Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014679.1 Kokia drynarioides strain JFW-HI SEQ_129718, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 331910
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 120 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:817 original size:14 final size:14
Alignment explanation
Indices: 798--828 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
788 TTGCATAAAT
798 TATGTATATATATA
1 TATGTATATATATA
*
812 TATGTATGTATATA
1 TATGTATATATATA
826 TAT
1 TAT
829 ATGTGTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:11992 original size:16 final size:15
Alignment explanation
Indices: 11971--12009 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
11961 TACCCCTTTT
11971 TTTATTTCTTATATA
1 TTTATTTCTTATATA
* *
11986 CTTTATTTTTTATTTA
1 -TTTATTTCTTATATA
12002 TTTATTTC
1 TTTATTTC
12010 AATTTGCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTCTTATATA
Found at i:15443 original size:18 final size:18
Alignment explanation
Indices: 15420--15456 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
15410 AATGTTTGAG
15420 TAGTGAAATTTGAAACAT
1 TAGTGAAATTTGAAACAT
15438 TAGTGAAATTTGAAACAT
1 TAGTGAAATTTGAAACAT
15456 T
1 T
15457 GATGTAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (18 bp):
TAGTGAAATTTGAAACAT
Found at i:16540 original size:33 final size:33
Alignment explanation
Indices: 16498--16563 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
16488 AGAGGACATG
16498 TATTGAATCTAAGAAAACGTAGAATTATCCTTT
1 TATTGAATCTAAGAAAACGTAGAATTATCCTTT
16531 TATTGAATCTAAGAAAACGTAGAATTATCCTTT
1 TATTGAATCTAAGAAAACGTAGAATTATCCTTT
16564 CTCTTTTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (33 bp):
TATTGAATCTAAGAAAACGTAGAATTATCCTTT
Found at i:18255 original size:34 final size:34
Alignment explanation
Indices: 18217--18284 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
18207 GAATTAAATT
*
18217 TTAGTATAAGCGATTTATGAAAAAGAGGTATTGG
1 TTAGTAGAAGCGATTTATGAAAAAGAGGTATTGG
*
18251 TTAGTAGAAGCGGTTTATGAAAAAGAGGTATTGG
1 TTAGTAGAAGCGATTTATGAAAAAGAGGTATTGG
18285 GACCTCGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (34 bp):
TTAGTAGAAGCGATTTATGAAAAAGAGGTATTGG
Found at i:20549 original size:109 final size:109
Alignment explanation
Indices: 20358--20746 Score: 496
Period size: 109 Copynumber: 3.6 Consensus size: 109
20348 ATAAACTATC
* *
20358 GTGATGGTTGAGATCCTGCATATGTTGCGGACTT-TCGACAGCTTGTGTGAGCAGCATCGTGAAC
1 GTGATGGTTGAGATCCTGCATATGTTGC-GAATTCTCAACAGCTTGTGTGAGCAGCATCGTGAAC
*
20422 TAGTGACTATTGAATGGATACTATGTTCTAATTATACAAACCGTA
65 TAGTGACTATTGAATGGATACTATGTTCTAATGATACAAACCGTA
* * * *
20467 GTGATGGTTGAGATCCTGCATATGTTGCGGATTTTCAACAGCTTGTGTGTGTAGCATCGTGAACT
1 GTGATGGTTGAGATCCTGCATATGTTGCGAATTCTCAACAGCTTGTGTGAGCAGCATCGTGAACT
20532 AGTGACTATTGAATGGATACTATGTTCTAATGATACAAACCGTA
66 AGTGACTATTGAATGGATACTATGTTCTAATGATACAAACCGTA
* * * * * * *
20576 GCGATGG-TGAAGATCCTGCATATGTTACGAATTCTCGATAGCTTGTGTGAGCAACATCATGAGC
1 GTGATGGTTG-AGATCCTGCATATGTTGCGAATTCTCAACAGCTTGTGTGAGCAGCATCGTGAAC
* * * * * * *
20640 -CGATGATTATTGAATGGATACTATATTTTGATGATACAAATCGTT
65 TAG-TGACTATTGAATGGATACTATGTTCTAATGATACAAACCGTA
** * * *
20685 GTGATGACTGAGATCCTGTATATGTTGCGAATTCTCAACAACTTGTGTGAGTAGCATCGTGA
1 GTGATGGTTGAGATCCTGCATATGTTGCGAATTCTCAACAGCTTGTGTGAGCAGCATCGTGA
20747 GCGGGTGATA
Statistics
Matches: 242, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
108 6 0.02
109 234 0.97
110 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (109 bp):
GTGATGGTTGAGATCCTGCATATGTTGCGAATTCTCAACAGCTTGTGTGAGCAGCATCGTGAACT
AGTGACTATTGAATGGATACTATGTTCTAATGATACAAACCGTA
Found at i:26058 original size:15 final size:15
Alignment explanation
Indices: 26038--26072 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
26028 ATAGAGGTTC
26038 AATAAAATATTAAAA
1 AATAAAATATTAAAA
26053 AAT-AAATATTAAAA
1 AATAAAATATTAAAA
26067 AA-AAAA
1 AATAAAA
26073 GACATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAAAATATTAAAA
Found at i:29994 original size:18 final size:19
Alignment explanation
Indices: 29967--30003 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29957 AGCACCACGA
*
29967 CCCCTCCCACGACCACCAG
1 CCCCTCCCACCACCACCAG
29986 CCCCT-CCACCACCACCAG
1 CCCCTCCCACCACCACCAG
30004 ATGCACCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.65, G:0.08, T:0.05
Consensus pattern (19 bp):
CCCCTCCCACCACCACCAG
Found at i:37236 original size:3 final size:3
Alignment explanation
Indices: 37228--37286 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
37218 AGACAACCTA
37228 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
37275 TTT ATT TTT ATT
1 ATT ATT ATT ATT
37287 TTTGTATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:37287 original size:6 final size:6
Alignment explanation
Indices: 37232--37315 Score: 60
Period size: 6 Copynumber: 13.0 Consensus size: 6
37222 AACCTAATTA
* * * * *
37232 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTAT TATATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATT-T T-TATTT TTATTT
*
37282 TTATTT TTGTATT TTATTTAT TTATTTT TTATTT
1 TTATTT TTAT-TT TTA-TT-T TTA-TTT TTATTT
37316 GTCCAAGAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
6 46 0.66
7 12 0.17
8 12 0.17
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (6 bp):
TTATTT
Found at i:37296 original size:13 final size:12
Alignment explanation
Indices: 37232--37309 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 12
37222 AACCTAATTA
37232 TTATTATTATTATT
1 TTATT-TTATT-TT
37246 ATTATTATTATTATT
1 -TTATT-TTATT-TT
37261 ATTATTATTATATTT
1 -TTATT-TTAT-TTT
37276 TTATTTTTATTTT
1 TTA-TTTTATTTT
37289 TGTATTTTATTTAT
1 T-TATTTTATTT-T
37303 TTATTTT
1 TTATTTT
37310 TTATTTGTCC
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
13 18 0.31
14 11 0.19
15 29 0.49
16 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:45871 original size:3 final size:3
Alignment explanation
Indices: 45863--45921 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
45853 AGACAACCTA
45863 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
45910 TTT ATT TTT ATT
1 ATT ATT ATT ATT
45922 TTTGTATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:45922 original size:6 final size:6
Alignment explanation
Indices: 45867--45950 Score: 60
Period size: 6 Copynumber: 13.0 Consensus size: 6
45857 AACCTAATTA
* * * * *
45867 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTAT TATATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATT-T T-TATTT TTATTT
*
45917 TTATTT TTGTATT TTATTTAT TTATTTT TTATTT
1 TTATTT TTAT-TT TTA-TT-T TTA-TTT TTATTT
45951 GTCCAAGAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
6 46 0.66
7 12 0.17
8 12 0.17
ACGTcount: A:0.25, C:0.00, G:0.01, T:0.74
Consensus pattern (6 bp):
TTATTT
Found at i:45931 original size:13 final size:12
Alignment explanation
Indices: 45867--45944 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 12
45857 AACCTAATTA
45867 TTATTATTATTATT
1 TTATT-TTATT-TT
45881 ATTATTATTATTATT
1 -TTATT-TTATT-TT
45896 ATTATTATTATATTT
1 -TTATT-TTAT-TTT
45911 TTATTTTTATTTT
1 TTA-TTTTATTTT
45924 TGTATTTTATTTAT
1 T-TATTTTATTT-T
45938 TTATTTT
1 TTATTTT
45945 TTATTTGTCC
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
13 18 0.31
14 11 0.19
15 29 0.49
16 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:49785 original size:21 final size:21
Alignment explanation
Indices: 49744--49791 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
49734 ACATGAAATT
49744 AAAAA-AAACTCTTAATTTTAA
1 AAAAATAAACTC-TAATTTTAA
49765 AAAAATAAACTC-AATTATTAA
1 AAAAATAAACTCTAATT-TTAA
49786 AAAAAT
1 AAAAAT
49792 GTTTCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.16
21 15 0.60
22 6 0.24
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATAAACTCTAATTTTAA
Found at i:51613 original size:7 final size:7
Alignment explanation
Indices: 51601--51640 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
51591 ACCCGACCCA
51601 TTGACCG
1 TTGACCG
51608 TTGACCG
1 TTGACCG
*
51615 TTGATCG
1 TTGACCG
*
51622 TTGATCG
1 TTGACCG
*
51629 TTAACCG
1 TTGACCG
51636 TTGAC
1 TTGAC
51641 TTTGACTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (7 bp):
TTGACCG
Found at i:62232 original size:80 final size:80
Alignment explanation
Indices: 62088--62242 Score: 240
Period size: 80 Copynumber: 1.9 Consensus size: 80
62078 AGCAAAACTG
* * * * *
62088 TTGGTTAATCCAACTAGTGCTAGGCTCACTTATTGTAGTTTATCCGCTAGGCACTGGGTGCCATG
1 TTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCAGTTTATCCGCTAGGCACTGCGTACCATG
62153 AATTGACAGACTTCA
66 AATTGACAGACTTCA
*
62168 TTGGTTAATCCAACTAGAGCTGGGCTCACTTATCGCAGTTTATCCGCTAGGCA-TCGCGTACCAT
1 TTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCAGTTTATCCGCTAGGCACT-GCGTACCAT
62232 GAATTGACAGA
65 GAATTGACAGA
62243 ATTGATTAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
79 1 0.01
80 67 0.99
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (80 bp):
TTGGTTAATCCAACTAGAGCTAGGCTCACTTATCGCAGTTTATCCGCTAGGCACTGCGTACCATG
AATTGACAGACTTCA
Found at i:63077 original size:21 final size:21
Alignment explanation
Indices: 63051--63097 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
63041 GGTTTTACAA
63051 ATACAACCCTGCATTCTACCG
1 ATACAACCCTGCATTCTACCG
63072 ATACAACCCTGCATTCTACCG
1 ATACAACCCTGCATTCTACCG
63093 ATACA
1 ATACA
63098 CTAAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.36, G:0.09, T:0.23
Consensus pattern (21 bp):
ATACAACCCTGCATTCTACCG
Found at i:65824 original size:52 final size:52
