATAATAAGTTTGGAT
ATGATTTTGTTATTTCATTGATCTCTAAATATGATTTCATAATAATAAATTGGTATATCTATCGA
TTTCTAAATATAAAATTTTGCTTTGAAATAACATACAAAATTTATTATGTATCAAATATGTTTTG
AGAAAGCATATAAATATTGATTTTGTCTATATTAGGTAATCGAAAAATATATTTTGATTTTTGGT
CTCTTAGTATGACTATGTTCTAACCCTGCCAATGGGGGTTAATTATTGACCATATCGACATGTAC
TTTATAATATCAATATTAGTTAAGAATAGTGAATTTTGTTTACCATACCATCAATGCTTTTGTTC
CATTACACTAAAAAGGTTACTTCTGTCCTATTGCACTAAAGGGGTTACTTCTATCCCATTTTACT
AGTTATTATGATACTAGTTTTGTTCCATTGCATAAACAAGGTTAATTATAATTGTCAGTGCAATG
ATCTAGTTATTTATGATATACTTCTGTTCCATTGTACTATATGGGTAATTCTGATTCTGACTTAT
TACTATTG
Found at i:5243942 original size:29 final size:30
Alignment explanation
Indices: 5243898--5243964 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
5243888 ATCAAGACCT
*
5243898 AGTCTTTGGCGCAGGCTTCACT-TCATAGA
1 AGTCTTTGGCGCAGGCTTCACTCCCATAGA
* *
5243927 AGTCTTTGGCGTAGGCTTCACTCCCATGGA
1 AGTCTTTGGCGCAGGCTTCACTCCCATAGA
5243957 AGTCTTTG
1 AGTCTTTG
5243965 CGTTACAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (30 bp):
AGTCTTTGGCGCAGGCTTCACTCCCATAGA
Found at i:5251117 original size:27 final size:27
Alignment explanation
Indices: 5251086--5251137 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
5251076 AAGATTATAA
*
5251086 TAGGA-TAGGATTAGATGATATTATCAG
1 TAGGATTA-GATTAAATGATATTATCAG
*
5251113 TAGGATTAGATTAAATGATGTTATC
1 TAGGATTAGATTAAATGATATTATC
5251138 TTATCTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (27 bp):
TAGGATTAGATTAAATGATATTATCAG
Found at i:5252566 original size:64 final size:64
Alignment explanation
Indices: 5252465--5252593 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
5252455 TAATGAAGGA
*
5252465 AGTTTGTGACATCCCAATTCTACAAAGGGATAATTTGAGGATCT-TATATGGTATATAAGTAAAG
1 AGTTTGTGACATCCCAATTCTACAAAGGGATAATTTGAGGAT-TAGATATGGTATATAAGTAAAG
* *
5252529 AGTTTGTGACATCCTAATTCTACAAAGGGATATTTTGAGGATTAGATATGGTATATAAGTAAAG
1 AGTTTGTGACATCCCAATTCTACAAAGGGATAATTTGAGGATTAGATATGGTATATAAGTAAAG
5252593 A
1 A
5252594 TTTAAACCTA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 1 0.02
64 60 0.98
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.33
Consensus pattern (64 bp):
AGTTTGTGACATCCCAATTCTACAAAGGGATAATTTGAGGATTAGATATGGTATATAAGTAAAG
Found at i:5253126 original size:37 final size:37
Alignment explanation
Indices: 5253066--5253138 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
5253056 CATATATATC
*
5253066 ATACCATATCCACACATTCTTCTAACGTGGGATTGTT
1 ATACCATATCCACACATTCTTCTAACGTGAGATTGTT
* * * *
5253103 ATACTATATCGACACATTTTTCTAATGTGAGATTGT
1 ATACCATATCCACACATTCTTCTAACGTGAGATTGT
5253139 GAGATACTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (37 bp):
ATACCATATCCACACATTCTTCTAACGTGAGATTGTT
Found at i:5257217 original size:28 final size:27
Alignment explanation
Indices: 5257163--5257227 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
5257153 ACCATCAATG
5257163 CTTTTGTTCCATTACACTAAAAAGGTTA
1 CTTTTG-TCCATTACACTAAAAAGGTTA
* * **
5257191 GTTTTGTCCTATTGCACTAAAGGGGTTA
1 CTTTTGTCC-ATTACACTAAAAAGGTTA
*
5257219 CTTCTGTCC
1 CTTTTGTCC
5257228 CATTTTATTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 3 0.10
28 27 0.90
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (27 bp):
CTTTTGTCCATTACACTAAAAAGGTTA
Found at i:5257599 original size:18 final size:20
Alignment explanation
Indices: 5257576--5257613 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5257566 TCGGGGTAAA
*
5257576 TCTTG-ATTTTTA-AATATT
1 TCTTGAATTATTAGAATATT
5257594 TCTTGAATTATTAGAATATT
1 TCTTGAATTATTAGAATATT
5257614 AAAAGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (20 bp):
TCTTGAATTATTAGAATATT
Found at i:5259052 original size:30 final size:30
Alignment explanation
Indices: 5259016--5259113 Score: 169
Period size: 30 Copynumber: 3.3 Consensus size: 30
5259006 ATCAAGTTCT
5259016 AGTCTTTGGCGCAGGCTTCACTTCCATGGA
1 AGTCTTTGGCGCAGGCTTCACTTCCATGGA
5259046 AGTCTTTGGCGCAGGCTTCACTTCCATGGA
1 AGTCTTTGGCGCAGGCTTCACTTCCATGGA
* * *
5259076 AGTCTTTGGCGTAGGCTTCACTCCCACGGA
1 AGTCTTTGGCGCAGGCTTCACTTCCATGGA
5259106 AGTCTTTG
1 AGTCTTTG
5259114 CGTTACAATT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.31
Consensus pattern (30 bp):
AGTCTTTGGCGCAGGCTTCACTTCCATGGA
Found at i:5267250 original size:2 final size:2
Alignment explanation
Indices: 5267243--5267273 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5267233 TTCTATTATG
*
5267243 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5267274 GAAATTTAAA
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5268161 original size:13 final size:13
Alignment explanation
Indices: 5268143--5268178 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
5268133 TAATGTAAGA
*
5268143 TTGTGAGAGATTT
1 TTGTGAGACATTT
5268156 TTGTGAGACATTT
1 TTGTGAGACATTT
5268169 TTGTGAGACA
1 TTGTGAGACA
5268179 AAACTGTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.42
Consensus pattern (13 bp):
TTGTGAGACATTT
Found at i:5275899 original size:32 final size:33
Alignment explanation
Indices: 5275863--5275934 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
5275853 TAATCTAATT
5275863 ATCATAATTTA-ACTTCTTA-AAAATCTCCAAA
1 ATCATAATTTATACTTCTTAGAAAATCTCCAAA
* * *
5275894 GATCATAA-TTATAGTTCTTAGAAAATTTTCAAA
1 -ATCATAATTTATACTTCTTAGAAAATCTCCAAA
5275927 ATCATAAT
1 ATCATAAT
5275935 ATAGGTTCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 3 0.09
32 21 0.62
33 10 0.29
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.38
Consensus pattern (33 bp):
ATCATAATTTATACTTCTTAGAAAATCTCCAAA
Found at i:5276601 original size:28 final size:27
Alignment explanation
Indices: 5276570--5276622 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
5276560 ATATTTCGTA
5276570 AATTCATAAATCAATATA-AAAATATGTC
1 AATTCATAAATC-AT-TACAAAATATGTC
5276598 AATTCATAAATCATTACAAAATATG
1 AATTCATAAATCATTACAAAATATG
5276623 CTACTATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 2 0.08
27 10 0.42
28 12 0.50
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (27 bp):
AATTCATAAATCATTACAAAATATGTC
Found at i:5276723 original size:23 final size:23
Alignment explanation
Indices: 5276649--5276724 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
5276639 GTAATCAAAC
*
5276649 CATCATGGATCAATCATTAAAGAT
1 CATCATGGATCAATCTTTAAA-AT
* **
5276673 CATCGTAAATC-ATCTTTATATAA-
1 CATCATGGATCAATCTTTA-A-AAT
*
5276696 AATCATGGATCAATCTTTAAAAT
1 CATCATGGATCAATCTTTAAAAT
5276719 CATCAT
1 CATCAT
5276725 AAATATCATT
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
22 2 0.05
23 19 0.49
24 17 0.44
25 1 0.03
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (23 bp):
CATCATGGATCAATCTTTAAAAT
Found at i:5281243 original size:19 final size:20
Alignment explanation
Indices: 5281213--5281250 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
5281203 ACGTAAAGAG
5281213 ATTAACCATGCAAATATAAT
1 ATTAACCATGCAAATATAAT
5281233 ATTAA-CATGCAAATATAA
1 ATTAACCATGCAAATATAA
5281251 GATAGTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (20 bp):
ATTAACCATGCAAATATAAT
Found at i:5282666 original size:24 final size:24
Alignment explanation
Indices: 5282563--5282660 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
5282553 GACTTTAACC
* *
5282563 TAAAACAAAAACTAAAA-TAAAAT
1 TAAAACTAAAACCAAAATTAAAAT
* *
5282586 TAAAACCAAAATCAAAATTAAAAT
1 TAAAACTAAAACCAAAATTAAAAT
5282610 TAAAACTAAAACCAAAATTAAAAT
1 TAAAACTAAAACCAAAATTAAAAT
* * **
5282634 CAAAATTAAAATTAAAATTAAAAT
1 TAAAACTAAAACCAAAATTAAAAT
