Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_pilon, 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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 32
Found at i:3695114 original size:36 final size:35
Alignment explanation
Indices: 3695061--3695331 Score: 211
Period size: 36 Copynumber: 7.6 Consensus size: 35
3695051 ATAGTTCCCA
*
3695061 AAAACT-TATATAATATATATTTTCAAAAATATTTT
1 AAAACTATATATTATATATATTTTC-AAAATATTTT
* * *
3695096 AAAACTATATATTATATATATTTTAAAAAAATATTC
1 AAAACTATATATTATATATATTTTCAAAATAT-TTT
* *
3695132 AAAACTATATACTATATA-AGCTTTTTCAAAATGTTTT
1 AAAACTATATATTATATATA---TTTTCAAAATATTTT
* *
3695169 CAAAA--ACTATATTATATATATATTTCAAATTTTTTT
1 -AAAACTA-TATATTATATATAT-TTTCAAAATATTTT
*
3695205 AAAACTATATATTATATATATGTTTCCAAAATGTTTT
1 AAAACTATATATTATATATAT-TTT-CAAAATATTTT
* * *
3695242 AAAACTATATA--ATATATGTTTTCAAAATGCTTTC
1 AAAACTATATATTATATATATTTTCAAAAT-ATTTT
*
3695276 ATAAACTATATA-TATATATA-GTTCAAAA-ATCATTT
1 A-AAACTATATATTATATATATTTTCAAAATAT--TTT
3695311 ACAAACTATA-ATATATATATA
1 A-AAACTATATAT-TATATATA
3695332 AATAAAATAA
Statistics
Matches: 194, Mismatches: 23, Indels: 37
0.76 0.09 0.15
Matches are distributed among these distances:
33 7 0.04
34 8 0.04
35 53 0.27
36 79 0.41
37 33 0.17
38 14 0.07
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (35 bp):
AAAACTATATATTATATATATTTTCAAAATATTTT
Found at i:3695182 original size:73 final size:69
Alignment explanation
Indices: 3695061--3695330 Score: 219
Period size: 73 Copynumber: 3.8 Consensus size: 69
3695051 ATAGTTCCCA
* *
3695061 AAAACT-TATATAATATATAT-TTTCAAAAATATTTTAAAACTATATATTATATATATTTTAAAA
1 AAAACTATATAT-ATATATATGTTTCCAAAATGTTTTAAAAC--TATATTATATATATTTTAAAA
3695124 AAATATTC
63 AAAT-TTC
* *
3695132 AAAACTATATACTATATA-A-GCTTTTTCAAAATGTTTTCAAAAACTATATTATATATATATTTC
1 AAAACTATATA-TATATATATG--TTTCCAAAATGTTTT--AAAACTATATTATATATAT-TTTA
*** *
3695195 AAATTTTTTT
60 AAAAAATTTC
* * *
3695205 AAAACTATATATTATATATATGTTTCCAAAATGTTTTAAAACTATATAATATATGTTTTCAAAAT
1 AAAACTATATA-TATATATATGTTTCCAAAATGTTTTAAAACTATATTATATATATTTT-AAAAA
**
3695270 GCTTTC
64 AATTTC
* ** *
3695276 ATAAACTATATATATATATA-G-TTCAAAAATCATTTACAAACTATAATATATATAT
1 A-AAACTATATATATATATATGTTTCCAAAATGTTTTA-AAACTATATTATATATAT
3695331 AAATAAAATA
Statistics
Matches: 164, Mismatches: 22, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
69 12 0.07
70 19 0.12
71 40 0.24
72 19 0.12
73 60 0.37
74 8 0.05
75 6 0.04
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (69 bp):
AAAACTATATATATATATATGTTTCCAAAATGTTTTAAAACTATATTATATATATTTTAAAAAAA
TTTC
Found at i:3695839 original size:85 final size:85
Alignment explanation
Indices: 3695703--3696363 Score: 795
Period size: 85 Copynumber: 7.8 Consensus size: 85
3695693 ACGTGTCATC
* * * * **** *
3695703 GAGCTGAGTGGAATCGAACTCGATAGTTTTTTGTTGACAGATAGTTTTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* *
3695768 CTGTAAATTTGATGTGCCTCT
65 CTGTAAATTTGATATGCCTTT
* *
3695789 GAGCTGAATGTAATCGAACTCGATGGTCTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
3695854 TGTAAATTTGATGTGCCTCT
66 TGTAAATTTGATATGCCTTT
* * * * * *
3695874 GAGCTTAATGTAATCGAACTCGAAGGTCTTTATTGACAAATAACCCTTCTTGCCTTGAGCTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
3695939 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* ** * ** *** * *
3695959 GAGCTGAATGTAATCGAACTCAAAAATCTTCGTTGACAGATAGA-TTTTCTTAACTTAAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA-ACCCTTCTCGCCTTGAGTTATG
* *
3696023 TTGTAAATTTGATATGTCTTT
65 CTGTAAATTTGATATGCCTTT
* * * * * * *
3696044 GAGCTAAATGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGGCTTAAGTTACGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
3696109 TGTAAAATTTGATATGCCTTT
66 TGT-AAATTTGATATGCCTTT
* * *
3696130 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
3696195 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * * *
3696215 GAGCTGAGTGTAATCGAACTCAAAGGTCTTGGTTGACAAATAACCCCTATCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
3696280 TGCAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * *
3696300 GAGCTGAGTGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAG-TATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
3696364 CACCAATAGT
Statistics
Matches: 506, Mismatches: 66, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
84 5 0.01
85 403 0.80
86 98 0.19
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
TGTAAATTTGATATGCCTTT
Found at i:3696546 original size:86 final size:86
Alignment explanation
Indices: 3696439--3696605 Score: 244
Period size: 86 Copynumber: 1.9 Consensus size: 86
3696429 AGGTCGTTCT
* *
3696439 CCTTAACGAGTCTGAACCAAGTGAGATGATATTTGGATGACTCCCCTTCACGGGAAAACCATGTG
1 CCTTAACGAGTCTAAACCAAGTGAGATGATATTTGGATGACTACCCTTCACGGGAAAACCATGTG
*
3696504 GTATGTTCTTCAAGTGGATCC
66 ATATGTTCTTCAAGTGGATCC
* * * * * *
3696525 CCTTAGCGGGTCTAAACCAAGTGAGATGATCTTTGGATGACTACCCTTTATGGGAAAGCCATGTG
1 CCTTAACGAGTCTAAACCAAGTGAGATGATATTTGGATGACTACCCTTCACGGGAAAACCATGTG
*
3696590 ATATGTTCTTCGAGTG
66 ATATGTTCTTCAAGTG
3696606 ACTCCTCTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (86 bp):
CCTTAACGAGTCTAAACCAAGTGAGATGATATTTGGATGACTACCCTTCACGGGAAAACCATGTG
ATATGTTCTTCAAGTGGATCC
Found at i:3723791 original size:36 final size:36
Alignment explanation
Indices: 3723559--3723790 Score: 313
Period size: 36 Copynumber: 6.4 Consensus size: 36
3723549 AGCAAAGTTA
*
3723559 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGA-ATAGTGAAGCAAACC
* *
3723595 ATCTGAAGCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* *
3723631 ATCCTAAGCCTTCACCGGAGAATAGTGAAGCTAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * *
3723667 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCA
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
*
3723703 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
* * * * *
3723739 ATCATAAGTCTTCACCAGAGAGTAGTGAAGTAAACC
1 ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
*
3723775 ATCTTAAGTCTTCACC
1 ATCTTAAGCCTTCACC
3723791 AAAAAGTAGT
Statistics
Matches: 174, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
35 1 0.01
36 173 0.99
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
Found at i:3723799 original size:36 final size:35
Alignment explanation
Indices: 3723559--3723823 Score: 282
Period size: 36 Copynumber: 7.4 Consensus size: 35
3723549 AGCAAAGTTA
3723559 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACC
1 ATCTTAAGCCTTCACCG-AGA-ATAGTGAAGCAAACC
* *
3723595 ATCTGAAGCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCAC-CGAGAATAGTGAAGCAAACC
* *
3723631 ATCCTAAGCCTTCACCGGAGAATAGTGAAGCTAACC
1 ATCTTAAGCCTTCACC-GAGAATAGTGAAGCAAACC
* * *
3723667 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCA
1 ATCTTAAGCCTTCACC-GAGAATAGTGAAGCAAACC
*
3723703 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACC-GAGAATAGTGAAGCAAACC
* * * *
3723739 ATCATAAGTCTTCACCAGAGAGTAGTGAAGTAAACC
1 ATCTTAAGCCTTCACC-GAGAATAGTGAAGCAAACC
* * * *
3723775 ATCTTAAGTCTTCACCAAAAAGTAGTG-AGCAGATCC
1 ATCTTAAGCCTTCACCGAGAA-TAGTGAAGCA-AACC
*
3723811 ATTTTAAGCCTTC
1 ATCTTAAGCCTTC
3723824 TCAGAAGAGT
Statistics
Matches: 197, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
35 6 0.03
36 190 0.96
37 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (35 bp):
ATCTTAAGCCTTCACCGAGAATAGTGAAGCAAACC
Found at i:3723820 original size:108 final size:108
Alignment explanation
Indices: 3723559--3723823 Score: 347
Period size: 108 Copynumber: 2.5 Consensus size: 108
3723549 AGCAAAGTTA
* * * *
3723559 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCTGAAGCCTTCACTGGAGAATAGTGAA
1 ATCTTAAGCCTTCACCGAAAAGTAGTGAAGCAATCCATCTGAAGCCTTCACCGGAGAATAGTGAA
* *
3723624 GCAAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCTAACC
66 GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCTAACC
* * *
3723667 ATCTGAAGCCTTCACCGGAGAA-TAGTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGA
1 ATCTTAAGCCTTCACC-GAAAAGTAGTGAAGCAATCCATCTGAAGCCTTCACCGGAGAATAGTGA
* *
3723731 AGCAAACCATCATAAGTCTTCACCAGAGAGTAGTGAAG-TAAACC
65 AGCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCT-AACC
* * * *
3723775 ATCTTAAGTCTTCACCAAAAAGTAGTG-AGCAGATCCATTTTAAGCCTTC
1 ATCTTAAGCCTTCACCGAAAAGTAGTGAAGCA-ATCCATCTGAAGCCTTC
3723824 TCAGAAGAGT
Statistics
Matches: 135, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
107 8 0.06
108 124 0.92
109 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (108 bp):
ATCTTAAGCCTTCACCGAAAAGTAGTGAAGCAATCCATCTGAAGCCTTCACCGGAGAATAGTGAA
GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCTAACC
Found at i:3724341 original size:51 final size:51
Alignment explanation
Indices: 3724185--3724633 Score: 488
Period size: 51 Copynumber: 8.8 Consensus size: 51
3724175 TGAATTATTT
* *
3724185 GAGTTCCATACTCCTTAAAG-AAG-AGGAGTGAACCCGTTTTGAAGA-GATGTC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCG-TTTGAAGATG-T-TC
* * * * * *
3724236 TGAGTTCCATACTCCCTAGAGAAAG-AGGAGCGAACCCGTGTGAAGATATGC
1 -GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
*
3724287 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTAAAGATGTTC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * *
3724338 GAGTTCCATACTCCTTAAAG-AGGAAGGAGCGAACCC-ATTGAAGATGTTC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
* * * * *
3724387 GAGTCCCATACTCCCTAGAG-AAGAGGGAGCGAACCCG--TGAAGAGATGTTC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTTC
* *
3724437 GAGTTCTATACTCCCTAAAGAAAG-AGGAGCGAACCCATTTGAAGATGTTC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
3724487 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
** *
3724538 GAGTTCTATACTCCTTAAAGAGGGAAGGAGCGAACCCGTTTGAAGAATATGTC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-ATGT-TC
* * * * *
3724591 TGAGTT-TCATACTCCCTAGAGAAATAGGGAGCGAACCCATTTG
1 -GAGTTCT-ATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG
3724634 TTGAAAATTG
Statistics
Matches: 344, Mismatches: 39, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
48 2 0.01
49 43 0.12
50 103 0.30
51 114 0.33
52 31 0.09
53 18 0.05
54 33 0.10
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (51 bp):
GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
Found at i:3724670 original size:53 final size:53
Alignment explanation
Indices: 3724610--3725067 Score: 334
Period size: 53 Copynumber: 8.6 Consensus size: 53
3724600 TACTCCCTAG
* * *
3724610 AGAAATAGGGAGCGAACCCATTTGTTGAAAATTGTGGGTCTTATACTCTATGA
1 AGAAATAGGGAGCGAACCCAATTGTTGAAGATTGTGGGTCTTATACTCTCTGA
* * * * * * * * * *
3724663 AGGAATAGGGAAC-ATACAC-GTT-TTCAAAAGATTTTCGAGTTTTATACTCCCTGG
1 AGAAATAGGGAGCGA-ACCCAATTGTT--GAAGATTGT-GGGTCTTATACTCTCTGA