Alignment explanation
Indices: 65751--65989 Score: 370
Period size: 52 Copynumber: 4.6 Consensus size: 52
65741 TTCTCATTTA
* *
65751 ATACTCACAATGACACATAGTCATTGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
* * * * * *
65803 ATACTCACGATGATACGTAGTCATCGGACCTCGTAATCCGTAAAAGATTGAT
1 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
*
65855 ATACTCACGATGACACATAGTCATTGGACCTCATAATCAGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
*
65907 ATACTCACGATGACACATAGTCATTGGACCTCCTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
* *
65959 ATACTCACGATGATACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATTGGACCT
65990 TTTGCATTTA
Statistics
Matches: 168, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 168 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAAGGATTCAT
Found at i:69397 original size:41 final size:41
Alignment explanation
Indices: 69313--69539 Score: 253
Period size: 41 Copynumber: 5.5 Consensus size: 41
69303 TTATGCTCTA
* * * *
69313 TCGAGGCATAAGTCTTCCTTTTTCCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATT-CATAATCTCATTCTCATC
*
69355 TCGAGACGTGAGTCTTCCTTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
69396 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
* * * *
69437 TTGAGACACGAGTCTTCCTTATTCATAATCCCATGCTCAT-
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
* * * * *
69477 TCTAAGTCAAGAGTCTTCCATT-TTACA-ATTTCTCATTCTCAAC
1 TC-GAGACATGAGTCTTCC-TTATT-CATA-ATCTCATTCTCATC
*
69520 CCGAGACATGAGTCTTCCTT
1 TCGAGACATGAGTCTTCCTT
69540 TTTATACACC
Statistics
Matches: 158, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
40 1 0.01
41 111 0.70
42 45 0.28
43 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.38
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
Found at i:76529 original size:36 final size:39
Alignment explanation
Indices: 76479--76619 Score: 189
Period size: 41 Copynumber: 3.6 Consensus size: 39
76469 TTATGCTCTA
* *
76479 TCGAGGCATAAGTCTTCCTT-TT-T-TCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATTATATCTCATTCTCATC
76515 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATT-AT-ATCTCATTCTCATC
76556 TCGAGACATGAGTCTTCCTTATTAATAATCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATT-AT-ATCTCATTCTCATC
* *
76597 TCAAGACATGAGTCCTCCTTATT
1 TCGAGACATGAGTCTTCCTTATT
76620 CGTAATTCCA
Statistics
Matches: 95, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
36 18 0.19
37 2 0.02
39 1 0.01
41 74 0.78
ACGTcount: A:0.23, C:0.26, G:0.11, T:0.40
Consensus pattern (39 bp):
TCGAGACATGAGTCTTCCTTATTATATCTCATTCTCATC
Found at i:76559 original size:41 final size:41
Alignment explanation
Indices: 76502--76655 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
76492 CTTCCTTTTT
76502 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCATAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCATAA
*
76543 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTAATAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCATAA
* * *
76584 TCTCATTCTCATCTCAAGACATGAGTCCTCCTTATTCGTAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCATAA
* *
76625 T-TCCATACTCAT-TCCGAGTCATGAGTCTTCC
1 TCT-CATTCTCATCT-CGAGACATGAGTCTTCC
76656 ATTTTATAGT
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.02
41 100 0.98
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.38
Consensus pattern (41 bp):
TCTCATTCTCATCTCGAGACATGAGTCTTCCTTATTCATAA
Found at i:77407 original size:3 final size:3
Alignment explanation
Indices: 77399--77429 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
77389 AACGGTGTAG
77399 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
77430 AGAAAATGTG
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:81523 original size:14 final size:14
Alignment explanation
Indices: 81501--81548 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
81491 CGGTAATATA
81501 TTTCTTTTCTTTTT
1 TTTCTTTTCTTTTT
* *
81515 TTTCCTTTCTTCTTC
1 TTTCTTTTCTT-TTT
81530 TTTCTTTTTCTTTCTT
1 TTTC-TTTTCTTT-TT
81546 TTT
1 TTT
81549 GTGAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 10 0.37
15 7 0.26
16 10 0.37
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTTCTTTTT
Found at i:81532 original size:10 final size:10
Alignment explanation
Indices: 81501--81548 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
81491 CGGTAATATA
81501 TTTC-TTTTC
1 TTTCTTTTTC
81510 TTT-TTTTTCC
1 TTTCTTTTT-C
*
81520 TTTCTTCTTC
1 TTTCTTTTTC
81530 TTTCTTTTTC
1 TTTCTTTTTC
81540 TTTCTTTTT
1 TTTCTTTTT
81549 GTGAAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 7 0.21
10 23 0.68
11 4 0.12
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:82157 original size:18 final size:17
Alignment explanation
Indices: 82121--82159 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
82111 AAATGTACTA
*
82121 ACAAATGAAATGCAGTG
1 ACAAATGAAATGCAATG
82138 ACAAATGAAGATGCAATG
1 ACAAATGAA-ATGCAATG
82156 ACAA
1 ACAA
82160 CTAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (17 bp):
ACAAATGAAATGCAATG
Found at i:90278 original size:52 final size:52
Alignment explanation
Indices: 90071--90284 Score: 347
Period size: 52 Copynumber: 4.1 Consensus size: 52
90061 TCATTTGCTA
* *
90071 ACTCACGATGACACATAGTCATCAGACCTCATAATTCGTAAAGGATTCATAA
1 ACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATAT
* * * * *
90123 ACTCACGATGACACATAGTCATCTGACCACGTAATTCGTAAAAGATTCATAT
1 ACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATAT
90175 ACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATAT
*
90227 ACTCACGATGACACATAGTCATCAGACCTCCTAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATAT
*
90279 ATTCAC
1 ACTCAC
90285 TGTAGACACT
Statistics
Matches: 150, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 150 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATAT
Found at i:90977 original size:147 final size:148
Alignment explanation
Indices: 90689--91267 Score: 548
Period size: 149 Copynumber: 3.9 Consensus size: 148
90679 AAATTTTGGT
* *
90689 TTTTTTTAACAATTTCGAAATAAAAGCTTT-GATTTTTAAGTAAAATAGTGATTTCCTTTAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAG-TTTAGATTTTTAAGTAAAGTAGTGA--T--TTT---AA
** ** * *
90753 AAAAAAAAAAAAATAGTTTAGATTTTTAAAAATAAAAA-ACTG--TTTT--TT-TTTT--AG-AA
58 TTAAAAGGAAGAA-AGTTTATATTTTTAAAAATAAAAATA-TGTTTTTTAATTATTTTAAAGAAA
* *
90809 AAGTTTAAATTTTTAAATAAAGTTTTGA
121 AATTTTAAATTTTTAAATAAAGTTTTCA
*
90837 TTTTTTTAACTATTTCAAAATAAAAGTTTAGATTTTTAAG-AAAGTAGTGATTTTAATTTTAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTAA--TTAAAA
* * * *
90901 GG-AGAAAGTTTATA-TTTTAAAAA-AATATATATGTTTTTTAGTTATTTTAGAGAAAATTTTTA
64 GGAAGAAAGTTTATATTTTTAAAAATAA-AAATATGTTTTTTAATTATTTTAAAGAAAAATTTTA
90963 AATTTTTAAATAAAG-TTTCA
128 AATTTTTAAATAAAGTTTTCA
* * *
90983 TTTTTTTTAACTATATCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAG
1 -TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTAATTAAAAG
*
91048 GAAAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAATTATTTTAAAGAAAAATTTTAA
65 G-AAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAATTATTTTAAAGAAAAATTTTAA
* ** *
91113 AATTTTAAATAATTTTTTTA
129 ATTTTTAAATAAAGTTTTCA
* * * * * *
91133 TTTTTTTAGCTATTTCGAAATAAAAATTTATATTTTAAAGTAAAATAGTGATTTTCATT-AAA--
1 TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTAATTAAAAGG
* * * * * * *
91195 AA-AAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTGATTTTAAATAAAAAAATTTAAA
66 AAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAATTATTTTAAA-GAAAAATTTTAAA
91259 TATTTTAAA
130 T-TTTTAAA
91268 GTAAGATAAA
Statistics
Matches: 369, Mismatches: 40, Indels: 46
0.81 0.09 0.10
Matches are distributed among these distances:
138 2 0.01
139 13 0.04
140 10 0.03
141 7 0.02
142 4 0.01
143 5 0.01
144 48 0.13
145 14 0.04
146 21 0.06
147 71 0.19
148 64 0.17
149 104 0.28
150 6 0.02
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (148 bp):
TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTAATTAAAAGG
AAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAATTATTTTAAAGAAAAATTTTAAAT
TTTTAAATAAAGTTTTCA
Found at i:91681 original size:158 final size:156
Alignment explanation
Indices: 91359--91658 Score: 449
Period size: 161 Copynumber: 1.9 Consensus size: 156
91349 TCATAATAAT
91359 GATAAAAAATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTTTTAA
1 GATAAAAAATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTTTTAA
* * * *
91424 TCTTTTTTAGGATTTTAAAATATAATTAATTTTAAGAAATGAAGGTATTTTACTAGAATTATTTA
66 TCTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAAATGAAAGTATTTTACTAAAATTATTTA
91489 AGTATCTTTACAAGTAAATCGGAGTAAA
131 AGTATCTTTACAAGT--ATCGGAGTAAA
* *
91517 GATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAATTTTTTT
1 GATAAAAAATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAA---CTTT
* * *
91582 TAGGT-TTTTTTAGGATTCTAAACTAGAATTAATTTTAAGAATTGAAAGTATTTTACTAAAATTA
63 TA-ATCTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAAATGAAAGTATTTTACTAAAATTA
*
91646 TTTATGTATCTTT
127 TTTAAGTATCTTT
91659 TAGGGTTCTT
Statistics
Matches: 128, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
158 57 0.45
161 70 0.55
162 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (156 bp):
GATAAAAAATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTTTTAA
TCTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAAATGAAAGTATTTTACTAAAATTATTTA
AGTATCTTTACAAGTATCGGAGTAAA
Found at i:94962 original size:4 final size:4
Alignment explanation
