Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004049.1 Hibiscus syriacus cultivar Beakdansim tig00008847_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: 82303
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7042 original size:21 final size:21
Alignment explanation
Indices: 7018--7058 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7008 ACGTTTTCAC
*
7018 CTTTCACTTTCTATCTTTTTA
1 CTTTCACTTTCTATCATTTTA
* *
7039 CTTTTACTTTTTATCATTTT
1 CTTTCACTTTCTATCATTTT
7059 CTTCTCCCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.66
Consensus pattern (21 bp):
CTTTCACTTTCTATCATTTTA
Found at i:9621 original size:20 final size:20
Alignment explanation
Indices: 9596--9638 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
9586 TCTAAAGGCC
9596 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
9616 CATTTAGAAGCATTTAGTTG
1 CATTTAGAACCATATAGATG
9636 CAT
1 CAT
9639 GTAGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:11147 original size:21 final size:20
Alignment explanation
Indices: 11122--11168 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
11112 TTTGCCACAT
11122 CATTTTCA-ATTACCATCATTC
1 CATTTTCACATTACC-T-ATTC
* *
11143 CATTTCCACATTAGCTATTC
1 CATTTTCACATTACCTATTC
11163 CATTTT
1 CATTTT
11169 GCCACAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.41
21 8 0.36
22 5 0.23
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.45
Consensus pattern (20 bp):
CATTTTCACATTACCTATTC
Found at i:18894 original size:22 final size:22
Alignment explanation
Indices: 18868--18971 Score: 113
Period size: 23 Copynumber: 4.7 Consensus size: 22
18858 ATAGGGCAGA
* *
18868 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
18890 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
* *
18913 GGGAACCTATTCCCCATTTGAAG
1 GGGAACCGATTCCCC-CTTGAAG
*
18936 GGGAACCAATTCCCCCTT--AG
1 GGGAACCGATTCCCCCTTGAAG
* *
18956 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
18972 CTGGGGTTCT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
20 15 0.21
22 16 0.23
23 40 0.56
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:18910 original size:23 final size:23
Alignment explanation
Indices: 18868--18953 Score: 120
Period size: 23 Copynumber: 3.8 Consensus size: 23
18858 ATAGGGCAGA
* *
18868 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
18890 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
18913 GGGAACCTATTCCCCATTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
18936 GGGAACCAATTCCCCCTT
1 GGGAACCGATTCCCCCTT
18954 AGGGGAATCG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 14 0.25
23 43 0.75
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.22
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:22461 original size:25 final size:24
Alignment explanation
Indices: 22398--22505 Score: 79
Period size: 24 Copynumber: 4.6 Consensus size: 24
22388 TAAGTAAAAT
*
22398 AAAAT-ATATATATAAAAAAAATA
1 AAAATAATATATATAAAAAAAAGA
* *
22421 TAAAA-AATA-A-AGAAAAAGAAGA
1 -AAAATAATATATATAAAAAAAAGA
22443 AAAAT-ATATATA-AATAAAACAA-A
1 AAAATAATATATATAA-AAAA-AAGA
*
22466 TAAATAATA-ATAATAAAAAAAAGTA
1 AAAATAATATAT-ATAAAAAAAAG-A
22491 AAAATAATATATATA