* *
3724717 AGAAAGAGGGAACGAACCCAATTGTTGAAGATTGTGGGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAACCCAATTGTTGAAGATTGTGGGTCTTATACTCTCTGA
* * *
3724770 AGAAATAGGG-G-G-ACGCAATAGTTGAAGATTGTTCGGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAACCCAATTGTTGAAGATTG-TGGGTCTTATACTCTCTGA
* * * *
3724821 AGAAATAGGGGGC-AACGCAATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGAACCCAATTGTTGAAGATTG-T-GGGTCTTATACTCTCTGA
* ** * * *
3724875 AGAAATAGGGGGC-AGATGCGATTGATGAAGATTGTGAGTCTTATACTCTCTGA
1 AGAAATAGGGAGCGA-ACCCAATTGTTGAAGATTGTGGGTCTTATACTCTCTGA
* * *
3724928 AGAAATAGGGAGC-AGACACGATTGATGAAGATTGTGGGTC-T-TACTCTCTGA
1 AGAAATAGGGAGCGA-ACCCAATTGTTGAAGATTGTGGGTCTTATACTCTCTGA
* ** *
3724979 AGAAATAGGGGGC-AGA--CAAGTTTGTTGAAGA-TGATTCAAGTCTTATACCCTCTGA
1 AGAAATAGGGAGCGA-ACCCAA--TTGTTGAAGATTG--T-GGGTCTTATACTCTCTGA
* *
3725034 AGAAATAGGGAGCGAACCCATTTTTCTGAAGATT
1 AGAAATAGGGAGCGAACCCAATTGT-TGAAGATT
3725068 TATTGAATTC
Statistics
Matches: 333, Mismatches: 47, Indels: 46
0.78 0.11 0.11
Matches are distributed among these distances:
49 2 0.01
50 19 0.06
51 65 0.20
52 6 0.02
53 120 0.36
54 66 0.20
55 43 0.13
56 9 0.03
57 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (53 bp):
AGAAATAGGGAGCGAACCCAATTGTTGAAGATTGTGGGTCTTATACTCTCTGA
Found at i:3724748 original size:54 final size:52
Alignment explanation
Indices: 3724244--3725216 Score: 279
Period size: 51 Copynumber: 18.6 Consensus size: 52
3724234 TCTGAGTTCC
* * * * * *
3724244 ATACTCCCT-AGAGAAAGA-GGAGCGAACCC-GTGTGAAGATATGCGAGTTCT
1 ATACTCCCTGA-AGAAATAGGGAGCGAACCCATTTTGAAGATTTTCGAGTTTT
* * * * * * * **
3724294 ATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTTTAAAGATGTTCGAGTTCC
1 ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTGAAGATTTTCGAGTTTT
* * * * ***
3724345 ATACTCCTTAAAGAGGA-A-GGAGCGAACCCA--TTGAAGATGTTCGAGTCCC
1 ATACTCCCTGAAGA-AATAGGGAGCGAACCCATTTTGAAGATTTTCGAGTTTT
* * *** * *
3724394 ATACTCCCT--AGAGAAGAGGGAGCGAACCCGTGAAG-AGATGTTCGAGTTCT
1 ATACTCCCTGAAGA-AATAGGGAGCGAACCCATTTTGAAGATTTTCGAGTTTT
* * * *
3724444 ATACTCCCTAAAGAAAGA-GGAGCGAACCCA-TTTGAAGATGTTCGAGTTCT
1 ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTGAAGATTTTCGAGTTTT
* * * * * * *
3724494 ATACTCCTTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTTCGAGTTCT
1 ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTGAAGATTTTCGAGTTTT
* * *** * * * *
3724545 ATACTCCTTAAAGAGGGAAGGAGCGAACCC-GTTTGAAGAATATGTCTGAGTTTC
1 ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTGAAG-AT-TTTC-GAGTTTT
* * * *
3724599 ATACTCCCT-AGAGAAATAGGGAGCGAACCCATTTGTTGAAAATTGT-GGGTCTT
1 ATACTCCCTGA-AGAAATAGGGAGCGAACCCA-TT-TTGAAGATTTTCGAGTTTT
** * * * * *
3724652 ATACTCTATGAAGGAATAGGGAAC-ATACACGTTTTCAAAAGATTTTCGAGTTTT
1 ATACTCCCTGAAGAAATAGGGAGCGA-ACCCATTTT--GAAGATTTTCGAGTTTT
* * * * * *
3724706 ATACTCCCTGGAGAAAGAGGGAACGAACCCAATTGTTGAAGATTGT-GGGTCTT
1 ATACTCCCTGAAGAAATAGGGAGCGAACCC-ATT-TTGAAGATTTTCGAGTTTT
* * * *
3724759 ATACTCTCTGAAGAAATAGGG-G-G-ACGCAATAGTTGAAGATTGTTCG-GTCTT
1 ATACTCCCTGAAGAAATAGGGAGCGAAC-CCAT-TTTGAAGATT-TTCGAGTTTT
* * * * *
3724810 ATACTCTCTGAAGAAATAGGGGGC-AACGCAATCGTTGAAGATTGTTCGAGTCTT
1 ATACTCCCTGAAGAAATAGGGAGCGAAC-CCAT-TTTGAAGATT-TTCGAGTTTT
* * ** * * * *
3724864 ATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAGATTGT-GAGTCTT
1 ATACTCCCTGAAGAAATAGGGAGC-GAACCCATT-TTGAAGATTTTCGAGTTTT
* * * * * *
3724917 ATACTCTCTGAAGAAATAGGGAGC-AGACACGATTGATGAAGATTGT-G-GGTCT
1 ATACTCCCTGAAGAAATAGGGAGCGA-AC-CCATT-TTGAAGATTTTCGAGTTTT
* * * * * *
3724969 -TACTCTCTGAAGAAATAGGGGGC-AGA-CAAGTTTGTTGAAGATGATTCAAGTCTT
1 ATACTCCCTGAAGAAATAGGGAGCGA-ACCCA--TT-TTGAAGAT-TTTCGAGTTTT
* * *
3725023 ATAC-CCTCTGAAGAAATAGGGAGCGAACCCATTTTTCTGAAGATTTATTGAATTCT
1 ATACTCC-CTGAAGAAATAGGGAGCGAACCCA--TTT-TGAAGATTT-TCGAGTTTT
* * ** * * * **
3725079 ATACTCCCTGAAAAGAATAAGGAGC-AAGTACGTGGATTGAAGATTGATCGAGTCCT
1 ATACTCCCTGAAGA-AATAGGGAGCGAA-CCCAT--TTTGAAGATT-TTCGAGTTTT
* * * * * * *
3725135 ATACTCTCTGAAGGAATA-GGAGC-AGACACGTTTTCAAAGGATTTTCGTGTTCT
1 ATACTCCCTGAAGAAATAGGGAGCGA-ACCCATTTT-GAA-GATTTTCGAGTTTT
*
3725188 ATACTCCCTGAAGAAAGAGGGAGCGAACC
1 ATACTCCCTGAAGAAATAGGGAGCGAACC
3725217 TGTAGGCAAA
Statistics
Matches: 739, Mismatches: 121, Indels: 122
0.75 0.12 0.12
Matches are distributed among these distances:
47 5 0.01
48 1 0.00
49 39 0.05
50 104 0.14
51 182 0.25
52 16 0.02
53 151 0.20
54 117 0.16
55 46 0.06
56 60 0.08
57 18 0.02
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (52 bp):
ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTGAAGATTTTCGAGTTTT
Found at i:3724858 original size:158 final size:156
Alignment explanation
Indices: 3724690--3725044 Score: 389
Period size: 158 Copynumber: 2.2 Consensus size: 156
3724680 ACGTTTTCAA
* * * *
3724690 AAGATTTTCGAGTTTTATACTCCCTGGAGAAAGAGGGAAC-GAACCCAATTGTTGAAGATTGTGG
1 AAGATTTTCGAGTCTTATACTCCCTGAAGAAAGAGGGAACAG-ACCCAATTGATGAAGATTGTGA
* *
3724754 GTCTTATACTCTCTGAAGAAATAGGG-G-GACGCAATAGTTGAAGATTGTTCGGTCTTATACTCT
65 GTCTTATACTCTCTGAAGAAATAGGGAGAGACACAATAGATGAAGATTG-TCGGTC-T-TACTCT
3724817 CTGAAGAAATAGGGGGCAACGCAATCGTTG
127 CTGAAGAAATAGGGGGCAACGCAATCGTTG
* * ** ** *
3724847 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAGATTGTGA
1 AAGATT-TTCGAGTCTTATACTCCCTGAAGAAAGAGGGAACAGACCCAATTGATGAAGATTGTGA
* * *
3724912 GTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGATGAAGATTGTGGGTCTTACTCTCT
65 GTCTTATACTCTCTGAAGAAATAGGGAG-AGACACAATAGATGAAGATTGTCGGTCTTACTCTCT
*
3724977 GAAGAAATAGGGGGC-A-GACAAGTTTGTTG
129 GAAGAAATAGGGGGCAACG-CAA--TCGTTG
* * *
3725006 AAGATGATTCAAGTCTTATAC-CCTCTGAAGAAATAGGGA
1 AAGAT-TTTCGAGTCTTATACTCC-CTGAAGAAAGAGGGA
3725045 GCGAACCCAT
Statistics
Matches: 167, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
156 1 0.01
157 10 0.06
158 95 0.57
159 40 0.24
160 5 0.03
161 16 0.10
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (156 bp):
AAGATTTTCGAGTCTTATACTCCCTGAAGAAAGAGGGAACAGACCCAATTGATGAAGATTGTGAG
TCTTATACTCTCTGAAGAAATAGGGAGAGACACAATAGATGAAGATTGTCGGTCTTACTCTCTGA
AGAAATAGGGGGCAACGCAATCGTTG
Found at i:3725876 original size:28 final size:28
Alignment explanation
Indices: 3725836--3725908 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
3725826 TCACGTGAGC
3725836 TCACCATTTCCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
3725864 TCACCATTTCCAACCCGTGCCAGTGCCT
1 TCACCATTTCCAACCCGTGCCAGTGCCT
3725892 TCACCATTTCCAACCCG
1 TCACCATTTCCAACCCG
3725909 GGCTTACCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.19, C:0.44, G:0.12, T:0.25
Consensus pattern (28 bp):
TCACCATTTCCAACCCGTGCCAGTGCCT
Found at i:3730703 original size:35 final size:34
Alignment explanation
Indices: 3730658--3730759 Score: 145
Period size: 35 Copynumber: 3.0 Consensus size: 34
3730648 ATATTCTAGC
3730658 AACTCTCTATATTATATTAATATTAATGCTTAACA
1 AACTCTCTATATTAT-TTAATATTAATGCTTAACA
* *
3730693 AACTCTCTATATTATGTTAATATGAATGCTAAACA
1 AACTCTCTATATTAT-TTAATATTAATGCTTAACA
*
3730728 AACTCTCTATA-T-TCTAATATTAATGCTTAACA
1 AACTCTCTATATTATTTAATATTAATGCTTAACA
3730760 TTCACCCTAC
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
32 16 0.26
33 1 0.02
34 1 0.02
35 43 0.70
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (34 bp):
AACTCTCTATATTATTTAATATTAATGCTTAACA
Found at i:3730967 original size:145 final size:147
Alignment explanation
Indices: 3730703--3730994 Score: 570
Period size: 145 Copynumber: 2.0 Consensus size: 147
3730693 AACTCTCTAT
3730703 ATTATGTTAATATGAATGCTAAACAAACTCTCTATATTCTAATATTAATGCTTAACATTCACCCT
1 ATTATGTTAATATGAATGCTAAACAAACTCTCTATATTCTAATATTAATGCTTAACATTCACCCT
3730768 ACTTTCCAGGACTTCAAGAATTCCATTTGAGACCTTCATCTTGTGGCGAAATGAGGAAAAATAAG
66 ACTTTCCAGGACTTCAAGAATTCCATTTGAGACCTTCATCTTGTGGCGAAATGAGGAAAAATAAG
3730833 CATGTG-AAGGGGTTTG
131 CATGTGAAAGGGGTTTG
3730849 ATTATGTTAATATGAATGCT-AACAAACTCTCTATATTCTAATATTAATGCTTAACATTCACCCT
1 ATTATGTTAATATGAATGCTAAACAAACTCTCTATATTCTAATATTAATGCTTAACATTCACCCT
3730913 ACTTTCCAGGACTTCAAGAATTCCATTTGAGACCTTCATCTTGTGGCGAAATGAGGAAAAATAAG
66 ACTTTCCAGGACTTCAAGAATTCCATTTGAGACCTTCATCTTGTGGCGAAATGAGGAAAAATAAG
3730978 CATGTGAAAGGGGTTTG
131 CATGTGAAAGGGGTTTG
3730995 GTAAGACCAT
Statistics
Matches: 145, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
145 115 0.79
146 30 0.21
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (147 bp):
ATTATGTTAATATGAATGCTAAACAAACTCTCTATATTCTAATATTAATGCTTAACATTCACCCT
ACTTTCCAGGACTTCAAGAATTCCATTTGAGACCTTCATCTTGTGGCGAAATGAGGAAAAATAAG
CATGTGAAAGGGGTTTG
Found at i:3735280 original size:42 final size:42
Alignment explanation
Indices: 3735215--3735327 Score: 176
Period size: 42 Copynumber: 2.7 Consensus size: 42
3735205 CCGATTCCCG
*
3735215 TGTTTGTTTCAC-TAATTCGTTTTCCGGAAAATGTTTTCACGA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC-CAA
*
3735257 -GTTTGTTTCACGAAATTCGTTTTCCGGAAAATGTTTTCCAA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCAA
*
3735298 TGTTTGTTTCACGTAATTAGTTTTCCGGAA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAA
3735328 CGTAATTAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
41 13 0.20
42 52 0.80
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (42 bp):
TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCAA
Found at i:3735541 original size:19 final size:19
Alignment explanation
Indices: 3735517--3735553 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3735507 TTTATTTATA
3735517 ATATTTATAATATAATATT
1 ATATTTATAATATAATATT
* *
3735536 ATATTTTTAATATTATAT
1 ATATTTATAATATAATAT
3735554 AAATAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTATAATATAATATT
Found at i:3735541 original size:28 final size:27
Alignment explanation
Indices: 3735505--3735560 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
3735495 AAATATTATT
3735505 TATTTATTTATAATATT-TATAATATAA
1 TATTTATTTATAATATTATATAA-ATAA
*
3735532 TATTATATTTTTAATATTATATAAATAA
1 TATT-TATTTATAATATTATATAAATAA
3735560 T
1 T
3735561 CAAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 4 0.15
28 17 0.65
29 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTTATTTATAATATTATATAAATAA
Found at i:3735560 original size:14 final size:14
Alignment explanation
Indices: 3735514--3735560 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3735504 TTATTTATTT
3735514 ATAATATT-TATAA
1 ATAATATTATATAA
**
3735527 TATAATATTATATTT
1 -ATAATATTATATAA
*
3735542 TTAATATTATATAA
1 ATAATATTATATAA
3735556 ATAAT
1 ATAAT
3735561 CAAATATTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 23 0.88
15 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATAATATTATATAA
Found at i:3735567 original size:28 final size:28
Alignment explanation
