Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 160 of 198
Found at i:50433016 original size:132 final size:132
Alignment explanation
Indices: 50432862--50433734 Score: 1405
Period size: 132 Copynumber: 6.6 Consensus size: 132
50432852 CTCTCGGTTC
* * * *
50432862 TAGTGGAGTAGGTTAAAGATTGCATATTCTGTCACCCTATGCAGTAGTGGAGCAGATCAAAGATG
1 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
*
50432927 GTGAATCTTATCTTCCCAGTACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGC
66 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGC
50432992 AG
131 AG
* *
50432994 TAGTGGAGTAGGTTAAATATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
1 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
50433059 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGC
66 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGC
50433124 AG
131 AG
* * *
50433126 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTATGCAGTAGTGGAACAGATCAAAGATG
1 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
* * *
50433191 GTGAATCTTATCTTCTCAGTACAGTGGAGAAGCAGATTTAAGCCGTTAGTCCTATCACCCTAAGC
66 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGC
50433256 AG
131 AG
50433258 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
1 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
50433323 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGC
66 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGC
50433388 AG
131 AG
*
50433390 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAACAGATCGAAGATG
1 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
* *
50433455 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCGTTAGTCTTATCACCCTAAGC
66 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGC
50433520 AG
131 AG
* *
50433522 TAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGAAGATCGAAGATG
1 TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
* * * * *
50433587 GTGAATCTTATCTTCCTAATACAGTGGAGAAGTAGATTTAAGTCATTATTCC-AT--CCCT-TGC
66 GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAG-
50433648 CAG
130 CAG
* * * * * ** *
50433651 CAATGGAATAGATTGAAGATTGCAGATTCTGTTC-CCTTAAATAGTAGTGGAGCAGATCAAAGAT
1 TAGTGGAGTAGGTTGAAGATTGCAGATTCTG-TCACCCTAAGCAGTAGTGGAGCAGATCGAAGAT
*
50433715 GCTGAATCTTATCTTCCCAA
65 GGTGAATCTTATCTTCCCAA
50433735 GATAGTAGAG
Statistics
Matches: 695, Mismatches: 44, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
128 1 0.00
129 76 0.11
130 2 0.00
131 2 0.00
132 614 0.88
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
TAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATG
GTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTAGTCCTATCACCCTAAGC
AG
Found at i:50433176 original size:44 final size:44
Alignment explanation
Indices: 50432978--50433585 Score: 250
Period size: 44 Copynumber: 13.8 Consensus size: 44
50432968 GCCATTAGTC
* * * *
50432978 CTATCACCCTAAGCAGTAGTGGAGTAGGTTAAATATTGCAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
* * ** *
50433022 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGGTGAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
* * * * * * *
50433065 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT--AG-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATTGAAG--ATTGCAGATT
* *
50433110 CTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
* * * ** ** *
50433154 CTGTCACCCTATGCAGTAGTGGAACAGATCAAAGA-TGGTGAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
** * * * * * * *
50433197 CTTATC-TTCTCAGTACAGTGGAGAAGCAGATTTAAGCCGTT--AG-TC
1 C-TATCACCCTAAG--CAGTAGTGGAGCAGATTGAAG--ATTGCAGATT
* *
50433242 CTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
* * ** *
50433286 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGA-TGGTGAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
* * * * * * *
50433329 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT--AG-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATTGAAG--ATTGCAGATT
* *
50433374 CTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
* * * ** *
50433418 CTGTCACCCTAAGCAGTAGTGGAACAGATCGAAGA-TGGTGAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
* * * * * * *
50433461 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCGTT--AG--T
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATTGAAG--ATTGCAGATT
* * *
50433505 CTTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATT
1 C-TATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
* * *
50433550 CTGTCACCCTAAGCAGTAGTGGAGAAGATCGAAGAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGAT
50433586 GGTGAATCTT
Statistics
Matches: 399, Mismatches: 124, Indels: 82
0.66 0.20 0.14
Matches are distributed among these distances:
41 10 0.03
43 103 0.26
44 196 0.49
45 80 0.20
46 4 0.01
47 2 0.01
48 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
CTATCACCCTAAGCAGTAGTGGAGCAGATTGAAGATTGCAGATT
Found at i:50460896 original size:44 final size:43
Alignment explanation
Indices: 50460614--50461428 Score: 286
Period size: 44 Copynumber: 18.8 Consensus size: 43
50460604 TCGGTGGCCG
* * * *
50460614 ATAATCTTATCTCTCTAAAGTTACAGTGGAGCAGATTAGAACC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * * * * *
50460657 GATAATCCTATCTCCCTAAAGTTACAGTGGAGCGGATGAAAACC
1 -ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * * * *** *
50460701 TTGGATCTTATCTCACTGAAGTTACAG-AGAGCAGATCCCA-TC
1 AT-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * * * *
50460743 -TAGTCTTATCTCCCTGAAGTTACAGTAGAGCAGACTAAGTGGGC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-AGCC
* * * *
50460787 A-AGTCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATG-G
1 ATAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-GCC
* *
50460831 AAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAGAGCC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* ** * *
50460874 GATAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACC
1 -ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* ** * * * * *
50460918 TTAGATCTTATCTCTTTGAAGTAGCAG-AGAGTAGA-TCGCA-TC
1 ATA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCC
* * *
50460960 -TAGTCTTATCTCCCTGAAGTTGCGGTGGAGCAGACTAAGTAAG-C
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG--AGCC
* * * *
50461004 A-AGTCTTATC-CTCCTGAAGATGCAGT-GAGGCAGACTGAAGATGGC
1 ATAATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-GCC
** * * *
50461049 A-AATCTTATCTCTTTAAAGTTGCAGTAGAGCAGATTAAAGCC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * *
50461091 GATAATCCTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAACC
1 -ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * * * *
50461135 -TCAGATCTTATCTCTCTGAAGTTGAAG-AGAGCAGA-TCGCA-TC
1 AT-A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCC
* * *
50461177 -TAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTA-AGCAA
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGC-C
* * * *
50461219 AGCAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGC
1 A-TAA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-GCC
* * *
50461267 A-AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
* * ** * *
50461309 GACAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACTTC
1 -ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGC--C
* ** * * *
50461355 A-GATCTTATCTCTATGAAGTTGCAG-AGAGCAGA-TCGCA-TC
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAG-AGCC
* *
50461395 -TAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
1 ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
50461429 CTGGCAGATC
Statistics
Matches: 587, Mismatches: 127, Indels: 117
0.71 0.15 0.14
Matches are distributed among these distances:
40 80 0.14
41 32 0.05
42 15 0.03
43 49 0.08
44 289 0.49
45 106 0.18
46 12 0.02
47 1 0.00
48 2 0.00
49 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
ATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAGCC
Found at i:50460993 original size:217 final size:217
Alignment explanation
Indices: 50460616--50461430 Score: 1231
Period size: 217 Copynumber: 3.8 Consensus size: 217
50460606 GGTGGCCGAT
* * *
50460616 AATCTTATCTCTCTAAAGTTACAGTGGAGCAGATTAGAA-CCGATAATCCTATCTCCCTAAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTA-AAGCCGATAATCCTATCTCCCTGAAGTT
* * * * *
50460680 ACAGTGGAGCGGATGAAAACCTTGGATCTTATCTCACTGAAGTTA-CAGAGAGCAGATCCCATCT
65 GCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAG-TAGCAGAGAGCAGATCGCATCT
* * **
50460744 AGTCTTATCTCCCTGAAGTTACAGTAGAGCAGACTAAGTGGGCAAGTCTTATCCTCCTGAAGTTG
129 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTG
* *
50460809 TAGTGAGGCAGACTGAAGATGGAA
194 CAGTGAGGCAGACTGAAGATGGCA
*
50460833 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
* * *
50460898 CAGTGGAGTGGATTAAAACCTTAGATCTTATCTCTTTGAAGTAGCAGAGAGTAGATCGCATCTAG
66 CAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTAGCAGAGAGCAGATCGCATCTAG
* *
50460963 TCTTATCTCCCTGAAGTTGCGGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGATGCA
131 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
50461028 GTGAGGCAGACTGAAGATGGCA
196 GTGAGGCAGACTGAAGATGGCA
** *
50461050 AATCTTATCTCTTTAAAGTTGCAGTAGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
* * * * *
50461115 CAGTGAAGCAGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGAAGAGAGCAGATCGCATCTAG
66 CAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTAGCAGAGAGCAGATCGCATCTAG
*
50461180 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAAGCAAGTCTTATCCTCCTGAAGTTGC
131 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-TAAGCAAGTCTTATCCTCCTGAAGTTGC
*
50461245 AGTGAGGTAGACTGAAGATGGCA
195 AGTGAGGCAGACTGAAGATGGCA
* * * *
50461268 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
* * *
50461333 CAGTGGAGTGGATTAAAA-CTTCAGATCTTATCTCTATGAAGTTGCAGAGAGCAGATCGCATCTA
66 CAGTGGAGCGGATTAAAACCTT-AGATCTTATCTCTCTGAAGTAGCAGAGAGCAGATCGCATCTA
*
50461397 GTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACT
130 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
50461431 GGCAGATCAA
Statistics
