Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008097.1 Hibiscus syriacus cultivar Beakdansim tig00110621_pilon, 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: 3094402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 12
Found at i:1177 original size:237 final size:232
Alignment explanation
Indices: 759--1654 Score: 1051
Period size: 237 Copynumber: 3.9 Consensus size: 232
749 GCTTCCCCCA
* * * *
759 CCACCAAATCCCATATGGTTACCTCCAAATCCGGCTGAACCATTGGTGGCAAAACTATCACCACC
1 CCACCAAATCCCATTTGGTTACCTCCGAATCCAGCTGAACCACTGGTGGCAAAACTATCACCACC
* * * *
824 AATGCCACCGGCGGCAGCATTGAACCCACCATCGTACTTGTTTGGACCAGATTGATCAGAGTTGC
66 AATGTCACCGGCAGCAGCATTGAACCCACCATCGCACTTGTTTGGACCAGATTGATCAGAATTGC
* *
889 TTCCATAGCTACCACCAGCGCCATCCTTGTTACCATCACCATAACTTCCTTGGCCTCCATAACCA
131 TTCCATAGCTACCACCAGCGCCATACTTGTTACCACCACCATAACTTCCTTGGCCTCCATAACCA
954 CTACCACCGCCACCAGTGTTACCATATCCAACATTACCG
196 CTACCA-C-CCACCAGTGTTACCATATCCAACATTACCG
* * * * * * * *
993 CCACCGAATCCCATTTGGTTACCTCTGAAGCCGGCTGAACCAATAGTGGAAAAATTATCACCACC
1 CCACCAAATCCCATTTGGTTACCTCCGAATCCAGCTGAACCACTGGTGGCAAAACTATCACCACC
* * * * *
1058 GATATCACCAGCAGCAGCATTGAAATTCCCACCATCGTACTTGTTTAGACCAGATTGATCAGAAT
66 AATGTCACCGGCAGCAGCATTG-AA--CCCACCATCGCACTTGTTTGGACCAGATTGATCAGAAT
** * *
1123 TGCTTCCATAGCTACCACCAATGCCATACTTGTTACCTCCACCATAACTTCCTTGGCCTCCATGA
128 TGCTTCCATAGCTACCACCAGCGCCATACTTGTTACCACCACCATAACTTCCTTGGCCTCCATAA
* * * *
1188 CCACTACCAACACCACAAGTCTTCCCATATCCAACATTATCG
193 CCACTACC-AC-CCACCAGTGTTACCATATCCAACATTACCG
*
1230 CCACCAAATCCCATTTGGTTACCTCCGAATCCAGCTGAACCACTGGTGGCAAAACTATCACCGCC
1 CCACCAAATCCCATTTGGTTACCTCCGAATCCAGCTGAACCACTGGTGGCAAAACTATCACCACC
** * * **
1295 AATGTTGCCGGCTGGAGCATTGAACCCACCATCGCACTTGTTTGGACCAGATTGATCAGAGCTGC
66 AATGTCACCGGCAGCAGCATTGAACCCACCATCGCACTTGTTTGGACCAGATTGATCAGAATTGC
* * *
1360 TTTCGTAGCTACCACCAGCGCCATACTTGTTACCACCACCATAACTTCCTT-G-ATCCATAACCA
131 TTCCATAGCTACCACCAGCGCCATACTTGTTACCACCACCATAACTTCCTTGGCCTCCATAACCA
*
1423 CT-------ACCAGTGTTACCATATCCAACATTACCT
196 CTACCACCCACCAGTGTTACCATATCCAACATTACCG
* * * ** **
1453 CCACCGAATTCCATTAT-GTTACCTCTGAATCCAGCTGAACTGCTGGTGGCAAAACTATTGCCAC
1 CCACCAAATCCCATT-TGGTTACCTCCGAATCCAGCTGAACCACTGGTGGCAAAACTATCACCAC
*** * ** *
1517 TGCTTTCACCGGCAGCAAAATTGAAATTCCCACCATCGCAATTGTTTGGACCAGATTGATCAGAA
65 CAATGTCACCGGCAGCAGCATTG-AA--CCCACCATCGCACTTGTTTGGACCAGATTGATCAGAA
** * * *
1582 --GCTTCCATAGCTACCACCAGTACCATAATTGTTTCCACCACCATAGCTTCCTTGGCCTCCATA
127 TTGCTTCCATAGCTACCACCAGCGCCATACTTGTTACCACCACCATAACTTCCTTGGCCTCCATA
*
1645 ACCACCACCA
192 ACCACTACCA
1655 GTGTTACCAT
Statistics
Matches: 560, Mismatches: 88, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
223 90 0.16
224 49 0.09
225 1 0.00
226 46 0.08
232 11 0.02
233 1 0.00
234 156 0.28
235 2 0.00
236 2 0.00
237 201 0.36
238 1 0.00
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (232 bp):
CCACCAAATCCCATTTGGTTACCTCCGAATCCAGCTGAACCACTGGTGGCAAAACTATCACCACC
AATGTCACCGGCAGCAGCATTGAACCCACCATCGCACTTGTTTGGACCAGATTGATCAGAATTGC
TTCCATAGCTACCACCAGCGCCATACTTGTTACCACCACCATAACTTCCTTGGCCTCCATAACCA
CTACCACCCACCAGTGTTACCATATCCAACATTACCG
Found at i:6027 original size:30 final size:30
Alignment explanation
Indices: 5992--6162 Score: 279
Period size: 30 Copynumber: 5.7 Consensus size: 30
5982 AAACTGAACA
* **
5992 GTTGAGAACATATTGCATAATAGCAACGCA
1 GTTGAGAACATATTGCATAATAGCAATGTG
*
6022 TTTGAGAACATATTGCATAATAGCAATGTG
1 GTTGAGAACATATTGCATAATAGCAATGTG
6052 GTTGAGAACATATTGCATAATAGCAATGTG
1 GTTGAGAACATATTGCATAATAGCAATGTG
6082 GTTGAGAACATATTGCATAATAGCAATGTG
1 GTTGAGAACATATTGCATAATAGCAATGTG
* *
6112 GTTGAGAACATATTGCATAATAGCAACGTC
1 GTTGAGAACATATTGCATAATAGCAATGTG
*
6142 GTTGAGAACATATTACATAAT
1 GTTGAGAACATATTGCATAAT
6163 TTCAGTACCA
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 133 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (30 bp):
GTTGAGAACATATTGCATAATAGCAATGTG
Found at i:13492 original size:14 final size:14
Alignment explanation
Indices: 13473--13502 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13463 CGTTCGTGAA
13473 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
13487 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
13501 CG
1 CG
13503 CTTATGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.30, T:0.47
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:13521 original size:24 final size:24
Alignment explanation
Indices: 13474--13524 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
13464 GTTCGTGAAC
* * *
13474 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGCTTATGTTCATTCAGTTAT
*
13498 GTTCGCTTATGTTCATTCATTTAT
1 GTTCGCTTATGTTCATTCAGTTAT
13522 GTT
1 GTT
13525 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.14, G:0.22, T:0.53
Consensus pattern (24 bp):
GTTCGCTTATGTTCATTCAGTTAT
Found at i:14609 original size:10 final size:10
Alignment explanation
Indices: 14594--14633 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
14584 GGGTCTCCAA
14594 CGTTTATGTT
1 CGTTTATGTT
14604 CGTTTATGTT
1 CGTTTATGTT
14614 CG----TGTT
1 CGTTTATGTT
14620 CGTTTATGTT
1 CGTTTATGTT
14630 CGTT
1 CGTT
14634 AATTTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.23
10 20 0.77
ACGTcount: A:0.07, C:0.12, G:0.23, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:14621 original size:16 final size:16
Alignment explanation
Indices: 14600--14632 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
14590 CCAACGTTTA
14600 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
14616 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
14632 T
1 T
14633 TAATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:18953 original size:3 final size:3
Alignment explanation
Indices: 18945--18996 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
18935 TTTTTGTATA
** * *
18945 TAT TAT TAT TAT CGT TAT T-T TAAT TAT TAT TAT TAG CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
18990 TAT TAT T
1 TAT TAT T
18997 TAACTTACAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:21374 original size:22 final size:22
Alignment explanation
Indices: 21349--21392 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
21339 TCAAACGATG
*
21349 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
21371 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
21393 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:22925 original size:31 final size:32
Alignment explanation
Indices: 22889--22950 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
22879 ATTTTACATG
22889 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
22920 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
22951 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:23968 original size:22 final size:23
Alignment explanation
Indices: 23925--23969 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
23915 AGTGCACCAT
*
23925 TTCCATCTAAGAAGCTCCAGACA
1 TTCCATCTAAGAAGCTCAAGACA
23948 TTCCA-CTAAGAA-CTGCAAGACA
1 TTCCATCTAAGAAGCT-CAAGACA
23970 CTAAAGCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 13 0.65
23 5 0.25
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.20
Consensus pattern (23 bp):
TTCCATCTAAGAAGCTCAAGACA
Found at i:25027 original size:24 final size:21
Alignment explanation
Indices: 24979--25033 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 21
24969 AAGATCAAAC
*
24979 CAAAGAAAAAAAAACAAAGAG
1 CAAAGAAAAAAAAACAAAAAG
*
25000 CAAAGAAAAAATCAAAGCAAAAAT
1 CAAAGAAAAAA--AAA-CAAAAAG
25024 CAAAGAAAAA
1 CAAAGAAAAA
25034 GCAAAGAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
23 3 0.10
24 15 0.52
ACGTcount: A:0.75, C:0.11, G:0.11, T:0.04
Consensus pattern (21 bp):
CAAAGAAAAAAAAACAAAAAG
Found at i:25032 original size:11 final size:12
Alignment explanation
Indices: 25000--25046 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
24990 AAACAAAGAG
25000 CAAAGAAAAAAT
1 CAAAGAAAAAAT
*
25012 CAAAGCAAAAAT
1 CAAAGAAAAAAT
*
25024 CAAAG-AAAAAG
1 CAAAGAAAAAAT
25035 CAAAGAACAAAA
1 CAAAGAA-AAAA
25047 GAGGACAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 10 0.32
12 17 0.55
13 4 0.13
ACGTcount: A:0.72, C:0.13, G:0.11, T:0.04
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:25046 original size:24 final size:25
Alignment explanation
Indices: 24991--25047 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
24981 AAGAAAAAAA
*
24991 AACAAAGAGCAAAGAAAAAATCAAAG
1 AACAAA-AGCAAAGAAAAAAGCAAAG
* *
25017 CA-AAAATCAAAG-AAAAAGCAAAG
1 AACAAAAGCAAAGAAAAAAGCAAAG
25040 AACAAAAG
1 AACAAAAG
25048 AGGACAAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
23 11 0.44
24 10 0.40
25 3 0.12
26 1 0.04
ACGTcount: A:0.70, C:0.12, G:0.14, T:0.04
Consensus pattern (25 bp):
AACAAAAGCAAAGAAAAAAGCAAAG
Found at i:26227 original size:4 final size:4
Alignment explanation
Indices: 26218--26281 Score: 76
Period size: 4 Copynumber: 16.2 Consensus size: 4
26208 GATCGAGAAA
* * * * *
26218 ACAT ACAT ACAT ACAA ACAT ATAT ACAT ACAT ACAT ATAT ACAC ATAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
26266 ACAT ACAT A-AT ACAT A
1 ACAT ACAT ACAT ACAT A
26282 AAATTTGCAT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
3 3 0.06
4 46 0.94
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:26873 original size:105 final size:102
Alignment explanation
Indices: 26732--26971 Score: 286
Period size: 105 Copynumber: 2.3 Consensus size: 102
26722 TGAGAATTTT
* * *
26732 AAAACAAATTGTGTTTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATT-TGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* ***
26796 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC
65 TT-AAACAAAATTAATCTCA-CTTGAGATCG-T-TTTCTCAA
* * *
26837 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTT-GTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* *
26902 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAA
65 TTAAACAAAATTAATCTCACTTGAGATCGTTTTCTCAA
*
26940 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTGTCTCGCTTGAGACATTTTC
26972 TCTAAAAACA
Statistics
Matches: 117, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
103 31 0.26
104 8 0.07
105 76 0.65
106 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (102 bp):
AAAACAAATTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACAT
TAAACAAAATTAATCTCACTTGAGATCGTTTTCTCAA
Found at i:26886 original size:156 final size:154
Alignment explanation
Indices: 26592--26877 Score: 368
Period size: 156 Copynumber: 1.9 Consensus size: 154
26582 AATTCAGTCT
* * * * *