Indices: 3735509--3735578 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 28
3735499 ATTATTTATT
*
3735509 TATTTATAATATTTATAATATAATATTA
1 TATTTATAATATTTATAATATAATATAA
*
3735537 TATTTTTAATATTATATAA-ATAATCA-AA
1 TATTTATAATATT-TATAATATAAT-ATAA
3735565 TATTATACTAATAT
1 TATT-TA-TAATAT
3735579 AAGATATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 22 0.63
29 7 0.20
30 6 0.17
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
TATTTATAATATTTATAATATAATATAA
Found at i:3735838 original size:18 final size:18
Alignment explanation
Indices: 3735815--3735863 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
3735805 AAAAATACTA
3735815 TTTAATAATAATAAATTT
1 TTTAATAATAATAAATTT
*
3735833 TTTAATAATAATAAGTTT
1 TTTAATAATAATAAATTT
* *
3735851 TATGATAATAATA
1 TTTAATAATAATA
3735864 TTATTTATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
TTTAATAATAATAAATTT
Found at i:3735870 original size:18 final size:17
Alignment explanation
Indices: 3735801--3735871 Score: 58
Period size: 18 Copynumber: 4.2 Consensus size: 17
3735791 ATTAATAAAA
* *
3735801 TTATAAAAATACTA-TT
1 TTATAATAATAATATTT
*
3735817 TAATAATAATAA-ATTT
1 TTATAATAATAATATTT
*
3735833 TT-TAATAATAATAAGTT
1 TTATAATAATAAT-ATTT
*
3735850 TTATGATAATAATATTAT
1 TTATAATAATAATATT-T
3735868 TTAT
1 TTAT
3735872 TGTATTTAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 10 0.23
16 12 0.28
17 7 0.16
18 14 0.33
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (17 bp):
TTATAATAATAATATTT
Found at i:3736067 original size:15 final size:15
Alignment explanation
Indices: 3736047--3736097 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
3736037 TCATTTCCAG
*
3736047 AATTCAAATTACAGT
1 AATTCAAATTTCAGT
**
3736062 AATTCATTTTTCAGT
1 AATTCAAATTTCAGT
3736077 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
3736092 AATTCA
1 AATTCA
3736098 TTTTTCGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (15 bp):
AATTCAAATTTCAGT
Found at i:3736083 original size:30 final size:29
Alignment explanation
Indices: 3736035--3736103 Score: 104
Period size: 30 Copynumber: 2.4 Consensus size: 29
3736025 CCAGAAATGT
*
3736035 ATTCA-TTTCCAGAATTCAAATTACAGTA
1 ATTCATTTTTCAGAATTCAAATTACAGTA
*
3736063 ATTCATTTTTCAGTAATTCAAATTTCAGTA
1 ATTCATTTTTCAG-AATTCAAATTACAGTA
3736093 ATTCATTTTTC
1 ATTCATTTTTC
3736104 GAAAACCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 5 0.14
29 6 0.16
30 26 0.70
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (29 bp):
ATTCATTTTTCAGAATTCAAATTACAGTA
Found at i:3736103 original size:15 final size:15
Alignment explanation
Indices: 3736058--3736103 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
3736048 ATTCAAATTA
3736058 CAGTAATTCATTTTT
1 CAGTAATTCATTTTT
**
3736073 CAGTAATTCAAATTT
1 CAGTAATTCATTTTT
3736088 CAGTAATTCATTTTT
1 CAGTAATTCATTTTT
3736103 C
1 C
3736104 GAAAACCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (15 bp):
CAGTAATTCATTTTT
Found at i:3737785 original size:4 final size:4
Alignment explanation
Indices: 3737776--3737811 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
3737766 AGATAAAGAT
*
3737776 TAAA TAAA TAAA CAAA TAAA TAAA TAAA -AAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
3737812 TGAGATAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:3737795 original size:16 final size:15
Alignment explanation
Indices: 3737776--3737811 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
3737766 AGATAAAGAT
3737776 TAAATAAATAAACAAA
1 TAAATAAATAAA-AAA
3737792 TAAATAAATAAAAAA
1 TAAATAAATAAAAAA
3737807 TAAAT
1 TAAAT
3737812 TGAGATAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAATAAATAAAAAA
Found at i:3742952 original size:23 final size:23
Alignment explanation
Indices: 3742926--3742995 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
3742916 CAACCTTATA
* *
3742926 TGGCCCTTCGATGCATTTCTATG
1 TGGCACTTCGGTGCATTTCTATG
* * *
3742949 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTATG
*
3742972 TGGCACTTCGGTGCAATTTATATG
1 TGGCACTTCGGTGC-ATTTCTATG
3742996 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 31 0.84
24 6 0.16
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTATG
Found at i:3746299 original size:21 final size:21
Alignment explanation
Indices: 3746259--3746299 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3746249 TCTGGGCTAG
* *
3746259 GGGAATCGGTACCCATTCAAT
1 GGGAATCGATACCCACTCAAT
*
3746280 GGGAATCGATACCCCCTCAA
1 GGGAATCGATACCCACTCAA
3746300 CCGAACTAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (21 bp):
GGGAATCGATACCCACTCAAT
Found at i:3748059 original size:23 final size:23
Alignment explanation
Indices: 3747997--3748060 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
3747987 TAACCTTATA
*
3747997 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
3748020 CGGCACTAT-GGTTCAATTCTACG
1 TGGCACT-TCGGTGCAATTCTACG
3748043 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
3748061 TATATGAGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:3751422 original size:22 final size:22
Alignment explanation
Indices: 3751381--3751422 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3751371 TCTGGGCTAG
* *
3751381 GGGAATCGGTACCCATTCAAAT
1 GGGAATCGATACCCACTCAAAT
*
3751403 GGGAATCGATACCCCCTCAA
1 GGGAATCGATACCCACTCAA
3751423 CCGAACCAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (22 bp):
GGGAATCGATACCCACTCAAAT
Found at i:3753164 original size:23 final size:23
Alignment explanation
Indices: 3753130--3753185 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3753120 TATGGAACTT
*
3753130 CGGTGCATTTCTACGCGGCACTA
1 CGGTGCAATTCTACGCGGCACTA
* *
3753153 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTA
*
3753176 CAGTGCAATT
1 CGGTGCAATT
3753186 TATATGAGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTA
Found at i:3756183 original size:197 final size:199
Alignment explanation
Indices: 3755846--3756220 Score: 664
Period size: 197 Copynumber: 1.9 Consensus size: 199
3755836 ATTTCTGTCG
* *
3755846 GTATCCAAGTTTTGAACAAAACAAACATTTAACAGGCGTATCAGTAGATTCATCGGATCAAATAT
1 GTATCCAAGTTTTGAACAAAACAAACATTTAACAGACGTATCAGTAGATTCATCAGATCAAATAT
3755911 ATATTTTTAGGGTTATTTCCTCTTTTAGAAACATTCCTTGTCTTTTAACATCACATGGGTATTTT
66 ATATTTTTAGGGTTATTTCCTCTTTTAGAAACATTCCTTGTCTTTTAACATCACATGGGTATTTT
* * *
3755976 CATAATTTCTTATCTATGTATTTTTGGTATTTAACCTTTAATGAAAAATAATCAGAATTTAAGGA
131 CATAATTTCTTATCCATGCATTTCTGGTATTTAACCTTTAATGAAAAATAATCAGAATTTAAGGA
3756041 TCCC
196 TCCC
*
3756045 GTATCCAAGTTTTGAACAAAACAAACATTTAACAGACGTATCAGTAGATTTATCAGATC-AA-AT
1 GTATCCAAGTTTTGAACAAAACAAACATTTAACAGACGTATCAGTAGATTCATCAGATCAAATAT
*
3756108 ATATTTTTAGGGTTATTTCCTCTTTTAGGAACATTCCTTGTCTTTTAACATCACATGGGTATTTT
66 ATATTTTTAGGGTTATTTCCTCTTTTAGAAACATTCCTTGTCTTTTAACATCACATGGGTATTTT
*
3756173 TATAATTTCTTATCCATGCATTTCTGGTATTTAACCTTTAATGAAAAA
131 CATAATTTCTTATCCATGCATTTCTGGTATTTAACCTTTAATGAAAAA
3756221 ATATCGTTAA
Statistics
Matches: 168, Mismatches: 8, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
197 110 0.65
198 2 0.01
199 56 0.33
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (199 bp):
GTATCCAAGTTTTGAACAAAACAAACATTTAACAGACGTATCAGTAGATTCATCAGATCAAATAT
ATATTTTTAGGGTTATTTCCTCTTTTAGAAACATTCCTTGTCTTTTAACATCACATGGGTATTTT
CATAATTTCTTATCCATGCATTTCTGGTATTTAACCTTTAATGAAAAATAATCAGAATTTAAGGA
TCCC
Found at i:3760614 original size:15 final size:15
Alignment explanation
Indices: 3760594--3760639 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3760584 CAAACACTCA
3760594 TTTTCTTCTTCCATC
1 TTTTCTTCTTCCATC
*
3760609 TTTTC-TCTTTTC-TC
1 TTTTCTTC-TTCCATC
*
3760623 TTTTCTTCTCCCATC
1 TTTTCTTCTTCCATC
3760638 TT
1 TT
3760640 CAAGTTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTCTTCTTCCATC
Found at i:3763930 original size:25 final size:27
Alignment explanation
Indices: 3763892--3763942 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
3763882 TCTCTTAAGA
3763892 GTTATTATTTAAAT-AA-AAATAATAC
1 GTTATTATTTAAATAAATAAATAATAC
3763917 GTTA-TATTTGAAATAAATAAATAATA
1 GTTATTATTT-AAATAAATAAATAATA
3763943 ATAGGAGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 8 0.35
26 2 0.09
27 8 0.35
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (27 bp):
GTTATTATTTAAATAAATAAATAATAC
Found at i:3766066 original size:261 final size:262
Alignment explanation
Indices: 3765602--3766124 Score: 1023
Period size: 261 Copynumber: 2.0 Consensus size: 262
3765592 TTTTTGATAG
3765602 TCTCGACTGTATTTGTTCAGTCTGTAATTGGCAAGACGTTTGTCGATACGACTTTCGGTAAATTA
1 TCTCGACTGTATTTGTTCAGTCTGTAATTGGCAAGACGTTTGTCGATACGACTTTCGGTAAATTA
3765667 AATTTGATGGTTATTTTTCAACACAAAAAAGTTGAAGCTAATGTGACAGTTAAAATATTTGATAT
66 AATTTGATGGTTATTTTTCAACACAAAAAAGTTGAAGCTAATGTGACAGTTAAAATATTTGATAT
3765732 AATTACACATTTGGTCACTCTTACTTATATATTTTATCAATTTGGTCTTAATTTTAATAAATTAA
131 AATTACACATTTGGTCACTCTTACTTATATATTTTATCAATTTGGTCTTAATTTTAATAAATTAA
3765797 AATACATTTAACCCTCAAATCAAATGGTGTATGTGTCACTGGTGCC-AGTGTAATGACATGTATC
196 AATACATTTAACCCTCAAATCAAATGGTGTATGTGTCACTGGTGCCAAGTGTAATGACATGTATC
3765861 AC
261 AC
3765863 TCTCGACTGTATTTGTTCAGTCTGTAATTGGCAAGACGTTTGTCGATACGACTTTCGGTAAATTA
1 TCTCGACTGTATTTGTTCAGTCTGTAATTGGCAAGACGTTTGTCGATACGACTTTCGGTAAATTA
3765928 AATTTGATGGTTA-TTTTCAACAACAAAAAAGTTGAAGCTAATGTGACAGTTAAAATATTTGATA
66 AATTTGATGGTTATTTTTCAAC-ACAAAAAAGTTGAAGCTAATGTGACAGTTAAAATATTTGATA
3765992 TAATTACACATTTGGTCACTCTTACTTATATATTTTATCAATTTGGTCTTAATTTTAATAAATTA
130 TAATTACACATTTGGTCACTCTTACTTATATATTTTATCAATTTGGTCTTAATTTTAATAAATTA
3766057 AAATACATTTAACCCTCAAATCAAATGGTGTATGTGTCACTGGTGCCAAGTGTAATGACATGTAT
195 AAATACATTTAACCCTCAAATCAAATGGTGTATGTGTCACTGGTGCCAAGTGTAATGACATGTAT
3766122 CAC
260 CAC
3766125 CATGTCCGAT
Statistics
Matches: 260, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
260 8 0.03
261 232 0.89
262 20 0.08
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (262 bp):
TCTCGACTGTATTTGTTCAGTCTGTAATTGGCAAGACGTTTGTCGATACGACTTTCGGTAAATTA
AATTTGATGGTTATTTTTCAACACAAAAAAGTTGAAGCTAATGTGACAGTTAAAATATTTGATAT
AATTACACATTTGGTCACTCTTACTTATATATTTTATCAATTTGGTCTTAATTTTAATAAATTAA
AATACATTTAACCCTCAAATCAAATGGTGTATGTGTCACTGGTGCCAAGTGTAATGACATGTATC
AC
Found at i:3766696 original size:30 final size:29
Alignment explanation
Indices: 3766450--3766739 Score: 200
Period size: 30 Copynumber: 10.0 Consensus size: 29
3766440 ACTTATTAAT
* * *
3766450 TATATTTTAATCTTGTCTTAACATAAAAA
1 TATATTTTATTCTTATCTTAACTTAAAAA
* * *
3766479 TATATTGTATTCTTATTTTAA-TTTAAAA
1 TATATTTTATTCTTATCTTAACTTAAAAA
*
3766507 TATATTTTAGTCTTTATCTTAACTTAAAAA
1 TATATTTTATTC-TTATCTTAACTTAAAAA
* * *
3766537 TTTTATTTTATTCTTATCTTAACTTATTACA
1 -TATATTTTATTCTTATCTTAACTTA-AAAA
* * * * *
3766568 TAAATTATATTCTTAACTTAAATTATTAAA
1 TATATTTTATTCTTATCTTAACTTA-AAAA