1 AAAATAATATATATA
22506 TATATATAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 23
0.69 0.06 0.24
Matches are distributed among these distances:
21 7 0.11
22 12 0.18
23 14 0.21
24 17 0.26
25 14 0.21
26 2 0.03
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (24 bp):
AAAATAATATATATAAAAAAAAGA
Found at i:22467 original size:47 final size:48
Alignment explanation
Indices: 22389--22505 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 48
22379 ATAAAATAGT
22389 AAGTAAAATAAA-ATATATATATAAAAAAAAT-ATAA-AA-AATAAAGAAA
1 AAGTAAAA-AAATATATATA-ATAAAAAAAATAATAATAATAATAAA-AAA
*
22436 AAG-AAGAAAAATATATATAAATAAAACAAATAAATAATAATAATAAAAAA
1 AAGTAA-AAAAATATATAT-AATAAAAAAAAT-AATAATAATAATAAAAAA
22486 AAGTAAAAATAATATATATA
1 AAGTAAAAA-AATATATATA
22506 TATATATAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
46 5 0.08
47 21 0.35
48 1 0.02
49 4 0.07
50 12 0.20
51 17 0.28
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.22
Consensus pattern (48 bp):
AAGTAAAAAAATATATATAATAAAAAAAATAATAATAATAATAAAAAA
Found at i:22500 original size:51 final size:48
Alignment explanation
Indices: 22389--22559 Score: 144
Period size: 51 Copynumber: 3.6 Consensus size: 48
22379 ATAAAATAGT
* * *
22389 AAGT-AAAATAAAATATATATATAAAAAAAATATAAAAAATAAAGAAA
1 AAGTAAAAATAATATATATAAATAAAAAAAAAATAAAAAATAAAGAAA
22436 AAG-AAGAAA-AATATATATAAATAAAACAAATAAATAATAATAATAAA-AAA
1 AAGTAA-AAATAATATATATAAATAAAA-AAA-AAATAA-AA-AATAAAGAAA
* * * *
22486 AAGTAAAAATAATATATATATATATATAATAAATAAAAACATAAA-AAA
1 AAGTAAAAATAATATATATAAATAAAAAAAAAATAAAAA-ATAAAGAAA
* *
22534 TAGT--AAAT-ATATATA-AATTAAAAAAA
1 AAGTAAAAATAATATATATAAATAAAAAAA
22560 TGGATAATAA
Statistics
Matches: 102, Mismatches: 13, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
44 6 0.06
45 7 0.07
46 4 0.04
47 20 0.20
48 19 0.19
49 11 0.11
50 13 0.13
51 22 0.22
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (48 bp):
AAGTAAAAATAATATATATAAATAAAAAAAAAATAAAAAATAAAGAAA
Found at i:23208 original size:37 final size:37
Alignment explanation
Indices: 23158--23228 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
23148 TTGTGGAGTC
*
23158 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATACTAAAACTCTATCA
*
23195 TATTTTTAGGAGTTTGAATCCTACTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATACTAAAACTCTA
23229 ACGTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATACTAAAACTCTATCA
Found at i:23794 original size:18 final size:18
Alignment explanation
Indices: 23762--23799 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
23752 AATAAGGTAC
*
23762 AAATGTGTAAAAC-AACA
1 AAATGTATAAAACAAACA
23779 AAATGTATACAAACAAACA
1 AAATGTATA-AAACAAACA
23798 AA
1 AA
23800 GGAAGGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 4 0.22
19 6 0.33
ACGTcount: A:0.63, C:0.13, G:0.08, T:0.16
Consensus pattern (18 bp):
AAATGTATAAAACAAACA
Found at i:25657 original size:20 final size:20
Alignment explanation
Indices: 25627--25685 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
25617 CACTGAATAT
*
25627 TTGTCCTGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* * *
25647 TTGTTCCGAAGAACCA-TTA
1 TTGTCCCGAAGGACCACTGA
*
25666 -TGTCCCGAAAGACCACTGA