Indices: 94953--95003 Score: 75
Period size: 4 Copynumber: 12.8 Consensus size: 4
94943 GTGCCCCAAT
* * *
94953 TTCA TTCA TTCA CTCA CTCA TTCA TTCA TTCA TTCA TTCA TTCA CTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTCA
95001 TTC
1 TTC
95004 GCTCATTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (4 bp):
TTCA
Found at i:95008 original size:8 final size:8
Alignment explanation
Indices: 94953--95010 Score: 62
Period size: 8 Copynumber: 7.2 Consensus size: 8
94943 GTGCCCCAAT
*
94953 TTCATTCA
1 TTCACTCA
94961 TTCACTCA
1 TTCACTCA
* *
94969 CTCATTCA
1 TTCACTCA
*
94977 TTCATTCA
1 TTCACTCA
*
94985 TTCATTCA
1 TTCACTCA
94993 TTCACTCA
1 TTCACTCA
*
95001 TTCGCTCA
1 TTCACTCA
95009 TT
1 TT
95011 TGTTAATTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.45
Consensus pattern (8 bp):
TTCACTCA
Found at i:103611 original size:42 final size:42
Alignment explanation
Indices: 103549--103847 Score: 343
Period size: 42 Copynumber: 7.4 Consensus size: 42
103539 AAGGAAAGAA
* *
103549 TTCATTGCATTTAGAAGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
103591 TTCATCACATTTAGAGGCCTAAGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
103633 TTCATCGCA--T-------T--GTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
** * * *
103664 TTTTTCGCATTTGGAGGCCCAGGT-TGGAGGTCCGTTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* *
103705 TTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
* * * *
103747 TTCATTGCATTTAGAGGCATAAGTGTAGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
** *
103789 TTCATTACATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTT
1 TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
*
103831 TTCATTGCATTTAGAGG
1 TTCATCGCATTTAGAGG
103848 TCCATTTACT
Statistics
Matches: 219, Mismatches: 26, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
31 27 0.12
33 2 0.01
40 1 0.00
41 37 0.17
42 152 0.69
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (42 bp):
TTCATCGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
Found at i:103650 original size:31 final size:31
Alignment explanation
Indices: 103613--103674 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
103603 AGAGGCCTAA
103613 GTGTGGAGGTCCATTTACTTTTCATCGCATT
1 GTGTGGAGGTCCATTTACTTTTCATCGCATT
**
103644 GTGTGGAGGTCCATTTACTTTTTTTCGCATT
1 GTGTGGAGGTCCATTTACTTTTCATCGCATT
103675 TGGAGGCCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.45
Consensus pattern (31 bp):
GTGTGGAGGTCCATTTACTTTTCATCGCATT
Found at i:103847 original size:70 final size:70
Alignment explanation
Indices: 103772--103917 Score: 265
Period size: 70 Copynumber: 2.1 Consensus size: 70
103762 GGCATAAGTG
103772 TAGAGGTCCATTTACTTTTCATTACATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTTTTCATT
1 TAGAGGTCCATTTACTTTTCATTACATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTTTTCATT
103837 GCATT
66 GCATT
* * *
103842 TAGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTTCATTTACTTTTCATT
1 TAGAGGTCCATTTACTTTTCATTACATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTTTTCATT
103907 GCATT
66 GCATT
103912 TAGAGG
1 TAGAGG
103918 CCAGGTGTGG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (70 bp):
TAGAGGTCCATTTACTTTTCATTACATTTAGAGGCCAAGGTGTGGAGGTCCATTTACTTTTCATT
GCATT
Found at i:103849 original size:28 final size:28
Alignment explanation
Indices: 103816--103875 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
103806 CCAAGGTGTG
103816 GAGGTCCATTTACTTTTCATTGCATTTA
1 GAGGTCCATTTACTTTTCATTGCATTTA
103844 GAGGTCCATTTACTTTTCATTGCATTTA
1 GAGGTCCATTTACTTTTCATTGCATTTA
103872 GAGG
1 GAGG
103876 CCCAGGTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (28 bp):
GAGGTCCATTTACTTTTCATTGCATTTA
Found at i:103896 original size:42 final size:42
Alignment explanation
Indices: 103844--104012 Score: 232
Period size: 42 Copynumber: 3.9 Consensus size: 42
103834 ATTGCATTTA
103844 GAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
*
103886 GAGGTTCATTTACTTTTCATTGCATTTAGAGG-CCAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
* *
103927 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTG
1 GAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
103969 GAGGCTTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCA
1 GAGG--T------CCATTTACTTTTCATTGCATTTAGAGGCCCA
104013 TTTACTTTTC
Statistics
Matches: 112, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
41 39 0.35
42 43 0.38
50 30 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (42 bp):
GAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
Found at i:103949 original size:83 final size:85
Alignment explanation
Indices: 103844--104010 Score: 248
Period size: 83 Copynumber: 1.9 Consensus size: 85
103834 ATTGCATTTA
* *
103844 GAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGG-TT-CATTTACTTTTCATT
1 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGGCTTGCATTTACTTTTCATT
103907 GCATTTAGAGGCCAGGTGTG
66 GCATTTAGAGGCCAGGTGTG
103927 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGGCTTGGAGGCCCATTTACTT
1 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGGCTT----G--CATTTACTT
103992 TTCATTGCATTTAGAGGCC
60 TTCATTGCATTTAGAGGCC
104011 CATTTACTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
83 44 0.59
84 2 0.03
91 28 0.38
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (85 bp):
GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGGCTTGCATTTACTTTTCATT
GCATTTAGAGGCCAGGTGTG
Found at i:104017 original size:28 final size:28
Alignment explanation
Indices: 103977--104040 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
103967 TGGAGGCTTG
103977 GAGGCCCATTTACTTTTCATTGCATTTA
1 GAGGCCCATTTACTTTTCATTGCATTTA
104005 GAGGCCCATTTACTTTTCATTGCATTTA
1 GAGGCCCATTTACTTTTCATTGCATTTA
104033 GAGGCCCA
1 GAGGCCCA
104041 GGTGTGGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (28 bp):
GAGGCCCATTTACTTTTCATTGCATTTA
Found at i:104034 original size:161 final size:153
Alignment explanation
Indices: 103698--104142 Score: 665
Period size: 161 Copynumber: 2.8 Consensus size: 153
103688 TGGAGGTCCG
* *
103698 TTTACTTTTCATCGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTTAGAG
1 TTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAG
* * * * *
103763 GCATAAGTGTAGAGGTCCATTTACTTTTCATTACATTTAGAGGCCAAGGTGTGGAGGTCCATTTA
66 GC-CAGGTGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTA
*
103828 CTTTTCATTGCATTTAGAGGTCCA
130 CTTTTCATTGCATTTAGAGGCCCA
*
103852 TTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTTCATTTACTTTTCATTGCATTTAGAG
1 TTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAG
103917 GCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGGCTTGGAGGC
66 GCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGG--T------
103982 CCATTTACTTTTCATTGCATTTAGAGGCCCA
123 CCATTTACTTTTCATTGCATTTAGAGGCCCA
*
104013 TTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAAAG
1 TTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAG
* * * * *
104078 GTCCAGGTGTGGAGGCCCATTTACTTTTTATTGCATTTAGGGGCCTAGGCGTAGAGGTCCATTTA
66 G-CCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTA
104143 TTTATTTTTT
Statistics
Matches: 266, Mismatches: 16, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
153 49 0.18
154 71 0.27
155 1 0.00
160 1 0.00
161 94 0.35
162 50 0.19
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (153 bp):
TTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAG
GCCAGGTGTGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGGTCCATTTAC
TTTTCATTGCATTTAGAGGCCCA
Found at i:104044 original size:78 final size:75
Alignment explanation
Indices: 103927--104074 Score: 209
Period size: 78 Copynumber: 2.0 Consensus size: 75
103917 GCCAGGTGTG
*
103927 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCAAGGTGTGGAGGCTTGGAGGCCCATTTACTT
1 GAGG-CCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGG-TTGGAGG-CCATTTACTT
103992 TTCATTGCATTTA
63 TTCATTGCATTTA
104005 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGG-T-----CCATTTACTTTT
1 GAGG-CCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTTGGAGGCCATTTACTTTT
104064 CATTGCATTTA
65 CATTGCATTTA
104075 AAGGTCCAGG
Statistics
Matches: 69, Mismatches: 1, Indels: 8
0.88 0.01 0.10
Matches are distributed among these distances:
70 23 0.33
76 1 0.01
78 45 0.65
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (75 bp):
GAGGCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTTGGAGGCCATTTACTTTTC
ATTGCATTTA
Found at i:104057 original size:42 final size:42
Alignment explanation
Indices: 104005--104142 Score: 195
Period size: 42 Copynumber: 3.3 Consensus size: 42
103995 ATTGCATTTA
104005 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
1 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
* * *
104047 GAGGTCCATTTACTTTTCATTGCATTTAAAGGTCCAGGTGTG
1 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
* * * * *
104089 GAGGCCCATTTACTTTTTATTGCATTTAGGGGCCTAGGCGTA
1 GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
*
104131 GAGGTCCATTTA
1 GAGGCCCATTTA
104143 TTTATTTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
GAGGCCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTG
Found at i:105563 original size:144 final size:146
Alignment explanation
Indices: 105204--105583 Score: 450
Period size: 143 Copynumber: 2.6 Consensus size: 146
105194 TTTTTTTTAG
*
105204 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTTTAACTATTTCAAAATAAAAGTTTAGA
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGA---TTTTTTTAACTATTTCGAAATAAAAGTTTAGA