* * * * *
3766598 TAT-TGTATATTGTTACCTTAAATTATTAAA
1 TATAT-TTTATTCTTATCTTAACTTA-AAAA
* * * *
3766628 TATAATTAATTCTTATTTTAACTTAAAGCA
1 TATATTTTATTCTTATCTTAACTTAAA-AA
* *
3766658 TATCTTTTATTATTATCTTAACTTAAAAA
1 TATATTTTATTCTTATCTTAACTTAAAAA
*
3766687 TATA---T-TT-TTAT-TTAACTAAAAAA
1 TATATTTTATTCTTATCTTAACTTAAAAA
*
3766710 TATATTTTATTTTTATCTTAACTATAAAAA
1 TATATTTTATTCTTATCTTAACT-TAAAAA
3766740 AATAAAAAAA
Statistics
Matches: 206, Mismatches: 41, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
23 15 0.07
24 4 0.02
25 2 0.01
26 2 0.01
27 2 0.01
28 19 0.09
29 37 0.18
30 113 0.55
31 12 0.06
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (29 bp):
TATATTTTATTCTTATCTTAACTTAAAAA
Found at i:3766707 original size:21 final size:23
Alignment explanation
Indices: 3766665--3766721 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
3766655 GCATATCTTT
* *
3766665 TATTATTATCTTAACTTAAAAATA
1 TATTTTTAT-TTAACTTAAAAAAA
3766689 TATTTTTATTTAAC-T-AAAAAA
1 TATTTTTATTTAACTTAAAAAAA
3766710 TATATTTTATTT
1 TAT-TTTTATTT
3766722 TTATCTTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 8 0.27
22 9 0.30
23 5 0.17
24 8 0.27
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTTTTATTTAACTTAAAAAAA
Found at i:3766708 original size:23 final size:23
Alignment explanation
Indices: 3766665--3766721 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
3766655 GCATATCTTT
* *
3766665 TATTATTATCTTAACTTAAAAATA
1 TATTTTTAT-TTAACTAAAAAATA
3766689 TATTTTTATTTAACTAAAAAATA
1 TATTTTTATTTAACTAAAAAATA
3766712 TA-TTTTATTT
1 TATTTTTATTT
3766722 TTATCTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 8 0.26
23 15 0.48
24 8 0.26
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTTTTATTTAACTAAAAAATA
Found at i:3766811 original size:31 final size:31
Alignment explanation
Indices: 3766757--3766876 Score: 111
Period size: 30 Copynumber: 4.0 Consensus size: 31
3766747 AAAAATTCTT
* * * *
3766757 ATATTTAAAATAATATCATAATAATATATAA
1 ATATTTAAATTAATATAAGAATAAAATATAA
*
3766788 ATATTTAAATTAATATAAGAAT-AAAT-TAT
1 ATATTTAAATTAATATAAGAATAAAATATAA
* * * *
3766817 ATTTTTAATTTAACATAAGATTAAAATAT-A
1 ATATTTAAATTAATATAAGAATAAAATATAA
* * *
3766847 TTTTTTAAATTAAAATAAGAATAAAATATA
1 ATATTTAAATTAATATAAGAATAAAATATA
3766877 TTTTTAGAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
29 20 0.28
30 32 0.44
31 20 0.28
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (31 bp):
ATATTTAAATTAATATAAGAATAAAATATAA
Found at i:3766834 original size:29 final size:29
Alignment explanation
Indices: 3766791--3766942 Score: 166
Period size: 29 Copynumber: 5.2 Consensus size: 29
3766781 TATATAAATA
*
3766791 TTTAAATTAATATAAGAATAAATTATATT
1 TTTAAATTAATATAAGAATAAAATATATT
* * *
3766820 TTTAATTTAACATAAGATTAAAATATATTT
1 TTTAAATTAATATAAGAATAAAATATA-TT
*
3766850 TTTAAATTAAAATAAGAATAAAATATATT
1 TTTAAATTAATATAAGAATAAAATATATT
3766879 TTTAGAA-TAGA-A-AACGAATAAAATATATT
1 TTTA-AATTA-ATATAA-GAATAAAATATATT
* * *
3766908 TAATAAGTTAATATAAAAATAAAATATATT
1 T-TTAAATTAATATAAGAATAAAATATATT
3766938 TTTAA
1 TTTAA
3766943 TGTTAAGATT
Statistics
Matches: 104, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
28 2 0.02
29 52 0.50
30 48 0.46
31 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (29 bp):
TTTAAATTAATATAAGAATAAAATATATT
Found at i:3766854 original size:30 final size:30
Alignment explanation
Indices: 3766791--3766940 Score: 155
Period size: 30 Copynumber: 5.1 Consensus size: 30
3766781 TATATAAATA
* *
3766791 TTTAAATTAATATAAGAATAAATTATA-TT
1 TTTAAATTAAAATAAGAATAAAATATATTT
* * *
3766820 TTTAATTTAACATAAGATTAAAATATATTT
1 TTTAAATTAAAATAAGAATAAAATATATTT
3766850 TTTAAATTAAAATAAGAATAAAATATA-TT
1 TTTAAATTAAAATAAGAATAAAATATATTT
*
3766879 TTTAGAA-TAGAAA-ACGAATAAAATATATTT
1 TTTA-AATTA-AAATAAGAATAAAATATATTT
** * * *
3766909 AATAAGTTAATATAAAAATAAAATATATTT
1 TTTAAATTAAAATAAGAATAAAATATATTT
3766939 TT
1 TT
3766941 AATGTTAAGA
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
29 47 0.47
30 52 0.53
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTAAATTAAAATAAGAATAAAATATATTT
Found at i:3766859 original size:59 final size:58
Alignment explanation
Indices: 3766791--3766948 Score: 185
Period size: 59 Copynumber: 2.7 Consensus size: 58
3766781 TATATAAATA
* *
3766791 TTTAAATTAATATAAGAATAAATTATATTTTTAATTTAACATAA-GATTAAAATATATTT
1 TTTAAATTAATATAAGAATAAAATATATTTTTAATTTAA-A-AACGAATAAAATATATTT
* *
3766850 TTTAAATTAAAATAAGAATAAAATATATTTTTAGA-ATAGAAAACGAATAAAATATATTT
1 TTTAAATTAATATAAGAATAAAATATATTTTTA-ATTTA-AAAACGAATAAAATATATTT
** * *
3766909 AATAAGTTAATATAAAAATAAAATATATTTTTAATGTTAA
1 TTTAAATTAATATAAGAATAAAATATATTTTTAAT-TTAA
3766949 GATTTAAACC
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
58 3 0.04
59 77 0.92
60 4 0.05
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (58 bp):
TTTAAATTAATATAAGAATAAAATATATTTTTAATTTAAAAACGAATAAAATATATTT
Found at i:3767197 original size:36 final size:36
Alignment explanation
Indices: 3767150--3767240 Score: 155
Period size: 36 Copynumber: 2.5 Consensus size: 36
3767140 TCGGGGATGA
3767150 TAAACGGGGACGGGGACGGAGAAACCCCATTTATGT
1 TAAACGGGGACGGGGACGGAGAAACCCCATTTATGT
*
3767186 TAAACGGGGACGGGGACGGAGAAACCCCGTTTATGT
1 TAAACGGGGACGGGGACGGAGAAACCCCATTTATGT
* *
3767222 TAAACGAGGACAGGGACGG
1 TAAACGGGGACGGGGACGG
3767241 GTTTGGTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.31, C:0.19, G:0.36, T:0.14
Consensus pattern (36 bp):
TAAACGGGGACGGGGACGGAGAAACCCCATTTATGT
Found at i:3767301 original size:12 final size:13
Alignment explanation
Indices: 3767252--3767300 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
3767242 TTTGGTAATC
*
3767252 CCCGCCCCGATTA
1 CCCGACCCGATTA
*
3767265 CCCGGCCCGATTA
1 CCCGACCCGATTA
*
3767278 CCCAACCCGA-TA
1 CCCGACCCGATTA
3767290 CCCGACCCGAT
1 CCCGACCCGAT
3767301 AAATATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 11 0.35
13 20 0.65
ACGTcount: A:0.20, C:0.51, G:0.16, T:0.12
Consensus pattern (13 bp):
CCCGACCCGATTA
Found at i:3773734 original size:37 final size:37
Alignment explanation
Indices: 3773693--3773875 Score: 129
Period size: 37 Copynumber: 5.3 Consensus size: 37
3773683 ATAATATATA
3773693 AGTGACCAAATAGGTAGTTTACCCTAAATTATAATCG
1 AGTGACCAAATAGGTAGTTTACCCTAAATTATAATCG
* ** ** ** *
3773730 AGTGATCAAA-ACATAAATTA-GAT-AA-TAT-AT-A
1 AGTGACCAAATAGGTAGTTTACCCTAAATTATAATCG
*
3773761 AGTGACCAAATAGGTAGTTTACCCTAAATAATAATCG
1 AGTGACCAAATAGGTAGTTTACCCTAAATTATAATCG
** ** ** *
3773798 AGTGACCAAA-ACATAAATTA-GAT-AA-TAT-AT-A
1 AGTGACCAAATAGGTAGTTTACCCTAAATTATAATCG
*
3773829 AGTGACCAAATAGGTAGTTTACCCTAAATAATAATCG
1 AGTGACCAAATAGGTAGTTTACCCTAAATTATAATCG
3773866 AGTGACCAAA
1 AGTGACCAAA
3773876 ACATAAATTA
Statistics
Matches: 101, Mismatches: 33, Indels: 24
0.64 0.21 0.15
Matches are distributed among these distances:
31 19 0.19
32 16 0.16
33 7 0.07
34 8 0.08
35 6 0.06
36 16 0.16
37 29 0.29
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (37 bp):
AGTGACCAAATAGGTAGTTTACCCTAAATTATAATCG
Found at i:3773765 original size:31 final size:31
Alignment explanation
Indices: 3773730--3773974 Score: 105
Period size: 31 Copynumber: 7.3 Consensus size: 31
3773720 ATTATAATCG
*
3773730 AGTGATCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
** ** ** *
3773761 AGTGACCAAATAGGTAGTTTACCCTAAATAATAATCG
1 AGTGACCAAA-ACATAAATTA-GAT-AAT-AT-AT-A
3773798 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
** ** ** *
3773829 AGTGACCAAATAGGTAGTTTACCCTAAATAATAATCG
1 AGTGACCAAA-ACATAAATTA-GAT-AAT-AT-AT-A
3773866 AGTGACCAAAACATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
* ** ** *
3773897 AGTGATCAAATAGGTAGTTTA-ACCTAAATAATAATCG
1 AGTGACCAAA-ACATAAATTAGA--T-AAT-AT-AT-A
* *
3773934 AGCGACCAAAATATAAATTAGATAATATATA
1 AGTGACCAAAACATAAATTAGATAATATATA
3773965 AGTGACCAAA
1 AGTGACCAAA
3773975 TAGGTAGTTT
Statistics
Matches: 151, Mismatches: 43, Indels: 40
0.65 0.18 0.17
Matches are distributed among these distances:
31 38 0.25
32 24 0.16
33 9 0.06
34 18 0.12
35 9 0.06
36 24 0.16
37 29 0.19
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.27
Consensus pattern (31 bp):
AGTGACCAAAACATAAATTAGATAATATATA
Found at i:3773769 original size:68 final size:68
Alignment explanation
Indices: 3773591--3773988 Score: 601
Period size: 68 Copynumber: 5.9 Consensus size: 68
3773581 ATTTGAAAAA
* * * * *
3773591 AATAATCAAATGATCAAAACATAAATTAGATAATATATAAGTTACCAAATAGGTAGTCTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
3773656 AAT
66 AAT
* * * * *
3773659 AAAAAT--A-T-A-TATGAA-TTATATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCT
1 AATAATCGAGTGACCA-AAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCT
3773718 AAAT
65 AAAT
* *
3773722 TATAATCGAGTGATCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
3773787 AAT
66 AAT
3773790 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
3773855 AAT
66 AAT
* *
3773858 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGATCAAATAGGTAGTTTAACCTA
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
3773923 AAT
66 AAT
* *
3773926 AATAATCGAGCGACCAAAATATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCC
1 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCC
3773989 AAAAAATCCC
Statistics
Matches: 302, Mismatches: 21, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
63 49 0.16
64 3 0.01
65 2 0.01
66 2 0.01
67 3 0.01
68 243 0.80
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (68 bp):
AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
AAT
Found at i:3778934 original size:15 final size:17
Alignment explanation
Indices: 3778914--3778949 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3778904 CTTATCAACC
3778914 CAAATT-AAATGTCCA-
1 CAAATTCAAATGTCCAT
3778929 CAAATTCAAATGTCCAT
1 CAAATTCAAATGTCCAT
3778946 CAAA
1 CAAA
3778950 AGTTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 9 0.47
17 4 0.21
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (17 bp):
CAAATTCAAATGTCCAT
Found at i:3783342 original size:14 final size:15
Alignment explanation
Indices: 3783323--3783351 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3783313 ATAACATAAT
3783323 TAATAAATG-TAACA
1 TAATAAATGATAACA
3783337 TAATAAATGATAACA
1 TAATAAATGATAACA
3783352 GGAGAGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (15 bp):
TAATAAATGATAACA
Found at i:3784523 original size:2 final size:2
Alignment explanation
Indices: 3784516--3784540 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3784506 GCGCATGCTC
3784516 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3784541 AACTCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3784717 original size:4 final size:4
