Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 38 of 198
Found at i:11400643 original size:25 final size:26
Alignment explanation
Indices: 11400615--11400673 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
11400605 TTTCTCATCC
**
11400615 CAATTTTA-CCCTAATAATTTTTTGA
1 CAATTTTACCCCTAATAAAATTTTGA
*
11400640 CAATTTTACCCCTGATAAAATTTTGA
1 CAATTTTACCCCTAATAAAATTTTGA
*
11400666 CGATTTTA
1 CAATTTTA
11400674 ATCTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (26 bp):
CAATTTTACCCCTAATAAAATTTTGA
Found at i:11400848 original size:6 final size:6
Alignment explanation
Indices: 11400837--11400872 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
11400827 TGCAAGTGTC
*
11400837 CATTTT CATTTT CATTTT CATTTT CATTTC CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT CATTTT
11400873 TTGGAAACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (6 bp):
CATTTT
Found at i:11404941 original size:14 final size:14
Alignment explanation
Indices: 11404922--11404949 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11404912 TTCGTCATCC
11404922 ACTCAGGATTTAAG
1 ACTCAGGATTTAAG
11404936 ACTCAGGATTTAAG
1 ACTCAGGATTTAAG
11404950 TATGCCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
ACTCAGGATTTAAG
Found at i:11409702 original size:15 final size:15
Alignment explanation
Indices: 11409682--11409714 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
11409672 ATATATATTT
11409682 TTTATA-AAAAATTAA
1 TTTATATAAAAA-TAA
11409697 TTTATATAAAAATAA
1 TTTATATAAAAATAA
11409712 TTT
1 TTT
11409715 GATCTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTATATAAAAATAA
Found at i:11410860 original size:14 final size:15
Alignment explanation
Indices: 11410838--11410914 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
11410828 CAATCAAACA
11410838 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
11410852 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
11410867 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
11410887 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
11410901 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
11410915 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:11410879 original size:20 final size:20
Alignment explanation
Indices: 11410854--11410893 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11410844 AATATTTTCC
*
11410854 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
11410874 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
11410894 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:11410899 original size:34 final size:35
Alignment explanation
Indices: 11410842--11410908 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
11410832 CAAACACCAG
*
11410842 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
11410877 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
11410909 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:11412452 original size:19 final size:18
Alignment explanation
Indices: 11412412--11412459 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
11412402 TTAGAGTTTT
* * *
11412412 TTTTTGTATTTTTATGAT
1 TTTTTATATTTTTAGGAA
11412430 TTTTTATATTTTTAAGGAA
1 TTTTTATATTTTT-AGGAA
11412449 TTTTTAT-TTTT
1 TTTTTATATTTT
11412460 AAAGTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (18 bp):
TTTTTATATTTTTAGGAA
Found at i:11413627 original size:13 final size:14
Alignment explanation
Indices: 11413609--11413637 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
11413599 TTAATTTGTC
11413609 TAAATTTAT-TTTT
1 TAAATTTATATTTT
11413622 TAAATTTATATTTT
1 TAAATTTATATTTT
11413636 TA
1 TA
11413638 TCTAAATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TAAATTTATATTTT
Found at i:11416468 original size:7 final size:7
Alignment explanation
Indices: 11416456--11416495 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
11416446 TAGTCGATTG
11416456 GTATTTA
1 GTATTTA
11416463 GTATTTA
1 GTATTTA
11416470 GTATTTA
1 GTATTTA
11416477 GTATTTA
1 GTATTTA
11416484 GTATTTA
1 GTATTTA
11416491 GTATT
1 GTATT
11416496 ATGTATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:11419109 original size:21 final size:22
Alignment explanation
Indices: 11419083--11419146 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 22
11419073 CTAAACTTAA
*
11419083 AAACCCCAAAACTCT-AACCCT
1 AAACCCCAAAACCCTAAACCCT
*
11419104 AAA-CCCTAAACCCTAAACCCT
1 AAACCCCAAAACCCTAAACCCT
*
11419125 AAA--CCAAAACCCAAAACCCT
1 AAACCCCAAAACCCTAAACCCT
11419145 AA
1 AA
11419147 TAGGAGACAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 26 0.68
21 12 0.32
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.11
Consensus pattern (22 bp):
AAACCCCAAAACCCTAAACCCT
Found at i:11419110 original size:7 final size:7
Alignment explanation
Indices: 11419098--11419146 Score: 73
Period size: 7 Copynumber: 7.1 Consensus size: 7
11419088 CCAAAACTCT
11419098 AACCCTA
1 AACCCTA
11419105 AACCCTA
1 AACCCTA
11419112 AACCCTA
1 AACCCTA
11419119 AACCCTA
1 AACCCTA
*
11419126 AA-CCAA
1 AACCCTA
*
11419132 AACCCAA
1 AACCCTA
11419139 AACCCTA
1 AACCCTA
11419146 A
1 A
11419147 TAGGAGACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
6 5 0.13
7 34 0.87
ACGTcount: A:0.49, C:0.41, G:0.00, T:0.10
Consensus pattern (7 bp):
AACCCTA
Found at i:11419662 original size:20 final size:21
Alignment explanation
Indices: 11419619--11419659 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11419609 AGCACCACCA
11419619 ATTTTTTTAATATATATTTTT
1 ATTTTTTTAATATATATTTTT
11419640 ATTTTTTTAA-ATATTATTTT
1 ATTTTTTTAATATA-TATTTT
11419660 ATTAGTGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTTTTAATATATATTTTT
Found at i:11419843 original size:16 final size:16
Alignment explanation
Indices: 11419822--11419852 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11419812 TCCCTTCCGC
11419822 CACGCCCTCCACACTA
1 CACGCCCTCCACACTA
*
11419838 CACGCCCTGCACACT
1 CACGCCCTCCACACT
11419853 GCATTTTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.55, G:0.10, T:0.13
Consensus pattern (16 bp):
CACGCCCTCCACACTA
Found at i:11420282 original size:108 final size:97
Alignment explanation
Indices: 11420148--11420825 Score: 544
Period size: 103 Copynumber: 6.8 Consensus size: 97
11420138 AAATTATTAG
* * *
11420148 TAATTTATGATTAT-GTTATAATTTGTTTGTTCTTTAGTTTAGTGTTTTGTGAATTTTTATTAAT
1 TAATTTATGATT-TGGTTATAAATTG-TTG-TGTTTAGTTTAGTGTTTTGTGATTTTTTATTAAT
*
11420212 GTAATTTTTTTGTTTTTTTAATTATTTTATAGTTATGTTGTTAA
63 GTAA---TTTT-TTTTTGT--TT-TTTTA-A-TTATGTTGTTAA
11420256 TAATTTATGATTTGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
1 TAATTTATGATTTGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
*
11420321 ATTTTTTTTTGTTTTTTTAATTATTTTGTTAA
66 ATTTTTTTTTGTTTTTTTAATTATGTTGTTAA
*
11420353 TAATTTATGATTAGGTTATAAATTGTTGTGTTTAG-TTAGTGTTTTGTGATTTTTTATTAATGTA
1 TAATTTATGATTTGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
** * * * * *
11420417 A-----AATT-ATTTTATAGTTATTTTGTTAG
66 ATTTTTTTTTGTTTTTTTAATTATGTTGTTAA
* *
11420443 TAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTTTTTTGTGATTTTTTATTAATGT
1 TAATTTATGATTTGGTTATAAATTGTT-GTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGT
*** ** * * * **
11420508 AAAATTTTTAAAAAATAATTTTATAGTTATTTTGTTTG
65 --AATTTTT---TTTTGTTTTTTTAATTATGTTGTTAA
** *
11420546 TAATTTATGATTAAGTTATAAATTGTTAGTGTCTAGTTTAGTGTTTTGTGATTTTTTATTAATGT
1 TAATTTATGATTTGGTTATAAATTGTT-GTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGT
* * * * *
11420611 AAAATTATTTTTTAAAATAATTTTATATAGTTATTTTGTTAG
65 --AATT-TTTTTT----T-GTTTT-TTTAATTATGTTGTTAA
* * * *
11420653 TAATTTATGATTAGGTTATAAATCGTTAGTGTTTAGCTTAGTGTTTTGCGATTTTTTATTAATGT
1 TAATTTATGATTTGGTTATAAATTGTT-GTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGT
**** * * * *
11420718 AATTTTTTAAAAAATTTTTATAGTTATTTTGTTAG
65 AATTTTTT--TTTGTTTTTTTAATTATGTTGTTAA
* * * * * * *
11420753 TAATTTAAGATTAGGTTATAAATTATTATGTTTAGTTTAATATTTTTTGATTTTTTATTAATGTA
1 TAATTTATGATTTGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
*
11420818 AATTTTTT
66 ATTTTTTT
11420826 ATAACGTAAT
Statistics
Matches: 505, Mismatches: 42, Indels: 57
0.84 0.07 0.09
Matches are distributed among these distances:
90 44 0.09
91 10 0.02
92 27 0.05
94 2 0.00
96 30 0.06
97 45 0.09
98 1 0.00
99 43 0.09
100 43 0.09
101 5 0.01
102 9 0.02
103 92 0.18
104 7 0.01
105 5 0.01
106 40 0.08
107 80 0.16
108 22 0.04
ACGTcount: A:0.27, C:0.01, G:0.14, T:0.58
Consensus pattern (97 bp):
TAATTTATGATTTGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGATTTTTTATTAATGTA
ATTTTTTTTTGTTTTTTTAATTATGTTGTTAA
Found at i:11420534 original size:103 final size:103
Alignment explanation
Indices: 11420416--11420848 Score: 606
Period size: 103 Copynumber: 4.2 Consensus size: 103
11420406 TTATTAATGT
*
11420416 AAAATTATTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTT
1 AAAATAATTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTT
*
11420481 TAGTTTTTTGTGATTTTTTATTAATGTAAAATTTTTAA
66 TAGTGTTTTGTGATTTTTTATTAATGTAAAATTTTTAA
* * *
11420519 AAAATAATTTTATAGTTATTTTGTTTGTAATTTATGATTAAGTTATAAATTGTTAGTGTCTAGTT
1 AAAATAATTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTT
**
11420584 TAGTGTTTTGTGATTTTTTATTAATGTAAAATTATTTTTT
66 TAGTGTTTTGTGATTTTTTATTAATGTAAAA-T-TTTTAA
*
11420624 AAAATAATTTTATATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATCGTTAGTGTTTAG
1 AAAATAA-TTT-TATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAG
* * *
11420689 CTTAGTGTTTTGCGATTTTTTATTAATGT-AATTTTTTAA
64 TTTAGTGTTTTGTGATTTTTTATTAATGTAAAATTTTTAA
* *
11420728 AAAAT--TTTTATAGTTATTTTGTTAGTAATTTAAGATTAGGTTATAAATTATTA-TGTTTAGTT
1 AAAATAATTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTT
* * * * *
11420790 TAATATTTTTTGATTTTTTATTAATGTAAATTTTTTAT
66 TAGTGTTTTGTGATTTTTTATTAATGTAAAATTTTTAA
** *
11420828 AACGTAATTTTAT-TTTATTTT
1 AAAATAATTTTATAGTTATTTT
11420849 TATTTATTTG
Statistics
Matches: 295, Mismatches: 28, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
99 31 0.11
100 54 0.18
101 10 0.03
102 6 0.02
103 91 0.31
104 10 0.03
105 12 0.04
