Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold293
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: 1704560
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 10 of 12
Found at i:1383076 original size:17 final size:18
Alignment explanation
Indices: 1383054--1383092 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1383044 GTATTATTAA
*
1383054 AATATTAAAAT-TTATAT
1 AATATTAAAATATAATAT
*
1383071 AATATTTAAATATAATAT
1 AATATTAAAATATAATAT
1383089 AATA
1 AATA
1383093 CAAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATTAAAATATAATAT
Found at i:1384427 original size:16 final size:15
Alignment explanation
Indices: 1384397--1384435 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1384387 AAATTCTTTT
*
1384397 TATTT-TATTTATCG
1 TATTTATATGTATCG
1384411 TATTATATATGTATCG
1 TATT-TATATGTATCG
1384427 TATTTATAT
1 TATTTATAT
1384436 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 6 0.27
16 12 0.55
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (15 bp):
TATTTATATGTATCG
Found at i:1384850 original size:30 final size:29
Alignment explanation
Indices: 1384802--1384886 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 29
1384792 TATTTAAAAT
*
1384802 TTTATAAATCTAACTAAATTTAAA-TTATTA
1 TTTATAAAT-TAAATAAATTTAAATTTA-TA
*
1384832 TTTAAAAATATAAATAAATTTAAAATTTATA
1 TTTATAAAT-TAAATAAATTT-AAATTTATA
1384863 TTT-TAAATTAAATTAAATTTAAAT
1 TTTATAAATTAAA-TAAATTTAAAT
1384887 ATATGTCTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 8 0.17
30 29 0.60
31 8 0.17
32 3 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTATAAATTAAATAAATTTAAATTTATA
Found at i:1386603 original size:3 final size:3
Alignment explanation
Indices: 1386590--1386631 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
1386580 CCAAGCCTTG
1386590 TTC TCTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1386632 TTGTTTCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1391593 original size:2 final size:2
Alignment explanation
Indices: 1391586--1391611 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1391576 CAATACGCAT
1391586 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1391612 CACAAGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1394063 original size:2 final size:2
Alignment explanation
Indices: 1394056--1394080 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1394046 CGTACACAAT
1394056 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1394081 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1394085 original size:2 final size:2
Alignment explanation
Indices: 1394080--1394112 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1394070 TCTCTCTCTC
1394080 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
1394113 TGCATCAATC
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:1396151 original size:27 final size:26
Alignment explanation
Indices: 1396133--1396195 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
1396123 ATTTTATAAT
*
1396133 TTATATAATTTTGATATATTAATTTAA
1 TTATATAAATTTGATATATT-ATTTAA
*
1396160 TTATATAAATTTGAAAATATATATTTATA
1 TTATATAAATTTG-ATATAT-TATTTA-A
1396189 TTATATA
1 TTATATA
1396196 TTTAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 12 0.39
28 10 0.32
29 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
TTATATAAATTTGATATATTATTTAA
Found at i:1396195 original size:13 final size:14
Alignment explanation
Indices: 1396177--1396206 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1396167 AATTTGAAAA
1396177 TATATATTT-ATAT
1 TATATATTTAATAT
1396190 TATATATTTAATAT
1 TATATATTTAATAT
1396204 TAT
1 TAT
1396207 TCGTATAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATATTTAATAT
Found at i:1396565 original size:2 final size:2
Alignment explanation
Indices: 1396558--1396587 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1396548 TTTTAGTGCA
1396558 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1396588 TCTAATTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1398138 original size:21 final size:20
Alignment explanation
Indices: 1398093--1398139 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
1398083 ATAGTACGTT
1398093 AATTATATTTTGAGTATTTA
1 AATTATATTTTGAGTATTTA
1398113 AATTATATTTTGAGTATTTAA
1 AATTATATTTTGAGTATTT-A
1398134 AATTAT
1 AATTAT
1398140 CAAAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (20 bp):
AATTATATTTTGAGTATTTA
Found at i:1399997 original size:27 final size:27
Alignment explanation
Indices: 1399942--1399997 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1399932 ATATTTTTAT
*
1399942 TAAAAATTCAAAAAATTAAAAGTAGAA
1 TAAAAATTCAAAAAATTAAAAGTAAAA
* *
1399969 TAAAATTTGAAAAAATTAAAA-TCAAAA
1 TAAAAATTCAAAAAATTAAAAGT-AAAA
1399996 TA
1 TA
1399998 TAGTTGCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.25
Consensus pattern (27 bp):
TAAAAATTCAAAAAATTAAAAGTAAAA
Found at i:1400472 original size:12 final size:11
Alignment explanation
Indices: 1400454--1400481 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1400444 CACACCTTGG
1400454 GAAAAAAAAAA
1 GAAAAAAAAAA
1400465 GAAAAAAAAAA
1 GAAAAAAAAAA
1400476 GAAAAA
1 GAAAAA
1400482 GGAAGAGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:1401339 original size:2 final size:2
Alignment explanation
Indices: 1401334--1401368 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1401324 TTTTTTCATG
*
1401334 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1401369 AGGTGTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1402562 original size:20 final size:20
Alignment explanation
Indices: 1402539--1402584 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1402529 ATATGAAAAA
1402539 AATAAAATAAAT-ATAATATT
1 AATAAAATAAATAATAAT-TT
* *
1402559 AATATAATATATAATAATTT
1 AATAAAATAAATAATAATTT
1402579 AA-AAAA
1 AATAAAA
1402585 AAACATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAAAATAAATAATAATTT
Found at i:1405649 original size:14 final size:16
Alignment explanation
Indices: 1405630--1405667 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 16
1405620 TAATTAAATT
1405630 TAAATAAATTTTAA-A
1 TAAATAAATTTTAATA
1405645 T-AAT-AATTTTAATA
1 TAAATAAATTTTAATA
1405659 TAAATAAAT
1 TAAATAAAT
1405668 AAATTCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 8 0.40
14 5 0.25
15 4 0.20
16 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATAAATTTTAATA
Found at i:1405888 original size:11 final size:11
Alignment explanation
Indices: 1405872--1405946 Score: 64
Period size: 11 Copynumber: 6.5 Consensus size: 11
1405862 TATCATTTGA
1405872 ATATTTATATT
1 ATATTTATATT
1405883 ATATTTATATATTT
1 ATA-TT-TATA-TT
*
1405897 ATTATTTACATT
1 A-TATTTATATT
1405909 ATATTTATA-T
1 ATATTTATATT
* *
1405919 ATTTATTATTTT
1 ATAT-TTATATT
1405931 ATATTTATATT
1 ATATTTATATT
1405942 A-ATTT
1 ATATTT
1405947 TAAATTGTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
10 8 0.15
11 21 0.40
12 9 0.17
13 7 0.13
14 5 0.10
15 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTTATATT
Found at i:1405889 original size:26 final size:26
Alignment explanation
Indices: 1405860--1405921 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
1405850 CTTATCTCAT
*
1405860 TTTATCAT-TTGAATATTTATATTATA
1 TTTAT-ATATTGAATATTTACATTATA
* *
1405886 TTTATATATTTATTATTTACATTATA
1 TTTATATATTGAATATTTACATTATA
1405912 TTTATATATT
1 TTTATATATT
1405922 TATTATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTATATATTGAATATTTACATTATA
Found at i:1405890 original size:6 final size:6