Alignment explanation
Indices: 3784708--3784756 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
3784698 TGATGTGAGA
* *
3784708 GAGG GAGG GACG GAGG GAGG GACG GAGG GA-G G-GG GAGG GAGG GAGG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG
3784754 GAG
1 GAG
3784757 AGAGAATGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 4 0.10
4 35 0.90
ACGTcount: A:0.24, C:0.04, G:0.71, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:3784725 original size:12 final size:12
Alignment explanation
Indices: 3784708--3784756 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
3784698 TGATGTGAGA
3784708 GAGGGAGGGACG
1 GAGGGAGGGACG
3784720 GAGGGAGGGACG
1 GAGGGAGGGACG
3784732 GAGGGAGGG--G
1 GAGGGAGGGACG
*
3784742 GAGGGAGGGAGG
1 GAGGGAGGGACG
3784754 GAG
1 GAG
3784757 AGAGAATGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.29
12 25 0.71
ACGTcount: A:0.24, C:0.04, G:0.71, T:0.00
Consensus pattern (12 bp):
GAGGGAGGGACG
Found at i:3791872 original size:17 final size:16
Alignment explanation
Indices: 3791832--3791878 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
3791822 ATTTGAAAAG
3791832 AATTTTT-TTTTT-TA
1 AATTTTTATTTTTATA
3791846 AATTTATTATTTTTATA
1 AATTT-TTATTTTTATA
3791863 ATATTTTTATTTTTAT
1 A-ATTTTTATTTTTAT
3791879 TACTTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.17
15 2 0.07
16 5 0.17
17 13 0.45
18 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
AATTTTTATTTTTATA
Found at i:3792357 original size:181 final size:182
Alignment explanation
Indices: 3792064--3792416 Score: 428
Period size: 181 Copynumber: 1.9 Consensus size: 182
3792054 TGCATATTCG
*
3792064 ATTTGATTTAGGGTTAACAAAATTATCAAGTAAGTAAAATAAAAATCATCTTCTCTATATTTTAC
1 ATTTAATTTAGGGTTAACAAAATTAT--A-TAAGTAAAATAAAAATCATCTTCTCTATATTTTAC
* * * ** * *
3792129 TTTTAAATAATCTTTTTTTAGAATTCTGTTATTTTACATTTTTTTTTTGTTTTGCT-CCAGATTA
63 TTTTAAATAATCTTGTTTAAGAATTCTATTATTTTACATAATTTTTTTATCTTG-TACCAGATTA
** * * *
3792193 TAGTTGTAGAAGTGGTTCGTCAATTTTAATATCCAAGTAATTGAATATTTTGATAAT
127 TAGTACTAGAAGCGGTT-ATCAATTTTAATACCCAAGTAATTGAATATTTTGATAAT
* * *
3792250 ATTTAATTTAGGGTTAA-AAAATTAT-TAAGTGAAATAGAAAT-ATTCTTCTCTGTATTTTACTT
1 ATTTAATTTAGGGTTAACAAAATTATATAAGTAAAATAAAAATCA-TCTTCTCTATATTTTACTT
* * *
3792312 TTGCAATAATCTTGTTTAAGAGTTCTATTGTTTTACA-AATTTTTTTATCTTGTACCAGATTATA
65 TT-AAATAATCTTGTTTAAGAATTCTATTATTTTACATAATTTTTTTATCTTGTACCAGATTATA
*
3792376 GTACTAGAAGCGGTTATCAATTTTAATACCCAGGTAATTGA
129 GTACTAGAAGCGGTTATCAATTTTAATACCCAAGTAATTGA
3792417 TTTTTTTTAT
Statistics
Matches: 144, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
180 25 0.17
181 67 0.47
182 28 0.19
185 8 0.06
186 16 0.11
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (182 bp):
ATTTAATTTAGGGTTAACAAAATTATATAAGTAAAATAAAAATCATCTTCTCTATATTTTACTTT
TAAATAATCTTGTTTAAGAATTCTATTATTTTACATAATTTTTTTATCTTGTACCAGATTATAGT
ACTAGAAGCGGTTATCAATTTTAATACCCAAGTAATTGAATATTTTGATAAT
Found at i:3795270 original size:191 final size:192
Alignment explanation
Indices: 3794891--3795274 Score: 469
Period size: 191 Copynumber: 2.0 Consensus size: 192
3794881 TATGTCGCTC
* *
3794891 AAAATGTGACAATATCTCTTTCGTCACATATAGGTTGATTCTAATGTATTATTCACGACTGTATA
1 AAAATGTGACAATATCTCTTTCATCACATATAGATTGATTCTAATGTATTATTCACGACTGTATA
* *
3794956 AATTATTAATTAAAAATATTATATAATTTAGTGGCATAACTAATTGTCATGAAATATAAGTTATA
66 AATTATCAATTAAAAATATTATATAATTTAGTGACATAACTAATTGTCATGAAATATAAGTTATA
* * * * *
3795021 AAGTGGCGTTATGCATAAGTGTCATTTATAATACTATTAGGTAGCATTGTATTACGTCACTA
131 AAGTGACGTTATGCATAAATGTCATTCATAATACTAATAGGTAGCATTGTACTACGTCACTA
* * * * *
3795083 AAAATGTGACGATATCTCTTTCATCACATATAGATTGCTTTTAATGTATTATTTTACTA-T-T-T
1 AAAATGTGACAATATCTCTTTCATCACATATAGATTGATTCTAATGTATTA-TTCACGACTGTAT
* * *
3795145 GAATTATCAA-TAACGAAATATTATATAATTTAGTGACATAACTAGTTGTCATTG-AGTATCAA-
65 AAATTATCAATTAA--AAATATTATATAATTTAGTGACATAACTAATTGTCA-TGAAATAT-AAG
* * *
3795207 TTATTAAGTGACGTTATGGATAAATGTCATTCATACTACTAATAGGT-GACGA-TGTACTACGTC
126 TTATAAAGTGACGTTATGCATAAATGTCATTCATAATACTAATAGGTAG-C-ATTGTACTACGTC
3795270 ACTA
189 ACTA
3795274 A
1 A
3795275 TATTGTAATA
Statistics
Matches: 165, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
189 3 0.02
190 10 0.06
191 95 0.58
192 52 0.32
193 5 0.03
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.39
Consensus pattern (192 bp):
AAAATGTGACAATATCTCTTTCATCACATATAGATTGATTCTAATGTATTATTCACGACTGTATA
AATTATCAATTAAAAATATTATATAATTTAGTGACATAACTAATTGTCATGAAATATAAGTTATA
AAGTGACGTTATGCATAAATGTCATTCATAATACTAATAGGTAGCATTGTACTACGTCACTA
Found at i:3795627 original size:2 final size:2
Alignment explanation
Indices: 3795607--3795759 Score: 84
Period size: 2 Copynumber: 78.0 Consensus size: 2
3795597 GGAGTTTAGG
* * * * *
3795607 GA GA AA GA GA GA TGG GA GA GA GA GG GA GA GG GA GA GG GA GA GA
1 GA GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * *
3795650 GA GA -A TGA GA GA GC GA GA GA GA GA TA -A G- GT GA GA GA GA AA
1 GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * ** * *
3795690 GG GA GA AA GA GA GA GA TT GA GA GA GA -A GA GA GG GA G- GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
3795730 GA GA GG GA GA GA GA GA TG- GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA -GA GA GA GA GA GA GA
3795760 TGGCAAGAGA
Statistics
Matches: 111, Mismatches: 31, Indels: 18
0.69 0.19 0.11
Matches are distributed among these distances:
1 6 0.05
2 102 0.92
3 3 0.03
ACGTcount: A:0.44, C:0.01, G:0.50, T:0.05
Consensus pattern (2 bp):
GA
Found at i:3795643 original size:12 final size:12
Alignment explanation
Indices: 3795612--3795758 Score: 101
Period size: 12 Copynumber: 12.7 Consensus size: 12
3795602 TTAGGGAGAA
*
3795612 AGAGAGATGG-G
1 AGAGAGAGGGAG
3795623 AGAGAGAGGGAG
1 AGAGAGAGGGAG
*
3795635 AGGGAGAGGGAG
1 AGAGAGAGGGAG
**
3795647 AGAGAGAATGAG
1 AGAGAGAGGGAG
* *
3795659 AGAGCGAGAGAG
1 AGAGAGAGGGAG
*
3795671 AGATA-AGGTGAG
1 AGAGAGAGG-GAG
*
3795683 AGAGAAAGGGAG
1 AGAGAGAGGGAG
3795695 A-A-AGA--GAG
1 AGAGAGAGGGAG
** *
3795703 AGATTGAGAGAG
1 AGAGAGAGGGAG
3795715 A-AGAGAGGGAGG
1 AGAGAGAGGGA-G
*
3795727 GGAGAGAGGGAG
1 AGAGAGAGGGAG
* *
3795739 AGAGAGATGGAA
1 AGAGAGAGGGAG
3795751 AGAGAGAG
1 AGAGAGAG
3795759 ATGGCAAGAG
Statistics
Matches: 105, Mismatches: 22, Indels: 17
0.73 0.15 0.12
Matches are distributed among these distances:
8 4 0.04
9 1 0.01
10 4 0.04
11 18 0.17
12 66 0.63
13 12 0.11
ACGTcount: A:0.44, C:0.01, G:0.51, T:0.05
Consensus pattern (12 bp):
AGAGAGAGGGAG
Found at i:3795768 original size:12 final size:14
Alignment explanation
Indices: 3795694--3795769 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
3795684 GAGAAAGGGA
*
3795694 GAAAGAGAGAGATT
1 GAAAGAGAGAGATG
*
3795708 GAGAGAGAAGAGA-G
1 GAAAGAG-AGAGATG
* * *
3795722 GGAGGGGAGAGA-G
1 GAAAGAGAGAGATG
*
3795735 G-GAGAGAGAGATG
1 GAAAGAGAGAGATG
3795748 GAAAGAGAGAGATG
1 GAAAGAGAGAGATG
*
3795762 GCAAGAGA
1 GAAAGAGA
3795770 AAGAGGGGGA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
12 7 0.15
13 9 0.19
14 27 0.56
15 5 0.10
ACGTcount: A:0.45, C:0.01, G:0.49, T:0.05
Consensus pattern (14 bp):
GAAAGAGAGAGATG
Found at i:3795774 original size:16 final size:15
Alignment explanation
Indices: 3795736--3795774 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
3795726 GGGAGAGAGG
3795736 GAGAGAGAGATGGAA
1 GAGAGAGAGATGGAA
3795751 -AGAGAGAGATGGCAA
1 GAGAGAGAGATGG-AA
*
3795766 GAGAAAGAG
1 GAGAGAGAG
3795775 GGGGAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 12 0.57
15 2 0.10
16 7 0.33
ACGTcount: A:0.49, C:0.03, G:0.44, T:0.05
Consensus pattern (15 bp):
GAGAGAGAGATGGAA
Found at i:3795796 original size:54 final size:54
Alignment explanation
Indices: 3795694--3795797 Score: 124
Period size: 54 Copynumber: 1.9 Consensus size: 54
3795684 GAGAAAGGGA
* * * *
3795694 GAAAGAGAGAGATTGAGAGAGAAGAGAGGGAGGGGAGAGAGGGAGAGAGAGATG
1 GAAAGAGAGAGATGGAGAGAGAAGAGAGGGAGGAGAAAGAGGAAGAGAGAGATG
3795748 GAAAGAGAGAGATGGCA-AGAGAA-AGAGGG-GGAGAAAGAGAGAACGAGAGA
1 GAAAGAGAGAGATGG-AGAGAGAAGAGAGGGAGGAGAAAGAG-GAA-GAGAGA
3795798 AGGGGATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
52 8 0.19
53 8 0.19
54 26 0.60
55 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.48, T:0.04
Consensus pattern (54 bp):
GAAAGAGAGAGATGGAGAGAGAAGAGAGGGAGGAGAAAGAGGAAGAGAGAGATG
Found at i:3799394 original size:25 final size:25
Alignment explanation
Indices: 3799366--3799421 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
3799356 ATATGAAAAG
*
3799366 ATAAAACGATAATTAAAACATATCT
1 ATAAAACAATAATTAAAACATATCT
** *
3799391 ATAAATTAATAATTAAAATATATCT
1 ATAAAACAATAATTAAAACATATCT
3799416 ATAAAA
1 ATAAAA
3799422 AATGTGTTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAAAACAATAATTAAAACATATCT
Found at i:3802881 original size:19 final size:19
Alignment explanation
Indices: 3802854--3802890 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3802844 ATTATTTGAC
*
3802854 AAAATTAATAGAAAACATA
1 AAAAATAATAGAAAACATA
*
3802873 AAAAATAATATAAAACAT
1 AAAAATAATAGAAAACAT
3802891 TTTATGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAAATAATAGAAAACATA
Found at i:3806135 original size:23 final size:24
Alignment explanation
Indices: 3806105--3806158 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
3806095 AATTACCACT
3806105 CACGTTACG-TTTTTCTCTGGGCG
1 CACGTTACGTTTTTTCTCTGGGCG
*
3806128 CACGTTACGTTTTTTTTCTGGGCG
1 CACGTTACGTTTTTTCTCTGGGCG
3806152 CACGTTA
1 CACGTTA
3806159 ACAGGACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (24 bp):
CACGTTACGTTTTTTCTCTGGGCG
Found at i:3809736 original size:15 final size:15
Alignment explanation
Indices: 3809718--3809767 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
3809708 TAAGAAGAAG
3809718 AGGATATGGAAGTTA
1 AGGATATGGAAGTTA
* *
3809733 AGGATAAGG-AG-AA
1 AGGATATGGAAGTTA
*
3809746 GAGGATATGAAAGTTA
1 -AGGATATGGAAGTTA
3809762 AGGATA
1 AGGATA
3809768 GGATAAATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 1 0.04
14 9 0.33
15 16 0.59
16 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (15 bp):
AGGATATGGAAGTTA
Found at i:3809750 original size:29 final size:29
Alignment explanation
Indices: 3809708--3809767 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
3809698 TTGAATTTCC
*
3809708 TAAGAAGAAGAGGATATGGAAGTTAAGGA
1 TAAGAAGAAGAGGATATGAAAGTTAAGGA
*
3809737 TAAGGAGAAGAGGATATGAAAGTTAAGGA
1 TAAGAAGAAGAGGATATGAAAGTTAAGGA
3809766 TA
1 TA
3809768 GGATAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.18
Consensus pattern (29 bp):
TAAGAAGAAGAGGATATGAAAGTTAAGGA
Found at i:3811082 original size:32 final size:31
Alignment explanation
Indices: 3811041--3811115 Score: 105
Period size: 32 Copynumber: 2.4 Consensus size: 31