106 5 0.02
107 76 0.26
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.56
Consensus pattern (103 bp):
AAAATAATTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTT
TAGTGTTTTGTGATTTTTTATTAATGTAAAATTTTTAA
Found at i:11420708 original size:210 final size:204
Alignment explanation
Indices: 11420426--11420840 Score: 632
Period size: 210 Copynumber: 2.0 Consensus size: 204
11420416 AAAATTATTT
* * *
11420426 TATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTAGTTTTTTG
1 TATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATCGTTAGTGTTTAGCTTAGTGTTTTG
* * *
11420491 TGATTTTTTATTAATGTAAAATTTTTAAAAAATAATTTTATAGTTATTTTGTTTGTAATTTATGA
66 CGATTTTTTATTAATGT-AAATTTTTAAAAAAT--TTTTATAGTTATTTTGTTAGTAATTTAAGA
* * *
11420556 TTAAGTTATAAATTGTTAGTGTCTAGTTTAGTGTTTTGTGATTTTTTATTAATGTAAAATTATTT
128 TTAAGTTATAAATTATTA-TGTCTAGTTTAATATTTTGTGATTTTTTATTAATGT-AAATT-TTT
*
11420621 TTTAAAATAATTTTA
190 TATAAAATAATTTTA
11420636 TATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATCGTTAGTGTTTAGCTTAGTGTTTTG
1 TATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATCGTTAGTGTTTAGCTTAGTGTTTTG
*
11420701 CGATTTTTTATTAATGTAATTTTTTAAAAAATTTTTATAGTTATTTTGTTAGTAATTTAAGATTA
66 CGATTTTTTATTAATGTAAATTTTTAAAAAATTTTTATAGTTATTTTGTTAGTAATTTAAGATTA
* * * *
11420766 GGTTATAAATTATTATGTTTAGTTTAATATTTTTTGATTTTTTATTAATGTAAATTTTTTATAAC
131 AGTTATAAATTATTATGTCTAGTTTAATATTTTGTGATTTTTTATTAATGTAAATTTTTTATAAA
*
11420831 GTAATTTTA
196 ATAATTTTA
11420840 T
1 T
11420841 TTTATTTTTA
Statistics
Matches: 189, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
204 16 0.08
205 5 0.03
206 32 0.17
207 44 0.23
209 14 0.07
210 78 0.41
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.56
Consensus pattern (204 bp):
TATAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATCGTTAGTGTTTAGCTTAGTGTTTTG
CGATTTTTTATTAATGTAAATTTTTAAAAAATTTTTATAGTTATTTTGTTAGTAATTTAAGATTA
AGTTATAAATTATTATGTCTAGTTTAATATTTTGTGATTTTTTATTAATGTAAATTTTTTATAAA
ATAATTTTA
Found at i:11423311 original size:46 final size:43
Alignment explanation
Indices: 11423244--11423477 Score: 239
Period size: 36 Copynumber: 5.6 Consensus size: 43
11423234 TTTGAGTACT
*
11423244 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG---TAGCTACACTTA
*
11423290 TCTGATCAAGTGACAAAGTGAT-A-----AGT-GCTAAACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTAGCTACACTTA
*
11423326 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG---TAGCTACACTTA
11423372 TCTGATCAAGTGACAAAGTGAT-A-----AGT-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTAGCTACACTTA
*
11423408 TCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG--TAGCTACACTTA
*
11423453 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
11423478 ATCATACGTA
Statistics
Matches: 161, Mismatches: 8, Indels: 41
0.77 0.04 0.20
Matches are distributed among these distances:
36 61 0.38
37 4 0.02
40 4 0.02
42 4 0.02
43 12 0.07
44 5 0.03
45 20 0.12
46 51 0.32
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (43 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGTAGCTACACTTA
Found at i:11423381 original size:82 final size:82
Alignment explanation
Indices: 11423244--11423477 Score: 384
Period size: 82 Copynumber: 2.9 Consensus size: 82
11423234 TTTGAGTACT
* *
11423244 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
11423309 GATAAGTGCTAAACTTA
66 GATAAGTGCTAAACTTA
*
11423326 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
*
11423391 GATAAGTGCTACACTTA
66 GATAAGTGCTAAACTTA
* * *
11423408 TCTGATCAAGTGGCAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AGGGAC-AAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
11423470 GATAAGTG
66 GATAAGTG
11423478 ATCATACGTA
Statistics
Matches: 144, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
79 12 0.08
80 5 0.03
81 19 0.13
82 108 0.75
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (82 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGCTAAACTTA
Found at i:11428912 original size:19 final size:19
Alignment explanation
Indices: 11428888--11428943 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
11428878 ATAACCTAAT
11428888 AAAATAACTTTCAAATAAC
1 AAAATAACTTTCAAATAAC
***
11428907 AAAATAA--AAAAATACTAAC
1 AAAATAACTTTCAA-A-TAAC
11428926 AAAATAACTTTCAAATAA
1 AAAATAACTTTCAAATAA
11428944 ATTAAAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
17 2 0.07
18 1 0.04
19 21 0.78
20 1 0.04
21 2 0.07
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATAACTTTCAAATAAC
Found at i:11429111 original size:25 final size:26
Alignment explanation
Indices: 11429083--11429131 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
11429073 AATAGCATTA
* *
11429083 AACTAAACAAAT-AATTTATAATAGT
1 AACTAAAAAAATAAATTTAAAATAGT
11429108 AACTAAAAAAATAAATTTAAAATA
1 AACTAAAAAAATAAATTTAAAATA
11429132 AATTAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (26 bp):
AACTAAAAAAATAAATTTAAAATAGT
Found at i:11429239 original size:18 final size:18
Alignment explanation
Indices: 11429216--11429250 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11429206 ATCCATATCA
* *
11429216 TTCTTTTTTTGTTCTCCT
1 TTCTTTCTTTCTTCTCCT
11429234 TTCTTTCTTTCTTCTCC
1 TTCTTTCTTTCTTCTCC
11429251 CTATCTTCTT
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:0.00, C:0.29, G:0.03, T:0.69
Consensus pattern (18 bp):
TTCTTTCTTTCTTCTCCT
Found at i:11429414 original size:27 final size:27
Alignment explanation
Indices: 11429340--11429415 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
11429330 AAAAATTGAC
*
11429340 CACTGGTGCCGCCTATCAGATAGGGGT
1 CACTAGTGCCGCCTATCAGATAGGGGT
* * *
11429367 CACCACTGGCGCCTA-CTAGATAGGGGT
1 CACTAGTGCCGCCTATC-AGATAGGGGT
11429394 CACTAGTGCCG-CTGATCAGATA
1 CACTAGTGCCGCCT-ATCAGATA
11429416 TGCACCACCC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
26 3 0.08
27 35 0.90
28 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.21
Consensus pattern (27 bp):
CACTAGTGCCGCCTATCAGATAGGGGT
Found at i:11436283 original size:3 final size:3
Alignment explanation
Indices: 11436275--11436312 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
11436265 GGTTTTGGGC
11436275 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
11436313 TTTATCTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:11436319 original size:6 final size:6
Alignment explanation
Indices: 11436278--11436386 Score: 51
Period size: 6 Copynumber: 18.2 Consensus size: 6
11436268 TTTGGGCTCA
* * * * * *
11436278 TCATCA TCATCA TCATCA TCATCA TCATCA TCATCT TTATCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * * * * *
11436326 TCACCT CCATTT TCA-CC TC-TACGT CCATCT TGATCT TAATCT TGATCT
1 TCATCT TCATCT TCATCT TCAT-C-T TCATCT TCATCT TCATCT TCATCT
*
11436374 TTATCT TCATCT T
1 TCATCT TCATCT T
11436387 GTTCTTTCGT
Statistics
Matches: 81, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
5 2 0.02
6 76 0.94
7 2 0.02
8 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:11436379 original size:18 final size:18
Alignment explanation
Indices: 11436352--11436393 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11436342 CTCTACGTCC
*
11436352 ATCTTGATCTTAATCTTG
1 ATCTTTATCTTAATCTTG
*
11436370 ATCTTTATCTTCATCTTG
1 ATCTTTATCTTAATCTTG
*
11436388 TTCTTT
1 ATCTTT
11436394 CGTGTTAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.07, T:0.57
Consensus pattern (18 bp):
ATCTTTATCTTAATCTTG
Found at i:11439844 original size:43 final size:41
Alignment explanation
Indices: 11439795--11439875 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 41
11439785 ATATGATTCG
* *
11439795 TGTAAGACCCTGTCTGGGATAGAGGCATCGATATGTGATAACA
1 TGTAAGACCATATCTGGGATA-AGGCATCG-TATGTGATAACA
* *
11439838 TGTAAGACCATATCTGGGATATGGCATTGTATGTGATA
1 TGTAAGACCATATCTGGGATAAGGCATCGTATGTGATA
11439876 TATGTGCTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 9 0.26
42 6 0.18
43 19 0.56
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (41 bp):
TGTAAGACCATATCTGGGATAAGGCATCGTATGTGATAACA
Found at i:11445964 original size:20 final size:20
Alignment explanation
Indices: 11445931--11446001 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
11445921 GAATAAGCAT
* *
11445931 TGAAAGTAAAGAAATGCAAA
1 TGAAAATAAGGAAATGCAAA
11445951 TGAAAATAAGGAAAT-C--A
1 TGAAAATAAGGAAATGCAAA
11445968 TGAAAGAGT-A--AAATGCAAA
1 TGAAA-A-TAAGGAAATGCAAA
11445987 TGAAAATAAGGAAAT
1 TGAAAATAAGGAAAT
11446002 CATGAAAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
16 4 0.10
17 8 0.20
18 4 0.10
19 8 0.20
20 17 0.41
ACGTcount: A:0.59, C:0.04, G:0.20, T:0.17
Consensus pattern (20 bp):
TGAAAATAAGGAAATGCAAA
Found at i:11445972 original size:17 final size:17
Alignment explanation
Indices: 11445950--11446008 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
11445940 AGAAATGCAA
11445950 ATGAAAATAAGGAAATC
1 ATGAAAATAAGGAAATC
11445967 ATGAAAGAGT-A--AAATGC
1 ATGAAA-A-TAAGGAAAT-C
11445984 AAATGAAAATAAGGAAATC
1 --ATGAAAATAAGGAAATC
11446003 ATGAAA
1 ATGAAA
11446009 GAGTAAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
16 4 0.12
17 14 0.41
18 4 0.12
19 8 0.24
20 4 0.12
ACGTcount: A:0.59, C:0.05, G:0.19, T:0.17
Consensus pattern (17 bp):
ATGAAAATAAGGAAATC
Found at i:11445983 original size:36 final size:36
Alignment explanation
Indices: 11445942--11446016 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
11445932 GAAAGTAAAG
11445942 AAATGCAAATGAAAATAAGGAAATCATGAAAGAGTA
1 AAATGCAAATGAAAATAAGGAAATCATGAAAGAGTA
11445978 AAATGCAAATGAAAATAAGGAAATCATGAAAGAGTA
1 AAATGCAAATGAAAATAAGGAAATCATGAAAGAGTA
11446014 AAA
1 AAA
11446017 CTTGCAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.60, C:0.05, G:0.19, T:0.16
Consensus pattern (36 bp):
AAATGCAAATGAAAATAAGGAAATCATGAAAGAGTA
Found at i:11450417 original size:41 final size:41
Alignment explanation
Indices: 11450315--11450423 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 41
11450305 GAGGTGTGAT
*
11450315 TTCGTGTAAGACCATGTTTGGGACATTGGCACCGATATGAGA
1 TTCGTGTAAGACCATGTCTGGGACATTGGCACCGATAT-AGA
* * *
11450357 TTACGTGTAAGACCTTGTCTAGGACTTTGGCACCG-TATATGA