* * ** *
105269 TTTTTAAGAAAGTAGTGATTTTCATTAAATATGAGAAAGTTTATATTTTTAAAAATAAAAATATG
63 TTTTTAAG-TAGTAGTGATTTTCATTAAATA-GAGAAAGTTTAGATTTAAAAAAATAAAAATATA
*
105334 TTTTTTAGTTATTCCAAAAGA
126 TTTTTTAGTGATTCCAAAAGA
* * *
105355 AAAAGTTT-AATTTTTAAAATAAAGTTTTGATTTTTTTAACTATTTCGAATTAAAATTTTGGATT
1 AAAAGTTTAAATTTTT-AAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
* *
105419 TTTAAGTA-TAGTGATTTTTATTAAA-A-A-AAAGTTTAGACTTTAAAAAAATAAAAATCTATTT
65 TTTAAGTAGTAGTGATTTTCATTAAATAGAGAAAGTTTAGA-TTTAAAAAAATAAAAATATATTT
**
105480 TTTAGTGATT-TTAAAGAA
129 TTTAGTGATTCCAAAAG-A
* *
105498 AAAAGTTTAAATTTTTAAACACAGTTTTGATTTTGTTTAACTATTTCGAAATAAAAGCTTT-GAT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTT-TTTAACTATTTCGAAATAAAAG-TTTAGAT
*
105562 TTTGAAGTAAAGTAGTGATTTT
64 TTTTAAGT--AGTAGTGATTTT
105584 ATTTTAATCA
Statistics
Matches: 201, Mismatches: 19, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
142 13 0.06
143 54 0.27
144 37 0.18
145 4 0.02
146 17 0.08
147 11 0.05
148 36 0.18
150 7 0.03
151 22 0.11
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.45
Consensus pattern (146 bp):
AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTT
TTAAGTAGTAGTGATTTTCATTAAATAGAGAAAGTTTAGATTTAAAAAAATAAAAATATATTTTT
TAGTGATTCCAAAAGA
Found at i:108002 original size:16 final size:16
Alignment explanation
Indices: 107978--108009 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
107968 TCCTTACAAA
*
107978 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
107994 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
108010 AAAAATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:111720 original size:21 final size:21
Alignment explanation
Indices: 111675--111723 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
111665 CCTCTGATAG
* * *
111675 TTCTACCTATACAAATGAAGT
1 TTCTACCTAAACAAATCAAGC
*
111696 TTCTACCTAAACAAATCATGC
1 TTCTACCTAAACAAATCAAGC
111717 TTCTACC
1 TTCTACC
111724 AGTACCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.33
Consensus pattern (21 bp):
TTCTACCTAAACAAATCAAGC
Found at i:112540 original size:52 final size:52
Alignment explanation
Indices: 112461--112697 Score: 309
Period size: 52 Copynumber: 4.6 Consensus size: 52
112451 TTCTCATTTA
* * *
112461 ATACTCACAATGACACATAGTCATCAGACTTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAAGATTCAT
** * *
112513 ATACTCACGATGACACATAGTTGTCAGACCTCGTAATCTGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAAGATTCAT
* * * * *
112565 ATATTCACGATGACAC--AGTCATCGGACCTCATATTCAGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAAGATTCAT
*
112615 ATACTCACGATGACACATAGTCATC-GAACCTCCTAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCAG-ACCTCATAATCCGTAAAAGATTCAT
* *
112667 ATACTCACGATGACACATAATCATCGGACCT
1 ATACTCACGATGACACATAGTCATCAGACCT
112698 TTTGCATTTA
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
50 42 0.26
51 1 0.01
52 116 0.73
53 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAAGATTCAT
Found at i:112658 original size:102 final size:103
Alignment explanation
Indices: 112461--112697 Score: 334
Period size: 102 Copynumber: 2.3 Consensus size: 103
112451 TTCTCATTTA
* * * *
112461 ATACTCACAATGACACATAGTCATCAGACTTCATAATCCGTAAAGGATTCATATACTCACGATGA
1 ATACTCACGATGACACA-AGTCATCGGACCTCATAATCAGTAAAGGATTCATATACTCACGATGA
** * *
112526 CACATAGTTGTCAGACCTCGTAATCTGTAAAAGATTCAT
65 CACATAGTCATCAGACCTCCTAATCCGTAAAAGATTCAT
* *
112565 ATATTCACGATGACAC-AGTCATCGGACCTCATATTCAGTAAAGGATTCATATACTCACGATGAC
1 ATACTCACGATGACACAAGTCATCGGACCTCATAATCAGTAAAGGATTCATATACTCACGATGAC
112629 ACATAGTCATC-GAACCTCCTAATCCGTAAAAGATTCAT
66 ACATAGTCATCAG-ACCTCCTAATCCGTAAAAGATTCAT
*
112667 ATACTCACGATGACACATAATCATCGGACCT
1 ATACTCACGATGACACA-AGTCATCGGACCT
112698 TTTGCATTTA
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
101 1 0.01
102 91 0.77
104 26 0.22
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (103 bp):
ATACTCACGATGACACAAGTCATCGGACCTCATAATCAGTAAAGGATTCATATACTCACGATGAC
ACATAGTCATCAGACCTCCTAATCCGTAAAAGATTCAT
Found at i:116109 original size:24 final size:24
Alignment explanation
Indices: 116059--116110 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
116049 AAACAAGGAG
* * * *
116059 CACATGGCCTGTGACACGGGTTGT
1 CACACGGCCTATGACACGGGCTAT
116083 CACACGGCCTATGACACGGGCTAT
1 CACACGGCCTATGACACGGGCTAT
116107 CACA
1 CACA
116111 GTGTCGTGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.23, C:0.31, G:0.27, T:0.19
Consensus pattern (24 bp):
CACACGGCCTATGACACGGGCTAT
Found at i:121304 original size:30 final size:30
Alignment explanation
Indices: 121250--121306 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
121240 TATCCACTTC
* *
121250 TCCCAGATTGGTACCTATAGTTTTTTTTTG
1 TCCCAGATTGGTACCGATACTTTTTTTTTG
121280 TCCCAGATTGGTACTCGA-ACTTTTTTT
1 TCCCAGATTGGTAC-CGATACTTTTTTT
121307 CCGGCCACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (30 bp):
TCCCAGATTGGTACCGATACTTTTTTTTTG
Found at i:127723 original size:25 final size:25
Alignment explanation
Indices: 127695--127755 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
127685 AATTACCAAG
127695 TTTTAGTTTTTAGATAATTATTTTA
1 TTTTAGTTTTTAGATAATTATTTTA
127720 TTTTAGTTTTTAGATAATTATTTTA
1 TTTTAGTTTTTAGATAATTATTTTA
*
127745 TTTTACTTTTT
1 TTTTAGTTTTT
127756 TCCGAATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (25 bp):
TTTTAGTTTTTAGATAATTATTTTA
Found at i:127763 original size:25 final size:25
Alignment explanation
Indices: 127695--127765 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
127685 AATTACCAAG
* * *
127695 TTTTAGTTTTTAGATAATTATTTTA
1 TTTTACTTTTTACAGAATTATTTTA
* * *
127720 TTTTAGTTTTTAGATAATTATTTTA
1 TTTTACTTTTTACAGAATTATTTTA
* *
127745 TTTTACTTTTTTCCGAATTAT
1 TTTTACTTTTTACAGAATTAT
127766 CATTTTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.63
Consensus pattern (25 bp):
TTTTACTTTTTACAGAATTATTTTA
Found at i:130196 original size:116 final size:115
Alignment explanation
Indices: 129970--130251 Score: 417
Period size: 116 Copynumber: 2.4 Consensus size: 115
129960 TTAATTTTAA
* *
129970 TTTTAATGTTTAATTTAATATG-AAATTTTTTTTATCTTAATTTGATATATAAATTTGATTTTAA
1 TTTTAATGTTTAATTTAATATGTATA-TTTTTTTATCTTAA-TTAATATATAAATTTGATTTTAA
**
130034 TATTCACTTTAATATTACTTTTTTTCAATTTGAAATTTAATTTTTTTTATCAG
64 TATTCACTTTAATATTAAGTTTTTTCAATTTGAAATTTAA-TTTTTTTATCAG
*
130087 TTTTATTGTTTAATTTAATATGTATATTTTTTTATCTTAATTAATATATAAATTTGATTTTAATA
1 TTTTAATGTTTAATTTAATATGTATATTTTTTTATCTTAATTAATATATAAATTTGATTTTAATA
130152 TTCACTTTAATATTAAAGTTTTTTCAATTTTGAAATTTAA-TTTTTTATCAG
66 TTCACTTTAATATT-AAGTTTTTTCAA-TTTGAAATTTAATTTTTTTATCAG
* * *
130203 TTTTAATGTTTAATTTAATATTTTTATATTTTTTATTTTAATTAA-ATAT
1 TTTTAATGTTTAATTTAATATGTATAT-TTTTTTATCTTAATTAATATAT
130252 TTTTATATTT
Statistics
Matches: 152, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
116 77 0.51
117 61 0.40
118 14 0.09
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (115 bp):
TTTTAATGTTTAATTTAATATGTATATTTTTTTATCTTAATTAATATATAAATTTGATTTTAATA
TTCACTTTAATATTAAGTTTTTTCAATTTGAAATTTAATTTTTTTATCAG
Found at i:130243 original size:28 final size:28
Alignment explanation
Indices: 130185--130267 Score: 114
Period size: 28 Copynumber: 2.9 Consensus size: 28
130175 TCAATTTTGA
* *
130185 AATTTAAT-TTTTTATCAGTTTTAATGTTT
1 AATTTAATATTTTTAT-ATTTTTTAT-TTT
130214 AATTTAATATTTTTATATTTTTTATTTT
1 AATTTAATATTTTTATATTTTTTATTTT
*
130242 AATTAAATATTTTTATATTTTTTATT
1 AATTTAATATTTTTATATTTTTTATT
130268 AGATCACATG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
28 28 0.56
29 15 0.30
30 7 0.14
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (28 bp):
AATTTAATATTTTTATATTTTTTATTTT
Found at i:134567 original size:18 final size:18
Alignment explanation
Indices: 134544--134584 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
134534 CAGGAATGGA
134544 AGAGAAAGAAGC-AGAGAT
1 AGAGAAAGAAGCAAGA-AT
*
134562 AGAGAAAGTAGCAAGAAT
1 AGAGAAAGAAGCAAGAAT
134580 AGAGA
1 AGAGA
134585 GCGTGAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.56, C:0.05, G:0.32, T:0.07
Consensus pattern (18 bp):
AGAGAAAGAAGCAAGAAT
Found at i:138316 original size:12 final size:12
Alignment explanation
Indices: 138299--138323 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
138289 TGGGTTTCCA
138299 TTCTTCTCTGGT
1 TTCTTCTCTGGT
138311 TTCTTCTCTGGT
1 TTCTTCTCTGGT
138323 T
1 T
138324 CTGCATGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.24, G:0.16, T:0.60
Consensus pattern (12 bp):
TTCTTCTCTGGT
Found at i:150354 original size:70 final size:69
Alignment explanation
Indices: 150280--150415 Score: 254
Period size: 69 Copynumber: 2.0 Consensus size: 69
150270 TGTTTCAGGT
*
150280 TTTTTTTTAATTAATGTTTTTATCATATAAGCTTTTTTTATTAGACGGTTAAATAATAGTAATTT
1 TTTTTTTTAATTAATGTTTTTATCATATAAGCGTTTTTTATTAGACGGTTAAATAATAGTAATTT
150345 CAAG
66 CAAG
*
150349 TTTTTTTTAATTAATGTTTTTATCATATCAGCGTTTTTTATTAGACGGTTAAATAATAGTAATTT
1 TTTTTTTTAATTAATGTTTTTATCATATAAGCGTTTTTTATTAGACGGTTAAATAATAGTAATTT
150414 CA
66 CA
150416 TTCCTAAGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (69 bp):
TTTTTTTTAATTAATGTTTTTATCATATAAGCGTTTTTTATTAGACGGTTAAATAATAGTAATTT
CAAG
Found at i:150593 original size:19 final size:18
Alignment explanation
Indices: 150571--150607 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
150561 AATAATTATT
*
150571 GTAAATATCATTATTTTTA
1 GTAAATATAATT-TTTTTA
150590 GTAAATATAATTTTTTTA
1 GTAAATATAATTTTTTTA
150608 TGTGTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (18 bp):