Alignment explanation
Indices: 1405872--1405941 Score: 60
Period size: 6 Copynumber: 11.8 Consensus size: 6
1405862 TATCATTTGA
*
1405872 ATATTT ATA-TT ATATTTAT ATATTT ATTATTT ACA-TT ATATTT ATATATT
1 ATATTT ATATTT ATA-TT-T ATATTT A-TATTT ATATTT ATATTT ATAT-TT
1405922 -TA-TT AT-TTT ATATTT ATATT
1 ATATTT ATATTT ATATTT ATATT
1405942 AATTTTAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
4 2 0.04
5 14 0.26
6 22 0.42
7 11 0.21
8 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:1405893 original size:8 final size:8
Alignment explanation
Indices: 1405882--1405940 Score: 70
Period size: 8 Copynumber: 7.4 Consensus size: 8
1405872 ATATTTATAT
1405882 TATATTTA
1 TATATTTA
1405890 TATATTTA
1 TATATTTA
1405898 T-TATTTACA
1 TATATTT--A
1405907 TTATATTTA
1 -TATATTTA
1405916 TATATTTA
1 TATATTTA
1405924 T-TATTT-
1 TATATTTA
1405930 TATATTTA
1 TATATTTA
1405938 TAT
1 TAT
1405941 TAATTTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
6 1 0.02
7 15 0.33
8 21 0.47
9 2 0.04
10 1 0.02
11 5 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATTTA
Found at i:1405922 original size:26 final size:26
Alignment explanation
Indices: 1405873--1405929 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1405863 ATCATTTGAA
*
1405873 TATTTATATTATATTTATATATTTAT
1 TATTTACATTATATTTATATATTTAT
1405899 TATTTACATTATATTTATATATTTAT
1 TATTTACATTATATTTATATATTTAT
1405925 TATTT
1 TATTT
1405930 TATATTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TATTTACATTATATTTATATATTTAT
Found at i:1406985 original size:26 final size:27
Alignment explanation
Indices: 1406953--1407003 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1406943 ACATACTAAT
*
1406953 TTTTATTTAATTTTT-TGTTTTTATAA
1 TTTTATTTAATTTTTATATTTTTATAA
*
1406979 TTTTATTTAGTTTTTATATTTTTAT
1 TTTTATTTAATTTTTATATTTTTAT
1407004 TAAGTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTATTTAATTTTTATATTTTTATAA
Found at i:1407080 original size:68 final size:69
Alignment explanation
Indices: 1406994--1407143 Score: 214
Period size: 69 Copynumber: 2.2 Consensus size: 69
1406984 TTTAGTTTTT
* * *
1406994 ATATTTTT-ATTAAGTAAATTAATATTAAATTCAGTCATTTATC-TCATAATGATTAAATTAAAT
1 ATATTTTTAATTAAGTAAATTAATATTAAATTCAGTCATTTATCTTAATAAAGATCAAATTAAAT
1407057 TTAA
66 TTAA
* * *
1407061 ATATTTTTAATTAAGTAAATTAATATTAAATTTAGTTATTTGTCTTAATAAAGATCAAATTAAAT
1 ATATTTTTAATTAAGTAAATTAATATTAAATTCAGTCATTTATCTTAATAAAGATCAAATTAAAT
*
1407126 TTGA
66 TTAA
*
1407130 ATAATTTTAATTAA
1 ATATTTTTAATTAA
1407144 ACTCGGATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
67 8 0.11
68 32 0.44
69 33 0.45
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (69 bp):
ATATTTTTAATTAAGTAAATTAATATTAAATTCAGTCATTTATCTTAATAAAGATCAAATTAAAT
TTAA
Found at i:1407545 original size:22 final size:22
Alignment explanation
Indices: 1407476--1407550 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
1407466 TTTATTTAAA
*
1407476 AATTATTTTTA-TATT-AATATT
1 AATT-TTTTTATTATTAAATAAT
* *
1407497 AATATATTTTATAATTAAAATTAAAT
1 AAT-TTTTTTATTATT-AAA-T-AAT
1407523 AATTTTTTTATTATTAAATAAT
1 AATTTTTTTATTATTAAATAAT
1407545 AATTTT
1 AATTTT
1407551 AATCTTATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
21 8 0.19
22 13 0.30
23 1 0.02
24 5 0.12
25 11 0.26
26 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTTTTTATTATTAAATAAT
Found at i:1408162 original size:26 final size:28
Alignment explanation
Indices: 1408129--1408186 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
1408119 AATTCGGATA
* *
1408129 TTTAAAATTATAATTTATTTAAT-A-AAT
1 TTTAAATTTA-AATTTATATAATCATAAT
1408156 TTTAAATTTAAATTTATATAATCATAAT
1 TTTAAATTTAAATTTATATAATCATAAT
1408184 TTT
1 TTT
1408187 TTCTTTCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 10 0.37
28 6 0.22
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTAAATTTAAATTTATATAATCATAAT
Found at i:1409300 original size:2 final size:2
Alignment explanation
Indices: 1409295--1409330 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1409285 TATGCACAGC
1409295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1409331 CAATCTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1409619 original size:14 final size:15
Alignment explanation
Indices: 1409600--1409629 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1409590 ATTAAATAGA
1409600 TTTTTT-AAAAAGTT
1 TTTTTTAAAAAAGTT
1409614 TTTTTTAAAAAAGTT
1 TTTTTTAAAAAAGTT
1409629 T
1 T
1409630 ATTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTTTTAAAAAAGTT
Found at i:1410904 original size:22 final size:21
Alignment explanation
Indices: 1410861--1410906 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1410851 ATTAACTAAT
* *
1410861 AAAAAATTAATTTAATCATTA
1 AAAAAATTAATTCAAACATTA
1410882 AAAAAATTAATTCAAACAGTTA
1 AAAAAATTAATTCAAACA-TTA
1410904 AAA
1 AAA
1410907 GTTAGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAAATTAATTCAAACATTA
Found at i:1411223 original size:25 final size:22
Alignment explanation
Indices: 1411195--1411247 Score: 52
Period size: 26 Copynumber: 2.2 Consensus size: 22
1411185 AATAAATGTA
*
1411195 TTAATATATAAAGTTTATTTAATTT
1 TTAATATATAAA-ATTA-TT-ATTT
*
1411220 TTAAATTTATAAAATTATTATTT
1 TT-AATATATAAAATTATTATTT
1411243 TTAAT
1 TTAAT
1411248 TTTGATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.12
23 6 0.24
24 2 0.08
25 5 0.20
26 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTAATATATAAAATTATTATTT
Found at i:1411505 original size:22 final size:25
Alignment explanation
Indices: 1411457--1411512 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
1411447 AAATTAATTG
*
1411457 TATTAATAATAAAAAATATTTATAA
1 TATTAATAATAAAAAATATATATAA
*
1411482 TATTAAT-TTAAAAAATA-ATA-AA
1 TATTAATAATAAAAAATATATATAA
*
1411504 TATTTATAA
1 TATTAATAA
1411513 ATTAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 8 0.31
23 2 0.08
24 9 0.35
25 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TATTAATAATAAAAAATATATATAA
Found at i:1411505 original size:31 final size:30
Alignment explanation
Indices: 1411446--1411522 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 30
1411436 ACTTATAAAT
*
1411446 TAAATTAATTGTATTAATAATAAAAAATATTTA
1 TAAATTAATT-TA--AAAAATAAAAAATATTTA
*
1411479 TAATATTAATTTAAAAAATAATAAATATTTA
1 TAA-ATTAATTTAAAAAATAAAAAATATTTA
1411510 TAAATTAATTTAA
1 TAAATTAATTTAA
1411523 GATATTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
30 10 0.24
31 19 0.46
33 5 0.12
34 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (30 bp):
TAAATTAATTTAAAAAATAAAAAATATTTA
Found at i:1412233 original size:24 final size:26
Alignment explanation
Indices: 1412182--1412235 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
1412172 TGCTTATCTT
* **
1412182 ATTTTATTTTAAAAAACTAAATCCCA
1 ATTTCATTTTAAAAAACTAAATAACA
1412208 ATTTCATTTTAAAAAA-T-AATAACA
1 ATTTCATTTTAAAAAACTAAATAACA
1412232 ATTT
1 ATTT
1412236 TTTAAATGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.36
25 1 0.04
26 15 0.60
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTTCATTTTAAAAAACTAAATAACA
Found at i:1412389 original size:34 final size:33
Alignment explanation
Indices: 1412328--1412403 Score: 82
Period size: 34 Copynumber: 2.3 Consensus size: 33
1412318 AATTATTTTT
*
1412328 AATAATAATATTTTTATTTAAATTTAATTATAAA
1 AATAAAAATATTTTTATTTAAATTTAATT-TAAA
** **
1412362 AATAAAAATATTTTTTATTTTCA-TTAATTTATG
1 AATAAAAATA-TTTTTATTTAAATTTAATTTAAA
1412395 AATAAAAAT
1 AATAAAAAT