26592 CTTGAGACATTTTTTTCCTTTGAGATCCAAATTTTGAATTTGTTTCACATTAAACAAAGTTGATT
1 CTTGAGACA-TTTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACATTAAACAAAATTAATC
* *
26657 TCATTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCACAAATTT
65 TCACTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACACTTTTCCAC--A-TT
26722 TGAGAATTTTAAAACAAATTGTGTTTCG
127 TGAGAATTTTAAAACAAATTGTGTTTCG
26750 CTTGAGACA-TTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-TTAAAACAAAATTAATC
1 CTTGAGACATTTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACATT-AAACAAAATTAATC
* * * *
26813 TCACCTT-AGATTGTTGTTTCTTTCAAAACAAATTTCGTCTCGCTTGAGAC-CTTTTCC-C-TTT
65 TCA-CTTGAGATCG-TATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACACTTTTCCACATTT
26874 GAGA
128 GAGA
26878 TCCAAATTTC
Statistics
Matches: 114, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
151 7 0.06
155 3 0.03
156 60 0.53
157 35 0.31
158 9 0.08
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (154 bp):
CTTGAGACATTTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACATTAAACAAAATTAATCT
CACTTGAGATCGTATCTATTTCAAAACAAATTTCGTCTCGCTTGAGACACTTTTCCACATTTGAG
AATTTTAAAACAAATTGTGTTTCG
Found at i:26979 original size:36 final size:35
Alignment explanation
Indices: 26904--27036 Score: 117
Period size: 36 Copynumber: 3.7 Consensus size: 35
26894 GTTTCACATT
* * ** *
26904 AAACAAAGTTGATCTCACTTGAGATCGTTTTCTCAAA
1 AAACAAATTTG-TCTCGCTTGAGA-CAATTTCTCTAA
26941 AAACAAACTTTGTCTCGCTTGAGACAATTTCTCTAA
1 AAACAAA-TTTGTCTCGCTTGAGACAATTTCTCTAA
** * *
26977 AAACAAATTTTGTCTCATTTGAGACTATATCT-T-A
1 AAACAAA-TTTGTCTCGCTTGAGACAATTTCTCTAA
*
27011 AAGCAAATTTCGTCTCGCTTGAGACA
1 AAACAAATTT-GTCTCGCTTGAGACA
27037 TTTTTCCTTT
Statistics
Matches: 80, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
33 3 0.04
34 19 0.24
35 1 0.01
36 36 0.45
37 18 0.22
38 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (35 bp):
AAACAAATTTGTCTCGCTTGAGACAATTTCTCTAA
Found at i:27419 original size:29 final size:27
Alignment explanation
Indices: 27381--27449 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
27371 GTTTCTCTTG
*
27381 AAAAATCTTTGAGTTTGTTCCTTTTGA
1 AAAAATCTTTGAGTTCGTTCCTTTTGA
*
27408 ATAAATATCTTTGAG-TCGTTTCTTTTGA
1 A-AAA-ATCTTTGAGTTCGTTCCTTTTGA
*
27436 AAAAAACTTTGAGT
1 AAAAATCTTTGAGT
27450 CTATTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 8 0.22
27 4 0.11
28 15 0.42
29 9 0.25
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (27 bp):
AAAAATCTTTGAGTTCGTTCCTTTTGA
Found at i:27538 original size:52 final size:53
Alignment explanation
Indices: 27460--27564 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 53
27450 CTATTTATTT
*
27460 TGAAACAAAGTTTTATCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTATATCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
* *
27512 TGAAACAAAGTTTTGTATCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAGT
1 TGAAACAAAGTTTTATATCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAGT
27565 TTGTTTCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 34 0.71
54 14 0.29
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTATATCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:27622 original size:67 final size:67
Alignment explanation
Indices: 27513--27706 Score: 254
Period size: 67 Copynumber: 3.0 Consensus size: 67
27503 CTTTGAGTCT
* * * * *
27513 GAAACAAAGTTTTGTATCTCTTGAGACAA-TT-TTGTG-AA-AAAAATCTTTGAGTTTGTTTCTT
1 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTT
27574 TG
66 TG
* *
27576 GAAACAAAATTCTT-TCTCTTTTAAGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
1 GAAACAAAATT-TTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
*
27640 TTT
65 TTG
* *
27643 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCT
1 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
27707 CTTAAAATGA
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
63 20 0.18
64 4 0.04
65 4 0.04
66 4 0.04
67 81 0.72
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (67 bp):
GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTT
TG
Found at i:27990 original size:120 final size:117
Alignment explanation
Indices: 27807--28027 Score: 263
Period size: 120 Copynumber: 1.9 Consensus size: 117
27797 TTAACAAAAT
* * *
27807 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTCTCTCTTGAGACAGTTTCTAATTAAAAAC
1 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATTAAAAA-
27872 TAACTTTTGAGATT-GTTTCATTTGAAAC-AAATTTGGTCTTACTTAAGATGTAATC
65 T--C-TTTGAG-TTGGTTTCATTTGAAACAAAATTTGGTCTTACTTAAGATGTAATC
** *
27927 CATCTTTGAGTCTATTTCTTTTGAAACAAAAT-TT-TATCTCTTAAAGACAATTTCT-TTTGAAA
1 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTATCTCTT-AAGACAATTTCTAATT-AAA
* *
27989 AATCTTTGAGTTGGTTTCCTTTGAAACAAAATTTTGTCT
63 AATCTTTGAGTTGGTTTCATTTGAAACAAAATTTGGTCT
28028 CTCGAGATAA
Statistics
Matches: 88, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
115 2 0.02
116 19 0.22
117 11 0.12
119 10 0.11
120 42 0.48
121 4 0.05
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (117 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTGTATCTCTTAAGACAATTTCTAATTAAAAAT
CTTTGAGTTGGTTTCATTTGAAACAAAATTTGGTCTTACTTAAGATGTAATC
Found at i:28520 original size:35 final size:37
Alignment explanation
Indices: 28454--28533 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 37
28444 TGTTTCTTTG
* * *
28454 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT-
1 GAAACAAAATTAAACATCTTTGAAACTGTTTCCCTTA
28490 GAAACAAAA-TAAACATCTTTGAGAAC-GTTTCCCTTA
1 GAAACAAAATTAAACATCTTTGA-AACTGTTTCCCTTA
*
28526 AAAACAAA
1 GAAACAAA
28534 TTTTGTCTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 20 0.53
36 18 0.47
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (37 bp):
GAAACAAAATTAAACATCTTTGAAACTGTTTCCCTTA
Found at i:28867 original size:40 final size:40
Alignment explanation
Indices: 28812--29176 Score: 173
Period size: 40 Copynumber: 8.6 Consensus size: 40
28802 TGGCCAGTAG
*
28812 TCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
** * ** * *
28852 TCCTCATCACGTAGGAGTCGTGTCAACCATTGGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCC---CCA-GACCAGATC
* * *
28895 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATTGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA----CCAGATC
* * * *
28943 TCTTCATCACGTATGAGCCGTGCCATTCCCCAGACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCCAGACCAGATC
* * * * * *
28984 TCCTCATCACGTATGAGCTGTGTCATCCCCTGACCATATT
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
* * *
29024 TCCTCATCACGTAGGAACCGGGTCA-CCCTTAGATAACCAG-TAG
1 TCCTCATCACGTAGGAACCGTGTCATCCC-CAG---ACCAGAT-C
* * *
29067 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 TCCTCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATC
* * * *
29113 TCTTCATCACGTATG-AGCGTGTCATTCCCC-GACCAGAGC
1 TCCTCATCACGTAGGAACCGTGTCA-TCCCCAGACCAGATC
* *
29152 TCTTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
29177 CCTTTAGACG
Statistics
Matches: 247, Mismatches: 50, Indels: 56
0.70 0.14 0.16
Matches are distributed among these distances:
39 23 0.09
40 65 0.26
41 28 0.11
42 3 0.01
43 31 0.13
44 30 0.12
45 15 0.06
46 23 0.09
47 26 0.11
48 3 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGATC
Found at i:28993 original size:41 final size:40
Alignment explanation
Indices: 28936--29036 Score: 130
Period size: 41 Copynumber: 2.5 Consensus size: 40
28926 TTTAGATTGG
* *
28936 CCAGAACTCTTCATCACGTATGAGCCGTGCCATTCCCCAGA
1 CCAGATCTCCTCATCACGTATGAGCCGTGCCA-TCCCCAGA
* * *
28977 CCAGATCTCCTCATCACGTATGAGCTGTGTCATCCCCTGA
1 CCAGATCTCCTCATCACGTATGAGCCGTGCCATCCCCAGA
* *
29017 CCATATTTCCTCATCACGTA
1 CCAGATCTCCTCATCACGTA
29037 GGAACCGGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 25 0.47
41 28 0.53
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.27
Consensus pattern (40 bp):
CCAGATCTCCTCATCACGTATGAGCCGTGCCATCCCCAGA
Found at i:29098 original size:171 final size:169
Alignment explanation
Indices: 28812--29176 Score: 543
Period size: 172 Copynumber: 2.1 Consensus size: 169
28802 TGGCCAGTAG
* * ** *
28812 TCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGTCGTGTCA
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAACCGGGTCA
* *
28877 ACCATTGGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATTGGCCAGAA
66 ACCATTAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGA-TGGCCAGAA
*
28942 CTCTTCATCACGTATGAGCCGTGCCATTCCCCAGACCAGATC
130 CTCTTCATCACGTATGAG-CGTGCCATTCCCC-GACCAGAGC
* * * * *
28984 TCCTCATCACGTATGAGCTGTGTCATCCCCTGACCATATTTCCTCATCACGTAGGAACCGGGTC-
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAACCGGGTCA
* *
29048 ACCCTTAGATAACCAGTAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
66 ACCATTAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
*
29113 TCTTCATCACGTATGAGCGTGTCATTCCCCGACCAGAGC
131 TCTTCATCACGTATGAGCGTGCCATTCCCCGACCAGAGC
*
29152 TCTTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAGCCGTGTCA
29177 CCTTTAGACG
Statistics
Matches: 174, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
168 30 0.17
169 12 0.07
170 27 0.16
171 51 0.29
172 54 0.31
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (169 bp):
TCCTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAACCGGGTCA
ACCATTAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
TCTTCATCACGTATGAGCGTGCCATTCCCCGACCAGAGC
Found at i:29202 original size:43 final size:43
Alignment explanation
Indices: 29027--29218 Score: 151
Period size: 43 Copynumber: 4.5 Consensus size: 43
29017 CCATATTTCC
* * * ** * * *
29027 TCATCACGTAGGAACCGGGTCACCCTTAGATAACCAGTAGTCC
1 TCATCACGTAGGAGCCGTGTCACCTTTAGACGACCAGAACTCT
* * *
29070 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTG---TCACCTTTAGACGACCAGAACTCT
* *** *
29116 TCATCACGTATGAG-CGTGTCA---TTCCCCGACCAGAGCTCT
1 TCATCACGTAGGAGCCGTGTCACCTTTAGACGACCAGAACTCT
29155 TCATCACGTAGGAGCCGTGTCACCTTTAGACGACCCA-AACTCT
1 TCATCACGTAGGAGCCGTGTCACCTTTAGACGA-CCAGAACTCT
* *
29198 TCATCACGTATGAGCAGTGTC
1 TCATCACGTAGGAGCCGTGTC
29219 GTCCCCAACA
Statistics
Matches: 119, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
39 25 0.21
40 7 0.06
42 3 0.03
43 47 0.39
44 3 0.03
45 4 0.03
46 30 0.25
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (43 bp):
TCATCACGTAGGAGCCGTGTCACCTTTAGACGACCAGAACTCT
Found at i:29224 original size:82 final size:83
Alignment explanation
Indices: 29070--29224 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 83
29060 CCAGTAGTCC
* *