GTAAATATAATTTTTTTA
Found at i:150769 original size:39 final size:43
Alignment explanation
Indices: 150679--150773 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 43
150669 TTTGTATGTG
*
150679 TATTTGAAATAATTATTTAAAATATTTCACATATAAATATAATAA
1 TATTTGAAATAATTAATTAAAATATTTCACA-AT-AATATAATAA
*
150724 TATTTGAAATAATTAATTGAAATATTTCAC-AT-ATA-AA-AA
1 TATTTGAAATAATTAATTAAAATATTTCACAATAATATAATAA
150763 TATTTGAAATA
1 TATTTGAAATA
150774 TCATACTCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
39 13 0.27
40 2 0.04
41 3 0.06
43 2 0.04
45 28 0.58
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (43 bp):
TATTTGAAATAATTAATTAAAATATTTCACAATAATATAATAA
Found at i:150774 original size:17 final size:17
Alignment explanation
Indices: 150713--150774 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
150703 TTTCACATAT
*
150713 AAATATAATAATATTTG
1 AAATATAAAAATATTTG
*
150730 AAATAATTAATTGAAATATTTC
1 AAAT-A-TAA---AAATATTTG
*
150752 ACATATAAAAATATTTG
1 AAATATAAAAATATTTG
150769 AAATAT
1 AAATAT
150775 CATACTCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 17 0.49
18 1 0.03
19 3 0.09
20 3 0.09
21 1 0.03
22 10 0.29
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (17 bp):
AAATATAAAAATATTTG
Found at i:152654 original size:16 final size:16
Alignment explanation
Indices: 152633--152666 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
152623 CTATTGATAT
152633 ATCGCGGTTCGTTGTA
1 ATCGCGGTTCGTTGTA
152649 ATCGCGGTTCGTTGTA
1 ATCGCGGTTCGTTGTA
152665 AT
1 AT
152667 AGATTAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.29, T:0.38
Consensus pattern (16 bp):
ATCGCGGTTCGTTGTA
Found at i:170955 original size:52 final size:52
Alignment explanation
Indices: 170878--171069 Score: 294
Period size: 52 Copynumber: 3.7 Consensus size: 52
170868 CCGTAAAGAA
* * *
170878 ATTCATATACTCACGATGACACTTAGTCATTGGACCTTATAATCCGTGAAGG
1 ATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATGAAGG
* * * * * *
170930 ATTCATGTACTCATGATGACGCTTAGTCATCGGACTTTAGAATCTATGAACG
1 ATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATGAAGG
*
170982 ATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATCAAGG
1 ATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATGAAGG
171034 ATTCATGTACTCACGATGACACTTAGTCATCGGACC
1 ATTCATGTACTCACGATGACACTTAGTCATCGGACC
171070 CTTTTCCATT
Statistics
Matches: 124, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (52 bp):
ATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATGAAGG
Found at i:171008 original size:104 final size:104
Alignment explanation
Indices: 170878--171068 Score: 328
Period size: 104 Copynumber: 1.8 Consensus size: 104
170868 CCGTAAAGAA
* * *
170878 ATTCATATACTCACGATGACACTTAGTCATTGGACCTTATAATCCGTGAAGGATTCATGTACTCA
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTATAATCCATCAAGGATTCATGTACTCA
* *
170943 TGATGACGCTTAGTCATCGGACTTTAGAATCTATGAACG
66 CGATGACACTTAGTCATCGGACTTTAGAATCTATGAACG
*
170982 ATTCATGTACTCACGATGACACTTAGTCATCGGACCTTATAATCCATCAAGGATTCATGTACTCA
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTATAATCCATCAAGGATTCATGTACTCA
171047 CGATGACACTTAGTCATCGGAC
66 CGATGACACTTAGTCATCGGAC
171069 CCTTTTCCAT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
104 81 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (104 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTTATAATCCATCAAGGATTCATGTACTCA
CGATGACACTTAGTCATCGGACTTTAGAATCTATGAACG
Found at i:171977 original size:20 final size:21
Alignment explanation
Indices: 171934--171977 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
171924 ACTTTCATCA
* *
171934 TTAATCTTTAATTAAACATTT
1 TTAACCTTTAATTAAACATAT
*
171955 TTAACCTTT-ATTAAACCTAT
1 TTAACCTTTAATTAAACATAT
171975 TTA
1 TTA
171978 TAATCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAACCTTTAATTAAACATAT
Found at i:178183 original size:52 final size:51
Alignment explanation
Indices: 178118--178304 Score: 216
Period size: 52 Copynumber: 3.6 Consensus size: 51
178108 CCTTAAAGAA
* * **
178118 ATTCATATACTCACAATGACAC-TCGCTCATCGGATCTTATAATCTGTGAAGG
1 ATTCATATACTCACGATGACACTTAG-TCATCGGA-CTTATAATCCATGAAGG
* *
178170 ATTCATATACTCACGATGACGCTTAGTCATCAGACTTTATAATCCATGAACGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGAC-TTATAATCCATGAA-GG
* *
178223 -TTCATGTACTCACGATGACACTTAGTCATCGGGCCTTATAATCCATGAAGG
1 ATTCATATACTCACGATGACACTTAGTCATC-GGACTTATAATCCATGAAGG
* * *
178274 ATTCATGTACTCCCGATAACACTTAGTCATC
1 ATTCATATACTCACGATGACACTTAGTCATC
178305 AGACCTTTTT
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
51 3 0.03
52 109 0.92
53 6 0.05
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACTTATAATCCATGAAGG
Found at i:178252 original size:104 final size:104
Alignment explanation
Indices: 178119--178308 Score: 265
Period size: 104 Copynumber: 1.8 Consensus size: 104
178109 CTTAAAGAAA
* * **
178119 TTCATATACTCACAATGACACTCGCTCATCGGATCTTATAATCTGTGAAGGATTCATATACTCAC
1 TTCATATACTCACAATGACACTAGCTCATCGGACCTTATAATCCATGAAGGATTCATATACTCAC
* *
178184 GATGACGCTTAGTCATCAGACTTTATAATCCATGAACGG
66 GATAACACTTAGTCATCAGACTTTATAATCCATGAACGG
* * * * *
178223 TTCATGTACTCACGATGACACTTAG-TCATCGGGCCTTATAATCCATGAAGGATTCATGTACTCC
1 TTCATATACTCACAATGACAC-TAGCTCATCGGACCTTATAATCCATGAAGGATTCATATACTCA
178287 CGATAACACTTAGTCATCAGAC
65 CGATAACACTTAGTCATCAGAC
178309 CTTTTTTCAT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 72 0.97
105 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (104 bp):
TTCATATACTCACAATGACACTAGCTCATCGGACCTTATAATCCATGAAGGATTCATATACTCAC
GATAACACTTAGTCATCAGACTTTATAATCCATGAACGG
Found at i:179090 original size:7 final size:7
Alignment explanation
Indices: 179078--179102 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
179068 TGTCGTGTGG
179078 AGAAGAA
1 AGAAGAA
179085 AGAAGAA
1 AGAAGAA
179092 AGAAGAA
1 AGAAGAA
179099 AGAA
1 AGAA
179103 AATGGGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:187220 original size:2 final size:2
Alignment explanation
Indices: 187213--187243 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
187203 AAATCCCGTT
187213 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
187244 GCATGTAGTT
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:187737 original size:31 final size:31
Alignment explanation
Indices: 187680--187744 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
187670 AACAACCTGA
*
187680 TGACTTAAATAAAAACTTTTGAATAGTTCAG
1 TGACTTAAATAAAAACTTTAGAATAGTTCAG
*
187711 TGACTTAAATAAAAACTTTCAG-ATAGTTGAG
1 TGACTTAAATAAAAACTTT-AGAATAGTTCAG
187742 TGA
1 TGA
187745 TCATTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTAGAATAGTTCAG
Found at i:192529 original size:11 final size:12
Alignment explanation
Indices: 192513--192579 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 12
192503 ATTTACTAAC
192513 ATTTAATTT-TT
1 ATTTAATTTATT
192524 ATTTAATTTATT
1 ATTTAATTTATT
192536 A-TT-ATTTATT
1 ATTTAATTTATT
*
192546 ATTT-CTTTATGT
1 ATTTAATTTAT-T
*
192558 A-TTATTTTATGAT
1 ATTTAATTTAT--T
192571 ATTTAATTT
1 ATTTAATTT
192580 TATTGACATT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.17
11 20 0.43
12 10 0.22
13 2 0.04
14 6 0.13
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.67
Consensus pattern (12 bp):
ATTTAATTTATT
Found at i:192549 original size:22 final size:23
Alignment explanation
Indices: 192518--192579 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
192508 CTAACATTTA
192518 ATTT-TTATTTAATTTAT-TATT
1 ATTTATTATTTAATTTATGTATT
*
192539 ATTTATTATTT-CTTTATGTATT
1 ATTTATTATTTAATTTATGTATT
192561 ATTTTATGATATTTAATTT
1 A-TTTAT--TATTTAATTT
192580 TATTGACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
21 9 0.27
22 11 0.33
23 5 0.15
25 5 0.15
26 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (23 bp):
ATTTATTATTTAATTTATGTATT
Found at i:197400 original size:30 final size:31
Alignment explanation
Indices: 197364--197423 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
197354 TGTCGTACAC
197364 AAATTTTGATTTTG-TGTAATTTT-ATAAATA
1 AAATTTT-ATTTTGATGTAATTTTCATAAATA
*
197394 AAATTTTATTTTGATTTAATTTTCATAAAT
1 AAATTTTATTTTGATGTAATTTTCATAAAT
197424 TATTGACAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.22
30 15 0.56
31 6 0.22
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.55
Consensus pattern (31 bp):
AAATTTTATTTTGATGTAATTTTCATAAATA
Found at i:197931 original size:4 final size:4
Alignment explanation
Indices: 197922--197964 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
197912 GATGAAAGTA
197922 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
197965 CAAAAGCAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:198367 original size:22 final size:21
Alignment explanation
Indices: 198341--198399 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
198331 TATCGTCCAC
198341 CTTTTTCTTCTTTTTTCTCACA
1 CTTTTTCTTCTTTTTTCT-ACA
* * *
198363 CTTTTTTTTCATTTTTGTACA
1 CTTTTTCTTCTTTTTTCTACA
*
198384 -TGTTTTCTTTTTTTTT
1 CT-TTTTCTTCTTTTTT
198400 TTTTTAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 14 0.47
22 15 0.50
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.71
Consensus pattern (21 bp):
CTTTTTCTTCTTTTTTCTACA
Found at i:200943 original size:28 final size:28
Alignment explanation
Indices: 200912--201008 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 28
200902 TTTTAGATCC
200912 CTTAAAAGTTGGAAAAAAATTGGACCCT
1 CTTAAAAGTTGGAAAAAAATTGGACCCT
*
200940 CTTAAAAGTTGGTAAAAAAATACTGG--TCT
1 CTTAAAAGTTGG-AAAAAAAT--TGGACCCT