1 TT-CGTGTAAGACCATGTCTGGGACATTGGCACCGATATA-GA
*
11450399 TTCGTGTAAGACCCTGTCTGGGACA
1 TTCGTGTAAGACCATGTCTGGGACA
11450424 GAGGCATCGA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
41 21 0.36
42 9 0.16
43 28 0.48
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (41 bp):
TTCGTGTAAGACCATGTCTGGGACATTGGCACCGATATAGA
Found at i:11451147 original size:12 final size:12
Alignment explanation
Indices: 11451127--11451172 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
11451117 GACGAGTGAG
11451127 TTATTATTTTAA
1 TTATTATTTTAA
*
11451139 TTATCATTTT-A
1 TTATTATTTTAA
11451150 --ATT-TTTTAA
1 TTATTATTTTAA
11451159 TTATTATTTTAA
1 TTATTATTTTAA
11451171 TT
1 TT
11451173 TTTTCAGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 4 0.14
9 3 0.11
11 4 0.14
12 17 0.61
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATTATTTTAA
Found at i:11451158 original size:20 final size:20
Alignment explanation
Indices: 11451133--11451176 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
11451123 TGAGTTATTA
11451133 TTTTAATTATCATTTTAATT
1 TTTTAATTATCATTTTAATT
*
11451153 TTTTAATTATTATTTTAATT
1 TTTTAATTATCATTTTAATT
11451173 TTTT
1 TTTT
11451177 CAGGACTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTAATTATCATTTTAATT
Found at i:11452372 original size:12 final size:12
Alignment explanation
Indices: 11452355--11452379 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11452345 TCTCCACAGC
11452355 TCGTGTGAGCAA
1 TCGTGTGAGCAA
11452367 TCGTGTGAGCAA
1 TCGTGTGAGCAA
11452379 T
1 T
11452380 GATGTAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (12 bp):
TCGTGTGAGCAA
Found at i:11453460 original size:12 final size:12
Alignment explanation
Indices: 11453443--11453472 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
11453433 TTAGTGAGTT
*
11453443 ACACGGCCTAGC
1 ACACGGCCTAAC
11453455 ACACGGCCTAAC
1 ACACGGCCTAAC
11453467 ACACGG
1 ACACGG
11453473 GCGTGTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.40, G:0.23, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAAC
Found at i:11460908 original size:3 final size:3
Alignment explanation
Indices: 11460900--11460928 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11460890 GCGATTATCC
11460900 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
11460929 CAAGTTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:11467203 original size:27 final size:27
Alignment explanation
Indices: 11467145--11467233 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
11467135 TAATAATATT
*
11467145 AATATAAACTTATAAATATTATAAAAA
1 AATAAAAACTTATAAATATTATAAAAA
*
11467172 AATAAAAACTTATAAATATTATACAAA
1 AATAAAAACTTATAAATATTATAAAAA
* * * *
11467199 TATAAAAA-TATAAAAAAATTATAAAATT
1 AATAAAAACT-TATAAATATTATAAAA-A
11467227 AATAAAA
1 AATAAAA
11467234 CATATTTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
26 1 0.02
27 45 0.87
28 6 0.12
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.30
Consensus pattern (27 bp):
AATAAAAACTTATAAATATTATAAAAA
Found at i:11467207 original size:8 final size:8
Alignment explanation
Indices: 11467145--11467214 Score: 50
Period size: 8 Copynumber: 8.2 Consensus size: 8
11467135 TAATAATATT
11467145 AATATAAA
1 AATATAAA
**
11467153 CTTATAAA
1 AATATAAA
*
11467161 TATTATAAA
1 -AATATAAA
*
11467170 AAAATAAA
1 AATATAAA
11467178 AACTTATAAA
1 AA--TATAAA
* *
11467188 TATTATACA
1 -AATATAAA
11467197 AATATAAA
1 AATATAAA
11467205 AATATAAA
1 AATATAAA
11467213 AA
1 AA
11467215 AATTATAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
8 30 0.62
9 12 0.25
10 5 0.10
11 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (8 bp):
AATATAAA
Found at i:11467224 original size:8 final size:8
Alignment explanation
Indices: 11467147--11467233 Score: 50
Period size: 9 Copynumber: 9.9 Consensus size: 8
11467137 ATAATATTAA
*
11467147 TATAAACT
1 TATAAAAT
11467155 TATAAATAT
1 TATAAA-AT
*
11467164 TATAAAAA
1 TATAAAAT
*
11467172 AATAAAAACT
1 TAT-AAAA-T
11467182 TATAAATAT
1 TATAAA-AT
11467191 TATACAAA-
1 TATA-AAAT
11467199 TATAAAAAT
1 TAT-AAAAT
*
11467208 ATAAAAAAAT
1 -T-ATAAAAT
11467218 TATAAAAT
1 TATAAAAT
11467226 TAATAAAA
1 T-ATAAAA
11467234 CATATTTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
8 22 0.35
9 28 0.45
10 11 0.18
11 1 0.02
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (8 bp):
TATAAAAT
Found at i:11467352 original size:9 final size:9
Alignment explanation
Indices: 11467087--11467354 Score: 98
Period size: 10 Copynumber: 27.7 Consensus size: 9
11467077 TAAAATCATT
11467087 TAAAAATTA
1 TAAAAATTA
*
11467096 TTAAAAATGAA
1 -TAAAAAT-TA
*
11467107 TAAATATTA
1 TAAAAATTA
*
11467116 -AGAATATT-
1 TA-AAAATTA
11467124 TAAAATATATA
1 TAAAA-AT-TA
11467135 TAATAATATTAA
1 TAA-AA-ATT-A
*
11467147 TATAAACTTA
1 TA-AAAATTA
*
11467157 TAAATATTA
1 TAAAAATTA
*
11467166 TAAAAA-AA
1 TAAAAATTA
11467174 TAAAAACTTA
1 TAAAAA-TTA
*
11467184 TAAATATTA
1 TAAAAATTA
*
11467193 TACAAA-TA
1 TAAAAATTA
11467201 TAAAAATATA
1 TAAAAAT-TA
*
11467211 AAAAAATTA
1 TAAAAATTA
11467220 T-AAAATTAA
1 TAAAAATT-A
*
11467229 TAAAACATATT
1 TAAAA-AT-TA
*
11467240 TAAAATATTT
1 TAAAA-ATTA
*
11467250 TAAAATTTTA
1 TAAAA-ATTA
*
11467260 TAAAAATTCT
1 TAAAAATT-A
*
11467270 TAAAAACATA
1 TAAAAA-TTA
* *
11467280 AAAAAATACA
1 TAAAAAT-TA
11467290 TAAAAAATTA
1 T-AAAAATTA
11467300 TAAGAATATT-
1 TAA-AA-ATTA
**
11467310 TGAAATTTTA
1 T-AAAAATTA
11467320 TAAAAATTGA
1 TAAAAATT-A
*
11467330 TATAAATGTA
1 TAAAAAT-TA
11467340 TAAAAATTA
1 TAAAAATTA
11467349 TAAAAA
1 TAAAAA
11467355 AAATCATAAA
Statistics
Matches: 196, Mismatches: 35, Indels: 55
0.69 0.12 0.19
Matches are distributed among these distances:
8 23 0.12
9 50 0.26
10 82 0.42
11 29 0.15
12 11 0.06
13 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:11467678 original size:12 final size:10
Alignment explanation
Indices: 11467640--11467755 Score: 84
Period size: 10 Copynumber: 12.2 Consensus size: 10
11467630 TAATAGTTGG
*
11467640 ATAATTTCTT
1 ATAATTTTTT
* *
11467650 AGATTTTTTT
1 ATAATTTTTT
11467660 ATAATTTTTT
1 ATAATTTTTT
*
11467670 ATAA-TATTT
1 ATAATTTTTT
*
11467679 ATAACTTTTT
1 ATAATTTTTT
* *
11467689 ATAACTTGTT
1 ATAATTTTTT
11467699 ATAA-TTTTT
1 ATAATTTTTT
* *
11467708 ATAAGTTTAT
1 ATAATTTTTT
11467718 ATCAA--TTTT
1 AT-AATTTTTT
*
11467727 -TAATTTTTA
1 ATAATTTTTT
11467736 ATAA-TTTTT
1 ATAATTTTTT
11467745 AT-ATTTTTT
1 ATAATTTTTT
11467754 AT
1 AT
11467756 GTTAGCTCGA
Statistics
Matches: 86, Mismatches: 13, Indels: 15
0.75 0.11 0.13
Matches are distributed among these distances:
7 2 0.02
8 2 0.02
9 35 0.41
10 45 0.52
11 2 0.02
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:11467681 original size:19 final size:18
Alignment explanation
Indices: 11467656--11467747 Score: 82
Period size: 19 Copynumber: 4.9 Consensus size: 18
11467646 TCTTAGATTT
11467656 TTTTATAATTTTTTATAA-
1 TTTTATAA-TTTTTATAAC
11467674 TATTTATAACTTTTTATAAC
1 T-TTTATAA-TTTTTATAAC
*
11467694 TTGTTATAATTTTTATAAG
1 TT-TTATAATTTTTATAAC
*
11467713 TTTATATCAA-TTTT-TAAT
1 TTT-TAT-AATTTTTATAAC
11467731 TTTTAATAATTTTTATA
1 TTTT-ATAATTTTTATA
11467748 TTTTTTATGT
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
17 3 0.05
18 14 0.22
19 37 0.59
20 9 0.14
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTATAATTTTTATAAC
Found at i:11467688 original size:29 final size:28
Alignment explanation
Indices: 11467655--11467755 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 28
11467645 TTCTTAGATT
*
11467655 TTTTTATAATTTTTTATAATATTTATAA
1 TTTTTATAATTTTTTATAATTTTTATAA
* *
11467683 CTTTTTATAACTTGTTATAATTTTTATAA
1 -TTTTTATAATTTTTTATAATTTTTATAA
*
11467712 GTTTATATCAA--TTTT-TAATTTTTAATAA
1 -TTTTTAT-AATTTTTTATAATTTTT-ATAA
11467740 TTTTTAT-ATTTTTTAT
1 TTTTTATAATTTTTTAT
11467756 GTTAGCTCGA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
25 1 0.02
27 18 0.30
28 8 0.13
29 31 0.52
30 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTTATAATTTTTTATAATTTTTATAA
Found at i:11467754 original size:19 final size:18
Alignment explanation
Indices: 11467640--11467752 Score: 70
Period size: 19 Copynumber: 5.9 Consensus size: 18
11467630 TAATAGTTGG
* *
11467640 ATAATTTCTTAGATTTTTTT
1 ATAATTT-TTATA-TTTTTA
*
11467660 ATAATTTTTTATAATATTT-
1 ATAA-TTTTTAT-ATTTTTA
*
11467679 ATAACTTTTTATAACTTGTT-
1 ATAA-TTTTTAT-A-TTTTTA
**
11467699 ATAATTTTTATAAGTTTA
1 ATAATTTTTATATTTTTA
11467717 TATCAATTTTTA-ATTTTTA
1 -AT-AATTTTTATATTTTTA
11467736 ATAATTTTTATATTTTT
1 ATAATTTTTATATTTTT
11467753 TATGTTAGCT
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
17 10 0.13
18 9 0.12
19 27 0.36
20 26 0.34
21 4 0.05
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (18 bp):
ATAATTTTTATATTTTTA
Found at i:11468019 original size:38 final size:38
Alignment explanation
Indices: 11467958--11468031 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
11467948 AGGACAATGT
11467958 TTAACATTACAATCTCCCTTAAGATTTCTACCCAAAATC
1 TTAACATTACAATCT-CCTTAAGATTTCTACCCAAAATC
* *
11467997 TTAATATTACAAATCT-CTTAAGATTTCTACTCAAA
1 TTAACATTAC-AATCTCCTTAAGATTTCTACCCAAA
11468032 CCTTAAGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
38 18 0.56
39 9 0.28
40 5 0.16
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (38 bp):
TTAACATTACAATCTCCTTAAGATTTCTACCCAAAATC
Found at i:11469409 original size:30 final size:30
Alignment explanation
Indices: 11469373--11469430 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
11469363 ACGAGCTTTG
*
11469373 GGGCAAAAGTGTAAATATGTAAAAGTTTAA
1 GGGCAAAAGTGTAAATATGAAAAAGTTTAA
* * *
11469403 GGGCAAAATTGTAATTTTGAAAAAGTTT
1 GGGCAAAAGTGTAAATATGAAAAAGTTT
11469431 GAGTCAATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.31
Consensus pattern (30 bp):
GGGCAAAAGTGTAAATATGAAAAAGTTTAA
Found at i:11469628 original size:22 final size:22
Alignment explanation
Indices: 11469600--11469650 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
11469590 CTAATAACAA
11469600 TATATTTTTATAAATTTTGAAT
1 TATATTTTTATAAATTTTGAAT
11469622 TATATTTTTATAAATTTTGAAT
1 TATATTTTTATAAATTTTGAAT
11469644 TATATTT
1 TATATTT
