Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009675.1 Kokia drynarioides strain JFW-HI SEQ_124393, 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: 254440
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:6992 original size:15 final size:15
Alignment explanation
Indices: 6974--7033 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
6964 TTCATCACTC
*
6974 TCACTTTCTTTTCCT
1 TCACTTTCTTTTCTT
* *
6989 TCACGCTCTCTTTTTGTT
1 TCA--CTTTC-TTTTCTT
*
7007 TCAATTTCTTTTCTT
1 TCACTTTCTTTTCTT
7022 TCACTTTCTTTT
1 TCACTTTCTTTT
7034 TCATTCTCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 20 0.57
16 3 0.09
17 4 0.11
18 8 0.23
ACGTcount: A:0.08, C:0.27, G:0.03, T:0.62
Consensus pattern (15 bp):
TCACTTTCTTTTCTT
Found at i:7044 original size:33 final size:33
Alignment explanation
Indices: 6972--7049 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
6962 CTTTCATCAC
* *
6972 TCTCACTTTCTTTTCCTTCACGCTCTCTTTTTGT
1 TCTCAATTTCTTTTCCTTCAC-CTCTCTTTTTAT
* *
7006 T-TCAATTTCTTTTCTTTCA-CTTTCTTTTTCAT
1 TCTCAATTTCTTTTCCTTCACCTCTCTTTTT-AT
7038 TCTCAATTTCTT
1 TCTCAATTTCTT
7050 GTTTCTTCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 9 0.24
32 2 0.05
33 26 0.68
34 1 0.03
ACGTcount: A:0.10, C:0.27, G:0.03, T:0.60
Consensus pattern (33 bp):
TCTCAATTTCTTTTCCTTCACCTCTCTTTTTAT
Found at i:10752 original size:9 final size:9
Alignment explanation
Indices: 10740--10772 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
10730 ATTAATTCAA
10740 TAATTAATC
1 TAATTAATC
10749 TAATTAA--
1 TAATTAATC
10756 TAATTAATC
1 TAATTAATC
10765 TAATTAAT
1 TAATTAAT
10773 GTGATAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.32
9 15 0.68
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTAATC
Found at i:10759 original size:16 final size:16
Alignment explanation
Indices: 10732--10772 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
10722 CAAATTAAAT
10732 TAATTCAATAATTAATC
1 TAATT-AATAATTAATC
10749 TAATTAATAATTAATC
1 TAATTAATAATTAATC
10765 TAATTAAT
1 TAATTAAT
10773 GTGATAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTAATAATTAATC
Found at i:15201 original size:45 final size:43
Alignment explanation
Indices: 15081--15211 Score: 149
Period size: 43 Copynumber: 3.0 Consensus size: 43
15071 GGTTGACAAG
** * *
15081 AAAAAAGGAAGCAATGTGGAAA-AAACCAAAACCAAGAAAACAT
1 AAAAAAGGAAGCAACATGGAAACAAA-CACAACCAAGAAAAGAT
* *
15124 AAAAAAGGAAGCAACGTGGAAACAATCACAACCAAGAAAAGAT
1 AAAAAAGGAAGCAACATGGAAACAAACACAACCAAGAAAAGAT
*
15167 AAAAAAAAGGAAGCAACAT-GAAAGCAAACGCAACCAAGAAAAGAT
1 --AAAAAAGGAAGCAACATGGAAA-CAAACACAACCAAGAAAAGAT
15212 GTCATCCTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
43 36 0.47
44 6 0.08
45 35 0.45
ACGTcount: A:0.61, C:0.15, G:0.18, T:0.06
Consensus pattern (43 bp):
AAAAAAGGAAGCAACATGGAAACAAACACAACCAAGAAAAGAT
Found at i:34275 original size:7 final size:7
Alignment explanation
Indices: 34263--34292 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
34253 AAATCAAATA
34263 TGTTGAG
1 TGTTGAG
34270 TGTTGAG
1 TGTTGAG
34277 TGTTGAG
1 TGTTGAG
34284 TGTTGAG
1 TGTTGAG
34291 TG
1 TG
34293 CTGAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
TGTTGAG
Found at i:35840 original size:20 final size:20
Alignment explanation
Indices: 35817--35882 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
35807 TTTTGGTACT
*
35817 TTTTTTACTGTTTTGGTTGC
1 TTTTTTGCTGTTTTGGTTGC
* * **
35837 -TTTTTGCTTTTTTATGTTAT
1 TTTTTTGCTGTTTT-GGTTGC
35857 TTTTTTGCTGTTTTGGTTGC
1 TTTTTTGCTGTTTTGGTTGC
35877 TGTTTT
1 T-TTTT
35883 CGTGTTGTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
19 11 0.32
20 7 0.21
21 16 0.47
ACGTcount: A:0.05, C:0.08, G:0.18, T:0.70
Consensus pattern (20 bp):
TTTTTTGCTGTTTTGGTTGC
Found at i:35912 original size:24 final size:23
Alignment explanation
Indices: 35885--35949 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
35875 GCTGTTTTCG
*
35885 TGTTGTTTTAGCTGTTATTTTTAT
1 TGTTGTTTT-GCTGTTATTTTTAA
* *
35909 TGTTATTTT--TGTTGTTTTTAA
1 TGTTGTTTTGCTGTTATTTTTAA
* *
35930 TATTGTTTTGCTATTATTTT
1 TGTTGTTTTGCTGTTATTTT
35950 AGTTATTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
21 17 0.53
23 7 0.22
24 8 0.25
ACGTcount: A:0.14, C:0.03, G:0.14, T:0.69
Consensus pattern (23 bp):
TGTTGTTTTGCTGTTATTTTTAA
Found at i:35925 original size:44 final size:43
Alignment explanation
Indices: 35873--35969 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 43
35863 GCTGTTTTGG
** * * *
35873 TTGCTGTTTTCGTGTTGTTTTAGCTGTTATTTTTA-TTGTTATTT
1 TTGCTGTTTTAATATTGTTTT-GCTATTA-TTTTAGTTATTATTT
*
35917 TTGTTGTTTTTAATATTGTTTTGCTATTATTTTAGTTATTATTT
1 TTGCTG-TTTTAATATTGTTTTGCTATTATTTTAGTTATTATTT
35961 TTGCTGTTT
1 TTGCTGTTT
35970 GGATGTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
43 8 0.18
44 24 0.55
45 12 0.27
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.67
Consensus pattern (43 bp):
TTGCTGTTTTAATATTGTTTTGCTATTATTTTAGTTATTATTT
Found at i:36148 original size:24 final size:23
Alignment explanation
Indices: 36096--36148 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
36086 TTAATATAAA
*
36096 TTTTTTTTAATGTATTTTAAATT
1 TTTTTTTTAATGTATTTTAAATG
* *
36119 TATTTTTTTAATGTTTGTTTTAATG
1 T-TTTTTTTAATGTAT-TTTAAATG
36144 TTTTT
1 TTTTT
36149 AAGTGTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 17 0.68
25 7 0.28
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (23 bp):
TTTTTTTTAATGTATTTTAAATG
Found at i:38499 original size:21 final size:22
Alignment explanation
Indices: 38459--38499 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
38449 GGGTTATGGA
38459 TTGACTATGTGGCACTATTTCG
1 TTGACTATGTGGCACTATTTCG
38481 TTGACTACT-TGGC-CTATTT
1 TTGACTA-TGTGGCACTATTT
38500 TTTATCTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 11 0.61
23 1 0.06
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.44
Consensus pattern (22 bp):
TTGACTATGTGGCACTATTTCG
Found at i:44130 original size:21 final size:20
Alignment explanation
Indices: 44084--44130 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
44074 CTACACAATG
44084 TTTCTTCTTCCTCCTCTTCT
1 TTTCTTCTTCCTCCTCTTCT
* * *
44104 TCTCTTCCTTCCTGCTCTTTT
1 TTTCTT-CTTCCTCCTCTTCT