Matches: 546, Mismatches: 48, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
216 3 0.01
217 347 0.64
218 196 0.36
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTG
CAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTAGCAGAGAGCAGATCGCATCTAG
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
GTGAGGCAGACTGAAGATGGCA
Found at i:50461707 original size:17 final size:17
Alignment explanation
Indices: 50461685--50461726 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
50461675 GACCCGAGGT
* *
50461685 GGCCCAAACCCAACTGA
1 GGCCCAAACCAAACAGA
50461702 GGCCCAAACCAAACAGA
1 GGCCCAAACCAAACAGA
*
50461719 AGCCCAAA
1 GGCCCAAA
50461727 GTAGATTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.43, C:0.38, G:0.17, T:0.02
Consensus pattern (17 bp):
GGCCCAAACCAAACAGA
Found at i:50464691 original size:3 final size:3
Alignment explanation
Indices: 50464683--50464771 Score: 115
Period size: 3 Copynumber: 29.7 Consensus size: 3
50464673 CCACTCATTT
* * * * * * *
50464683 TAA TAA TAA TGA TAA TGA TGA TGA TGA TGA TGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50464731 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
50464772 CTTACCTCAC
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:50465532 original size:16 final size:17
Alignment explanation
Indices: 50465502--50465534 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
50465492 TTGTTTATTA
*
50465502 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
50465519 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
50465535 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:50465662 original size:5 final size:5
Alignment explanation
Indices: 50465654--50465692 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
50465644 TTATTTATTT
*
50465654 TATAA TATAA TATAA TATAA TAATAA TAATAA TTTAA TA
1 TATAA TATAA TATAA TATAA T-ATAA T-ATAA TATAA TA
50465693 ACATATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:50473546 original size:8 final size:8
Alignment explanation
Indices: 50473515--50473566 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
50473505 AGGTCTATTT
*
50473515 AAAATAAA
1 AAAATTAA
50473523 AAAATTAA
1 AAAATTAA
50473531 ATTTAAATTAA
1 A---AAATTAA
*
50473542 AAAATAAA
1 AAAATTAA
50473550 AAAATTAA
1 AAAATTAA
*
50473558 ACAATTAA
1 AAAATTAA
50473566 A
1 A
50473567 GAACACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 29 0.78
11 8 0.22
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAATTAA
Found at i:50486727 original size:23 final size:23
Alignment explanation
Indices: 50486701--50486746 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
50486691 ATTATAACTT
50486701 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
50486724 TTTTTTATTTACCAAAATATATA
1 TTTTTTATTTACCAAAATATATA
50486747 AAAAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTTATTTACCAAAATATATA
Found at i:50486787 original size:23 final size:23
Alignment explanation
Indices: 50486744--50486787 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
50486734 ACCAAAATAT
*
50486744 ATAAAAAACAAAAAAATAAAAAA
1 ATAAAAAACAAAAAAAAAAAAAA
**
50486767 ATAAAAAACCGAAAAAAAAAA
1 ATAAAAAACAAAAAAAAAAAA
50486788 CTGAACTGAT
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:0.84, C:0.07, G:0.02, T:0.07
Consensus pattern (23 bp):
ATAAAAAACAAAAAAAAAAAAAA
Found at i:50486874 original size:27 final size:27
Alignment explanation
Indices: 50486813--50486895 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 27
50486803 AACTCCCTGG
50486813 GTGGAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
****
50486840 AACAAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
** **
50486867 GTGGAGGGATCCCTGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
50486894 GT
1 GT
50486896 CCTGCCAACC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.23, C:0.22, G:0.42, T:0.13
Consensus pattern (27 bp):
GTGGAGGGAAGCAGGTTGGCGGCACCA
Found at i:50487216 original size:3 final size:3
Alignment explanation
Indices: 50487208--50487238 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
50487198 AATTCTATAG
50487208 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
50487239 GTTGTTGTTG
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):
TAT
Found at i:50487243 original size:3 final size:3
Alignment explanation
Indices: 50487237--50487331 Score: 181
Period size: 3 Copynumber: 31.7 Consensus size: 3
50487227 ATTATTATTA
50487237 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
*
50487285 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG CTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
50487332 AGTAAAAAAC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.00, C:0.01, G:0.33, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:50487703 original size:15 final size:15
Alignment explanation
Indices: 50487679--50487717 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
50487669 CAATAACCAC
*
50487679 AATAACTAAAACTAG
1 AATAATTAAAACTAG
*
50487694 AATAATT-AAATTAG
1 AATAATTAAAACTAG
50487708 AATAATTAAA
1 AATAATTAAA
50487718 TTGATACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (15 bp):
AATAATTAAAACTAG
Found at i:50487710 original size:14 final size:14
Alignment explanation
Indices: 50487691--50487719 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
50487681 TAACTAAAAC
50487691 TAGAATAATTAAAT
1 TAGAATAATTAAAT
50487705 TAGAATAATTAAAT
1 TAGAATAATTAAAT
50487719 T
1 T
50487720 GATACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:50488707 original size:17 final size:17
Alignment explanation
Indices: 50488685--50488721 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
50488675 AGTAAGATGT
50488685 CATGAATATTAAAATAG
1 CATGAATATTAAAATAG
*
50488702 CATGAATATTAGAATAG
1 CATGAATATTAAAATAG
50488719 CAT
1 CAT
50488722 CTTACCCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.30
Consensus pattern (17 bp):
CATGAATATTAAAATAG
Found at i:50491308 original size:10 final size:10
Alignment explanation
Indices: 50491293--50491409 Score: 75
Period size: 10 Copynumber: 11.7 Consensus size: 10
50491283 AAAAATTACC
50491293 TTCTTTCCTT
1 TTCTTTCCTT
50491303 TTCTTTCCTTATTT
1 TTCTTTCC----TT
50491317 TTCTTTCCTT
1 TTCTTTCCTT
50491327 ATT-TTT-C-T
1 -TTCTTTCCTT
*
50491335 TTCTTTCCTC
1 TTCTTTCCTT
**
50491345 CCCTTTCCTT
1 TTCTTTCCTT
50491355 TTCTTTCCTT
1 TTCTTTCCTT
50491365 CTT-TTT-C-T
1 -TTCTTTCCTT
*
50491373 TTCTTTCCTC
1 TTCTTTCCTT
*
50491383 TCCTTTCCTT
1 TTCTTTCCTT
* *
50491393 TTCCTTCTTT
1 TTCTTTCCTT
50491403 TTCTTTC
1 TTCTTTC
50491410 TTCCTTTCTT
Statistics
Matches: 82, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
7 4 0.05
8 8 0.10
9 4 0.05
10 52 0.63
11 4 0.05
14 10 0.12
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (10 bp):
TTCTTTCCTT
Found at i:50491320 original size:14 final size:14
Alignment explanation
Indices: 50491301--50491337 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
50491291 CCTTCTTTCC
50491301 TTTTCTTTCCTTAT
1 TTTTCTTTCCTTAT
50491315 TTTTCTTTCCTTAT
1 TTTTCTTTCCTTAT
50491329 TTTTCTTTC
1 TTTTCTTTC
50491338 TTTCCTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTCTTTCCTTAT
Found at i:50491323 original size:18 final size:18
Alignment explanation
Indices: 50491316--50491426 Score: 95
Period size: 18 Copynumber: 6.1 Consensus size: 18
50491306 TTTCCTTATT
*
50491316 TTTCTTTCCTTATTTTTC
1 TTTCTTTCCTTCTTTTTC
* * *
50491334 TTTCTTTCCTCCCCTTTCC
1 TTTCTTTCCT-TCTTTTTC
50491353 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTCTTTTTC
*
50491372 TTTCTTTCC-TCTCCTTTC
1 TTTCTTTCCTTCT-TTTTC
*
50491390 -CT-TTTCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
50491406 TTTC-TTCCTTTCTTTCTTC
1 TTTCTTTCC-TTCTTT-TTC
50491425 TT
1 TT
50491427 CTTCCCCTCT
Statistics
Matches: 74, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
16 9 0.12
17 12 0.16
18 29 0.39
19 14 0.19
20 10 0.14
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:50491357 original size:38 final size:38
Alignment explanation
Indices: 50491315--50491417 Score: 145
Period size: 38 Copynumber: 2.7 Consensus size: 38
50491305 CTTTCCTTAT
50491315 TTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCC
1 TTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCC
* *
50491353 TTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCC
1 TTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCC
* * *
50491391 TTTTCCTT-CTTTTTCTTTCTTCCTTTC
1 TTTTCTTTCCTTATT-TTTCTTTCTTTC
50491418 TTTCTTCTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 5 0.08
38 54 0.92
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (38 bp):
TTTTCTTTCCTTATTTTTCTTTCTTTCCTCCCCTTTCC
Found at i:50491370 original size:14 final size:14
Alignment explanation
Indices: 50491353--50491426 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
50491343 TCCCCTTTCC
50491353 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
50491367 TTTTCTTTCTTTCCT
1 TTTTCTTTCCTT-CT
50491382 CTCCTTTCCTTTTCCTTCT
1 -T--TTT-C-TTTCCTTCT
50491401 TTTTCTTT-CTTC-
1 TTTTCTTTCCTTCT
*
50491413 CTTTCTTT-CTTCT
1 TTTTCTTTCCTTCT
50491426 T
1 T
50491427 CTTCCCCTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
12 11 0.22
13 4 0.08
14 14 0.29
15 3 0.06
16 4 0.08
18 4 0.08
19 3 0.06
20 6 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:50491378 original size:28 final size:28
Alignment explanation
Indices: 50491293--50491426 Score: 93
Period size: 28 Copynumber: 4.8 Consensus size: 28
50491283 AAAAATTACC
*
50491293 TTCTTTCCTTTTCTTTCCTTATTTTTCT
1 TTCTTTCCTTTTCTTTCCTTCTTTTTCT
* ** **
50491321 TTCCTTATTTTTCTTT-C-T-TTCCTC-
1 TTCTTTCCTTTTCTTTCCTTCTTTTTCT
**
50491345 CCCTTTCCTTTTCTTTCCTTCTTTTTCT
1 TTCTTTCCTTTTCTTTCCTTCTTTTTCT
50491373 TTCTTTCCTCTCCTTTCCTTTTCCTTCTTTTTCT
1 TTCTTT-C-CT--TTT-C-TTTCCTTCTTTTTCT
50491407 TTC-TTCC-TTTCTTT-CTTCTT
1 TTCTTTCCTTTTCTTTCCTTCTT
50491427 CTTCCCCTCT
Statistics
Matches: 82, Mismatches: 14, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
24 11 0.13
25 11 0.13
26 5 0.06
27 6 0.07
28 20 0.24
29 1 0.01
30 2 0.02
31 1 0.01
32 4 0.05
33 3 0.04
34 18 0.22