29070 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCGTGT
1 TCATCACGTAGGAACCGTG-T-TCACCTTTAGACGCCCAGAACTCTTCATCACGTATGAGCGTGT
*
29135 CATTCCCCGACCAGAGCTCT
64 CAGTCCCCGACCAGAGCTCT
*
29155 TCATCACGTAGGAGCCGTG-TCACCTTTAGACGACCCA-AACTCTTCATCACGTATGAGCAGTGT
1 TCATCACGTAGGAACCGTGTTCACCTTTAGACG-CCCAGAACTCTTCATCACGTATGAGC-GTGT
29218 C-GTCCCC
64 CAGTCCCC
29225 AACAACCAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
82 38 0.59
83 8 0.12
85 18 0.28
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (83 bp):
TCATCACGTAGGAACCGTGTTCACCTTTAGACGCCCAGAACTCTTCATCACGTATGAGCGTGTCA
GTCCCCGACCAGAGCTCT
Found at i:31794 original size:22 final size:22
Alignment explanation
Indices: 31769--31812 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31759 TCAAACGATG
*
31769 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
31791 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
31813 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:33348 original size:17 final size:14
Alignment explanation
Indices: 33324--33363 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 14
33314 TTTAATTAAG
33324 ATTAAATTTATAAAA
1 ATTAAATTT-TAAAA
33339 TATATAAATTTTAAAA
1 -AT-TAAATTTTAAAA
33355 ATTAAATTT
1 ATTAAATTT
33364 GTCGTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 2 0.09
16 7 0.30
17 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTAAATTTTAAAA
Found at i:42944 original size:18 final size:19
Alignment explanation
Indices: 42921--42964 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
42911 TCAGTAATCC
*
42921 TATTCC-CTGATAATCTTT
1 TATTCCACTGATAATCTTA
*
42939 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGATAATCTTA
42959 TATTCC
1 TATTCC
42965 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (19 bp):
TATTCCACTGATAATCTTA
Found at i:53437 original size:15 final size:16
Alignment explanation
Indices: 53417--53447 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53407 ACGTTTAGTA
53417 TTTTAT-AATTAATTT
1 TTTTATAAATTAATTT
53432 TTTTATAAATTAATTT
1 TTTTATAAATTAATTT
53448 AATATTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATAAATTAATTT
Found at i:54619 original size:182 final size:181
Alignment explanation
Indices: 54312--54764 Score: 676
Period size: 182 Copynumber: 2.5 Consensus size: 181
54302 ACTTTTTTAC
* * *
54312 TACCGATTTTGTCATTTCGAGACCGATTTTATTATATTTTTACATGTTATATTATTATGGATCGA
1 TACCGATTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
* *
54377 TACATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
* **
54442 TGTCGATACTTATAATAAAATATCGACACT-TTCAACATATCCGGTAGTTCTT
131 TGTCGATACTTATAATAAAATATCGACACTATT-AACATAT-CGATAGCGCTT
* *
54494 TACCGATTTTATCATTTCGAGACCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGA
1 TACCGATTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
* *
54559 TACATTTTTATAAAGTATCGACACTTTATTAGTGTTATAACTTCTTCTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
* *
54624 TGTCTATACTTATAATAAAGTATCGACACTATTAACATATCGATAGCGCTT
131 TGTCGATACTTATAATAAAATATCGACACTATTAACATATCGATAGCGCTT
* ** * * * *
54675 TACATG-TTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATAGATCG
1 TAC-CGATTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCG
54739 ATACATTTTTATAAAGTATCGACACT
65 ATACATTTTTATAAAGTATCGACACT
54765 ATCAACATAT
Statistics
Matches: 247, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
181 88 0.36
182 157 0.64
183 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (181 bp):
TACCGATTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAATATCGACACTATTAACATATCGATAGCGCTT
Found at i:54830 original size:20 final size:20
Alignment explanation
Indices: 54785--54830 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
54775 CCGGTAGCGC
* *
54785 TTTACCTGTTTTGTCATTTA
1 TTTACCAGTTTTATCATTTA
* *
54805 TATACCAGTTTTATCATTTT
1 TTTACCAGTTTTATCATTTA
54825 TTTACC
1 TTTACC
54831 TGTTATATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTACCAGTTTTATCATTTA
Found at i:54834 original size:112 final size:112
Alignment explanation
Indices: 54638--55210 Score: 882
Period size: 112 Copynumber: 5.1 Consensus size: 112
54628 TATACTTATA
* * *
54638 ATAAAGTATCGACACTATT-AACATAT-CGATAGCGCTTTACATGTTTTGTCATTTATAGACCGG
1 ATAAAGTATCGACACT-TTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG
*
54701 TTTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
54749 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACCAGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
54814 TTTATCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * * * *
54861 ATAATGTATTGACACTTTTAATATATCTGGTAGCGCTTTACCTATTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
54926 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
54973 ATAAAATATCGACACTTTCAATATATCCGGTAGCGCTTTACCT-ATTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
55037 TTTGTAATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
55084 ATAAAGTATCAACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTTTCATTTATAGATCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* ** *
55149 TTTGTCATTTTTTTACCTGTTATATTATTATGGATTAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
55196 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
55211 AAACCGACAA
Statistics
Matches: 421, Mismatches: 38, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
110 1 0.00
111 129 0.31
112 291 0.69
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:55144 original size:223 final size:223
Alignment explanation
Indices: 54638--55210 Score: 889
Period size: 223 Copynumber: 2.6 Consensus size: 223
54628 TATACTTATA
* * * *
54638 ATAAAGTATCGACACTATTAACATAT-CGATAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACT-TTAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
*
54702 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTAT
65 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
* * *
54767 CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACCAGTTTTATCATTTTTTTACCT
130 CAACATATCCGGTAGCGCTTTACCTGATTTGTCATTTATAGACCAGTTTTATAATTTTTTTACCT
54832 GTTATATTGTTATGGATCGATACATTTTT
195 GTTATATTGTTATGGATCGATACATTTTT
* * * *
54861 ATAATGTATTGACACTTTTAATATATCTGGTAGCGCTTTACCTATTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACAC-TTTAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
* *
54926 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAATATCGACACTTT
65 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
* * *
54991 CAATATATCCGGTAGCGCTTTACCT-ATTTGTCATTTATAGACCGGTTTTGTAATTTTTTTACCT
130 CAACATATCCGGTAGCGCTTTACCTGATTTGTCATTTATAGACCAGTTTTATAATTTTTTTACCT
55055 GTTATATTGTTATGGATCGATACATTTTT
195 GTTATATTGTTATGGATCGATACATTTTT
* * *
55084 ATAAAGTATCAACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTTTCATTTATAGATCGAT
1 ATAAAGTATCGACACTTT-AATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
* ** *
55149 TTTGTCATTTTTTTACCTGTTATATTATTATGGATTAATATATTTTTATAAAGTATCGACAC
65 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
55211 AAACCGACAA
Statistics
Matches: 318, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
222 3 0.01
223 195 0.61
224 120 0.38
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (223 bp):
ATAAAGTATCGACACTTTAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGTT
TTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTATC
AACATATCCGGTAGCGCTTTACCTGATTTGTCATTTATAGACCAGTTTTATAATTTTTTTACCTG
TTATATTGTTATGGATCGATACATTTTT
Found at i:64768 original size:16 final size:17
Alignment explanation
Indices: 64727--64768 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
64717 ACTCAGTTTA
64727 TATCTATACATATAATAT
1 TATCTA-ACATATAATAT
* *
64745 TATTTAACCTATAA-AT
1 TATCTAACATATAATAT
64761 TATCTAAC
1 TATCTAAC
64769 TTAGAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 7 0.33
18 5 0.24
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (17 bp):
TATCTAACATATAATAT
Found at i:68393 original size:25 final size:28
Alignment explanation
Indices: 68337--68392 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
68327 GTTCGCAAAC
*
68337 AATAAATAAACGAACATGAATACTTCAAA
1 AATAAATAAAAGAACATGAATACTT-AAA
68366 AATAAATAAAAGAACATG-ATA-TTAAA
1 AATAAATAAAAGAACATGAATACTTAAA
68392 A
1 A
68393 TTTTAAACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 2 0.08
28 3 0.12
29 17 0.65
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.21
Consensus pattern (28 bp):
AATAAATAAAAGAACATGAATACTTAAA
Found at i:70616 original size:35 final size:36
Alignment explanation
Indices: 70544--70692 Score: 182
Period size: 35 Copynumber: 4.2 Consensus size: 36
70534 TGAAAGTATT
* **
70544 AAAATGGTTTTC-AAGTTTGGT-AAT-TAACTTTGAA
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG-A
70578 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTT-A
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
*
70613 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGA
1 AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
* * *
70649 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GATTTTCAAAGTTTGGTAAATGTTTCTTTGA
70685 AAAATGAT
1 AAAATGAT
70693 AATGAGATAA
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
34 11 0.11
35 45 0.44
36 18 0.18
37 28 0.27
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
AAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTGA
Found at i:70651 original size:72 final size:69
Alignment explanation
Indices: 70544--70690 Score: 197
Period size: 72 Copynumber: 2.1 Consensus size: 69
70534 TGAAAGTATT
70544 AAAATGGTTTTCAAGTTTGGTAATTAACTTTGAAAAA-ATGATTTTCAAAGTTTGGTAAATGTTT
1 AAAATGGTTTTCAAGTTTGGTAATTAACTTTGAAAAATA-GATTTTCAAAGTTTGGTAAATGTTT
*
70608 CTTTA
65 CTTGA
** * *
70613 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGT
1 AAAATGGTTTTC-AAGTTTGGT-AAT-TAACTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGT
*
70678 TTGTTGA
63 TTCTTGA
70685 AAAATG
1 AAAATG
70691 ATAATGAGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
69 12 0.18
70 9 0.13
71 3 0.04
72 43 0.63
73 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (69 bp):
AAAATGGTTTTCAAGTTTGGTAATTAACTTTGAAAAATAGATTTTCAAAGTTTGGTAAATGTTTC
TTGA
Found at i:71120 original size:16 final size:17
Alignment explanation
Indices: 71099--71130 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
71089 TTACTATTCA
71099 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
71115 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