44125 TTTCTT
1 TTTCTT
44131 TAGAGCGCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTCTTCTTCCTCCTCTTCT
Found at i:47622 original size:14 final size:15
Alignment explanation
Indices: 47603--47632 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
47593 TTTGGGTGTT
47603 TTACTATTCAT-TTA
1 TTACTATTCATCTTA
47617 TTACTATTCATCTTA
1 TTACTATTCATCTTA
47632 T
1 T
47633 CATTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.57
Consensus pattern (15 bp):
TTACTATTCATCTTA
Found at i:48589 original size:53 final size:52
Alignment explanation
Indices: 48478--48655 Score: 205
Period size: 52 Copynumber: 3.4 Consensus size: 52
48468 TTTCACTTCG
* * * * * * *
48478 TTCATATACTCCCGATAACACATAGCCA-CTGAACCTTATAATCCATAAGGGA
1 TTCATATACTCACGATGACACAGAGTCATC-GGACCTTTTAATCCATAAAGGA
* *
48530 TTCATATACTCATGATGACACAGAGTCATCGGACCCTTTTAATCCGTAAAGGA
1 TTCATATACTCACGATGACACAGAGTCATCGGA-CCTTTTAATCCATAAAGGA
** *
48583 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGA
1 TTCATATACTCACGATGACACAGAGTCATCGGACCTTTTAATCCATAAAGGA
* *
48635 TTCATATACTGACGAAGACAC
1 TTCATATACTCACGATGACAC
48656 TTATTCATCA
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
52 61 0.56
53 47 0.44
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (52 bp):
TTCATATACTCACGATGACACAGAGTCATCGGACCTTTTAATCCATAAAGGA
Found at i:48655 original size:52 final size:52
Alignment explanation
Indices: 48516--48673 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
48506 CTGAACCTTA
* * ** *
48516 TAATCCATAAGGGATTCATATACTCATGATGACACAGAGTCATCGGACCCTTT
1 TAATCCATAAAGGATTCATATACTCACGATGACACTTAGTCATCGGA-CCTCT
*
48569 TAATCCGTAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTCT
1 TAATCCATAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTCT
* * * **
48621 TAATCCATAAAGGATTCATATACTGACGAAGACACTTATTCATCAAACCTCT
1 TAATCCATAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTCT
48673 T
1 T
48674 CGTTTATGGC
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
52 51 0.55
53 42 0.45
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (52 bp):
TAATCCATAAAGGATTCATATACTCACGATGACACTTAGTCATCGGACCTCT
Found at i:54615 original size:14 final size:15
Alignment explanation
Indices: 54596--54624 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54586 TCGGTGTTTT
54596 ACTGTTCAT-TTATC
1 ACTGTTCATCTTATC
54610 ACTGTTCATCTTATC
1 ACTGTTCATCTTATC
54625 GATATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.24, G:0.07, T:0.48
Consensus pattern (15 bp):
ACTGTTCATCTTATC
Found at i:55618 original size:53 final size:52
Alignment explanation
Indices: 55503--55698 Score: 261
Period size: 52 Copynumber: 3.8 Consensus size: 52
55493 TTTCATTTCG
* * * * ** *
55503 TTCATATACTCAC-AGTGACACATAGCCACCGGACCT-TATAATCCACAAGGGA
1 TTCATATACTCACGA-TGACACTTAGTCATCAGACCTCT-TAATCCGTAAAGGA
**
55555 TTCATATACTCACGATGACACAGAGTCATCAGACCCTCTTAATCCGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCAGA-CCTCTTAATCCGTAAAGGA
*
55608 TTCATATACTCACAATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGGA
55660 TTCATATACTCACGATGACACTTAGTCATCAGACCTCTT
1 TTCATATACTCACGATGACACTTAGTCATCAGACCTCTT
55699 CGTTTATGGC
Statistics
Matches: 130, Mismatches: 11, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
52 84 0.65
53 45 0.35
54 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (52 bp):
TTCATATACTCACGATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGGA
Found at i:55687 original size:105 final size:104
Alignment explanation
Indices: 55503--55698 Score: 277
Period size: 105 Copynumber: 1.9 Consensus size: 104
55493 TTTCATTTCG
* * *
55503 TTCATATACTCACAGTGACACATAGCCACCGGACCTTATAATCCACAAGGGATTCATATACTCAC
1 TTCATATACTCACAATGACACATAGCCACCAGACCTTATAATCCACAAAGGATTCATATACTCAC
55568 GATGACACAGAGTCATCAGACCCTCTTAATCCGTAAAGGA
66 GATGACACAGAGTCATCAGA-CCTCTTAATCCGTAAAGGA
* * * **
55608 TTCATATACTCACAATGACACTTAGTCATCAGACCTCT-TAATCCGTAAAGGATTCATATACTCA
1 TTCATATACTCACAATGACACATAGCCACCAGACCT-TATAATCCACAAAGGATTCATATACTCA
**
55672 CGATGACACTTAGTCATCAGACCTCTT
65 CGATGACACAGAGTCATCAGACCTCTT
55699 CGTTTATGGC
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
104 6 0.08
105 73 0.91
106 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (104 bp):
TTCATATACTCACAATGACACATAGCCACCAGACCTTATAATCCACAAAGGATTCATATACTCAC
GATGACACAGAGTCATCAGACCTCTTAATCCGTAAAGGA
Found at i:62562 original size:21 final size:21
Alignment explanation
Indices: 62538--62598 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
62528 GGAGTGAAAG
62538 TATGATTATTTAATTGTTTAA
1 TATGATTATTTAATTGTTTAA
* *
62559 TATGA--A--T--TT-TTCAT
1 TATGATTATTTAATTGTTTAA
62573 TATGATTATTTAATTGTTTAA
1 TATGATTATTTAATTGTTTAA
62594 TATGA
1 TATGA
62599 ATTTTTCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 8 0.28
15 2 0.07
16 1 0.03
17 1 0.03
18 1 0.03
19 1 0.03
20 2 0.07
21 13 0.45
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (21 bp):
TATGATTATTTAATTGTTTAA
Found at i:62584 original size:35 final size:35
Alignment explanation
Indices: 62538--62608 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
62528 GGAGTGAAAG
62538 TATGATTATTTAATTGTTTAATATGAATTTTTCAT
1 TATGATTATTTAATTGTTTAATATGAATTTTTCAT
62573 TATGATTATTTAATTGTTTAATATGAATTTTTCAT
1 TATGATTATTTAATTGTTTAATATGAATTTTTCAT
62608 T
1 T
62609 TCGGATCAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (35 bp):
TATGATTATTTAATTGTTTAATATGAATTTTTCAT
Found at i:65099 original size:36 final size:39
Alignment explanation
Indices: 65059--65136 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 39
65049 TTTTTCAAAC
65059 TTGAGTAC-TCATGCTC-TTTTCTCTTTTT-TTTTTC-TT
1 TTGAGTACAT-ATGCTCATTTTCTCTTTTTCTTTTTCATT
*
65095 TTGAGTACATATGCTCTATTTTTTCTTTTTCTTTTTCATT
1 TTGAGTACATATGCTC-ATTTTCTCTTTTTCTTTTTCATT
65135 TT
1 TT
65137 TTTCGGAGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
36 14 0.39
37 1 0.03
38 11 0.31
39 6 0.17
40 4 0.11
ACGTcount: A:0.12, C:0.17, G:0.08, T:0.64
Consensus pattern (39 bp):
TTGAGTACATATGCTCATTTTCTCTTTTTCTTTTTCATT
Found at i:69247 original size:17 final size:17
Alignment explanation
Indices: 69217--69257 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
69207 AAACTAAAAG