*
200969 -TTAAAAG-T-AAAAAAAATTGGACCC-
1 CTTAAAAGTTGGAAAAAAATTGGACCCT
*
200993 CTTAAAAATTGGAAAA
1 CTTAAAAGTTGGAAAA
201009 CAATATTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
23 3 0.05
25 15 0.27
26 1 0.02
27 5 0.09
28 19 0.34
29 10 0.18
31 3 0.05
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.26
Consensus pattern (28 bp):
CTTAAAAGTTGGAAAAAAATTGGACCCT
Found at i:203169 original size:6 final size:6
Alignment explanation
Indices: 203158--203202 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
203148 TGATCAAAAT
* * * *
203158 TGAAAG TGAAAG TGAAAG TGAAAA TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
203203 TATGAATTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:204845 original size:18 final size:18
Alignment explanation
Indices: 204822--204864 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
204812 TTTTTAGTTG
204822 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
204840 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
204858 TAATTAA
1 TAATTAA
204865 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:209704 original size:33 final size:33
Alignment explanation
Indices: 209656--209722 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
209646 CTAGAAACAC
*
209656 TAGAATGAAATAAATACAATCTTCAATAATACT
1 TAGAATGAAAGAAATACAATCTTCAATAATACT
*
209689 TAGAATGGAAGAAATACAATCTTCAATAATACT
1 TAGAATGAAAGAAATACAATCTTCAATAATACT
209722 T
1 T
209723 CAACAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (33 bp):
TAGAATGAAAGAAATACAATCTTCAATAATACT
Found at i:212434 original size:9 final size:10
Alignment explanation
Indices: 212417--212446 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
212407 TTTAATAAAC
212417 TTATATTTTT
1 TTATATTTTT
212427 TT-TATTTTT
1 TTATATTTTT
212436 TTATATTTTT
1 TTATATTTTT
212446 T
1 T
212447 GTAATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTATATTTTT
Found at i:214405 original size:28 final size:28
Alignment explanation
Indices: 214369--214425 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
214359 TTCTGACACC
* * *
214369 TCTTGTTTGAAATCAATGCTTTTATTTT
1 TCTTCTTTGAAATCAATGCCTTGATTTT
214397 TCTTCTTTGAAATCAATGCCTTGATTTT
1 TCTTCTTTGAAATCAATGCCTTGATTTT
214425 T
1 T
214426 ACTCTAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (28 bp):
TCTTCTTTGAAATCAATGCCTTGATTTT
Found at i:215189 original size:22 final size:22
Alignment explanation
Indices: 215163--215208 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
215153 ATCATTTTCC
215163 AAATACTATTTTGAATGAAACA
1 AAATACTATTTTGAATGAAACA
215185 AAATACTATTTTGAATGAAACA
1 AAATACTATTTTGAATGAAACA
215207 AA
1 AA
215209 CACCCCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (22 bp):
AAATACTATTTTGAATGAAACA
Found at i:215345 original size:30 final size:32
Alignment explanation
Indices: 215304--215369 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
215294 CATTTAACTA
* *
215304 AAAAAAGTTATCGTTT-GGTCACTAAACTATT
1 AAAAAAGTTATCATTTAAGTCACTAAACTATT
*
215335 AAAAAA-TTATCATTTAAGTCACTAAACTGTT
1 AAAAAAGTTATCATTTAAGTCACTAAACTATT
215366 AAAA
1 AAAA
215370 CCGATGCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (32 bp):
AAAAAAGTTATCATTTAAGTCACTAAACTATT
Found at i:215356 original size:31 final size:31
Alignment explanation
Indices: 215288--215369 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
215278 AAATTTTTGT
* * *
215288 TTTAGTCATTTAACTA--AAAAAAGTTATCG
1 TTTAGTCACTAAACTATTAAAAAAGTTATCA
*
215317 TTTGGTCACTAAACTATTAAAAAA-TTATCA
1 TTTAGTCACTAAACTATTAAAAAAGTTATCA
*
215347 TTTAAGTCACTAAACTGTTAAAA
1 TTT-AGTCACTAAACTATTAAAA
215370 CCGATGCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
29 13 0.30
30 8 0.18
31 23 0.52
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.37
Consensus pattern (31 bp):
TTTAGTCACTAAACTATTAAAAAAGTTATCA
Found at i:220237 original size:13 final size:14
Alignment explanation
Indices: 220211--220240 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
220201 AGAATAAATT
220211 TTTAATTAAATAAA
1 TTTAATTAAATAAA
220225 TTTAATT-AATAAA
1 TTTAATTAAATAAA
220238 TTT
1 TTT
220241 TTTTTAATTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:220250 original size:32 final size:32
Alignment explanation
Indices: 220209--220269 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
220199 TAAGAATAAA
220209 TTTTTAATTAAATA-AATTTAATTAATAAATTT
1 TTTTTAATTAAATACAATTTAATT-ATAAATTT
* *
220241 TTTTTAATTAATTACACTTTAATTATAAA
1 TTTTTAATTAAATACAATTTAATTATAAA
220270 AAAAAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (32 bp):
TTTTTAATTAAATACAATTTAATTATAAATTT
Found at i:221932 original size:82 final size:82
Alignment explanation
Indices: 221835--221997 Score: 265
Period size: 82 Copynumber: 2.0 Consensus size: 82
221825 TCTATTTTGA
* *
221835 TTGCGCTAATAATTCTCGAATTGA-TTAGATTAGTAATTGCTTAGCTAGTAATTAATTTGGCAAA
1 TTGCACTAATAATTCTCGAATTGATTTA-ATTAGTAATTGCTTAGCTAGTAATTAATTTGACAAA
* *
221899 CATGTTTACCAATTGACG
65 CACGTTTAACAATTGACG
*
221917 TTGCACTAATAATTCTCGAATTGATTTAATTAGTAATTGCTTAGCTAGTAATTAGTTTGACAAAC
1 TTGCACTAATAATTCTCGAATTGATTTAATTAGTAATTGCTTAGCTAGTAATTAATTTGACAAAC
221982 ACGTTTAACAATTGAC
66 ACGTTTAACAATTGAC
221998 AATCCTTTGG
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
82 72 0.96
83 3 0.04
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (82 bp):
TTGCACTAATAATTCTCGAATTGATTTAATTAGTAATTGCTTAGCTAGTAATTAATTTGACAAAC
ACGTTTAACAATTGACG
Found at i:228072 original size:19 final size:19
Alignment explanation
Indices: 228031--228074 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
228021 CATTCTTTAG
* *
228031 AATTTTTTAAAAAAATTTT
1 AATTTTTTAAAAAAATATA
*
228050 AATTTTTTTAAAAAATATA
1 AATTTTTTAAAAAAATATA
228069 AATTTT
1 AATTTT
228075 GGAATTGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTTTTAAAAAAATATA
Found at i:228110 original size:19 final size:18
Alignment explanation
Indices: 228084--228131 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
228074 TGGAATTGTA
228084 TAAA-TATTTTGAAAATT
1 TAAATTATTTTGAAAATT
*
228101 TAAATTTATTTTGAAATTT
1 TAAA-TTATTTTGAAAATT
*
228120 TGAATTATTTTG
1 TAAATTATTTTG
228132 TAATTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 4 0.15
18 8 0.30
19 15 0.56
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TAAATTATTTTGAAAATT
Found at i:228119 original size:18 final size:17
Alignment explanation
Indices: 228084--228137 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
228074 TGGAATTGTA
228084 TAAA-TATTTTGAAAATT
1 TAAATTATTTTG-AAATT
228101 TAAATTTATTTTGAAATTT
1 TAAA-TTATTTTGAAA-TT
* *
228120 TGAATTATTTTGTAATT
1 TAAATTATTTTGAAATT
228137 T
1 T
228138 TTGTATTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 7 0.22
18 13 0.41
19 12 0.38
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (17 bp):
TAAATTATTTTGAAATT
Found at i:228872 original size:150 final size:150
Alignment explanation
Indices: 228600--228876 Score: 412
Period size: 150 Copynumber: 1.8 Consensus size: 150
228590 TTGGGTCCGG
* * ** * * *
228600 GGTGAGCAAAAAACTGCCTTGCCATGTTGCCAATCCTGCTTCTATTTCTTTAAATGAAGGTTGAC
1 GGTGAGCAAAAAACTGCCCTGCCATGTTGCCAACCCCACTTCCATTTCGTTAAATGAAGGTCGAC
* *
228665 CATTATCTATTATACATGTGAAGTAGTTAATTTGGGTTTACGGAGAAATAACCAACTATGCACTT
66 CATTATCTACTATACATGTGAAGTACTTAATTTGGGTTTACGGAGAAATAACCAACTATGCACTT
228730 AAGATTTAGTTTGGATTTAT
131 AAGATTTAGTTTGGATTTAT
*
228750 GGTGAGC-GAAAACTGCCCTGCCATGTTGCCAACCCCACTTCCATTTCAGTTAAATGAAGGTCGA
1 GGTGAGCAAAAAACTGCCCTGCCATGTTGCCAACCCCACTTCCATTTC-GTTAAATGAAGGTCGA
* * **
228814 CCATTATCTACTATACATGTGAAGTACTTAGTTTGGGTTTATGGAGAAATAATTAACTATGCA
65 CCATTATCTACTATACATGTGAAGTACTTAATTTGGGTTTACGGAGAAATAACCAACTATGCA
228877 TCTTGTGTCT
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
149 34 0.30
150 78 0.70
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (150 bp):
GGTGAGCAAAAAACTGCCCTGCCATGTTGCCAACCCCACTTCCATTTCGTTAAATGAAGGTCGAC
CATTATCTACTATACATGTGAAGTACTTAATTTGGGTTTACGGAGAAATAACCAACTATGCACTT
AAGATTTAGTTTGGATTTAT
Found at i:229691 original size:16 final size:16
Alignment explanation
Indices: 229670--229706 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
229660 TTCTTACAAT
229670 TTTGACAAGTCCTTGC
1 TTTGACAAGTCCTTGC
229686 TTTGACAAGTCCTTGC
1 TTTGACAAGTCCTTGC
229702 TTTGA
1 TTTGA
229707 AACTGTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (16 bp):
TTTGACAAGTCCTTGC
Found at i:235272 original size:27 final size:27
Alignment explanation
Indices: 235219--235275 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
235209 AATGTTTTTG
*
235219 TTTTTATTTATGTTACTTTCATGTTAT
1 TTTTTATTTATGTTAATTTCATGTTAT
* *
235246 TTTTTATTTAATTTTAATTTTAT-TTAT
1 TTTTTATTT-ATGTTAATTTCATGTTAT
235273 TTT
1 TTT
235276 AATTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (27 bp):
TTTTTATTTATGTTAATTTCATGTTAT
Found at i:235276 original size:15 final size:16
Alignment explanation
Indices: 235247--235283 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
235237 TCATGTTATT
235247 TTTTATTTAATTTTAA
1 TTTTATTTAATTTTAA
235263 TTTTATTT-ATTTTAA
1 TTTTATTTAATTTTAA
235278 TTTTAT
1 TTTTAT
235284 ATTTATATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTTAATTTTAA
Found at i:235278 original size:21 final size:22
Alignment explanation
Indices: 235248--235292 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
235238 CATGTTATTT
235248 TTTATTTAATTTTA-ATTT-TA
1 TTTATTTAATTTTATATTTATA
235268 TTTATTTTAATTTTATATTTATA
1 TTTA-TTTAATTTTATATTTATA
235291 TT
1 TT