71131 CGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:75227 original size:21 final size:21
Alignment explanation
Indices: 75203--75263 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
75193 AACTTTGAAA
75203 AAATGATTTTCAAAGTTTGGT
1 AAATGATTTTCAAAGTTTGGT
*
75224 AAATG--TTTC----TTT-GA
1 AAATGATTTTCAAAGTTTGGT
75238 AAATGATTTTCAAAGTTTGGT
1 AAATGATTTTCAAAGTTTGGT
75259 AAATG
1 AAATG
75264 TTTCCTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 6 0.19
15 3 0.10
16 4 0.13
19 4 0.13
20 3 0.10
21 11 0.35
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (21 bp):
AAATGATTTTCAAAGTTTGGT
Found at i:75309 original size:36 final size:36
Alignment explanation
Indices: 75201--75316 Score: 173
Period size: 35 Copynumber: 3.2 Consensus size: 36
75191 CCAACTTTGA
*
75201 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCCTTG
75237 -AAAATGATTTTCAAAGTTTGGTAAATGTTTCCTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCCTTG
* * *
75272 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 AAAAAT-GATTTTCAAAGTTTGGTAAATGTTTCCTTG
75308 AAAAATGAT
1 AAAAATGAT
75317 AATGGGATAA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 36 0.49
36 14 0.19
37 23 0.32
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (36 bp):
AAAAATGATTTTCAAAGTTTGGTAAATGTTTCCTTG
Found at i:75743 original size:16 final size:17
Alignment explanation
Indices: 75722--75753 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
75712 TTACTATTCA
75722 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
75738 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
75754 CGTCGGCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:79924 original size:36 final size:36
Alignment explanation
Indices: 79810--79931 Score: 167
Period size: 35 Copynumber: 3.4 Consensus size: 36
79800 TGGTAACCAA
79810 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
79847 CTTTG-AAAATGGTTTTCAAAGTTTAGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
79882 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
79919 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
79932 AATGGGATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 35 0.46
36 14 0.18
37 27 0.36
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:88392 original size:36 final size:36
Alignment explanation
Indices: 88352--88443 Score: 166
Period size: 36 Copynumber: 2.6 Consensus size: 36
88342 ATTGCCGCTG
* *
88352 ATCTCTCGTACACGATCAATATCACCATTGTTGTCA
1 ATCTCTCGTTCACAATCAATATCACCATTGTTGTCA
88388 ATCTCTCGTTCACAATCAATATCACCATTGTTGTCA
1 ATCTCTCGTTCACAATCAATATCACCATTGTTGTCA
88424 ATCTCTCGTTCACAATCAAT
1 ATCTCTCGTTCACAATCAAT
88444 GCGCTTTTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (36 bp):
ATCTCTCGTTCACAATCAATATCACCATTGTTGTCA
Found at i:90066 original size:17 final size:17
Alignment explanation
Indices: 90044--90082 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
90034 AAATATTCAC
90044 AAATAATAAAGTTCAAT
1 AAATAATAAAGTTCAAT
*
90061 AAATAATCAAGTTCAAT
1 AAATAATAAAGTTCAAT
90078 AAATA
1 AAATA
90083 TTCACAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (17 bp):
AAATAATAAAGTTCAAT
Found at i:100667 original size:21 final size:25
Alignment explanation
Indices: 100643--100687 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 25
100633 ATTATCCAGC
100643 TGATA-AT-CAAAA-ATT-AATTAG
1 TGATATATACAAAATATTCAATTAG
100664 TGATATATACAAAATATTCAATTA
1 TGATATATACAAAATATTCAATTA
100688 TTATTAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.25
22 2 0.10
23 5 0.25
24 3 0.15
25 5 0.25
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (25 bp):
TGATATATACAAAATATTCAATTAG
Found at i:105219 original size:16 final size:16
Alignment explanation
Indices: 105200--105230 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
105190 AATTGAATTA
*
105200 TATTTAAATTATTTGT
1 TATTGAAATTATTTGT
105216 TATTGAAATTATTTG
1 TATTGAAATTATTTG
105231 AGTATCGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (16 bp):
TATTGAAATTATTTGT
Found at i:107122 original size:191 final size:191
Alignment explanation
Indices: 106797--107171 Score: 662
Period size: 191 Copynumber: 2.0 Consensus size: 191
106787 TTTGACTATC
106797 GATGTTTTAATTTAATCAATCAGATCACTCAACTATTTAGATGGTTTAATCAAGCCACATGTCAT
1 GATGTTTTAATTTAATCAATCAGATCACTCAACTATTTAGATGGTTTAATCAAGCCACATGTCAT
* *
106862 TAATATTTAACGAAATATGTGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATTCT
66 TAATATTTAACGAAATATATGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATCCT
*
106927 AGTACTTATATATTATTTTAATTTGGTCATAATTGTAATAAATCAAAATAAATTATATTTA
131 AGTACTTATATATTATTTCAATTTGGTCATAATTGTAATAAATCAAAATAAATTATATTTA
* * *
106988 GATGTTTTAATTTGATCAATCATATCACTCAACTATTTATAT-GTTTCAATCAAGCCACATGTCA
1 GATGTTTTAATTTAATCAATCAGATCACTCAACTATTTAGATGGTTT-AATCAAGCCACATGTCA
* *
107052 TTAATATTTAACGGAGTATATGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATCC
65 TTAATATTTAACGAAATATATGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATCC
107117 TAGTACTTATATATTATTTCAATTTGGTCATAATTGTAATAAATCAAAATAAATT
130 TAGTACTTATATATTATTTCAATTTGGTCATAATTGTAATAAATCAAAATAAATT
107172 TAATAATCAA
Statistics
Matches: 175, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
190 4 0.02
191 171 0.98
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (191 bp):
GATGTTTTAATTTAATCAATCAGATCACTCAACTATTTAGATGGTTTAATCAAGCCACATGTCAT
TAATATTTAACGAAATATATGATGTGACAGTTAAAATATTTTGATATAATTATATAATTGATCCT
AGTACTTATATATTATTTCAATTTGGTCATAATTGTAATAAATCAAAATAAATTATATTTA
Found at i:107181 original size:18 final size:20
Alignment explanation
Indices: 107148--107187 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
107138 ATTTGGTCAT
107148 AATTGTAATAAATCAAAATA
1 AATTGTAATAAATCAAAATA
*
107168 AATT-TAAT-AATCAAATTA
1 AATTGTAATAAATCAAAATA
107186 AA
1 AA
107188 AGGTGCTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 4 0.21
20 4 0.21
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AATTGTAATAAATCAAAATA
Found at i:107585 original size:28 final size:30
Alignment explanation
Indices: 107549--107610 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
107539 ATTTTCACTG
* *
107549 AAAATTATATTTTATTCTTAT-TTCAA-ATT
1 AAAATTATATGTTATTATTATCTT-AACATT
107578 AAAA-TATATGTTATTATTATCTTAACATT
1 AAAATTATATGTTATTATTATCTTAACATT
107607 AAAA
1 AAAA
107611 AACATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (30 bp):
AAAATTATATGTTATTATTATCTTAACATT
Found at i:107658 original size:59 final size:58
Alignment explanation
Indices: 107595--107833 Score: 168
Period size: 59 Copynumber: 4.1 Consensus size: 58
107585 ATGTTATTAT
* *
107595 TATCTTAACATTAAAAAACATATTAAAATATATTTTTAATTTAAA-ATAAGAATAAAATA
1 TATCTTAACATTAAAAAA-ATA-TAAAATATATTTTTAAGTTAAACATAATAATAAAATA
* * ** * * *
107654 TATCTTAAC-TTCAAAATATATTTTAATATATTCTTAAAAGTTAAAGATAATAATAAATTA
1 TATCTTAACATTAAAAAAATA-TAAAATATATT-TT-TAAGTTAAACATAATAATAAAATA
* * * * *
107714 TATTTTTAA-TTTGAAATAAGA-ATAAAATATATTTTTAAGTGAAA-ATAATAGTAAAATA
1 TA-TCTTAACATT-AAA-AAAATATAAAATATATTTTTAAGTTAAACATAATAATAAAATA
* * * *
107772 TATATTATATATTAAAATAAACATAAAATATATTTGTTAAGTTAAACA-AA-AATAAAAGA
1 TATCTTA-ACATTAAAA-AAATATAAAATATATTT-TTAAGTTAAACATAATAATAAAATA
107831 TAT
1 TAT
107834 ATAAAATATT
Statistics
Matches: 144, Mismatches: 23, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
57 18 0.12
58 28 0.19
59 48 0.33
60 27 0.19
61 17 0.12
62 3 0.02
63 3 0.02
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (58 bp):
TATCTTAACATTAAAAAAATATAAAATATATTTTTAAGTTAAACATAATAATAAAATA
Found at i:107787 original size:89 final size:88
Alignment explanation
Indices: 107618--107833 Score: 217
Period size: 89 Copynumber: 2.4 Consensus size: 88
107608 AAAAACATAT
* * **
107618 TAAAATATATTTTTAATTTAAAATAAGAATAAAATATA-TCTTAACTTCAAAATATATTTTAATA
1 TAAAATATATTTTTAATTT-AAATAAGAATAAAATATATTCTTAACGTCAAAATATAGTAAAATA
*
107682 TATTCTTAAAAGTTAAAGATAATA-A
65 TATTATTAAAAGTTAAA-ATAA-ACA
* * *
107707 TAAATTATATTTTTAATTTGAAATAAGAATAAAATATATTTTTAA-GTGAAAATAATAGTAAAAT
1 TAAAATATATTTTTAATTT-AAATAAGAATAAAATATATTCTTAACGTCAAAAT-ATAGTAAAAT
*
107771 ATA-TATTATATA-TTAAAATAAACA
64 ATATTATTA-AAAGTTAAAATAAACA
* * * *
107795 TAAAATATATTTGTTAAGTTAAACAAAAATAAAAGATAT
1 TAAAATATATTT-TTAATTTAAATAAGAATAAAATATAT
107834 ATAAAATATT
Statistics
Matches: 107, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
87 1 0.01
88 32 0.30
89 57 0.53
90 17 0.16
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (88 bp):
TAAAATATATTTTTAATTTAAATAAGAATAAAATATATTCTTAACGTCAAAATATAGTAAAATAT
ATTATTAAAAGTTAAAATAAACA
Found at i:107817 original size:30 final size:29
Alignment explanation
Indices: 107618--107833 Score: 165
Period size: 29 Copynumber: 7.3 Consensus size: 29
107608 AAAAACATAT
* *
107618 TAAAATATATTTTTAATTTAAAATAAGAA
1 TAAAATATATTTTTAAGTTAAAATAATAA
* * *
107647 TAAAATATA-TCTTAACTTCAAAAT-ATAT
1 TAAAATATATTTTTAAGTT-AAAATAATAA
** *
107675 TTTAATATATTCTTAAAAGTTAAAGATAATAA
1 TAAAATATATT-TT-TAAGTTAAA-ATAATAA
* * * *
107707 TAAATTATATTTTTAATTTGAAATAAGAA
1 TAAAATATATTTTTAAGTTAAAATAATAA
* *
107736 TAAAATATATTTTTAAGTGAAAATAATAG
1 TAAAATATATTTTTAAGTTAAAATAATAA
*
107765 TAAAATATATATTATATA-TTAAAATAA-ACA
1 TAAAATATAT-TTTTA-AGTTAAAATAATA-A
107795 TAAAATATATTTGTTAAGTTAAACA-AA-AA
1 TAAAATATATTT-TTAAGTTAAA-ATAATAA
*
107824 TAAAAGATAT
1 TAAAATATAT
107834 ATAAAATATT
Statistics
Matches: 147, Mismatches: 28, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
28 16 0.11
29 68 0.46
30 42 0.29
31 10 0.07
32 11 0.07
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (29 bp):
TAAAATATATTTTTAAGTTAAAATAATAA
Found at i:110176 original size:16 final size:16
Alignment explanation
Indices: 110139--110177 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
110129 TTTCGATTTA
*
110139 AAAAAAAACCGGTTTT
1 AAAAAAAACCGGTTAT
**
110155 TTAAAAAACCGGTTAT
1 AAAAAAAACCGGTTAT
110171 AAAAAAA
1 AAAAAAA
110178 CCAATTTTAA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (16 bp):
AAAAAAAACCGGTTAT
Found at i:110586 original size:21 final size:21
Alignment explanation
Indices: 110562--110615 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
110552 CTCGGAGGGA
110562 ACCGATTCCCCCATAGGGGGT
1 ACCGATTCCCCCATAGGGGGT
*
110583 ACCGATTCTCCCATAGGGGGT
1 ACCGATTCCCCCATAGGGGGT
110604 ACCGATTCCCCC
1 ACCGATTCCCCC
110616 TATTCAACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.37, G:0.24, T:0.20
Consensus pattern (21 bp):
ACCGATTCCCCCATAGGGGGT
Found at i:110903 original size:13 final size:13
Alignment explanation
