Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 19 of 24
Found at i:2447777 original size:2 final size:2
Alignment explanation
Indices: 2447770--2447800 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2447760 TTCCATTTCC
2447770 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 T
2447801 GATTGTCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2448181 original size:18 final size:17
Alignment explanation
Indices: 2448158--2448227 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 17
2448148 AAAGAATTTT
2448158 AAAAAATAAAAATAATTA
1 AAAAAATAAAAA-AATTA
*
2448176 AAAAAATTAAAAAAATCA
1 AAAAAA-TAAAAAAATTA
* *
2448194 TAAAAATTAAAAAAATTT
1 -AAAAAATAAAAAAATTA
*
2448212 AAAAGATAAAATAAAT
1 AAAAAATAAAA-AAAT
2448228 AACATAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 9 0.21
18 23 0.53
19 11 0.26
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (17 bp):
AAAAAATAAAAAAATTA
Found at i:2448188 original size:27 final size:26
Alignment explanation
Indices: 2448158--2448227 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
2448148 AAAGAATTTT
2448158 AAAAAATAAAAATAATTAAAAAAATTA
1 AAAAAATAAAAA-AATTAAAAAAATTA
* *
2448185 AAAAAATCATAAAAATTAAAAAAATTT
1 AAAAAAT-AAAAAAATTAAAAAAATTA
*
2448212 AAAAGATAAAATAAAT
1 AAAAAATAAAA-AAAT
2448228 AACATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.08
27 30 0.81
28 4 0.11
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (26 bp):
AAAAAATAAAAAAATTAAAAAAATTA
Found at i:2448197 original size:11 final size:9
Alignment explanation
Indices: 2448158--2448215 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
2448148 AAAGAATTTT
2448158 AAAAAA-TA
1 AAAAAATTA
2448166 AAAATAATTA
1 AAAA-AATTA
2448176 AAAAAATTA
1 AAAAAATTA
*
2448185 AAAAAATCA
1 AAAAAATTA
*
2448194 TAAAAATTA
1 AAAAAATTA
2448203 AAAAAATTTA
1 AAAAAA-TTA
2448213 AAA
1 AAA
2448216 GATAAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 4 0.09
9 27 0.63
10 12 0.28
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAAATTA
Found at i:2449444 original size:3 final size:3
Alignment explanation
Indices: 2449436--2449464 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2449426 AAATTTTAAC
2449436 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2449465 CCTGAAATCC
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2449497 original size:2 final size:2
Alignment explanation
Indices: 2449490--2449530 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2449480 TAATTAAAGT
2449490 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2449531 CTAAATTCAT
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:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2450220 original size:2 final size:2
Alignment explanation
Indices: 2450215--2450244 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2450205 ATGTGTGTGC
2450215 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
2450245 ACATAAAAAA
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):
TA
Found at i:2451571 original size:7 final size:7
Alignment explanation
Indices: 2451559--2451587 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2451549 ATCTTTATTA
2451559 TTAAAAT
1 TTAAAAT
2451566 TTAAAAT
1 TTAAAAT
2451573 TTAAAAT
1 TTAAAAT
2451580 TTAAAAT
1 TTAAAAT
2451587 T
1 T
2451588 AATTAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTAAAAT
Found at i:2451645 original size:24 final size:23
Alignment explanation
Indices: 2451600--2451653 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
2451590 TTAATTTATA
* *
2451600 TAATTATTTTAAAA-ATATAATATT
1 TAATTAATTTAAAATTTA-AATA-T
*
2451624 TAATTAATTTAAAATTTAAATAC
1 TAATTAATTTAAAATTTAAATAT
2451647 TAATTAA
1 TAATTAA
2451654 AAAATTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 7 0.27
24 17 0.65
25 2 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATTAATTTAAAATTTAAATAT
Found at i:2451878 original size:14 final size:14
Alignment explanation
Indices: 2451859--2451955 Score: 53
Period size: 14 Copynumber: 6.9 Consensus size: 14
2451849 TTTTTGTTTG
2451859 TATTAATAAATTTA
1 TATTAATAAATTTA
2451873 TATTAAT--ATTTA
1 TATTAATAAATTTA
*
2451885 TA-TAATTATATTTAA
1 TATTAA-TAAATTT-A
* * *
2451900 AATATATTATATTTA
1 TAT-TAATAAATTTA
*
2451915 TATTAAT--TTTAATA
1 TATTAATAAATT--TA
2451929 TATTAAT-AATTTA
1 TATTAATAAATTTA
2451942 TATTATATAAATTT
1 TATTA-ATAAATTT
2451956 TAAAAATATA
Statistics
Matches: 66, Mismatches: 6, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
11 3 0.05
12 10 0.15
13 7 0.11
14 25 0.38
15 12 0.18
16 7 0.11
17 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATTAATAAATTTA
Found at i:2451910 original size:16 final size:16
Alignment explanation
Indices: 2451871--2451914 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2451861 TTAATAAATT
*
2451871 TATATTAATATTT-ATA
1 TATATT-ATATTTAAAA
2451887 TA-ATTATATTTAAAA
1 TATATTATATTTAAAA
2451902 TATATTATATTTA
1 TATATTATATTTA
2451915 TATTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
16 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTATATTTAAAA
Found at i:2451931 original size:27 final size:28
Alignment explanation
Indices: 2451871--2451946 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 28
2451861 TTAATAAATT
*
2451871 TATATTAATATTTATATAATTATATTTAAAA
1 TATATT-ATATTTATAT--TAATATTTAAAA
2451902 TATATTATATTTATATTAAT-TTT--AA
1 TATATTATATTTATATTAATATTTAAAA
2451927 TATATTAATAATTTATATTA
1 TATATT-AT-ATTTATATTA
2451947 TATAAATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
25 8 0.19
26 2 0.05
27 13 0.31
28 3 0.07
30 10 0.24
31 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TATATTATATTTATATTAATATTTAAAA
Found at i:2452047 original size:2 final size:2
Alignment explanation
Indices: 2452034--2452067 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2452024 ATTGAATCGA
*
2452034 AT AT AT AA 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
2452068 TATGGTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2453104 original size:19 final size:19
Alignment explanation
Indices: 2453071--2453132 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
2453061 ACTTAAAAAG
* *
2453071 TAATTATAATATAATATTA
1 TAATTATTATTTAATATTA
*
2453090 TAATTATTATTTAATAATTT
1 TAATTATTATTTAAT-ATTA
* *
2453110 TAA-TATTTTTTATTATTAA
1 TAATTATTATTTAATATT-A
2453129 TAAT
1 TAAT
2453133 ATAATCGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 3 0.09
19 25 0.74
20 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATTATTATTTAATATTA
Found at i:2453151 original size:29 final size:29
Alignment explanation
Indices: 2453112--2453167 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2453102 AATAATTTTA
*
2453112 ATATTTTTTATTATTAATAAT-ATAATCG
1 ATATTTTTTATAATTAATAATCATAATCG
*
2453140 ATATTTTATTATAATTAATTATCATAAT
1 ATATTTT-TTATAATTAATAATCATAAT
2453168 ATTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 12 0.50
30 5 0.21
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (29 bp):
ATATTTTTTATAATTAATAATCATAATCG
Found at i:2453202 original size:26 final size:30
Alignment explanation
Indices: 2453148--2453202 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
2453138 CGATATTTTA
*
2453148 TTATAATTAATTATCATAATATTATTATAT
1 TTATAATTAATTATCATAATATTAATATAT
2453178 TTATAATT-ATTAT-A-AATA-TAATATA
1 TTATAATTAATTATCATAATATTAATATA
2453203 AAAAAATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 4 0.17
28 1 0.04
29 5 0.21
30 8 0.33
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
TTATAATTAATTATCATAATATTAATATAT
Found at i:2453830 original size:38 final size:38