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (28 bp):
TTCTTTCCTTTTCTTTCCTTCTTTTTCT
Found at i:50491401 original size:42 final size:44
Alignment explanation
Indices: 50491330--50491446 Score: 111
Period size: 42 Copynumber: 2.8 Consensus size: 44
50491320 TTTCCTTATT
* *
50491330 TTTCTTT-CTTTCC-TCCCCTTTCCTTTTCTTTCCTTCTTT-TT-C
1 TTTCTTTCCTCTCCTTCCCCTCTCC--TTCTTTCCTTCTTTCTTCC
* * *
50491372 TTTCTTTCCTCTCCTTTCCTTTTCCTTCTTT--TTCTTTCTTCC
1 TTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTCCTTCTTTCTTCC
* *
50491414 TTTCTTTCTTCTTCTTCCCCTCTCCTTCTTTCC
1 TTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTCC
50491447 CCCACCAACC
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
40 6 0.10
41 2 0.03
42 40 0.66
43 5 0.08
44 8 0.13
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (44 bp):
TTTCTTTCCTCTCCTTCCCCTCTCCTTCTTTCCTTCTTTCTTCC
Found at i:50491410 original size:10 final size:10
Alignment explanation
Indices: 50491358--50491429 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
50491348 TTTCCTTTTC
*
50491358 TTTCCTTCTT
1 TTTCTTTCTT
50491368 TTTCTTTCTT
1 TTTCTTTCTT
*
50491378 TCCTCTCCTTTCCT
1 T--T-T-CTTTCTT
*
50491392 TTTCCTTCTT
1 TTTCTTTCTT
50491402 TTTCTTTCTT
1 TTTCTTTCTT
50491412 CCTTTCTTTCTT
1 --TTTCTTTCTT
*
50491424 CTTCTT
1 TTTCTT
50491430 CCCCTCTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 29 0.58
11 1 0.02
12 12 0.24
13 1 0.02
14 7 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:50491422 original size:22 final size:23
Alignment explanation
Indices: 50491387--50491429 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
50491377 TTCCTCTCCT
*
50491387 TTCCTTTTCCTTCTTTTTCTTTC
1 TTCCTTTTCCTTCTTCTTCTTTC
*
50491410 TTCC-TTTCTTTCTTCTTCTT
1 TTCCTTTTCCTTCTTCTTCTT
50491430 CCCCTCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (23 bp):
TTCCTTTTCCTTCTTCTTCTTTC
Found at i:50491516 original size:27 final size:27
Alignment explanation
Indices: 50491478--50491544 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
50491468 AATTCAAGGG
*
50491478 TGGTGCCGCCAACAGGGATCCCTCCAC
1 TGGTGCCGCCAACACGGATCCCTCCAC
*
50491505 TGGTGCCGCCAACACGGATCCCTCCAT
1 TGGTGCCGCCAACACGGATCCCTCCAC
50491532 TGGTGCCGCCAAC
1 TGGTGCCGCCAAC
50491545 CTGCTTCCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.18, C:0.40, G:0.25, T:0.16
Consensus pattern (27 bp):
TGGTGCCGCCAACACGGATCCCTCCAC
Found at i:50491614 original size:9 final size:10
Alignment explanation
Indices: 50491586--50491613 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
50491576 CAGTTCAGGT
50491586 TTTTTTTTTG
1 TTTTTTTTTG
50491596 TTTTTTTTTG
1 TTTTTTTTTG
50491606 TTTTTTTT
1 TTTTTTTT
50491614 GATATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:50491681 original size:28 final size:27
Alignment explanation
Indices: 50491623--50491683 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
50491613 TGATATATTT
* * *
50491623 TGGTAAATAAAAAATTTATATATATTT
1 TGGTAAATAAAAAAGTTATATACATTC
50491650 TGGTAAATAAAAAAAAGTTATA-ACATTC
1 TGGTAAAT--AAAAAAGTTATATACATTC
50491678 TGGTAA
1 TGGTAA
50491684 TTTTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 8 0.28
28 10 0.34
29 11 0.38
ACGTcount: A:0.49, C:0.03, G:0.11, T:0.36
Consensus pattern (27 bp):
TGGTAAATAAAAAAGTTATATACATTC
Found at i:50492054 original size:40 final size:41
Alignment explanation
Indices: 50491990--50492089 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 41
50491980 GATAAAGCAG
*
50491990 GAAAACGCTTCCTCAAGGAAGCGC-TT-TGTCCACGTGGAC
1 GAAAACGCTTCCTTAAGGAAGCGCTTTGTGTCCACGTGGAC
* ** *
50492029 AGAAAACGCTTCCTTGAGGGTGCGCTTTGTGTTCACGTGGAC
1 -GAAAACGCTTCCTTAAGGAAGCGCTTTGTGTCCACGTGGAC
*
50492071 -AAAGCGCTTCCTTAAGGAA
1 GAAAACGCTTCCTTAAGGAA
50492090 TCACTTTCCC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
40 35 0.71
41 2 0.04
42 12 0.24
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (41 bp):
GAAAACGCTTCCTTAAGGAAGCGCTTTGTGTCCACGTGGAC
Found at i:50492295 original size:45 final size:44
Alignment explanation
Indices: 50492246--50492346 Score: 175
Period size: 45 Copynumber: 2.3 Consensus size: 44
50492236 AAAAAATTAG
*
50492246 ATTAGGGTTTAGTTTTTATGGTTTTTAAGGAAAAAAATCAAATAA
1 ATTAGGGTTTAGTGTTTATGGTTTTTAAGG-AAAAAATCAAATAA
50492291 ATTAGGGTTTAGTGTTTATGGTTTTTAAGGAAAAAATCAAATAA
1 ATTAGGGTTTAGTGTTTATGGTTTTTAAGGAAAAAATCAAATAA
*
50492335 ATAAGGGTTTAG
1 ATTAGGGTTTAG
50492347 GGTTACTTGA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
44 25 0.46
45 29 0.54
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.39
Consensus pattern (44 bp):
ATTAGGGTTTAGTGTTTATGGTTTTTAAGGAAAAAATCAAATAA
Found at i:50492424 original size:141 final size:141
Alignment explanation
Indices: 50492172--50492442 Score: 314
Period size: 141 Copynumber: 1.9 Consensus size: 141
50492162 GATTTTAGGG
* ** * *
50492172 TTTTAAGAAAAAAATTAAATAAATAAGGGTCTAGGGTTTTTTAATTAAATTAATTATAAATTTTA
1 TTTTAAGAAAAAAATCAAATAAATAAGGGTCTAGGGTTACTTAAGTAAATTAATTATAAACTTTA
** ** * *
50492237 AAAAATTAGATTAGGGTTTAGTTTTTATGGTTTTTAAGGAAAAAAATCAAATAAATTAGGGTTTA
66 AAAAATTAGATTAGGGCATAGTGATTATGATTTTTAAGGAAAAAAATCAAATAAATGAGGGTTTA
50492302 GTGTTTATGGT
131 GTGTTTATGGT
* * *
50492313 TTTTAAGGAAAAAATCAAATAAATAAGGGTTTAGGGTTACTTGAGTAAATTAATTAT-AACTTTA
1 TTTTAAGAAAAAAATCAAATAAATAAGGGTCTAGGGTTACTTAAGTAAATTAATTATAAACTTTA
** * * * *
50492377 AAGCCGATTTGATTAGGGCATAGTGATTA-GTATTTTTTAGG-ACAAAATCTAATAAATGAGGGT
66 AA--AAATTAGATTAGGGCATAGTGATTATG-ATTTTTAAGGAAAAAAATCAAATAAATGAGGGT
50492440 TTA
128 TTA
50492443 AGCGGCTTGA
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
140 8 0.07
141 73 0.68
142 26 0.24
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (141 bp):
TTTTAAGAAAAAAATCAAATAAATAAGGGTCTAGGGTTACTTAAGTAAATTAATTATAAACTTTA
AAAAATTAGATTAGGGCATAGTGATTATGATTTTTAAGGAAAAAAATCAAATAAATGAGGGTTTA
GTGTTTATGGT
Found at i:50511285 original size:21 final size:20
Alignment explanation
Indices: 50511252--50511300 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
50511242 ATAAATAAAA
50511252 TCATTCATGTCAATTCCCTG
1 TCATTCATGTCAATTCCCTG
*
50511272 TCATTCACTGTCAATTTCCTG
1 TCATTCA-TGTCAATTCCCTG
50511293 TCATTCAT
1 TCATTCAT
50511301 AACTTCTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.20, C:0.29, G:0.08, T:0.43
Consensus pattern (20 bp):
TCATTCATGTCAATTCCCTG
Found at i:50511529 original size:19 final size:19
Alignment explanation
Indices: 50511479--50511532 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
50511469 CGAATACGCC
* * *
50511479 AACAGAAGCTCGAAAGTTG
1 AACAGAAGCTCGTAAGCTA
*
50511498 AGCAGAAGCTCGTAAGCTA
1 AACAGAAGCTCGTAAGCTA
50511517 AACAGAAGCTCGTAAG
1 AACAGAAGCTCGTAAG
50511533 AGCTGATTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.19, G:0.26, T:0.15
Consensus pattern (19 bp):
AACAGAAGCTCGTAAGCTA
Found at i:50512039 original size:17 final size:17
Alignment explanation
Indices: 50512004--50512047 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
50511994 ACAATTTTTG
50512004 TAATTAATC-TCATAAT
1 TAATTAATCTTCATAAT
50512020 TAATTAATCTATCA-AAT
1 TAATTAATCT-TCATAAT
*
50512037 TAACTAATCTT
1 TAATTAATCTT
50512048 GTAATACCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 10 0.40
17 12 0.48
18 3 0.12
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTAATCTTCATAAT
Found at i:50520673 original size:17 final size:17
Alignment explanation
Indices: 50520631--50520681 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
50520621 TATATTTTTA
50520631 TAATTTAAATAAAAATT
1 TAATTTAAATAAAAATT
** * *
50520648 TAAGATAAATCAAATTT
1 TAATTTAAATAAAAATT
50520665 TAATTTAAAATAAAAAT
1 TAATTT-AAATAAAAAT
50520682 ATTTTTGATA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TAATTTAAATAAAAATT
Found at i:50524959 original size:39 final size:39
Alignment explanation
Indices: 50524914--50524992 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
50524904 TCTTTGTCCC
50524914 TTCCAAGTAAGTAATTTGTTAATTTCTTGCAGATATATT
1 TTCCAAGTAAGTAATTTGTTAATTTCTTGCAGATATATT
50524953 TTCCAAGTAAGTAATTTGTTAATTTCTTGCAGATATATT
1 TTCCAAGTAAGTAATTTGTTAATTTCTTGCAGATATATT
50524992 T
1 T
50524993 ACCATCACCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (39 bp):
TTCCAAGTAAGTAATTTGTTAATTTCTTGCAGATATATT
Found at i:50526026 original size:32 final size:33
Alignment explanation
Indices: 50525968--50526032 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
50525958 ATGATGAAAA
50525968 ACCTTGTTTGCTGGTGCTTTTTTTCTTCTTGTT
1 ACCTTGTTTGCTGGTGCTTTTTTTCTTCTTGTT
50526001 ACCTTGTTTGCTGGTG-TTTTTTTCTTCTTGTT
1 ACCTTGTTTGCTGGTGCTTTTTTTCTTCTTGTT
50526033 GTCGAAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.03, C:0.17, G:0.18, T:0.62
Consensus pattern (33 bp):
ACCTTGTTTGCTGGTGCTTTTTTTCTTCTTGTT
Found at i:50531219 original size:3 final size:3
Alignment explanation
Indices: 50531211--50531235 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
50531201 ATAAACCCAT
50531211 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
50531236 ACAGAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:50536095 original size:20 final size:20
Alignment explanation
Indices: 50536070--50536110 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
50536060 GGATAACTAG
50536070 AATATTCACACGCAACAACC
1 AATATTCACACGCAACAACC
50536090 AATATTCACACGCAACAACC
1 AATATTCACACGCAACAACC
50536110 A
1 A
50536111 GTAGATGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.34, G:0.05, T:0.15
Consensus pattern (20 bp):
AATATTCACACGCAACAACC
Found at i:50541743 original size:15 final size:15
Alignment explanation
Indices: 50541723--50541757 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
50541713 ATACAGAGCC
50541723 AATTTTGTTTTATTT
1 AATTTTGTTTTATTT
*
50541738 AATTTTTTTTTATTT
1 AATTTTGTTTTATTT
*
50541753 CATTT
1 AATTT
50541758 GCTTAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
AATTTTGTTTTATTT
Found at i:50547686 original size:10 final size:10
Alignment explanation
Indices: 50547671--50547696 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
50547661 AAAAAATTTA
50547671 AAATTATTAG
1 AAATTATTAG
50547681 AAATTATTAG
1 AAATTATTAG