5282658 TAA
1 TAA
5282661 GATTAAGATT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
23 14 0.22
24 50 0.78
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.22
Consensus pattern (24 bp):
TAAAACTAAAACCAAAATTAAAAT
Found at i:5282670 original size:6 final size:6
Alignment explanation
Indices: 5282570--5282666 Score: 106
Period size: 6 Copynumber: 16.3 Consensus size: 6
5282560 ACCTAAAACA
* ** * *
5282570 AAAACT AAAA-T AAAATT AAAACC AAAATC AAAATT AAAATT AAAACT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
** * *
5282617 AAAACC AAAATT AAAATC AAAATT AAAATT AAAATT AAAATT AAGATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
5282665 AA
1 AA
5282667 GATTTTTAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
5 5 0.06
6 74 0.94
ACGTcount: A:0.67, C:0.08, G:0.01, T:0.24
Consensus pattern (6 bp):
AAAATT
Found at i:5283193 original size:20 final size:20
Alignment explanation
Indices: 5283168--5283205 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5283158 ACTATAAATC
5283168 TCATCGAAAAATTTAAATAT
1 TCATCGAAAAATTTAAATAT
5283188 TCATCGAAAAATTTAAAT
1 TCATCGAAAAATTTAAAT
5283206 TTAAACCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (20 bp):
TCATCGAAAAATTTAAATAT
Found at i:5283929 original size:24 final size:24
Alignment explanation
Indices: 5283893--5283953 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
5283883 AACAATAACT
**
5283893 AAAA-TAAAATTAAAACCAAAGGC
1 AAAATTAAAATTAAAACCAAAACC
*
5283916 AAAATTAAAATTAAAACTAAAACC
1 AAAATTAAAATTAAAACCAAAACC
*
5283940 AAACTTAAAATTAA
1 AAAATTAAAATTAA
5283954 GGTTAAGATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
23 4 0.12
24 29 0.88
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (24 bp):
AAAATTAAAATTAAAACCAAAACC
Found at i:5283950 original size:30 final size:29
Alignment explanation
Indices: 5283892--5283953 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
5283882 AAACAATAAC
* *
5283892 TAAAATAAAATTAAAACCAAAGGCAAAAT
1 TAAAATAAAACTAAAACCAAACGCAAAAT
**
5283921 TAAAATTAAAACTAAAACCAAACTTAAAAT
1 TAAAA-TAAAACTAAAACCAAACGCAAAAT
5283951 TAA
1 TAA
5283954 GGTTAAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.21
Consensus pattern (29 bp):
TAAAATAAAACTAAAACCAAACGCAAAAT
Found at i:5284208 original size:48 final size:48
Alignment explanation
Indices: 5284155--5284250 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
5284145 CAAAAATCAA
* *
5284155 AAAAGAAAATTGCAAAAGCTCTCCGACAATTGAGGCTTTAAAACTTTT
1 AAAAGAAAATTGCAAAAGCTCTCCGACAACTAAGGCTTTAAAACTTTT
* ** *
5284203 AAAAGAAAATTGCAAAAGTTCTTTGACAACTAAGGCTTTGAAACTTTT
1 AAAAGAAAATTGCAAAAGCTCTCCGACAACTAAGGCTTTAAAACTTTT
5284251 GGAAAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (48 bp):
AAAAGAAAATTGCAAAAGCTCTCCGACAACTAAGGCTTTAAAACTTTT
Found at i:5287159 original size:59 final size:58
Alignment explanation
Indices: 5286987--5287226 Score: 340
Period size: 60 Copynumber: 4.1 Consensus size: 58
5286977 AAAAAAACAC
5286987 TTTTTTAGAAAA-TTATTTTCAA-AGAAAATTGATACTTTCAACTTTTCCTCAAAAATA
1 TTTTTTAGAAAACTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATA
* * * * **
5287044 ATTTTTAGAAAACTTATTTTCAAGGAAATTTGATACTTTCAATTTTTCCTTGAAAATA
1 TTTTTTAGAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA
* * * *
5287102 TTTTTTAGAAAAACTTGTTTTTAAGAAAAATTGATACTTTAAACTTTTTCTCAAAAATAA
1 TTTTTTAG-AAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-A
5287162 TTTTTTAGAAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA
1 TTTTTTAG-AAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA
5287221 TTTTTT
1 TTTTTT
5287227 TTGGAATTTT
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
57 11 0.07
58 46 0.29
59 47 0.30
60 55 0.35
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (58 bp):
TTTTTTAGAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA
Found at i:5287276 original size:19 final size:19
Alignment explanation
Indices: 5287254--5287291 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5287244 GAAAATCATT
5287254 TAAAAAAAAGAT-AAATAAA
1 TAAAAAAAA-ATAAAATAAA
*
5287273 TAAAATAAAATAAAATAAA
1 TAAAAAAAAATAAAATAAA
5287292 ATAAGGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
TAAAAAAAAATAAAATAAA
Found at i:5287280 original size:5 final size:5
Alignment explanation
Indices: 5287266--5287295 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
5287256 AAAAAAAGAT
5287266 AAAT- AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
5287296 GGAATACTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:5288231 original size:24 final size:24
Alignment explanation
Indices: 5288194--5288274 Score: 110
Period size: 24 Copynumber: 3.3 Consensus size: 24
5288184 GATAAATAAT
*
5288194 AATAAAAAATATATATTAATAGATA
1 AATAATAAA-ATATATTAATAGATA
*
5288219 AATAATAAAATATGTTAATAGATA
1 AATAATAAAATATATTAATAGATA
*
5288243 AATAATAAAATATATATATTA-ATA
1 AATAATAAAATATAT-TAATAGATA
5288267 AATAATAA
1 AATAATAA
5288275 TGGTAATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
24 39 0.76
25 12 0.24
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
AATAATAAAATATATTAATAGATA
Found at i:5293934 original size:3 final size:3
Alignment explanation
Indices: 5293928--5293989 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
5293918 CTTCAAAGTG
5293928 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5293976 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
5293990 TTATTATTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5293994 original size:3 final size:3
Alignment explanation
Indices: 5293988--5294014 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5293978 ATAATAATAA
5293988 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
5294015 ATGCAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5298718 original size:14 final size:14
Alignment explanation
Indices: 5298701--5298739 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5298691 TTTTTTTCCA
*
5298701 TTTTCTTTTTATTT
1 TTTTCCTTTTATTT
5298715 TTTTCCTTTTATTT
1 TTTTCCTTTTATTT
*
5298729 ATTTCCATTTT
1 TTTTCC-TTTT
5298740 TTGATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCCTTTTATTT
Found at i:5298790 original size:3 final size:3
Alignment explanation
Indices: 5298784--5298817 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
5298774 TTATTAGTAT
*
5298784 TAC TAC TAC TAT TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
5298818 TATTAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (3 bp):
TAC
Found at i:5298796 original size:12 final size:12
Alignment explanation
Indices: 5298781--5298822 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
5298771 TTATTATTAG
5298781 TATTACTACTAC
1 TATTACTACTAC
5298793 TATTACTACTAC
1 TATTACTACTAC
*
5298805 TACTACTACTAC
1 TATTACTACTAC
5298817 TTATTA
1 -TATTA
5298823 AATTAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (12 bp):
TATTACTACTAC
Found at i:5298957 original size:21 final size:21
Alignment explanation
Indices: 5298919--5298962 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5298909 ATGATTATTA
** *
5298919 ATTAATTGCATGTTAATTTAT
1 ATTAATTGCATGACAATTGAT
5298940 ATTAATTGCATGACAATTGAT
1 ATTAATTGCATGACAATTGAT
5298961 AT
1 AT
5298963 ATTATATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (21 bp):
ATTAATTGCATGACAATTGAT
Found at i:5303486 original size:19 final size:17
Alignment explanation
Indices: 5303439--5303477 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