11469651 GATATGAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TATATTTTTATAAATTTTGAAT
Found at i:11469895 original size:23 final size:23
Alignment explanation
Indices: 11469865--11469984 Score: 170
Period size: 23 Copynumber: 5.2 Consensus size: 23
11469855 ATGTTATTGA
11469865 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
* *
11469888 TCAATGGTAGCTACGGCTAC-TT
1 TCAGTGGTAGCTTCGGCTACATT
11469910 ATCAGTGGTAGCTTCGGCTACATT
1 -TCAGTGGTAGCTTCGGCTACATT
* * *
11469934 TCAGTGGTAGCTACGGCTACGTA
1 TCAGTGGTAGCTTCGGCTACATT
*
11469957 TCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
11469980 TCAGT
1 TCAGT
11469985 ATGGCACTTA
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
22 2 0.02
23 82 0.95
24 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:11469984 original size:46 final size:46
Alignment explanation
Indices: 11469864--11469984 Score: 215
Period size: 46 Copynumber: 2.6 Consensus size: 46
11469854 AATGTTATTG
* *
11469864 ATCAGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGGCTACTT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACGT
11469910 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACGT
*
11469956 ATCAGTGGTAGCTTCGGCTACATATCAGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGT
11469985 ATGGCACTTA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACGT
Found at i:11470977 original size:45 final size:45
Alignment explanation
Indices: 11470926--11471020 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
11470916 TTTCAATTAG
*
11470926 TTATTATGACTTGAATTGTAAATTCATATGGATGAAACCAAACAA
1 TTATTATGAATTGAATTGTAAATTCATATGGATGAAACCAAACAA
11470971 TTATTATGAATTGAATTGTAAATTCATATGGATGAAACCAAACAA
1 TTATTATGAATTGAATTGTAAATTCATATGGATGAAACCAAACAA
11471016 TTATT
1 TTATT
11471021 TGTTAGTATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (45 bp):
TTATTATGAATTGAATTGTAAATTCATATGGATGAAACCAAACAA
Found at i:11478110 original size:18 final size:19
Alignment explanation
Indices: 11478066--11478111 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
11478056 TTTTTAAAAG
11478066 AAAAAGAAAGAAAAAGATAA
1 AAAAAG-AAGAAAAAGATAA
*
11478086 AAGAAGAAG-AAAAGA-AGA
1 AAAAAGAAGAAAAAGATA-A
11478104 AAAAAGAA
1 AAAAAGAA
11478112 AAATGAGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 3 0.13
20 5 0.22
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAAAGAAGAAAAAGATAA
Found at i:11479518 original size:89 final size:90
Alignment explanation
Indices: 11479333--11479955 Score: 668
Period size: 89 Copynumber: 7.0 Consensus size: 90
11479323 AGATAGCAGG
** * * * *
11479333 TCTTGCCTTCCTGTACTGACAGCAAATCAGA-TCGAAGACACCAG-TCTTGCTTTCCTGTACTGA
1 TCTTGCCTTCCTGTACTGACAGCGGAGCAGACT-GAAGATAGCAGATCTTGCCTTCCTGTACTGA
* * * *
11479396 CAGTGAAGCAGACTGAAGATAACAGA
65 CAGCGAAGCAGATTGAAGACACCAGA
* * *
11479422 TCTTGCCTTCCTGTACTGACAACGGAGCAGACTGAAGATAGTAGATCTTGCCTTCCTGTATTGAC
1 TCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
11479487 AGCGAAGCAGATTGAAGACACCAG-
66 AGCGAAGCAGATTGAAGACACCAGA
* * * * * *
11479511 CCTTGCCTTCCTATATTGACAACGGAGCAGACTAAAGATAGTAGATCTTGCCTTCCTGTACTGAC
1 TCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
* * *
11479576 AACGAAGCAGATCGAAGACACTAG-
66 AGCGAAGCAGATTGAAGACACCAGA
* *
11479600 TTTTGCCTTCCTGTACTAACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
1 TCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
* * * ** *
11479665 AACGAAGTAGACTGAAGGGAGCAGA
66 AGCGAAGCAGATTGAAGACACCAGA
* * * * * * *
11479690 TCTTGCCTTTCTATACTGACAGCGAAGCAGA-TCGAAGACACCAG-CCTTGCCTTCTTGTACTGA
1 TCTTGCCTTCCTGTACTGACAGCGGAGCAGACT-GAAGATAGCAGATCTTGCCTTCCTGTACTGA
* * ** *
11479753 CAGCGGAGCAGACTGAAGGTAGCAGA
65 CAGCGAAGCAGATTGAAGACACCAGA
* * *
11479779 TCTTGTCTTCCTGTACTGACAGCGGAGCAAACTGAAGATAACAGATCTTGCCTTCCTGTACTGAC
1 TCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
*
11479844 AGCGAAGCCA-ATCGAAGACACCA-A
66 AGCGAAG-CAGATTGAAGACACCAGA
* * * * * * * *
11479868 CCTCGCCTTCTTGTTCTGACAGTGGAGCAGAATGAAGATAGTAGATCTTGCTTTCCTGTACTGAC
1 TCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
*
11479933 AGCGAAGCAGATCGAAGACACCA
66 AGCGAAGCAGATTGAAGACACCA
11479956 TAGTTTGAGC
Statistics
Matches: 451, Mismatches: 75, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
88 2 0.00
89 340 0.75
90 107 0.24
91 2 0.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (90 bp):
TCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGAC
AGCGAAGCAGATTGAAGACACCAGA
Found at i:11479712 original size:223 final size:222
Alignment explanation
Indices: 11479322--11479955 Score: 810
Period size: 223 Copynumber: 2.8 Consensus size: 222
11479312 CAGATCAGTG
* * * *
11479322 AAGATAGCAGGTCTTGCCTTCCTGTACTGACAGCAAATCAGATCGAAGACACCAGTCTTGCTTTC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACA-CAGTCTTGCCTTC
*
11479387 CTGTACTGACAGTGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGGAGCAG
65 CTGTACTGACAGCGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGGAGCAG
* * *
11479452 ACTGAAGATAGTAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGATTGAAGACACCAGCCTTGC
130 ACTGAAGATAGTAGATCTTGCCTTTCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
*
11479517 CTTCCTATATTGACAACGGAGCAGACTA
195 CTTCCTATACTGACAACGGAGCAGACTA
* * *
11479545 AAGATAGTAGATCTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACACTAGTTTTGCCTTC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACAC-AGTCTTGCCTTC
* * * * *
11479610 CTGTACTAACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAACGAAGTAG
65 CTGTACTGACAGCGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGGAGCAG
** * *
11479675 ACTGAAGGGAGCAGATCTTGCCTTTCTATACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
130 ACTGAAGATAGTAGATCTTGCCTTTCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
* * * *
11479740 CTTCTTGTACTGACAGCGGAGCAGACTG
195 CTTCCTATACTGACAACGGAGCAGACTA
* * * * *
11479768 AAGGTAGCAGATCTTGTCTTCCTGTACTGACAGCGGAGCA-AACTGAAGATAACAGATCTTGCCT
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC-GAAGA-CACAG-TCTTGCCT
* * * * * * **
11479832 TCCTGTACTGACAGCGAAGCCA-A-TCGAAGACACCA-ACCTCGCCTTCTTGTTCTGACAGTGGA
63 TCCTGTACTGACAGCGAAG-CAGACT-GAAGATAACAGATCTTGCCTTCCTGTACTGACAACGGA
*
11479894 GCAGAATGAAGATAGTAGATCTTG-CTTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCA
126 GCAGACTGAAGATAGTAGATCTTGCCTTT-CTGTACTGACAGCGAAGCAGATCGAAGACACCA
11479956 TAGTTTGAGC
Statistics
Matches: 354, Mismatches: 50, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
222 7 0.02
223 310 0.88
224 35 0.10
225 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (222 bp):
AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACAGTCTTGCCTTCC
TGTACTGACAGCGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGGAGCAGA
CTGAAGATAGTAGATCTTGCCTTTCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCC
TTCCTATACTGACAACGGAGCAGACTA
Found at i:11479950 original size:134 final size:134
Alignment explanation
Indices: 11479334--11479943 Score: 674
Period size: 134 Copynumber: 4.6 Consensus size: 134
11479324 GATAGCAGGT
** * * *
11479334 CTTGCCTTCCTGTACTGACAGCAAATCAGA-TCGAAGACACCAG-TCTTGCTTTCCTGTACTGAC
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACT-GAAGATAGCAGATCTTGCTTTCCTGTACTGAC
* * *
11479397 AGTGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGGAGCAGA-CTGAAGAT
65 AGCGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGAAGCAGATC-GAAGAC
** *
11479461 AGTAGAT
129 ACCA-AC
* * * * * * * * *
11479468 CTTGCCTTCCTGTATTGACAGCGAAGCAGATTGAAGACACCAG-CCTTGCCTTCCTATATTGACA
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCTTTCCTGTACTGACA
* * * **
11479532 ACGGAGCAGACTAAAGATAGTAGATCTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACAC
66 GCGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACAC
* **
11479597 TAGT
131 CAAC
* * *
11479601 TTTGCCTTCCTGTACTAACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACA
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCTTTCCTGTACTGACA
* * ** * * * *
11479666 ACGAAGTAGACTGAAGGGAGCAGATCTTGCCTTTCTATACTGACAGCGAAGCAGATCGAAGACAC
66 GCGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACAC
*
11479731 CAGC
131 CAAC
* *
11479735 CTTGCCTTCTTGTACTGACAGCGGAGCAGACTGAAGGTAGCAGATCTTG-TCTTCCTGTACTGAC
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCT-TTCCTGTACTGAC
* * *
11479799 AGCGGAGCAAACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAGCGAAGCCA-ATCGAAGAC
65 AGCGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGAAG-CAGATCGAAGAC
11479863 ACCAAC
129 ACCAAC
* * * * * *
11479869 CTCGCCTTCTTGTTCTGACAGTGGAGCAGAATGAAGATAGTAGATCTTGCTTTCCTGTACTGACA
1 CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCTTTCCTGTACTGACA
11479934 GCGAAGCAGA
66 GCGAAGCAGA
11479944 TCGAAGACAC
Statistics
Matches: 409, Mismatches: 61, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
133 37 0.09
134 367 0.90
135 5 0.01
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (134 bp):
CTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCTTTCCTGTACTGACA
GCGAAGCAGACTGAAGATAACAGATCTTGCCTTCCTGTACTGACAACGAAGCAGATCGAAGACAC
CAAC
Found at i:11480039 original size:44 final size:44
Alignment explanation
Indices: 11479989--11480203 Score: 227
Period size: 44 Copynumber: 4.8 Consensus size: 44
11479979 GATAGCAGAC
*
11479989 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAGT
* * * * **
11480033 CTTATCTCCCTAAAGTTGCAGTAGAGCAGACT-AAAGATAGCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAA-TTA-CAAGT
* * * *
11480078 CTTATCTCTCTGAATTTGCAGTAGAGCAGGTTGAAGA-TACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA-ATTACAAGT
* *
11480122 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAGT
* * * *
11480166 CCTATCTCCCTGAAGTTTACAGTGGAGCGGATTAAAAT
1 CTTATCTCCCTGAAG-TTGCAGTGGAGCAGATTGAAAT
11480204 GATAGATTTT
Statistics
Matches: 140, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
43 3 0.02
44 84 0.60
45 50 0.36
46 2 0.01
47 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAGT
Found at i:11480119 original size:89 final size:89
Alignment explanation
Indices: 11479968--11480151 Score: 289