50547691 AAATTA
1 AAATTA
50547697 GAAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (10 bp):
AAATTATTAG
Found at i:50547988 original size:59 final size:58
Alignment explanation
Indices: 50547922--50548051 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 58
50547912 TTTCACAAAA
*
50547922 TTTATATTTCTTTACATTTTGTATAA-TTTCCTTACGA-CTTTATAAAATTTTACAATTTT
1 TTTATATTTCTTTACA-TTT-TATAATTTTCCTTACGATCTTTATAAAATGTTACAA-TTT
* * ** *
50547981 TTTATATTTCTATATATTTTATAATTTTTTTTACGATTTTTATAAAATGTTACAATTT
1 TTTATATTTCTTTACATTTTATAATTTTCCTTACGATCTTTATAAAATGTTACAATTT
50548039 TTTATATTTCTTT
1 TTTATATTTCTTT
50548052 TACAACTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
57 5 0.08
58 27 0.44
59 30 0.48
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.60
Consensus pattern (58 bp):
TTTATATTTCTTTACATTTTATAATTTTCCTTACGATCTTTATAAAATGTTACAATTT
Found at i:50548024 original size:28 final size:28
Alignment explanation
Indices: 50547968--50548049 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 28
50547958 ACTTTATAAA
*
50547968 ATTTTACAATTTTTTTATATTTCTATAT
1 ATTTTACAATTTTTTTAGATTTCTATAT
* * *
50547996 ATTTTATAATTTTTTTTACGATTTTTATAAA
1 ATTTTACAA-TTTTTTTA-GATTTCTAT-AT
* *
50548027 ATGTTACAA-TTTTTTATATTTCT
1 ATTTTACAATTTTTTTAGATTTCT
50548050 TTTACAACTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
28 13 0.30
29 15 0.35
30 7 0.16
31 8 0.19
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (28 bp):
ATTTTACAATTTTTTTAGATTTCTATAT
Found at i:50548078 original size:58 final size:58
Alignment explanation
Indices: 50547960--50548080 Score: 149
Period size: 59 Copynumber: 2.1 Consensus size: 58
50547950 TCCTTACGAC
* * *
50547960 TTTATAAAATTTTACAATTTTTTTATATTTCTATATATTTTATAATTTTTTTTACGATT
1 TTTATAAAATGTTACAATTTTTTTATATTTCTATAAACTTTATAATTTTTTTTAC-ATT
*
50548019 TTTATAAAATGTTACAA-TTTTTTATATTTCTTTTACAACTTTAT-ATTTTTTTCTA-ATT
1 TTTATAAAATGTTACAATTTTTTTATATTTC-TATA-AACTTTATAATTTTTTT-TACATT
50548077 TTTA
1 TTTA
50548081 ATATTTGATT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
58 20 0.36
59 27 0.49
60 8 0.15
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (58 bp):
TTTATAAAATGTTACAATTTTTTTATATTTCTATAAACTTTATAATTTTTTTTACATT
Found at i:50548080 original size:19 final size:20
Alignment explanation
Indices: 50548030--50548086 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
50548020 TTATAAAATG
50548030 TTACAATTTTTTATATTTCTT
1 TTACAA-TTTTTATATTTCTT
*
50548051 TTACAA-CTTTATATTT-TT
1 TTACAATTTTTATATTTCTT
50548069 TT-CTAATTTTTAATATTT
1 TTAC-AATTTTT-ATATTT
50548087 GATTTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 1 0.03
18 6 0.19
19 12 0.39
20 6 0.19
21 6 0.19
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (20 bp):
TTACAATTTTTATATTTCTT
Found at i:50548282 original size:88 final size:89
Alignment explanation
Indices: 50548180--50548359 Score: 258
Period size: 89 Copynumber: 2.0 Consensus size: 89
50548170 GCTTAAAATT
* * *
50548180 TTTTTTGATGCATTTTGAAAGTTTAAGTA-CTCAATTGAGTGC-AAAAAAAATAG-GGACTTAAT
1 TTTTTTGATACATTTTGAAAGTTTAAGTATC-CAAATGAATGCAAAAAAAAATAGAGG-CTTAAT
** * *
50548242 TGTTTTTTTTGAAAAAGTTTGAGGGC
64 TGCATTTTTTGAAAAACTTTGAGAGC
50548268 TTTTTTGATACATTTTGAAAGTTTAAGTATCCAAATGAATGCAAAAAAAAATAGAGGCTTAATTG
1 TTTTTTGATACATTTTGAAAGTTTAAGTATCCAAATGAATGCAAAAAAAAATAGAGGCTTAATTG
50548333 CATTTTTTGAAAAACTTTGAGAGC
66 CATTTTTTGAAAAACTTTGAGAGC
50548357 TTT
1 TTT
50548360 GAGGCTTAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
88 37 0.45
89 43 0.52
90 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.39
Consensus pattern (89 bp):
TTTTTTGATACATTTTGAAAGTTTAAGTATCCAAATGAATGCAAAAAAAAATAGAGGCTTAATTG
CATTTTTTGAAAAACTTTGAGAGC
Found at i:50554780 original size:42 final size:42
Alignment explanation
Indices: 50554685--50554872 Score: 227
Period size: 42 Copynumber: 4.5 Consensus size: 42
50554675 TGATTCAGTA
* * *
50554685 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGA-AATGTTT
1 CACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATATTGTTT
* * *
50554726 CATCGGTATTAAGCCTGCTAGATGTAAAGTCTGATATTGTTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTT
* * * *
50554768 CACCGGTATTAAGCCTGCTAGACGTAAAGTCTAAAATTATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTT
*
50554810 CATCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTT
* * *
50554852 CACTGGCAATAAGTCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
50554873 GCACTAAGCC
Statistics
Matches: 125, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
40 2 0.02
41 26 0.21
42 97 0.78
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTT
Found at i:50554830 original size:84 final size:83
Alignment explanation
Indices: 50554685--50554872 Score: 259
Period size: 84 Copynumber: 2.3 Consensus size: 83
50554675 TGATTCAGTA
* * * * * * *
50554685 CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAATGTTTCATCGGTATTAAGCCTGCTAGATG
1 CACCGGCAATAAGCCTGCTAGACATAAAGTCTAAAATATTTCATCGGCATTAAGCCTGCTAGACG
50554750 TAAAGTCTGATATTGTTT
66 TAAAGTCTGATATTGTTT
* * *
50554768 CACCGGTATTAAGCCTGCTAGACGTAAAGTCTAAAATTATTTCATCGGCATTAAGCCTGCTAGAC
1 CACCGGCAATAAGCCTGCTAGACATAAAGTCTAAAA-TATTTCATCGGCATTAAGCCTGCTAGAC
50554833 GTAAAGTCTGATATTGTTT
65 GTAAAGTCTGATATTGTTT
* *
50554852 CACTGGCAATAAGTCTGCTAG
1 CACCGGCAATAAGCCTGCTAG
50554873 GCACTAAGCC
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
83 30 0.33
84 61 0.67
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (83 bp):
CACCGGCAATAAGCCTGCTAGACATAAAGTCTAAAATATTTCATCGGCATTAAGCCTGCTAGACG
TAAAGTCTGATATTGTTT
Found at i:50556728 original size:10 final size:10
Alignment explanation
Indices: 50556715--50556800 Score: 92
Period size: 9 Copynumber: 9.1 Consensus size: 10
50556705 TATATATATA
50556715 TATAATTTTT
1 TATAATTTTT
*
50556725 TATATTTTTT
1 TATAATTTTT
50556735 TATAATTTTT
1 TATAATTTTT
50556745 TATAA-TTTT
1 TATAATTTTT
* *
50556754 CATAA-TTTC
1 TATAATTTTT
*
50556763 TAT-ATATTT
1 TATAATTTTT
50556772 TAT-ATTTTT
1 TATAATTTTT
*
50556781 TATGA-TTTT
1 TATAATTTTT
50556790 TATAATTTTT
1 TATAATTTTT
50556800 T
1 T
50556801 GTATTTTTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
8 1 0.02
9 34 0.53
10 29 0.45
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (10 bp):
TATAATTTTT
Found at i:50556733 original size:9 final size:9
Alignment explanation
Indices: 50556719--50556824 Score: 90
Period size: 9 Copynumber: 11.4 Consensus size: 9
50556709 TATATATATA
50556719 ATTTTTTAT
1 ATTTTTTAT
50556728 ATTTTTTTAT
1 A-TTTTTTAT
50556738 AATTTTTTAT
1 -ATTTTTTAT
* *
50556748 AATTTTCAT
1 ATTTTTTAT
* *
50556757 AATTTCTAT
1 ATTTTTTAT
*
50556766 ATATTTTAT
1 ATTTTTTAT
50556775 ATTTTTTAT
1 ATTTTTTAT
50556784 GA-TTTTTAT
1 -ATTTTTTAT
*
50556793 AATTTTTTGT
1 -ATTTTTTAT
*
50556803 ATTTTTCA-
1 ATTTTTTAT
50556811 ATATTTTTAT
1 AT-TTTTTAT
50556821 ATTT
1 ATTT
50556825 GTAGTAGTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
8 2 0.03
9 50 0.64
10 25 0.32
11 1 0.01
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:50556743 original size:18 final size:19
Alignment explanation
Indices: 50556715--50556798 Score: 75
Period size: 20 Copynumber: 4.5 Consensus size: 19
50556705 TATATATATA
* *
50556715 TATAATTTTTTATATTTTTT
1 TATAATTTTATATA-ATTTT
*
50556735 TATAATTTTTTATAATTTT
1 TATAATTTTATATAATTTT
*
50556754 CATAATTTCTATAT-A-TTT
1 TATAATTT-TATATAATTTT
* *
50556772 TAT-ATTTTTTATGATTTT
1 TATAATTTTATATAATTTT
50556790 TATAATTTT
1 TATAATTTT
50556799 TTGTATTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.07
17 5 0.09
18 11 0.20
19 17 0.31
20 18 0.33
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (19 bp):
TATAATTTTATATAATTTT
Found at i:50557712 original size:21 final size:23
Alignment explanation
Indices: 50557669--50557714 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
50557659 CGATGTTACA
50557669 CGAACCCTAATTGTTTATGACATG
1 CGAACCCTAA-TGTTTATGACATG
*
50557693 CGAACCCTAA-G-TTATTACATG
1 CGAACCCTAATGTTTATGACATG
50557714 C
1 C
50557715 AAATCTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
24 10 0.48
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (23 bp):
CGAACCCTAATGTTTATGACATG
Found at i:50572415 original size:100 final size:99
Alignment explanation
Indices: 50572237--50572430 Score: 289
Period size: 100 Copynumber: 1.9 Consensus size: 99
50572227 TCGTCTGGAG
* * * * *
50572237 TCATCTTATTCCTCGGGTGCCATGCTTTATCTGCTAAAAACCCTTTGGTTTATGTTTGTTTGAGA
1 TCATCTTATTCCTCGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGAGA
* * *
50572302 ATATATTTCTTAAAATTATTCAATACCATGTTCCA
66 AAACATTTATT-AAATTATTCAATACCATGTTCCA
* *
50572337 TCATCTTATTCCTTGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGTGA
1 TCATCTTATTCCTCGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGAGA
50572402 AAACATTTATTAAATTATTCAATACCATG
66 AAACATTTATTAAATTATTCAATACCATG
50572431 CGTCATTACT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 18 0.21
100 66 0.79
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.42
Consensus pattern (99 bp):
TCATCTTATTCCTCGGGTGCCAAGCTTTATCTGCTAAAAACCATTTGCTTAATGTCTGTTTGAGA
AAACATTTATTAAATTATTCAATACCATGTTCCA
Found at i:50592705 original size:25 final size:25
Alignment explanation
Indices: 50592660--50592708 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
50592650 ATATAGTTTT
*
50592660 TATATTAATTATAAATGTTATAATA
1 TATATTAATTATAAATATTATAATA
50592685 TATATTATATTAT-AATATTATAAT
1 TATATTA-ATTATAAATATTATAAT
50592709 TAAACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TATATTAATTATAAATATTATAATA
Found at i:50594492 original size:41 final size:41
Alignment explanation
Indices: 50594429--50594553 Score: 151
Period size: 41 Copynumber: 3.0 Consensus size: 41
50594419 ACTAATCTGA
* * *
50594429 TTTATTGCCAGTGAAATAATTCAGACTTTATGTCTAGCAGGC
1 TTTA-TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
*
50594471 TTTATGCCGGTGAAATTATTCAGACTATACGTCTAGCAGGC
1 TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
* * * * * *
50594512 TTAATGCCGGTGATACATTTCGGACTATAAGTCTAGCAGGC
1 TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
50594553 T
1 T