1412404 TTAAGTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 11 0.31
34 15 0.42
35 10 0.28
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (33 bp):
AATAAAAATATTTTTATTTAAATTTAATTTAAA
Found at i:1413313 original size:2 final size:2
Alignment explanation
Indices: 1413306--1413371 Score: 71
Period size: 2 Copynumber: 32.5 Consensus size: 2
1413296 ATGACAGCAA
* * *
1413306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T GAT AT AA AC AGC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A-T AT
*
1413349 AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1413372 AAATACAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
1 1 0.02
2 52 0.93
3 3 0.05
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1413762 original size:25 final size:26
Alignment explanation
Indices: 1413725--1413773 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
1413715 GTATCATGTA
1413725 TTTAAATATTTTAATTT-ATTTAAAT
1 TTTAAATATTTTAATTTAATTTAAAT
1413750 TTTAAA-ATGTTTAATTTAATTTAA
1 TTTAAATAT-TTTAATTTAATTTAA
1413774 TTATATTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 2 0.09
25 14 0.64
26 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TTTAAATATTTTAATTTAATTTAAAT
Found at i:1420995 original size:12 final size:12
Alignment explanation
Indices: 1420980--1421044 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
1420970 AGAGATGAGA
1420980 AAAGAGAAAGAG
1 AAAGAGAAAGAG
*
1420992 AAAGA-AACAAAG
1 AAAGAGAA-AGAG
1421004 AAAG-GAAAGA-
1 AAAGAGAAAGAG
*
1421014 AAAGA-ATAGA-
1 AAAGAGAAAGAG
1421024 AAAGAGAAAGAG
1 AAAGAGAAAGAG
*
1421036 GAAGAGAAA
1 AAAGAGAAA
1421045 AAAAAGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
10 13 0.30
11 8 0.19
12 22 0.51
ACGTcount: A:0.69, C:0.02, G:0.28, T:0.02
Consensus pattern (12 bp):
AAAGAGAAAGAG
Found at i:1421017 original size:14 final size:14
Alignment explanation
Indices: 1421000--1421091 Score: 53
Period size: 14 Copynumber: 6.2 Consensus size: 14
1420990 AGAAAGAAAC
1421000 AAAGAAAGGAAAGA
1 AAAGAAAGGAAAGA
*
1421014 AAAGAATAGAAAAGA
1 AAAGAA-AGGAAAGA
*
1421029 GAAAGAGGAAGAGAAAAA
1 -AAAGA--AAG-GAAAGA
** *
1421047 AAAGAAAAAAAAGG
1 AAAGAAAGGAAAGA
1421061 AAA-AAAGGCAAAGA
1 AAAGAAAGG-AAAGA
*
1421075 AAA-AGAGGGAAAGA
1 AAAGA-AAGGAAAGA
1421089 AAA
1 AAA
1421092 AAAAAAGAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
13 3 0.05
14 28 0.47
15 12 0.20
16 5 0.08
17 7 0.12
18 5 0.08
ACGTcount: A:0.72, C:0.01, G:0.26, T:0.01
Consensus pattern (14 bp):
AAAGAAAGGAAAGA
Found at i:1434759 original size:2 final size:2
Alignment explanation
Indices: 1434752--1434786 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1434742 TGTATCTGCG
1434752 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1434787 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1434791 original size:2 final size:2
Alignment explanation
Indices: 1434786--1434820 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1434776 TCTCTCTCTC
*
1434786 TA TA TA TA TA TA TA TA TG 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 TA T
1434821 GTACACACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1434828 original size:2 final size:2
Alignment explanation
Indices: 1434823--1434863 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1434813 ATATATATGT
1434823 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1434864 TGCATTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1436633 original size:4 final size:4
Alignment explanation
Indices: 1436624--1436659 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
1436614 CAATGGCCTT
*
1436624 CATA CATA CATA CATA CATG CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1436660 TATATTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:1436882 original size:15 final size:16
Alignment explanation
Indices: 1436864--1436896 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1436854 TTTTTTCATC
*
1436864 ATTTTTTTACT-CAAA
1 ATTTTTTAACTACAAA
1436879 ATTTTTTAACTACAAA
1 ATTTTTTAACTACAAA
1436895 AT
1 AT
1436897 ATTGAGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTTTTAACTACAAA
Found at i:1441072 original size:16 final size:17
Alignment explanation
Indices: 1441037--1441094 Score: 68
Period size: 16 Copynumber: 3.5 Consensus size: 17
1441027 TAATATAATG
* *
1441037 TTATGATTATTATTTATT
1 TTATAATTATTA-ATATT
1441055 TTATAATT-TTAATATT
1 TTATAATTATTAATATT
1441071 TTAT-ATTATTAATA-T
1 TTATAATTATTAATATT
1441086 TTATAATTA
1 TTATAATTA
1441095 ATAGTAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.22
16 18 0.50
17 3 0.08
18 7 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTATAATTATTAATATT
Found at i:1441142 original size:16 final size:16
Alignment explanation
Indices: 1441123--1441197 Score: 55
Period size: 16 Copynumber: 4.4 Consensus size: 16
1441113 ATGTTTATAA
1441123 TTATAATAAAAATATT
1 TTATAATAAAAATATT
*
1441139 TTATAATTGTAATAAATATA
1 TTATAA---TAA-AAATATT
*
1441159 ATATAATAAAAATATAT
1 TTATAATAAAAATAT-T
*
1441176 TT-TTA-AAAAATATT
1 TTATAATAAAAATATT
1441190 ATTATAAT
1 -TTATAAT
1441198 TTTTATATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
14 1 0.02
15 10 0.22
16 16 0.36
17 4 0.09
19 3 0.07
20 11 0.24
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (16 bp):
TTATAATAAAAATATT
Found at i:1441142 original size:31 final size:32
Alignment explanation
Indices: 1441076--1441139 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
1441066 ATATTTTATA
*
1441076 TTATTAATATTTATAATTAATAGTAATAAAAT
1 TTATTAATATTTATAATTAATAATAATAAAAT
*
1441108 TTATT-ATGTTTATAATT-ATAATAA-AAATAT
1 TTATTAATATTTATAATTAATAATAATAAA-AT
1441138 TT
1 TT
1441140 TATAATTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.10
30 10 0.34
31 11 0.38
32 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
TTATTAATATTTATAATTAATAATAATAAAAT
Found at i:1441210 original size:6 final size:6
Alignment explanation
Indices: 1441199--1441298 Score: 64
Period size: 6 Copynumber: 16.8 Consensus size: 6
1441189 TATTATAATT
* * *
1441199 TTTATA TTTATA TTTTATA TTTGTA TTGA-A TATATA TTTATA -TTA-A
1 TTTATA TTTATA -TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
* * * * * *
1441245 TTTAT- TTTAATT TTTATA TTTATA TTAAACA TATATA TATATA TATATA
1 TTTATA TTT-ATA TTTATA TTTATA TT-TATA TTTATA TTTATA TTTATA
1441294 TTTAT
1 TTTAT
1441299 TTTGATTTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
4 1 0.01
5 12 0.16
6 49 0.66
7 12 0.16
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (6 bp):
TTTATA
Found at i:1441262 original size:45 final size:49
Alignment explanation
Indices: 1441211--1441307 Score: 130
Period size: 45 Copynumber: 2.1 Consensus size: 49
1441201 TATATTTATA
* * *
1441211 TTTTATATTTGTATT-GA-ATATATATTTATAT-TA-ATTTATTTTAAT
1 TTTTATATTTATATTAAACATATATATATATATATATATTTATTTTAAT
*
1441256 TTTTATATTTATATTAAACATATATATATATATATATATTTATTTTGAT
1 TTTTATATTTATATTAAACATATATATATATATATATATTTATTTTAAT
1441305 TTT
1 TTT
1441308 AATAAATGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
45 14 0.32
46 1 0.02
47 13 0.30
48 2 0.05
49 14 0.32
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (49 bp):
TTTTATATTTATATTAAACATATATATATATATATATATTTATTTTAAT
Found at i:1444377 original size:220 final size:220
Alignment explanation
Indices: 1443634--1444516 Score: 1597
Period size: 220 Copynumber: 4.0 Consensus size: 220
1443624 TCTCAAATCA
* * * * *
1443634 CATCAAAACGACTTCCAAAGATCATAATAAGAAA-GACAGACAACAAAATATGAAAGCACGCTGG