Period size: 89 Copynumber: 2.1 Consensus size: 89
11479958 GTTTGAGCAA
* * *
11479968 AGCAGATTAAAGATAGCAGACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACAAGT
1 AGCAGACTAAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAATTACAAGT
11480033 CTTATCTCCCTAAAGTTGCAGTAG
66 CTTATCTCCCTAAAGTTGCAGTAG
* *
11480057 AGCAGACTAAAGATAGCAAACCTTATCTCTCTGAATTTGCAGTAGAGCAGGTTGAAGA-TACAAG
1 AGCAGACTAAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAA-ATTACAAG
* *
11480121 TCTTATCTCCCTGAAGTTGCAGTGG
65 TCTTATCTCCCTAAAGTTGCAGTAG
11480146 AGCAGA
1 AGCAGA
11480152 TTGAAGTTAC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 86 0.99
90 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (89 bp):
AGCAGACTAAAGATAGCAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAATTACAAGT
CTTATCTCCCTAAAGTTGCAGTAG
Found at i:11480217 original size:45 final size:45
Alignment explanation
Indices: 11479989--11480227 Score: 150
Period size: 44 Copynumber: 5.4 Consensus size: 45
11479979 GATAGCAGAC
* * * * *
11479989 CTTATCTCCCTGAAG-TTGCAGTGGAGCAGGTTGAAATTACAAGT
1 CTTATCTCCCTGAAGTTTACAGTGGAGCAGATTAAAATGACTAGT
* * * * * **
11480033 CTTATCTCCCTAAAG-TTGCAGTAGAGCAGACTAAAGAT-AGCAAAC
1 CTTATCTCCCTGAAGTTTACAGTGGAGCAGATTAAA-ATGA-CTAGT
* * * * * *
11480078 CTTATCTCTCTGAA-TTTGCAGTAGAGCAGGTTGAAGAT-ACAAGT
1 CTTATCTCCCTGAAGTTTACAGTGGAGCAGATT-AAAATGACTAGT
* * * *
11480122 CTTATCTCCCTGAAG-TTGCAGTGGAGCAGATTGAAGTTACTAGT
1 CTTATCTCCCTGAAGTTTACAGTGGAGCAGATTAAAATGACTAGT
* *
11480166 CCTATCTCCCTGAAGTTTACAGTGGAGCGGATTAAAATGA-TAGAT
1 CTTATCTCCCTGAAGTTTACAGTGGAGCAGATTAAAATGACTAG-T
* * *
11480211 TTTATCTCTCTAAAGTT
1 CTTATCTCCCTGAAGTT
11480228 GTACTAGAGC
Statistics
Matches: 156, Mismatches: 31, Indels: 15
0.77 0.15 0.07
Matches are distributed among these distances:
43 2 0.01
44 84 0.54
45 68 0.44
46 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (45 bp):
CTTATCTCCCTGAAGTTTACAGTGGAGCAGATTAAAATGACTAGT
Found at i:11480236 original size:133 final size:131
Alignment explanation
Indices: 11479989--11480239 Score: 315
Period size: 133 Copynumber: 1.9 Consensus size: 131
11479979 GATAGCAGAC
* * *
11479989 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATTACAAGTCTTATCTCCCTAAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAGTCCTATCTCCCTAAAGTTACAG
* * *
11480054 TAGAGCAGACTAAAGATAGCAAACCTTATCTCTCTGAATTTGCAGTAGAGCAGGTTGAAGATACA
66 TAGAGCAGACTAAAGATAG--AACCTTATCTCTCTAAAGTTGCACTAGAGCAGGTTGAAGATACA
11480119 AGT
129 AGT
* * *
11480122 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTACTAGTCCTATCTCCCTGAAGTTTACA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAGTCCTATCTCCCTAAAG-TTACA
* * * ** *
11480187 GTGGAGCGGATTAAAATGATAG-ATTTTATCTCTCTAAAGTTGTACTAGAGCAG
65 GTAGAGCAGACT-AAA-GATAGAACCTTATCTCTCTAAAGTTGCACTAGAGCAG
11480240 ATCACACCAT
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
133 79 0.79
134 13 0.13
135 3 0.03
136 5 0.05
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (131 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAATTACAAGTCCTATCTCCCTAAAGTTACAG
TAGAGCAGACTAAAGATAGAACCTTATCTCTCTAAAGTTGCACTAGAGCAGGTTGAAGATACAAG
T
Found at i:11480425 original size:131 final size:131
Alignment explanation
Indices: 11480250--11480503 Score: 348
Period size: 131 Copynumber: 1.9 Consensus size: 131
11480240 ATCACACCAT
*
11480250 AACCAGTCCTATCTCCCTAAGCAGCAATGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAG
1 AACCAATCCTATCTCCCTAA-CAGCAATGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAG
* * ***
11480315 TAGTAGCGGAGCAGATTGTGGACGGCGAATCTTATCTTCCCAAAGTAGTAGAGAAGCAAATTTAG
65 CAGTAGCGGAGCAGACTAAAGACGGCGAATCTTATCTTCCCAAAGTAGTAGAGAAGCAAATTTAG
11480380 GC
130 GC
* * *
11480382 AACCAATCCTATCTCCCTGAA-AGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTTTCCCTAAG
1 AACCAATCCTATCTCCCT-AACAGCAATGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAG
* * * * * *
11480446 CAGTAGTGGAGCAGACTAAAGATGGTGAATCTTATCTTCTCAAGGTAGTAGGGAAGCA
65 CAGTAGCGGAGCAGACTAAAGACGGCGAATCTTATCTTCCCAAAGTAGTAGAGAAGCA
11480504 GACTAAAACC
Statistics
Matches: 106, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
131 87 0.82
132 17 0.16
133 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (131 bp):
AACCAATCCTATCTCCCTAACAGCAATGGAGTAGGTTGAAGATTGCAGATCCTATCTCCCTAAGC
AGTAGCGGAGCAGACTAAAGACGGCGAATCTTATCTTCCCAAAGTAGTAGAGAAGCAAATTTAGG
C
Found at i:11481951 original size:3 final size:3
Alignment explanation
Indices: 11481937--11481975 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
11481927 AATTTAGTAC
*
11481937 TAT TAT TGT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
11481976 TACTCATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11483334 original size:11 final size:10
Alignment explanation
Indices: 11483300--11483467 Score: 55
Period size: 10 Copynumber: 17.8 Consensus size: 10
11483290 TTAACAAATT
*
11483300 ATAATTGTTA
1 ATAATTTTTA
* * *
11483310 CTATTTTTTT
1 ATAATTTTTA
11483320 ATAAGTTTTTA
1 ATAA-TTTTTA
11483331 ATAATTTTTA
1 ATAATTTTTA
*
11483341 TACAATTTTATA
1 -ATAATTTT-TA
*
11483353 AT-ATTTATA
1 ATAATTTTTA
11483362 AT-ATATTTTA
1 ATAAT-TTTTA
*
11483372 TTAATTTTATA
1 ATAATTTT-TA
*
11483383 A-AA--ATT-
1 ATAATTTTTA
11483389 ATAATTTTT-
1 ATAATTTTTA
11483398 AT-ATTTTT-
1 ATAATTTTTA
*
11483406 ATAATATTT-
1 ATAATTTTTA
11483415 ATAAGTTTTT-
1 ATAA-TTTTTA
11483425 AT--TTTTT-
1 ATAATTTTTA
*
11483432 ATAA-ATTTA
1 ATAATTTTTA
*
11483441 TATCATTTTTA
1 -ATAATTTTTA
11483452 AT-ATTTTTA
1 ATAATTTTTA
11483461 AT-ATTTT
1 ATAATTTT
11483468 CAATTTTCAA
Statistics
Matches: 122, Mismatches: 20, Indels: 33
0.70 0.11 0.19
Matches are distributed among these distances:
6 1 0.01
7 10 0.08
8 12 0.10
9 33 0.27
10 39 0.32
11 25 0.20
12 2 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:11483351 original size:30 final size:30
Alignment explanation
Indices: 11483316--11483418 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 30
11483306 GTTACTATTT
11483316 TTTTATAAGT-TTT-TAATA-ATTTTTATACAA
1 TTTTATAA-TATTTATAATATA-TTTTAT-CAA
*
11483346 TTTTATAATATTTATAATATATTTTATTAA
1 TTTTATAATATTTATAATATATTTTATCAA
* * *
11483376 TTTTATAAAAATTAT-A-AT-TTTTAT-AT
1 TTTTATAATATTTATAATATATTTTATCAA
11483402 TTTTATAATATTTATAA
1 TTTTATAATATTTATAA
11483419 GTTTTTATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
26 14 0.22
27 7 0.11
28 2 0.03
29 2 0.03
30 26 0.41
31 11 0.17
32 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTTATAATATTTATAATATATTTTATCAA
Found at i:11483399 original size:9 final size:9
Alignment explanation
Indices: 11483315--11483460 Score: 95
Period size: 9 Copynumber: 15.7 Consensus size: 9
11483305 TGTTACTATT
11483315 TTTTTATAA
1 TTTTTATAA
11483324 GTTTTTAATAA
1 -TTTTT-ATAA
11483335 TTTTTATACA
1 TTTTTATA-A
*
11483345 ATTTTATAA
1 TTTTTATAA
*
11483354 TATTTATAATA
1 TTTTTAT-A-A
11483365 TATTTTATTAA
1 T-TTTTA-TAA
11483376 -TTTTATAA
1 TTTTTATAA
***
11483384 AAATTATAA
1 TTTTTATAA
11483393 TTTTTAT-A
1 TTTTTATAA
11483401 TTTTTATAA
1 TTTTTATAA
*
11483410 TATTTATAA
1 TTTTTATAA
11483419 GTTTTTAT--
1 -TTTTTATAA
11483427 TTTTTATAAA
1 TTTTTAT-AA
* *
11483437 TTTATATCA
1 TTTTTATAA
11483446 TTTTTA-ATA
1 TTTTTATA-A
11483455 TTTTTA
1 TTTTTA
11483461 ATATTTTCAA
Statistics
Matches: 108, Mismatches: 15, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
7 7 0.06
8 11 0.10
9 46 0.43
10 31 0.29
11 7 0.06
12 5 0.05
13 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11483405 original size:26 final size:26
Alignment explanation
Indices: 11483393--11483460 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 26
11483383 AAAATTATAA
*
11483393 TTTTTATATTTTTATAATATTTATAAGT
1 TTTT-ATATTTTTATAAAATTTATAA-T
11483421 TTTTAT-TTTTTAT-AAATTTATATCAT
1 TTTTATATTTTTATAAAATTTATA--AT
11483447 TTTTAATATTTTTA
1 TTTT-ATATTTTTA
11483461 ATATTTTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 8 0.23
26 12 0.34
27 5 0.14
28 10 0.29
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (26 bp):
TTTTATATTTTTATAAAATTTATAAT
Found at i:11483464 original size:21 final size:20
Alignment explanation
Indices: 11483440--11483524 Score: 57
Period size: 21 Copynumber: 4.0 Consensus size: 20
11483430 TTATAAATTT
*
11483440 ATATCATTTTTAATATTTTTA
1 ATATCAATTTTAA-ATTTTTA
*
11483461 ATATTTTCAATTTTCAATTTTTA
1 ATA---TCAATTTTAAATTTTTA
* *
11483484 ATTTTCAATTTTCAATTTTT-
1 A-TATCAATTTTAAATTTTTA
11483504 ATAT-AATTTATAATATTTTTA
1 ATATCAATTT-TAA-ATTTTTA
11483525 TAAGAAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
18 5 0.10
19 4 0.08
20 7 0.13
21 19 0.37
23 8 0.15
24 9 0.17
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATCAATTTTAAATTTTTA
Found at i:11483475 original size:7 final size:7
Alignment explanation
Indices: 11483463--11483502 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
11483453 TATTTTTAAT
11483463 ATTTTCA
1 ATTTTCA
11483470 ATTTTCA
1 ATTTTCA
*
11483477 ATTTTTA
1 ATTTTCA
11483484 ATTTTCA
1 ATTTTCA
11483491 ATTTTCA
1 ATTTTCA
11483498 ATTTT
1 ATTTT
11483503 TATATAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTCA
Found at i:11484011 original size:75 final size:76
Alignment explanation
Indices: 11483923--11484065 Score: 234
Period size: 76 Copynumber: 1.9 Consensus size: 76
11483913 ACTATTAAGG
* *
11483923 ACATTAAATTAATAATTAAATATAA-AAAACTTTTAAATTATTTTATTTTAATGAAATTATTAAA
1 ACATTAAACTAATAATTAAATATAACAAAACTTTTAAATTATTTCATTTTAATGAAATTATTAAA
11483987 AATATGTCAAA
66 AATATGTCAAA
* * *
11483998 ACATTAAACTAATAATTTAATATAACAAAAGTTTTAAATTATTTCATTTTTATGAAATTATTAAA
1 ACATTAAACTAATAATTAAATATAACAAAACTTTTAAATTATTTCATTTTAATGAAATTATTAAA
11484063 AAT
66 AAT
11484066 GTCCAATTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
75 23 0.37
76 39 0.63
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (76 bp):
ACATTAAACTAATAATTAAATATAACAAAACTTTTAAATTATTTCATTTTAATGAAATTATTAAA
AATATGTCAAA
Found at i:11498348 original size:11 final size:11
Alignment explanation
Indices: 11498328--11498373 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
11498318 TAGTTTTAGG
11498328 TTTA-GTTTTC