1 TTGTCCCGAAGGACCACTGA
25685 T
1 T
25686 AATCCCTCGA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
18 12 0.41
19 4 0.14
20 13 0.45
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:27821 original size:13 final size:14
Alignment explanation
Indices: 27797--27827 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
27787 GGAGATACGG
27797 GAAGAGAGGAAGAA
1 GAAGAGAGGAAGAA
27811 GAAGA-AGGAAGAA
1 GAAGAGAGGAAGAA
27824 GAAG
1 GAAG
27828 TTCTGGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (14 bp):
GAAGAGAGGAAGAA
Found at i:30747 original size:8 final size:8
Alignment explanation
Indices: 30734--32001 Score: 1920
Period size: 8 Copynumber: 160.5 Consensus size: 8
30724 AAATATATAT
30734 ATACATAC
1 ATACATAC
30742 ATACATAC
1 ATACATAC
30750 ATACATAC
1 ATACATAC
30758 ATACATAC
1 ATACATAC
30766 ATACATAC
1 ATACATAC
30774 ATACATAC
1 ATACATAC
30782 ATACATAC
1 ATACATAC
30790 ATACATAC
1 ATACATAC
30798 ATACATAC
1 ATACATAC
30806 ATACATAC
1 ATACATAC
30814 ATACATAC
1 ATACATAC
30822 ATACATAC
1 ATACATAC
30830 ATACATAC
1 ATACATAC
30838 ATACATAC
1 ATACATAC
30846 ATACATAC
1 ATACATAC
30854 ATACATAC
1 ATACATAC
30862 ATACATAC
1 ATACATAC
30870 ATACATAC
1 ATACATAC
30878 ATACATAC
1 ATACATAC
30886 ATACATAC
1 ATACATAC
30894 ATACATAC
1 ATACATAC
30902 ATACATAC
1 ATACATAC
30910 ATACATAC
1 ATACATAC
30918 ATACATAC
1 ATACATAC
30926 ATACATAC
1 ATACATAC
30934 ATACATAC
1 ATACATAC
30942 ATACATAC
1 ATACATAC
30950 ATACATAC
1 ATACATAC
30958 ATACATAC
1 ATACATAC
30966 ATACATAC
1 ATACATAC
30974 ATACATAC
1 ATACATAC
30982 ATACATAC
1 ATACATAC
30990 ATACATAC
1 ATACATAC
30998 ATACATAC
1 ATACATAC
31006 ATACATAC
1 ATACATAC
31014 ATACATAC
1 ATACATAC
31022 ATACATAC
1 ATACATAC
31030 ATACATAC
1 ATACATAC
31038 ATACAT--
1 ATACATAC
31044 ATACATAC
1 ATACATAC
31052 ATACATAC
1 ATACATAC
31060 ATACATAC
1 ATACATAC
31068 ATACATAC
1 ATACATAC
31076 ATACATAC
1 ATACATAC
31084 ATACATAC
1 ATACATAC
31092 ATACATAC
1 ATACATAC
31100 ATACATAC
1 ATACATAC
31108 ATACATAC
1 ATACATAC
31116 ATACATAC
1 ATACATAC
31124 ATACATAC
1 ATACATAC
31132 ATACATAC
1 ATACATAC
31140 ATACATAC
1 ATACATAC
31148 ATACATAC
1 ATACATAC
31156 ATACATAC
1 ATACATAC
31164 ATACATAC
1 ATACATAC
31172 ATACATAC
1 ATACATAC
31180 ATACATAC
1 ATACATAC
31188 ATACATAC
1 ATACATAC
31196 ATACATAC
1 ATACATAC
31204 ATACATAC
1 ATACATAC
31212 ATACATAC
1 ATACATAC
31220 ATACATAC
1 ATACATAC
31228 ATACATAC
1 ATACATAC
31236 ATACATAC
1 ATACATAC
31244 ATACATAC
1 ATACATAC
31252 ATAC--AC
1 ATACATAC
31258 ATACATAC
1 ATACATAC
31266 ATACATAC
1 ATACATAC
31274 ATACATAC
1 ATACATAC
31282 ATACATAC
1 ATACATAC
31290 ATACATAC
1 ATACATAC
31298 ATACATAC
1 ATACATAC
31306 ATACATAC
1 ATACATAC
31314 ATACATAC
1 ATACATAC
31322 ATACATAC
1 ATACATAC
31330 ATACATAC
1 ATACATAC
31338 ATACATAC
1 ATACATAC
31346 ATACATAC
1 ATACATAC
31354 ATACATAC
1 ATACATAC
31362 ATACATAC
1 ATACATAC
31370 ATACATAC
1 ATACATAC
31378 ATACATAC
1 ATACATAC
31386 ATACATAC
1 ATACATAC
31394 ATACATAC
1 ATACATAC
31402 ATACATAC
1 ATACATAC
31410 ATACATAC
1 ATACATAC
31418 ATACATAC
1 ATACATAC
31426 ATACATAC
1 ATACATAC
31434 ATACATAC
1 ATACATAC
31442 ATACATAC
1 ATACATAC
31450 ATACATAC
1 ATACATAC
31458 ATACATAC
1 ATACATAC
31466 ATACATAC