69217 GAATGCAGTGATAATTAA
1 GAATGCAGTGATAA-TAA
69235 -AATGCAG-GCATAATAA
1 GAATGCAGTG-ATAATAA
69251 GAATGCA
1 GAATGCA
69258 TGAAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (17 bp):
GAATGCAGTGATAATAA
Found at i:75073 original size:17 final size:19
Alignment explanation
Indices: 75051--75087 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
75041 TTAAAAATCT
75051 GAAAAAGAA-AACA-ATTA
1 GAAAAAGAACAACAGATTA
*
75068 GAAAAATAACAACAGATTA
1 GAAAAAGAACAACAGATTA
75087 G
1 G
75088 TAAAGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.65, C:0.08, G:0.14, T:0.14
Consensus pattern (19 bp):
GAAAAAGAACAACAGATTA
Found at i:89383 original size:22 final size:22
Alignment explanation
Indices: 89355--89408 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
89345 CTGATTTTTT
89355 TGTCGCGACACAAGTCCTGGTG
1 TGTCGCGACACAAGTCCTGGTG
89377 TGTCGCGACACAAGTCCTGGTG
1 TGTCGCGACACAAGTCCTGGTG
89399 TGTCGCGACA
1 TGTCGCGACA
89409 TCAACCCCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.19, C:0.28, G:0.31, T:0.22
Consensus pattern (22 bp):
TGTCGCGACACAAGTCCTGGTG
Found at i:89605 original size:17 final size:17
Alignment explanation
Indices: 89571--89603 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
89561 CATTCAATAG
*
89571 ATTTTAGTTTTTAGTTT
1 ATTTTAGTTTTCAGTTT
89588 ATTTTA-TTTTCAGTTT
1 ATTTTAGTTTTCAGTTT
89604 TAAAACGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.70
Consensus pattern (17 bp):
ATTTTAGTTTTCAGTTT
Found at i:104834 original size:29 final size:29
Alignment explanation
Indices: 104800--104873 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
104790 CGTAACCTTC
104800 ATATTATTTTAATAAATAAT-TTATAACCT
1 ATATTATTTTAATAAATAATATTA-AACCT
* ***
104829 ATATTATTTTAGA-AACTAATATTAATTTT
1 ATATTATTTTA-ATAAATAATATTAAACCT
104858 ATATTATTTTAATAAA
1 ATATTATTTTAATAAA
104874 ACCCCAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 1 0.03
29 32 0.86
30 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (29 bp):
ATATTATTTTAATAAATAATATTAAACCT
Found at i:104839 original size:17 final size:19
Alignment explanation
Indices: 104819--104860 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
104809 TAATAAATAA
*
104819 TTTATAACCT-ATATT-AT
1 TTTATAAACTAATATTAAT
*
104836 TTTAGAAACTAATATTAAT
1 TTTATAAACTAATATTAAT
104855 TTTATA
1 TTTATA
104861 TTATTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 8 0.40
18 5 0.25
19 7 0.35
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (19 bp):
TTTATAAACTAATATTAAT
Found at i:108716 original size:29 final size:30
Alignment explanation
Indices: 108683--108756 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
108673 CATAACTTTC
108683 ATATTATTTTAATAAA-TAAT-TTATAACCT
1 ATATTATTTTAATAAACTAATATTA-AACCT
* ***
108712 ATATTA-TTTAAGAAACTAATATTAATTTT
1 ATATTATTTTAATAAACTAATATTAAACCT
108741 ATATTATTTTAATAAA
1 ATATTATTTTAATAAA
108757 ACCCCAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 8 0.22
29 18 0.49
30 11 0.30
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (30 bp):
ATATTATTTTAATAAACTAATATTAAACCT
Found at i:110072 original size:35 final size:34
Alignment explanation
Indices: 110005--110084 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 34
109995 AACTGAACTT
* * *
110005 CAAAGGTCATTATTCATTTTACTCCCTGTTGACA
1 CAAAGGTCATGATTCATTTGACTCCCTATTGACA
*
110039 CAAAGGTCATGATGCTCATTTGA-TCCCTATTGACC
1 CAAAGGTCATGAT--TCATTTGACTCCCTATTGACA
110074 CAAAGGTCATG
1 CAAAGGTCATG
110085 TCTGTTACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 12 0.30
35 21 0.52
36 7 0.17
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (34 bp):
CAAAGGTCATGATTCATTTGACTCCCTATTGACA
Found at i:111073 original size:3 final size:3
Alignment explanation
Indices: 111065--111096 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
111055 TGGCCATGTA
111065 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
111097 AATATGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:116057 original size:6 final size:6
Alignment explanation
Indices: 116046--116070 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
116036 AATCATTCAC
116046 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
116071 TAATTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:117170 original size:20 final size:20
Alignment explanation
Indices: 117145--117284 Score: 101
Period size: 20 Copynumber: 7.1 Consensus size: 20
117135 AAGTCAATAG
117145 TCAAAGTCAATGGTCAACGA
1 TCAAAGTCAATGGTCAACGA
* * **
117165 TTAAAGTCAACGGTCAATAA
1 TCAAAGTCAATGGTCAACGA
* * *
117185 TTAACGGTC-ATGGTCAA-TA
1 TCAA-AGTCAATGGTCAACGA
117204 GTCAAAGTCAATGGTCAACGA
1 -TCAAAGTCAATGGTCAACGA
*
117225 TCAAAGTCAATGTTCAAC-A
1 TCAAAGTCAATGGTCAACGA
* * *
117244 GTCAACGTCAACGGTCAACAA
1 -TCAAAGTCAATGGTCAACGA
* *
117265 TC-GA-TCAACGGTCAACGA
1 TCAAAGTCAATGGTCAACGA
117283 TC
1 TC
117285 GATCAACTGT
Statistics
Matches: 97, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
18 15 0.15
19 5 0.05
20 72 0.74
21 5 0.05
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
TCAAAGTCAATGGTCAACGA
Found at i:117213 original size:13 final size:13
Alignment explanation
Indices: 117197--117254 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
117187 AACGGTCATG
*
117197 GTCAATAGTCAAA
1 GTCAATAGTCAAC
*
117210 GTCAATGGTCAAC
1 GTCAATAGTCAAC
*
117223 GATCAA-AGTCAAT
1 G-TCAATAGTCAAC
*
117236 GTTCAACAGTCAAC
1 G-TCAATAGTCAAC
117250 GTCAA
1 GTCAA
117255 CGGTCAACAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 26 0.70
14 11 0.30
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (13 bp):
GTCAATAGTCAAC
Found at i:117255 original size:13 final size:13
Alignment explanation
Indices: 117197--117262 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
117187 AACGGTCATG
* *
117197 GTCAATAGTCAAA
1 GTCAACAGTCAAC
**
117210 GTCAATGGTCAAC
1 GTCAACAGTCAAC
*
117223 GATCAA-AGTCAAT
1 G-TCAACAGTCAAC
117236 GTTCAACAGTCAAC
1 G-TCAACAGTCAAC
*
117250 GTCAACGGTCAAC
1 GTCAACAGTCAAC
117263 AATCGATCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
13 33 0.75
14 11 0.25
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (13 bp):
GTCAACAGTCAAC
Found at i:117260 original size:60 final size:60