Indices: 110882--110936 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
110872 AAGTTCGATA
*
110882 AATTCAAATACTT
1 AATTGAAATACTT
110895 AATTGAAATACTT
1 AATTGAAATACTT
* *
110908 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
110922 AATTGAAATACTT
1 AATTGAAATACTT
110935 AA
1 AA
110937 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:110967 original size:33 final size:33
Alignment explanation
Indices: 110922--111020 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
110912 AACTCAACAT
* * *
110922 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
110955 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
110988 AATTCAAATACTTAAAAACTT-CAAATTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
111020 A
1 A
111021 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 11 0.18
33 50 0.82
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:111039 original size:21 final size:21
Alignment explanation
Indices: 111015--111056 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
111005 ACTTCAAATT
*
111015 CGATAATTGAAACAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
*
111036 CGATAATTAAAATAAAGTTTA
1 CGATAATTAAAACAAAGTTTA
111057 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTAAAACAAAGTTTA
Found at i:118630 original size:50 final size:50
Alignment explanation
Indices: 118567--118668 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
118557 TTTATCCTAT
*
118567 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGAGATATCTTGTTTTGTA
118617 TTTAGTATGTATTTATTTTAAAATTGATTATTGAGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGAGATATCTTGTTTTGTA
118667 TT
1 TT
118669 CAATAATTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTGATTATTGAGATATCTTGTTTTGTA
Found at i:119890 original size:24 final size:26
Alignment explanation
Indices: 119837--119891 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
119827 GAGATTAATG
* * *
119837 TAAAATTTTATAGTAGTACGAACTTT
1 TAAAATTTTATAGGAGTACAAACTTA
119863 TAAAATTTT-TAGGA-TACAAACTTA
1 TAAAATTTTATAGGAGTACAAACTTA
119887 TAAAA
1 TAAAA
119892 AATTTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 13 0.50
25 4 0.15
26 9 0.35
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.38
Consensus pattern (26 bp):
TAAAATTTTATAGGAGTACAAACTTA
Found at i:119945 original size:15 final size:17
Alignment explanation
Indices: 119925--119961 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
119915 TTATCAATAG
119925 AAAATATA-AA-AATCT
1 AAAATATACAATAATCT
*
119940 AAAATATACAATAATTT
1 AAAATATACAATAATCT
119957 AAAAT
1 AAAAT
119962 TTTAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 9 0.47
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATATACAATAATCT
Found at i:120092 original size:25 final size:25
Alignment explanation
Indices: 120039--120092 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
120029 TTTACTATGC
* *
120039 TTTTAGTTTATATAATTACTCTAAT
1 TTTTAGTTTATATAATTAATCTAAA
*
120064 TTTTAGTTTATATAA-TAATTTAAAA
1 TTTTAGTTTATATAATTAATCT-AAA
120089 TTTT
1 TTTT
120093 TAGAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTAGTTTATATAATTAATCTAAA
Found at i:126010 original size:18 final size:16
Alignment explanation
Indices: 125974--126029 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
125964 CTCTAAAAAT
125974 TTTAATTTTTTTTATA
1 TTTAATTTTTTTTATA
125990 TTTAATTTTTTTTATA
1 TTTAATTTTTTTTATA
126006 ---AATTTTTTTTAATTA
1 TTTAATTTTTTTT-A-TA
126021 TTTAATTTT
1 TTTAATTTT
126030 GTATATTCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 10 0.29
14 1 0.03
15 2 0.06
16 16 0.46
18 6 0.17
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTAATTTTTTTTATA
Found at i:126034 original size:29 final size:28
Alignment explanation
Indices: 125977--126034 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
125967 TAAAAATTTT
*
125977 AATTTTTTTTATATTTAATTTTTTTTATA
1 AATTTTTTTTATATTTAA-TTTTTGTATA
126006 AATTTTTTTTAATTATTTAA-TTTTGTATA
1 AATTTTTTTT-A-TATTTAATTTTTGTATA
126035 TTCTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 18 0.69
30 1 0.04
31 7 0.27
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
AATTTTTTTTATATTTAATTTTTGTATA
Found at i:143175 original size:14 final size:14
Alignment explanation
Indices: 143158--143184 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
143148 AAGAGAGCAG
143158 AAAAAGAAATAATA
1 AAAAAGAAATAATA
143172 AAAAAGAAATAAT
1 AAAAAGAAATAAT
143185 TGTTGGTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAAGAAATAATA
Found at i:143378 original size:2 final size:2
Alignment explanation
Indices: 143373--143399 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
143363 TTTTTCTATG
143373 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
143400 TTCATATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:148390 original size:14 final size:14
Alignment explanation
Indices: 148371--148405 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
148361 ACAGCATCTT
148371 GCTGGAAAATAGGG
1 GCTGGAAAATAGGG
148385 GCTGGAAAATAGGG
1 GCTGGAAAATAGGG
148399 GCTGGAA
1 GCTGGAA
148406 TTGGGGCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.43, T:0.14
Consensus pattern (14 bp):
GCTGGAAAATAGGG
Found at i:156618 original size:5 final size:5
Alignment explanation
Indices: 156608--156633 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
156598 TATTATTATT
156608 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
156634 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:161501 original size:15 final size:16
Alignment explanation
Indices: 161457--161504 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
161447 GTAACTTTAA
161457 TAAATATTAATAATTTTAT
1 TAAA-ATTAATAA--TTAT
*
161476 TAAAATAAATAATTAT
1 TAAAATTAATAATTAT
161492 T-AAATTAATAATT
1 TAAAATTAATAATT
161505 TAGAACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 11 0.41
16 5 0.19
18 7 0.26
19 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAAATTAATAATTAT
Found at i:165043 original size:18 final size:18
Alignment explanation
Indices: 165020--165054 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
165010 AATAAGGAGC
*
165020 AGAAGGAATTGGTTAAAT
1 AGAAGGAATTAGTTAAAT
165038 AGAAGGAATTAGTTAAA
1 AGAAGGAATTAGTTAAA
165055 ATCAAACGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (18 bp):
AGAAGGAATTAGTTAAAT
Found at i:169964 original size:30 final size:30
Alignment explanation
Indices: 169926--169990 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
169916 AAGGGAGATC
169926 AACA-GAACGTGGCTAAAGTAGCAGTCACA
1 AACATGAACGTGGCTAAAGTAGCAGTCACA
169955 AACATGAACGTGGCTAAAGTAGCAGTCACA
1 AACATGAACGTGGCTAAAGTAGCAGTCACA
169985 AACATG
1 AACATG
169991 GTAGATCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (30 bp):
AACATGAACGTGGCTAAAGTAGCAGTCACA
Found at i:175763 original size:65 final size:65
Alignment explanation
Indices: 175603--175763 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
175593 TTGTTTAAGG
* * * ** *
175603 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATATGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
175666 A
65 A
*
175667 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
175731 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
175764 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:176115 original size:18 final size:18
Alignment explanation
Indices: 176080--176115 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
176070 AAAATGGGTA
* *
176080 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
176098 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
176116 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:177212 original size:21 final size:21
Alignment explanation
Indices: 177186--177248 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
177176 GTCGAGGGTT
177186 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
177207 TCATAGGTCCTTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
*
177229 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
177249 ATTTCATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:177239 original size:22 final size:22
Alignment explanation
Indices: 177185--177256 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
177175 AGTCGAGGGT
177185 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
177206 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
177228 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
177250 TTTCATA
1 -TTCATA
177257 TGCCACTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.40
22 22 0.49
23 5 0.11
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:180812 original size:65 final size:65
Alignment explanation
Indices: 180652--180812 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
180642 TTATTTAAGG
* * * ** *
180652 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATATGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
180715 A
65 A
*
180716 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
180780 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
180813 ACCTTTATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:181164 original size:18 final size:18
Alignment explanation
Indices: 181130--181164 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
181120 AAATGGGTAT
* *
181130 ATATGTTATATGTATTGC
1 ATATGTTACATGAATTGC
181148 ATATGTTACATGAATTG
1 ATATGTTACATGAATTG
181165 AATGAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (18 bp):
ATATGTTACATGAATTGC
Found at i:182246 original size:21 final size:21
Alignment explanation
Indices: 182220--182260 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
182210 GTCGAGGGTT
182220 TCATAGGTCCTTCAGGACAAC
1 TCATAGGTCCTTCAGGACAAC
*
182241 TCATAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCAGGACAA
182261 ATTCACAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCAGGACAAC
Found at i:182275 original size:22 final size:22
Alignment explanation
Indices: 182219--182290 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
182209 AGTCGAGGGT
*
182219 TTCATAGGTCCTTCAGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
182240 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
* *
182262 TTCACAGGTTCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
182284 TTTCATA
1 -TTCATA
182291 TGCCACTCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.40
22 21 0.49
23 5 0.12
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:191860 original size:2 final size:2
Alignment explanation