3811031 AGAGTCGAGG
*
3811041 GTTACCTATGTCTTTCGAGACATATGGACAGT
1 GTTACCTATGTCTTTCGAGACATATGAACA-T
* *
3811073 GTTACCTATGTCTTTTGGGACATATGAACAT
1 GTTACCTATGTCTTTCGAGACATATGAACAT
3811104 GATTACCTATGT
1 G-TTACCTATGT
3811116 TCCAAGGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (31 bp):
GTTACCTATGTCTTTCGAGACATATGAACAT
Found at i:3815617 original size:32 final size:31
Alignment explanation
Indices: 3815575--3815650 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 31
3815565 AAGAGTCGAG
3815575 GGTTACCTATG-CCTTTCGAGACATATGGACA
1 GGTTACCTATGTCC-TTCGAGACATATGGACA
3815606 GTGTTACCTATGTCCTTCGAGACATATGGACA
1 G-GTTACCTATGTCCTTCGAGACATATGGACA
3815638 GGATTACCTATGT
1 GG-TTACCTATGT
3815651 TCTAAGGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
31 2 0.05
32 38 0.90
33 2 0.05
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGAGACATATGGACA
Found at i:3829856 original size:229 final size:228
Alignment explanation
Indices: 3829451--3829937 Score: 884
Period size: 229 Copynumber: 2.1 Consensus size: 228
3829441 GTAAATTATC
* * *
3829451 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
3829516 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
3829581 TGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTG
*
3829646 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTTAAAAAAAGTATA
*
3829679 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
3829744 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* *
3829809 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATT
3829874 GAAACATAAATTACATAACTTTAAAAAAAGTATA
195 GAAACATAAATTACATAACTTTAAAAAAAGTATA
3829908 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
3829938 AAAAGTAGGT
Statistics
Matches: 249, Mismatches: 9, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
228 36 0.14
229 213 0.86
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAAGTATA
Found at i:3830219 original size:20 final size:19
Alignment explanation
Indices: 3830196--3830242 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
3830186 CGATATACCA
3830196 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
3830216 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
3830236 GGTAAAA
1 GGTAAAA
3830243 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:3830400 original size:20 final size:19
Alignment explanation
Indices: 3830377--3830423 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
3830367 CGATATAACA
3830377 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
3830397 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
3830417 GGTAAAA
1 GGTAAAA
3830424 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:3830409 original size:181 final size:183
Alignment explanation
Indices: 3829992--3830456 Score: 702
Period size: 181 Copynumber: 2.6 Consensus size: 183
3829982 CCGGTTCGTG
* *
3829992 TCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTAT-AGAAATGATAAAACCGGT
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCA-AAATGATAAAACCGGT
* * * * * *
3830056 CAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCGTGAATTT
65 AAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTT
* * *
3830121 AAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTAAAAAAAATGTA
130 AAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAAAAAAATATA
* *
3830175 TCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
* * *
3830240 AAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAATGATCGACACTTTGTGAATTTA
66 AAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
** *
3830304 AAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATACTTT-AAAAAAATATA
131 AAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAAAAAAATATA
*
3830356 TCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
* *
3830421 AAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACGATACCGGATATATTAAAAGTGTCGATACTTT
3830457 CGTAAGTACG
Statistics
Matches: 257, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
181 105 0.41
182 62 0.24
183 89 0.35
184 1 0.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (183 bp):
TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATAAAACCGGTA
AAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
AAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTAAAAAAAATATA
Found at i:3830425 original size:17 final size:19
Alignment explanation
Indices: 3830386--3830428 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
3830376 AGGTAAAAAT
3830386 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
3830406 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
3830423 ATGATA
1 ATGATA
3830429 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:3832683 original size:21 final size:21
Alignment explanation
Indices: 3832656--3832720 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
3832646 AAGACAATCA
*
3832656 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
* * *
3832677 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
3832698 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
3832719 AG
1 AG
3832721 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:3832796 original size:33 final size:33
Alignment explanation
Indices: 3832754--3832819 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3832744 AAATAGATGG
*
3832754 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
3832787 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
3832820 TATAAGATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:3834628 original size:19 final size:19
Alignment explanation
Indices: 3834604--3834652 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3834594 AATGTAGGGT
3834604 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3834623 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
3834642 TATTTTTGTAT
1 TAATTTTGTAT
3834653 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3835354 original size:198 final size:200
Alignment explanation
Indices: 3834771--3835542 Score: 1394
Period size: 198 Copynumber: 3.9 Consensus size: 200
3834761 CAATATGGCC
* *
3834771 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
*
3834836 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
3834901 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
3834966 TGGAA
196 TGGAA
*
3834971 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATTGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
*
3835036 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
3835101 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
*
3835166 TGAAA
196 TGGAA
*
3835171 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCG-AAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
*
3835234 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
3835299 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
3835364 TGGAA
196 TGGAA
*
3835369 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
*
3835433 CCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAAGTATACCGGTATTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
3835497 GAATATGTCTAAATAATGTGTCGACACGT--TATAGTTTGTGTCGATA
131 GAATATGTCTAAATAATGTGTCGACAC-TAATATAGTTTGTGTCGATA
3835543 CTAATTTAAA
Statistics
Matches: 558, Mismatches: 12, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
197 17 0.03
198 234 0.42
199 77 0.14
200 230 0.41
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (200 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
TGGAA
Found at i:3839956 original size:24 final size:25
Alignment explanation
Indices: 3839927--3839990 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
3839917 ATATCATTAA
3839927 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
3839952 A-TTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
3839976 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
3839991 TCTTTTGAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 20 0.67
25 10 0.33
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:3840317 original size:22 final size:22
Alignment explanation
Indices: 3840272--3840317 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3840262 ATTACATAAC
*
3840272 TTTTAAAAAAAGTATCGATCCT
1 TTTTAAAAAAAGTATCGAACCT
*
3840294 TTTTATAAAAAGTAT-GAACACT
1 TTTTAAAAAAAGTATCGAAC-CT
3840316 TT
1 TT
3840318 CAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTTAAAAAAAGTATCGAACCT
Found at i:3840366 original size:23 final size:23
Alignment explanation
Indices: 3840335--3840407 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
3840325 ATAGGTAAAC
*
3840335 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3840358 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3840381 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
3840404 ATAT
1 ATAT
3840408 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:3840823 original size:23 final size:23
Alignment explanation
Indices: 3840763--3840823 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
3840753 ATAGGTAAAA
* *
3840763 ATATGATGTAATAGATAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
3840786 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
3840809 ATATAATGTAATAGG
1 ATATAATGTAATAGG
3840824 CAGTGGTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:3840833 original size:23 final size:23
Alignment explanation
Indices: 3840784--3840835 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3840774 TAGATAGCGC
* *
3840784 TTATATAATGTAATAGGTATCGT
1 TTATATAATGTAATAGGCATCGG
3840807 TTATATAATGTAATAGGCAGT-GG
1 TTATATAATGTAATAGGCA-TCGG
3840830 TTATAT
1 TTATAT
3840836 TGTAAAGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (23 bp):
TTATATAATGTAATAGGCATCGG
Found at i:3840929 original size:428 final size:429
Alignment explanation
Indices: 3840132--3841067 Score: 1698
Period size: 428 Copynumber: 2.2 Consensus size: 429
3840122 GTTAATGTTG
* * *
3840132 TTAAATT-TAAATTATAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
1 TTAAATTACAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
3840196 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
3840261 AATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAA
131 AATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAA
* *
3840326 TAGGTAAACATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGATAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
* *
3840391 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCATTTTATAAAAGTATCCATATTTTTTTCACTG
261 ATAGGCAGTGGTTATATTGTAAAGTATCTATCCATTTTATAAAAGTATCCATACTTTTTTCACTG
3840456 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
3840521 CGTCTAATGATTTATTTTTTACGTTACGATATATTATTA