Alignment explanation
Indices: 117137--117261 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
117127 TTCAGAAAAA
* * * *
117137 GTCAATAGTCAAAGTCAATGGTCAACGATTAAAGTCAACGGTCAATAATTAACGGTCATG
1 GTCAATAGTCAAAGTCAATGGTCAACGATCAAAGTCAACGGTCAACAATCAACGGTCACG
* * *
117197 GTCAATAGTCAAAGTCAATGGTCAACGATCAAAGTCAATGTTCAACAGTCAAC-GTCAACG
1 GTCAATAGTCAAAGTCAATGGTCAACGATCAAAGTCAACGGTCAACAATCAACGGTC-ACG
117257 GTCAA
1 GTCAA
117262 CAATCGATCA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 3 0.05
60 54 0.95
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (60 bp):
GTCAATAGTCAAAGTCAATGGTCAACGATCAAAGTCAACGGTCAACAATCAACGGTCACG
Found at i:117262 original size:40 final size:40
Alignment explanation
Indices: 117145--117266 Score: 131
Period size: 40 Copynumber: 3.0 Consensus size: 40
117135 AAGTCAATAG
* *
117145 TCAAAGTCAATGGTCAAC-GATTAAAGTCAACGGTCAATAA
1 TCAAAGTCAATGGTCAACAG-TCAAAGTCAACGGTCAACAA
* * * * *
117185 TTAACGGTC-ATGGTCAATAGTCAAAGTCAATGGTCAACGA
1 TCAA-AGTCAATGGTCAACAGTCAAAGTCAACGGTCAACAA
* *
117225 TCAAAGTCAATGTTCAACAGTCAACGTCAACGGTCAACAA
1 TCAAAGTCAATGGTCAACAGTCAAAGTCAACGGTCAACAA
117265 TC
1 TC
117267 GATCAACGGT
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
39 3 0.05
40 58 0.89
41 4 0.06
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (40 bp):
TCAAAGTCAATGGTCAACAGTCAAAGTCAACGGTCAACAA
Found at i:117274 original size:18 final size:18
Alignment explanation
Indices: 117251--117291 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
117241 ACAGTCAACG
117251 TCAACGGTCAACAATCGA
1 TCAACGGTCAACAATCGA
*
117269 TCAACGGTCAACGATCGA
1 TCAACGGTCAACAATCGA
117287 TCAAC
1 TCAAC
117292 TGTAAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (18 bp):
TCAACGGTCAACAATCGA
Found at i:123137 original size:6 final size:6
Alignment explanation
Indices: 123126--123156 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
123116 AATCATTCAC
*
123126 AAATAT AAATAT AACTAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT AAATAT A
123157 TAATTTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:123808 original size:18 final size:19
Alignment explanation
Indices: 123785--123820 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
123775 TTATATCAAT
123785 ATTTAAAT-CCTAAGTTCA
1 ATTTAAATCCCTAAGTTCA
123803 ATTTAAATCCCTAAGTTC
1 ATTTAAATCCCTAAGTTC
123821 CAAATGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (19 bp):
ATTTAAATCCCTAAGTTCA
Found at i:124046 original size:21 final size:20
Alignment explanation
Indices: 124021--124073 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
124011 CTTGTGCTAG
*
124021 ATCTACCGATACAAGTATGGT
1 ATCTACCGATACAAGTAT-GC
* *
124042 TTCTACCGGTACAAGTATGC
1 ATCTACCGATACAAGTATGC
124062 ATCTACCGATAC
1 ATCTACCGATAC
124074 CAAAAACTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (20 bp):
ATCTACCGATACAAGTATGC
Found at i:129717 original size:29 final size:30
Alignment explanation
Indices: 129673--129755 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
129663 TTAAATTACC
129673 ATAACTTTCATATTATTTTAATAAATAAT-TT
1 ATAAC-TT-ATATTATTTTAATAAATAATATT
*
129704 ATAACTTATATTATTTTAGA-AACTAATATT
1 ATAACTTATATTATTTTA-ATAAATAATATT
**
129734 A-ATTTTATATTATTTTAATAAA
1 ATAACTTATATTATTTTAATAAA
129756 ACCCCAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
28 1 0.02
29 33 0.73
30 6 0.13
31 5 0.11
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (30 bp):
ATAACTTATATTATTTTAATAAATAATATT
Found at i:136780 original size:48 final size:48
Alignment explanation
Indices: 136696--136801 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
136686 TGGTTTATTA
* ** * * *
136696 ACAACTATATGTATTGGTAGTTTGTCTGCGATTTTAGTGACTTTGACC
1 ACAACTATGTGTATTGACAGCTTGTCTGCAAATTTAGTGACTTTGACC
* * *
136744 ACAACTATGTGTATTGACAGCTTGTTTGCAAATTTAGTGGCTTTGTCC
1 ACAACTATGTGTATTGACAGCTTGTCTGCAAATTTAGTGACTTTGACC
136792 AC-AC-ATGTGT
1 ACAACTATGTGT
136802 TGAGTGTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
46 6 0.12
47 2 0.04
48 41 0.84
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (48 bp):
ACAACTATGTGTATTGACAGCTTGTCTGCAAATTTAGTGACTTTGACC
Found at i:143700 original size:37 final size:38
Alignment explanation
Indices: 143645--143742 Score: 144
Period size: 37 Copynumber: 2.6 Consensus size: 38
143635 TAGATCTACT
*
143645 ATTGTGGTATGCAGGGTGGACGGGCCTACCATAGCC-A
1 ATTGTGGTGTGCAGGGTGGACGGGCCTACCATAGCCTA
* * *
143682 ATTGTGGTGTGCAAGGTGGATGGGCCTACCTTAGCCTA
1 ATTGTGGTGTGCAGGGTGGACGGGCCTACCATAGCCTA
*
143720 ATTGTGGTGTGTAGGGTGGACGG
1 ATTGTGGTGTGCAGGGTGGACGG
143743 AATGGTGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 32 0.60
38 21 0.40
ACGTcount: A:0.18, C:0.16, G:0.39, T:0.27
Consensus pattern (38 bp):
ATTGTGGTGTGCAGGGTGGACGGGCCTACCATAGCCTA
Found at i:151706 original size:25 final size:25
Alignment explanation
Indices: 151678--151725 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
151668 AGAACTTTGT
*
151678 AGAAGAGATTGGAGGG-TGCAAATTC
1 AGAAGA-ATTCGAGGGATGCAAATTC
*
151703 AGAAGATTTCGAGGGATGCAAAT
1 AGAAGAATTCGAGGGATGCAAAT
151726 ACTGCTGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (25 bp):
AGAAGAATTCGAGGGATGCAAATTC
Found at i:156205 original size:24 final size:26
Alignment explanation
Indices: 156158--156215 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 26
156148 ATTCAAATTC
*
156158 TCTTAGAGTTTTTCTTTTCAAGAATTGT
1 TCTTA-AGTTTTTCTTTT-AAGAATAGT
156186 TCTTAAGTTTTT-TTTT-AGAATAGT
1 TCTTAAGTTTTTCTTTTAAGAATAGT
*
156210 TTTTAA
1 TCTTAA
156216 CAATATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 12 0.43
26 4 0.14
27 7 0.25
28 5 0.18
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57
Consensus pattern (26 bp):
TCTTAAGTTTTTCTTTTAAGAATAGT
Found at i:156457 original size:17 final size:17
Alignment explanation
Indices: 156407--156459 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
156397 TTCCAATCTT
*
156407 TTTATTTA-TTGTTCTA
1 TTTATTTATTTGTTTTA
156423 TTTATTTATCTTAG--TTA
1 TTTATTTAT-TT-GTTTTA
156440 TTTATTTATTTGTTTTA
1 TTTATTTATTTGTTTTA
156457 TTT
1 TTT
156460 GACTTGAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
15 1 0.03
16 10 0.32
17 17 0.55
18 2 0.06