1 TTTAGGTTTTC
*
11498338 TCTAGGTTTTC
1 TTTAGGTTTTC
*
11498349 TTTAGTTTTTC
1 TTTAGGTTTTC
*
11498360 TTTAGTTTTTC
1 TTTAGGTTTTC
11498371 TTT
1 TTT
11498374 GCACTTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 3 0.09
11 29 0.91
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.70
Consensus pattern (11 bp):
TTTAGGTTTTC
Found at i:11498353 original size:21 final size:22
Alignment explanation
Indices: 11498328--11498373 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
11498318 TAGTTTTAGG
11498328 TTTAG-TTTTCTCTAGGTTTTC
1 TTTAGTTTTTCTCTAGGTTTTC
* *
11498349 TTTAGTTTTTCTTTAGTTTTTC
1 TTTAGTTTTTCTCTAGGTTTTC
11498371 TTT
1 TTT
11498374 GCACTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.70
Consensus pattern (22 bp):
TTTAGTTTTTCTCTAGGTTTTC
Found at i:11499608 original size:35 final size:35
Alignment explanation
Indices: 11499562--11499633 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
11499552 TTAACTTAGA
11499562 TTTATTAAAACTATGTTCATACTATTACGAATAAT
1 TTTATTAAAACTATGTTCATACTATTACGAATAAT
*
11499597 TTTATTAAAACTATGTTCATACTGTTACGAATAAT
1 TTTATTAAAACTATGTTCATACTATTACGAATAAT
11499632 TT
1 TT
11499634 CATGGCAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTATTAAAACTATGTTCATACTATTACGAATAAT
Found at i:11502823 original size:18 final size:18
Alignment explanation
Indices: 11502790--11502837 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
11502780 ATTCACCTAA
*
11502790 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
* *
11502809 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
11502827 ACCCAACCCAA
1 ACCCAACCCAA
11502838 TCATAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.42, C:0.46, G:0.02, T:0.10
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:11502830 original size:13 final size:13
Alignment explanation
Indices: 11502814--11502838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11502804 CAAGTATCCA
11502814 ACCCAACCCAATT
1 ACCCAACCCAATT
11502827 ACCCAACCCAAT
1 ACCCAACCCAAT
11502839 CATAAAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:11503152 original size:9 final size:9
Alignment explanation
Indices: 11503138--11503175 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
11503128 GTAGTGATTC
11503138 AATTCGGTT
1 AATTCGGTT
11503147 AATTCGGTT
1 AATTCGGTT
*
11503156 AATTCGGGT
1 AATTCGGTT
11503165 AATTCGGTT
1 AATTCGGTT
11503174 AA
1 AA
11503176 ATGCGTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:11503185 original size:18 final size:18
Alignment explanation
Indices: 11503142--11503186 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
11503132 TGATTCAATT
*
11503142 CGGTTAATTCGGTTAATT
1 CGGTTAATTCGGTTAATG
*
11503160 CGGGTAATTCGGTTAAATG
1 CGGTTAATTCGGTT-AATG
11503179 C-GTTAATT
1 CGGTTAATT
11503187 TTAACCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.40
Consensus pattern (18 bp):
CGGTTAATTCGGTTAATG
Found at i:11517986 original size:42 final size:42
Alignment explanation
Indices: 11517901--11517985 Score: 111
Period size: 41 Copynumber: 2.0 Consensus size: 42
11517891 CAAAAAAATA
* *
11517901 TTCAAAAATTCCAAAAATATTTTCCATTTTTATTTTTAATTT
1 TTCAAAAATTCCAAAAATATTTTCCACTTTCATTTTTAATTT
* *
11517943 TTCAAAAA-TCCAAAAATATTTAT-TACTTTCATTTTTATTTT
1 TTCAAAAATTCCAAAAATATTT-TCCACTTTCATTTTTAATTT
11517984 TT
1 TT
11517986 TTATTGCATG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 29 0.76
42 9 0.24
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (42 bp):
TTCAAAAATTCCAAAAATATTTTCCACTTTCATTTTTAATTT
Found at i:11524848 original size:95 final size:95
Alignment explanation
Indices: 11524714--11524891 Score: 277
Period size: 95 Copynumber: 1.9 Consensus size: 95
11524704 TCAATATATA
* * * * * *
11524714 TTCATAGTTGATTATAATGACTCATTAATCTAAGAAAGCAAATTAAAATTGAATTATAGAAGCAT
1 TTCATACTTGATTACAATGACTAATTAATCTAAAAAAGCAAATTAAAATTGAAGTATAGAAGCAC
11524779 AAACCACAAAAGCTATACGACTTCCGTCTT
66 AAACCACAAAAGCTATACGACTTCCGTCTT
*
11524809 TTCATACTTGATTACAATGACTAATTAA-CTTAAAAAAGCAAATTGAAATTGAAGTATAGAAGCA
1 TTCATACTTGATTACAATGACTAATTAATC-TAAAAAAGCAAATTAAAATTGAAGTATAGAAGCA
11524873 CAAACCACAAAAGCTATAC
65 CAAACCACAAAAGCTATAC
11524892 AACGTTTATC
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
94 1 0.01
95 74 0.99
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (95 bp):
TTCATACTTGATTACAATGACTAATTAATCTAAAAAAGCAAATTAAAATTGAAGTATAGAAGCAC
AAACCACAAAAGCTATACGACTTCCGTCTT
Found at i:11526579 original size:6 final size:6
Alignment explanation
Indices: 11526568--11526599 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
11526558 CTTATCCTCC
*
11526568 TTTTAT TTTTAT TTTTAT TTTTAT TTTAAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
11526600 GTGACATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:11529231 original size:20 final size:20
Alignment explanation
Indices: 11529185--11529234 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
11529175 TATATGTACG
*
11529185 TATATATATTATACTTTCTA
1 TATATATATTATAATTTCTA
* * *
11529205 AACATATTTTATAATTTCTA
1 TATATATATTATAATTTCTA
11529225 TATATATATT
1 TATATATATT
11529235 TTTCTTTATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (20 bp):
TATATATATTATAATTTCTA
Found at i:11542043 original size:44 final size:43
Alignment explanation
Indices: 11541980--11542100 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 43
11541970 GAAGATGGCA
* *
11541980 AATCTTATCTCCCTAAAGTTGCAGAGGAGCAGATTAAAGCCTAT
1 AATCTTATCTCCCTGAAGTTGCAGAGGAGCAGATTAAAACC-AT
* *
11542024 AATCCTATCTCCCTGAAGTTGCAGTA-GAGCAGATTAAAATCAT
1 AATCTTATCTCCCTGAAGTTGCAG-AGGAGCAGATTAAAACCAT
*
11542067 AGATCTTATCTCTCTGAAGTTGCAGAGG-GCAGAT
1 A-ATCTTATCTCCCTGAAGTTGCAGAGGAGCAGAT
11542101 CGCATCTAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
43 10 0.15
44 57 0.84
45 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGAGGAGCAGATTAAAACCAT
Found at i:11542158 original size:44 final size:45
Alignment explanation
Indices: 11542108--11542303 Score: 139
Period size: 44 Copynumber: 4.6 Consensus size: 45
11542098 GATCGCATCT
* *
11542108 AGTCTTATCTCCCTGAAGTGGCAGTGGAGCAAACTGAGTAAGA-A-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAA-ACAC
* * * * *
11542152 AGTCTTATTTCCCTAAAATTGCAGTGGGGCAGACTGAATAAACAC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAAACAC
* *
11542197 A-TCCTATCTCCCTGAAGTTGCAGTGGAGC--A--GACT---CA-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAAACAC
* * *
11542233 AGTCTTATCCCCCTGAAATTGCAGTAGG-GCAGACTGAATAAACA-
1 AGTCTTATCTCCCTGAAGTTGCAGT-GGAGCAAACTGAATAAACAC
* * * *
11542277 AATCCTATCTCCCTAAAGTTGTAGTGG
1 AGTCTTATCTCCCTGAAGTTGCAGTGG
11542304 GGTGGATTAG
Statistics
Matches: 118, Mismatches: 23, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
36 1 0.01
37 24 0.20
38 2 0.02
39 1 0.01
40 3 0.03
41 3 0.03
42 1 0.01
43 3 0.03
44 79 0.67
45 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAATAAACAC
Found at i:11542254 original size:81 final size:81
Alignment explanation
Indices: 11542151--11542303 Score: 243
Period size: 81 Copynumber: 1.9 Consensus size: 81
11542141 CTGAGTAAGA
** * * *
11542151 AAGTCTTATTTCCCTAAAATTGCAGTGGGGCAGACTGAATAAACACATCCTATCTCCCTGAAGTT
1 AAGTCTTATCCCCCTAAAATTGCAGTAGGGCAGACTGAATAAACAAATCCTATCTCCCTAAAGTT
11542216 GCAGTGGAGCAGACTC
66 GCAGTGGAGCAGACTC
*
11542232 AAGTCTTATCCCCCTGAAATTGCAGTAGGGCAGACTGAATAAACAAATCCTATCTCCCTAAAGTT
1 AAGTCTTATCCCCCTAAAATTGCAGTAGGGCAGACTGAATAAACAAATCCTATCTCCCTAAAGTT
*
11542297 GTAGTGG
66 GCAGTGG
11542304 GGTGGATTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (81 bp):
AAGTCTTATCCCCCTAAAATTGCAGTAGGGCAGACTGAATAAACAAATCCTATCTCCCTAAAGTT
GCAGTGGAGCAGACTC
Found at i:11542330 original size:125 final size:127
Alignment explanation
Indices: 11542024--11542353 Score: 321
Period size: 125 Copynumber: 2.6 Consensus size: 127
11542014 TAAAGCCTAT
* * * * *
11542024 AATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAATCATAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTAAAGTTGCAGTGGGGCAGATTAGAATAATAGATCTTATCTCTCTGAAGTTG
* * * * *
11542089 CAGAGG-GCAGATCGCATCTAGTCTTATCTCCCTGAAGTGGCAGTGGAGCAAACTGAGTAAGAA
66 CAGTGGAGCAGA-C-CATCAAGTCTTATCCCCCTGAAATGGCAGTGGAGCAAACTGAATAAGAA
* * * * * * * * *
11542152 AGTCTTATTTCCCTAAAATTGCAGTGGGGCAGACT-GAATAAACACATCCTATCTCCCTGAAGTT
1 AATCCTATCTCCCTAAAGTTGCAGTGGGGCAGATTAGAAT-AATAGATCTTATCTCTCTGAAGTT
* *
11542216 GCAGTGGAGCAGA-C-TCAAGTCTTATCCCCCTGAAATTGCAGTAGG-GCAGACTGAATAA-ACA
65 GCAGTGGAGCAGACCATCAAGTCTTATCCCCCTGAAATGGCAGT-GGAGCAAACTGAATAAGA-A
* ** * * *
11542277 AATCCTATCTCCCTAAAGTTGTAGTGGGGTGGATTAGAATAATGGATCTTATCTCTCTGAAATTA
1 AATCCTATCTCCCTAAAGTTGCAGTGGGGCAGATTAGAATAATAGATCTTATCTCTCTGAAGTTG
*
11542342 CAGTAGAGCAGA
66 CAGTGGAGCAGA
11542354 ACGCGTCAAA
Statistics
Matches: 160, Mismatches: 37, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
124 1 0.01
125 92 0.57
126 7 0.04
127 3 0.02
128 52 0.32
129 5 0.03
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (127 bp):
AATCCTATCTCCCTAAAGTTGCAGTGGGGCAGATTAGAATAATAGATCTTATCTCTCTGAAGTTG
CAGTGGAGCAGACCATCAAGTCTTATCCCCCTGAAATGGCAGTGGAGCAAACTGAATAAGAA
Found at i:11544080 original size:18 final size:18
Alignment explanation
Indices: 11544036--11544090 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 18
11544026 TATGTACGTA
*
11544036 TATATATATTATACTTTC
1 TATATATATTATAATTTC
* *
11544054 TAAACATATTTTATAATTTC
1 T--ATATATATTATAATTTC
11544074 TATATATA-TAT-ATTTC
1 TATATATATTATAATTTC
11544090 T
1 T
11544091 TTATTTTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 6 0.20
17 3 0.10
18 6 0.20
20 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATATATTATAATTTC
Found at i:11544082 original size:20 final size:20
Alignment explanation
Indices: 11544034--11544084 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
11544024 TATATGTACG
*
11544034 TATATATATATTATACTTTC
1 TATATATATATTATAATTTC
* * *
11544054 TAAACATATTTTATAATTTC
1 TATATATATATTATAATTTC
11544074 TATATATATAT
1 TATATATATAT
11544085 ATTTCTTTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATATATATTATAATTTC
Found at i:11554968 original size:3 final size:3