50594554 AAAAGTCGGT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 68 0.94
42 4 0.06
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (41 bp):
TTTATGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGC
Found at i:50594766 original size:13 final size:13
Alignment explanation
Indices: 50594750--50594774 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50594740 ATATTAAATA
50594750 TATATGCATTTGG
1 TATATGCATTTGG
50594763 TATATGCATTTG
1 TATATGCATTTG
50594775 ATAAGCAATT
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:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
TATATGCATTTGG
Found at i:50594793 original size:2 final size:2
Alignment explanation
Indices: 50594786--50594833 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
50594776 TAAGCAATTG
*
50594786 AT AT AT AT CT 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 AT AT
50594828 AT AT AT
1 AT AT AT
50594834 TCGGCAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50598375 original size:2 final size:2
Alignment explanation
Indices: 50598368--50598392 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50598358 ATTCACAATA
50598368 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
50598393 TGTTAAACAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:50603208 original size:5 final size:5
Alignment explanation
Indices: 50603198--50603222 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
50603188 TTAGTTGTTA
50603198 ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT
50603223 TAACTATTTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:50617794 original size:30 final size:30
Alignment explanation
Indices: 50617722--50617794 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
50617712 GTTTGATTTT
* *
50617722 TTTTTTCAGATTAAGATCTAAATTTGATAA
1 TTTTTTCATATTAAGATCTAAATTTGACAA
* *
50617752 TTTTTCTCATATT-AGAGTTTAAATTTGGCAA
1 TTTTT-TCATATTAAGA-TCTAAATTTGACAA
50617783 TTTTTTCATATT
1 TTTTTTCATATT
50617795 GGGGACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (30 bp):
TTTTTTCATATTAAGATCTAAATTTGACAA
Found at i:50618029 original size:59 final size:60
Alignment explanation
Indices: 50617935--50618050 Score: 155
Period size: 59 Copynumber: 1.9 Consensus size: 60
50617925 AAATTTAGGG
* * *
50617935 CCTAATTTGGACTAAAAAAAAGTTTAGACCCCAATGTGTGAACAATTG-TCAAGTTCAGAA
1 CCTAATTTGAACTAAAAAAAAGTTCAGACCCCAATGTGGGAACAATTGCT-AAGTTCAGAA
* * *
50617995 CCTAATTTGAAC-AAAAAAAAGTTCAGGCTCCAATGTGGGAAGAATTGCTAAGTTCA
1 CCTAATTTGAACTAAAAAAAAGTTCAGACCCCAATGTGGGAACAATTGCTAAGTTCA
50618051 AGCCCCAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 37 0.76
60 12 0.24
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (60 bp):
CCTAATTTGAACTAAAAAAAAGTTCAGACCCCAATGTGGGAACAATTGCTAAGTTCAGAA
Found at i:50625159 original size:35 final size:36
Alignment explanation
Indices: 50625119--50625198 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
50625109 TGTAAAATCA
* * *
50625119 TATTCTAATAGGA-GTATAGTAAGATTTAAACACCT
1 TATTCTAATAGAATATATAGTAAGATTGAAACACCT
50625154 TATTCTAATAGAATATATAGTAAGATTGAAACACCT
1 TATTCTAATAGAATATATAGTAAGATTGAAACACCT
50625190 TATTCTAAT
1 TATTCTAAT
50625199 CAATATCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 12 0.29
36 29 0.71
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (36 bp):
TATTCTAATAGAATATATAGTAAGATTGAAACACCT
Found at i:50631046 original size:15 final size:15
Alignment explanation
Indices: 50631026--50631055 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
50631016 AATCTTCAAA
50631026 ACCAACAACAACAAC
1 ACCAACAACAACAAC
*
50631041 ACCAACACCAACAAC
1 ACCAACAACAACAAC
50631056 GGCAACAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.43, G:0.00, T:0.00
Consensus pattern (15 bp):
ACCAACAACAACAAC
Found at i:50633526 original size:58 final size:59
Alignment explanation
Indices: 50633464--50633576 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
50633454 TGAATTAGCC
* * * * * *
50633464 AATTGTTCTCACATTTGGG-TTGAATTTTTTTTTGTTCGAGTTAAGTCCTGAACTAGAT
1 AATTGTTCTCACATTGGGGCTTAAACTTTTTTTTATCCAAGTTAAGTCCTGAACTAGAT
* * *
50633522 AATTGTTCTTATATTGGGGCTTAAACTTTTTTTTATCCAAGTTAGGTCCTGAACT
1 AATTGTTCTCACATTGGGGCTTAAACTTTTTTTTATCCAAGTTAAGTCCTGAACT
50633577 TTACAAATGC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
58 16 0.36
59 29 0.64
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (59 bp):
AATTGTTCTCACATTGGGGCTTAAACTTTTTTTTATCCAAGTTAAGTCCTGAACTAGAT
Found at i:50636464 original size:19 final size:20
Alignment explanation
Indices: 50636442--50636480 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
50636432 TCAAATTTAT
50636442 TTTTTAAACTTA-AATATTC
1 TTTTTAAACTTATAATATTC
* *
50636461 TTTTTACATTTATAATATTC
1 TTTTTAAACTTATAATATTC
50636481 GAATGCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTAAACTTATAATATTC
Found at i:50641041 original size:14 final size:14
Alignment explanation
Indices: 50641018--50641052 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
50641008 TATATGTGTC
*
50641018 AGTATCTTTCCTTA
1 AGTATATTTCCTTA
*
50641032 AGTATATTTCCTTC
1 AGTATATTTCCTTA
50641046 AGTATAT
1 AGTATAT
50641053 CCAATGATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (14 bp):
AGTATATTTCCTTA
Found at i:50647359 original size:17 final size:17
Alignment explanation
Indices: 50647339--50647399 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
50647329 ATTTCAAGAC
50647339 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
50647356 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
50647375 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
50647393 TTATGTA
1 TTATGTA
50647400 GTGATTCAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 15 0.45
18 5 0.15
19 5 0.15
20 8 0.24
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:50647375 original size:37 final size:37
Alignment explanation
Indices: 50647334--50647445 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
50647324 TGTTAATTTC
50647334 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
50647371 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
* * *
50647408 AAGATTTATGTAATGTTTTTAATTATGTTGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
50647445 A
1 A
50647446 TTCGGGTAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.47
Consensus pattern (37 bp):
AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:50647381 original size:20 final size:19
Alignment explanation
Indices: 50647355--50647419 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
50647345 AATATTTTTA
50647355 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
* ***
50647374 ACTTATGTAAT-ATTTTTA-
1 A-TTATGTAGTGATTCAAAG
50647392 ATTATGTAGTGATTCAAAG
1 ATTATGTAGTGATTCAAAG
50647411 ATTTATGTA
1 A-TTATGTA
50647420 ATGTTTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 8 0.24
18 5 0.15
19 6 0.18
20 15 0.44
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (19 bp):
ATTATGTAGTGATTCAAAG
Found at i:50647435 original size:17 final size:17
Alignment explanation
Indices: 50647339--50647435 Score: 50
Period size: 17 Copynumber: 5.4 Consensus size: 17
50647329 ATTTCAAGAC
*
50647339 TTATGTAATATTTTTAA
1 TTATGTAATGTTTTTAA
* ***
50647356 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
*
50647375 CTTATGTAATATTTTTAA
1 -TTATGTAATGTTTTTAA
* ***
50647393 TTATGTAGTGATTCAAAGA
1 TTATGTAATG-TTTTTA-A
50647412 TTTATGTAATGTTTTTAA
1 -TTATGTAATGTTTTTAA
50647430 TTATGT
1 TTATGT
50647436 TGTGATTCAA
Statistics
Matches: 55, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 22 0.40
18 8 0.15
19 8 0.15
20 17 0.31
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (17 bp):
TTATGTAATGTTTTTAA
Found at i:50650417 original size:15 final size:15
Alignment explanation
Indices: 50650397--50650426 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
50650387 TAAATTGCCT
50650397 ATGTATTTATAAATA
1 ATGTATTTATAAATA
50650412 ATGTATTTATAAATA
1 ATGTATTTATAAATA
50650427 TTTGTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
ATGTATTTATAAATA
Found at i:50651963 original size:42 final size:42
Alignment explanation
Indices: 50651904--50652072 Score: 243
Period size: 42 Copynumber: 4.0 Consensus size: 42
50651894 CGGCTCTTAG
50651904 TAGCGGCGCTTAGA-AAAAAACGCCGCTAAAGACCATGTTCTT
1 TAGCGGCGCTTA-ATAAAAAACGCCGCTAAAGACCATGTTCTT
* *
50651946 TAGCGGCGCTT-AGAAAAAACGCCGCTAAAGTCCATGTTCTT
1 TAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCATGTTCTT
* *
50651987 TAGCGACGCTTAATAAAAAACGCCGCTAAATACCATGTTCTT
1 TAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCATGTTCTT
* * * *
50652029 TAGCGGCACTTAATAATAAACGCCGCTAAAGAACATGATCTT
1 TAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCATGTTCTT
50652071 TA
1 TA
50652073 ACAGCGTTTT
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.01
41 37 0.32
42 76 0.67
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (42 bp):
TAGCGGCGCTTAATAAAAAACGCCGCTAAAGACCATGTTCTT
Found at i:50652100 original size:42 final size:42
Alignment explanation
Indices: 50652049--50652252 Score: 288
Period size: 42 Copynumber: 4.9 Consensus size: 42
50652039 TAATAATAAA
* * *
50652049 CGCCGCTAAAGAACATGATCTTTAACAGCGTTTTTAGCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTATCTAAG
* * *
50652091 CGCCTCTAAAGAACAAGGTCTTTAGCGGCGTTTTTTAT-TAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTATCTAAG
50652133 CGCCGCTAAAGAACATGGA-CTTTAGCGGCGTTTTT-TCTAAG
1 CGCCGCTAAAGAACAT-GATCTTTAGCGGCGTTTTTATCTAAG
* *
50652174 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTATCTAAG
*
50652216 CGCCGATAAAGAACATGATCTTTAGCGGCGTTTTTAT
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTAT
50652253 ACAAAAACGC
Statistics
Matches: 144, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.01
41 41 0.28
42 94 0.65
43 7 0.05
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTATCTAAG
Found at i:50652203 original size:83 final size:84
Alignment explanation
Indices: 50652007--50652251 Score: 316
Period size: 83 Copynumber: 2.9 Consensus size: 84
50651997 TAATAAAAAA
* * * ** ** * *