1 CATCAAAACGACTTCCAAGGATCATAACAAGAAAGGACAGATAACAAAATATGAAACCACCCTGG
* *
1443698 AACAAAGCAGATCAATCAAACTACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
66 AACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
1443763 TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGAT
131 TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGAT
1443828 TGATCAAAGATTCAATTTAGAAAAAG
196 TGATCAAAGATTCAATTTAG-AAAAG
*
1443854 CATCAAAACGACTTCCAAGGATCATAGCAAGAAAGGACAGATAACAAAATATGAAACCACCCTGG
1 CATCAAAACGACTTCCAAGGATCATAACAAGAAAGGACAGATAACAAAATATGAAACCACCCTGG
* *
1443919 AACAAAGCAGATCAATCAAAATACATAAAGCCGATCATCAAAAACAATGTGACATGATCAAAGCA
66 AACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
1443984 TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAAAGTGGAAAAAAAAG
131 TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTT--AAAAAAAGTGGAAAAAAAAG
1444049 ATTGATCAAAGATTCAATTTAGAAAAG
194 ATTGATCAAAGATTCAATTTAGAAAAG
* *
1444076 CATCAAAAGGACTTCCAAGGATCATAATAAGAAAGGACAGATAACAAAATATGAAACCACCCTGG
1 CATCAAAACGACTTCCAAGGATCATAACAAGAAAGGACAGATAACAAAATATGAAACCACCCTGG
1444141 AACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
66 AACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
1444206 TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGAT
131 TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGAT
1444271 TGATCAAAGATTCAATTTAGAAAAG
196 TGATCAAAGATTCAATTTAGAAAAG
*
1444296 CATCAAAACGACTTCCAAGGATCATAGCAAGAAAGGACAGATAACAAAATATGAAACCACCCTGG
1 CATCAAAACGACTTCCAAGGATCATAACAAGAAAGGACAGATAACAAAATATGAAACCACCCTGG
1444361 AACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
66 AACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
*
1444426 TCAAACATCAACAAATCACGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAAGA
131 TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGG-AAAAAAAAGA
1444491 TTGATCAAAGATTCAATTTAGAAAAG
195 TTGATCAAAGATTCAATTTAGAAAAG
1444517 GATAGATCTA
Statistics
Matches: 642, Mismatches: 17, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
220 258 0.40
221 169 0.26
222 173 0.27
223 42 0.07
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (220 bp):
CATCAAAACGACTTCCAAGGATCATAACAAGAAAGGACAGATAACAAAATATGAAACCACCCTGG
AACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGAT
TGATCAAAGATTCAATTTAGAAAAG
Found at i:1444458 original size:442 final size:441
Alignment explanation
Indices: 1443634--1444516 Score: 1635
Period size: 442 Copynumber: 2.0 Consensus size: 441
1443624 TCTCAAATCA
* *
1443634 CATCAAAACGACTTCCAAAGATCATAATAAGAAAGACAGACAACAAAATATGAAAGCACGCTGGA
1 CATCAAAACGACTTCCAAAGATCATAATAAGAAAGACAGACAACAAAATATGAAACCACCCTGGA
* *
1443699 ACAAAGCAGATCAATCAAACTACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCAT
66 ACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCAT
1443764 CAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGATT
131 CAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGATT
1443829 GATCAAAGATTCAATTTAGAAAAAGCATCAAAACGACTTCCAAGGATCATAGCAAGAAAGGACAG
196 GATCAAAGATTCAATTTAGAAAAAGCATCAAAACGACTTCCAAGGATCATAGCAAGAAAGGACAG
*
1443894 ATAACAAAATATGAAACCACCCTGGAACAAAGCAGATCAATCAAAATACATAAAGCCGATCATCA
261 ATAACAAAATATGAAACCACCCTGGAACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCA
1443959 AAAACAATGTGACATGATCAAAGCATCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTC
326 AAAACAATGTGACATGATCAAAGCATCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTC
1444024 GTTAAAAAAAAAGTGG-AAAAAAAAGATTGATCAAAGATTCAATTTAGAAAAG
391 GTT--AAAAAAAGTGGAAAAAAAAAGATTGATCAAAGATTCAATTTAGAAAAG
* * *
1444076 CATCAAAAGGACTTCCAAGGATCATAATAAGAAAGGACAGATAACAAAATATGAAACCACCCTGG
1 CATCAAAACGACTTCCAAAGATCATAATAAGAAA-GACAGACAACAAAATATGAAACCACCCTGG
1444141 AACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
65 AACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCA
1444206 TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGAT
130 TCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGAT
1444271 TGATCAAAGATTCAATTTAG-AAAAGCATCAAAACGACTTCCAAGGATCATAGCAAGAAAGGACA
195 TGATCAAAGATTCAATTTAGAAAAAGCATCAAAACGACTTCCAAGGATCATAGCAAGAAAGGACA
1444335 GATAACAAAATATGAAACCACCCTGGAACAAAGCAGATCAAACAAAATACATAAAGCCGATCATC
260 GATAACAAAATATGAAACCACCCTGGAACAAAGCAGATCAAACAAAATACATAAAGCCGATCATC
* *
1444400 CAAAACAATGTGACATGATCAAAGCATCAAACATCAACAAATCACGTAAAAGAAAGGCATCTTTT
325 AAAAACAATGTGACATGATCAAAGCATCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTT
1444465 CGTTAAAAAAAGTGGAAAAAAAAAGATTGATCAAAGATTCAATTTAGAAAAG
390 CGTTAAAAAAAGTGGAAAAAAAAAGATTGATCAAAGATTCAATTTAGAAAAG
1444517 GATAGATCTA
Statistics
Matches: 429, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
440 11 0.03
441 36 0.08
442 207 0.48
443 175 0.41
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (441 bp):
CATCAAAACGACTTCCAAAGATCATAATAAGAAAGACAGACAACAAAATATGAAACCACCCTGGA
ACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCCAAAACAATGTGACATGATCAAAGCAT
CAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTCGTTAAAAAAAGTGGAAAAAAAAGATT
GATCAAAGATTCAATTTAGAAAAAGCATCAAAACGACTTCCAAGGATCATAGCAAGAAAGGACAG
ATAACAAAATATGAAACCACCCTGGAACAAAGCAGATCAAACAAAATACATAAAGCCGATCATCA
AAAACAATGTGACATGATCAAAGCATCAAACATCAACAAATCAAGTAAAAGAAAGGCATCTTTTC
GTTAAAAAAAGTGGAAAAAAAAAGATTGATCAAAGATTCAATTTAGAAAAG
Found at i:1445083 original size:15 final size:14
Alignment explanation
Indices: 1445063--1445094 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1445053 TTATAAAAGA
1445063 ATTTTAATATTTAAT
1 ATTTTAATATTT-AT
1445078 ATTTTAATATTTAT
1 ATTTTAATATTTAT
1445092 ATT
1 ATT
1445095 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTAATATTTAT
Found at i:1445159 original size:16 final size:16
Alignment explanation
Indices: 1445130--1445164 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1445120 ATATTATCAA
* *
1445130 TTAATTAAATATTAAT
1 TTAATAAAAAATTAAT
1445146 TTAATAAAAAATTAAT
1 TTAATAAAAAATTAAT
1445162 TTA
1 TTA
1445165 TATTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATAAAAAATTAAT
Found at i:1445188 original size:25 final size:24
Alignment explanation
Indices: 1445145--1445194 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
1445135 TAAATATTAA
*
1445145 TTTAATAAAAAATTAATTTATATT
1 TTTAATAAAAAATTAATTTAAATT
1445169 TTTATATATAAAAATT-ATTTAAATT
1 TTTA-ATA-AAAAATTAATTTAAATT
1445194 T
1 T
1445195 AAAATTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 12 0.52
26 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTAATAAAAAATTAATTTAAATT
Found at i:1445365 original size:13 final size:13
Alignment explanation
Indices: 1445310--1445366 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1445300 ACTTATTTTT
*
1445310 TAAATATTTATTTA
1 TAAATATTT-TTAA
*
1445324 TTAAT-TTTTTAA
1 TAAATATTTTTAA
*
1445336 T-AATATTTTAAA
1 TAAATATTTTTAA
*
1445348 AAAATATTTTTAA
1 TAAATATTTTTAA
1445361 TAAATA
1 TAAATA
1445367 AATATAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 3 0.09
12 10 0.29
13 18 0.51
14 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TAAATATTTTTAA
Found at i:1445369 original size:17 final size:18
Alignment explanation
Indices: 1445344--1445381 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1445334 AATAATATTT
1445344 TAAAAAAATAT-TTTTAA
1 TAAAAAAATATATTTTAA
*
1445361 TAAATAAATATAATTTTAA
1 TAAAAAAATAT-ATTTTAA
1445380 TA
1 TA
1445382 TTTATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
19 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAAAAATATATTTTAA
Found at i:1446837 original size:22 final size:23
Alignment explanation
Indices: 1446796--1446851 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1446786 TAAAATGGTA
* *
1446796 AATAAATATGTTATTGAAAAGT-T
1 AATAAA-ATTTTATTGAAAAATAT
*
1446819 AATAAAATTTTATTTAAAAATAT
1 AATAAAATTTTATTGAAAAATAT
*
1446842 TATAAAATTT
1 AATAAAATTT
1446852 CTAAAAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
AATAAAATTTTATTGAAAAATAT
Found at i:1446984 original size:13 final size:13
Alignment explanation
Indices: 1446966--1446991 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1446956 CAACATGGAA
1446966 AAAATTAAATTAT
1 AAAATTAAATTAT
1446979 AAAATTAAATTAT
1 AAAATTAAATTAT
1446992 TTTATGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTAAATTAT
Found at i:1449128 original size:22 final size:22
Alignment explanation
Indices: 1449103--1449146 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1449093 GGTGTTGGTG
1449103 GTGATGCTGTTTTTATTGGAAA
1 GTGATGCTGTTTTTATTGGAAA
1449125 GTGATGCTGTTTTTATTGGAAA
1 GTGATGCTGTTTTTATTGGAAA
1449147 ACTGTCGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.27, T:0.45
Consensus pattern (22 bp):
GTGATGCTGTTTTTATTGGAAA
Found at i:1452729 original size:2 final size:2
Alignment explanation
Indices: 1452722--1452761 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1452712 ACATAAATTT
1452722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1452762 AGATTTAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1459291 original size:29 final size:29
Alignment explanation
Indices: 1459258--1459315 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1459248 ACATGTATGT
*
1459258 ATATATGTATATATTGTTAAGAGAGACTA
1 ATATATGTATATATTGTTAAGAGAAACTA
1459287 ATATATGTATATATTGTTAAGAGAAACTA
1 ATATATGTATATATTGTTAAGAGAAACTA
1459316 TCTTATTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (29 bp):
ATATATGTATATATTGTTAAGAGAAACTA
Found at i:1462127 original size:27 final size:27
Alignment explanation
Indices: 1462103--1462157 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
1462093 CCATTAGACT
1462103 TAGATAACTGACTCTT-CCCTGTAGAA
1 TAGATAACTGACTCTTCCCCTGTAGAA
**
1462129 TATCTAACTGACTCTTCCCCTGTAGAA
1 TAGATAACTGACTCTTCCCCTGTAGAA
1462156 TA
1 TA
1462158 TCTAATAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (27 bp):
TAGATAACTGACTCTTCCCCTGTAGAA
Found at i:1462136 original size:26 final size:27
Alignment explanation
Indices: 1462107--1462162 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
1462097 TAGACTTAGA
1462107 TAACTGACTCTT-CCCTGTAGAATATC
1 TAACTGACTCTTCCCCTGTAGAATATC
1462133 TAACTGACTCTTCCCCTGTAGAATATC
1 TAACTGACTCTTCCCCTGTAGAATATC
1462160 TAA
1 TAA
1462163 TAGATAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (27 bp):
TAACTGACTCTTCCCCTGTAGAATATC
Found at i:1467319 original size:44 final size:47
Alignment explanation
Indices: 1467231--1467329 Score: 109
Period size: 47 Copynumber: 2.1 Consensus size: 47
1467221 TAACATAAAT
1467231 ATTTTTTAATTTATATTTTATTATTTAATACAAGCATAATTTTAA-TA
1 ATTTTTTAATTTATATTTTATTATTTAATACAAGCAT-ATTTTAATTA
* *
1467278 ATTTTTTTATTTAT-TATTTATTTTTTATATAC-A-CAT-TTTTAATTTA
1 ATTTTTTAATTTATAT-TTTATTATTTA-ATACAAGCATATTTTAA-TTA
1467324 ATTTTT
1 ATTTTT
1467330 AATAATTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
44 6 0.13
46 12 0.26
47 24 0.52
48 4 0.09
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (47 bp):
ATTTTTTAATTTATATTTTATTATTTAATACAAGCATATTTTAATTA
Found at i:1468020 original size:2 final size:2
Alignment explanation
Indices: 1468013--1468040 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1468003 TCTTCCCCAA
1468013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1468041 GTTCTTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1468121 original size:18 final size:20
Alignment explanation
Indices: 1468098--1468164 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 20
1468088 TGAATTTATA
1468098 TTATATAATT-TATAAT-TT
1 TTATATAATTATATAATATT
* *
1468116 TTATATTATTATATCATATT
1 TTATATAATTATATAATATT
*
1468136 TTATATTATATTTTAATTAATATT
1 TTATA-TA-ATTAT-A-TAATATT
1468160 TTATA
1 TTATA
1468165 CATTATAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.24
19 5 0.13
20 7 0.18
21 1 0.03
22 4 0.11
23 1 0.03
24 11 0.29
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATAATTATATAATATT
Found at i:1468141 original size:12 final size:12
Alignment explanation
Indices: 1468118--1468164 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1468108 TATAATTTTT
*
1468118 ATATTATTATATC
1 ATATT-TTATATA
*
1468131 ATATTTTATATT
1 ATATTTTATATA
1468143 ATATTTTA-ATTA
1 ATATTTTATA-TA
1468155 ATATTTTATA
1 ATATTTTATA
1468165 CATTATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 1 0.03
12 23 0.77
13 6 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTTTATATA
Found at i:1469172 original size:8 final size:8
Alignment explanation
Indices: 1469161--1469193 Score: 52
Period size: 7 Copynumber: 4.4 Consensus size: 8
1469151 AATTTAATGA
1469161 AAATTATT
1 AAATTATT
1469169 AAATTATT
1 AAATTATT
1469177 AAA-TATT
1 AAATTATT
1469184 AAATT-TT
1 AAATTATT
1469191 AAA
1 AAA
1469194 AAATATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 12 0.50
8 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AAATTATT
Found at i:1469643 original size:3 final size:3
Alignment explanation
Indices: 1469635--1469665 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1469625 TTTAAATCCC
1469635 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1469666 ATGAAATCGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1469831 original size:26 final size:25
Alignment explanation
Indices: 1469802--1469864 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
1469792 TTATTAATAA
* *
1469802 ATTAAATTTAATAGTTAAATAACATT
1 ATTAAA-TTAATAATCAAATAACATT
*
1469828 ATTAAGATTAATAATCAAATTACATT
1 ATTAA-ATTAATAATCAAATAACATT
*
1469854 ATCAAAATTAA
1 AT-TAAATTAA
1469865 GTATGTAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 28 0.90
27 3 0.10
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.38
Consensus pattern (25 bp):
ATTAAATTAATAATCAAATAACATT
Found at i:1470349 original size:19 final size:19
Alignment explanation
Indices: 1470308--1470359 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
1470298 TTGACAAATT
* *
1470308 ATATTAAT-TTAATTTTAA
1 ATATTAATATAAAATTTAA
*
1470326 ATATTAATGTAAAATTTAA
1 ATATTAATATAAAATTTAA
* *
1470345 TTATTTATATAAAAT
1 ATATTAATATAAAAT
1470360 ATATATGTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATTAATATAAAATTTAA
Found at i:1470396 original size:18 final size:18
Alignment explanation
Indices: 1470370--1470419 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1470360 ATATATGTTC
1470370 AATATATAAAATTTTATA
1 AATATATAAAATTTTATA
* *
1470388 AATAAATAAATTTTTTATA
1 AATATATAAA-ATTTTATA
1470407 ATATATATAAAAT
1 A-ATATATAAAAT
1470420 CATATTACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 9 0.35
19 9 0.35
20 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATATAAAATTTTATA
Found at i:1478715 original size:13 final size:13
Alignment explanation
Indices: 1478697--1478727 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1478687 TTGTTAATAT
1478697 TTTAAATTTTTTA
1 TTTAAATTTTTTA
1478710 TTTAAATTTTTTA
1 TTTAAATTTTTTA
1478723 TTTAA
1 TTTAA
1478728 TCAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTAAATTTTTTA
Found at i:1479440 original size:25 final size:24