5303429 GATGAAAGTG
5303439 AAAA-AAAAAAAAAGAT
1 AAAATAAAAAAAAAGAT
5303455 AAAATAAGCAAAAAAAGAT
1 AAAATAA--AAAAAAAGAT
5303474 AAAA
1 AAAA
5303478 AGTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 2 0.10
19 14 0.70
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAATAAAAAAAAAGAT
Found at i:5303486 original size:28 final size:25
Alignment explanation
Indices: 5303439--5303499 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
5303429 GATGAAAGTG
*
5303439 AAAAAAAAAAAAAGATAAAATAAGCA
1 AAAAAAAAAAAAAGAAAAAATAAG-A
* *
5303465 AAAAAAGATAAAAAGTAAAAAATGAGA
1 AAAAAA-AAAAAAAG-AAAAAATAAGA
5303492 AAAAAAAA
1 AAAAAAAA
5303500 TTGATGGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 7 0.24
27 14 0.48
28 8 0.28
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (25 bp):
AAAAAAAAAAAAAGAAAAAATAAGA
Found at i:5303496 original size:19 final size:17
Alignment explanation
Indices: 5303433--5303497 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
5303423 AAAAATGATG
*
5303433 AAAGTGAAAAAAA-AAA
1 AAAGAGAAAAAAAGAAA
* *
5303449 AAAGATAAAATAAGCAAA
1 AAAGAGAAAAAAAG-AAA
*
5303467 AAA-AGATAAAAAGTAAA
1 AAAGAGAAAAAAAG-AAA
5303484 AAATGAGAAAAAAA
1 AAA-GAGAAAAAAA
5303498 AATTGATGGA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
16 10 0.27
17 13 0.35
18 6 0.16
19 8 0.22
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (17 bp):
AAAGAGAAAAAAAGAAA
Found at i:5303836 original size:31 final size:31
Alignment explanation
Indices: 5303784--5303842 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5303774 GAGATGTGCA
** *
5303784 AAAAAAAAAAAAAGAGCAAAAAATGAAATGT
1 AAAAAAAAAAAAAGAAAAAAAAAGGAAATGT
*
5303815 AAAAAAAAAAAGAGAAAAAAAAAGGAAA
1 AAAAAAAAAAAAAGAAAAAAAAAGGAAA
5303843 AATGAAGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (31 bp):
AAAAAAAAAAAAAGAAAAAAAAAGGAAATGT
Found at i:5303842 original size:11 final size:12
Alignment explanation
Indices: 5303788--5303844 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 12
5303778 TGTGCAAAAA
5303788 AAAAAAAAAGAG
1 AAAAAAAAAGAG
*
5303800 CAAAAAATGAAATGTAA
1 -AAAAAA--AAA-G-AG
5303817 AAAAAAAAAGAG
1 AAAAAAAAAGAG
5303829 AAAAAAAAAG-G
1 AAAAAAAAAGAG
5303840 AAAAA
1 AAAAA
5303845 TGAAGATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 6 0.16
12 11 0.29
13 7 0.18
14 3 0.08
15 3 0.08
16 7 0.18
17 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:5305002 original size:45 final size:44
Alignment explanation
Indices: 5304953--5305112 Score: 133
Period size: 45 Copynumber: 3.6 Consensus size: 44
5304943 ATTTTGGATG
*
5304953 TGAAATCCTAAAATTTTTCAAATGAGAACCTTTGAAGTTTGGGTA
1 TGAAATCCTAAAGTTTTTCAAATGAGAACCTTTGAAGTTTGGG-A
* * * * * * *
5304998 TGAAATCATAAAGTTTTT-GAATGAAAATCTTTCAAATTTTGGA
1 TGAAATCCTAAAGTTTTTCAAATGAGAACCTTTGAAGTTTGGGA
* * * * *
5305041 TGTAAAACACTAAAGTTTTTCAAATGTGAACATTTGAAGTTTCGAA
1 TG-AAATC-CTAAAGTTTTTCAAATGAGAACCTTTGAAGTTTGGGA
* * *
5305087 TGTGAATCCTCAAGTTATTCAAATGA
1 TG-AAATCCTAAAGTTTTTCAAATGA
5305113 AAATCTTTTG
Statistics
Matches: 88, Mismatches: 24, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
43 3 0.03
44 22 0.25
45 41 0.47
46 22 0.25
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (44 bp):
TGAAATCCTAAAGTTTTTCAAATGAGAACCTTTGAAGTTTGGGA
Found at i:5305102 original size:90 final size:90
Alignment explanation
Indices: 5304921--5305120 Score: 233
Period size: 90 Copynumber: 2.2 Consensus size: 90
5304911 CACTATTTTT
* * * *
5304921 TTTTTGAATGAGAATTTTTAAAATTTTGGATGTGAAATCCTAAAATTTTTCAAATGAGAACCTTT
1 TTTTTGAATGAAAATCTTTAAAATTTTGGATGTGAAAACCTAAAATTTTTCAAATGAGAACATTT
* *
5304986 GAAGTTTGGGTATGAAATCATAAAG
66 GAAGTTTGCGAATGAAATCATAAAG
* * *
5305011 TTTTTGAATGAAAATCTTTCAAATTTTGGATGT-AAAACACTAAAGTTTTTCAAATGTGAACATT
1 TTTTTGAATGAAAATCTTTAAAATTTTGGATGTGAAAAC-CTAAAATTTTTCAAATGAGAACATT
* * *
5305075 TGAAGTTT-CGAATGTGAATCCTCAAG
65 TGAAGTTTGCGAATG-AAATCATAAAG
**
5305101 TTATTCAAATGAAAATCTTT
1 TT-TTTGAATGAAAATCTTT
5305121 TGGGTCTGAA
Statistics
Matches: 93, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
89 8 0.09
90 70 0.75
91 15 0.16
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (90 bp):
TTTTTGAATGAAAATCTTTAAAATTTTGGATGTGAAAACCTAAAATTTTTCAAATGAGAACATTT
GAAGTTTGCGAATGAAATCATAAAG
Found at i:5305430 original size:18 final size:18
Alignment explanation
Indices: 5305409--5305451 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5305399 TCTTACAAAT
5305409 CTTTAAAG-TCTTGTGAAC
1 CTTTAAAGAT-TTGTGAAC
* *
5305427 CTTTGAAGATTTGTGAAT
1 CTTTAAAGATTTGTGAAC
5305445 CTTTAAA
1 CTTTAAA
5305452 ATTCTTGCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (18 bp):
CTTTAAAGATTTGTGAAC
Found at i:5305473 original size:17 final size:18
Alignment explanation
Indices: 5305448--5305481 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5305438 TGTGAATCTT
5305448 TAAAATTCTTGC-AAATC
1 TAAAATTCTTGCGAAATC
*
5305465 TAAAGTTCTTGCGAAAT
1 TAAAATTCTTGCGAAAT
5305482 TCTTGCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TAAAATTCTTGCGAAATC
Found at i:5305554 original size:17 final size:16
Alignment explanation
Indices: 5305527--5305581 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 16
5305517 TTTTTGAAAA
5305527 TTGAATTCTTGCAAAC
1 TTGAATTCTTGCAAAC
*
5305543 TTGAAGTTCTTGCGAAC
1 TTGAA-TTCTTGCAAAC
*
5305560 TTGAAATTCTTGCAAAT
1 TTG-AATTCTTGCAAAC
5305577 TTGAA
1 TTGAA
5305582 AATTCTTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.21
17 25 0.74
18 2 0.06
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (16 bp):
TTGAATTCTTGCAAAC
Found at i:5305582 original size:17 final size:17
Alignment explanation
Indices: 5305477--5305589 Score: 95
Period size: 18 Copynumber: 6.6 Consensus size: 17
5305467 AAGTTCTTGC
5305477 GAAATTCTTGCAAATCTT
1 GAAATTCTTGCAAAT-TT
* * *
5305495 TAAATTCTTGTGAATTTT
1 GAAATTCTTG-CAAATTT
* * *
5305513 TAAATTTTTG-AAAATT
1 GAAATTCTTGCAAATTT
*
5305529 G-AATTCTTGCAAACTT
1 GAAATTCTTGCAAATTT
* * *
5305545 GAAGTTCTTGCGAACTT
1 GAAATTCTTGCAAATTT
5305562 GAAATTCTTGCAAATTT
1 GAAATTCTTGCAAATTT
5305579 GAAAATTCTTG
1 G-AAATTCTTG
5305590 TGAAAATGAA
Statistics
Matches: 77, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
15 7 0.09
16 10 0.13
17 28 0.36
18 29 0.38
19 3 0.04
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (17 bp):
GAAATTCTTGCAAATTT
Found at i:5305641 original size:53 final size:53
Alignment explanation
Indices: 5305530--5305708 Score: 145
Period size: 53 Copynumber: 3.4 Consensus size: 53
5305520 TTGAAAATTG
* * * * * *
5305530 AATTCTTGCAAACTTGAAGTTCTT-GCGAACTTGAAATTCTTGCAAATTTGAA
1 AATTCTTGTAAAATTGAAATTTTTGGCGAAATTGAAATTCTTACAAATTTGAA
*
5305582 AATTCTTGTGAAAA-TG-AATTTTTGGCGAAATTGAAAATTCTTACGAATCTT-AA
1 AATTCTTGT-AAAATTGAAATTTTTGGCGAAATTG-AAATTCTTACAAAT-TTGAA
*** * *
5305635 AATTCTTGTAAAATTGAAATTTTTTATG-AATCTAAAATTCTTATAAATTT-AA
1 AATTCTTGTAAAATTGAAATTTTTGGCGAAAT-TGAAATTCTTACAAATTTGAA
* *
5305687 AATTCTTGCAAATATTTAAATT
1 AATTCTTGTAAA-ATTGAAATT
5305709 CTTATAAAAT
Statistics
Matches: 104, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
51 5 0.05
52 37 0.36
53 51 0.49
54 11 0.11
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (53 bp):
AATTCTTGTAAAATTGAAATTTTTGGCGAAATTGAAATTCTTACAAATTTGAA
Found at i:5305655 original size:35 final size:35
Alignment explanation
Indices: 5305609--5305727 Score: 125
Period size: 35 Copynumber: 3.4 Consensus size: 35