Indices: 191853--191881 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
191843 ATGCTCTGTT
191853 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
191882 GAAAGTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:192805 original size:31 final size:31
Alignment explanation
Indices: 192767--192837 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
192757 GTAATACATA
*
192767 TGTATATATGTTAATCAAACTTGGTTGCTGG
1 TGTATATATGCTAATCAAACTTGGTTGCTGG
192798 TGTATATATGCTAATCAAACTTGGTTGCTGG
1 TGTATATATGCTAATCAAACTTGGTTGCTGG
192829 TGTGATATA
1 TGT-ATATA
192838 GGGATATGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 33 0.87
32 5 0.13
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.41
Consensus pattern (31 bp):
TGTATATATGCTAATCAAACTTGGTTGCTGG
Found at i:196353 original size:2 final size:2
Alignment explanation
Indices: 196346--196376 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
196336 TATGTCACTA
196346 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
196377 CATTTTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:201722 original size:37 final size:36
Alignment explanation
Indices: 201678--201796 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
201668 TGGCAACCAA
201678 CTTTGAAAAATTAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TAGTTTTCAAAGTTTGGTAAATGTTT
*
201715 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
201750 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
201787 -GTTGAAAAAT
1 CTTTGAAAAAT
201797 GATAATGGGA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 30 0.39
36 19 0.25
37 27 0.36
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:212101 original size:64 final size:64
Alignment explanation
Indices: 211969--212125 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 64
211959 AATTGGTCTT
* * * *
211969 CAAACTTTTAAATATTTTAATTTCAT-CCC---TAAACTATGTCTCACATTCTAAATTAATCCT
1 CAAACTTTTGAATATTTTAATTTCATCCCCAAAAAAACTATATCTCACATTCTAAATTAATCCC
* * *
212029 GAAGCTTTTGAACATTTTAATTTCATCCCCAAAAAAACTATATC-CATCATTCTAAATTAGA-CC
1 CAAACTTTTGAATATTTTAATTTCATCCCCAAAAAAACTATATCTCA-CATTCTAAATTA-ATCC
212092 C
64 C
* *
212093 CAAACTTTTGAATATTTCAATTTCATCCACAAA
1 CAAACTTTTGAATATTTTAATTTCATCCCCAAA
212126 CTATCAATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
60 22 0.28
61 3 0.04
63 2 0.03
64 51 0.65
65 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (64 bp):
CAAACTTTTGAATATTTTAATTTCATCCCCAAAAAAACTATATCTCACATTCTAAATTAATCCC
Found at i:216123 original size:27 final size:27
Alignment explanation
Indices: 216093--216148 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
216083 TAGATCTAGG
*
216093 ACAATCAAATTTAATAATTTATTATAC
1 ACAATCAAATTTAACAATTTATTATAC
216120 ACAATCAAATTTAACAATTTATTATAC
1 ACAATCAAATTTAACAATTTATTATAC
216147 AC
1 AC
216149 GTCTCTATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (27 bp):
ACAATCAAATTTAACAATTTATTATAC
Found at i:219703 original size:17 final size:18
Alignment explanation
Indices: 219655--219703 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
219645 TTAAAAAATA
219655 ATATTTTGATTAATTATT
1 ATATTTTGATTAATTATT
219673 AT-TTTATGGAATTAATTATT
1 ATATTT-T-G-ATTAATTATT
219693 ATATTTT-ATTA
1 ATATTTTGATTA
219704 TTTCACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
17 7 0.26
18 3 0.11
19 1 0.04
20 13 0.48
21 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
ATATTTTGATTAATTATT
Found at i:220308 original size:6 final size:6
Alignment explanation
Indices: 220297--220346 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
220287 GTGACTATGA
220297 GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT
1 GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT GGGTGT
220345 GG
1 GG
220347 TTGGTTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (6 bp):
GGGTGT
Found at i:221220 original size:2 final size:2
Alignment explanation
Indices: 221213--221247 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
221203 CTTATAACGG
221213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
221248 AAAATTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:221324 original size:24 final size:24
Alignment explanation
Indices: 221286--221355 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
221276 CAAATCAGAG
* *
221286 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
221310 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
221334 TCCATGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
221356 CTATTTATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:221355 original size:48 final size:47
Alignment explanation
Indices: 221261--221355 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 47
221251 ATTAAAACAT
* ** *
221261 AATTCAGGTCAAATACAAATCAGAGTCCATGTCAAGTATCATATAAA
1 AATTCAGGTCAAATACAAATCAGAATCCATGTCAAAAATCAGATAAA
*
221308 AATTCAGGTCAAATATCATATCAGAATCCATGTCAAAAATCAGATAAA
1 AATTCAGGTCAAATA-CAAATCAGAATCCATGTCAAAAATCAGATAAA
221356 CTATTTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 15 0.36
48 27 0.64
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (47 bp):
AATTCAGGTCAAATACAAATCAGAATCCATGTCAAAAATCAGATAAA
Found at i:222120 original size:57 final size:57
Alignment explanation
Indices: 222051--222207 Score: 205
Period size: 57 Copynumber: 2.7 Consensus size: 57
222041 ATTTTTAAAA
222051 TAATTACCAAAATAGCAACTTTTCGAATTAAATTCCCAAAATAGCA-CTTTTCGAAT
1 TAATTACCAAAATAGCAACTTTTCGAATTAAATTCCCAAAATAGCACCTTTTCGAAT
*
222107 TAAATTACCAAAATAGC-ACATTTTCCGAA-TAAATTCCCAAAATAGCACTCTTTTTGAAT
1 T-AATTACCAAAATAGCAAC-TTTT-CGAATTAAATTCCCAAAATAGCAC-CTTTTCGAAT
* * *
222166 TAATTCCCAAAATAGCACCTATTTCGTATT-AATTCCCAAAAT
1 TAATTACCAAAATAGCAACT-TTTCGAATTAAATTCCCAAAAT
222208 GTCACCCGGT
Statistics
Matches: 89, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
56 3 0.03
57 37 0.42
58 34 0.38
59 15 0.17
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.32
Consensus pattern (57 bp):
TAATTACCAAAATAGCAACTTTTCGAATTAAATTCCCAAAATAGCACCTTTTCGAAT
Found at i:222203 original size:58 final size:56
Alignment explanation
Indices: 222031--222207 Score: 221
Period size: 58 Copynumber: 3.1 Consensus size: 56
222021 CATTTTACAG
* * *
222031 AAATAGCATCATTTTTAAAATAATTACCAAAATAGCAACTTTTCGAATTAAATTCCCA
1 AAATAGCATC-TTTTTGAATTAATTACCAAAATAGCACCTTTTCGAATT-AATTCCCA
* * *
222089 AAATAGCA-CTTTTCGAATTAAATTACCAAAATAGCACATTTTCCGAATAAATTCCCA
1 AAATAGCATCTTTTTGAATT-AATTACCAAAATAGCACCTTTT-CGAATTAATTCCCA
* *
222146 AAATAGCACTCTTTTTGAATTAATTCCCAAAATAGCACCTATTTCGTATTAATTCCCA
1 AAATAGCA-TCTTTTTGAATTAATTACCAAAATAGCACCT-TTTCGAATTAATTCCCA
222204 AAAT
1 AAAT
222208 GTCACCCGGT
Statistics
Matches: 103, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
56 7 0.07
57 37 0.36
58 46 0.45
59 13 0.13
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (56 bp):
AAATAGCATCTTTTTGAATTAATTACCAAAATAGCACCTTTTCGAATTAATTCCCA
Found at i:222213 original size:29 final size:28
Alignment explanation
Indices: 222051--222207 Score: 199
Period size: 29 Copynumber: 5.5 Consensus size: 28
222041 ATTTTTAAAA
* *
222051 TAATTACCAAAATAGCAACTTTTCGAAT
1 TAATTCCCAAAATAGCACCTTTTCGAAT
222079 TAAATTCCCAAAATAGCA-CTTTTCGAAT
1 T-AATTCCCAAAATAGCACCTTTTCGAAT
* *
222107 TAAATTACCAAAATAGCACATTTTCCGAAT
1 T-AATTCCCAAAATAGCACCTTTT-CGAAT
* *
222137 AAATTCCCAAAATAGCACTCTTTTTGAAT
1 TAATTCCCAAAATAGCAC-CTTTTCGAAT
*
222166 TAATTCCCAAAATAGCACCTATTTCGTAT
1 TAATTCCCAAAATAGCACCT-TTTCGAAT
222195 TAATTCCCAAAAT
1 TAATTCCCAAAAT
222208 GTCACCCGGT
Statistics
Matches: 114, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
28 30 0.26
29 75 0.66
30 9 0.08
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.32
Consensus pattern (28 bp):
TAATTCCCAAAATAGCACCTTTTCGAAT
Found at i:222239 original size:12 final size:13
Alignment explanation
Indices: 222222--222250 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
222212 CCCGGTCAAC
222222 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
222234 GGTCAACGGGTCG
1 GGTCAACGGGTCG
222247 GGTC
1 GGTC
222251 GGATCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:224409 original size:14 final size:14
Alignment explanation
Indices: 224372--224411 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
224362 TGTTTTTTGT
224372 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
* *
224385 GTTTATATTCGTTC
1 GTTTGTGTTCGTTC
224399 GTTTGTGTTCGTT
1 GTTTGTGTTCGTT
224412 TATCATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.05, C:0.10, G:0.25, T:0.60
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:225698 original size:20 final size:20
Alignment explanation
Indices: 225614--225691 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
225604 GAATACCAGT
* *
225614 TTCGCAACACAGTTTTCAAA
1 TTCGCAACGCGGTTTTCAAA
* * *
225634 TTAGCAACGCGATTCTCCAAA
1 TTCGCAACGCGGTT-TTCAAA
*
225655 ATCGCAACGCGGTTTTCAAA
1 TTCGCAACGCGGTTTTCAAA
225675 TTCGCAACGCGGTTTTC
1 TTCGCAACGCGGTTTTC
225692 GTTTTCGTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 31 0.66
21 16 0.34
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGGTTTTCAAA
Found at i:225763 original size:71 final size:70
Alignment explanation
Indices: 225657--225795 Score: 188
Period size: 71 Copynumber: 2.0 Consensus size: 70
225647 TCTCCAAAAT
* * * ** * * *
225657 CGCAACGCGGTTTTCAAATTCGCAACGCGGTTTTCGTTTTCGTAATGCTAATTATCGATATAGGT
1 CGCAACGCGATTTCCAAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATAGGT
225722 AAACA
66 AAACA
*
225727 CGCAACGCGATTCTCCAAAATCGCAACGTGAATTTCGTTTTCGCAACGCTAATTACCGATATAGG
1 CGCAACGCGATT-TCCAAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATAGG
225792 TAAA
65 TAAA
225796 TACAACTATT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
70 11 0.19
71 48 0.81
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (70 bp):
CGCAACGCGATTTCCAAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCGATATAGGT
AAACA
Found at i:227873 original size:2 final size:2
Alignment explanation
Indices: 227866--227928 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
227856 GTAATCATGC
227866 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
227908 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
227929 GAAAAGTTAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:230378 original size:2 final size:2
Alignment explanation
Indices: 230371--230426 Score: 53
Period size: 2 Copynumber: 28.5 Consensus size: 2
230361 GCGTATAGTC
* * *
230371 AT AT AT AT AT AT AT AT AT AT AT AT AT TT A- AA AA AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