235293 CATATTCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 10 0.45
22 4 0.18
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTATTTAATTTTATATTTATA
Found at i:235288 original size:6 final size:6
Alignment explanation
Indices: 235250--235335 Score: 58
Period size: 6 Copynumber: 14.8 Consensus size: 6
235240 TGTTATTTTT
*
235250 TATTTA -ATTT- TAATTT- TATTTA T-TTTA -ATTTTA TATTTA TATTCA
1 TATTTA TATTTA T-ATTTA TATTTA TATTTA TA-TTTA TATTTA TATTTA
* * * *
235295 TATTCT- TATTCA TATTTC TATTTC TATTTC TATTTA TATTT
1 TATT-TA TATTTA TATTTA TATTTA TATTTA TATTTA TATTT
235336 TACTATACAC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
5 12 0.18
6 53 0.80
7 1 0.02
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (6 bp):
TATTTA
Found at i:238254 original size:18 final size:18
Alignment explanation
Indices: 238231--238266 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
238221 AGCACCTTAT
238231 AACTCGAACTCGACGATC
1 AACTCGAACTCGACGATC
238249 AACTCGAACTCGACGATC
1 AACTCGAACTCGACGATC
238267 GAGTCGGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (18 bp):
AACTCGAACTCGACGATC
Found at i:238616 original size:52 final size:52
Alignment explanation
Indices: 238538--238643 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
238528 TATATATACC
*
238538 ACATTCATGCTTGGAGTGACATGTCTAATTATTACAGTAAGGTTGATCATTT
1 ACATTAATGCTTGGAGTGACATGTCTAATTATTACAGTAAGGTTGATCATTT
238590 ACATTAATGCTTGGAGTGACATGTCTAATTATTACAGTAAGGTTGATCATTT
1 ACATTAATGCTTGGAGTGACATGTCTAATTATTACAGTAAGGTTGATCATTT
238642 AC
1 AC
238644 TACACATTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (52 bp):
ACATTAATGCTTGGAGTGACATGTCTAATTATTACAGTAAGGTTGATCATTT
Found at i:240037 original size:13 final size:12
Alignment explanation
Indices: 240021--240110 Score: 62
Period size: 13 Copynumber: 7.2 Consensus size: 12
240011 TTTCTATTCA
240021 TTAATTTTATTT
1 TTAATTTTATTT
240033 GTTAATTTTATCTT
1 -TTAATTTTAT-TT
240047 TTAATTTTA---
1 TTAATTTTATTT
*
240056 ATAATTTTATCTT
1 TTAATTTTAT-TT
240069 TTAAATTTTTATTT
1 TT-AA-TTTTATTT
*
240083 GTTAATTTT-TATA
1 -TTAATTTTAT-TT
*
240096 TTATTTTTATTT
1 TTAATTTTATTT
240108 TTA
1 TTA
240111 TTATCATGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
9 8 0.13
12 12 0.19
13 26 0.42
14 8 0.13
15 8 0.13
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (12 bp):
TTAATTTTATTT
Found at i:240061 original size:22 final size:23
Alignment explanation
Indices: 240035--240077 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
240025 TTTTATTTGT
240035 TAATTTTATCTTTT-AATTTTAA
1 TAATTTTATCTTTTAAATTTTAA
240057 TAATTTTATCTTTTAAATTTT
1 TAATTTTATCTTTTAAATTTT
240078 TATTTGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (23 bp):
TAATTTTATCTTTTAAATTTTAA
Found at i:240107 original size:6 final size:6
Alignment explanation
Indices: 240025--240112 Score: 52
Period size: 6 Copynumber: 13.2 Consensus size: 6
240015 TATTCATTAA
* *
240025 TTTTAT TTGTTAA TTTTAT CTTTTAAT TTTAATAA TTTTAT CTTTTAAAT
1 TTTTAT TT-TTAT TTTTAT -TTTT-AT TTT--TAT TTTTAT -TTTT--AT
*
240075 TTTTAT TTGTTAAT TTTTA- TATTAT TTTTAT TTTTAT T
1 TTTTAT TT-TT-AT TTTTAT TTTTAT TTTTAT TTTTAT T
240113 ATCATGATAA
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
5 4 0.06
6 24 0.37
7 20 0.31
8 14 0.22
9 3 0.05
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (6 bp):
TTTTAT
Found at i:240109 original size:17 final size:19
Alignment explanation
Indices: 240077--240111 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
240067 TTTTAAATTT
240077 TTATTTGTTAATTTTTATA
1 TTATTTGTTAATTTTTATA
240096 TTATTT-TT-ATTTTTAT
1 TTATTTGTTAATTTTTAT
240112 TATCATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
TTATTTGTTAATTTTTATA
Found at i:243730 original size:18 final size:18
Alignment explanation
Indices: 243702--243752 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
243692 ATATCATCCT
*
243702 CAAATGCATCCTCCACCA
1 CAAATGTATCCTCCACCA
* * *
243720 CTAATGTATCCTCCTCCT
1 CAAATGTATCCTCCACCA
*
243738 CAAATATATCCTCCA
1 CAAATGTATCCTCCA
243753 TATCAATTAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.29, C:0.39, G:0.04, T:0.27
Consensus pattern (18 bp):
CAAATGTATCCTCCACCA
Found at i:253752 original size:16 final size:15
Alignment explanation
Indices: 253732--253774 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 15
253722 GGCTTCTCCT
253732 TTTCCTTCATTTTCC
1 TTTCCTTCATTTTCC
253747 TATTCCTTCA-TTT-C
1 T-TTCCTTCATTTTCC
253761 -TTCCTTCATTTTCC
1 TTTCCTTCATTTTCC
253775 ATGATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 8 0.32
13 3 0.12
14 2 0.08
15 4 0.16
16 8 0.32
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTCCTTCATTTTCC
Found at i:255051 original size:15 final size:15
Alignment explanation
Indices: 255031--255059 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
255021 ATTTCAATAC
255031 AATCATTCATCCTCG
1 AATCATTCATCCTCG
255046 AATCATTCATCCTC
1 AATCATTCATCCTC
255060 AAATGGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.34, G:0.03, T:0.34
Consensus pattern (15 bp):
AATCATTCATCCTCG
Found at i:262396 original size:24 final size:24
Alignment explanation
Indices: 262369--262414 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
262359 GGGTTGTGGC
262369 AGGAAATTTCTCAACATCTAAGGT
1 AGGAAATTTCTCAACATCTAAGGT
262393 AGGAAATTTCTCAACATCTAAG
1 AGGAAATTTCTCAACATCTAAG
262415 ATGTACAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (24 bp):
AGGAAATTTCTCAACATCTAAGGT
Found at i:281223 original size:29 final size:29
Alignment explanation
Indices: 281089--281401 Score: 150
Period size: 30 Copynumber: 10.5 Consensus size: 29
281079 TTTGGGGTCA
* * * *
281089 AAATGTAATTCTAGGAAAGATTAGGGGTCA
1 AAATGTAATTTTTGGAAAGTTTAGGGGT-T
* * * * *
281119 AAAGGTAATATTAGAAAAATTTAGGGGTT
1 AAATGTAATTTTTGGAAAGTTTAGGGGTT
* *
281148 AAAATGTAATTTTTGAAAAGTTTCAGGGTCAACTT
1 -AAATGTAATTTTTGGAAAGTTT-AGGG----GTT
281183 AAAATGT-ATTTTTGGAAAGTTTAGGGGTT
1 -AAATGTAATTTTTGGAAAGTTTAGGGGTT
*
281212 AAATGTAATTTTTGGAAAGTTT-GGGGTAG
1 AAATGTAATTTTTGGAAAGTTTAGGGGT-T
* ** * * *
281241 AAATGTAATTTATATAAAGTTCAAGAGTCT
1 AAATGTAATTTTTGGAAAGTTTAGGGGT-T
* *
281271 AAATGTAATTTATGGAAAGTTT-GGGGTCA
1 AAATGTAATTTTTGGAAAGTTTAGGGGT-T
* * * * *
281300 AAATGAAATTTTAGAAAATTTTA-TGGTT
1 AAATGTAATTTTTGGAAAGTTTAGGGGTT
* * * * *
281328 AAAATATGATTTTGGGAAAGTATAGGGTTT
1 -AAATGTAATTTTTGGAAAGTTTAGGGGTT
* * * * * *
281358 AAAATATGATTTTGGGAAAGTGTAAGGGTA
1 -AAATGTAATTTTTGGAAAGTTTAGGGGTT
281388 AAATGT-ATTTTTGG
1 AAATGTAATTTTTGG
281402 GTAAAATAGG
Statistics
Matches: 220, Mismatches: 51, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
28 18 0.08
29 80 0.36
30 91 0.41
31 4 0.02
33 4 0.02
34 14 0.06
35 9 0.04
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
AAATGTAATTTTTGGAAAGTTTAGGGGTT
Found at i:283428 original size:209 final size:207
Alignment explanation
Indices: 283055--283655 Score: 694
Period size: 209 Copynumber: 2.9 Consensus size: 207
283045 GCTTCATCTC
* * * * *
283055 TTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTACTTCGATCCACTTCTCTGT
1 TTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTGCTTTGACCCACTTCTCTGT
* * * * *
283120 ATCTCATCAGGAAGATAGGGGTTTGAAGTTT-TACTCGCATTAAATTTCGCTTCATTGATTTGAT
66 ATCTTATAAGGAAGAT--GGGTTTGAAGTTTCT-CTCGCATTGAACTTCGCTTCATTGATTTGGT
* * * * *
283184 CTACTTCTTTATATCTCATCAGGAAGATAACCGCTTCATTGATTTAATCCACTTCTCTGTGTCTC
128 CTACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTC
* *
283249 GCCATGAAGACAGAT
193 ACCAGGAAGACAGAT
* * *
283264 TTGGTTCACTTCTCTATATCTCATTAGGAAAGATGACCTCTTTATTGCTTTGACCCACTTCTCTA
1 TTGGTTCACTTCTCTGTATCTCATCAGG-AAGATGACCTCTTTATTGCTTTGACCCACTTCTCTG
** * *
283329 TATCTTATAAGGAAGATGGAGTTTGGAAGTTTCTCT-AAATTGAGCTTCGCTTCATTGAATTGGT
65 TATCTTATAAGGAAGATGG-GTTT-GAAGTTTCTCTCGCATTGAACTTCGCTTCATTGATTTGGT
* *
283393 CTACTTCTCTGTATCTTATCAAGAAGATGACCGCTTCATT-ATTTTAATCCACTTCTCTATATCT
128 CTACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATTGA-TTTAATCCACTTCTCTATATCT
* *
283457 CATCAGGAAGACGGAT
192 CACCAGGAAGACAGAT
* * * * * * *
283473 TT-GTTCCACTTCTTTGTATTTTATCAAGAAGATGA-TTGCTTTCTTGCTTTGACCCACTTCTTT
1 TTGGTT-CACTTCTCTGTATCTCATCAGGAAGATGACCT-CTTTATTGCTTTGACCCACTTCTCT
* *
283536 GTATCTCT-CAA-GAAGATGGGATTTGAAGTTTCACTCGCATTGAACTTCGCTTCATTGATTTGG
64 GTATCT-TATAAGGAAGATGGG-TTTGAAGTTTCTCTCGCATTGAACTTCGCTTCATTGATTTGG
* **
283599 TCTACTTCTCTATTTCTCATCAAGAAGATGATTGCTTCATTGATTTAATCCACTTCT
127 TCTACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCT
283656 GTAACACTTT
Statistics
Matches: 332, Mismatches: 49, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
206 11 0.03
207 85 0.26
208 44 0.13
209 136 0.41
210 55 0.17
211 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (207 bp):
TTGGTTCACTTCTCTGTATCTCATCAGGAAGATGACCTCTTTATTGCTTTGACCCACTTCTCTGT
ATCTTATAAGGAAGATGGGTTTGAAGTTTCTCTCGCATTGAACTTCGCTTCATTGATTTGGTCTA
CTTCTCTATATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTCACC
AGGAAGACAGAT
Found at i:283541 original size:85 final size:85
Alignment explanation
Indices: 283395--283560 Score: 192
Period size: 85 Copynumber: 2.0 Consensus size: 85
283385 GAATTGGTCT
* *
283395 ACTTCTCTGTATCTTATCAAGAAGATGACCGCTTCATTATTTTAATCCACTTCTCTATATCTCAT
1 ACTTCTCTGTATCTTATCAAGAAGATGACCGCTTCATTACTTTAACCCACTTCTCTATATCTC-T
*
283460 CAGGAAGA-CGGATTTGTTCC
65 CAAGAAGATCGGATTTGTTCC
* * ** * * * *
283480 ACTTCTTTGTATTTTATCAAGAAGATGATTGCTTTC-TTGCTTTGACCCACTTCTTTGTATCTCT
1 ACTTCTCTGTATCTTATCAAGAAGATGACCGC-TTCATTACTTTAACCCACTTCTCTATATCTCT
*
283544 CAAGAAGATGGGATTTG