5305599 ATTTTTGGCG
*
5305609 AAATTGAAAATTCTTACGAATCTTAAAATTCTTGTA
1 AAATTG-AAATTCTTACGAATCTTAAAATTCTTATA
* *
5305645 AAATTGAAATTTTTTATGAATC-TAAAATTCTTATA
1 AAATTGAAA-TTCTTACGAATCTTAAAATTCTTATA
* * * * * *
5305680 AATTTAAAATTCTTGCAAATATTTAAATTCTTATA
1 AAATTGAAATTCTTACGAATCTTAAAATTCTTATA
5305715 AAATTG-AATTCTT
1 AAATTGAAATTCTT
5305728 GTGAAATCTA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 14 0.21
35 38 0.56
36 16 0.24
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (35 bp):
AAATTGAAATTCTTACGAATCTTAAAATTCTTATA
Found at i:5305666 original size:36 final size:35
Alignment explanation
Indices: 5305609--5305722 Score: 113
Period size: 36 Copynumber: 3.2 Consensus size: 35
5305599 ATTTTTGGCG
* *
5305609 AAATTGAAAATTCTTACGAATCTTAAAATTCTTGTA
1 AAATTGAAATTTCTTACGAATC-TAAAATTCTTATA
* *
5305645 AAATTGAAATTTTTTATGAATCTAAAATTCTTAT-
1 AAATTGAAATTTCTTACGAATCTAAAATTCTTATA
* * * * * *
5305679 AAATTTAAAATTCTTGCAAATATTTAAATTCTTATA
1 AAATTGAAATTTCTTACGAAT-CTAAAATTCTTATA
5305715 AAATTGAA
1 AAATTGAA
5305723 TTCTTGTGAA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
34 15 0.24
35 22 0.35
36 26 0.41
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (35 bp):
AAATTGAAATTTCTTACGAATCTAAAATTCTTATA
Found at i:5305687 original size:17 final size:17
Alignment explanation
Indices: 5305609--5305716 Score: 81
Period size: 17 Copynumber: 6.2 Consensus size: 17
5305599 ATTTTTGGCG
* *
5305609 AAATTGAAAATTCTTAC
1 AAATTTAAAATTCTTAT
* *
5305626 GAATCTTAAAATTCTTGT
1 AAAT-TTAAAATTCTTAT
* * *
5305644 AAAATTGAAATTTTTTAT
1 -AAATTTAAAATTCTTAT
* *
5305662 GAATCTAAAATTCTTAT
1 AAATTTAAAATTCTTAT
**
5305679 AAATTTAAAATTCTTGC
1 AAATTTAAAATTCTTAT
*
5305696 AAATATTTAAATTCTTAT
1 AAAT-TTAAAATTCTTAT
5305714 AAA
1 AAA
5305717 ATTGAATTCT
Statistics
Matches: 67, Mismatches: 21, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
17 32 0.48
18 32 0.48
19 3 0.04
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.43
Consensus pattern (17 bp):
AAATTTAAAATTCTTAT
Found at i:5305742 original size:70 final size:69
Alignment explanation
Indices: 5305609--5305751 Score: 164
Period size: 70 Copynumber: 2.1 Consensus size: 69
5305599 ATTTTTGGCG
* * * *
5305609 AAATTGAAAATTCTTACGAATCTTAAAATTCTTGTAAAATTGAAATTTTTTATGAATCTAAAATT
1 AAATTGAAAATTCTTACAAATATTAAAATTCTTATAAAATTGAAATTTCTTATGAATCTAAAA-T
*
5305674 CTTAT
65 CTTAC
* * * *
5305679 AAATTTAAAATTCTTGCAAATATTTAAATTCTTATAAAATTG-AA-TTCTTGTGAAATCTAAAAA
1 AAATTGAAAATTCTTACAAATATTAAAATTCTTATAAAATTGAAATTTCTTATG-AATCT-AAAA
5305742 TCTTAC
64 TCTTAC
5305748 AAAT
1 AAAT
5305752 CTTTCATTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
68 6 0.10
69 16 0.26
70 40 0.65
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.41
Consensus pattern (69 bp):
AAATTGAAAATTCTTACAAATATTAAAATTCTTATAAAATTGAAATTTCTTATGAATCTAAAATC
TTAC
Found at i:5305803 original size:40 final size:41
Alignment explanation
Indices: 5305722--5305803 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
5305712 ATAAAATTGA
** *
5305722 ATTCTTGTGAAATCTAAAAATCTTACAAATCTTTCATTCTT
1 ATTCTTGTGAAATCTAAAAATCTTACAAATCTTAAAGTCTT
* *
5305763 ATTCTTGT-AAATCTAAAAATCTTGCAACTCTTAAAGTCTT
1 ATTCTTGTGAAATCTAAAAATCTTACAAATCTTAAAGTCTT
5305803 A
1 A
5305804 GAATCTGTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 28 0.78
41 8 0.22
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.41
Consensus pattern (41 bp):
ATTCTTGTGAAATCTAAAAATCTTACAAATCTTAAAGTCTT
Found at i:5306200 original size:16 final size:16
Alignment explanation
Indices: 5306156--5306203 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
5306146 TAATTTCATC
5306156 AAAAGTAAAAAAAAAA
1 AAAAGTAAAAAAAAAA
* * **
5306172 AAAAGCAAGAAAAATC
1 AAAAGTAAAAAAAAAA
*
5306188 TAAAGTAAAAAAAAAA
1 AAAAGTAAAAAAAAAA
5306204 GTCAAAACAA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.79, C:0.04, G:0.08, T:0.08
Consensus pattern (16 bp):
AAAAGTAAAAAAAAAA
Found at i:5307306 original size:14 final size:13
Alignment explanation
Indices: 5307271--5307349 Score: 58
Period size: 13 Copynumber: 6.3 Consensus size: 13
5307261 AATTATAGGT
**
5307271 TTTTCTTTTTCCA
1 TTTTCTTTTTTTA
5307284 TTTTC--TTTTTA
1 TTTTCTTTTTTTA
*
5307295 TTTTCATTTTTTA
1 TTTTCTTTTTTTA
*
5307308 TTTT-TTATTTT-
1 TTTTCTTTTTTTA
* *
5307319 TTCTCTTTATTTA
1 TTTTCTTTTTTTA
*
5307332 TTTCCATTTTTTTA
1 TTTTC-TTTTTTTA
5307346 TTTT
1 TTTT
5307350 TTTACTACCT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
11 12 0.24
12 10 0.20
13 18 0.36
14 10 0.20
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTTTTTTA
Found at i:5308667 original size:14 final size:14
Alignment explanation
Indices: 5308648--5308690 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
5308638 ATATCATGCA
5308648 ATCATGCAATAAAT
1 ATCATGCAATAAAT
*
5308662 ATCATGTCGA-AAAT
1 ATCATG-CAATAAAT
5308676 ATCATGCAATAAAT
1 ATCATGCAATAAAT
5308690 A
1 A
5308691 AAACCATGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 2 0.08
14 21 0.84
15 2 0.08
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (14 bp):
ATCATGCAATAAAT
Found at i:5308768 original size:14 final size:13
Alignment explanation
Indices: 5308719--5308773 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
5308709 AACAACAAAT
5308719 ATGCAAAAATATC
1 ATGCAAAAATATC
*
5308732 ATGCAATAATAT-
1 ATGCAAAAATATC
5308744 -T---AAAATATC
1 ATGCAAAAATATC
5308753 ATGCAAAAATTATC
1 ATGCAAAAA-TATC
5308767 ATGCAAA
1 ATGCAAA
5308774 GAGATTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
8 6 0.18
10 1 0.03
11 1 0.03
13 15 0.44
14 11 0.32
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (13 bp):
ATGCAAAAATATC
Found at i:5308802 original size:20 final size:20
Alignment explanation
Indices: 5308777--5308823 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
5308767 ATGCAAAGAG
*
5308777 ATTAATCACGCAAATATAAT
1 ATTAATCACGCAAACATAAT
*
5308797 ATTAATCATGCAAACATAAT
1 ATTAATCACGCAAACATAAT
5308817 A-TAATCA
1 ATTAATCA
5308824 TACTATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (20 bp):
ATTAATCACGCAAACATAAT
Found at i:5309059 original size:6 final size:6
Alignment explanation
Indices: 5309048--5309139 Score: 61
Period size: 6 Copynumber: 16.3 Consensus size: 6
5309038 AAATCTTATC
* * *
5309048 TTAATT TTAATT TTGATT TTAA-T TTGATT TTAATT TTAA-- TTAGTT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
* * * ** *
5309093 TTGATT TT-AGT TTGATT TTGCTT TTAA-T TTAA-T TTAATT TTAGTT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
5309138 TT
1 TT
5309140 CGTTTAATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
4 3 0.04
5 18 0.26
6 47 0.69
ACGTcount: A:0.25, C:0.01, G:0.09, T:0.65
Consensus pattern (6 bp):
TTAATT
Found at i:5309075 original size:11 final size:11
Alignment explanation
Indices: 5309051--5309134 Score: 62
Period size: 11 Copynumber: 7.5 Consensus size: 11
5309041 TCTTATCTTA
5309051 ATTTTAATTTTG
1 ATTTTAA-TTTG
5309063 ATTTTAATTTG
1 ATTTTAATTTG
*
5309074 ATTTTAATTTT
1 ATTTTAATTTG
* *
5309085 A-ATTAGTTTTG
1 ATTTTA-ATTTG
*
5309096 ATTTTAGTTTG
1 ATTTTAATTTG
** *
5309107 ATTTTGCTTTT
1 ATTTTAATTTG
* *
5309118 AATTTAATTTA
1 ATTTTAATTTG
5309129 ATTTTA
1 ATTTTA
5309135 GTTTTCGTTT
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
10 3 0.05
11 43 0.77
12 10 0.18
ACGTcount: A:0.26, C:0.01, G:0.08, T:0.64
Consensus pattern (11 bp):
ATTTTAATTTG
Found at i:5309133 original size:33 final size:33
Alignment explanation