19 1 0.03
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTATTTATTTGTTTTA
Found at i:160738 original size:20 final size:20
Alignment explanation
Indices: 160715--160790 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
160705 TTAAAATCCA
160715 ATCCAAATTCCAAAAATAAC
1 ATCCAAATTCCAAAAATAAC
160735 ATCCAAAAATATCCAATATTTAA-AATC
1 ATCC--AAAT-TCCAA-A---AATAA-C
160762 AAATCCAAATTCCAAAAATAAC
1 --ATCCAAATTCCAAAAATAAC
160784 ATCCAAA
1 ATCCAAA
160791 AATATCCAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 22
0.67 0.00 0.33
Matches are distributed among these distances:
20 11 0.24
22 7 0.16
23 7 0.16
24 1 0.02
25 1 0.02
26 7 0.16
27 7 0.16
29 4 0.09
ACGTcount: A:0.55, C:0.22, G:0.00, T:0.22
Consensus pattern (20 bp):
ATCCAAATTCCAAAAATAAC
Found at i:160800 original size:49 final size:49
Alignment explanation
Indices: 160693--160800 Score: 198
Period size: 49 Copynumber: 2.2 Consensus size: 49
160683 ATGTAGAAAT
* *
160693 AATATCCAAAATTTAAAATCCAATCCAAATTCCAAAAATAACATCCAAA
1 AATATCCAATATTTAAAATCAAATCCAAATTCCAAAAATAACATCCAAA
160742 AATATCCAATATTTAAAATCAAATCCAAATTCCAAAAATAACATCCAAA
1 AATATCCAATATTTAAAATCAAATCCAAATTCCAAAAATAACATCCAAA
160791 AATATCCAAT
1 AATATCCAAT
160801 CCAAATTCCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 57 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (49 bp):
AATATCCAATATTTAAAATCAAATCCAAATTCCAAAAATAACATCCAAA
Found at i:164776 original size:846 final size:846
Alignment explanation
Indices: 163145--164837 Score: 3233
Period size: 846 Copynumber: 2.0 Consensus size: 846
163135 TTTGAGGAGA
163145 AGTCTCGATCCCCAAATGACATAGTAACGAATCTTTCGAGAGACTACATGAAGAAACCGAACGAA
1 AGTCTCGATCCCCAAATGACATAGTAACGAATCTTTCGAGAGACTACATGAAGAAACCGAACGAA
163210 AAGAACAAGAACAAAAGGAGAAGCCATGTATTGAACAGGACAAGGAAACTTTTGAGGAACCAATT
66 AAGAACAAGAACAAAAGGAGAAGCCATGTATTGAACAGGACAAGGAAACTTTTGAGGAACCAATT
163275 GACCAGAGAATTGGGTATACAAAAGAGTCATCAGTGGAAGAGGACATTGAACATATTTTGAGAAT
131 GACCAGAGAATTGGGTATACAAAAGAGTCATCAGTGGAAGAGGACATTGAACATATTTTGAGAAT
163340 AAAAAATGAACCTCGATCTAGTGACCCCATTATTTCTTTAGATAAAAGTGATGGTCTCCATTTAT
196 AAAAAATGAACCTCGATCTAGTGACCCCATTATTTCTTTAGATAAAAGTGATGGTCTCCATTTAT
163405 AGAGCATAGATTTTCAATTAATCACTGTTATGGACAGAAACACAAAAGAAATGTTGGCAATTGAA
261 AGAGCATAGATTTTCAATTAATCACTGTTATGGACAGAAACACAAAAGAAATGTTGGCAATTGAA
*
163470 ATATATATGGATCAAGAAATAGGTTTTAAATGGGAAATGGCCATAATGTACAATATGTCTCTGTT
326 ATATATATGGATCAAGAAATAGGTTTTAAATGGGAAATGGCCATAATGTACAATATCTCTCTGTT
*
163535 GAAATATATCCTCAAAGAAATCAATAATATCAAAATTTTCCATACACTTCAGATAATCGAGGAGA
391 GAAATATATCCCCAAAGAAATCAATAATATCAAAATTTTCCATACACTTCAGATAATCGAGGAGA
163600 TTTACATCTTCGAGCCATCACCTCAGTCTTCGAATGTCAAAGTAATTATGTCTTTACAAAAGAAG
456 TTTACATCTTCGAGCCATCACCTCAGTCTTCGAATGTCAAAGTAATTATGTCTTTACAAAAGAAG
163665 GAAACAAATTCATGGAAAGTTCAACCCATTCAATGGCTTCAAGAACCTTGTGTGAAAATGTCATT
521 GAAACAAATTCATGGAAAGTTCAACCCATTCAATGGCTTCAAGAACCTTGTGTGAAAATGTCATT
163730 TAAAATCATGGGAATATATGATGATGGTTGGAAACAAAGCTTAGGAGAGAATACAGTTGCACCAG
586 TAAAATCATGGGAATATATGATGATGGTTGGAAACAAAGCTTAGGAGAGAATACAGTTGCACCAG
*
163795 TATTAATACTAGCAAATGTAAAATCAGTGATAGAACCATTTTTGCTAAATGAGATGATTGAGCAG
651 TATTAATACTAGCAAATGTAAAATCAGTGATAGAACCAGTTTTGCTAAATGAGATGATTGAGCAG
163860 TTGTTAGGGCACTACGTCCAAACTTACAATTTTTAAAAGTGGCCCAATAATGGAAGCAGACACAA
716 TTGTTAGGGCACTACGTCCAAACTTACAATTTTTAAAAGTGGCCCAATAATGGAAGCAGACACAA
163925 GATCAAGTGGTGGCATCAATTCATGTTCGTCATCGATAAATATGACCGGCAGCAGGAAATGGCAG
781 GATCAAGTGGTGGCATCAATTCATGTTCGTCATCGATAAATATGACCGGCAGCAGGAAATGGCAG
163990 T
846 T
*
163991 AGTCTCGATCCCCAAATGACATAGTAACGAATCTTTCGAGAGACTACATGTAGAAACCGAACGAA
1 AGTCTCGATCCCCAAATGACATAGTAACGAATCTTTCGAGAGACTACATGAAGAAACCGAACGAA
*
164056 AAGAACAAGAACAAAAGGAGAAGCCATGTATTGAATAGGACAAGGAAACTTTTGAGGAACCAATT
66 AAGAACAAGAACAAAAGGAGAAGCCATGTATTGAACAGGACAAGGAAACTTTTGAGGAACCAATT
*
164121 GACCAGAGAATTGGGTATACAAAAGTGTCATCAGTGGAAGAGGACATTGAACATATTTTGAGAAT
131 GACCAGAGAATTGGGTATACAAAAGAGTCATCAGTGGAAGAGGACATTGAACATATTTTGAGAAT
*
164186 AAAAAATGAACCTCGATCTAGTGACCCTATTATTTCTTTAGATAAAAGTGATGGTCTCCATTTAT
196 AAAAAATGAACCTCGATCTAGTGACCCCATTATTTCTTTAGATAAAAGTGATGGTCTCCATTTAT
*
164251 AGAGCATAGATTTTCAATTAATCACTGTTATGGATAGAAACACAAAAGAAATGTTGGCAATTGAA
261 AGAGCATAGATTTTCAATTAATCACTGTTATGGACAGAAACACAAAAGAAATGTTGGCAATTGAA
*
164316 ATATATATGGATCAAGAAATAGGTTTTGAATGGGAAATGGCCATAATGTACAATATCTCTCTGTT
326 ATATATATGGATCAAGAAATAGGTTTTAAATGGGAAATGGCCATAATGTACAATATCTCTCTGTT
164381 GAAATATATCCCCAAAGAAATCAATAATATCAAAATTTTCCATACACTTCAGATAATCGAGGAGA
391 GAAATATATCCCCAAAGAAATCAATAATATCAAAATTTTCCATACACTTCAGATAATCGAGGAGA
* *
164446 TTTACATCTTTGAGCCATCACCTCAGTCTTCGGATGTCAAAGTAATTATGTCTTTACAAAAGAAG
456 TTTACATCTTCGAGCCATCACCTCAGTCTTCGAATGTCAAAGTAATTATGTCTTTACAAAAGAAG
*
164511 GAAACAAATTCATGGAAAGTTCAACCCATTCATTGGCTTCAAGAACCTTGTGTGAAAATGTCATT
521 GAAACAAATTCATGGAAAGTTCAACCCATTCAATGGCTTCAAGAACCTTGTGTGAAAATGTCATT
*
164576 TAAAATCATGGGAATATATGATGATGGTTGGAAACAAAGCTTAGGAGAGAATATAGTTGCACCAG
586 TAAAATCATGGGAATATATGATGATGGTTGGAAACAAAGCTTAGGAGAGAATACAGTTGCACCAG
164641 TATTAATACTAGCAAATGTAAAATCAGTGATAGAACCAGTTTTGCTAAATGAGATGATTGAGCAG
651 TATTAATACTAGCAAATGTAAAATCAGTGATAGAACCAGTTTTGCTAAATGAGATGATTGAGCAG
*
164706 TTGTTAGGGCACTACGTCCAAACTTACAATTTTTAAAAGTGGCCTAATAATGGAAGCAGACACAA
716 TTGTTAGGGCACTACGTCCAAACTTACAATTTTTAAAAGTGGCCCAATAATGGAAGCAGACACAA
* * *
164771 GATCAAGTGGTGGCATCAATTCATGTTCGTCCTCGATAGATATGACCTGCAGCAGGAAATGGCAG
781 GATCAAGTGGTGGCATCAATTCATGTTCGTCATCGATAAATATGACCGGCAGCAGGAAATGGCAG
164836 T
846 T
164837 A
1 A
164838 ATTAATTGAT
Statistics
Matches: 830, Mismatches: 17, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
846 830 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (846 bp):
AGTCTCGATCCCCAAATGACATAGTAACGAATCTTTCGAGAGACTACATGAAGAAACCGAACGAA
AAGAACAAGAACAAAAGGAGAAGCCATGTATTGAACAGGACAAGGAAACTTTTGAGGAACCAATT
GACCAGAGAATTGGGTATACAAAAGAGTCATCAGTGGAAGAGGACATTGAACATATTTTGAGAAT
AAAAAATGAACCTCGATCTAGTGACCCCATTATTTCTTTAGATAAAAGTGATGGTCTCCATTTAT
AGAGCATAGATTTTCAATTAATCACTGTTATGGACAGAAACACAAAAGAAATGTTGGCAATTGAA
ATATATATGGATCAAGAAATAGGTTTTAAATGGGAAATGGCCATAATGTACAATATCTCTCTGTT
GAAATATATCCCCAAAGAAATCAATAATATCAAAATTTTCCATACACTTCAGATAATCGAGGAGA