Alignment explanation
Indices: 2453739--2453847 Score: 112
Period size: 38 Copynumber: 2.9 Consensus size: 38
2453729 AGCCAGCCAC
* ** **
2453739 CAACCAATTCCAAATTGAATTCTCTAGTCATCAGTCAT
1 CAACCAATTTCAAATTGAATTCTCTAACCATCAACCAT
*
2453777 CAACGAA-TTCTAAATTGAATTCTCTAACCATCAACCAT
1 CAACCAATTTC-AAATTGAATTCTCTAACCATCAACCAT
** * *
2453815 CTGCCAATTTCAAATTAAATTTTCTAACCATCA
1 CAACCAATTTCAAATTGAATTCTCTAACCATCA
2453848 GCAATTCAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
37 2 0.03
38 53 0.91
39 3 0.05
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (38 bp):
CAACCAATTTCAAATTGAATTCTCTAACCATCAACCAT
Found at i:2457980 original size:35 final size:35
Alignment explanation
Indices: 2457928--2457996 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
2457918 AAATATGAGT
*
2457928 AAGGAAGTAAATAGCACCAAAAATTTTAACGTAGC
1 AAGGAAGAAAATAGCACCAAAAATTTTAACGTAGC
*
2457963 AAGGAAGAAAATGGCACCAAAAATTTTAACGTAG
1 AAGGAAGAAAATAGCACCAAAAATTTTAACGTAG
2457997 TTCACCCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (35 bp):
AAGGAAGAAAATAGCACCAAAAATTTTAACGTAGC
Found at i:2458950 original size:15 final size:14
Alignment explanation
Indices: 2458930--2458972 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
2458920 GGCGGTCTTT
2458930 TATTTTACAATTAAA
1 TATTTTA-AATTAAA
*
2458945 TATTTTAAGTATAAA
1 TATTTTAAAT-TAAA
2458960 TGATTTTAAATTA
1 T-ATTTTAAATTA
2458973 TTAAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 2 0.08
15 14 0.58
16 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (14 bp):
TATTTTAAATTAAA
Found at i:2459097 original size:16 final size:15
Alignment explanation
Indices: 2459049--2459100 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2459039 TAAATTTTAT
2459049 TTTTAATAAAATTAAA
1 TTTTAA-AAAATTAAA
* * *
2459065 TTATATTAAATTTAAA
1 TTTTA-AAAAATTAAA
2459081 TTTTAAAAAATTAAAA
1 TTTTAAAAAATT-AAA
2459097 TTTT
1 TTTT
2459101 TTTGTGAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTTAAAAAATTAAA
Found at i:2459539 original size:20 final size:21
Alignment explanation
Indices: 2459510--2459548 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2459500 TATAATTAAA
2459510 TTTAAATAAAAATA-TATTAT
1 TTTAAATAAAAATACTATTAT
*
2459530 TTTAATTAAAAATACTATT
1 TTTAAATAAAAATACTATT
2459549 CTAAACTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAAATAAAAATACTATTAT
Found at i:2460074 original size:25 final size:25
Alignment explanation
Indices: 2460042--2460097 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
2460032 ATATAAAATT
*
2460042 TAAAATATTATAT-TTTTATCATATA
1 TAAAATATTATATATATTAT-ATATA
* *
2460067 TAAAATATTTTATATATTATATTTA
1 TAAAATATTATATATATTATATATA
2460092 TAAAAT
1 TAAAAT
2460098 TATATTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TAAAATATTATATATATTATATATA
Found at i:2460481 original size:17 final size:17
Alignment explanation
Indices: 2460459--2460493 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2460449 TGAGTGGAGC
*
2460459 TTTTATTTTTATGAAAT
1 TTTTATATTTATGAAAT
*
2460476 TTTTATATTTATTAAAT
1 TTTTATATTTATGAAAT
2460493 T
1 T
2460494 ATCAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTATATTTATGAAAT
Found at i:2460793 original size:21 final size:21
Alignment explanation
Indices: 2460768--2460832 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
2460758 TATTTGATTT
*
2460768 ATTTAATTTATATTTAATTAA
1 ATTTAAATTATATTTAATTAA
*
2460789 ATTTAAATAATATTT--TTATA
1 ATTTAAATTATATTTAATTA-A
*
2460809 ATTTAAATTA-AATTAATTTAA
1 ATTTAAATTATATTTAA-TTAA
2460830 ATT
1 ATT
2460833 ATTATTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 6 0.17
20 10 0.28
21 17 0.47
22 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAAATTATATTTAATTAA
Found at i:2460845 original size:35 final size:35
Alignment explanation
Indices: 2460771--2460845 Score: 91
Period size: 35 Copynumber: 2.1 Consensus size: 35
2460761 TTGATTTATT
* *
2460771 TAATTTATATTTAATTAAATTTAAATAATATTTTTA
1 TAATTTAAATTAAATTAAATTTAAAT-ATATTTTTA
2460807 TAATTTAAATTAAATT-AATTTAAAT-TATTATTTAA
1 TAATTTAAATTAAATTAAATTTAAATATATT-TTT-A
2460842 TAAT
1 TAAT
2460846 AAAAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 4 0.11
34 3 0.09
35 14 0.40
36 14 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
TAATTTAAATTAAATTAAATTTAAATATATTTTTA
Found at i:2460851 original size:20 final size:20
Alignment explanation
Indices: 2460828--2460914 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
2460818 AAATTAATTT
2460828 AAATTATTATTTAATAATAA
1 AAATTATTATTTAATAATAA
* *
2460848 AAATTTTTATTTAATTTATTAA
1 AAATTATTATTTAA--TAATAA
*
2460870 AAATATATAAATATTAAT-ATAA
1 AAAT-TAT-TAT-TTAATAATAA
*
2460892 AAATTATTTTTTAATAATAA
1 AAATTATTATTTAATAATAA
2460912 AAA
1 AAA
2460915 AGATTATCGA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
19 5 0.09
20 21 0.39
21 3 0.06
22 16 0.30
23 3 0.06
24 2 0.04
25 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTATTATTTAATAATAA
Found at i:2463517 original size:2 final size:2
Alignment explanation
Indices: 2463510--2463555 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2463500 AACAAGACCT
2463510 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
2463552 TA TA
1 TA TA
2463556 AAAGAATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2464373 original size:5 final size:5
Alignment explanation
Indices: 2464365--2464389 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2464355 CATAAAAAAA
2464365 AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT
2464390 CGTAAGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:2464714 original size:3 final size:3
Alignment explanation
Indices: 2464708--2464733 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2464698 ATCGTCATCA
2464708 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
2464734 CTTTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:2466118 original size:4 final size:4
Alignment explanation
Indices: 2466109--2466184 Score: 71
Period size: 4 Copynumber: 19.0 Consensus size: 4
2466099 AATATACATT
* * * * * * * * *
2466109 TATG TATG TATG TGTG TGTG TGTG TGTG TCTA TATA TATA TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2466157 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
2466185 CATGGACAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.24, C:0.01, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:2467586 original size:111 final size:111
Alignment explanation
Indices: 2467439--2467640 Score: 359
Period size: 111 Copynumber: 1.8 Consensus size: 111
2467429 TTGAACCCTA
* * *
2467439 ATCAAACTTCATTGTTCAACTGCTTTATTATTATTTTGGTTTCTAATCATTTATACCAAATTTGA
1 ATCAAAATTCATTATTCAACTGCTTTATTATTATTTTGGTTACTAATCATTTATACCAAATTTGA
2467504 TGTGGAAGACTATATAACCCATAACAAGGGAAATATCACTTTTGCT
66 TGTGGAAGACTATATAACCCATAACAAGGGAAATATCACTTTTGCT
2467550 ATCAAAATTCATTATTCAACTGCTTTATTATTATTTTGGTTACTAATCATTTATACCAAATTTGA
1 ATCAAAATTCATTATTCAACTGCTTTATTATTATTTTGGTTACTAATCATTTATACCAAATTTGA
* *
2467615 TGTGGAATATTATATAACCCATAACA
66 TGTGGAAGACTATATAACCCATAACA
2467641 TTAGAAATAT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 86 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (111 bp):
ATCAAAATTCATTATTCAACTGCTTTATTATTATTTTGGTTACTAATCATTTATACCAAATTTGA
TGTGGAAGACTATATAACCCATAACAAGGGAAATATCACTTTTGCT
Found at i:2471768 original size:2 final size:2
Alignment explanation
Indices: 2471761--2471799 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2471751 CAAAAGCAAC
2471761 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2471800 AAGCACCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2472475 original size:69 final size:69