Indices: 5309048--5309138 Score: 103
Period size: 33 Copynumber: 2.7 Consensus size: 33
5309038 AAATCTTATC
*
5309048 TTAATTTTAATTTTGATTTTAATTTGATTTTAATT
1 TTAA-TTTAA-TTTGATTTTAGTTTGATTTTAATT
* **
5309083 TTAA-TTAGTTTTGATTTTAGTTTGATTTTGCTT
1 TTAATTTA-ATTTGATTTTAGTTTGATTTTAATT
*
5309116 TTAATTTAATTTAATTTTAGTTT
1 TTAATTTAATTTGATTTTAGTTT
5309139 TCGTTTAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
33 41 0.85
34 3 0.06
35 4 0.08
ACGTcount: A:0.25, C:0.01, G:0.09, T:0.65
Consensus pattern (33 bp):
TTAATTTAATTTGATTTTAGTTTGATTTTAATT
Found at i:5309734 original size:27 final size:23
Alignment explanation
Indices: 5309711--5309794 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
5309701 ATTATGATTA
*
5309711 ATTATACATTTATTTGCATGATG
1 ATTATATATTTATTTGCATGATG
5309734 ATTATATATTTATTTGCATG-T-
1 ATTATATATTTATTTGCATGATG
*
5309755 -TT-TATACTGTTAATTGCATGAT-
1 ATTATATA-T-TTATTTGCATGATG
5309777 A--ATATATTTATTTGCATG
1 ATTATATATTTATTTGCATG
5309795 TCTTATATTG
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
19 4 0.08
20 13 0.25
21 11 0.21
22 6 0.11
23 19 0.36
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (23 bp):
ATTATATATTTATTTGCATGATG
Found at i:5309787 original size:41 final size:41
Alignment explanation
Indices: 5309731--5310041 Score: 408
Period size: 41 Copynumber: 7.6 Consensus size: 41
5309721 TATTTGCATG
* *
5309731 ATGATTATATATTTATTTGCATGTTTTATACTGTTAATTGC
1 ATGATTATATATTTAATTGCATGTTTTATATTGTTAATTGC
* * *
5309772 ATGATAATATATTTATTTGCATGTCTTATATTGTTAATTGC
1 ATGATTATATATTTAATTGCATGTTTTATATTGTTAATTGC
* *
5309813 TTGATTATATATTTCATTGCATGTTTTATATTGTTAATTGC
1 ATGATTATATATTTAATTGCATGTTTTATATTGTTAATTGC
*
5309854 ATGATTATATATTTAATTACATGTTTTATATTGTTAATTGC
1 ATGATTATATATTTAATTGCATGTTTTATATTGTTAATTGC
* * * * *
5309895 ATGATAATATCTTTAATTGTATGATTTATAACT-TTAATTGC
1 ATGATTATATATTTAATTGCATGTTTTAT-ATTGTTAATTGC
* * * *
5309936 ATGATCATATATTTAACTGCATATTTTACATTGTTAATTGC
1 ATGATTATATATTTAATTGCATGTTTTATATTGTTAATTGC
* *
5309977 ATGATTAGATATTTAATGGCATGTTTTATATTGTTAATTGC
1 ATGATTATATATTTAATTGCATGTTTTATATTGTTAATTGC
* * *
5310018 AAGATTATACATTTAATTGTATGT
1 ATGATTATATATTTAATTGCATGT
5310042 CTATTTGCAT
Statistics
Matches: 232, Mismatches: 36, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
40 2 0.01
41 228 0.98
42 2 0.01
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (41 bp):
ATGATTATATATTTAATTGCATGTTTTATATTGTTAATTGC
Found at i:5310064 original size:32 final size:32
Alignment explanation
Indices: 5310013--5310093 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
5310003 TATATTGTTA
*
5310013 ATTGCAAGATTA-TACATTTAATTGTATGTCT-
1 ATTGCATGATTATTA-ATTTAATTGTATGTCTG
* * *
5310044 ATTTGCATGATTATTAATTTATTTGTTTGTTTG
1 A-TTGCATGATTATTAATTTAATTGTATGTCTG
*
5310077 ATTGTATGATTATTAAT
1 ATTGCATGATTATTAAT
5310094 ATATTTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
31 1 0.02
32 38 0.90
33 3 0.07
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (32 bp):
ATTGCATGATTATTAATTTAATTGTATGTCTG
Found at i:5310099 original size:32 final size:32
Alignment explanation
Indices: 5310050--5310111 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
5310040 GTCTATTTGC
* * *
5310050 ATGATTATTAATTTATTTGTTTGTTTGATTGT
1 ATGATTATTAATATATTTATTTGTGTGATTGT
5310082 ATGATTATTAATATATTTATTTGTGTGATT
1 ATGATTATTAATATATTTATTTGTGTGATT
5310112 ATTATTATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.60
Consensus pattern (32 bp):
ATGATTATTAATATATTTATTTGTGTGATTGT
Found at i:5310153 original size:19 final size:19
Alignment explanation
Indices: 5310116--5310153 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5310106 GTGATTATTA
* *
5310116 TTATTGCATGATTTTATAT
1 TTATTGCATGATATGATAT
5310135 TTATTGCATGATATGATAT
1 TTATTGCATGATATGATAT
5310154 AATATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (19 bp):
TTATTGCATGATATGATAT
Found at i:5310312 original size:20 final size:17
Alignment explanation
Indices: 5310252--5310316 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
5310242 ATTGTATTAG
5310252 ATTTGCATGATATTATGT
1 ATTTGCATGATATTAT-T
* *
5310270 ATTTACACGATTATTATT
1 ATTTGCATGA-TATTATT
5310288 A-TTGCATGATAATTAATAT
1 ATTTGCATGAT-ATT-AT-T
5310307 ATTTGCATGA
1 ATTTGCATGA
5310317 CATTCTTGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 9 0.24
18 12 0.32
19 8 0.21
20 8 0.21
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (17 bp):
ATTTGCATGATATTATT
Found at i:5311015 original size:27 final size:25
Alignment explanation
Indices: 5310983--5311033 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
5310973 GATAGAAAAT
*
5310983 AAAAATATGAAACGAAACAAAAAATAG
1 AAAAATAAGAAA-GAAA-AAAAAATAG
*
5311010 AAAAATAAGAAAGAAAATAAAATA
1 AAAAATAAGAAAGAAAAAAAAATA
5311034 AAAGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
27 11 0.50
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.12
Consensus pattern (25 bp):
AAAAATAAGAAAGAAAAAAAAATAG
Found at i:5312092 original size:6 final size:6
Alignment explanation
Indices: 5312083--5312194 Score: 88
Period size: 6 Copynumber: 19.3 Consensus size: 6
5312073 ACCCAAAACA
* * *
5312083 AAAATT AAAA-T AAAATT AAAATT AAAATC AAAATC AAAA-T CAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
* ** * * * *
5312129 AAAATT AAAACT AAAACC AAAATT AAAA-T CAAA-T CAAATC AAAATC
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
* *
5312175 AAATTT AAAATT AAGATT AA
1 AAAATT AAAATT AAAATT AA
5312195 GATCTTTTAG
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
5 17 0.19
6 71 0.81
ACGTcount: A:0.65, C:0.09, G:0.01, T:0.25
Consensus pattern (6 bp):
AAAATT
Found at i:5312121 original size:29 final size:29
Alignment explanation
Indices: 5312083--5312194 Score: 113
Period size: 29 Copynumber: 3.9 Consensus size: 29
5312073 ACCCAAAACA
*
5312083 AAAATTAAAATAAAATTAAAATTAAAATC
1 AAAATCAAAATAAAATTAAAATTAAAATC
*
5312112 AAAATCAAAATCAAATTAAAATTAAAA-C
1 AAAATCAAAATAAAATTAAAATTAAAATC
* * *
5312140 TAAAACCAAAATTAAAA-TCAAA-TCAAATC
1 -AAAATCAAAA-TAAAATTAAAATTAAAATC
* *
5312169 AAAATCAAATTTAAAATTAAGATTAA
1 AAAATCAAA-ATAAAATTAAAATTAA
5312195 GATCTTTTAG
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
28 18 0.27
29 42 0.64
30 6 0.09
ACGTcount: A:0.65, C:0.09, G:0.01, T:0.25
Consensus pattern (29 bp):
AAAATCAAAATAAAATTAAAATTAAAATC
Found at i:5312648 original size:5 final size:5
Alignment explanation
Indices: 5312638--5312662 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5312628 CTTACTTATC
5312638 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
5312663 ACATTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:5314073 original size:23 final size:23
Alignment explanation
Indices: 5314042--5314089 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5314032 CCAAGTGTTA
5314042 AATAAAAAATA-ATAAATAATTAT
1 AATAAAAAATATA-AAATAATTAT
* *
5314065 AATATAAAATATAAAATGATTAT
1 AATAAAAAATATAAAATAATTAT
5314088 AA
1 AA
5314090 AATTAACTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AATAAAAAATATAAAATAATTAT
Found at i:5314424 original size:30 final size:31
Alignment explanation
Indices: 5314366--5314630 Score: 127
Period size: 30 Copynumber: 9.1 Consensus size: 31
5314356 AAACCCCAAG
*
5314366 CCTC-AAATCTTAAAATCAAAACCCTTAAAC
1 CCTCTAAATCCTAAAATCAAAACCCTTAAAC
*
5314396 CCTCTAAATCCTAAAATCGAAA-CCTTAAAC
1 CCTCTAAATCCTAAAATCAAAACCCTTAAAC
* * * *
5314426 TCTCTAAATCCTAAAATCAAAGCCC--CAAG