1 ATACATAC
31474 ATACATAC
1 ATACATAC
*
31482 AAACA-AC
1 ATACATAC
31489 ATACATAC
1 ATACATAC
31497 ATACATAC
1 ATACATAC
31505 ATACA-AC
1 ATACATAC
31512 ATACATAC
1 ATACATAC
*
31520 AAACATAC
1 ATACATAC
31528 ATAC--AC
1 ATACATAC
*
31534 ATACACAC
1 ATACATAC
*
31542 ATACACAC
1 ATACATAC
*
31550 ATACACAC
1 ATACATAC
*
31558 ATACACAC
1 ATACATAC
*
31566 ATACACAC
1 ATACATAC
31574 ATAC--AC
1 ATACATAC
*
31580 ATACACAC
1 ATACATAC
*
31588 ATACACAC
1 ATACATAC
*
31596 ATACACAC
1 ATACATAC
*
31604 ATACACAC
1 ATACATAC
31612 ATAC--AC
1 ATACATAC
*
31618 ATACACAC
1 ATACATAC
31626 ATAC--AC
1 ATACATAC
*
31632 ATACACAC
1 ATACATAC
*
31640 ATACACAC
1 ATACATAC
*
31648 ATACACAC
1 ATACATAC
*
31656 ATACACAC
1 ATACATAC
*
31664 ATACACAC
1 ATACATAC
* *
31672 ATACACAT
1 ATACATAC
*
31680 ACACATAC
1 ATACATAC
*
31688 ACACATAC
1 ATACATAC
*
31696 ACACATAC
1 ATACATAC
*
31704 ACACATAC
1 ATACATAC
*
31712 ACACATAC
1 ATACATAC
*
31720 ACACATAC
1 ATACATAC
*
31728 ACACATAC
1 ATACATAC
*
31736 ACACATAC
1 ATACATAC
*
31744 ACACATAC
1 ATACATAC
*
31752 ACACATAC
1 ATACATAC
* *
31760 ACACACAC
1 ATACATAC
*
31768 ATACACAC
1 ATACATAC
*
31776 ATACACAC
1 ATACATAC
*
31784 ATACACAC
1 ATACATAC
*
31792 ATACACAC
1 ATACATAC
*
31800 ATACACAC
1 ATACATAC
*
31808 ATACACAC
1 ATACATAC
*
31816 ATACACAC
1 ATACATAC
31824 ATAC--AC
1 ATACATAC
*
31830 ATACACAC
1 ATACATAC
*
31838 ATACACAC
1 ATACATAC
*
31846 ATACACAC
1 ATACATAC
*
31854 ATACACAC
1 ATACATAC
*
31862 ATACACAC
1 ATACATAC
*
31870 ATACACAC
1 ATACATAC
*
31878 ATACACAC
1 ATACATAC
*
31886 ATACACAC
1 ATACATAC
*
31894 ATACACAC
1 ATACATAC
*
31902 ATACACAC
1 ATACATAC
*
31910 ATACACAC
1 ATACATAC
*
31918 ATACACAC
1 ATACATAC
*
31926 ATACACAC
1 ATACATAC
*
31934 ATACACAC
1 ATACATAC
*
31942 ATACACAC
1 ATACATAC
*
31950 ATACACAC
1 ATACATAC
*
31958 ATACACAC
1 ATACATAC
31966 ATACATAC
1 ATACATAC
31974 ATACATAC
1 ATACATAC
*
31982 ATATATAC
1 ATACATAC
31990 ATACATAC
1 ATACATAC
31998 ATAC
1 ATAC
32002 GTGTATGTCA
Statistics
Matches: 1231, Mismatches: 13, Indels: 32
0.96 0.01 0.03
Matches are distributed among these distances:
6 42 0.03
7 13 0.01
8 1176 0.96
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (8 bp):
ATACATAC
Found at i:32371 original size:20 final size:20
Alignment explanation
Indices: 32341--32401 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
32331 CACTGAATAT
*
32341 TTGTCTCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* * * *
32361 TTGTTCTGAAGAACCACTGT
1 TTGTCCCGAAGGACCACTGA
*
32381 TTGTCCCGAATGACCACTGA
1 TTGTCCCGAAGGACCACTGA
32401 T
1 T
32402 AATCCCTCGA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:33375 original size:32 final size:34
Alignment explanation
Indices: 33339--33408 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
33329 CCTTACAAAC
*
33339 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACATT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACATT
* *
33371 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACATT
33405 TCCC
1 TCCC
33409 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACATT
Found at i:34792 original size:20 final size:19
Alignment explanation
Indices: 34767--34820 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