Alignment explanation
Indices: 2472364--2472500 Score: 274
Period size: 69 Copynumber: 2.0 Consensus size: 69
2472354 TTGGCATTTA
2472364 GGAAACTGTCCCTAAACATCAGATACATCTGATCAACAATCAAAAGAGGCTCCATTGCAAGAGGC
1 GGAAACTGTCCCTAAACATCAGATACATCTGATCAACAATCAAAAGAGGCTCCATTGCAAGAGGC
2472429 CAAT
66 CAAT
2472433 GGAAACTGTCCCTAAACATCAGATACATCTGATCAACAATCAAAAGAGGCTCCATTGCAAGAGGC
1 GGAAACTGTCCCTAAACATCAGATACATCTGATCAACAATCAAAAGAGGCTCCATTGCAAGAGGC
2472498 CAA
66 CAA
2472501 GGGGTAGCCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (69 bp):
GGAAACTGTCCCTAAACATCAGATACATCTGATCAACAATCAAAAGAGGCTCCATTGCAAGAGGC
CAAT
Found at i:2474277 original size:31 final size:32
Alignment explanation
Indices: 2474242--2474302 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
2474232 GCGCCATATA
*
2474242 TTATGC-TTTCACTAGAAAATCATCCATTAAG
1 TTATGCTTTTCACTAGAAAATCATACATTAAG
*
2474273 TTATGCTTTTCACTAGAAGATCATACATTA
1 TTATGCTTTTCACTAGAAAATCATACATTA
2474303 TATGAAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (32 bp):
TTATGCTTTTCACTAGAAAATCATACATTAAG
Found at i:2478062 original size:2 final size:2
Alignment explanation
Indices: 2478055--2478104 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2478045 GTCTTCCATG
2478055 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
*
2478097 TA CA TA TA
1 TA TA TA TA
2478105 AAACTACTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2483158 original size:3 final size:3
Alignment explanation
Indices: 2483150--2483186 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2483140 CATTTATTGC
2483150 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2483187 ATAATTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2483316 original size:2 final size:2
Alignment explanation
Indices: 2483304--2483345 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2483294 TTAGTATTAG
*
2483304 TA TA CA 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
2483346 CACTTGTAAA
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:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2485516 original size:17 final size:17
Alignment explanation
Indices: 2485494--2485528 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2485484 AATCAGCAAA
2485494 TTAAAAACAGAAATGAT
1 TTAAAAACAGAAATGAT
*
2485511 TTAAAATCAGAAATGAT
1 TTAAAAACAGAAATGAT
2485528 T
1 T
2485529 CCTAGAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (17 bp):
TTAAAAACAGAAATGAT
Found at i:2491090 original size:25 final size:28
Alignment explanation
Indices: 2491062--2491126 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 28
2491052 AATAAATTAT
2491062 TAATTTTATTTA-TAAAATAAA-AA-AA
1 TAATTTTATTTATTAAAATAAAGAATAA
* *
2491087 TAATTCT-TTTATTAATATAAAGAATAA
1 TAATTTTATTTATTAAAATAAAGAATAA
*
2491114 TAATAATTATTTA
1 TAAT-TTTATTTA
2491127 CACAAGTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 4 0.13
25 14 0.45
26 2 0.06
27 6 0.19
28 1 0.03
29 4 0.13
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
TAATTTTATTTATTAAAATAAAGAATAA
Found at i:2491559 original size:2 final size:2
Alignment explanation
Indices: 2491552--2491587 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2491542 TACTTTAAAT
*
2491552 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2491588 CAAGTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2499440 original size:72 final size:72
Alignment explanation
Indices: 2499289--2499613 Score: 373
Period size: 72 Copynumber: 4.5 Consensus size: 72
2499279 GCACACAAAG
* * * *
2499289 TTATTTATTGTAATTATCGTACAAATTATCTCAGA-TAATTGTTGATAATAATTTTCAATATGCA
1 TTATTGATTGTAATTATCGTACAAATTATCTCGGATTAATTGTTGATAATAGTTTTAAATATGCA
2499353 GAAATAT
66 GAAATAT
* * * * * * * * **
2499360 TTGTTGATTGTAGTTATCGTGCAAATTATTTTGGATTAGTTGTCGATAGTAGTTTTAAATATATA
1 TTATTGATTGTAATTATCGTACAAATTATCTCGGATTAATTGTTGATAATAGTTTTAAATATGCA
2499425 GAAATAT
66 GAAATAT
* * * * *
2499432 TTATTGATTGTAATTATCATACAGATTATTTCGGATTAGTTGTTGATAGTAGTTTTAAATATGCA
1 TTATTGATTGTAATTATCGTACAAATTATCTCGGATTAATTGTTGATAATAGTTTTAAATATGCA
*
2499497 TAAATAT
66 GAAATAT
* * * *
2499504 TTGTTGATTGTAGTTATCGTACAAATTATCTCGAATTAATTATTGATAATAGTTTTAAATATGCA
1 TTATTGATTGTAATTATCGTACAAATTATCTCGGATTAATTGTTGATAATAGTTTTAAATATGCA
* *
2499569 AAAATAA
66 GAAATAT
* * * *
2499576 TTATTGATTATATTTATCGTGCAAATTATCTCGAATTA
1 TTATTGATTGTAATTATCGTACAAATTATCTCGGATTA
2499614 TCGTTTCATC
Statistics
Matches: 214, Mismatches: 39, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
71 28 0.13
72 186 0.87
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.45
Consensus pattern (72 bp):
TTATTGATTGTAATTATCGTACAAATTATCTCGGATTAATTGTTGATAATAGTTTTAAATATGCA
GAAATAT
Found at i:2502578 original size:22 final size:22
Alignment explanation
Indices: 2502553--2502605 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
2502543 TTTGGTATTA
* * *
2502553 ATTTTACTTTTATTATTATAAT
1 ATTTTAATTTAATTATTAAAAT
2502575 ATTTTAATTTAATTATTAAAAT
1 ATTTTAATTTAATTATTAAAAT
*
2502597 A-ATTAATTT
1 ATTTTAATTT
2502606 TTTTTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTAATTTAATTATTAAAAT
Found at i:2505246 original size:15 final size:15
Alignment explanation
Indices: 2505216--2505265 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2505206 AAAATATACC
*
2505216 TAAAATATATAATATA
1 TAAAAAATA-AATATA
* *
2505232 TATAAATTAAATATA
1 TAAAAAATAAATATA
*
2505247 CAAAAAATAAATATA
1 TAAAAAATAAATATA
2505262 TAAA
1 TAAA
2505266 TATTTTAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
15 21 0.78
16 6 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAAAAATAAATATA
Found at i:2505274 original size:32 final size:31
Alignment explanation
Indices: 2505238--2505307 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
2505228 TATATATAAA
2505238 TTAAATATACAA-AAAATAAATATATAAATATT
1 TTAAATATA-AATAAAATAAAT-TATAAATATT
* * *
2505270 TTAAAATTTAAATAATATAAATTATTAATATT
1 TT-AAATATAAATAAAATAAATTATAAATATT
2505302 TTAAAT
1 TTAAAT
2505308 TTTATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 4 0.12
32 15 0.45
33 14 0.42
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (31 bp):
TTAAATATAAATAAAATAAATTATAAATATT
Found at i:2505304 original size:25 final size:24
Alignment explanation
Indices: 2505254--2505321 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 24
2505244 ATACAAAAAA
*
2505254 TAAATATATAAATATTTTAAAATT
1 TAAATATATAAATATATTAAAATT
*
2505278 TAAATAATATAAAT-TATTAATATTT
1 TAAAT-ATATAAATATATTAA-AATT
2505303 TAAATTTTATATAAATATA
1 TAAA---TATATAAATATA
2505322 AAATCTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
24 10 0.28
25 15 0.42
27 8 0.22
28 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAATATATAAATATATTAAAATT
Found at i:2505320 original size:33 final size:33
Alignment explanation
Indices: 2505253--2505323 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
2505243 TATACAAAAA
2505253 ATAAATATATAAATATTTTAAAATTTAAATAAT
1 ATAAATATATAAATATTTTAAAATTTAAATAAT
* * *
2505286 ATAAAT-TATTAATATTTTAAATTTTATATAAAT
1 ATAAATATATAAATATTTTAAAATTTAAAT-AAT
2505319 ATAAA
1 ATAAA
2505324 ATCTTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 20 0.59
33 14 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
ATAAATATATAAATATTTTAAAATTTAAATAAT
Found at i:2505344 original size:20 final size:20
Alignment explanation
Indices: 2505307--2505344 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2505297 ATATTTTAAA
*
2505307 TTTTATATAAATATAAAATC
1 TTTTATATAAATAAAAAATC
2505327 TTTTA-ATATAATAAAAAA