1 CCTCTAAATCCTAAAATCAAAACCCTTAAAC
* *
5314455 CCTC-AAA-CCTTAAAATCAAAATCCTAAAAC
1 CCTCTAAATCC-TAAAATCAAAACCCTTAAAC
** * * * * *
5314485 TTTC-AAACCCTAAAATTAAAGCCC--CAAG
1 CCTCTAAATCCTAAAATCAAAACCCTTAAAC
* * * *
5314513 CAT-TAAACCCTTAAATCAAAACCCTAAAAC
1 CCTCTAAATCCTAAAATCAAAACCCTTAAAC
* *
5314543 TCTC-AAACCCTAAAATCAAAACTCC--AAA-
1 CCTCTAAATCCTAAAATCAAAAC-CCTTAAAC
* *
5314571 CCTC-AAACCCTAAAATC-AAGCCC-TAAAC
1 CCTCTAAATCCTAAAATCAAAACCCTTAAAC
* * * *
5314599 CTTTTAAA-CTCTAAAACCAAAACTC-TAAAC
1 CCTCTAAATC-CTAAAATCAAAACCCTTAAAC
5314629 CC
1 CC
5314631 AAAACTTTCC
Statistics
Matches: 182, Mismatches: 37, Indels: 32
0.73 0.15 0.13
Matches are distributed among these distances:
26 2 0.01
27 8 0.04
28 54 0.30
29 18 0.10
30 79 0.43
31 21 0.12
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.21
Consensus pattern (31 bp):
CCTCTAAATCCTAAAATCAAAACCCTTAAAC
Found at i:5314594 original size:13 final size:13
Alignment explanation
Indices: 5314457--5314597 Score: 77
Period size: 14 Copynumber: 9.9 Consensus size: 13
5314447 GCCCCAAGCC
*
5314457 TCAAACCTTAAAA
1 TCAAACCCTAAAA
*
5314470 TCAAAATCCTAAAA
1 TC-AAACCCTAAAA
5314484 CTTTCAAACCCTAAAA
1 ---TCAAACCCTAAAA
* * *
5314500 TTAAAGCCCCAAGCA
1 TCAAA-CCCTAA-AA
* *
5314515 TTAAACCCTTAAA
1 TCAAACCCTAAAA
5314528 TCAAAACCCTAAAA
1 TC-AAACCCTAAAA
5314542 CTCTCAAACCCTAAAA
1 ---TCAAACCCTAAAA
*
5314558 TCAAAACTCC-AAACC
1 TC-AAAC-CCTAAA-A
5314573 TCAAACCCTAAAA
1 TCAAACCCTAAAA
*
5314586 TCAAGCCCTAAA
1 TCAAACCCTAAA
5314598 CCTTTTAAAC
Statistics
Matches: 100, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
13 23 0.23
14 42 0.42
15 10 0.10
16 21 0.21
17 4 0.04
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.19
Consensus pattern (13 bp):
TCAAACCCTAAAA
Found at i:5314623 original size:14 final size:14
Alignment explanation
Indices: 5314604--5314636 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5314594 TAAACCTTTT
5314604 AAACTCTAAAACCA
1 AAACTCTAAAACCA
*
5314618 AAACTCTAAACCCA
1 AAACTCTAAAACCA
5314632 AAACT
1 AAACT
5314637 TTCCAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACTCTAAAACCA
Found at i:5314623 original size:57 final size:58
Alignment explanation
Indices: 5314376--5314621 Score: 235
Period size: 58 Copynumber: 4.2 Consensus size: 58
5314366 CCTCAAATCT
* * * * * *
5314376 TAAAATCAAAACCCTTAAACCCTCTAAATCCTAAAATCGAAA-CCTTAAACTCTCTAAATCC
1 TAAAATCAAAACCC-CAAA-CCTC-AAACCCTAAAATCAAAACCCTAAAACTTTC-AAACCC
* * * *
5314437 TAAAATCAAAGCCCCAAGCCTCAAACCTTAAAATCAAAATCCTAAAACTTTCAAACCC
1 TAAAATCAAAACCCCAAACCTCAAACCCTAAAATCAAAACCCTAAAACTTTCAAACCC
* * * * * * *
5314495 TAAAATTAAAGCCCCAAGCATTAAACCCTTAAATCAAAACCCTAAAACTCTCAAACCC
1 TAAAATCAAAACCCCAAACCTCAAACCCTAAAATCAAAACCCTAAAACTTTCAAACCC
* * * * *
5314553 TAAAATCAAAACTCCAAACCTCAAACCCTAAAATC-AAGCCCTAAACCTTTTAAACTC
1 TAAAATCAAAACCCCAAACCTCAAACCCTAAAATCAAAACCCTAAAACTTTCAAACCC
*
5314610 TAAAACCAAAAC
1 TAAAATCAAAAC
5314622 TCTAAACCCA
Statistics
Matches: 155, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
57 28 0.18
58 98 0.63
59 14 0.09
60 2 0.01
61 13 0.08
ACGTcount: A:0.47, C:0.30, G:0.02, T:0.20
Consensus pattern (58 bp):
TAAAATCAAAACCCCAAACCTCAAACCCTAAAATCAAAACCCTAAAACTTTCAAACCC
Found at i:5314709 original size:14 final size:14
Alignment explanation
Indices: 5314692--5314737 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
5314682 TTGAAACCAT
5314692 AAACCCTAAAATCA
1 AAACCCTAAAATCA
* * *
5314706 AAACCTTAAACTCC
1 AAACCCTAAAATCA
5314720 AAACCCTAAAATCCA
1 AAACCCTAAAAT-CA
5314735 AAA
1 AAA
5314738 ACTTTAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 21 0.84
15 4 0.16
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:5314709 original size:21 final size:21
Alignment explanation
Indices: 5314670--5314716 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5314660 TTAAAACCTT
* **
5314670 TAAACCTTAAAATTGAAACCA
1 TAAACCCTAAAATCAAAACCA
*
5314691 TAAACCCTAAAATCAAAACCT
1 TAAACCCTAAAATCAAAACCA
5314712 TAAAC
1 TAAAC
5314717 TCCAAACCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.21
Consensus pattern (21 bp):
TAAACCCTAAAATCAAAACCA
Found at i:5316064 original size:1 final size:1
Alignment explanation
Indices: 5316058--5316108 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
5316048 AGTTTCATGC
*** **
5316058 TTTTTTTTTTTTTGGCTTTTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5316109 GCTTTGCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:5316559 original size:55 final size:54
Alignment explanation
Indices: 5316478--5316620 Score: 148
Period size: 55 Copynumber: 2.6 Consensus size: 54
5316468 TGAATGGATC
* * *
5316478 TTTTTTATT--AAAAGAAATTTATAAAGACTACATTTTTTAAAATAGAAACATAG
1 TTTTTTATTGAAAAAAAAAATTATAAAGACTACATTTTGT-AAATAGAAACATAG
* * * *
5316531 TTTTTTATTGAAAAAAAAAATTATAAAGACTACGTTTTGTAATTAGAAGCATGG
1 TTTTTTATTGAAAAAAAAAATTATAAAGACTACATTTTGTAAATAGAAACATAG
* *
5316585 TCTTTGATTGGAAAAAAAAAATT-TAGGAAGACTACA
1 TTTTTTATT-GAAAAAAAAAATTATA--AAGACTACA
5316621 AGTGTGAAAG
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
53 9 0.12
54 20 0.27
55 38 0.51
56 8 0.11
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (54 bp):
TTTTTTATTGAAAAAAAAAATTATAAAGACTACATTTTGTAAATAGAAACATAG
Found at i:5317072 original size:18 final size:18
Alignment explanation
Indices: 5317044--5317078 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5317034 CTTTTTCATA
5317044 ATTTGTTTTATTATTTTTT
1 ATTTGTTTTATT-TTTTTT
5317063 ATTT-TTTTATTTTTTT
1 ATTTGTTTTATTTTTTT
5317079 ATCCATACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (18 bp):
ATTTGTTTTATTTTTTTT
Found at i:5317988 original size:105 final size:102
Alignment explanation
Indices: 5317810--5318013 Score: 227
Period size: 105 Copynumber: 2.0 Consensus size: 102
5317800 AATTTTTAAT
*
5317810 TTTTAAATTAATAAAAATATAATTATTTTTATCTAAATATTTACTTAAATATAAATAATAATTAA
1 TTTTAAATTAATAAAAATATAATAATTTTTATCTAAATATTTACTTAAATATAAATAATAATTAA
*
5317875 TGCTAAAAAA-AT-TTATGTATATTTAATATTTTAACA
66 TGC-AAAAAATATATTATATATATTTAATATTTTAACA
* * * *
5317911 TTTTAAATTAATCAAAATATATATAATAATTTTTTATCTTAATA-TTATTTGAATATAAAATTAT
1 TTTTAAATTAAT--AAA-A-ATATAATAA-TTTTTATCTAAATATTTACTTAAATAT-AAATAAT
* * *
5317975 AATATATTG-AAAAAATATATTTTATATATTTTATATTTT
60 AAT-TAATGCAAAAAATATATTATATATATTTAATATTTT
5318014 TAAGTAATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
101 12 0.14
103 3 0.04
104 1 0.01
105 24 0.28
106 24 0.28
107 21 0.25
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.49
Consensus pattern (102 bp):
TTTTAAATTAATAAAAATATAATAATTTTTATCTAAATATTTACTTAAATATAAATAATAATTAA
TGCAAAAAATATATTATATATATTTAATATTTTAACA
Found at i:5318024 original size:16 final size:16
Alignment explanation
Indices: 5318005--5318046 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
5317995 TTTATATATT
*
5318005 TTATATTTTTAAGTAA
1 TTATATTTTTAACTAA
5318021 TTATAATTTTTTAACTAA
1 TTAT-A-TTTTTAACTAA
5318039 TTAT-TTTT
1 TTATATTTT
5318047 ACATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 4 0.17
16 4 0.17
17 1 0.04
18 14 0.61
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
TTATATTTTTAACTAA
Found at i:5319383 original size:22 final size:22
Alignment explanation
Indices: 5319358--5319401 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5319348 GTTTGACATT
*
5319358 TTTTAT-TTTTCTTTATTTTTTA
1 TTTTATGTTTT-TTTATTGTTTA
*
5319380 TTTTGTGTTTTTTTATTGTTTA
1 TTTTATGTTTTTTTATTGTTTA