50652007 CGCCGCTAAATACCATGTTCTTTAGCGGCACTTAATAATAAACGCCGCTAAAGAACATGATCTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGATCTTT
* *
50652072 AACAGCGTTTTTAGCTAAG
66 AGCGGCGTTTTTAGCTAAG
* *
50652091 CGCCTCTAAAGAACAAGGTCTTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGGA-CTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACAT-GATCTT
*
50652155 TAGCGGCGTTTTT-TCTAAG
65 TAGCGGCGTTTTTAGCTAAG
*
50652174 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT-TCTAAGCGCCGATAAAGAACATGATCTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTAT-TAAGCGCCGCTAAAGAACATGATCTT
50652238 TAGCGGCGTTTTTA
65 TAGCGGCGTTTTTA
50652252 TACAAAAACG
Statistics
Matches: 140, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
82 3 0.02
83 74 0.53
84 61 0.44
85 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (84 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGATCTTT
AGCGGCGTTTTTAGCTAAG
Found at i:50652593 original size:21 final size:21
Alignment explanation
Indices: 50652568--50652635 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
50652558 TTTTGCTCTG
*
50652568 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCTCTCGCTGCAGC
*
50652589 CTCTGCTTCTCTCGCTGCAGT
1 CTCTGCTTCTCTCGCTGCAGC
* * *
50652610 CGCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCTCTCGCTGCAGC
50652631 CTCTG
1 CTCTG
50652636 TTTTAAGTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.43, G:0.21, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCTCTCGCTGCAGC
Found at i:50656827 original size:6 final size:6
Alignment explanation
Indices: 50656818--50656843 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
50656808 AGCAGAGAGC
50656818 GACGGT GACGGT GACGGT GACGGT GA
1 GACGGT GACGGT GACGGT GACGGT GA
50656844 TGCAGTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.15, G:0.50, T:0.15
Consensus pattern (6 bp):
GACGGT
Found at i:50658462 original size:16 final size:17
Alignment explanation
Indices: 50658425--50658499 Score: 127
Period size: 16 Copynumber: 4.5 Consensus size: 17
50658415 ACATTATATA
50658425 ATATAATAAACTACATT
1 ATATAATAAACTACATT
50658442 ATATAATAAACTACA-T
1 ATATAATAAACTACATT
*
50658458 ATATAATAAACTA-AAT
1 ATATAATAAACTACATT
50658474 ATATAATAAACTACATT
1 ATATAATAAACTACATT
50658491 ATATAATAA
1 ATATAATAA
50658500 TCTAGCGGCG
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
15 1 0.02
16 28 0.51
17 26 0.47
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAATAAACTACATT
Found at i:50658467 original size:33 final size:33
Alignment explanation
Indices: 50658425--50658499 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
50658415 ACATTATATA
*
50658425 ATATAATAAACTACATTATATAATAAACTACA-T
1 ATATAATAAACTA-AATATATAATAAACTACATT
50658458 ATATAATAAACTAAATATATAATAAACTACATT
1 ATATAATAAACTAAATATATAATAAACTACATT
50658491 ATATAATAA
1 ATATAATAA
50658500 TCTAGCGGCG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 17 0.43
33 23 0.57
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.33
Consensus pattern (33 bp):
ATATAATAAACTAAATATATAATAAACTACATT
Found at i:50658704 original size:113 final size:113
Alignment explanation
Indices: 50658519--50658872 Score: 390
Period size: 114 Copynumber: 3.1 Consensus size: 113
50658509 GCTTCCCACA
* * * *
50658519 ACGCGCCGCTAATAATATGTTTTAGCGGCGTTTTACCATAAGCGCAAC-AACTGCTAGTATACAT
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTACCATAAGCGCCACTAA-TGCTAATATACAT
*
50658583 CAAGACCAAAGCACTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAAT
65 CAAGACCAAAGCACTGCGTTTTGGTTAATATTTTGCAGCGCTTTACAAT
* * * *
50658632 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTT-CAAATAAGCGCCACTAATCCTAATGTACCT
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTAC-CATAAGCGCCACTAATGCTAATATACAT
* * * * ** * *
50658696 CAACACCAAA-CTCTGCGTTTCGGTTAAGAAAGATTGCAGCGCTTTTCAGT
65 CAAGACCAAAGCACTGCGTTTTGGTT-A-ATATTTTGCAGCGCTTTACAAT
* * * * *
50658746 ACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCATAAGTGCCACTAATGCTACTATACATC
1 ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTACCATAAGCGCCACTAATGCTAATATACATC
* * * *
50658811 AAGACCAAAGCGCAGCGTTTTGGTTAATATTTTGCAGCGTTTTCCAAAT
66 AAGACCAAAGCACTGCGTTTTGGTTAATATTTTGCAGCGCTTTAC-AAT
* *
50658860 AAGCGCCACTAAT
1 ACGCGCCGCTAAT
50658873 CCTAATATAC
Statistics
Matches: 195, Mismatches: 39, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
112 14 0.07
113 75 0.38
114 94 0.48
115 12 0.06
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (113 bp):
ACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTACCATAAGCGCCACTAATGCTAATATACATC
AAGACCAAAGCACTGCGTTTTGGTTAATATTTTGCAGCGCTTTACAAT
Found at i:50659088 original size:114 final size:112
Alignment explanation
Indices: 50658847--50659098 Score: 292
Period size: 114 Copynumber: 2.2 Consensus size: 112
50658837 ATATTTTGCA
* * * *
50658847 GCGTTTTCCAAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTTTGTGTTTTGGTTAA
1 GCGTTTT-CACATAAGCGCCACTAATCCTAATATACCGCAACACCAAACTCTGCGTTTTGGTTAA
* ** * *
50658912 TATTTTGTGACACTTTACAATACGCGCCGCTAATACTATGCTTTAGCG
65 AAGATTGCGACACTTTACAATACGCGCCGCTAATACTATACTTTAGCG
* * * * *
50658960 GCGTTTTCATATAAGCGCCACTAATCGTAATGTACCTCAACACTAAACTCTGCGTTTTGGTTAAG
1 GCGTTTTCACATAAGCGCCACTAATCCTAATATACCGCAACACCAAACTCTGCGTTTTGGTT-A-
* * *
50659025 AAAGATTGCGACGCTTTTA-AGTACTCGCCGCTAATACTATACTTTAGCG
64 AAAGATTGCGACAC-TTTACAATACGCGCCGCTAATACTATACTTTAGCG
50659074 GCGTTTT-AGCATAAGCGCCACTAAT
1 GCGTTTTCA-CATAAGCGCCACTAAT
50659099 GTTACTATAC
Statistics
Matches: 118, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
112 47 0.40
113 9 0.08
114 58 0.49
115 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (112 bp):
GCGTTTTCACATAAGCGCCACTAATCCTAATATACCGCAACACCAAACTCTGCGTTTTGGTTAAA
AGATTGCGACACTTTACAATACGCGCCGCTAATACTATACTTTAGCG
Found at i:50659303 original size:187 final size:188
Alignment explanation
Indices: 50658957--50659306 Score: 515
Period size: 188 Copynumber: 1.9 Consensus size: 188
50658947 CTATGCTTTA
* * *
50658957 GCGGCGTTTTCATATAAGCGCCACTAATCGTAATGTACCTCAACACTAAACTCTGCGTTTTGGTT
1 GCGGCGTTTTCATATAAGCGCCACTAATCCTAATATACCTCAACACCAAACTCTGCGTTTTGGTT
*
50659022 AAGAAAGATTGCGACGCTTTTAAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCATA
66 AAGAAAGATTGCGACGCTTTTAACTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCATA
*
50659087 AGCGCCACTAATGTTACTATACATTAAGACCAATGGGCAGCGTTTTGGTTAATATTTT
131 AGCGCCACTAATGCTACTATACATTAAGACCAATGGGCAGCGTTTTGGTTAATATTTT
* *
50659145 GCGGCGTTTTCCA-ATAAGCGCCACTAATCCTAATATACCTTAAGACCAAACTCTGCGTTTTGGT
1 GCGGCGTTTT-CATATAAGCGCCACTAATCCTAATATACCTCAACACCAAACTCTGCGTTTTGGT
* * ** * * * *
50659209 TAAGAAATATTGCGGCGC-TTTCCCTACTCGCCGCTAATACTATGCTTTCGCGGCGTTTTTGTAT
65 TAAGAAAGATTGCGACGCTTTTAACTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCAT
* * *
50659273 AAGCGCCACTAATGCTAGTGTACCTTAAGACCAA
130 AAGCGCCACTAATGCTACTATACATTAAGACCAA
50659307 ACTCTGCGTT
Statistics
Matches: 143, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
187 69 0.48
188 72 0.50
189 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (188 bp):
GCGGCGTTTTCATATAAGCGCCACTAATCCTAATATACCTCAACACCAAACTCTGCGTTTTGGTT
AAGAAAGATTGCGACGCTTTTAACTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCATA
AGCGCCACTAATGCTACTATACATTAAGACCAATGGGCAGCGTTTTGGTTAATATTTT
Found at i:50659380 original size:301 final size:299
Alignment explanation
Indices: 50658538--50659326 Score: 1136
Period size: 301 Copynumber: 2.6 Consensus size: 299
50658528 TAATAATATG
* * * * *
50658538 TTTTAGCGGCGTTTTACC-ATAAGCGCAAC-AACTGCTAGTATACATCAAGACCAAAGCACTGCG
1 TTTT-GCGGCGTTTT-CCAATAAGCGCCACTAA-TCCTAATATACCTCAAGACCAAA-CTCTGCG
50658601 TTTTGGTTAATATTTTGCGGCGCTTTACAATACGCGCCGCTAATACTATGCTTTAGCGGCGTTTT
62 TTTTGGTTAATATTTTGCGGCGCTTTACAATACGCGCCGCTAATACTATGCTTTAGCGGCGTTTT
*
50658666 CAAATAAGCGCCACTAATCCTAATGTACCTCAACACCAAACTCTGCG-TTTCGGTTAAGAAAGAT
127 CATATAAGCGCCACTAAT-CTAATGTACCTCAACACCAAACTCTGCGTTTTC-GTTAAGAAAGAT
* * *
50658730 TGCAGCGCTTTTCAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCATAAGTGCCACT
190 TGCGGCGCTTTTAAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCATAAGCGCCACT
50658795 AATGCTACTATACATCAAGACCAAAGCGCAGCGTTTTGGTTAATA
255 AATGCTACTATACATCAAGACCAAAGCGCAGCGTTTTGGTTAATA
* * * *
50658840 TTTTGCAGCGTTTTCCAAATAAGCGCCACTAATCCTAATATACCGCAAGACCAAACTTTGTGTTT
1 TTTTGCGGCGTTTTCC-AATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTT
* * *
50658905 TGGTTAATATTTTGTGACACTTTACAATACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCAT
65 TGGTTAATATTTTGCGGCGCTTTACAATACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCAT
* *
50658970 ATAAGCGCCACTAATCGTAATGTACCTCAACACTAAACTCTGCGTTTTGGTTAAGAAAGATTGCG
130 ATAAGCGCCACTAATC-TAATGTACCTCAACACCAAACTCTGCGTTTTCGTTAAGAAAGATTGCG
*
50659035 ACGCTTTTAAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCATAAGCGCCACTAATG
194 GCGCTTTTAAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCATAAGCGCCACTAATG
* * * *
50659100 TTACTATACATTAAGACCAATGGGCAGCGTTTTGGTTAATA
259 CTACTATACATCAAGACCAAAGCGCAGCGTTTTGGTTAATA
*
50659141 TTTTGCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCTTAAGACCAAACTCTGCGTTTT
1 TTTTGCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTT
* * ** * * **
50659206 GGTTAAGAAATATTGCGGCGCTTT-CCCTACTCGCCGCTAATACTATGCTTTCGCGGCGTTTTTG
66 GGTT-A-ATATTTTGCGGCGCTTTACAATACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCA
* * *
50659270 TATAAGCGCCACTAATGCTAGTGTACCTTAAGACCAAACTCTGCGTTTTCGTTAAGA
129 TATAAGCGCCACTAAT-CTAATGTACCTCAACACCAAACTCTGCGTTTTCGTTAAGA
50659327 TGTATTGCGG
Statistics
Matches: 435, Mismatches: 44, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
300 52 0.12
301 332 0.76
302 49 0.11
303 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (299 bp):
TTTTGCGGCGTTTTCCAATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTT
GGTTAATATTTTGCGGCGCTTTACAATACGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCATA
TAAGCGCCACTAATCTAATGTACCTCAACACCAAACTCTGCGTTTTCGTTAAGAAAGATTGCGGC
GCTTTTAAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAGCATAAGCGCCACTAATGCT
ACTATACATCAAGACCAAAGCGCAGCGTTTTGGTTAATA