1 TTTTATATA-AATAAAAAA
2505345 ATATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTTATATAAATAAAAAATC
Found at i:2505602 original size:20 final size:20
Alignment explanation
Indices: 2505574--2505613 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2505564 ATATATTTAT
2505574 ATTTATTTATTTAAAATAAA
1 ATTTATTTATTTAAAATAAA
* *
2505594 ATTTTTTTATTTAAATTAAA
1 ATTTATTTATTTAAAATAAA
2505614 TTAAATTAAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTATTTATTTAAAATAAA
Found at i:2506530 original size:21 final size:22
Alignment explanation
Indices: 2506488--2506530 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2506478 TTGTTTATCA
* *
2506488 TAAAATTAAATAATTATATTTT
1 TAAAATAAAAAAATTATATTTT
2506510 TAAAATAAAAAAATTAT-TTTT
1 TAAAATAAAAAAATTATATTTT
2506531 ACTTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAATAAAAAAATTATATTTT
Found at i:2507598 original size:21 final size:19
Alignment explanation
Indices: 2507560--2507600 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2507550 ATAATGATCA
*
2507560 AATTGAATTTAAAATTTTT
1 AATTGAATTGAAAATTTTT
2507579 AATTGAATTCGAATAATTTTT
1 AATTGAATT-GAA-AATTTTT
2507600 A
1 A
2507601 TATATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 2 0.11
21 8 0.42
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (19 bp):
AATTGAATTGAAAATTTTT
Found at i:2508088 original size:20 final size:19
Alignment explanation
Indices: 2508082--2508142 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
2508072 ATTAATATTA
2508082 AAAATTTTAAATTTAAATT
1 AAAATTTTAAATTTAAATT
*
2508101 AAAATTTTAAGTTTAAA-T
1 AAAATTTTAAATTTAAATT
*
2508119 ATAAATAATTAAATTTAAAATT
1 A-AAAT-TTTAAATTT-AAATT
2508141 AA
1 AA
2508143 GCATAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 2 0.06
19 20 0.57
20 7 0.20
21 4 0.11
22 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATTTTAAATTTAAATT
Found at i:2508091 original size:19 final size:18
Alignment explanation
Indices: 2508067--2508142 Score: 64
Period size: 19 Copynumber: 3.9 Consensus size: 18
2508057 ATTTATTTAT
2508067 TTTTAA-TTAATATTAAAAA
1 TTTTAATTTAA-ATT-AAAA
2508086 TTTTAAATTTAAATTAAAA
1 TTTT-AATTTAAATTAAAA
2508105 TTTTAAGTTTAAATATAAATA
1 TTTTAA-TTTAAAT-TAAA-A
* *
2508126 ATTAAATTTAAAATTAA
1 TTTTAATTT-AAATTAA
2508143 GCATAAAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.04
19 19 0.39
20 15 0.31
21 13 0.27
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
TTTTAATTTAAATTAAAA
Found at i:2510680 original size:2 final size:2
Alignment explanation
Indices: 2510673--2510701 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2510663 CTTTATCCTT
2510673 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 T
2510702 GAAATCGGCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2512703 original size:20 final size:20
Alignment explanation
Indices: 2512655--2512703 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2512645 ATTTTCGTAT
2512655 CATAAAA-ATATAAAATACG
1 CATAAAATATATAAAATACG
* *
2512674 CATAACATATATAAGATACG
1 CATAAAATATATAAAATACG
**
2512694 GTTAAAATAT
1 CATAAAATAT
2512704 GATTAATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (20 bp):
CATAAAATATATAAAATACG
Found at i:2512763 original size:65 final size:65
Alignment explanation
Indices: 2512694--2512857 Score: 163
Period size: 65 Copynumber: 2.5 Consensus size: 65
2512684 ATAAGATACG
* *
2512694 GTTAAAATATGATTAATTAATCATATCATAAATGGGTAATCGTATC-ATATC-TATCCATTTACA
1 GTTAAAATATGATTAATTAATCATATCATAAATGGATAATCGTATCAATA-CATATCCATTAACA
2512757 C
65 C
* * * * * * * * * *
2512758 AGTTAAGACATAATTAATTAATCGTGTCATAAATGTATAATTGTGTTAATACATATCCGTTAACA
1 -GTTAAAATATGATTAATTAATCATATCATAAATGGATAATCGTATCAATACATATCCATTAACA
2512823 C
65 C
*
2512824 GTTTAAAATATGATTATTTAA-CATATCATAAATG
1 G-TTAAAATATGATTAATTAATCATATCATAAATG
2512858 AATAGACACG
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
65 49 0.63
66 29 0.37
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (65 bp):
GTTAAAATATGATTAATTAATCATATCATAAATGGATAATCGTATCAATACATATCCATTAACAC
Found at i:2513257 original size:20 final size:20
Alignment explanation
Indices: 2513234--2513273 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2513224 AATGTTTGGA
*
2513234 TTAAATTTTAAATATGATAT
1 TTAAAATTTAAATATGATAT
*
2513254 TTAAAATTTAATTATGATAT
1 TTAAAATTTAAATATGATAT
2513274 GATATGAATA
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:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TTAAAATTTAAATATGATAT
Found at i:2513640 original size:127 final size:127
Alignment explanation
Indices: 2513489--2513724 Score: 377
Period size: 127 Copynumber: 1.9 Consensus size: 127
2513479 TCGGTTTTAT
*
2513489 CTTGTCCATAAAAAATTAGAAATAAAGCCAATCAATCAACTAAAATATGA-TTTTATTGAATCCT
1 CTTGTCCATAAAAAATTAGAAATAAAACCAATCAATCAACTAAAATA-GAGTTTTATTGAATCCT
* *
2513553 CTCATCCACTCCACTTAGACAAGCACCTTTCTCTTAATTTCACTTGTCACAATTGCCCAAATC
65 CTCATCCACTCCACTTAGACAAACACCTTTCTCCTAATTTCACTTGTCACAATTGCCCAAATC
*
2513616 CTTGTCCATAGAAAAA-TAGAAATAAAACCAATCAATTAACTAAAATAGAGTTTTATTGAATCCT
1 CTTGTCCATA-AAAAATTAGAAATAAAACCAATCAATCAACTAAAATAGAGTTTTATTGAATCCT
* * *
2513680 CTCATCCACTCGACTTCGACAAACACCTTTTTCCTAATTTCACTT
65 CTCATCCACTCCACTTAGACAAACACCTTTCTCCTAATTTCACTT
2513725 ATAGACAATC
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
126 2 0.02
127 93 0.93
128 5 0.05
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (127 bp):
CTTGTCCATAAAAAATTAGAAATAAAACCAATCAATCAACTAAAATAGAGTTTTATTGAATCCTC
TCATCCACTCCACTTAGACAAACACCTTTCTCCTAATTTCACTTGTCACAATTGCCCAAATC
Found at i:2517046 original size:25 final size:23
Alignment explanation
Indices: 2516996--2517046 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
2516986 TTGAACTTTT
* **
2516996 ATTTTGTTTGTTGATACATTTGA
1 ATTTTGTTTGTTAATACATTAAA
2517019 ATTTTGTTTGTGTAATTACATTAAA
1 ATTTTGTTTGT-TAA-TACATTAAA
2517044 ATT
1 ATT
2517047 GGATAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 11 0.48
24 2 0.09
25 10 0.43
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (23 bp):
ATTTTGTTTGTTAATACATTAAA
Found at i:2517349 original size:35 final size:34
Alignment explanation
Indices: 2517280--2517349 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
2517270 TTGTGTCGTG
**
2517280 TCGTATCATATTAACATAAACGGATCAAGTTTAA
1 TCGTATCATATTAACATAAACAAATCAAGTTTAA
* * *
2517314 TCGTATCATATTAAACGTTAACAAATCAATTTTAA
1 TCGTATCATATT-AACATAAACAAATCAAGTTTAA
2517349 T
1 T
2517350 TGTGTCGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (34 bp):
TCGTATCATATTAACATAAACAAATCAAGTTTAA
Found at i:2518144 original size:2 final size:2
Alignment explanation
Indices: 2518139--2518168 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2518129 ACACACACAC
2518139 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
2518169 CCTCTCTTTA
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:2525102 original size:11 final size:11
Alignment explanation
Indices: 2525083--2525125 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
2525073 TTTGGATCTG
*
2525083 AAAAAATAATT
1 AAAATATAATT
2525094 AAAATATAATGT
1 AAAATATAAT-T
2525106 AAAATATAA-T
1 AAAATATAATT
2525116 ATAAATATAA
1 A-AAATATAA
2525126 ATGTAATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 2 0.07
11 17 0.59
12 10 0.34
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (11 bp):
AAAATATAATT
Found at i:2525110 original size:12 final size:12
Alignment explanation
Indices: 2525083--2525131 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
2525073 TTTGGATCTG
*
2525083 AAAAAATAAT-T
1 AAAATATAATGT
2525094 AAAATATAATGT