TTTACATCTTCGAGCCATCACCTCAGTCTTCGAATGTCAAAGTAATTATGTCTTTACAAAAGAAG
GAAACAAATTCATGGAAAGTTCAACCCATTCAATGGCTTCAAGAACCTTGTGTGAAAATGTCATT
TAAAATCATGGGAATATATGATGATGGTTGGAAACAAAGCTTAGGAGAGAATACAGTTGCACCAG
TATTAATACTAGCAAATGTAAAATCAGTGATAGAACCAGTTTTGCTAAATGAGATGATTGAGCAG
TTGTTAGGGCACTACGTCCAAACTTACAATTTTTAAAAGTGGCCCAATAATGGAAGCAGACACAA
GATCAAGTGGTGGCATCAATTCATGTTCGTCATCGATAAATATGACCGGCAGCAGGAAATGGCAG
T
Found at i:168752 original size:36 final size:36
Alignment explanation
Indices: 168711--169021 Score: 173
Period size: 36 Copynumber: 8.7 Consensus size: 36
168701 TAAAATGACC
*
168711 TTATGCTCTAACCGAGACATAAGCAATCACATGA-CA
1 TTATGCTCTAACCGAGACGTAAGCAATCAC-TGAGCA
* * * *
168747 TTATGCTCTAACAGAGATGTAAACAATCACTAAGCA
1 TTATGCTCTAACCGAGACGTAAGCAATCACTGAGCA
* * * * *
168783 ATATGCTCTAATCAAGACGTATGCAATCACTTAGCA
1 TTATGCTCTAACCGAGACGTAAGCAATCACTGAGCA
* ** * *
168819 TTACGCTCTAATTGAGACGTAAGTAATCACTTAGCA
1 TTATGCTCTAACCGAGACGTAAGCAATCACTGAGCA
* ** * * * *
168855 ATATGCTCTAATTGACATGTATGCAATCACTTAG-A
1 TTATGCTCTAACCGAGACGTAAGCAATCACTGAGCA
** ** * * *
168890 TTACACTCTAATTGAGATGTAAGTAATTACAT-AGCA
1 TTATGCTCTAACCGAGACGTAAGCAATCAC-TGAGCA
* * * * * *
168926 ATATGCTCTAATCGAGATGTATGAAATCACTTAGCGA
1 TTATGCTCTAACCGAGACGTAAGCAATCACTGAGC-A
* * * *
168963 -TACGCTCTAATCGAGACGTATGCAAT-AATGTAGCA
1 TTATGCTCTAACCGAGACGTAAGCAATCACTG-AGCA
* * *
168998 TTACGCTCTAACCGAAATGTAAGC
1 TTATGCTCTAACCGAGACGTAAGC
169022 TCTTTGTTGA
Statistics
Matches: 220, Mismatches: 48, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
35 32 0.15
36 187 0.85
37 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (36 bp):
TTATGCTCTAACCGAGACGTAAGCAATCACTGAGCA
Found at i:168829 original size:72 final size:72
Alignment explanation
Indices: 168712--168978 Score: 299
Period size: 72 Copynumber: 3.7 Consensus size: 72
168702 AAAATGACCT
* * * * * ** **
168712 TATGCTCTAACCGAGACATAAGCAATCACAT-GACATTATGCTCTAACAGAGATGTAAACAATCA
1 TATGCTCTAATCGAGACGTATGCAATCACTTAG-CATTACGCTCTAATTGAGATGTAAGTAATCA
168776 CTAAGCAA
65 CTAAGCAA
* *
168784 TATGCTCTAATCAAGACGTATGCAATCACTTAGCATTACGCTCTAATTGAGACGTAAGTAATCAC
1 TATGCTCTAATCGAGACGTATGCAATCACTTAGCATTACGCTCTAATTGAGATGTAAGTAATCAC
*
168849 TTAGCAA
66 TAAGCAA
* * * * *
168856 TATGCTCTAATTGACATGTATGCAATCACTTAG-ATTACACTCTAATTGAGATGTAAGTAATTAC
1 TATGCTCTAATCGAGACGTATGCAATCACTTAGCATTACGCTCTAATTGAGATGTAAGTAATCAC
168920 -ATAGCAA
66 TA-AGCAA
* * *
168927 TATGCTCTAATCGAGATGTATGAAATCACTTAGCGA-TACGCTCTAATCGAGA
1 TATGCTCTAATCGAGACGTATGCAATCACTTAGC-ATTACGCTCTAATTGAGA
168979 CGTATGCAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
71 63 0.38
72 101 0.61
73 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.28
Consensus pattern (72 bp):
TATGCTCTAATCGAGACGTATGCAATCACTTAGCATTACGCTCTAATTGAGATGTAAGTAATCAC
TAAGCAA
Found at i:168926 original size:71 final size:72
Alignment explanation
Indices: 168771--168982 Score: 286
Period size: 71 Copynumber: 3.0 Consensus size: 72
168761 AGATGTAAAC
* * *
168771 AATCAC-TAAGCAATATGCTCTAATCAAGACGTATGCAATCACTTAGCATTACGCTCTAATTGAG
1 AATCACAT-AGCAATATGCTCTAATCGAGATGTATGCAATCACTTAGCATTACACTCTAATTGAG
168835 ACGTAAGT
65 ACGTAAGT
* * *
168843 AATCACTTAGCAATATGCTCTAATTGACATGTATGCAATCACTTAG-ATTACACTCTAATTGAGA
1 AATCACATAGCAATATGCTCTAATCGAGATGTATGCAATCACTTAGCATTACACTCTAATTGAGA
*
168907 TGTAAGT
66 CGTAAGT
* * * *
168914 AATTACATAGCAATATGCTCTAATCGAGATGTATGAAATCACTTAGCGA-TACGCTCTAATCGAG
1 AATCACATAGCAATATGCTCTAATCGAGATGTATGCAATCACTTAGC-ATTACACTCTAATTGAG
168978 ACGTA
65 ACGTA
168983 TGCAATAATG
Statistics
Matches: 123, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
71 64 0.52
72 57 0.46
73 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (72 bp):
AATCACATAGCAATATGCTCTAATCGAGATGTATGCAATCACTTAGCATTACACTCTAATTGAGA
CGTAAGT
Found at i:174694 original size:53 final size:53
Alignment explanation
Indices: 174614--174888 Score: 365
Period size: 53 Copynumber: 5.2 Consensus size: 53
174604 ATAACTCTGG
* **
174614 GTCATCGTGAGTTGTATGAATCCTATCATGGATTAGAGGTCTGATGACTGAGT
1 GTCATCGTGAGTTATATGAATCCTATCATGGATTAGAGGTCTGATGACTTTGT
* *
174667 GTCATCGTGAGTTATATGAATCTTATCATGGATTAGAGGTCTGATGACTCTGT
1 GTCATCGTGAGTTATATGAATCCTATCATGGATTAGAGGTCTGATGACTTTGT
* *
174720 GTCATTGTGAGTTATATGAATCCTATCATGGATTAGAGGTCTAATGACTTTGT
1 GTCATCGTGAGTTATATGAATCCTATCATGGATTAGAGGTCTGATGACTTTGT
* * * * *
174773 GTTATCGTGAGTTATATGAATCTTATCACGGATTAAATGT-TCGATGACTCTTGT
1 GTCATCGTGAGTTATATGAATCCTATCATGGATTAGAGGTCT-GATGACT-TTGT
* * * *
174827 GTCATCATGAGTTATATGAATCCTATTACGGAATA-AGGGTCTGATGACTTTGT
1 GTCATCGTGAGTTATATGAATCCTATCATGGATTAGA-GGTCTGATGACTTTGT
174880 GTCATCGTG
1 GTCATCGTG
174889 CCATGGATTA
Statistics
Matches: 196, Mismatches: 22, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
52 1 0.01
53 151 0.77
54 43 0.22
55 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (53 bp):
GTCATCGTGAGTTATATGAATCCTATCATGGATTAGAGGTCTGATGACTTTGT
Found at i:174792 original size:106 final size:106
Alignment explanation
Indices: 174593--174888 Score: 416
Period size: 106 Copynumber: 2.8 Consensus size: 106
174583 GTGCCAAAGG
* * *
174593 TTAAAGGTTCGATAACTCTGGGTCATCGTGAGTTGTATGAATCCTATCATGGATTAGAGGTCTGA
1 TTAAAGGTTCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAGAGGTCTGA
** *
174658 TGACTGAGTGTCATCGTGAGTTATATGAATCTTATCATGGA
66 TGACTTTGTGTCATCGTGAGTTATATGAATCTTATCACGGA
* * *
174699 TTAGAGG-TCTGATGACTCTGTGTCATTGTGAGTTATATGAATCCTATCATGGATTAGAGGTCTA
1 TTAAAGGTTC-GATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAGAGGTCTG
*
174763 ATGACTTTGTGTTATCGTGAGTTATATGAATCTTATCACGGA
65 ATGACTTTGTGTCATCGTGAGTTATATGAATCTTATCACGGA
* * * * *
174805 TTAAATGTTCGATGACTCTTGTGTCATCATGAGTTATATGAATCCTATTACGGAATA-AGGGTCT
1 TTAAAGGTTCGATGACTC-TGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAGA-GGTCT
174869 GATGACTTTGTGTCATCGTG
64 GATGACTTTGTGTCATCGTG
174889 CCATGGATTA
Statistics
Matches: 167, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
105 2 0.01
106 107 0.64
107 58 0.35
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (106 bp):
TTAAAGGTTCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAGAGGTCTGA
TGACTTTGTGTCATCGTGAGTTATATGAATCTTATCACGGA