Found at i:50659816 original size:26 final size:22
Alignment explanation
Indices: 50659769--50659812 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
50659759 TAAAAAGAAA
50659769 AGAAACGATGAACATATTCTTT
1 AGAAACGATGAACATATTCTTT
50659791 AGAAACGATGAACATATTCTTT
1 AGAAACGATGAACATATTCTTT
50659813 CTTTTTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (22 bp):
AGAAACGATGAACATATTCTTT
Found at i:50667724 original size:9 final size:9
Alignment explanation
Indices: 50667710--50667855 Score: 175
Period size: 9 Copynumber: 15.6 Consensus size: 9
50667700 TTTGGTTAAA
50667710 AATTACCCG
1 AATTACCCG
50667719 AATTACCCG
1 AATTACCCG
*
50667728 AATTACCTG
1 AATTACCCG
*
50667737 ACTTACCCG
1 AATTACCCG
50667746 AATTACCCG
1 AATTACCCG
50667755 AATTACCCG
1 AATTACCCG
* *
50667764 AAAATGACCCA
1 --AATTACCCG
50667775 AATTACCCG
1 AATTACCCG
50667784 AATTACCCG
1 AATTACCCG
**
50667793 AAAATTACCTA
1 --AATTACCCG
50667804 AATTACCCG
1 AATTACCCG
50667813 AATTACCCG
1 AATTACCCG
*
50667822 AAAATTACCCA
1 --AATTACCCG
50667833 AATTACCCG
1 AATTACCCG
50667842 AATTACCCG
1 AATTACCCG
50667851 AATTA
1 AATTA
50667856 AATCACTACA
Statistics
Matches: 117, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
9 95 0.81
11 22 0.19
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:50667783 original size:29 final size:29
Alignment explanation
Indices: 50667708--50667852 Score: 222
Period size: 29 Copynumber: 5.1 Consensus size: 29
50667698 TTTTTGGTTA
* *
50667708 AAAATTACCCGAATTACCCGAATTACCTG
1 AAAATTACCCAAATTACCCGAATTACCCG
* *
50667737 --ACTTACCCGAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCGAATTACCCG
*
50667764 AAAATGACCCAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCGAATTACCCG
*
50667793 AAAATTACCTAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCGAATTACCCG
50667822 AAAATTACCCAAATTACCCGAATTACCCG
1 AAAATTACCCAAATTACCCGAATTACCCG
50667851 AA
1 AA
50667853 TTAAATCACT
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
27 25 0.24
29 81 0.76
ACGTcount: A:0.39, C:0.30, G:0.09, T:0.21
Consensus pattern (29 bp):
AAAATTACCCAAATTACCCGAATTACCCG
Found at i:50667846 original size:38 final size:36
Alignment explanation
Indices: 50667710--50667855 Score: 166
Period size: 38 Copynumber: 3.9 Consensus size: 36
50667700 TTTGGTTAAA
* * *
50667710 AATTACCCGAATTACCCGAATTACCTGACTTACCCG
1 AATTACCCAAATTACCCGAATTACCCGAATTACCCG
* * *
50667746 AATTACCCGAATTACCCGAAAATGACCCAAATTACCCG
1 AATTACCCAAATTACCCG--AATTACCCGAATTACCCG
**
50667784 AATTACCCGAAAATTACCTAAATTACCCGAATTACCCG
1 AATTACCC--AAATTACCCGAATTACCCGAATTACCCG
50667822 AAAATTACCCAAATTACCCGAATTACCCGAATTA
1 --AATTACCCAAATTACCCGAATTACCCGAATTA
50667856 AATCACTACA
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
36 18 0.19
38 60 0.65
40 15 0.16
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.23
Consensus pattern (36 bp):
AATTACCCAAATTACCCGAATTACCCGAATTACCCG
Found at i:50667902 original size:37 final size:37
Alignment explanation
Indices: 50667856--50667968 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
50667846 ACCCGAATTA
* *
50667856 AATCACTACATAATTAAAAACATTACATAAATCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
*
50667893 AATCACTACATAATTAAAAATATTAAATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
50667930 AATCACTACATAATTAAAAATATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
50667966 AAT
1 AAT
50667969 TAACACATAA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 6 0.08
37 66 0.92
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:50667958 original size:17 final size:17
Alignment explanation
Indices: 50667862--50667959 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
50667852 ATTAAATCAC
*
50667862 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
*** *
50667879 TACATAAATCTTTGAATCAC
1 TACAT-AAT-TAAAAAT-AT
50667899 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
* *** *
50667916 TAAATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
50667936 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
50667953 TACATAA
1 TACATAA
50667960 GTCTTGAATT
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 20 0.36
18 12 0.21
19 11 0.20
20 13 0.23
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:50668036 original size:24 final size:24
Alignment explanation
Indices: 50668009--50668091 Score: 139
Period size: 24 Copynumber: 3.5 Consensus size: 24
50667999 ATTCTCCATT
*
50668009 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
50668033 TATAGCCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
50668057 TATATCCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
50668081 TATCTCCATTT
1 TATATCCATTT
50668092 GCATTAAACC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.31, C:0.28, G:0.01, T:0.40
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:50670830 original size:37 final size:37
Alignment explanation
Indices: 50670783--50670853 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
50670773 TTTTTATAAA
50670783 AAAAAATTATAATTAGAAACCTTACCTAAAATTATAT
1 AAAAAATTATAATTAGAAACCTTACCTAAAATTATAT
50670820 AAAAAATTATAATTAGAAACCTTACCTAAAATTA
1 AAAAAATTATAATTAGAAACCTTACCTAAAATTA
50670854 CAAACAGAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (37 bp):
AAAAAATTATAATTAGAAACCTTACCTAAAATTATAT
Found at i:50672926 original size:16 final size:16
Alignment explanation
Indices: 50672905--50672937 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
50672895 TTCGCTATAT
50672905 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
50672921 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
50672937 T
1 T
50672938 AACAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:50674267 original size:91 final size:91
Alignment explanation
Indices: 50674127--50674422 Score: 511
Period size: 91 Copynumber: 3.3 Consensus size: 91
50674117 ATGATTATAA
* * *
50674127 ATAATAAATTTTCTTATATGAATTTGTATAATTTAAAATATTTATTATTAAATATAATTTAATAA
1 ATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAA
* *
50674192 TAATATATAATTTTATAAAATTCTTG
66 TGATATATAATTTCATAAAATTCTTG
50674218 ATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAA
1 ATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAA
*
50674283 TGGTATATAATTTCATAAAATTCTTG
66 TGATATATAATTTCATAAAATTCTTG
*
50674309 ATAATAATTTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAA
1 ATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAA
*
50674374 TGATATATAATTTCATAAAATTCTTA
66 TGATATATAATTTCATAAAATTCTTG
*
50674400 ATAATAAATGTTCTTATATGAAT
1 ATAATAAATTTTCTTATATGAAT
50674423 ATACTAAAAT
Statistics
Matches: 194, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 194 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
ATAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAA
TGATATATAATTTCATAAAATTCTTG
Found at i:50677752 original size:6 final size:6
Alignment explanation
Indices: 50677741--50677770 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
50677731 TAGTTTGAAC
50677741 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
50677771 TTTCGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:50677824 original size:96 final size:96
Alignment explanation
Indices: 50677657--50677832 Score: 266
Period size: 96 Copynumber: 1.8 Consensus size: 96
50677647 TTTATAACAT
* * * *
50677657 TTTAAATTTACATTTCATTTCGTATAAATATATTGATTAGTTTATTAAAGCATGTTCAAAGTTTG
1 TTTAAATTTAAATTTAATTTCGTATAAATAAATTGA-TAGTTTAATAAAGCATGTTCAAAGTTTG
50677722 AACATTGATTAGTTTGAACATTTAAATTTAAA
65 AACATTGATTAGTTTGAACATTTAAATTTAAA
50677754 TTTAAATTTAAATTTAATTTCGTAT-AATGAAATTGA-AGGTTTAATAAAGCATGTTCAAAGTTT
1 TTTAAATTTAAATTTAATTTCGTATAAAT-AAATTGATA-GTTTAATAAAGCATGTTCAAAGTTT
*
50677817 GATCATTGATTAGTTT
64 GAACATTGATTAGTTT
50677833 ATTTATTGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
95 1 0.01
96 42 0.58
97 29 0.40
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (96 bp):
TTTAAATTTAAATTTAATTTCGTATAAATAAATTGATAGTTTAATAAAGCATGTTCAAAGTTTGA
ACATTGATTAGTTTGAACATTTAAATTTAAA
Found at i:50678402 original size:31 final size:31
Alignment explanation
Indices: 50678364--50678425 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
50678354 AGGCAAATTG
50678364 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
50678395 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
50678426 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:50683980 original size:11 final size:11
Alignment explanation
Indices: 50683964--50684005 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
50683954 GGTAGGCAAC
50683964 TTTTTTTTGCG
1 TTTTTTTTGCG
50683975 TTTTTTTTGCG
1 TTTTTTTTGCG
* *
50683986 --CTTTTTGCT
1 TTTTTTTTGCG
50683995 TTTTTTTTGCG
1 TTTTTTTTGCG
50684006 CGTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 7 0.28
11 18 0.72
ACGTcount: A:0.00, C:0.12, G:0.17, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGCG
Found at i:50683992 original size:20 final size:19
Alignment explanation
Indices: 50683967--50684018 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
50683957 AGGCAACTTT
50683967 TTTTTGCGTTTTTTTTGCGC
1 TTTTTGC-TTTTTTTTGCGC
50683987 TTTTTGCTTTTTTTTTGCGC
1 TTTTTGC-TTTTTTTTGCGC
*
50684007 GTTTTGCTTTTT
1 TTTTTGCTTTTT
50684019 CTTTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.00, C:0.13, G:0.17, T:0.69
Consensus pattern (19 bp):
TTTTTGCTTTTTTTTGCGC
Found at i:50684581 original size:31 final size:31
Alignment explanation
Indices: 50684543--50684603 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
50684533 GACAAATTAT
50684543 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTC
50684574 AAGAGTAATTGAATCCTAATAAAACTCTTT
1 AAGAGTAATTGAATCCTAATAAAACTCTTT
50684604 AAAATTATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTC
Found at i:50685542 original size:13 final size:13
Alignment explanation
Indices: 50685524--50685548 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50685514 ATCAAATTTG
50685524 TATGTACTCTTTA
1 TATGTACTCTTTA
50685537 TATGTACTCTTT
1 TATGTACTCTTT
50685549 CACTAATAAA