1 AAAATATAATGT
*
2525106 AAAATATAATAT
1 AAAATATAATGT
2525118 -AAATATAAATGT
1 AAAATAT-AATGT
2525130 AA
1 AA
2525132 TATGAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 15 0.47
12 16 0.50
13 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (12 bp):
AAAATATAATGT
Found at i:2525114 original size:23 final size:24
Alignment explanation
Indices: 2525083--2525131 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2525073 TTTGGATCTG
2525083 AAAAAATAAT-TAAA-ATATAATGT
1 AAAAAATAATATAAATATA-AATGT
*
2525106 AAAATATAATATAAATATAAATGT
1 AAAAAATAATATAAATATAAATGT
2525130 AA
1 AA
2525132 TATGAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 9 0.39
24 11 0.48
25 3 0.13
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAAAATAATATAAATATAAATGT
Found at i:2525221 original size:11 final size:11
Alignment explanation
Indices: 2525178--2525223 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
2525168 TAATATTTAA
*
2525178 AATATAATTAT
1 AATATAAATAT
*
2525189 GATATATAAAAAT
1 -A-ATATAAATAT
2525202 AATATAAATAT
1 AATATAAATAT
2525213 AATATAAATAT
1 AATATAAATAT
2525224 TTTATTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 20 0.67
12 2 0.07
13 8 0.27
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
AATATAAATAT
Found at i:2526692 original size:5 final size:5
Alignment explanation
Indices: 2526682--2526709 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2526672 TTAATAATTT
2526682 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
2526710 TGCAGATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:2527560 original size:2 final size:2
Alignment explanation
Indices: 2527544--2527584 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2527534 TCCACTGACC
* *
2527544 TA TA TA CA TA CA 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
2527585 TCTTAGGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2528027 original size:20 final size:22
Alignment explanation
Indices: 2527989--2528032 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
2527979 ATTTATAGTT
2527989 AAAATAAAAAATAAATTTT-TA
1 AAAATAAAAAATAAATTTTGTA
* *
2528010 AAAATAATAAAT-AGTTTTGTA
1 AAAATAAAAAATAAATTTTGTA
2528031 AA
1 AA
2528033 TATACTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (22 bp):
AAAATAAAAAATAAATTTTGTA
Found at i:2528257 original size:19 final size:18
Alignment explanation
Indices: 2528230--2528269 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2528220 AATTATGTGG
*
2528230 ATTTGTATATTTATATTAT
1 ATTTATATATTTATA-TAT
*
2528249 ATTTATATATTTTTATAT
1 ATTTATATATTTATATAT
2528267 ATT
1 ATT
2528270 ATAATTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTATATATTTATATAT
Found at i:2528435 original size:20 final size:20
Alignment explanation
Indices: 2528407--2528447 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2528397 GTTAACAATG
*
2528407 TTATTTAAAATATTATATAT
1 TTATATAAAATATTATATAT
* *
2528427 TTATATAAATTTTTATATAT
1 TTATATAAAATATTATATAT
2528447 T
1 T
2528448 AATAATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATATAAAATATTATATAT
Found at i:2531336 original size:22 final size:22
Alignment explanation
Indices: 2531310--2531361 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2531300 ATTTTAAAAA
* *
2531310 TTTTAAAACGATTAATAA-TTAT
1 TTTTAAAA-GATAAAAAATTTAT
*
2531332 TTTTAAAATATAAAAAATTTAT
1 TTTTAAAAGATAAAAAATTTAT
2531354 TTTTAAAA
1 TTTTAAAA
2531362 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
TTTTAAAAGATAAAAAATTTAT
Found at i:2531395 original size:29 final size:31
Alignment explanation
Indices: 2531329--2531395 Score: 93
Period size: 29 Copynumber: 2.2 Consensus size: 31
2531319 GATTAATAAT
*
2531329 TATTTTTAAAATATAAAAAATTTATTTTTAA
1 TATTTTTAAAATATAAAAAATTTATTTCTAA
* *
2531360 AAATTTTAAAA-ATAAAAAA-TTATTTCTAA
1 TATTTTTAAAATATAAAAAATTTATTTCTAA
2531389 TATTTTT
1 TATTTTT
2531396 TTAAAATCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 14 0.45
30 8 0.26
31 9 0.29
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
TATTTTTAAAATATAAAAAATTTATTTCTAA
Found at i:2531480 original size:51 final size:50
Alignment explanation
Indices: 2531301--2531487 Score: 146
Period size: 51 Copynumber: 3.6 Consensus size: 50
2531291 TACTGTAAAA
* * * *
2531301 TTTTAAAAATTTTAAAACGATTAATAATTATTTTTAAAATATAAAAAATTTAT
1 TTTTAAAAATTTTAAAA--ATAAAAAATTA-TTTTAAATTATAAAAAAATTAT
* *** *
2531354 TTTTAAAAATTTTAAAAATAAAAAATTATTTCTAATATTTTTTTAAAATCGTCT
1 TTTTAAAAATTTTAAAAATAAAAAATTATTT-TAA-ATTATAAAAAAAT--TAT
** ** * *
2531408 TTCCAAAAA--TT-ATGATTAAAAATTATCTTTAAATTACAAAAAAATTAT
1 TTTTAAAAATTTTAAAAATAAAAAATTAT-TTTAAATTATAAAAAAATTAT
2531456 TTTTAAAAATTTTAAAAATAAAAAATTATTTT
1 TTTTAAAAATTTTAAAAATAAAAAATTATTTT
2531488 GAACTTTTAT
Statistics
Matches: 101, Mismatches: 25, Indels: 19
0.70 0.17 0.13
Matches are distributed among these distances:
48 9 0.09
50 16 0.16
51 39 0.39
52 11 0.11
53 17 0.17
54 9 0.09
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (50 bp):
TTTTAAAAATTTTAAAAATAAAAAATTATTTTAAATTATAAAAAAATTAT
Found at i:2532280 original size:22 final size:21
Alignment explanation
Indices: 2532252--2532305 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
2532242 ATAATTTATT
**
2532252 TTTTATATATAAATTTTTAAAA
1 TTTTATATATAAA-TTAAAAAA
*
2532274 TTTTATAAATAAATTAAAAAA
1 TTTTATATATAAATTAAAAAA
2532295 TTATTATATAT
1 TT-TTATATAT
2532306 TTTATTTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTATATATAAATTAAAAAA
Found at i:2534630 original size:2 final size:2
Alignment explanation
Indices: 2534623--2534651 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2534613 TAATGTCTTT
2534623 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 T
2534652 TATTTCTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2538444 original size:2 final size:2
Alignment explanation
Indices: 2538437--2538475 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2538427 AAATACATGA
2538437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2538476 AAATTAGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2539060 original size:30 final size:30
Alignment explanation
Indices: 2539026--2539117 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 30
2539016 ATAATACCTT
*
2539026 AAATTTTAATTTATATTTAAATAAATTTTA
1 AAATTTTAATTTATATCTAAATAAATTTTA
* * * * *
2539056 AAATTTTAATATGTACCAAAATAAATTTTT
1 AAATTTTAATTTATATCTAAATAAATTTTA
*
2539086 AACTTTTAATTTATATCTAAATAAACTTTTA
1 AAATTTTAATTTATATCTAAATAAA-TTTTA
2539117 A
1 A
2539118 TATACATAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 44 0.90
31 5 0.10
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (30 bp):
AAATTTTAATTTATATCTAAATAAATTTTA
Found at i:2543717 original size:21 final size:21
Alignment explanation
Indices: 2543692--2543732 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2543682 TATTTTTAAT
2543692 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TATAAAATATA
2543713 TAAATATTAATATAAAATAT
1 TAAATATTAATATAAAATAT
2543733 TTTTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:2544913 original size:28 final size:30
Alignment explanation
Indices: 2544881--2544937 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2544871 AAAATTAAGG
2544881 TAAAAG-ATATTTATTTT-TTAAAGTTTTA
1 TAAAAGAATATTTATTTTCTTAAAGTTTTA
*
2544909 TAAAAGATATATTTATTTTCTTAATGTTT
1 TAAAAGA-ATATTTATTTTCTTAAAGTTT
2544938 AAAAAATACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
30 11 0.44
31 8 0.32
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (30 bp):
TAAAAGAATATTTATTTTCTTAAAGTTTTA