5319402 CATGCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (22 bp):
TTTTATGTTTTTTTATTGTTTA
Found at i:5324542 original size:26 final size:22
Alignment explanation
Indices: 5324487--5324542 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
5324477 ATTTCATGTC
5324487 TTTTGCTTTTCTTTTTTTTTTT
1 TTTTGCTTTTCTTTTTTTTTTT
*
5324509 TTCT-CTTTTCTTATCTATTTTTTT
1 TTTTGCTTTTCTT-T-T-TTTTTTT
5324533 TTATTGCTTT
1 TT-TTGCTTT
5324543 CAATTATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 8 0.30
22 4 0.15
23 1 0.04
24 9 0.33
25 1 0.04
26 4 0.15
ACGTcount: A:0.05, C:0.12, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTGCTTTTCTTTTTTTTTTT
Found at i:5325724 original size:16 final size:16
Alignment explanation
Indices: 5325707--5325739 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
5325697 ATTTTAATTT
5325707 AAATATTTTTATTATTA
1 AAAT-TTTTTATTATTA
5325724 AAATTTTTTATTATTA
1 AAATTTTTTATTATTA
5325740 TTAACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AAATTTTTTATTATTA
Found at i:5327906 original size:15 final size:14
Alignment explanation
Indices: 5327848--5327908 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
5327838 CTAAGCCCAA
*
5327848 TTATCTATTTTTATT
1 TTAT-TATTTTTGTT
*
5327863 TTATT-TTTTAGTT
1 TTATTATTTTTGTT
*
5327876 TATATTA-TTTTATT
1 T-TATTATTTTTGTT
5327890 TTATTATTTTTGGTT
1 TTATTATTTTT-GTT
5327905 TTAT
1 TTAT
5327909 CTTTTGTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 12 0.32
14 15 0.41
15 10 0.27
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.74
Consensus pattern (14 bp):
TTATTATTTTTGTT
Found at i:5328769 original size:21 final size:21
Alignment explanation
Indices: 5328745--5328799 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
5328735 ACTGTTTATG
*
5328745 TTTTGATTTTTTTAATTA-TTA
1 TTTT-ATTTATTTAATTAGTTA
*
5328766 TTTTATTTATTTAGTTAGTTA
1 TTTTATTTATTTAATTAGTTA
5328787 TTTTATTTATTTA
1 TTTTATTTATTTA
5328800 CAATATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTATTTATTTAATTAGTTA
Found at i:5330910 original size:22 final size:22
Alignment explanation
Indices: 5330375--5330907 Score: 152
Period size: 22 Copynumber: 24.4 Consensus size: 22
5330365 GCAAATCAAC
* * *
5330375 AATAATGTAATAGTAGATAATT
1 AATAATTTAATAGTAAATCATT
* * * * *
5330397 GATAACTTATTAATTAATCATT
1 AATAATTTAATAGTAAATCATT
* *
5330419 GAA-AATTTAAAAGT-AATCAGT
1 -AATAATTTAATAGTAAATCATT
* *
5330440 -ATAATTTAGTAGT-AATCATC
1 AATAATTTAATAGTAAATCATT
* *
5330460 AATAATTTAATAATTAATCGA-T
1 AATAATTTAATAGTAAATC-ATT
* * *
5330482 AATAACTTAATAGTAAATTATG
1 AATAATTTAATAGTAAATCATT
* * * * *
5330504 GATAACTTAGTAGTAAATTAGT
1 AATAATTTAATAGTAAATCATT
* * * * *
5330526 GATAACTTAATAATAAATAAAT
1 AATAATTTAATAGTAAATCATT
* * * * *
5330548 GATTATTTAGTAGTCAATAATT
1 AATAATTTAATAGTAAATCATT
* * *
5330570 GATAATTTAGTAGTAAATCAAT
1 AATAATTTAATAGTAAATCATT
* * *
5330592 AATAATAT-ATAGT--TTTATGT
1 AATAATTTAATAGTAAATCAT-T
*
5330612 AATAGTTTAATAGTAAATCAATT
1 AATAATTTAATAGTAAATC-ATT
* * * **
5330635 -ATAATATAGTTGTAAATGTTT
1 AATAATTTAATAGTAAATCATT
* * * * *
5330656 AACAATATAGTAGTAAATTAAT
1 AATAATTTAATAGTAAATCATT
* * ** * *
5330678 AATAACTTATTAAAAAAATAAGT
1 AATAATTTAAT-AGTAAATCATT
* *
5330701 AATAACTTACTAGGT-AATCATT
1 AATAATTTAATA-GTAAATCATT
* * * * * * *
5330723 GATAACTTAGTAATACATGAAT
1 AATAATTTAATAGTAAATCATT
* * * * *
5330745 GATAACTTAATAATAAATTAGT
1 AATAATTTAATAGTAAATCATT
* * *
5330767 AATAACTTT-ATAATAAATTATC
1 AATAA-TTTAATAGTAAATCATT
* *
5330789 AATAACTTAGTAGTAAATCATT
1 AATAATTTAATAGTAAATCATT
* * *
5330811 CATATTTTAATGGTAAATCATT
1 AATAATTTAATAGTAAATCATT
* * *
5330833 CATATTTTAATGGTAAATCATT
1 AATAATTTAATAGTAAATCATT
* * *
5330855 CATATTTTAATGGTAAATCATT
1 AATAATTTAATAGTAAATCATT
* * *
5330877 AATAAATTATTAGTAAATCATA
1 AATAATTTAATAGTAAATCATT
5330899 AATAATTTA
1 AATAATTTA
5330908 TTACTAATAT
Statistics
Matches: 385, Mismatches: 109, Indels: 34
0.73 0.21 0.06
Matches are distributed among these distances:
19 3 0.01
20 21 0.05
21 32 0.08
22 304 0.79
23 23 0.06
24 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (22 bp):
AATAATTTAATAGTAAATCATT
Found at i:5330945 original size:22 final size:22
Alignment explanation
Indices: 5330912--5330998 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
5330902 AATTTATTAC
5330912 TAAT-ATAAATCATTGATAACT
1 TAATAATAAATCATTGATAACT
* * * *
5330933 TAGTAGTAAATCATTGAAAACA
1 TAATAATAAATCATTGATAACT
* *
5330955 TAATAATCAATCAATGATAACT
1 TAATAATAAATCATTGATAACT
* *
5330977 TAATTATCAATCATTG-TAACT
1 TAATAATAAATCATTGATAACT
5330998 T
1 T
5330999 TTTTTATACT
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 9 0.17
22 44 0.83
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (22 bp):
TAATAATAAATCATTGATAACT
Found at i:5331239 original size:20 final size:21
Alignment explanation
Indices: 5331214--5331254 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
5331204 AAAAAACTAA
5331214 ATTAATAA-AATTAAACCTAC
1 ATTAATAACAATTAAACCTAC
5331234 ATTAATAACTAATTAAACCTA
1 ATTAATAAC-AATTAAACCTA
5331255 AAAATTATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTAATAACAATTAAACCTAC
Found at i:5333445 original size:3 final size:3
Alignment explanation
Indices: 5333437--5333487 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
5333427 TAAATGTAAT
*
5333437 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5333485 TAA
1 TAA
5333488 CAACAACAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5333551 original size:21 final size:20
Alignment explanation
Indices: 5333527--5333575 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
5333517 CAAAAAATGG
5333527 AAAATAAT-AAAGAAAAAAAT
1 AAAATAATCAAA-AAAAAAAT
*
5333547 CAAAAAAATCAAAAACAAAAAT
1 -AAAATAATCAAAAA-AAAAAT
5333569 AAAATAA
1 AAAATAA
5333576 AATAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.80, C:0.06, G:0.02, T:0.12
Consensus pattern (20 bp):
AAAATAATCAAAAAAAAAAT
Found at i:5333552 original size:22 final size:20
Alignment explanation
Indices: 5333505--5333590 Score: 57
Period size: 22 Copynumber: 4.0 Consensus size: 20
5333495 AACAACATAG
**
5333505 TAAAAAAAT-AATCAAAAAA
1 TAAAAAAATAAAAAAAAAAA
* *
5333524 TGGAAAATAATAAAGAAAAAAA
1 T--AAAAAAATAAAAAAAAAAA
*
5333546 TCAAAAAAATCAAAAACAAAAA
1 T-AAAAAAAT-AAAAAAAAAAA
5333568 TAAAATAAAATAAAATAAAAAAA
1 T-AAA-AAAATAAAA-AAAAAAA
5333591 AAACCAACGA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
19 1 0.02
21 14 0.27
22 26 0.50
23 11 0.21
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (20 bp):
TAAAAAAATAAAAAAAAAAA
Found at i:5333554 original size:10 final size:9
Alignment explanation
Indices: 5333539--5333591 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
5333529 AATAATAAAG
*
5333539 AAAAAAATC
1 AAAAAAATA
5333548 AAAAAAATCA
1 AAAAAAAT-A
*
5333558 AAAACAA-A
1 AAAAAAATA
*
5333566 AATAAAATA
1 AAAAAAATA
5333575 AAATAAAATA
1 AAA-AAAATA
5333585 AAAAAAA
1 AAAAAAA
5333592 AACCAACGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
8 6 0.17
9 15 0.42
10 15 0.42
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATA
Found at i:5333582 original size:15 final size:14
Alignment explanation
Indices: 5333527--5333593 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 14
5333517 CAAAAAATGG
5333527 AAAATAATAAAGAAA-
1 AAAATAA-AAA-AAAT
*
5333542 AAAATCAAAAAAAT
1 AAAATAAAAAAAAT
* *
5333556 CAAA-AACAAAAAT
1 AAAATAAAAAAAAT
5333569 AAAATAAAATAAAAT
1 AAAATAAAA-AAAAT
5333584 AAAA-AAAAAA
1 AAAATAAAAAA