Alignment explanation
Indices: 11554960--11555002 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
11554950 ATATGTAGGT
*
11554960 ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA ATA ATA A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11555003 CAAAATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11555002 original size:12 final size:12
Alignment explanation
Indices: 11554960--11555016 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
11554950 ATATGTAGGT
*
11554960 ATAATAATAATA
1 ATAATAAAAATA
*
11554972 AT-ATATAATATA
1 ATAATA-AAAATA
11554984 ATAATAAAAATA
1 ATAATAAAAATA
11554996 ATAATAACAAA-A
1 ATAATAA-AAATA
*
11555008 TTAATAAAA
1 ATAATAAAA
11555017 TAGACTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.13
12 27 0.71
13 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATAAAAATA
Found at i:11555002 original size:15 final size:15
Alignment explanation
Indices: 11554962--11555018 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
11554952 ATGTAGGTAT
*
11554962 AATAATAATAATATAT
1 AATAATAATAATA-AA
11554978 AAT-ATAATAATAAA
1 AATAATAATAATAAA
*
11554992 AATAATAATAACAAA
1 AATAATAATAATAAA
*
11555007 ATTAATAA-AATA
1 AATAATAATAATA
11555019 GACTAAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.19
15 26 0.72
16 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:11555469 original size:23 final size:22
Alignment explanation
Indices: 11555426--11555483 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
11555416 AAAGGGTATC
* *
11555426 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
11555447 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
11555470 TACATATCATATCT
1 TACAAATCATATCT
11555484 AGGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:11555499 original size:21 final size:21
Alignment explanation
Indices: 11555473--11555537 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
11555463 CTAAGATTAC
*
11555473 ATATCATATCTAGGATTGCAT
1 ATATCATATCTAAGATTGCAT
*
11555494 ATATCATATCTAAGATTTCAT
1 ATATCATATCTAAGATTGCAT
*
11555515 ATACCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
11555536 AT
1 AT
11555538 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:11555538 original size:40 final size:36
Alignment explanation
Indices: 11555455--11555549 Score: 100
Period size: 40 Copynumber: 2.5 Consensus size: 36
11555445 ATTACAAAAT
*
11555455 CATATCTTCTAAGATTACATATCATATCTAGGATTG
1 CATATCTTCTAAGATTACATATCATATCTAAGATTG
*
11555491 CATATATCATATCTAAGATTTCATATACCATATCTAAGATTG
1 C--ATATC-T-TCTAAGATTACATAT--CATATCTAAGATTG
* *
11555533 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
11555550 TGTTTCCATA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
36 1 0.02
38 13 0.27
39 1 0.02
40 19 0.40
42 14 0.29
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (36 bp):
CATATCTTCTAAGATTACATATCATATCTAAGATTG
Found at i:11556374 original size:44 final size:44
Alignment explanation
Indices: 11556305--11556598 Score: 362
Period size: 44 Copynumber: 6.7 Consensus size: 44
11556295 GCTATTTTCC
* * * *
11556305 ACCTACTCCACTGCTG-CTCAAGGAGATAGGGTTCACGATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCA
* *
11556349 ACCTATTCAACTGCTGACCAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* *
11556393 ATCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
*
11556437 ACCTATTCCACTGCT-ACCCAGGGAGAT-GGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGA-CCAGGGAGATAGG-ATTCACAATCTTCA
* * *
11556481 ACTTATTCCACTGCTGACCAGGGAGATAGGATTCATAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * *
11556525 ACATATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * *
11556569 ACCTATTCCACTGTTGATCAGGGAAATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
11556599 GCTGGGGTCA
Statistics
Matches: 218, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
43 4 0.02
44 209 0.96
45 5 0.02
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
Found at i:11556657 original size:88 final size:88
Alignment explanation
Indices: 11556598--11556852 Score: 402
Period size: 88 Copynumber: 2.9 Consensus size: 88
11556588 AGGGAAATAG
* * * *
11556598 GGCTGGGGTCATCAATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
*
11556663 TCCGCTGCAACCCAAGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
11556686 GGCTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTAC
1 GGCTGGTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
11556751 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * * *
11556774 GGCTGGTGTGTTCGATCTGCTTTGTTATCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
11556839 TCCGCTGCAACCCA
66 TCCGCTGCAACCCA
11556853 AGANNNNNNN
Statistics
Matches: 152, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 152 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:11556686 original size:44 final size:44
Alignment explanation
Indices: 11556636--11556774 Score: 111
Period size: 44 Copynumber: 3.2 Consensus size: 44
11556626 CGGTGCAGGA
*
11556636 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAAGG
1 AGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAACCCAAGG
* * * * ** * * ****
11556680 AGGCAAG-GCTGGTGTCTTCGATCTACTTCGCTGTCGGTGC-AGG
1 AGGCAAGATCTGCTATTTTTAACCTACTCCGCTG-CAACCCAAGG
* *
11556723 AAGGCAAGATCTGCTATTTTTAGCCTACTCCGCTGCAACCCAGGG
1 -AGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAACCCAAGG
11556768 AGGCAAG
1 AGGCAAG
11556775 GCTGGTGTGT
Statistics
Matches: 64, Mismatches: 27, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
43 20 0.31
44 25 0.39
45 19 0.30
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (44 bp):
AGGCAAGATCTGCTATTTTTAACCTACTCCGCTGCAACCCAAGG
Found at i:11556757 original size:45 final size:45
Alignment explanation
Indices: 11556621--11556757 Score: 111
Period size: 45 Copynumber: 3.1 Consensus size: 45
11556611 AATCTGCTTT
* *
11556621 GCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCC
1 GCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTACTCC
**** * * * * * * *
11556666 GCTG-CAACCCAAGG-AGGCAAG-GCTGGT-GTCTTCGATCTACTTC
1 GCTGTCGGTGC-AGGAAGGCAAGATCTGCTATTTTTAG-CCTACTCC
11556709 GCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTACTCC
1 GCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTACTCC
11556754 GCTG
1 GCTG
11556758 CAACCCAGGG
Statistics
Matches: 62, Mismatches: 24, Indels: 12
0.63 0.24 0.12
Matches are distributed among these distances:
42 3 0.05
43 16 0.26
44 18 0.29
45 21 0.34
46 4 0.06
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.27
Consensus pattern (45 bp):
GCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTACTCC
Found at i:11563355 original size:3 final size:3
Alignment explanation
Indices: 11563347--11563389 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
11563337 ATATGTAGGT
*
11563347 ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA ATA ATA A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11563390 CAAAATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11563389 original size:12 final size:12
Alignment explanation
Indices: 11563347--11563403 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
11563337 ATATGTAGGT
*
11563347 ATAATAATAATA
1 ATAATAAAAATA
*
11563359 AT-ATATAATATA
1 ATAATA-AAAATA
11563371 ATAATAAAAATA
1 ATAATAAAAATA
11563383 ATAATAACAAA-A
1 ATAATAA-AAATA
*
11563395 TTAATAAAA
1 ATAATAAAA
11563404 TAGACTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.13
12 27 0.71
13 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAATAAAAATA
Found at i:11563389 original size:15 final size:15
Alignment explanation
Indices: 11563349--11563405 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
11563339 ATGTAGGTAT
*
11563349 AATAATAATAATATAT
1 AATAATAATAATA-AA
11563365 AAT-ATAATAATAAA
1 AATAATAATAATAAA
*
11563379 AATAATAATAACAAA
1 AATAATAATAATAAA
*
11563394 ATTAATAA-AATA
1 AATAATAATAATA
11563406 GACTAAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.19
15 26 0.72
16 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:11563856 original size:23 final size:22
Alignment explanation
Indices: 11563813--11563870 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
11563803 AAAGGGTATC
* *
11563813 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
11563834 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
11563857 TACATATCATATCT
1 TACAAATCATATCT
11563871 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:11563873 original size:19 final size:19
Alignment explanation
Indices: 11563826--11563923 Score: 106
Period size: 19 Copynumber: 4.8 Consensus size: 19
11563816 AAATTAAATC
*
11563826 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
11563846 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
11563868 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
11563889 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
11563908 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
11563924 CTCGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
19 33 0.48
21 18 0.26
22 7 0.10
23 11 0.16
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:11563886 original size:21 final size:21
Alignment explanation
Indices: 11563860--11563922 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
11563850 CTAAGATTAC
11563860 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
11563881 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
11563900 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
11563921 AT
1 AT
11563923 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:11592147 original size:20 final size:21
Alignment explanation
Indices: 11592101--11592160 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 21
11592091 TTATTTTATT
*
11592101 TAATATTAATATA-TTTTTAA
1 TAATATTATTATATTTTTTAA
**
11592121 TTTTATTATTATATTTTTTAA
1 TAATATTATTATATTTTTTAA
*
11592142 -AATATT-TATGTATTTTTTA
1 TAATATTAT-TATATTTTTTA
11592161 TATATTTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.03
20 24 0.75