Found at i:2545524 original size:25 final size:27
Alignment explanation
Indices: 2545481--2545535 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
2545471 TATCTTTAAA
** *
2545481 ATTTTTAAAATAATGATAAT-TAATTT
1 ATTTTTAAAATAAAAATAATATAATAT
2545507 ATTTTT-AAATAAAAATAATATAATAT
1 ATTTTTAAAATAAAAATAATATAATAT
2545533 ATT
1 ATT
2545536 AATATCAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTTTAAAATAAAAATAATATAATAT
Found at i:2547244 original size:26 final size:28
Alignment explanation
Indices: 2547215--2547303 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 28
2547205 TGGGTGGTTA
* *
2547215 GTCAACAAA-AATCA-TCCTTTGTGTTT
1 GTCAAAAAATAATCATTCCTTTGTATTT
*
2547241 GTCAAAAAATAATGATTCCTTTGTATTT
1 GTCAAAAAATAATCATTCCTTTGTATTT
* * * *
2547269 GTC-AAAAATATTGATTTCTTTTTATTT
1 GTCAAAAAATAATCATTCCTTTGTATTT
*
2547296 GTTAAAAA
1 GTCAAAAA
2547304 TAGTGACTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.15
27 27 0.51
28 18 0.34
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (28 bp):
GTCAAAAAATAATCATTCCTTTGTATTT
Found at i:2547283 original size:27 final size:27
Alignment explanation
Indices: 2547229--2547305 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
2547219 ACAAAAATCA
*
2547229 TCCTTTGTGTTTGTCAAAAAATAATGAT
1 TCCTTTGTATTTGTC-AAAAATAATGAT
*
2547257 TCCTTTGTATTTGTCAAAAATATTGAT
1 TCCTTTGTATTTGTCAAAAATAATGAT
* * *
2547284 TTCTTTTTATTTGTTAAAAATA
1 TCCTTTGTATTTGTCAAAAATA
2547306 GTGACTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 30 0.68
28 14 0.32
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.49
Consensus pattern (27 bp):
TCCTTTGTATTTGTCAAAAATAATGAT
Found at i:2551817 original size:24 final size:25
Alignment explanation
Indices: 2551760--2551826 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 25
2551750 AAAGCCACCT
*
2551760 TTTG-TGTTTGTCAAAAATGGTGGT
1 TTTGTTGTTTGTCAAAAATGGTGGA
*
2551784 TCCTTTTTGTTTGTCAAAAATGGT-GA
1 T--TTGTTGTTTGTCAAAAATGGTGGA
2551810 TTTGTTGTTTGTCAAAA
1 TTTGTTGTTTGTCAAAA
2551827 TTAGTGGCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 16 0.43
26 4 0.11
27 17 0.46
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (25 bp):
TTTGTTGTTTGTCAAAAATGGTGGA
Found at i:2552008 original size:17 final size:16
Alignment explanation
Indices: 2551978--2552024 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
2551968 CCTCGTTAAA
2551978 TTTTTAATATTTTATT
1 TTTTTAATATTTTATT
*
2551994 TTTTTATTATCTTTA-T
1 TTTTTAATAT-TTTATT
*
2552010 TTTTTAATAATTTAT
1 TTTTTAATATTTTAT
2552025 AAATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 4 0.15
16 18 0.69
17 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTAATATTTTATT
Found at i:2554618 original size:2 final size:2
Alignment explanation
Indices: 2554606--2554640 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2554596 ATTTGCCACT
*
2554606 TA TA AA 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 T
2554641 GTTCAGTTAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2561090 original size:19 final size:20
Alignment explanation
Indices: 2561063--2561112 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
2561053 ATAATAAATT
*
2561063 TAATAAATATAA-AATAAGA
1 TAATTAATATAATAATAAGA
*
2561082 TAATTAATATAATTAATAATA
1 TAATTAATATAA-TAATAAGA
2561103 T-ATTAATATA
1 TAATTAATATA
2561113 TATTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATTAATATAATAATAAGA
Found at i:2561095 original size:9 final size:9
Alignment explanation
Indices: 2561053--2561145 Score: 55
Period size: 9 Copynumber: 10.1 Consensus size: 9
2561043 TGGTATGACC
*
2561053 ATAATAAAT
1 ATAATTAAT
* *
2561062 TTAATAAAT
1 ATAATTAAT
* *
2561071 ATAAAATAAG
1 AT-AATTAAT
2561081 ATAATTAAT
1 ATAATTAAT
2561090 ATAATTAAT
1 ATAATTAAT
2561099 AATATATTAAT
1 -ATA-ATTAAT
2561110 ATATATT-AT
1 ATA-ATTAAT
* *
2561119 ATATTTAAG
1 ATAATTAAT
*
2561128 AT-TTTAAT
1 ATAATTAAT
*
2561136 ATATTTAAT
1 ATAATTAAT
2561145 A
1 A
2561146 ATAAAAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
8 9 0.13
9 38 0.55
10 16 0.23
11 6 0.09
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (9 bp):
ATAATTAAT
Found at i:2561102 original size:24 final size:23
Alignment explanation
Indices: 2561053--2561149 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 23
2561043 TGGTATGACC
2561053 ATAATAA-AT-TTAATA-AATATA
1 ATAATAAGATATTAATATAAT-TA
2561074 A-AATAAGATAATTAATATAATTA
1 ATAATAAGAT-ATTAATATAATTA
2561097 ATAAT---ATATTAATATATATTA
1 ATAATAAGATATTAATATA-ATTA
* * *
2561118 TATATTTAAGATTTTAATATATTTA
1 -ATA-ATAAGATATTAATATAATTA
2561143 ATAATAA
1 ATAATAA
2561150 AAAAAATAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
20 14 0.23
21 9 0.15
22 3 0.05
23 13 0.21
24 9 0.15
25 3 0.05
26 10 0.16
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAATAAGATATTAATATAATTA
Found at i:2563325 original size:156 final size:153
Alignment explanation
Indices: 2562944--2563387 Score: 393
Period size: 156 Copynumber: 2.9 Consensus size: 153
2562934 ATTATATTGA
* * * *
2562944 ACTTGATTTTAAAAAATCACGAAAATACCT-TCAAGTATAACTTCGACATGAAAGTATCCAGTAA
1 ACTTGATTATAAAAAATTACCAAAATACCTCT-AAGTATACCTTCGACATGAAAGTATCCAGTAA
* * * * * *
2563008 CCTTAAATGACAC-GAAAAGATAA-TAAAAAGATGAACATATCCTAAATGCACACCTTTAGCATA
65 CTTTAAAGGACACATAAAAGATAAGTAAAAAGATGAACCTATCCTAAATACACACATTTAGCATA
* *
2563071 AAAGCGACTCAATGACAACTTAGG
130 AAAGCGACTCAATGACAACCTAAG
* * * * * * * * * *
2563095 AC-TCACTTATATAAAAATTATCAAAATGCCCCTGAGATTTACTTTCGACATCAAAGCATCCCGG
1 ACTTGA-TTATA-AAAAATTACCAAAATACCTCTAAG-TATACCTTCGACATGAAAGTAT-CCAG
* *
2563159 TAA-TCCTAAAGGACACATAAAAGATAAGAAAAAAGACT-AACCTATCCTAAATACACACATTTA
62 TAACT-TTAAAGGACACATAAAAGATAAGTAAAAAGA-TGAACCTATCCTAAATACACACATTTA
* * ** *
2563222 GCATAAAAGTGATTCGGTGACGACCTAAG
125 GCATAAAAGCGACTCAATGACAACCTAAG
* * *
2563251 ACTTGATTCTAAAAAACTTACCAAAATACCTCTAAAGTATACCTTCGACGTGAAAGTATCTCAAT
1 ACTTGATTATAAAAAA-TTACCAAAATACCTCT-AAGTATACCTTCGACATGAAAGTATC-CAGT
* * *
2563316 AACTTTAAAGGACATGAT-AAAGATAAGTAAAGAGATGAACAC-ATCCTAAATACACACGTTT-G
63 AACTTTAAAGGACA-CATAAAAGATAAGTAAAAAGATGAAC-CTATCCTAAATACACACATTTAG
2563378 ACATAAAAGC
126 -CATAAAAGC
2563388 AACCCGGTAA
Statistics
Matches: 227, Mismatches: 48, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
150 2 0.01
151 6 0.03
152 16 0.07
153 18 0.08
154 15 0.07
155 17 0.07
156 144 0.63
157 9 0.04
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (153 bp):
ACTTGATTATAAAAAATTACCAAAATACCTCTAAGTATACCTTCGACATGAAAGTATCCAGTAAC
TTTAAAGGACACATAAAAGATAAGTAAAAAGATGAACCTATCCTAAATACACACATTTAGCATAA
AAGCGACTCAATGACAACCTAAG
Found at i:2563621 original size:30 final size:29
Alignment explanation
Indices: 2563585--2563670 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
2563575 TTAGATTTTC
* *
2563585 AAAATTATATTTTTGATCTCTAAACTTTGT
1 AAAATTACA-TTTTGATCTCAAAACTTTGT
*
2563615 AAAATTACATTTTGA-CATCAAAACTTTTT
1 AAAATTACATTTTGATC-TCAAAACTTTGT
*
2563644 AAAATCACATTTTGATCTCAAAACTTT
1 AAAATTACATTTTGATCTCAAAACTTT
2563671 TCAAATTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
28 1 0.02
29 40 0.80
30 9 0.18
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (29 bp):
AAAATTACATTTTGATCTCAAAACTTTGT
Found at i:2563696 original size:29 final size:29
Alignment explanation
Indices: 2563664--2563766 Score: 103
Period size: 29 Copynumber: 3.8 Consensus size: 29
2563654 TTTGATCTCA
* *
2563664 AAACTTTTCAAATTTTCACTTTAACCCTT
1 AAACTTTTCAAAATTACACTTTAACCCTT
2563693 AAAC-TTTCAAAATT--AC---AA-CCTCT
1 AAACTTTTCAAAATTACACTTTAACCCT-T
* *
2563716 AAACTTTTCAAAATTACATTTTAACCTTT
1 AAACTTTTCAAAATTACACTTTAACCCTT
*