Alignment explanation
Indices: 1479392--1479452 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
1479382 TATTTATACA
1479392 AAATATATAATAAAAATAATTATT
1 AAATATATAATAAAAATAATTATT
*
1479416 AAATATATAAATTAAAATTAA-TATT
1 AAATATAT-AA-TAAAAATAATTATT
1479441 -AATAT-TAATAAA
1 AAATATATAATAAA
1479453 TACTCTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 4 0.12
22 2 0.06
23 1 0.03
24 13 0.38
25 6 0.18
26 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATATATAATAAAAATAATTATT
Found at i:1479580 original size:6 final size:6
Alignment explanation
Indices: 1479574--1479613 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1479564 TATTTTTATT
* *
1479574 TAAATT TAATTA TAAAATA TAAATA TAAATA TAAATA TAA
1 TAAATA TAAATA T-AAATA TAAATA TAAATA TAAATA TAA
1479614 TATTTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
TAAATA
Found at i:1479623 original size:25 final size:25
Alignment explanation
Indices: 1479554--1479623 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
1479544 TTATTTAATA
* * *
1479554 ATAAAAATAATATTTTTATTTAAAT
1 ATAAATATAATATTTTAATATAAAT
* * * * *
1479579 TTAATTATAAAATATAAATATAAAT
1 ATAAATATAATATTTTAATATAAAT
1479604 ATAAATATAATATTTTAATA
1 ATAAATATAATATTTTAATA
1479624 ATATAATAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATAAATATAATATTTTAATATAAAT
Found at i:1484231 original size:12 final size:12
Alignment explanation
Indices: 1484214--1484239 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1484204 GACGTATTTA
1484214 ATAATTTATATT
1 ATAATTTATATT
1484226 ATAATTTATATT
1 ATAATTTATATT
1484238 AT
1 AT
1484240 GTTGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATAATTTATATT
Found at i:1484387 original size:24 final size:24
Alignment explanation
Indices: 1484342--1484387 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1484332 ATTGTAAAAT
*
1484342 ATATACTTTTTAGGAGGTATATGC
1 ATATACTTTTTAGGAGGGATATGC
*
1484366 ATATA-TTTTTAGGTGGAGATAT
1 ATATACTTTTTAGGAGG-GATAT
1484388 TTATTCTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.43
Consensus pattern (24 bp):
ATATACTTTTTAGGAGGGATATGC
Found at i:1492604 original size:30 final size:31
Alignment explanation
Indices: 1492568--1492626 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
1492558 TGTTTCTAAT
1492568 AAATAATAATATGTCAAAACAAAA-AAAATA
1 AAATAATAATATGTCAAAACAAAATAAAATA
*
1492598 AAATAATAATATGTCAAAATAAAATAAAA
1 AAATAATAATATGTCAAAACAAAATAAAA
1492627 AACATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.22
Consensus pattern (31 bp):
AAATAATAATATGTCAAAACAAAATAAAATA
Found at i:1493040 original size:2 final size:2
Alignment explanation
Indices: 1493033--1493057 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1493023 CTTTATTTTA
1493033 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
1493058 CAAATTTTTA
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:1496778 original size:16 final size:17
Alignment explanation
Indices: 1496757--1496794 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1496747 TAAATATTTC
1496757 ATTTTATTA-ATTAATT
1 ATTTTATTATATTAATT
*
1496773 ATTTTATTATTTTAATT
1 ATTTTATTATATTAATT
1496790 -TTTTA
1 ATTTTA
1496795 ACTGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATTATATTAATT
Found at i:1500721 original size:3 final size:3
Alignment explanation
Indices: 1500713--1500741 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1500703 GTTTGCATGT
1500713 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1500742 TTAAATTTTA
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:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1502375 original size:9 final size:9
Alignment explanation
Indices: 1502361--1502392 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1502351 TGCTCGCAGG
1502361 TCCGACTCC
1 TCCGACTCC
1502370 TCCGACTCC
1 TCCGACTCC
*
1502379 TCCAACTCC
1 TCCGACTCC
1502388 TCCGA
1 TCCGA
1502393 GGCCACCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.16, C:0.53, G:0.09, T:0.22
Consensus pattern (9 bp):
TCCGACTCC
Found at i:1504674 original size:14 final size:15
Alignment explanation
Indices: 1504649--1504708 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
1504639 AAAACTGATA
1504649 ATATTAAATATAATT
1 ATATTAAATATAATT
1504664 ATATT-AATATAA-T
1 ATATTAAATATAATT
* *
1504677 ATGA-AAAAAATAATT
1 AT-ATTAAATATAATT
*
1504692 AAATTATAATATAATT
1 ATATTA-AATATAATT
1504708 A
1 A
1504709 CAACATCACA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
13 3 0.09
14 15 0.43
15 8 0.23
16 9 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
ATATTAAATATAATT
Found at i:1507614 original size:13 final size:13
Alignment explanation
Indices: 1507596--1507620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1507586 ATGCGTGTTA
1507596 AACATAAATATTG
1 AACATAAATATTG
1507609 AACATAAATATT
1 AACATAAATATT
1507621 TAAAAAAAAT
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:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (13 bp):
AACATAAATATTG
Found at i:1509507 original size:2 final size:2
Alignment explanation
Indices: 1509500--1509552 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1509490 CAGTTCCTTT
1509500 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1509542 TA TA TA TA TA T
1 TA TA TA TA TA T
1509553 GACATGAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1513121 original size:22 final size:22
Alignment explanation
Indices: 1513077--1513123 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1513067 AAATTTTAGA
*
1513077 TAATTAATTCAATTAATTTAAT
1 TAATTAATTCAATTAATTCAAT
*
1513099 TAATTAGTTCAATTAGA-TCAAT
1 TAATTAATTCAATTA-ATTCAAT
1513121 TAA
1 TAA
1513124 AAATAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (22 bp):
TAATTAATTCAATTAATTCAAT
Found at i:1513638 original size:2 final size:2
Alignment explanation
Indices: 1513626--1513666 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1513616 GAAAACACTC
*
1513626 TA TA CA TA 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 TA TA TA TA T
1513667 TAGTCTGGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1513769 original size:2 final size:2
Alignment explanation
Indices: 1513762--1513787 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1513752 GGATGAAGAA
1513762 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
1513788 GAAAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1514870 original size:28 final size:28
Alignment explanation
Indices: 1514834--1514892 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1514824 AATGTTAATC
*
1514834 TTAAGTACTAACA-TAACAAAATAAAAA-T
1 TTAAATACTAA-ATTAACAAAA-AAAAAGT
1514862 TTAAATACTAAATTAACAAAAAAAAAGT
1 TTAAATACTAAATTAACAAAAAAAAAGT
1514890 TTA
1 TTA
1514893 GATATAAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.27
Consensus pattern (28 bp):
TTAAATACTAAATTAACAAAAAAAAAGT
Found at i:1515674 original size:22 final size:21
Alignment explanation
Indices: 1515639--1515679 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1515629 TAAAAAAATT
1515639 TATTTTTAATTTAATATTTATA
1 TATTTTTAATTTAA-ATTTATA
1515661 TATTTTATAA-TTAAATTTA
1 TATTTT-TAATTTAAATTTA
1515680 AATTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTTAATTTAAATTTATA
Found at i:1518284 original size:3 final size:3
Alignment explanation
Indices: 1518278--1518305 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1518268 AAAACTGTTC