Found at i:176966 original size:13 final size:14
Alignment explanation
Indices: 176948--176977 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
176938 GTTAACATAA
176948 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
176961 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
176975 TCA
1 TCA
176978 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:181487 original size:14 final size:14
Alignment explanation
Indices: 181460--181500 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
181450 ACAACAAAAG
181460 TAAAAGTGAAATAAA
1 TAAAAGT-AAATAAA
181475 TAAAAGTAAATAAA
1 TAAAAGTAAATAAA
181489 -AAAA-TAAA-AAA
1 TAAAAGTAAATAAA
181500 T
1 T
181501 GTGTCGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.12
12 4 0.16
13 4 0.16
14 7 0.28
15 7 0.28
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
TAAAAGTAAATAAA
Found at i:187929 original size:20 final size:19
Alignment explanation
Indices: 187892--187931 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
187882 AATAATAAAC
*
187892 AGAATAAAAGCATTAAATA
1 AGAATAAAAGCATCAAATA
*
187911 AGAATCAAAAGGATCAAATA
1 AGAAT-AAAAGCATCAAATA
187931 A
1 A
187932 TAAAAGATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.17
Consensus pattern (19 bp):
AGAATAAAAGCATCAAATA
Found at i:199229 original size:35 final size:35
Alignment explanation
Indices: 199151--199230 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
199141 GGTAATAGGC
*
199151 GTGACCC-TTGGGTCAATAGGGAGCAAATAAGCAA
1 GTGACCCTTTGGGTCAATAGGGAGCAAATAAGAAA
* * *
199185 GATGA-CCTTTGTGTCAATAGGGAGTAAA-AGGAATA
1 G-TGACCCTTTGGGTCAATAGGGAGCAAATAAGAA-A
199220 GTGACCCTTTG
1 GTGACCCTTTG
199231 AAGTTCAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
34 9 0.24
35 29 0.76
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.24
Consensus pattern (35 bp):
GTGACCCTTTGGGTCAATAGGGAGCAAATAAGAAA
Found at i:213835 original size:27 final size:27
Alignment explanation
Indices: 213805--213886 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
213795 ATGAATCCTA
213805 TCATGGATTAGAGGTTCGATGACTGTG
1 TCATGGATTAGAGGTTCGATGACTGTG
* ** * * *
213832 TCATCG--T-GA-GTTATATGAATCCTA
1 TCATGGATTAGAGGTTCGATGACT-GTG
213856 TCATGGATTAGAGGTTCGATGACTGTG
1 TCATGGATTAGAGGTTCGATGACTGTG
213883 TCAT
1 TCAT
213887 CGTGAGTTAT
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
23 8 0.21
24 8 0.21
25 1 0.03
26 1 0.03
27 12 0.32
28 8 0.21
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.35
Consensus pattern (27 bp):
TCATGGATTAGAGGTTCGATGACTGTG
Found at i:213959 original size:53 final size:52
Alignment explanation
Indices: 213763--214154 Score: 501
Period size: 51 Copynumber: 7.5 Consensus size: 52
213753 AATAGGTTAA
* * *
213763 AGGTTTGACGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAG
1 AGGTTCGATGACT-TGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAG
*
213816 AGGTTCGATGAC-TGTGTCATCGTGAGTTATATGAATCCTATCATGGATTAG
1 AGGTTCGATGACTTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAG
213867 AGGTTCGATGAC-TGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAG
1 AGGTTCGATGACTTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAG
* * * *
213918 AGGTCCGATGACTTTGTGTCATCATGAGTTATATGAATCCTATCACAGATTAA
1 AGGTTCGATGAC-TTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAG
* **
213971 AGGTTCGATGAC-TGTGTCATCGTGAGTTATGTGAATCCTATCACATATTA-
1 AGGTTCGATGACTTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAG
* *
214021 AGG-TCAGATGAATCTT-TGTCATCGTGAGTTATATGAATCCTATCATGGATTAA
1 AGGTTC-GATG-A-CTTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAG
* * *
214074 AGGTTCGATGACTATATGTCATCGTGAGTTATATGAATCCTATTACAGATTA-
1 AGGTTCGATGACT-TGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAG
* *
214126 AGGATCTAATGACTTTGTGTCATCGTGAG
1 AGGTTC-GATGAC-TTGTGTCATCGTGAG
214155 ATACACGAAT
Statistics
Matches: 306, Mismatches: 21, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
49 2 0.01
50 7 0.02
51 138 0.45
52 40 0.13
53 116 0.38
54 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (52 bp):
AGGTTCGATGACTTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAG
Found at i:214869 original size:21 final size:21
Alignment explanation
Indices: 214836--214892 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
214826 TAGAATTAAG
* *
214836 ACTTGTTTTGGTA-AAAGAGTC
1 ACTTGTATCGGTAGAAAGA-TC
**
214857 ACTTGTATCGGTAGAACTATC
1 ACTTGTATCGGTAGAAAGATC
*
214878 ACTTGTATCGATAGA
1 ACTTGTATCGGTAGA
214893 GGTCTGCACT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAAGATC
Found at i:216546 original size:36 final size:36
Alignment explanation
Indices: 216449--216548 Score: 101
Period size: 36 Copynumber: 2.8 Consensus size: 36
216439 CGTTATTCGC
* *** *
216449 TTTACACCCTGTTAACATGAAGGTCATGGTGCTCAT
1 TTTACTCCCTGTTAACCCAAAGGTCATGATGCTCAT
* * * * *
216485 TTTACTTCCTGTTAACCTAATGGTCATGATTCTTAT
1 TTTACTCCCTGTTAACCCAAAGGTCATGATGCTCAT
*
216521 TTTACTCCCTGTTGACCCAAAGGTCATG
1 TTTACTCCCTGTTAACCCAAAGGTCATG
216549 CCTATTACCA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (36 bp):
TTTACTCCCTGTTAACCCAAAGGTCATGATGCTCAT
Found at i:223557 original size:36 final size:36
Alignment explanation
Indices: 223520--223649 Score: 154
Period size: 36 Copynumber: 3.6 Consensus size: 36
223510 ATGGCCTTAT
* *
223520 GCTCTAACCGAGACATAAGCAATCACATGGCATTAT
1 GCTCTAACCGAGACATAAGCAATCACATAGCATTAC
* * * * *
223556 GCTTTAACCGAGACATGAGTAATCACTTAGCAATAC
1 GCTCTAACCGAGACATAAGCAATCACATAGCATTAC
* * *
223592 GCTCTAACCGAGACATATGCAATCACTTAGTATTAC
1 GCTCTAACCGAGACATAAGCAATCACATAGCATTAC
*
223628 ACTCT-ACCGAGACATAAGCAAT
1 GCTCTAACCGAGACATAAGCAAT
223650 TATATTACTA
Statistics
Matches: 79, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 16 0.20
36 63 0.80
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (36 bp):
GCTCTAACCGAGACATAAGCAATCACATAGCATTAC
Found at i:225637 original size:11 final size:11
Alignment explanation
Indices: 225621--225654 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
225611 TTGTTATTAC
225621 ATTTTTCTTTT
1 ATTTTTCTTTT
*
225632 ATTTTTCATTT
1 ATTTTTCTTTT
225643 ATTTTTTCTTTT
1 A-TTTTTCTTTT
225655 GATGTATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (11 bp):