65 CAAGAAGATCGGATTTG
283561 AAGTTTCACT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
84 8 0.12
85 56 0.84
86 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (85 bp):
ACTTCTCTGTATCTTATCAAGAAGATGACCGCTTCATTACTTTAACCCACTTCTCTATATCTCTC
AAGAAGATCGGATTTGTTCC
Found at i:284437 original size:26 final size:27
Alignment explanation
Indices: 284383--284436 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
284373 AAACCAACCT
*
284383 AACCCAGAACCCTTATTACCCATTTAA
1 AACCCAGAACCCTTATAACCCATTTAA
284410 AACCCA-AA-CCTTATAAACCC-TTTAA
1 AACCCAGAACCCTTAT-AACCCATTTAA
284435 AA
1 AA
284437 ATCTTTAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 13 0.52
26 6 0.24
27 6 0.24
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.24
Consensus pattern (27 bp):
AACCCAGAACCCTTATAACCCATTTAA
Found at i:284499 original size:15 final size:16
Alignment explanation
Indices: 284467--284501 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
284457 ACCCAATAAC
284467 CCAAACCCAAAGTGAA
1 CCAAACCCAAAGTGAA
*
284483 CCAAACCC-AATTGAA
1 CCAAACCCAAAGTGAA
284498 CCAA
1 CCAA
284502 GTCCAAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.49, C:0.34, G:0.09, T:0.09
Consensus pattern (16 bp):
CCAAACCCAAAGTGAA
Found at i:284613 original size:20 final size:20
Alignment explanation
Indices: 284588--284629 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
284578 CGGTTGACCA
284588 TTGACCATTGACCATTGACT
1 TTGACCATTGACCATTGACT
* * *
284608 TTGACCGTTGATCGTTGACT
1 TTGACCATTGACCATTGACT
284628 TT
1 TT
284630 TTCTGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGACCATTGACCATTGACT
Found at i:284618 original size:7 final size:7
Alignment explanation
Indices: 284581--284606 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
284571 ACTTTGGCGG
284581 TTGACCA
1 TTGACCA
284588 TTGACCA
1 TTGACCA
284595 TTGACCA
1 TTGACCA
284602 TTGAC
1 TTGAC
284607 TTTGACCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (7 bp):
TTGACCA
Found at i:286162 original size:124 final size:123
Alignment explanation
Indices: 285891--286172 Score: 422
Period size: 123 Copynumber: 2.3 Consensus size: 123
285881 GAAGATAGAT
* * *
285891 TTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCTCTTTATTGCTTTGACCCACTTCTCTGT
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGAACTATTTATTGCTTTGACCCACTTCTCTGT
* * * * *
285956 ATCTCATCAGGAAGATGGGGTTCGAAGTCTCATTCATATTGAGCTTCGCTTCATTTAT
66 ATCTCATCAGGAAGATGGGGTTCGAAGTCTCACTCACATTGAGCTCCGCTTCATTGAA
286014 TTGGTCTACTTCTCTGTATCTCATCAGGAAGAT-AACTGATTTATTGCTTTGACCCACTTCTCTG
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGAACT-ATTTATTGCTTTGACCCACTTCTCTG
* * *
286078 TATCTCATCAGGAATATTGGGGTTTGAAGTTTCACTCACATTGAGCTCCGCTTCATTGAA
65 TATCTCATCAGGAAGA-TGGGGTTCGAAGTCTCACTCACATTGAGCTCCGCTTCATTGAA
* *
286138 TTGGTCCACTTCTCTGTATCTCATCAGGAAAATGA
1 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA
286173 CCTCAATTTG
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
122 3 0.02
123 72 0.50
124 67 0.47
125 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.38
Consensus pattern (123 bp):
TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGAACTATTTATTGCTTTGACCCACTTCTCTGT
ATCTCATCAGGAAGATGGGGTTCGAAGTCTCACTCACATTGAGCTCCGCTTCATTGAA
Found at i:286365 original size:46 final size:44
Alignment explanation
Indices: 286175--286452 Score: 384
Period size: 43 Copynumber: 6.3 Consensus size: 44
286165 GAAAATGACC
* *
286175 TCAATTTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAAAGGCCT
1 TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAATGG-CT
* *
286220 TCAATCTACCCCTCTTGA-TTAGGGGTAAAAGATTGGAATGACT
1 TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAATGGCT
* * * *
286263 TTAATCTGCCCCTCTTGA-TTAGGGGTAGAAGATTAGAATGACT
1 TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAATGGCT
*
286306 TCAATCTGCCCCTCTTGACTTTGGGGTAAAAGATTGGATGATGGCT
1 TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGA--ATGGCT
286352 TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAATGTGGCT
1 TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAA--TGGCT
*
286398 TCAATCTACCCCTCTTGAC-TAGGGGTAAAAGATTGGAATGGCT
1 TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAATGGCT
286441 GT-AATCTGCCCC
1 -TCAATCTGCCCC
286453 ATGATCGGGG
Statistics
Matches: 211, Mismatches: 16, Indels: 14
0.88 0.07 0.06
Matches are distributed among these distances:
43 72 0.34
44 39 0.18
45 35 0.17
46 65 0.31
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (44 bp):
TCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGAATGGCT
Found at i:286624 original size:49 final size:50
Alignment explanation
Indices: 286525--286631 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 50
286515 GACCTCAACG
* * * *
286525 TTTCCCTTCATATCTTCATGGTATCGGATTCACCGTCGTAGCCTCGATCC
1 TTTCCCATCACATCTTCAAGGTATCGGATTCACCGTCGCAGCCTCGATCC
* *
286575 -TTCCCATCACATCTTCTAAGGTATCAGG-TTCACCGTTGCGGCCTC-ATCC
1 TTTCCCATCACATCTTC-AAGGTATC-GGATTCACCGTCGCAGCCTCGATCC
286624 TTTCCCAT
1 TTTCCCAT
286632 TGTGTTCGGG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
49 18 0.38
50 28 0.58
51 2 0.04
ACGTcount: A:0.17, C:0.34, G:0.15, T:0.35
Consensus pattern (50 bp):
TTTCCCATCACATCTTCAAGGTATCGGATTCACCGTCGCAGCCTCGATCC
Found at i:288809 original size:2 final size:2
Alignment explanation
Indices: 288802--288829 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
288792 AGAACACAAA
288802 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
288830 TTTTGAGTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:293910 original size:2 final size:2
Alignment explanation
Indices: 293903--293932 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
293893 ATAACACAAA
293903 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
293933 TTTTGAGTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:298970 original size:30 final size:29
Alignment explanation
Indices: 298887--299176 Score: 191
Period size: 30 Copynumber: 9.8 Consensus size: 29
298877 TTTTGGGGCC
* * * * *
298887 AAAATGTAATTTTGGGAAGATT-GGGGGT
1 AAAATGTAATTTTAGAAAGTTTAAGGGTT
* * *
298915 AAAATGTAATATTATAAAATTTAAGGGTT
1 AAAATGTAATTTTAGAAAGTTTAAGGGTT
*
298944 AAAATGTAAATTTTAGAAAGTTTAAGGGTC
1 AAAATGT-AATTTTAGAAAGTTTAAGGGTT
* * * * *
298974 AAATTGTAAATTTGGAAAAATTTAGGGGTT
1 AAAATGTAATTTTAG-AAAGTTTAAGGGTT
* *
299004 AAAATATAAATTTTAGAAAGTTT-A-GCTAT
1 AAAATGT-AATTTTAGAAAGTTTAAGGGT-T
*
299033 CAAAATGTAATTTGTGGAAAGTTT--GGAAGTT
1 -AAAATGTAATTT-TAGAAAGTTTAAGG--GTT
*
299064 GAAATGTAA-TTTATGTAAAGTTTAAGGGTT
1 AAAATGTAATTTTA-G-AAAGTTTAAGGGTT
*
299094 AAAATGTAA-TTTATGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTA-G-AAAGTTTAAGGGTT
*
299124 AAAATGTAATTTTAGGAAA-TTTTAGAGGTT
1 AAAATGTAATTTTA-GAAAGTTTAAG-GGTT
* *
299154 AAAATGTGATTGTAGGAAAGTTT
1 AAAATGTAATTTTA-GAAAGTTT
299177 GGGGTCAAAA
Statistics
Matches: 207, Mismatches: 38, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
28 19 0.09
29 30 0.14
30 140 0.68
31 15 0.07
32 3 0.01
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAGTTTAAGGGTT
Found at i:299174 original size:90 final size:88
Alignment explanation
Indices: 298887--299176 Score: 243
Period size: 90 Copynumber: 3.2 Consensus size: 88
298877 TTTTGGGGCC
* * * * * *
298887 AAAATGTAATTTTGGGAAGATT-GGGGGTAAAATGTAATATTATAAAA-TTTAAGGGTTAAAATG
1 AAAATGTAATTTAGGAAAGTTTAAGGGTTAAAATGTAAT-TTATAAAAGTTTAGGGGTTAAAATG
*
298950 TAAATTTTA-GAAAGTTTA-AGGGTC
65 T-AATTTTAGGAAAGTTTAGA-GGTT
* * * * *** *
298974 AAATTGTAAATTT-GGAAAAATTTAGGGGTTAAAATATAAATTT-TAGAAAGTTTAGCTATCAAA
1 AAAATGT-AATTTAGG-AAAGTTTAAGGGTTAAAATGT-AATTTATA-AAAGTTTAGGGGTTAAA
* *
299037 ATGTAATTTGT-GGAAAGTTTGGAAGTT
62 ATGTAATTT-TAGGAAAGTTTAGAGGTT
* *
299064 GAAATGTAATTTATGTAAAGTTTAAGGGTTAAAATGTAATTTATGAAAAGTTTAGGGGTTAAAAT
1 AAAATGTAATTTA-GGAAAGTTTAAGGGTTAAAATGTAATTTAT-AAAAGTTTAGGGGTTAAAAT
*
299129 GTAATTTTAGGAAATTTTAGAGGTT
64 GTAATTTTAGGAAAGTTTAGAGGTT
*
299154 AAAATGTGATTGTAGGAAAGTTT
1 AAAATGTAATT-TAGGAAAGTTT
299177 GGGGTCAAAA
Statistics
Matches: 158, Mismatches: 30, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
87 8 0.05
88 11 0.07
89 32 0.20
90 102 0.65
91 5 0.03
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (88 bp):
AAAATGTAATTTAGGAAAGTTTAAGGGTTAAAATGTAATTTATAAAAGTTTAGGGGTTAAAATGT
AATTTTAGGAAAGTTTAGAGGTT
Found at i:303432 original size:22 final size:22
Alignment explanation
Indices: 303404--303448 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
303394 TATAATCCTA
303404 TGTTTATATGTCGATGACATAC
1 TGTTTATATGTCGATGACATAC
303426 TGTTTATATGTCGATGACATAC
1 TGTTTATATGTCGATGACATAC
303448 T
1 T
303449 CATTGTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (22 bp):
TGTTTATATGTCGATGACATAC
Found at i:307268 original size:20 final size:20
Alignment explanation
Indices: 307240--307280 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
307230 TATAATACTA
*
307240 TATATTTTATTT-TGTTATTT
1 TATAATTTATTTAT-TTATTT
307260 TATAATTTATTTATTTATTT
1 TATAATTTATTTATTTATTT
307280 T
1 T
307281 TGGACCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TATAATTTATTTATTTATTT
Found at i:309272 original size:21 final size:22
Alignment explanation
Indices: 309237--309278 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
309227 TCAAAGTAGT
309237 CCACGATCCTTTTGGGAATTGC
1 CCACGATCCTTTTGGGAATTGC
*
309259 CCACGA-CTTTTTGGGAATTG
1 CCACGATCCTTTTGGGAATTG
309279 GGGCTAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (22 bp):
CCACGATCCTTTTGGGAATTGC
Done.