2563745 AAATTTTTCAAAATTACACTTT
1 AAACTTTTCAAAATTACACTTT
2563767 GATCTTCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
22 3 0.05
23 7 0.11
24 10 0.16
26 3 0.05
28 9 0.15
29 27 0.44
30 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (29 bp):
AAACTTTTCAAAATTACACTTTAACCCTT
Found at i:2563777 original size:29 final size:29
Alignment explanation
Indices: 2563720--2563777 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
2563710 ACCTCTAAAC
* *
2563720 TTTTCAAAATTACATTTTAACCTTTAAAT
1 TTTTCAAAATTACACTTTAACCTTCAAAT
* *
2563749 TTTTCAAAATTACACTTTGATCTTCAAAT
1 TTTTCAAAATTACACTTTAACCTTCAAAT
2563778 GGTTTAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTTCAAAATTACACTTTAACCTTCAAAT
Found at i:2564299 original size:21 final size:23
Alignment explanation
Indices: 2564273--2564321 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
2564263 TTAAACCACG
*
2564273 AAAATAAACACCAAA-TATAT-C
1 AAAATAAACACAAAATTATATCC
*
2564294 AAAATAATCACAAAATTATATCC
1 AAAATAAACACAAAATTATATCC
2564317 AAAAT
1 AAAAT
2564322 CTCTAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 5 0.21
23 6 0.25
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAATAAACACAAAATTATATCC
Found at i:2564547 original size:17 final size:17
Alignment explanation
Indices: 2564527--2564559 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2564517 AACGAATTTG
2564527 CAAAAATTATGAATTAC
1 CAAAAATTATGAATTAC
2564544 CAAAAATTATGAATTA
1 CAAAAATTATGAATTA
2564560 GCCCTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (17 bp):
CAAAAATTATGAATTAC
Found at i:2565321 original size:15 final size:16
Alignment explanation
Indices: 2565301--2565335 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2565291 AAAAAAAATG
*
2565301 AAAATGAAG-TGAATA
1 AAAATGAAGTTGAAGA
2565316 AAAATGAAGTTGAAGA
1 AAAATGAAGTTGAAGA
2565332 AAAA
1 AAAA
2565336 AAACTACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (16 bp):
AAAATGAAGTTGAAGA
Found at i:2566212 original size:10 final size:10
Alignment explanation
Indices: 2566194--2566244 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
2566184 CTAGTTAAAA
*
2566194 AAATAAAATA
1 AAATAAAATT
*
2566204 AAATTAAATT
1 AAATAAAATT
*
2566214 AAATTAAATT
1 AAATAAAATT
2566224 AAA-AAAATT
1 AAATAAAATT
2566233 AAA-AAAATT
1 AAATAAAATT
2566242 AAA
1 AAA
2566245 ATTAATAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
9 17 0.45
10 21 0.55
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAATAAAATT
Found at i:2566217 original size:15 final size:15
Alignment explanation
Indices: 2566194--2566249 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
2566184 CTAGTTAAAA
*
2566194 AAATAAAATAAAATT
1 AAATAAAATTAAATT
*
2566209 AAATTAAATTAAATT
1 AAATAAAATTAAATT
*
2566224 AAA-AAAATTAAA-A
1 AAATAAAATTAAATT
2566237 AAATTAAAATTAA
1 AAA-TAAAATTAA
2566250 TAATCATAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 3 0.09
14 8 0.23
15 24 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAAAATTAAATT
Found at i:2566233 original size:9 final size:9
Alignment explanation
Indices: 2566209--2566245 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
2566199 AAATAAAATT
*
2566209 AAATTAAATT
1 AAATTAAA-A
2566219 AAATTAAAA
1 AAATTAAAA
2566228 AAATTAAAA
1 AAATTAAAA
2566237 AAATTAAAA
1 AAATTAAAA
2566246 TTAATAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAATTAAAA
Found at i:2580230 original size:2 final size:2
Alignment explanation
Indices: 2580223--2580250 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2580213 TCTATCTATC
2580223 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
2580251 ATTTTAACTA
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):
TA
Found at i:2580351 original size:16 final size:15
Alignment explanation
Indices: 2580330--2580368 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2580320 GGTAAAAGTG
*
2580330 AAAAAAATAGAGAATA
1 AAAAAAATAAAGAA-A
*
2580346 AAAAAAAGAAAGAAA
1 AAAAAAATAAAGAAA
2580361 AAAAAAAT
1 AAAAAAAT
2580369 TATGCATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (15 bp):
AAAAAAATAAAGAAA
Found at i:2580947 original size:18 final size:20
Alignment explanation
Indices: 2580924--2580966 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2580914 TATATTCATA
2580924 TCATATT-CATATT-ATTTT
1 TCATATTACATATTAATTTT
*
2580942 TCATATTACGTATTAATTTT
1 TCATATTACATATTAATTTT
2580962 T-ATAT
1 TCATAT
2580967 ATATTAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 9 0.41
20 6 0.27
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.58
Consensus pattern (20 bp):
TCATATTACATATTAATTTT
Found at i:2581930 original size:2 final size:2
Alignment explanation
Indices: 2581923--2581953 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2581913 TTCATACTCT
2581923 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2581954 GTTTTAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2581991 original size:21 final size:22
Alignment explanation
Indices: 2581966--2582015 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2581956 TTTAGATTAT
*
2581966 AAATAAAAACAAACATAAAT-A
1 AAATAAAAACAAAAATAAATAA
* * *
2581987 AAATAATAAGAAAAATATATAA
1 AAATAAAAACAAAAATAAATAA
2582009 AAATAAA
1 AAATAAA
2582016 CAGTGATGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (22 bp):
AAATAAAAACAAAAATAAATAA
Found at i:2583069 original size:13 final size:13
Alignment explanation
Indices: 2583051--2583076 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2583041 ATATAACATG
2583051 TGATTAAATTAAT
1 TGATTAAATTAAT
2583064 TGATTAAATTAAT
1 TGATTAAATTAAT
2583077 CTTGTAAGTT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TGATTAAATTAAT
Found at i:2583956 original size:16 final size:16
Alignment explanation
Indices: 2583935--2583982 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
2583925 AATTTCATTT
2583935 AAATTAATACTATGTA
1 AAATTAATACTATGTA
2583951 AAATT-A-A-TA-GT-
1 AAATTAATACTATGTA
2583962 AAATTAATACTATGTA
1 AAATTAATACTATGTA
2583978 AAATT
1 AAATT
2583983 TTCAAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
11 5 0.19
12 3 0.11
13 3 0.11
14 3 0.11
15 3 0.11
16 10 0.37
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (16 bp):
AAATTAATACTATGTA
Found at i:2586147 original size:16 final size:15
Alignment explanation
Indices: 2586126--2586173 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2586116 AATTTCATTT
2586126 AAATTACTACTATGTA
1 AAATTA-TACTATGTA
2586142 AAATTA-A-TA-GT-
1 AAATTATACTATGTA
2586153 AAATTAATACTATGTA
1 AAATT-ATACTATGTA
2586169 AAATT
1 AAATT
2586174 TTCAAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
11 5 0.19
12 3 0.11
13 3 0.11
14 3 0.11
15 2 0.07
16 11 0.41
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (15 bp):
AAATTATACTATGTA
Found at i:2586969 original size:2 final size:2
Alignment explanation
Indices: 2586964--2586990 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2586954 AAAAAGAGTT
2586964 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 T
2586991 CTAATGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2587311 original size:34 final size:34
Alignment explanation
Indices: 2587244--2587459 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
2587234 GTGAATATTC
* * *
2587244 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
2587277 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
2587311 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
2587344 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
2587378 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