ATTTTTCTTTT
Found at i:232198 original size:37 final size:37
Alignment explanation
Indices: 232148--232222 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
232138 CTTCTAGCAT
* **
232148 AACCAACACTTCCAGAGCAATTTCAGTCCCAAAAATC
1 AACCAACACTTCCAAAAAAATTTCAGTCCCAAAAATC
*
232185 AACCAGCACTTCCAAAAAAATTTCAGTCCCAAAAATC
1 AACCAACACTTCCAAAAAAATTTCAGTCCCAAAAATC
232222 A
1 A
232223 TTCTCTATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.44, C:0.31, G:0.07, T:0.19
Consensus pattern (37 bp):
AACCAACACTTCCAAAAAAATTTCAGTCCCAAAAATC
Found at i:233315 original size:9 final size:9
Alignment explanation
Indices: 233301--233362 Score: 65
Period size: 9 Copynumber: 6.7 Consensus size: 9
233291 GTAACAGTAA
233301 ACATAACAT
1 ACATAACAT
233310 ACATAACA-
1 ACATAACAT
*
233318 AAATGAACCAT
1 ACAT-AA-CAT
233329 AACAT-ACAT
1 -ACATAACAT
233338 ACATAACAAT
1 ACATAAC-AT
233348 ACATAACAT
1 ACATAACAT
233357 ACATAA
1 ACATAA
233363 TTATACGTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
8 7 0.16
9 23 0.51
10 12 0.27
12 3 0.07
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (9 bp):
ACATAACAT
Found at i:233358 original size:19 final size:18
Alignment explanation
Indices: 233301--233362 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
233291 GTAACAGTAA
233301 ACATAACATACATAACA-
1 ACATAACATACATAACAT
*
233318 AAATGAACCATAACAT-ACAT
1 ACAT-AA-CAT-ACATAACAT
233338 ACATAACAATACATAACAT
1 ACATAAC-ATACATAACAT
233357 ACATAA
1 ACATAA
233363 TTATACGTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 3 0.08
18 7 0.19
19 20 0.54
20 7 0.19
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (18 bp):
ACATAACATACATAACAT
Found at i:233374 original size:23 final size:23
Alignment explanation
Indices: 233301--233361 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
233291 GTAACAGTAA
*
233301 ACATAACATACATA-ACAA-AAT
1 ACATAACATACATACATAACAAT
233322 GAACCATAACATACATACATAACAAT
1 --A-CATAACATACATACATAACAAT
233348 ACATAACATACATA
1 ACATAACATACATA
233362 ATTATACGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 14 0.41
24 14 0.41
25 3 0.09
26 3 0.09
ACGTcount: A:0.57, C:0.21, G:0.02, T:0.20
Consensus pattern (23 bp):
ACATAACATACATACATAACAAT
Found at i:233769 original size:44 final size:44
Alignment explanation
Indices: 233706--233796 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
233696 TCGAATACTG
233706 CAAATAGCAGGATAATCGAAACAAACGA-CTACTCGATCATGAAA
1 CAAATAGCAGGATAATCGAAACAAAC-ATCTACTCGATCATGAAA
* * * *
233750 CAAATAGTAGGGTAATCGAAACAGACATTTACTCGATCATGAAA
1 CAAATAGCAGGATAATCGAAACAAACATCTACTCGATCATGAAA
233794 CAA
1 CAA
233797 GGGCTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (44 bp):
CAAATAGCAGGATAATCGAAACAAACATCTACTCGATCATGAAA
Found at i:236506 original size:20 final size:20
Alignment explanation
Indices: 236471--236508 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
236461 GCTGACAAAA
* *
236471 TAGTCACTCTAGTTTCAATC
1 TAGTCACTCAACTTTCAATC
236491 TAGTCACTCAACTTTCAA
1 TAGTCACTCAACTTTCAA
236509 AAAATAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.37
Consensus pattern (20 bp):
TAGTCACTCAACTTTCAATC
Found at i:236666 original size:153 final size:153
Alignment explanation
Indices: 236481--236761 Score: 449
Period size: 153 Copynumber: 1.8 Consensus size: 153
236471 TAGTCACTCT
* *
236481 AGTTTCAATCTAGTCACTCAACTTTCAAAAAATAACAAAAT-AGTCACTAACGTTATTGAAAAGT
1 AGTTTCAATCTAGTCACTCAACTTTCAAAAAATAAC-AAATCAGTCACTAACATTATCGAAAAGT
* ***
236545 GACAA-ATCAGTCACCCATTAACATTTTCCGTTACAGGCTTAATGGGATAGGTGACGTGGCTAGT
65 GACAATA-CAGTCACCCATTAACATTTTCCGTTACAGGCCTAACAAGATAGGTGACGTGGCTAGT
236609 TAACTTGCCTTATTGGATGAGGCAA
129 TAACTTGCCTTATTGGATGAGGCAA
*
236634 AGTTTCAATTTAGTCACTCAACTTTCAAAAAATAACAAATCAGTCACTAACATTATCGAAAAGTG
1 AGTTTCAATCTAGTCACTCAACTTTCAAAAAATAACAAATCAGTCACTAACATTATCGAAAAGTG
* *
236699 ACAATACAGTCACTCATTAACATTTTTCGTTACAGGCCTAACAAGATAGGTGACGTGGCTAGT
66 ACAATACAGTCACCCATTAACATTTTCCGTTACAGGCCTAACAAGATAGGTGACGTGGCTAGT
236762 AATTAGCAGA
Statistics
Matches: 117, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
152 4 0.03
153 112 0.96
154 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (153 bp):
AGTTTCAATCTAGTCACTCAACTTTCAAAAAATAACAAATCAGTCACTAACATTATCGAAAAGTG
ACAATACAGTCACCCATTAACATTTTCCGTTACAGGCCTAACAAGATAGGTGACGTGGCTAGTTA
ACTTGCCTTATTGGATGAGGCAA
Found at i:245118 original size:33 final size:33
Alignment explanation
Indices: 245071--245136 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
245061 CTTTGAGCCC
* * *
245071 ATGCTTATATGTTTCAAGTCTATTTTATGTCAA
1 ATGCCTATATGTTTCAAGTCCATTTTATATCAA
245104 ATGCCTATATGTTTCAAGTCCATTTTATATCAA
1 ATGCCTATATGTTTCAAGTCCATTTTATATCAA
245137 TTTGAGGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (33 bp):
ATGCCTATATGTTTCAAGTCCATTTTATATCAA
Found at i:246236 original size:17 final size:16
Alignment explanation
Indices: 246205--246251 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
246195 AATCATTTTA
*
246205 TTTTTATTTTTTAATC
1 TTTTTATTTTCTAATC
246221 TTTTTATTGTTCTAAT-
1 TTTTTATT-TTCTAATC
*
246237 TGTTTATTTTC-AATC
1 TTTTTATTTTCTAATC
246252 CTTTCTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.11
15 3 0.11
16 15 0.56
17 6 0.22
ACGTcount: A:0.19, C:0.09, G:0.04, T:0.68
Consensus pattern (16 bp):
TTTTTATTTTCTAATC
Found at i:250567 original size:6 final size:6
Alignment explanation
Indices: 250553--250586 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
250543 TGGGCTCATT
*
250553 ACACGC ACACAC ACACGC ACACGC ACACGC ACAC
1 ACACGC ACACGC ACACGC ACACGC ACACGC ACAC
250587 ATACATGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.50, G:0.12, T:0.00
Consensus pattern (6 bp):
ACACGC
Found at i:254140 original size:28 final size:28
Alignment explanation
Indices: 254103--254177 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
254093 AATGAGCATT
254103 ATGACCTTTGGGTCAATAGGGAATAAGC
1 ATGACCTTTGGGTCAATAGGGAATAAGC
*
254131 ATGACCTTTGGGTCAACAGGGAATAAGC
1 ATGACCTTTGGGTCAATAGGGAATAAGC
* *
254159 ATGACCCTTGGGTAAATAG
1 ATGACCTTTGGGTCAATAG
254178 AGAGTAAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (28 bp):
ATGACCTTTGGGTCAATAGGGAATAAGC
Done.