1518278 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1518306 CTCTAGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1519721 original size:3 final size:3
Alignment explanation
Indices: 1519713--1519751 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1519703 ATAGATTTGT
1519713 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1519752 AAGTGACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1520222 original size:2 final size:2
Alignment explanation
Indices: 1520215--1520239 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1520205 TTAAATTACT
1520215 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 T
1520240 TCCAAAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1520976 original size:147 final size:148
Alignment explanation
Indices: 1520776--1521063 Score: 354
Period size: 147 Copynumber: 1.9 Consensus size: 148
1520766 TATGTACTCA
* * * **
1520776 ATTTGGATATATATTTAATTTTTAAAATTTTTTATATATTTAAATTAGTATACCCTCGTACTTAT
1 ATTTGGATATATATTTAATTTTTAAAATTTTTAATATATTTAAATAAGCATACCCTAATACTTAT
* *
1520841 ATTCG-A-ATATATCATATACATGTATTG-GTGACAAGAATTT-TAAAA-AAAAAATTCTAGTAA
66 ATTCGAATATATATCATATACATGTATTGAG-GACAAGAATTTAAAAAATAAAAAATTCAAGTAA
1520901 CTTAGGTAATTCCTGTTCG
130 CTTAGGTAATTCCTGTTCG
* **
1520920 ATTTGGATATATATGTTTAATTTTTTAAAATTTTTAATATATCTT-AATAAGCATACCGTAATTT
1 ATTTGGATATATA--TTTAA-TTTTTAAAATTTTTAATATAT-TTAAATAAGCATACCCTAATAC
* * * *
1520984 TTATATTCGAATATATATTATATACATGTGTTGAGGGCGAGAATTTAAAAAAATAAAAAATTCAA
62 TTATATTCGAATATATATCATATACATGTATTGAGGACAAGAATTT-AAAAAATAAAAAATTCAA
1521049 GTAACTTAGGTAATT
126 GTAACTTAGGTAATT
1521064 TCTTGGCGTA
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
144 13 0.11
146 5 0.04
147 41 0.34
148 3 0.03
149 28 0.23
150 1 0.01
151 4 0.03
152 25 0.21
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (148 bp):
ATTTGGATATATATTTAATTTTTAAAATTTTTAATATATTTAAATAAGCATACCCTAATACTTAT
ATTCGAATATATATCATATACATGTATTGAGGACAAGAATTTAAAAAATAAAAAATTCAAGTAAC
TTAGGTAATTCCTGTTCG
Found at i:1521570 original size:2 final size:2
Alignment explanation
Indices: 1521565--1521606 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1521555 GTGTGTGTGT
*
1521565 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 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
1521607 CAGTTTGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1522402 original size:2 final size:2
Alignment explanation
Indices: 1522395--1522436 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
1522385 ATTTGTAAAT
1522395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
1522437 TGGTGAGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1522496 original size:18 final size:18
Alignment explanation
Indices: 1522473--1522546 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 18
1522463 GAATCACATA
*
1522473 TTTTTAAAAATTTTAAAT
1 TTTTTAAAAATTATAAAT
* * *
1522491 TTTTTAAGAATCATAGAT
1 TTTTTAAAAATTATAAAT
*
1522509 ATTTTAAAAATTATAAA-
1 TTTTTAAAAATTATAAAT
*
1522526 TTTTT-ATAATTATAAAT
1 TTTTTAAAAATTATAAAT
1522543 TTTT
1 TTTT
1522547 AATACAAAAC
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
16 10 0.22
17 8 0.18
18 27 0.60
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTTAAAAATTATAAAT
Found at i:1522496 original size:35 final size:36
Alignment explanation
Indices: 1522457--1522530 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
1522447 AAATCACAGA
* * *
1522457 TTTTATGAATCACATAT-TTTTAAAAATTTTAAATT
1 TTTTAAGAATCACAGATATTTTAAAAATTATAAATT
*
1522492 TTTTAAGAATCATAGATATTTTAAAAATTATAAATT
1 TTTTAAGAATCACAGATATTTTAAAAATTATAAATT
1522528 TTT
1 TTT
1522531 ATAATTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
35 14 0.41
36 20 0.59
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (36 bp):
TTTTAAGAATCACAGATATTTTAAAAATTATAAATT
Found at i:1522546 original size:16 final size:16
Alignment explanation
Indices: 1522517--1522547 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1522507 ATATTTTAAA
1522517 AATTATAAATTTTTAT
1 AATTATAAATTTTTAT
1522533 AATTATAAATTTTTA
1 AATTATAAATTTTTA
1522548 ATACAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTATAAATTTTTAT
Found at i:1523393 original size:22 final size:23
Alignment explanation
Indices: 1523356--1523400 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1523346 GATAAAATAC
*
1523356 ATTGGTCTATGCTAATT-GTTTT
1 ATTGGTCTATGATAATTAGTTTT
*
1523378 ATTGGTCTATTATAATTAGTTTT
1 ATTGGTCTATGATAATTAGTTTT
1523401 TATTATGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.22, C:0.07, G:0.16, T:0.56
Consensus pattern (23 bp):
ATTGGTCTATGATAATTAGTTTT
Found at i:1526986 original size:16 final size:16
Alignment explanation
Indices: 1526961--1527006 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1526951 ATGAGATTTG
*
1526961 ATAAAGTTATTTTAAA
1 ATAAAATTATTTTAAA
1526977 ATAAAATTATTTTAAA
1 ATAAAATTATTTTAAA
* **
1526993 TTTGAATTATTTTA
1 ATAAAATTATTTTA
1527007 TATATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
ATAAAATTATTTTAAA
Found at i:1527626 original size:20 final size:21
Alignment explanation
Indices: 1527579--1527641 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
1527569 CAATTGTCAT
1527579 AAATAATCTTTTAATTTTATCA
1 AAATAATCTTTTAATTTTA-CA
* * *
1527601 ATATAATTTTTTTATTTTA-A
1 AAATAATCTTTTAATTTTACA
*
1527621 AAATAATAATTTTAATATTTA
1 AAATAAT-CTTTTAAT-TTTA
1527642 AAATTTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 7 0.21
21 6 0.18
22 20 0.61
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATAATCTTTTAATTTTACA
Found at i:1527629 original size:23 final size:23
Alignment explanation
Indices: 1527580--1527633 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
1527570 AATTGTCATA
* **
1527580 AATAATCTTTTAATTTTATCAAT
1 AATAATTTTTTAATTTTAAAAAT
*
1527603 -ATAATTTTTTTATTTTAAAAAT
1 AATAATTTTTTAATTTTAAAAAT
1527625 AATAATTTT
1 AATAATTTT
1527634 AATATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (23 bp):
AATAATTTTTTAATTTTAAAAAT
Found at i:1528367 original size:21 final size:23
Alignment explanation
Indices: 1528327--1528369 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1528317 TTTTAGTTCA
*
1528327 ATATTTTAATTTTGTTAAAAATT
1 ATATATTAATTTTGTTAAAAATT
1528350 ATATATTAA-TTT-TTAAAAAT
1 ATATATTAATTTTGTTAAAAAT
1528370 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATATTAATTTTGTTAAAAATT
Found at i:1528447 original size:21 final size:20
Alignment explanation
Indices: 1528417--1528463 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1528407 AATAAAATTT
*
1528417 AAATATTTTATATTTTAAAA
1 AAATTTTTTATATTTTAAAA
* *
1528437 ATAATTTTTTATTTTTTACAA
1 A-AATTTTTTATATTTTAAAA
1528458 AAATTT
1 AAATTT
1528464 ATATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATTTTTTATATTTTAAAA
Found at i:1528470 original size:21 final size:21
Alignment explanation
Indices: 1528417--1528470 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
1528407 AATAAAATTT
1528417 AAAT-ATTTTATA--TTTTAA
1 AAATAATTTTATATTTTTTAA
* *
1528435 AAATAATTTTTTATTTTTTAC
1 AAATAATTTTATATTTTTTAA
1528456 AAA-AATTTATATATT
1 AAATAATTT-TATATT
1528471 AATTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.14
19 7 0.24
20 5 0.17
21 13 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATAATTTTATATTTTTTAA
Found at i:1529013 original size:27 final size:27
Alignment explanation
Indices: 1528944--1529013 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
1528934 AAATCACTTT
*
1528944 TTTTTATTTGTAAAAAATGATGATCCC
1 TTTTTATTTGTAAAAAATGATAATCCC