2587412 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
2587446 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2587460 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:2587425 original size:68 final size:67
Alignment explanation
Indices: 2587244--2587461 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
2587234 GTGAATATTC
* * * * *
2587244 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
2587309 AT
66 AT
* * * *
2587311 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
2587376 AT
66 AT
* * *
2587378 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
2587443 CAT
65 CAT
2587446 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
2587462 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:2589911 original size:14 final size:14
Alignment explanation
Indices: 2589892--2589919 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2589882 TTTTTAAATT
2589892 TTAAATATATTTTA
1 TTAAATATATTTTA
2589906 TTAAATATATTTTA
1 TTAAATATATTTTA
2589920 AATATTTGAA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:2592998 original size:4 final size:4
Alignment explanation
Indices: 2592991--2593015 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2592981 TTAAGAAAGA
2592991 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2593016 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2593386 original size:20 final size:21
Alignment explanation
Indices: 2593348--2593386 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2593338 TCTTTATATT
*
2593348 TTTATTTTTATAATAATTTTA
1 TTTAATTTTATAATAATTTTA
*
2593369 TTTAATTTT-TAATTATTT
1 TTTAATTTTATAATAATTT
2593387 GTAATTGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTAATTTTATAATAATTTTA
Found at i:2593841 original size:16 final size:16
Alignment explanation
Indices: 2593820--2593858 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2593810 TAATATATCA
2593820 ATTATTTTT-GAATTAT
1 ATTATTTTTAGAATT-T
*
2593836 ATTATTTTTATAATTT
1 ATTATTTTTAGAATTT
2593852 ATTATTT
1 ATTATTT
2593859 AAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
ATTATTTTTAGAATTT
Found at i:2613808 original size:34 final size:34
Alignment explanation
Indices: 2613739--2613952 Score: 279
Period size: 34 Copynumber: 6.4 Consensus size: 34
2613729 AAGTGGGAGA
* * *
2613739 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
** * * *
2613772 ATTGTTGATTAAATGGTTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
2613806 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
2613839 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2613873 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2613907 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2613941 ATTGTTGATTAA
1 ATTGTTGATTAA
2613953 TGGTGGTTTT
Statistics
Matches: 158, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
33 41 0.26
34 117 0.74
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2613847 original size:67 final size:66
Alignment explanation
Indices: 2613739--2613957 Score: 296
Period size: 67 Copynumber: 3.3 Consensus size: 66
2613729 AAGTGGGAGA
* * **
2613739 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGTTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TTG
2613804 CC
65 CC
* * * * *
2613806 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTG
2613871 CC
65 CC
* *
2613873 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTT
2613938 GCC
64 GCC
2613941 ATTGTTGATT-AATGGTG
1 ATTGTTGATTAAATGGTG
2613958 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
66 4 0.03
67 72 0.54
68 58 0.43
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (66 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTGC
C
Found at i:2613885 original size:101 final size:101
Alignment explanation
Indices: 2613739--2613957 Score: 336
Period size: 101 Copynumber: 2.2 Consensus size: 101
2613729 AAGTGGGAGA
* * * *
2613739 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGTTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
2613804 CCATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
2613839 ATTGTTGATTAAATGG-GAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCT
1 ATTGTTGATTAAATGGTG--ATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCT
* *
2613903 TACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
64 TACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
2613941 ATTGTTGATT-AATGGTG
1 ATTGTTGATTAAATGGTG
2613958 GTTTTTACCA
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
99 1 0.01
100 16 0.15
101 63 0.58
102 28 0.26
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:2614697 original size:1 final size:1
Alignment explanation
Indices: 2614338--2614685 Score: 462
Period size: 1 Copynumber: 348.0 Consensus size: 1
2614328 TTATTAGTTT
* * *
2614338 AAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2614403 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAATAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
2614468 AAAAAAAGAAAAAAAAAAAAAAAAAAAAATAACAAAAAAATAAAAAAGAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *** * * ** *
2614533 TAAAAAAAAAAAAATTTAATAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** * *
2614598 AAAAAGAATAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
2614663 AAAAAAATAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
2614686 TTATTATAAA
Statistics
Matches: 303, Mismatches: 44, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 303 1.00
ACGTcount: A:0.93, C:0.00, G:0.01, T:0.06
Consensus pattern (1 bp):
A
Found at i:2614738 original size:18 final size:15
Alignment explanation
Indices: 2614714--2614756 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 15
2614704 GTTAATATTG
2614714 GTAAAAATTCTTATGAT
1 GTAAAAATTCTTA--AT
2614731 GATAAAAATT-TTAAT
1 G-TAAAAATTCTTAAT
2614746 GTAAAAATTCT
1 GTAAAAATTCT
2614757 AACTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
17 4 0.17
18 8 0.33
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (15 bp):
GTAAAAATTCTTAAT
Found at i:2617026 original size:16 final size:17
Alignment explanation
Indices: 2616979--2617022 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
2616969 TAAATTTTAT
2616979 AAATTAGATTAATATAATAA
1 AAATTA-ATTAA-A-AATAA
2616999 AAATTAATTAAAAATAA
1 AAATTAATTAAAAATAA
2617016 AATATTA
1 AA-ATTA
2617023 TAAATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.30
18 5 0.22
19 5 0.22
20 6 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAATTAATTAAAAATAA
Found at i:2617549 original size:19 final size:19
Alignment explanation
Indices: 2617525--2617588 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
2617515 TTTTAAATTT
2617525 AATTTTTAATAATTTAATA
1 AATTTTTAATAATTTAATA
* *
2617544 AATTTTTATTAAATTTTA-A
1 AATTTTTAAT-AATTTAATA
* *
2617563 AATTATAAATAATTTAATA
1 AATTTTTAATAATTTAATA
*
2617582 TATTTTT
1 AATTTTT
2617589 TAAAGTTTAT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
18 6 0.18
19 22 0.65
20 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTTTTAATAATTTAATA
Found at i:2617589 original size:29 final size:31
Alignment explanation
Indices: 2617557--2617617 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2617547 TTTTATTAAA
2617557 TTTTAAA-ATTATAA-ATAAT-TTAATATATT
1 TTTTAAAGATTATAATATAATATT-ATATATT
*
2617586 TTTTAAAGTTTATAATATAATATTATATATT
1 TTTTAAAGATTATAATATAATATTATATATT
2617617 T
1 T
2617618 ATTTTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.25
30 6 0.21
31 13 0.46
32 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (31 bp):
TTTTAAAGATTATAATATAATATTATATATT
Done.