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:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTACTCTTTA
Found at i:50685568 original size:51 final size:52
Alignment explanation
Indices: 50685513--50685618 Score: 151
Period size: 52 Copynumber: 2.1 Consensus size: 52
50685503 TATATATTAG
** * *
50685513 TATCAAATTTGTAT-GTACTCTTTATATGTACTCTTTCACTAATAAATTATA
1 TATCAAATTTGTATCAAAATCTTTATATGTACACTTTCACTAATAAATTATA
* *
50685564 TATCAAATTTGTATCAAAATTTTTTTATGTACACTTTCACTAATAAATTATA
1 TATCAAATTTGTATCAAAATCTTTATATGTACACTTTCACTAATAAATTATA
50685616 TAT
1 TAT
50685619 TAGTAAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 14 0.29
52 34 0.71
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (52 bp):
TATCAAATTTGTATCAAAATCTTTATATGTACACTTTCACTAATAAATTATA
Found at i:50686259 original size:23 final size:24
Alignment explanation
Indices: 50686199--50686261 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
50686189 TCTACTCACT
50686199 AACAAATCAAGAACAATTTCCAGC
1 AACAAATCAAGAACAATTTCCAGC
*
50686223 AGAC-TATCAA-AACAATTTCCAG-
1 A-ACAAATCAAGAACAATTTCCAGC
50686245 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
50686262 ATCAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 6 0.18
23 18 0.53
24 6 0.18
25 2 0.06
ACGTcount: A:0.52, C:0.22, G:0.08, T:0.17
Consensus pattern (24 bp):
AACAAATCAAGAACAATTTCCAGC
Found at i:50686270 original size:22 final size:22
Alignment explanation
Indices: 50686228--50686273 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
50686218 CCAGCAGACT
* *
50686228 ATCAAAACAATTTCCAGAACAA
1 ATCAAAACAATATCCAAAACAA
50686250 ATCAAGAACAATAT-CAAAACAA
1 ATCAA-AACAATATCCAAAACAA
50686272 AT
1 AT
50686274 GCAACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (22 bp):
ATCAAAACAATATCCAAAACAA
Found at i:50686317 original size:23 final size:23
Alignment explanation
Indices: 50686291--50686369 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 23
50686281 TTTCCAGTTT
50686291 CATTGAAAATAGCAGACAATTTC
1 CATTGAAAATAGCAGACAATTTC
* * * *
50686314 CATTGCAACAATATCAAAAAACTGTCTG
1 CATTG-AA-AATAGCAGACAA-T-T-TC
* *
50686342 AATTGAAAACAGCAGACAATTTC
1 CATTGAAAATAGCAGACAATTTC
50686365 CATTG
1 CATTG
50686370 CTCACTGTAT
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
23 10 0.25
24 3 0.08
25 10 0.25
26 9 0.22
27 3 0.08
28 5 0.12
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (23 bp):
CATTGAAAATAGCAGACAATTTC
Found at i:50691309 original size:14 final size:14
Alignment explanation
Indices: 50691290--50691316 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50691280 TTGCATGGCA
50691290 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
50691304 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
50691317 GGGGCCGGGG
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:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (14 bp):
TTTTTTTGTTTTTT
Found at i:50702476 original size:6 final size:6
Alignment explanation
Indices: 50702454--50702543 Score: 81
Period size: 6 Copynumber: 14.7 Consensus size: 6
50702444 CTCTTGTACT
* * * * * *
50702454 TACATA TACATA TACACA TACACA TGCACA TGCACA TGCACA TGCACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACACA TACACA
* * *
50702502 TGCACG TGCACA TAGACACA TACACA TACACA TACACA TACA
1 TACACA TACACA T--ACACA TACACA TACACA TACACA TACA
50702544 TATATTGTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
6 72 0.94
8 5 0.06
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (6 bp):
TACACA
Found at i:50722333 original size:17 final size:16
Alignment explanation
Indices: 50722300--50722333 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50722290 TTCATTTTGT
*
50722300 AAATAATTGGCATTGA
1 AAATAATTGGAATTGA
50722316 AAATAATTGAGAATTGA
1 AAATAATTG-GAATTGA
50722333 A
1 A
50722334 CTCTAACCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (16 bp):
AAATAATTGGAATTGA
Found at i:50738665 original size:30 final size:30
Alignment explanation
Indices: 50738629--50738715 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 30
50738619 GCCACATGGT
* * *
50738629 CGTGTGCCAAGTTGTATAGTAGTACACAGC
1 CGTGTGCCAAGCTGTATAGTAGCACACAAC
* * * *
50738659 CGTGTGCTAGGCTGTTTGGTAGCACACAAC
1 CGTGTGCCAAGCTGTATAGTAGCACACAAC
* * *
50738689 CGTGTGCCAGGCTGTTTGGTAGCACAC
1 CGTGTGCCAAGCTGTATAGTAGCACAC
50738716 GGTCATGTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (30 bp):
CGTGTGCCAAGCTGTATAGTAGCACACAAC
Found at i:50739881 original size:21 final size:20
Alignment explanation
Indices: 50739853--50739892 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
50739843 GTCAATAACC
50739853 AAAAGTTCCCACAAACAGAT
1 AAAAGTTCCCACAAACAGAT
**
50739873 AAAATGTTCTGACAAACAGA
1 AAAA-GTTCCCACAAACAGA
50739893 CATATATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.50, C:0.20, G:0.12, T:0.17
Consensus pattern (20 bp):
AAAAGTTCCCACAAACAGAT
Found at i:50740607 original size:21 final size:21
Alignment explanation
Indices: 50740580--50740650 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
50740570 AGACACACAT
* *
50740580 CCGTGTGACCAAGTTATACGT
1 CCGTGTGACCAAGTTACACGG
*
50740601 CTGTGTGACCAAGTTACACGG
1 CCGTGTGACCAAGTTACACGG
*
50740622 CCGTGTGACCAAGTTACACGA
1 CCGTGTGACCAAGTTACACGG
50740643 CCGTGTGA
1 CCGTGTGA
50740651 GTAGCCCGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (21 bp):
CCGTGTGACCAAGTTACACGG
Found at i:50742016 original size:41 final size:41
Alignment explanation
Indices: 50741843--50741992 Score: 255
Period size: 41 Copynumber: 3.7 Consensus size: 41
50741833 TTTAACATAT
* *
50741843 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
50741884 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
50741925 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
50741966 TCACCGGCACGTAGCCTGCTAGACTTA
1 TCACCGGCACGTAGCCTGCTAGGCTTA
50741993 AAGTCTGAAT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 104 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (41 bp):
TCACCGGCACGTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:50742566 original size:2 final size:2
Alignment explanation
Indices: 50742517--50742546 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
50742507 AAAATTCAGC
50742517 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
50742547 TCGGCTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50747684 original size:21 final size:21
Alignment explanation
Indices: 50747637--50747684 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
50747627 GTGTAAAGAT
*
50747637 AATTTGTGAATGAAATGATAA
1 AATTAGTGAATGAAATGATAA
*
50747658 AGATTAGTG-ATGAAATTATGAA
1 A-ATTAGTGAATGAAATGAT-AA
50747680 AATTA
1 AATTA
50747685 CATGTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (21 bp):
AATTAGTGAATGAAATGATAA
Found at i:50761027 original size:31 final size:29
Alignment explanation
Indices: 50760984--50761045 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
50760974 TTTTATAAAT
*
50760984 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTAATATTTATAT-ATT-AAAATATTAAC
*
50761014 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATA-TTTATATATTAAAATATTAAC
50761044 AA
1 AA
50761046 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 8 0.29
32 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTAATATTTATATATTAAAATATTAAC
Found at i:50761848 original size:2 final size:2
Alignment explanation
Indices: 50761841--50761877 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
50761831 CAAGTGAATA
50761841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50761878 GGGGGAGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50763641 original size:19 final size:19
Alignment explanation
Indices: 50763617--50763656 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
50763607 ATCTAAAATG
50763617 ATAAAATATTTATCCTTCA
1 ATAAAATATTTATCCTTCA
50763636 ATAAAATATTTATCCTTCA
1 ATAAAATATTTATCCTTCA
50763655 AT
1 AT
50763657 TCTTATCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAAAATATTTATCCTTCA
Found at i:50765055 original size:37 final size:39
Alignment explanation
Indices: 50764969--50765056 Score: 99
Period size: 37 Copynumber: 2.3 Consensus size: 39
50764959 ATGTTGTTTC
* * * * *
50764969 ATATATTGAAAGTACACTCTATCGAGCCAAATCTTATTG
1 ATATATTGAATGTAAACTCAATCGAGCCAAATCATACTG
* *
50765008 TTATACTGAATG-AAACTCAATCGAG-CAAATCATACTG
1 ATATATTGAATGTAAACTCAATCGAGCCAAATCATACTG
50765045 ATATATTGAATG
1 ATATATTGAATG
50765057 GAGCTTAACT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
37 20 0.50
38 11 0.28
39 9 0.22
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (39 bp):
ATATATTGAATGTAAACTCAATCGAGCCAAATCATACTG
Found at i:50768147 original size:25 final size:25
Alignment explanation
Indices: 50768102--50768151 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
50768092 GTGAGCCATG
* **
50768102 TAACAGGAAGCTTATCCGAGCTTAA
1 TAACAGGAAGCTCATAAGAGCTTAA
50768127 TAACAGGAAGCTCATAAGAGCTTAA
1 TAACAGGAAGCTCATAAGAGCTTAA
50768152 ATAGAAAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (25 bp):
TAACAGGAAGCTCATAAGAGCTTAA
Found at i:50772870 original size:50 final size:52
Alignment explanation
Indices: 50772813--50772913 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 52
50772803 TCTCATTTTT
* *
50772813 CATTTTGGACAAAACCAGATTCA-TTCCAAATAATT-TCATTTCTTCATTTA
1 CATTTTGGACAAAACCAGAATCATTTCCAAATAATTCTCATTTCTCCATTTA
* * *
50772863 CATTTTGGAGAAAACCATAATCATTTCCAAATATTTCTCATTTCTCCATTT
1 CATTTTGGACAAAACCAGAATCATTTCCAAATAATTCTCATTTCTCCATTT
50772914 TCACCATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 20 0.45
51 11 0.25
52 13 0.30
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.41
Consensus pattern (52 bp):
CATTTTGGACAAAACCAGAATCATTTCCAAATAATTCTCATTTCTCCATTTA
Found at i:50779908 original size:14 final size:14
Alignment explanation
Indices: 50779889--50779927 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
50779879 TTGTTTTACT
*
50779889 GAAAATGGCTTCTG
1 GAAAATGACTTCTG
50779903 GAAAATGACTTCTG
1 GAAAATGACTTCTG
50779917 GAAAATGACTT
1 GAAAATGACTT
50779928 ACTTTCCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAAATGACTTCTG
Done.