391 CGTCTAATGATTTATTTTTTACGTTACGATATATTATTA
3840560 TTAAATTACAAATTCTAAATATTATTTTATAAAATATCAAAA-AATCAAATAATTTTTTGTGCAA
1 TTAAATTACAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
3840624 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACAT
* *
3840689 AAATTACATAAC-TTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
130 AAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATA
3840753 ATAGGTAAAAATATGATGTAATAGATAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGT
195 ATAGGTAAAAATATGATGTAATAGATAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGT
* * * *
3840818 AATAGGCAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACT
260 AATAGGCAGTGGTTATATTGTAAAGTATCTATCCATTTTATAAAAGTATCCATACTTTTTTCACT
*
3840883 GTGGAAAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
325 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
3840948 GCGTCTAATGATTTATTTTTTACGTTACGATATATTATTA
390 GCGTCTAATGATTTATTTTTTACGTTACGATATATTATTA
3840988 TTAAATTACAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTACAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
3841053 ATAAAATTATTAAAT
66 ATGAAATTATTAAAT
3841068 CAAATTACTT
Statistics
Matches: 489, Mismatches: 16, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
428 393 0.80
429 96 0.20
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.40
Consensus pattern (429 bp):
TTAAATTACAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
AATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAA
TAGGTAAAAATATGATGTAATAGATAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
ATAGGCAGTGGTTATATTGTAAAGTATCTATCCATTTTATAAAAGTATCCATACTTTTTTCACTG
TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
CGTCTAATGATTTATTTTTTACGTTACGATATATTATTA
Found at i:3841282 original size:18 final size:18
Alignment explanation
Indices: 3841261--3841297 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3841251 GTAATTGGAG
3841261 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3841279 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3841297 T
1 T
3841298 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:3841305 original size:24 final size:24
Alignment explanation
Indices: 3841253--3841299 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3841243 TTTCATATGT
* *
3841253 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
3841277 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
3841300 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:3841601 original size:39 final size:39
Alignment explanation
Indices: 3841555--3841641 Score: 120
Period size: 39 Copynumber: 2.2 Consensus size: 39
3841545 TCTGATGCTC
* * *
3841555 ATCAAAATCCAAAGCTCGTATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAACAAAAGGAA
* * *
3841594 ATTAAAATTCAAATCTCATATGATGCCAAACAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAACAAAAGGAA
3841633 ATCAAAATC
1 ATCAAAATC
3841642 TACAACTTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAACAAAAGGAA
Found at i:3842130 original size:25 final size:24
Alignment explanation
Indices: 3842057--3842133 Score: 104
Period size: 23 Copynumber: 3.2 Consensus size: 24
3842047 AATAGTAAAA
* *
3842057 ATATGATGTAATAGGTAG-CGCTT
1 ATATAATGTAATAGGTAGTCGTTT
3842080 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGTCGTTT
*
3842103 ATATAATGTAATAGGTAGTGGTTAT
1 ATATAATGTAATAGGTAGTCGTT-T
3842128 ATATAA
1 ATATAA
3842134 AGTGTCTATC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
23 37 0.77
24 4 0.08
25 7 0.15
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (24 bp):
ATATAATGTAATAGGTAGTCGTTT
Found at i:3842171 original size:22 final size:22
Alignment explanation
Indices: 3842127--3842170 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3842117 GTAGTGGTTA
*
3842127 TATATAAAGTGTCTATCCTTTT
1 TATATAAAGTGTCCATCCTTTT
*
3842149 TATA-AAAGTGTCCATACTTTT
1 TATATAAAGTGTCCATCCTTTT
3842170 T
1 T
3842171 TCACTGTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (22 bp):
TATATAAAGTGTCCATCCTTTT
Found at i:3843286 original size:7 final size:7
Alignment explanation
Indices: 3843274--3843325 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
3843264 AATAAAGTAA
*
3843274 CTTCTCT
1 CTTCCCT
*
3843281 CTTCTCT
1 CTTCCCT
3843288 CTTCCCT
1 CTTCCCT
3843295 CTTCCCT
1 CTTCCCT
3843302 CTTCCCT
1 CTTCCCT
3843309 CTTCCCT
1 CTTCCCT
3843316 CTTCCCT
1 CTTCCCT
3843323 CTT
1 CTT
3843326 TTTATTTCCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (7 bp):
CTTCCCT
Found at i:3863021 original size:29 final size:30
Alignment explanation
Indices: 3862973--3863052 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
3862963 CTTTTTGTTA
*
3862973 TTTCTATTTTAG-TCCCTTAAGCTTCTATT
1 TTTCTATTTTAGATCCTTTAAGCTTCTATT
**
3863002 TTTCTATTTTAGAT-CTTTAAATTTCTATT
1 TTTCTATTTTAGATCCTTTAAGCTTCTATT
*
3863031 TGTACTATTTT-GATCCTTTAAG
1 T-TTCTATTTTAGATCCTTTAAG
3863053 TTTTTGTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 28 0.65
30 15 0.35
ACGTcount: A:0.21, C:0.15, G:0.07, T:0.56
Consensus pattern (30 bp):
TTTCTATTTTAGATCCTTTAAGCTTCTATT
Found at i:3863041 original size:30 final size:29
Alignment explanation
Indices: 3862995--3863051 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
3862985 TCCCTTAAGC
*
3862995 TTCTATTTTTCTATTTTAGAT-CTTTAAAT
1 TTCTATTTTACTATTTT-GATCCTTTAAAT
3863024 TTCTATTTGTACTATTTTGATCCTTTAA
1 TTCTATTT-TACTATTTTGATCCTTTAA
3863052 GTTTTTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (29 bp):
TTCTATTTTACTATTTTGATCCTTTAAAT
Found at i:3866765 original size:24 final size:24
Alignment explanation
Indices: 3866728--3866777 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3866718 AAAATGGTTG
* *
3866728 CTCTACTAATGGGAGTAGTCAAAC
1 CTCTACTAACGGGAGTAGTAAAAC
*
3866752 CTCTATTAACGGGAGTAGTAAAAC
1 CTCTACTAACGGGAGTAGTAAAAC
3866776 CT
1 CT
3866778 ATACCATGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (24 bp):
CTCTACTAACGGGAGTAGTAAAAC
Found at i:3870559 original size:9 final size:9
Alignment explanation
Indices: 3870545--3870580 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
3870535 AGTCTTCATA
*
3870545 CTTCTCCTT
1 CTTCTCCTC
3870554 CTTCTCCTC
1 CTTCTCCTC
3870563 CTTCTCCTC
1 CTTCTCCTC
*
3870572 CTCCTCCTC
1 CTTCTCCTC
3870581 GATTTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCTCCTC
Found at i:3872536 original size:44 final size:41
Alignment explanation
Indices: 3872459--3872540 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
3872449 GCAACGCGAT
* *
3872459 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTAAAAAAGTGTTGCGAGAG
3872500 TTTGAAAAACATGTTGTTGCGATAGTAAAAAAGTGTTGCGA
1 TTTG-AAAA-ATG-TGTTGCGATAGTAAAAAAGTGTTGCGA
3872541 TAGTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 4 0.11
42 4 0.11
43 3 0.08
44 25 0.69
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTAAAAAAGTGTTGCGAGAG
Found at i:3872550 original size:19 final size:20
Alignment explanation
Indices: 3872461--3872551 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
3872451 AACGCGATTT
3872461 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
3872481 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
3872500 TTTGAAAAACATGTTGTTGCGATAG
1 --TG-AAAA-ATG-TGTTGCGATAG
*
3872525 T-AAAAAAGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
3872544 TGAAAAAT
1 TGAAAAAT
3872552 CCAAAATAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 28 0.48
20 8 0.14
21 5 0.09
23 4 0.07
24 3 0.05
25 10 0.17
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.31
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:3873003 original size:40 final size:40
Alignment explanation
Indices: 3872956--3873033 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
3872946 TTGAACTTGG
* * **
3872956 ACTATCGCAACGAATTTGAAAAATTGCAACGCGAACTTAA
1 ACTATCGCAACAAATTAGAAAAATCACAACGCGAACTTAA
*
3872996 ACTATCGCAACAAATTAGGAAAATCACAACGCGAACTT
1 ACTATCGCAACAAATTAGAAAAATCACAACGCGAACTT
3873034 CGACTAACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.21
Consensus pattern (40 bp):
ACTATCGCAACAAATTAGAAAAATCACAACGCGAACTTAA
Found at i:3873071 original size:21 final size:20
Alignment explanation
Indices: 3873047--3873213 Score: 76
Period size: 21 Copynumber: 8.2 Consensus size: 20
3873037 CTAACTATTA
*
3873047 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTT-GAATATCG
* *
3873068 CAA--CGAATTTGAAAAATCG
1 CAACGCGAACTTG-AATATCG
* ** *
3873087 TAACTTGAACTTGGACTATCG
1 CAACGCGAACTT-GAATATCG
* *
3873108 CAA--CGAATTTGAAAAATCG
1 CAACGCGAACTTG-AATATCG
**
3873127 CAACATGAACTTGAATTATCG
1 CAACGCGAACTTGAA-TATCG
*
3873148 CAACGTGAACTTGAACTATCG
1 CAACGCGAACTTGAA-TATCG
* * *
3873169 CAA--CGAATTTAGAAAATCA
1 CAACGCGAACTT-GAATATCG
*
3873188 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTT-GAATATCG
3873209 CAACG
1 CAACG
3873214 TAAATTTAGA
Statistics
Matches: 108, Mismatches: 27, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
18 2 0.02
19 37 0.34
20 5 0.05
21 63 0.58
22 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (20 bp):
CAACGCGAACTTGAATATCG
Found at i:3873108 original size:40 final size:40
Alignment explanation
Indices: 3873053--3873152 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
3873043 ATTACAACGC
* * *
3873053 GAACTTCGACTATCGCAACGAATTTGAAAAATCGTAACTT
1 GAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACAT
3873093 GAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACAT
1 GAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACAT
* *
3873133 GAACTTGAATTATCGCAACG
1 GAACTTGGACTATCGCAACG
3873153 TGAACTTGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (40 bp):
GAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACAT
Found at i:3873157 original size:61 final size:61
Alignment explanation
Indices: 3873083--3873242 Score: 189
Period size: 61 Copynumber: 2.6 Consensus size: 61
3873073 AATTTGAAAA
* * * * *
3873083 ATCGTAACTTGAACTTGGACTATCGCAACGAATTT-GAAAAATCGCAACATGAACTT-GAATT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTAG-AAAATCACAACACGAACTTCG-ACT
* *
3873144 ATCGCAACGTGAACTTGAACTATCGCAACGAATTTAGAAAATCACAACGCGAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTAGAAAATCACAACACGAACTTCGACT
* * * *
3873205 ATCGCAACGTAAATTTAGACTATCGTAACGAATTTAGA
1 ATCGCAACGTGAACTTGGACTATCGCAACGAATTTAGA
3873243 CTAACGTAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
61 83 0.98
62 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (61 bp):
ATCGCAACGTGAACTTGGACTATCGCAACGAATTTAGAAAATCACAACACGAACTTCGACT
Found at i:3873225 original size:21 final size:19
Alignment explanation
Indices: 3873162--3873245 Score: 78