21 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TAATATTATTATATTTTTTAA
Found at i:11592737 original size:20 final size:20
Alignment explanation
Indices: 11592709--11592756 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
11592699 ATATAAACAT
* *
11592709 TAAAAATATAAAAATTGAAA
1 TAAATATATAAAAATTCAAA
11592729 TAAATATATAAAAATTCAAA
1 TAAATATATAAAAATTCAAA
*
11592749 TATATATA
1 TAAATATA
11592757 ATCTATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAATATATAAAAATTCAAA
Found at i:11592753 original size:18 final size:17
Alignment explanation
Indices: 11592690--11592757 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 17
11592680 ATTTTCTCTT
* *
11592690 ATTAAATGTATATAAAC
1 ATTAAATATATATAAAA
11592707 ATTAAA-A-ATATAAAA
1 ATTAAATATATATAAAA
11592722 ATTGAAATAAATATATAAAA
1 ATT-AAAT--ATATATAAAA
11592742 ATTCAAATATATATAA
1 ATT-AAATATATATAA
11592758 TCTATAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
15 10 0.23
16 3 0.07
17 6 0.14
18 8 0.19
19 1 0.02
20 15 0.35
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
ATTAAATATATATAAAA
Found at i:11593055 original size:23 final size:22
Alignment explanation
Indices: 11593019--11593077 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
11593009 ATTATTTTTA
* *
11593019 ATTTTTAAAATTTAAAATCATAT
1 ATTTTTAAATTTTAAAA-CAAAT
*
11593042 A-TTTTAGAATTTTATAACAAAT
1 ATTTTTA-AATTTTAAAACAAAT
11593064 ATTTTTAAAATTTT
1 ATTTTT-AAATTTT
11593078 TAATCAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 10 0.33
23 19 0.63
24 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTTTAAATTTTAAAACAAAT
Found at i:11593086 original size:22 final size:22
Alignment explanation
Indices: 11593019--11593087 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
11593009 ATTATTTTTA
**
11593019 ATTTTTAAAATTTAAAATC-AT
1 ATTTTTAAAATTTTTAATCAAT
*
11593040 ATATTTTAGAATTTTATAA-CAAAT
1 AT-TTTTAAAATTTT-TAATC-AAT
11593064 ATTTTTAAAATTTTTAATCAAT
1 ATTTTTAAAATTTTTAATCAAT
11593086 AT
1 AT
11593088 AATATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 2 0.05
22 19 0.49
23 14 0.36
24 4 0.10
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (22 bp):
ATTTTTAAAATTTTTAATCAAT
Found at i:11600654 original size:21 final size:21
Alignment explanation
Indices: 11600628--11600669 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11600618 ATCGAAGGTT
*
11600628 TCTGGTTCACATAAATCAAAA
1 TCTGGTACACATAAATCAAAA
11600649 TCTGGTACACATAAATCAAAA
1 TCTGGTACACATAAATCAAAA
11600670 CATTGCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (21 bp):
TCTGGTACACATAAATCAAAA
Found at i:11608102 original size:54 final size:54
Alignment explanation
Indices: 11607968--11608105 Score: 163
Period size: 54 Copynumber: 2.6 Consensus size: 54
11607958 GACACATAAC
* * *
11607968 CGTGTCTCAGCCCGTGTCTTAAACCGTGTAACTCACTGACTTAGATCACACGGT
1 CGTGTCGCAGACCGTGTCTCAAACCGTGTAACTCACTGACTTAGATCACACGGT
* * * *
11608022 CATGTTGCAAACCGTGTGC-CAAACCGTGTGACTCACTGACTT-GATACACACGGT
1 CGTGTCGCAGACCGTGT-CTCAAACCGTGTAACTCACTGACTTAGAT-CACACGGT
* *
11608076 CGTGTCGCAGGCCGTGTCTCAGACCGTGTA
1 CGTGTCGCAGACCGTGTCTCAAACCGTGTA
11608106 TGGCACACGG
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
53 4 0.06
54 63 0.93
55 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (54 bp):
CGTGTCGCAGACCGTGTCTCAAACCGTGTAACTCACTGACTTAGATCACACGGT
Found at i:11611209 original size:13 final size:13
Alignment explanation
Indices: 11611193--11611221 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
11611183 TGTAAAAAAA
11611193 TTATTTTAATTTT
1 TTATTTTAATTTT
11611206 TTA-TTTAATTTT
1 TTATTTTAATTTT
11611218 TTAT
1 TTAT
11611222 ATTTTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTAATTTT
Found at i:11631662 original size:31 final size:31
Alignment explanation
Indices: 11631627--11631687 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
11631617 ACAAAATAGT
*
11631627 CACTAAACAATTTAAAAGTTTTTATTTAAGC
1 CACTAAACAATATAAAAGTTTTTATTTAAGC
* * *
11631658 CACTAGACTATATGAAAGTTTTTATTTAAG
1 CACTAAACAATATAAAAGTTTTTATTTAAG
11631688 ATACTACGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (31 bp):
CACTAAACAATATAAAAGTTTTTATTTAAGC
Found at i:11632758 original size:9 final size:9
Alignment explanation
Indices: 11632732--11632800 Score: 51
Period size: 8 Copynumber: 8.1 Consensus size: 9
11632722 AGAAACATTA
11632732 AAAATAT-T
1 AAAATATAT
11632740 AAAATA-AT
1 AAAATATAT
11632748 AAAATATAT
1 AAAATATAT
11632757 -AAAT-TA-
1 AAAATATAT
*
11632763 AAAATATAG
1 AAAATATAT
* *
11632772 AAAATTGTTT
1 AAAA-TATAT
11632782 AAAATATTAT
1 AAAATA-TAT
11632792 AAAA-ATAT
1 AAAATATAT
11632800 A
1 A
11632801 GGAAAGTGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
7 6 0.12
8 23 0.47
9 8 0.16
10 12 0.24
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAATATAT
Found at i:11632777 original size:16 final size:16
Alignment explanation
Indices: 11632722--11632777 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
11632712 AAAAAAAGCA
11632722 AGAAACATTAAAAATAT
1 AGAAA-ATTAAAAATAT
* *
11632739 -TAAAATAATAAAATAT
1 AGAAAATTA-AAAATAT
*
11632755 A-TAAATTAAAAATAT
1 AGAAAATTAAAAATAT
11632770 AGAAAATT
1 AGAAAATT
11632778 GTTTAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (16 bp):
AGAAAATTAAAAATAT
Found at i:11632797 original size:30 final size:29
Alignment explanation
Indices: 11632761--11632826 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
11632751 ATATATAAAT
**
11632761 TAAAAATATAGAAAATTGTTTAAAATA-TTA
1 TAAAAATATAGAAAA--GTGCAAAATATTTA
*
11632791 TAAAAATATAGGAAAGTGCAAAATATTTA
1 TAAAAATATAGAAAAGTGCAAAATATTTA
11632820 TAAAAAT
1 TAAAAAT
11632827 GGAAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 8 0.25
29 10 0.31
30 14 0.44
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32
Consensus pattern (29 bp):
TAAAAATATAGAAAAGTGCAAAATATTTA
Found at i:11633064 original size:38 final size:38
Alignment explanation
Indices: 11633022--11633094 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
11633012 CCCCTTGATT
11633022 TTTATAGTTTTTATTTTTAATATTTTTTTAGATTTAAA
1 TTTATAGTTTTTATTTTTAATATTTTTTTAGATTTAAA
11633060 TTTATAGTTTTTATTTTTAATATTTTTTTAGATTT
1 TTTATAGTTTTTATTTTTAATATTTTTTTAGATTT
11633095 TTCTTATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (38 bp):
TTTATAGTTTTTATTTTTAATATTTTTTTAGATTTAAA
Found at i:11637286 original size:11 final size:11
Alignment explanation
Indices: 11637270--11637313 Score: 88
Period size: 11 Copynumber: 4.0 Consensus size: 11
11637260 TGGGTGTGTG
11637270 AAAGTTGCTCT
1 AAAGTTGCTCT
11637281 AAAGTTGCTCT
1 AAAGTTGCTCT
11637292 AAAGTTGCTCT
1 AAAGTTGCTCT
11637303 AAAGTTGCTCT
1 AAAGTTGCTCT
11637314 CAAGGTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (11 bp):
AAAGTTGCTCT
Found at i:11648604 original size:119 final size:120
Alignment explanation
Indices: 11648474--11648762 Score: 553
Period size: 120 Copynumber: 2.4 Consensus size: 120
11648464 CAAACTTTAG
11648474 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGT-
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
11648538 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
*
11648593 ATTAAATTATATATTTTTATTAAATTATATTTAATAATTATTATTTTAAATTATATTTTATAGTA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
11648658 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
66 TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
*
11648713 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
11648763 ATATGATTAA
Statistics
Matches: 166, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
119 63 0.38
120 103 0.62
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (120 bp):
ATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTA
TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTT
Found at i:11650415 original size:33 final size:34
Alignment explanation
Indices: 11650378--11650448 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
11650368 TTTATAATTT
* * *
11650378 TTTATACTTTTAA-TGATTTTTATTTTTTAAAAA
1 TTTATACTTATAATTGATTTTGAATTTTTAAAAA
* *
11650411 TTTATTCTTATAATTTATTTTGAATTTTTAAAAA
1 TTTATACTTATAATTGATTTTGAATTTTTAAAAA
11650445 TTTA
1 TTTA
11650449 AAAATTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (34 bp):
TTTATACTTATAATTGATTTTGAATTTTTAAAAA
Found at i:11655271 original size:2 final size:2
Alignment explanation
Indices: 11655266--11655294 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11655256 ACACACACAC
11655266 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11655295 ACAATGCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11655489 original size:30 final size:30
Alignment explanation
Indices: 11655439--11655527 Score: 116
Period size: 25 Copynumber: 3.1 Consensus size: 30
11655429 ATTTCTTATG
* *
11655439 CCAATATCTCGATACTCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
11655470 CCAATATTTGATACCCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
11655499 ----TATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
11655525 CCA
1 CCA
11655528 TAAATATGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
25 23 0.44
26 2 0.04
29 2 0.04
30 18 0.35
31 7 0.13
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:11661212 original size:2 final size:2
Alignment explanation
Indices: 11661205--11661233 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11661195 GAATTTACAA
11661205 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
11661234 ACAATGCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11661428 original size:30 final size:30
Alignment explanation
Indices: 11661378--11661466 Score: 116
Period size: 25 Copynumber: 3.1 Consensus size: 30
11661368 ATTTCTTATG
*
11661378 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
11661409 CCAATATTTGATACTCATATCTTTGAC-TT
1 CCAATATTTGATACCCATATCTTTGACTTT
11661438 ----TATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
11661464 CCA
1 CCA
11661467 TAAATATAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
25 22 0.43
26 2 0.04
29 2 0.04
30 18 0.35
31 7 0.14
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Done.