230411 AT AT TT AT AT CAT AT A
1 AT AT AT AT AT -AT AT A
230427 ATTTATATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
1 2 0.04
2 42 0.91
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:230428 original size:18 final size:17
Alignment explanation
Indices: 230364--230426 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
230354 ACTTGTGGCG
*
230364 TATAGTCATATATATATA
1 TATA-TCATATATATATT
230382 TATAT-ATATATATATT
1 TATATCATATATATATT
* **
230398 TAAAAAATATAATATATT
1 TATATCATAT-ATATATT
230416 TATATCATATA
1 TATATCATATA
230427 ATTTATATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.35
17 6 0.16
18 18 0.49
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (17 bp):
TATATCATATATATATT
Found at i:239531 original size:34 final size:34
Alignment explanation
Indices: 239493--239577 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 34
239483 AGTTCTACTT
*
239493 GGACTCAAAATGC-TTCAGTTTTAGTGTTTCAATA
1 GGACTCAAAATACGTT-AGTTTTAGTGTTTCAATA
* *
239527 GGACT-TAAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAAATACGTTAGTTTTAGTGTTTCAATA
*
239560 --ACTC-AAATACGTTGGTTT
1 GGACTCAAAATACGTTAGTTT
239578 ATTTTCTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
31 17 0.37
33 22 0.48
34 7 0.15
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (34 bp):
GGACTCAAAATACGTTAGTTTTAGTGTTTCAATA
Found at i:239571 original size:31 final size:32
Alignment explanation
Indices: 239510--239577 Score: 111
Period size: 31 Copynumber: 2.1 Consensus size: 32
239500 AAATGCTTCA
*
239510 GTTTTAGTGTTTCAATAGGACTTAAATACGTTG
1 GTTTTAGTGTTTCAATA-GACTCAAATACGTTG
239543 GTTTTAGTGTTTCAATA-ACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAGACTCAAATACGTTG
239574 GTTT
1 GTTT
239578 ATTTTCTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 17 0.50
33 17 0.50
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.44
Consensus pattern (32 bp):
GTTTTAGTGTTTCAATAGACTCAAATACGTTG
Found at i:239686 original size:20 final size:20
Alignment explanation
Indices: 239626--239679 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
239616 AGGCCTGTAA
*
239626 AAAT-AATAA-AATAAAAAT
1 AAATAAATAATAATAATAAT
* *
239644 ATATTAATAATAATAATAAT
1 AAATAAATAATAATAATAAT
239664 AAATAAATATATAATA
1 AAATAAATA-ATAATA
239680 TAGTAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 15 0.52
21 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATAAATAATAATAATAAT
Found at i:240156 original size:84 final size:83
Alignment explanation
Indices: 240028--241125 Score: 970
Period size: 84 Copynumber: 13.3 Consensus size: 83
240018 AGCTTAATGG
* * * *
240028 AATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT-
* * * *
240090 GTTCCTTTGAGCTGAGTGG
65 GTGCCTTAGAGCTGAGCGT
* * * * * * * *
240109 AGTCTAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAGTTATGCCGTAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * *
240174 TGCCCTCAAAACTGAGTGT
66 TG-CCTTAGAGCTGAGCGT
* *
240193 AATCGAACTCGAGGGTCTTTG--G-CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* *
240255 TGCCTTGGAGCTAAGCGT
66 TGCCTTAGAGCTGAGCGT
* *
240273 AGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* *
240338 ATGCCTTGGAGCTGAGCGT
65 GTGCCTTAGAGCTGAGCGT
* * * * * * * * * *
240357 AGTCGAACTCGAAGGTATTTTGGTCACAAATAACCCTTCTAGCCTTGAGTTATGATGTAAATGAT
1 AATCGAACTCGAAGGT-CTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * *
240422 GTGCCCTCGAAGCTGAGTGT
65 GTGCCTTAG-AGCTGAGCGT
* * * * * * * *
240442 AATAGAATTCGAGGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCCGTAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* *
240507 TGCCTTCAAAGCTGAGTGT
66 TGCCTT-AGAGCTGAGCGT
* *
240526 AATCGAACTCGAGGGTCTTTG--G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
*
240588 TGCCTTAGAGCTGAGCAT
66 TGCCTTAGAGCTGAGCGT
* *
240606 AGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * *
240671 ATGCCTTGGAGCTAAGCGT
65 GTGCCTTAGAGCTGAGCGT
* ** * * * * * * *
240690 AGTTAAACTCAAAGGT-TTT-TTGGACATAGATAACCCTTATAGCCTTGAGTTATGTTGTAAATG
1 AATCGAACTCGAAGGTCTTTGTT-GAC--AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
* * *
240753 ATGTGCCCTCGAAGCTGAGTGT
63 ATGTGCCTTAG-AGCTGAGCGT
* * * *
240775 AATCGAACTCGAGGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAAGTTATG-T--AAATCATA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
*
240834 TGCCCTAGAGCTGAGCGT
66 TGCCTTAGAGCTGAGCGT
* * * *
240852 AATTGAACTCGAAAGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * * *
240917 ATGTCTTGGGGCTGAGCGT
65 GTGCCTTAGAGCTGAGCGT
* * * * * * * *
240936 AGTCGAAATCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 AATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * * *
241001 ATGCCCTCGAAGCTGAGTGT
65 GTGCCTTAG-AGCTGAGCGT
* * * * *
241021 AATCGAACTCGAGGGTCTTCGGTTGGCAGATAACCCTTTTTGACTTAAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * * *
241086 ATGTCTTGGAGCTGAGCAT
65 GTGCCTTAGAGCTGAGCGT
* *
241105 AGTCGAACTCGAAGGCCTTTG
1 AATCGAACTCGAAGGTCTTTG
241126 GTGGGCACGA
Statistics
Matches: 832, Mismatches: 154, Indels: 60
0.80 0.15 0.06
Matches are distributed among these distances:
77 26 0.03
78 14 0.02
80 57 0.07
81 148 0.18
82 5 0.01
83 10 0.01
84 459 0.55
85 110 0.13
86 3 0.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (83 bp):
AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
TGCCTTAGAGCTGAGCGT
Found at i:240550 original size:249 final size:248
Alignment explanation
Indices: 240011--241127 Score: 1216
Period size: 249 Copynumber: 4.5 Consensus size: 248
240001 CGGTTGATAC
* * * * * * * *
240011 GCCCTCG-AGCTTAATGGAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCT
1 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTT
* * * * * *
240075 ATGCTGCAAATGATGGTTCCTTTGAGCTGAGTGGAGTCTAACTCGAAGGTCTTT-GTTGACAGAT
66 ATGCTGCAAATGAT-ATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGAT
* * * * * * * * * *
240139 AACTCTTCTAGCCTTGAGTTATGCCGTAAATGATGTGCCCTCAAAACTGAGTGTAATCGAACTCG
130 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTCGAAGCTGAGCGTAATAGAACTCG
* * * *
240204 AGGGTCTTTG--G-CAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
194 AAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * * * * *
240256 G-CCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTA
* * *
240320 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGG-TCAC
62 AGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGGTTGAC
* * * * * * *
240384 AAATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGAAGCTGAGTGTAATAGAA
126 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTCGAAGCTGAGCGTAATAGAA
* * *
240449 TTCGAGGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCCGTAAATGATGT
190 CTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* * *
240508 GCCTTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCT
1 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTT
* * *
240573 ATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATA
66 ATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATA
* * * * * *
240638 ACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTAAGCGTAGTTA-AACTCAA
131 ACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTCGAAGCTGAGCGTA-ATAGAACTCGA
* *
240702 AGGT-TTT-TTGGACATAGATAACCCTTATAGCCTTGAGTTATGTTGTAAATGATGT
195 AGGTCTTTGTT-GAC--AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
*
240757 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTT
1 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTT
* * * * * *
240822 ATG-T--AAATCATATGCCCTAGAGCTGAGCGTAATTGAACTCGAAAGTCTTTGGTTGGCAGATA
66 ATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATA
* * * * ** * * *
240884 ACCTTTCTCGACTTAAGTTATGCTGCAAATGATATGTCTTGGGGCTGAGCGTAGTCGAAATCGAA
131 ACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTCGAAGCTGAGCGTAATAGAACTCGAA
* * *
240949 GGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATAT
196 GGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* *
241003 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTCGGTTGGCAGATAACCCTTTTTGACTTA
1 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-T---TTGGCAGATAACCCTTCTCGACTTA
* * * *
241068 AGTTATGCTGCAAATGATATGTCTTGGAGCTGAGCATAGTCGAACTCGAAGGCCTTTGGT
62 AGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
241128 GGGCACGATT
Statistics
Matches: 746, Mismatches: 99, Indels: 46
0.84 0.11 0.05
Matches are distributed among these distances:
244 4 0.01
245 24 0.03
246 183 0.25
247 8 0.01
248 61 0.08
249 330 0.44
250 30 0.04
251 3 0.00
252 38 0.05
253 65 0.09
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (248 bp):
GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTT
ATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGACAGATA
ACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTCGAAGCTGAGCGTAATAGAACTCGAA
GGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
Found at i:240659 original size:333 final size:331
Alignment explanation
Indices: 240030--241032 Score: 1326
Period size: 333 Copynumber: 3.0 Consensus size: 331
240020 CTTAATGGAA
* * * * * *
240030 TCGAACTCGAAGGTCTTTGG--CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGGTT
1 TCGAACTCGAAGGTTTTTGGCACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGAT-GTG
* * * * * * *
240093 CCTTTG-AGCTGAGTGGAGTCTAACTCGAAGGTCTTTGTTGACAGATAACTCTTCTAGCCTTGAG
65 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAG
*
240157 TTATGCCGTAAATGATGTGCCCTCAAAACTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAA
130 TTATGCCGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAA
* *
240222 CCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAACTCGAAG
195 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
240287 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTG
260 GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTG
240352 AGCGTAG
325 AGCGTAG
*
240359 TCGAACTCGAAGGTATTTTGGTCACAAATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGT
1 TCGAACTCGAAGGT-TTTTGG-CACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGT
* *
240424 GCCCTCGAAGCTGAGTGTAATAGAATTCGAGGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGA
64 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGA
*
240489 GTTATGCCGTAAATGATGTGCCTTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATA
129 GTTATGCCGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATA
* * *
240554 ACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTCGAACTCGAA
194 ACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
240619 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCT
259 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCT
*
240684 AAGCGTAG
324 GAGCGTAG
** * * * *
240692 TTAAACTCAAAGGTTTTTTGGACATAGATAACCCTTATAGCCTTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGG-TTTTTGG-CACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGT
* * * *
240757 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAA
64 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGA
* * * * * **
240819 GTTAT---GTAAATCATATGCCCT-AGAGCTGAGCGTAATTGAACTCGAAAGTCTTTGGTTGGCA
129 GTTATGCCGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCA
* * * * *
240880 GATAACCTTTCTCGACTTAAGTTATGCTGCAAATGATATGTCTTGGGGCTGAGCGTAGTCGAAAT
190 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
** * * * * *
240945 CGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTC
255 CGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTT
* * *
241009 GAAGCTGAGTGTAA
318 GGAGCTGAGCGTAG
241023 TCGAACTCGA
1 TCGAACTCGA
241033 GGGTCTTCGG
Statistics
Matches: 594, Mismatches: 68, Indels: 22
0.87 0.10 0.03
Matches are distributed among these distances:
326 24 0.04
327 13 0.02
328 1 0.00
329 14 0.02
330 138 0.23
331 26 0.04
332 6 0.01
333 371 0.62
334 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (331 bp):
TCGAACTCGAAGGTTTTTGGCACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGATGTGC
CCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGT
TATGCCGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAAC
CCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
TCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGA
GCGTAG
Found at i:241231 original size:34 final size:34
Alignment explanation
Indices: 241138--241231 Score: 88
Period size: 34 Copynumber: 2.8 Consensus size: 34
241128 GGGCACGATT
*
241138 CCCTTCGTCGTGAAGTTGAAACC---GTGGATAG
1 CCCTTCGTCGTGAAGTTGAAACCAAATTGGATAG
* **
241169 CCCATTCGTTGTGAAGTTGAGCCTCAAATTGGATA-
1 CCC-TTCGTCGTGAAGTTGAAAC-CAAATTGGATAG
*
241204 TCCTTCGTCGTGAAGTTGAAATCCAAAT
1 CCCTTCGTCGTGAAGTTGAAA-CCAAAT
241232 ATTTTTGTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
31 3 0.06
32 16 0.33
33 1 0.02
34 20 0.41
35 3 0.06
36 6 0.12
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (34 bp):
CCCTTCGTCGTGAAGTTGAAACCAAATTGGATAG
Found at i:241558 original size:110 final size:110
Alignment explanation
Indices: 241237--241888 Score: 983
Period size: 110 Copynumber: 6.0 Consensus size: 110
241227 CAAATATTTT
* * * * ** * *
241237 TGTTGTTTCGAGGCCGATATCCTTTGCCATGAAATTGAAATTGACT-T---TGAAACTGGAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
* * * * *
241298 TATTTGTTGACA-ACTAGTCACCCATTCGCTGTGAAGTTGGGCTTG
66 TGTTTGTTGACAGTC-AGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
* * *
241343 TGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATCGACTC-AAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
*
241407 TGTTTGTTGACAGTCAGTCGCCTCTTCGCTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
*
241452 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
* * *
241517 TATTTATTGACAGTCAGTCTCCCCTTCGCTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
* *
241562 TGTTGTCTCGAGTCCAATATTCTTCGCTGTGAAATTGAAATTGACTCTGAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
*
241627 TGTTTGTTAACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
*
241672 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
*
241737 TGTTTGTTGACAGTCAGTCGCCTCTTCGCTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
* * *
241782 TATTGTCTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
*
241847 TGTTTGTTGACCGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
241889 AACCACCATC
Statistics
Matches: 500, Mismatches: 40, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
106 37 0.07
109 95 0.19
110 368 0.74
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (110 bp):
TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
Found at i:244490 original size:15 final size:16
Alignment explanation
Indices: 244470--244500 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
244460 TATGCAAGTG
244470 ATGAAAAT-AAAATAA
1 ATGAAAATGAAAATAA
244485 ATGAAAATGAAAATAA
1 ATGAAAATGAAAATAA
244501 TTAGTGAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
ATGAAAATGAAAATAA
Found at i:245447 original size:13 final size:13
Alignment explanation
Indices: 245429--245470 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
245419 TAAACATGAG
245429 AAAATAATAATAA
1 AAAATAATAATAA
245442 AAAATAATAATATA
1 AAAATAATAATA-A
* *
245456 ATAATATTAATAA
1 AAAATAATAATAA
245469 AA
1 AA
245471 TGAAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:245485 original size:27 final size:25
Alignment explanation
Indices: 245430--245486 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
245420 AAACATGAGA
* *
245430 AAATAATAATAAAAAATAATAATAT
1 AAATAATAATAAAAAATAAAAAAAT
*
245455 -AATAATATTAATAAAATGAAAAAAAT
1 AAATAATAATAA-AAAAT-AAAAAAAT
245481 AAATAA
1 AAATAA
245487 ATAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 10 0.38
25 5 0.19
26 6 0.23
27 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (25 bp):
AAATAATAATAAAAAATAAAAAAAT
Found at i:245494 original size:32 final size:31
Alignment explanation
Indices: 245431--245502 Score: 76
Period size: 32 Copynumber: 2.2 Consensus size: 31
245421 AACATGAGAA
245431 AATAATAATAAAAAATAATAATATAATAATATT
1 AATAA-AATAAAAAATAATAATATAATAATA-T
*
245464 AATAAAATGAAAAA-AATAA-ATAAATAAATAT
1 AATAAAATAAAAAATAATAATAT-AAT-AATAT
245495 ATATAAAA
1 A-ATAAAA
245503 CAATGTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
30 2 0.06
31 10 0.29
32 18 0.51
33 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (31 bp):
AATAAAATAAAAAATAATAATATAATAATAT
Found at i:245513 original size:35 final size:34
Alignment explanation
Indices: 245439--245513 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 34
245429 AAAATAATAA
245439 TAAAAAATAATAATATAATAATATTAATAAAATG
1 TAAAAAATAATAATATAATAATATTAATAAAATG
*
245473 AAAAAAATAAATAA-ATAA-ATATATATAA-AACAATG
1 TAAAAAAT-AATAATATAATA-ATAT-TAATAA-AATG
245508 TAAAAA
1 TAAAAA
245514 GAAAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
33 1 0.03
34 17 0.49
35 17 0.49
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (34 bp):
TAAAAAATAATAATATAATAATATTAATAAAATG
Found at i:245902 original size:34 final size:35
Alignment explanation
Indices: 245864--245950 Score: 103
Period size: 33 Copynumber: 2.6 Consensus size: 35
245854 AGTTTTACTT
*
245864 GGACTCAAAATGC-TTCGGTTTTAGTGTTTCAA-TA
1 GGACTCAAAATACGTT-GGTTTTAGTGTTTCAATTA
*
245898 GGACT-TAAATACGTTGGTTTTAGTGTTTCAATTA
1 GGACTCAAAATACGTTGGTTTTAGTGTTTCAATTA
*
245932 -GACTC-AAATATGTTGGTTT
1 GGACTCAAAATACGTTGGTTT
245951 ATTTTATGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
33 38 0.81
34 9 0.19
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.41
Consensus pattern (35 bp):
GGACTCAAAATACGTTGGTTTTAGTGTTTCAATTA
Found at i:245921 original size:33 final size:33
Alignment explanation
Indices: 245880--245950 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
245870 AAAATGCTTC
*
245880 GGTTTTAGTGTTTCAA-TAGGACTTAAATACGTT
1 GGTTTTAGTGTTTCAATTA-GACTCAAATACGTT
*
245913 GGTTTTAGTGTTTCAATTAGACTCAAATATGTT
1 GGTTTTAGTGTTTCAATTAGACTCAAATACGTT
245946 GGTTT
1 GGTTT
245951 ATTTTATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.45
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATTAGACTCAAATACGTT
Found at i:252223 original size:29 final size:31
Alignment explanation
Indices: 252191--252249 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
252181 TGTATGGTTT
*
252191 TGAAAC-AAA-TAAAAATTTAAGTATTAAAA
1 TGAAACAAAACTAAAAATTTAAGTAATAAAA
*
252220 TGAAACAAAACTAATAATTTAAGTAATAAA
1 TGAAACAAAACTAAAAATTTAAGTAATAAA
252250 TGTATATCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 3 0.12
31 17 0.65
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (31 bp):
TGAAACAAAACTAAAAATTTAAGTAATAAAA
Found at i:253828 original size:17 final size:19
Alignment explanation
Indices: 253806--253844 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
253796 CATTAGTCTA
*
253806 ATAACGATA-TGATT-TGT
1 ATAACGAAATTGATTATGT
253823 ATAACGAAATTGATTATGT
1 ATAACGAAATTGATTATGT
253842 ATA
1 ATA
253845 TCAGGGCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 5 0.26
19 6 0.32
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (19 bp):
ATAACGAAATTGATTATGT
Found at i:253985 original size:56 final size:56
Alignment explanation
Indices: 253909--254037 Score: 186
Period size: 56 Copynumber: 2.3 Consensus size: 56
253899 CTATTTTTTT
* * * * *
253909 TAGATATATTCAATTCCGGGACCCCTATTTTTATATTTTTTAATGACAACAACTGA
1 TAGATATACTCAATTTCGGGACCCCTATTTTTATACTTCTTAATGACAACAACTAA
* * *
253965 TAGATATACTCGATTTCGGGACCTCTATTTTTATGCTTCTTAATGACAACAACTAA
1 TAGATATACTCAATTTCGGGACCCCTATTTTTATACTTCTTAATGACAACAACTAA
254021 TAGATATACTCAATTTC
1 TAGATATACTCAATTTC
254038 TACTTATTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (56 bp):
TAGATATACTCAATTTCGGGACCCCTATTTTTATACTTCTTAATGACAACAACTAA
Found at i:271330 original size:163 final size:163
Alignment explanation
Indices: 271060--271386 Score: 638
Period size: 163 Copynumber: 2.0 Consensus size: 163
271050 TAGGTATAAC
271060 ACTTAAAGAAATACAAAGAAAGGGTCGAAGGGAACCAAGGTTGAAATTAAAGAAAATGGATTGAA
1 ACTTAAAGAAATACAAAGAAAGGGTCGAAGGGAACCAAGGTTGAAATTAAAGAAAATGGATTGAA
271125 AACAAAGGAGGAAATTAGAGAATCAGCTAACCCTGGGAAAAAGGGAAAGTTTTCCTGGA-TTGAG
66 AACAAAGGAGGAAATTAGAGAATCAGCTAACCCTGGGAAAAAGGGAAAGTTTTCCTGGATTTGAG
271189 TTTGTTTTCGTGTTTTTTTAATGTTTGGAACGGG
131 TTTGTTTTCGT-TTTTTTTAATGTTTGGAACGGG
271223 ACTTAAAGAAATACAAAGAAAGGGTCGAAGGGAACCAAGGTTGAAATTAAAGAAAATGGATTGAA
1 ACTTAAAGAAATACAAAGAAAGGGTCGAAGGGAACCAAGGTTGAAATTAAAGAAAATGGATTGAA
271288 AACAAAGGAGGAAATTAGAGAATCAGCTAACCCTGGGAAAAAGGGAAAGTTTTCCTGGATTTGAG
66 AACAAAGGAGGAAATTAGAGAATCAGCTAACCCTGGGAAAAAGGGAAAGTTTTCCTGGATTTGAG
271353 TTTGTTTTCGTTTTTTTTAATGTTTGGAACGGG
131 TTTGTTTTCGTTTTTTTTAATGTTTGGAACGGG
271386 A
1 A
271387 AATTATACCG
Statistics
Matches: 163, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
163 147 0.90
164 16 0.10
ACGTcount: A:0.39, C:0.09, G:0.26, T:0.26
Consensus pattern (163 bp):
ACTTAAAGAAATACAAAGAAAGGGTCGAAGGGAACCAAGGTTGAAATTAAAGAAAATGGATTGAA
AACAAAGGAGGAAATTAGAGAATCAGCTAACCCTGGGAAAAAGGGAAAGTTTTCCTGGATTTGAG
TTTGTTTTCGTTTTTTTTAATGTTTGGAACGGG
Done.