5333594 CCAACGAGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 15 0.35
14 13 0.30
15 15 0.35
ACGTcount: A:0.82, C:0.04, G:0.01, T:0.12
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:5334602 original size:22 final size:22
Alignment explanation
Indices: 5334577--5334624 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
5334567 AGTAAAAAGA
*
5334577 ATGAAAATTTTTGTACCTTGAT
1 ATGAAAATTTTTATACCTTGAT
5334599 ATGAAAATTTTTATACCTTGAT
1 ATGAAAATTTTTATACCTTGAT
5334621 ATGA
1 ATGA
5334625 TTCTCGCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.44
Consensus pattern (22 bp):
ATGAAAATTTTTATACCTTGAT
Found at i:5340831 original size:25 final size:24
Alignment explanation
Indices: 5340812--5340862 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
5340802 GTAATAACAT
5340812 TTCTATGGTCGATAATTAATTGAAC
1 TTCTATGGTCGATAATTAA-TGAAC
*
5340837 TTCTATGGTTGATAATTAATTGAAC
1 TTCTATGGTCGATAATTAA-TGAAC
5340862 T
1 T
5340863 CATTCCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (24 bp):
TTCTATGGTCGATAATTAATGAAC
Found at i:5342258 original size:37 final size:38
Alignment explanation
Indices: 5342191--5342265 Score: 134
Period size: 37 Copynumber: 2.0 Consensus size: 38
5342181 TAGATTTTTT
*
5342191 TTTTTCTTCTCTTTTGTTTTTTTATTTTATACTAATAA
1 TTTTTCTTCTATTTTGTTTTTTTATTTTATACTAATAA
5342229 TTTTTCTTCTATTTTG-TTTTTTATTTTATACTAATAA
1 TTTTTCTTCTATTTTGTTTTTTTATTTTATACTAATAA
5342266 CACTCATGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 21 0.58
38 15 0.42
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.68
Consensus pattern (38 bp):
TTTTTCTTCTATTTTGTTTTTTTATTTTATACTAATAA
Found at i:5343593 original size:28 final size:28
Alignment explanation
Indices: 5343534--5343593 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
5343524 TTATACTTAT
*
5343534 TTTTTAAATAATTAATAAACTATTAAAC
1 TTTTTAAATAATTAATAAACTAATAAAC
* * *
5343562 TTTTTAATTTAATTATTAAAGTAATAAA-
1 TTTTTAA-ATAATTAATAAACTAATAAAC
5343590 TTTT
1 TTTT
5343594 GAATAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (28 bp):
TTTTTAAATAATTAATAAACTAATAAAC
Found at i:5350853 original size:2 final size:2
Alignment explanation
Indices: 5350846--5350878 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5350836 GCTTAAACCC
5350846 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5350879 AAGGAAAGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5353882 original size:20 final size:22
Alignment explanation
Indices: 5353824--5353905 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 22
5353814 CTCGTACCTC
*
5353824 ATATATATTTATATATTTAATA
1 ATATAAATTTATATATTTAATA
* *
5353846 A-ATTAATTTCT-TATTTAATA
1 ATATAAATTTATATATTTAATA
5353866 ATATAAATTT-TAT-TTTAGATTA
1 ATATAAATTTATATATTTA-A-TA
*
5353888 AT-TAAAATTAATATATTT
1 ATAT-AAATTTATATATTT
5353906 GTATTTTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 15 0.31
21 17 0.35
22 10 0.21
23 3 0.06
24 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (22 bp):
ATATAAATTTATATATTTAATA
Found at i:5357719 original size:32 final size:31
Alignment explanation
Indices: 5357653--5357721 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
5357643 TACATTTTAT
* *
5357653 ATTTTTATATTAATATAAATTATAATCCATA
1 ATTTTTATATAAATATAAATTATAATACATA
5357684 ATTTTTATATAAA-ATATAA-TATAAATACATA
1 ATTTTTATATAAATATA-AATTAT-AATACATA
*
5357715 AATTTTA
1 ATTTTTA
5357722 ATATTTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (31 bp):
ATTTTTATATAAATATAAATTATAATACATA
Found at i:5358420 original size:19 final size:18
Alignment explanation
Indices: 5358396--5358433 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5358386 TGACCCGATT
5358396 TAAAATATTATTATATTAA
1 TAAAATATTATTAT-TTAA
*
5358415 TAAAATATTTTTATTTAA
1 TAAAATATTATTATTTAA
5358433 T
1 T
5358434 TTTACTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAAATATTATTATTTAA
Found at i:5358496 original size:15 final size:15
Alignment explanation
Indices: 5358476--5358525 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
5358466 AGCCTTTTGG
5358476 TATTTTAATTTTAAA
1 TATTTTAATTTTAAA
5358491 TATTTTAATTTT--A
1 TATTTTAATTTTAAA
* *
5358504 TATTATTAAATATAAA
1 TATT-TTAATTTTAAA
5358520 TATTTT
1 TATTTT
5358526 TTATATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 5 0.17
14 6 0.20
15 14 0.47
16 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTTAATTTTAAA
Found at i:5358610 original size:17 final size:18
Alignment explanation
Indices: 5358555--5358652 Score: 95
Period size: 21 Copynumber: 5.7 Consensus size: 18
5358545 TATTATGTTG
5358555 TTATTTTAATAA-T-A-A
1 TTATTTTAATAATTAATA
5358570 TTA--TTAAT-ATTAATA
1 TTATTTTAATAATTAATA
* *
5358585 CTA-TTTAATAATT-TTA
1 TTATTTTAATAATTAATA
5358601 TTATTTTAATAATTAATA
1 TTATTTTAATAATTAATA
5358619 TTATTTAATACATAATTAATA
1 TTATTT--TA-ATAATTAATA
5358640 TTATTTTAATAAT
1 TTATTTTAATAAT
5358653 ATAAGCTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
12 1 0.01
13 6 0.09
14 1 0.01
15 6 0.09
16 9 0.13
17 13 0.19
18 13 0.19
19 2 0.03
20 2 0.03
21 16 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTTTAATAATTAATA
Found at i:5358833 original size:43 final size:44
Alignment explanation
Indices: 5358786--5358874 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 44
5358776 AATAATAGAC
*
5358786 ATTTTTAATA-TAAAATA-CAACTATTTTAATATTAAATATTACT
1 ATTTTTAATATTAAAATAGCAA-TATTTTAATACTAAATATTACT
** * *
5358829 A-TTTTAATATTATTATAGTAATATTTTAATACTAAATATTATT
1 ATTTTTAATATTAAAATAGCAATATTTTAATACTAAATATTACT
5358872 ATT
1 ATT
5358875 AAAATTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
42 8 0.21
43 27 0.71
44 3 0.08
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (44 bp):
ATTTTTAATATTAAAATAGCAATATTTTAATACTAAATATTACT
Found at i:5358839 original size:21 final size:21
Alignment explanation
Indices: 5358788--5358874 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
5358778 TAATAGACAT
* **
5358788 TTTTAATATAAAATACAACTA
1 TTTTAATATTAAATATTACTA
5358809 TTTTAATATTAAATATTACTA
1 TTTTAATATTAAATATTACTA
* * *
5358830 TTTTAATATTATTATAGTAATA
1 TTTTAATATTA-AATATTACTA
* *
5358852 TTTTAATACTAAATATTATTA
1 TTTTAATATTAAATATTACTA
5358873 TT
1 TT
5358875 AAAATTAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 38 0.69
22 17 0.31
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.51
Consensus pattern (21 bp):
TTTTAATATTAAATATTACTA
Found at i:5363195 original size:32 final size:32
Alignment explanation
Indices: 5363159--5363224 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
5363149 GGCCACGCCT
*
5363159 TCTAATCTCCTGCATATAAAACAGACTATTTG
1 TCTAATCTCCTACATATAAAACAGACTATTTG
*
5363191 TCTAATCTCCTACATATAAAACAGTCTATTTG
1 TCTAATCTCCTACATATAAAACAGACTATTTG
5363223 TC
1 TC
5363225 CAAAACAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (32 bp):
TCTAATCTCCTACATATAAAACAGACTATTTG
Found at i:5366141 original size:33 final size:33
Alignment explanation
Indices: 5366068--5366142 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
5366058 TTTATTAAAT
* *
5366068 TAAA-ATATTAAATAATATATTTATTAATATAA
1 TAAATATATTAAATAATAAATTTAATAATATAA
*
5366100 TACATATATATAAAT-ATAAATTTAATAA-ATAA
1 TAAATATAT-TAAATAATAAATTTAATAATATAA
5366132 TAAATTATATT
1 TAAA-TATATT
5366143 TTTTATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
32 11 0.31
33 20 0.56
34 5 0.14
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
TAAATATATTAAATAATAAATTTAATAATATAA
Done.