Period size: 21 Copynumber: 4.2 Consensus size: 19
3873152 GTGAACTTGA
3873162 ACTATCGCAACGAATTTAG
1 ACTATCGCAACGAATTTAG
** * * *
3873181 AAAATCACAACGCGAACTTCG
1 ACTATCGCAA--CGAATTTAG
3873202 ACTATCGCAACGTAAATTTAG
1 ACTATCGCAACG--AATTTAG
*
3873223 ACTATCGTAACGAATTTAG
1 ACTATCGCAACGAATTTAG
3873242 ACTA
1 ACTA
3873246 ACGTAAATTT
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
19 20 0.40
21 30 0.60
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.25
Consensus pattern (19 bp):
ACTATCGCAACGAATTTAG
Found at i:3873240 original size:19 final size:20
Alignment explanation
Indices: 3873201--3873251 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
3873191 CGCGAACTTC
*
3873201 GACTATCGCAACGTAAATTTA
1 GACTATCGTAACG-AAATTTA
3873222 GACTATCGTAACG-AATTTA
1 GACTATCGTAACGAAATTTA
*
3873241 GACTAACGTAA
1 GACTATCGTAA
3873252 ATTTAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.57
21 12 0.43
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
GACTATCGTAACGAAATTTA
Found at i:3873256 original size:16 final size:16
Alignment explanation
Indices: 3873210--3873258 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 16
3873200 CGACTATCGC
3873210 AACGTAAATTTAGACT
1 AACGTAAATTTAGACT
*
3873226 ATCGTAACGAATTTAGACT
1 AACGT-A--AATTTAGACT
3873245 AACGTAAATTTAGA
1 AACGTAAATTTAGA
3873259 AAATCGCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 12 0.43
17 1 0.04
18 1 0.04
19 14 0.50
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (16 bp):
AACGTAAATTTAGACT
Found at i:3879183 original size:18 final size:18
Alignment explanation
Indices: 3879162--3879196 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3879152 TAATTTACTC
3879162 TATTTTAATAAATTCAAT
1 TATTTTAATAAATTCAAT
* *
3879180 TATTTTATTCAATTCAA
1 TATTTTAATAAATTCAA
3879197 CGTTGAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTAATAAATTCAAT
Found at i:3880477 original size:21 final size:21
Alignment explanation
Indices: 3880452--3880495 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3880442 AAAATTATAA
3880452 TTATTT-AAATTTAATTTAATT
1 TTATTTGAAA-TTAATTTAATT
* *
3880473 TTATTTGTAATTAATTTTATT
1 TTATTTGAAATTAATTTAATT
3880494 TT
1 TT
3880496 TATAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATTTGAAATTAATTTAATT
Found at i:3900554 original size:17 final size:17
Alignment explanation
Indices: 3900532--3900587 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
3900522 ATATATATTT
3900532 TTATTTAACTACTTAAA
1 TTATTTAACTACTTAAA
**
3900549 TTATTTTATA-TA-TT-TT
1 TTA-TTTA-ACTACTTAAA
3900565 TTATTTAACTACTTAAA
1 TTATTTAACTACTTAAA
3900582 TTATTT
1 TTATTT
3900588 TTATTCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 1 0.03
15 6 0.20
16 5 0.17
17 11 0.37
18 6 0.20
19 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTTAACTACTTAAA
Found at i:3900591 original size:34 final size:34
Alignment explanation
Indices: 3900520--3900588 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
3900510 TATATCTAAA
3900520 TTATATATATTTTTATTTAACTACTTAAATTATT
1 TTATATATATTTTTATTTAACTACTTAAATTATT
3900554 TTATATAT-TTTTTATTTAACTACTTAAATTATT
1 TTATATATATTTTTATTTAACTACTTAAATTATT
3900587 TT
1 TT
3900589 TATTCAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (34 bp):
TTATATATATTTTTATTTAACTACTTAAATTATT
Found at i:3900605 original size:28 final size:29
Alignment explanation
Indices: 3900574--3900647 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 29
3900564 TTTATTTAAC
3900574 TACTTAAATTATTTTTAT-TCAAAATAAA
1 TACTTAAATTATTTTTATGTCAAAATAAA
* *
3900602 TACTTAAAGTTATATCTTTTTGTCAAAATAAG
1 TACTTAAA-TTAT-T-TTTATGTCAAAATAAA
* *
3900634 TATTTAAAATATTT
1 TACTTAAATTATTT
3900648 AAATTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 8 0.21
29 5 0.13
30 2 0.05
31 7 0.18
32 16 0.42
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (29 bp):
TACTTAAATTATTTTTATGTCAAAATAAA
Found at i:3912520 original size:20 final size:20
Alignment explanation
Indices: 3912495--3912549 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
3912485 TTTTGGTGCA
*
3912495 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
*
3912515 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCCCTT
3912536 GAAGGGGAACCGAT
1 G-A-GGGAACCGAT
3912550 TCCCACCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 10 0.33
21 9 0.30
22 2 0.07
23 9 0.30
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:3912547 original size:23 final size:21
Alignment explanation
Indices: 3912495--3912553 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
3912485 TTTTGGTGCA
*
3912495 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
3912515 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
3912536 GAAGGGGAACCGATTCCC
1 G-A-GGGAACCGATTCCC
3912554 ACCACAGGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 1 0.03
23 14 0.41
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:3917941 original size:32 final size:32
Alignment explanation
Indices: 3917878--3917963 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 32
3917868 AACAATGAAA
* * *
3917878 GCATCTTTGAAGATTCAACATCAAATGTTGGG
1 GCATATTTAAAGATTCAACATCAAATATTGGG
***
3917910 GCATATTTAAAGATTCAACATTGGATATTGGG
1 GCATATTTAAAGATTCAACATCAAATATTGGG
* ***
3917942 GCATCTTTGGGGATTCAACATC
1 GCATATTTAAAGATTCAACATC
3917964 TTGTTGCAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (32 bp):
GCATATTTAAAGATTCAACATCAAATATTGGG
Found at i:3918091 original size:34 final size:34
Alignment explanation
Indices: 3918052--3918147 Score: 129
Period size: 34 Copynumber: 2.8 Consensus size: 34
3918042 TGTTTCTCTT
3918052 AAAACAAATTTTGTCTCACTTGAGACAATTTCTC
1 AAAACAAATTTTGTCTCACTTGAGACAATTTCTC
** * * *
3918086 AAAACAACGTTTGTCTCACTTGATATAATTTTTC
1 AAAACAAATTTTGTCTCACTTGAGACAATTTCTC
* *
3918120 AAAACAAATTTCGTCTCGCTTGAGACAA
1 AAAACAAATTTTGTCTCACTTGAGACAA
3918148 CTTATCTATG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.34
Consensus pattern (34 bp):
AAAACAAATTTTGTCTCACTTGAGACAATTTCTC
Found at i:3918323 original size:40 final size:41
Alignment explanation
Indices: 3918268--3918351 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 41
3918258 AAAACCTTTG
3918268 AGTCTATTTCTTTGGAAACAAAA-TTTATCTATTTGGAGAC
1 AGTCTATTTCTTTGGAAACAAAATTTTATCTATTTGGAGAC
* * *
3918308 AGTCTGTTTCTTTGGAAATAAAATTTTATCTCTTTGGAGAC
1 AGTCTATTTCTTTGGAAACAAAATTTTATCTATTTGGAGAC
3918349 AGT
1 AGT
3918352 TTCTCGTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 21 0.52
41 19 0.47
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.42
Consensus pattern (41 bp):
AGTCTATTTCTTTGGAAACAAAATTTTATCTATTTGGAGAC
Found at i:3919135 original size:92 final size:94
Alignment explanation
Indices: 3919028--3919217 Score: 287
Period size: 92 Copynumber: 2.0 Consensus size: 94
3919018 CATATGAGCA
* * *
3919028 GTGTTATCATTATTCCTAAAGATGACCGAGAACTCTTCATCGCGTATGAGCAGTGTCATC-CCCC
1 GTGTTATCATCATTCCTAAAGATGACCGAGAACTCTTCATCACGGATGAGCAGTGTCATCTCCCC
**
3919092 GACCAGATTTTCC-CAGTAGAGT-GAAACC
66 GACCAGA-TTTCCTCAACAGAGTGGAAACC
* *
3919120 GTGTTATCATCATTCCTAAAGATGGCCTAGAACTCTTCATCACGGATGAGCAGTGTCATCTCCCC
1 GTGTTATCATCATTCCTAAAGATGACCGAGAACTCTTCATCACGGATGAGCAGTGTCATCTCCCC
3919185 GACCAGATTTCCTCAACAGAGTGGAAACC
66 GACCAGATTTCCTCAACAGAGTGGAAACC
3919214 GTGT
1 GTGT
3919218 CAACCTCAGA
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
92 60 0.68
93 18 0.20
94 10 0.11
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (94 bp):
GTGTTATCATCATTCCTAAAGATGACCGAGAACTCTTCATCACGGATGAGCAGTGTCATCTCCCC
GACCAGATTTCCTCAACAGAGTGGAAACC
Found at i:3921866 original size:23 final size:23
Alignment explanation
Indices: 3921836--3921895 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
3921826 AGATTTGTTA
3921836 AAAT-ATATCAATATAATAAAA-T
1 AAATAATAT-AATATAATAAAATT
*
3921858 AAATAATATATATATATTAAAATT
1 AAATAATATA-ATATAATAAAATT
*
3921882 AAATAAAATAATAT
1 AAATAATATAATAT
3921896 TTTTTGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 5 0.15
23 18 0.55
24 10 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATAATATAATATAATAAAATT
Found at i:3926027 original size:2 final size:2
Alignment explanation
Indices: 3926015--3926047 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
3926005 CAAACCTCAA
3926015 AT AT CAT 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
3926048 TAAGTAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3928373 original size:29 final size:29
Alignment explanation
Indices: 3928336--3928392 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3928326 TGACCAAATA
3928336 AAAATTAAATAATAAATAAGTGACTAAAAC
1 AAAATTAAATAATAAATAAGTGAC-AAAAC
3928366 AAAA-TAAATAATAAATAAGTGACAAAA
1 AAAATTAAATAATAAATAAGTGACAAAA
3928393 TAGATAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 4 0.15
29 19 0.70
30 4 0.15
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (29 bp):
AAAATTAAATAATAAATAAGTGACAAAAC
Found at i:3936988 original size:17 final size:17
Alignment explanation
Indices: 3936966--3937001 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3936956 GACAATCATT
3936966 TTTAAACAAATATTATC
1 TTTAAACAAATATTATC
3936983 TTTAAACAAATATTATC
1 TTTAAACAAATATTATC
3937000 TT
1 TT
3937002 ATAATCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAACAAATATTATC
Found at i:3937758 original size:2 final size:2
Alignment explanation
Indices: 3937751--3937801 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
3937741 TTAAGCGCGG
*
3937751 AT AT AT AT AT GT 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 AT AT AT
*
3937792 AA AT AT AT AT
1 AT AT AT AT AT
3937802 TTTATGACCT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3949318 original size:2 final size:2
Alignment explanation
Indices: 3949313--3949345 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3949303 TTATTTTGTT
3949313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3949346 GAATGATTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3956354 original size:14 final size:14
Alignment explanation
Indices: 3956335--3956367 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3956325 ATATATTTTT
3956335 TTAAACGATCAATG
1 TTAAACGATCAATG
3956349 TTAAACGATCAATG
1 TTAAACGATCAATG
3956363 -TAAAC
1 TTAAAC
3956368 AAAACGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (14 bp):
TTAAACGATCAATG
Found at i:3958812 original size:14 final size:16
Alignment explanation
Indices: 3958788--3958819 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3958778 CAAACGGGTG
3958788 TTAGATCAATAAA-AT
1 TTAGATCAATAAATAT
3958803 TTAG-TCAATAAATAT
1 TTAGATCAATAAATAT
3958818 TT
1 TT
3958820 GATAAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
TTAGATCAATAAATAT
Done.