* *
1528971 TTTTTATTTTATAAAAAAT-AGTAAT-TC
1 TTTTTA-TTTGTAAAAAATGA-TAATCCC
*
1528998 TTTTTATTTGTCAAAA
1 TTTTTATTTGTAAAAA
1529014 TTAAAGGCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 8 0.22
27 14 0.39
28 14 0.39
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (27 bp):
TTTTTATTTGTAAAAAATGATAATCCC
Found at i:1533480 original size:27 final size:26
Alignment explanation
Indices: 1533450--1533525 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 26
1533440 AAAATCACCA
1533450 TTTTTATTTGTAAAAAATGATGGTTC
1 TTTTTATTTGTAAAAAATGATGGTTC
* * * * *
1533476 CTTTTAGTTTGTCAAAAATGACGATTT
1 TTTTTA-TTTGTAAAAAATGATGGTTC
* *
1533503 TTTTTGTTTGTAAAAGATGATGG
1 TTTTTATTTGTAAAAAATGATGG
1533526 CTTGTTATTT
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
26 18 0.47
27 20 0.53
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (26 bp):
TTTTTATTTGTAAAAAATGATGGTTC
Found at i:1533506 original size:26 final size:26
Alignment explanation
Indices: 1533450--1533522 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
1533440 AAAATCACCA
* *
1533450 TTTTTA-TTTGTAAAAAATGATGGTTC
1 TTTTTAGTTTGT-AAAAATGACGATTC
*
1533476 CTTTTAGTTTGTCAAAAATGACGATT-
1 TTTTTAGTTTGT-AAAAATGACGATTC
*
1533502 TTTTTTGTTTGTAAAAGATGA
1 TTTTTAGTTTGTAAAA-ATGA
1533523 TGGCTTGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 4 0.10
26 19 0.49
27 16 0.41
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.48
Consensus pattern (26 bp):
TTTTTAGTTTGTAAAAATGACGATTC
Found at i:1535730 original size:5 final size:5
Alignment explanation
Indices: 1535722--1535787 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
1535712 TTTGATTTAT
* * ***
1535722 TAAAA TAAAA TAAAA TTATAA TAAAA TAATTA TTGTA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA -TAAAA TAAAA TAA-AA TAAAA T-AAAA TAAAA
1535770 TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAA
1535788 TTATAATTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
5 42 0.84
6 8 0.16
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (5 bp):
TAAAA
Found at i:1535744 original size:16 final size:16
Alignment explanation
Indices: 1535720--1535785 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
1535710 TATTTGATTT
1535720 ATTAAAATAAAATAAA
1 ATTAAAATAAAATAAA
* *
1535736 ATTATAATAAAATAATT
1 ATTAAAATAAAATAA-A
**
1535753 ATT-GTATAAAAATAAA
1 ATTAAAAT-AAAATAAA
1535769 A-TAAAATAAAATAAA
1 ATTAAAATAAAATAAA
1535784 AT
1 AT
1535786 AATTATAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
15 10 0.26
16 19 0.49
17 10 0.26
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
ATTAAAATAAAATAAA
Found at i:1537303 original size:26 final size:24
Alignment explanation
Indices: 1537274--1537348 Score: 60
Period size: 27 Copynumber: 2.9 Consensus size: 24
1537264 TTTTTTTGAT
1537274 TTAATATTTGTTAATATATTTAATAG
1 TTAA-ATTT-TTAATATATTTAATAG
* * *
1537300 TTAAAATTTTTTATATTAAATAAATAG
1 TT-AAATTTTTAATA-T-ATTTAATAG
*
1537327 TTAAATTTTTTAATTTATTTAA
1 TTAAA-TTTTTAATATATTTAA
1537349 AATTTAATGC
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
25 9 0.24
26 11 0.29
27 18 0.47
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
TTAAATTTTTAATATATTTAATAG
Found at i:1537351 original size:27 final size:26
Alignment explanation
Indices: 1537274--1537349 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
1537264 TTTTTTTGAT
* *
1537274 TTAATATTTGTTAATATATTT-AATAG
1 TTAA-ATTTTTTAATTTATTTAAATAG
**
1537300 TTAAAATTTTTT-ATATTAAATAAATAG
1 TT-AAATTTTTTAAT-TTATTTAAATAG
1537327 TTAAATTTTTTAATTTATTTAAA
1 TTAAATTTTTTAATTTATTTAAA
1537350 ATTTAATGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
25 2 0.05
26 27 0.68
27 11 0.28
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TTAAATTTTTTAATTTATTTAAATAG
Found at i:1537423 original size:19 final size:19
Alignment explanation
Indices: 1537378--1537423 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1537368 ATGTGAATAG
*
1537378 AATATAAATATTTATAATT
1 AATATAAATAATTATAATT
*
1537397 AATTTAAATAATTATAAATT
1 AATATAAATAATTAT-AATT
1537417 AA-ATAAA
1 AATATAAA
1537424 AAGTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATAAATAATTATAATT
Found at i:1537690 original size:3 final size:3
Alignment explanation
Indices: 1537682--1537711 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1537672 TTGTAAAGCA
1537682 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1537712 CATCATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1538531 original size:27 final size:27
Alignment explanation
Indices: 1538501--1538564 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
1538491 ATTATTTGTA
*
1538501 TATTTTTATAATTTTATATATAAT-TTT
1 TATTTTTATAATTTAAT-TATAATATTT
*
1538528 TATTTATT-TAATTTAATTATTATATTT
1 TATTT-TTATAATTTAATTATAATATTT
1538555 TATATTTTAT
1 TAT-TTTTAT
1538565 TCATATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
26 5 0.16
27 21 0.68
28 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TATTTTTATAATTTAATTATAATATTT
Found at i:1538561 original size:20 final size:20
Alignment explanation
Indices: 1538506--1538561 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1538496 TTGTATATTT
* *
1538506 TTATAATTTTATATATAATTT
1 TTAT-ATTTTATATTTAATTA
*
1538527 TTATTTATTTA-ATTTAATTA
1 TTATAT-TTTATATTTAATTA
1538547 TTATATTTTATATTT
1 TTATATTTTATATTT
1538562 TATTCATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.14
20 17 0.59
21 8 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATATTTTATATTTAATTA
Found at i:1539118 original size:19 final size:18
Alignment explanation
Indices: 1539087--1539165 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 18
1539077 TTAAATTTTA
*
1539087 AAAAT-TTAATTTAAAAT
1 AAAATATTAAATTAAAAT
1539104 AAAATATTAAATTTAAAAT
1 AAAATATTAAA-TTAAAAT
1539123 --AAT-TTAAATTAAAACT
1 AAAATATTAAATTAAAA-T
*
1539139 AAAAATATT-TATTAAAAT
1 -AAAATATTAAATTAAAAT
1539157 AAATATATT
1 AAA-ATATT
1539166 TTTTTATAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
15 6 0.12
16 6 0.12
17 11 0.21
18 10 0.19
19 17 0.33
20 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATATTAAATTAAAAT
Found at i:1539127 original size:34 final size:35
Alignment explanation
Indices: 1539071--1539147 Score: 104
Period size: 34 Copynumber: 2.2 Consensus size: 35
1539061 ATAAAAAGAT
* *
1539071 AAATATTTAAATTTTAAAAATTTAATTTAAAA-T-A
1 AAATA-TTAAATTTAAAAAATTTAAATTAAAACTAA
1539105 AAATATTAAATTTAAAATAATTTAAATTAAAACTAA
1 AAATATTAAATTTAAAA-AATTTAAATTAAAACTAA
1539141 AAATATT
1 AAATATT
1539148 TATTAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 11 0.29
34 18 0.47
35 1 0.03
36 8 0.21
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (35 bp):
AAATATTAAATTTAAAAAATTTAAATTAAAACTAA
Found at i:1539166 original size:18 final size:19
Alignment explanation
Indices: 1539130--1539166 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1539120 AATAATTTAA
1539130 ATTAAAACTAAAAATATTT
1 ATTAAAACTAAAAATATTT
*
1539149 ATTAAAA-TAAATATATTT
1 ATTAAAACTAAAAATATTT
1539167 TTTTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAAAACTAAAAATATTT
Found at i:1540463 original size:15 final size:15
Alignment explanation
Indices: 1540413--1540456 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
1540403 TTTCAAAATC
*
1540413 TAAAATAATTTAACT
1 TAAAATAACTTAACT
1540428 TAAAATAACTTAACT
1 TAAAATAACTTAACT
1540443 TAAAATAACTTAAC
1 TAAAATAACTTAAC
1540457 CAAAAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATAACTTAACT
Done.