34757 GCAAAATAAA
34767 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
34787 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
34807 AATCGCAACGCGAT
1 AATCGCAACGCGAT
34821 TATGAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:34833 original size:21 final size:20
Alignment explanation
Indices: 34807--34919 Score: 72
Period size: 21 Copynumber: 5.5 Consensus size: 20
34797 CAGTTCCCAG
34807 AATCGCAACGCGATTATGAAT
1 AATCGCAACGCGA-TATGAAT
*
34828 AATCGCAATGCGATA-GTACA-
1 AATCGCAACGCGATATG-A-AT
** * **
34848 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGA-TATGAAT
34870 AATCGCAACGCGAATATGAA-
1 AATCGCAACGCG-ATATGAAT
*
34890 AATCGCAACGCGATACTGACT
1 AATCGCAACGCGATA-TGAAT
34911 -ATCGCAACG
1 AATCGCAACG
34920 AGTATCCGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 19
0.71 0.11 0.19
Matches are distributed among these distances:
19 4 0.06
20 29 0.40
21 35 0.49
22 4 0.06
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
AATCGCAACGCGATATGAAT
Found at i:34895 original size:20 final size:20
Alignment explanation
Indices: 34870--35138 Score: 158
Period size: 20 Copynumber: 13.7 Consensus size: 20
34860 GATTTTCCAT
*
34870 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
*
34890 AATCGCAACGCG-ATACTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
34910 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
34931 AATCGCAACG-TATATCCGTA
1 AATCGCAACGCGA-ATACGAA
*
34951 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATACG-AA
* * *
34972 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
34992 AATCGTAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
35012 AATCGCAACGCG-----G-A
1 AATCGCAACGCGAATACGAA
* *
35026 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
35046 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * * *
35066 AATCACAATGTGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
35086 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
35106 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
35126 AATCGCAACGCGA
1 AATCGCAACGCGA
35139 TTTTTATAGC
Statistics
Matches: 199, Mismatches: 38, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
14 12 0.06
15 1 0.01
19 4 0.02
20 147 0.74
21 35 0.18
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:34933 original size:41 final size:42
Alignment explanation
Indices: 34870--35139 Score: 243
Period size: 40 Copynumber: 6.8 Consensus size: 42
34860 GATTTTCCAT
* * *
34870 AATCGCAACGCGAATATG-AAAATCGCAACGCGATA-CTG-A
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGATATCCGTA
* * * *
34909 CTATCGCAACGAGTATCCGTAAAATCGCAACG-TATATCCGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGATATCCGTA
34951 AATCGCAACGAGAATACGTAAAATCGCAACGCG-TATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGATATCCGTA
*
34992 AATCGTAACGAGAATACGT-AAATCGCAACGCG------G-A
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGATATCCGTA
*
35026 AATCGCAACGAGAATACGT-AAATCGCAATGCG-TATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGATATCCGTA
* * * * *
35066 AATCACAATGTGAATACGT-AAATCGCAATGCGA-ATACGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGATATCCGTA
* * * *
35106 AATCGCAATGCGTATCCGT-AAATCGCAACGCGAT
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGAT
35140 TTTTATAGCG
Statistics
Matches: 195, Mismatches: 23, Indels: 23
0.81 0.10 0.10
Matches are distributed among these distances:
34 31 0.16
35 1 0.01
39 1 0.01
40 93 0.48
41 68 0.35
42 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (42 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGATATCCGTA
Found at i:34954 original size:61 final size:61
Alignment explanation
Indices: 34870--35138 Score: 191
Period size: 61 Copynumber: 4.5 Consensus size: 61
34860 GATTTTCCAT
* * * **
34870 AATCGCAACGCGAATATGAAAATCGCAACGCG-ATAC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGAATACGT-AAAATCGCAACGAGTATCCGT-A
* * * *
34931 AATCGCAACGTA-TATCCGTAAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACG-AGAATACGTAAATCGCAACGCGAATACGTAAAATCGCAACGAGTATCCGTA
* * *
34992 AATCGTAACGAGAATACGTAAATCGCAACGCG-----G--AAATCGCAACGAGAATACGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGAATACGTAAAATCGCAACGAGTATCCGTA
* * * * * * * * * * *
35046 AATCGCAATGCGTATCCGTAAATCACAATGTGAATACGT-AAATCGCAATGCGAATACGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGAATACGTAAAATCGCAACGAGTATCCGTA
* * * *
35106 AATCGCAATGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGA
35139 TTTTTATAGC
Statistics
Matches: 169, Mismatches: 29, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
54 42 0.25
56 1 0.01
59 1 0.01
60 50 0.30
61 52 0.31
62 22 0.13
63 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (61 bp):
AATCGCAACGAGAATACGTAAATCGCAACGCGAATACGTAAAATCGCAACGAGTATCCGTA
Found at i:35081 original size:74 final size:75
Alignment explanation
Indices: 34950--35093 Score: 236
Period size: 74 Copynumber: 1.9 Consensus size: 75
34940 GTATATCCGT
**
34950 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGTAACGAGAATACGTAAAT
1 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAAAT
35015 CGCAACGCGG
66 CGCAACGCGG
* * *
35025 AAATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCACAATGTGAATACGTAAAT
1 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAAAT
35089 CGCAA
66 CGCAA
35094 TGCGAATACG
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 44 0.69
75 20 0.31
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (75 bp):
AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGTAAAT
CGCAACGCGG
Found at i:35719 original size:21 final size:21
Alignment explanation
Indices: 35658--35736 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
35648 TTCTAAACTT
35658 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
35678 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
35698 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
*
35719 AAAATCGTAACGAGAGAA
1 AAAATCGCAACGAGAGAA
35737 TAGCAACGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:35751 original size:33 final size:33
Alignment explanation
Indices: 35713--35791 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
35703 CGCAACGAGA
35713 GAAATGAAAATCGTAACGAGAGAATAGCAACGC
1 GAAATGAAAATCGTAACGAGAGAATAGCAACGC
* *
35746 GAAATGAAAATCGTAACGAGATAATCGCAACGC
1 GAAATGAAAATCGTAACGAGAGAATAGCAACGC
**
35779 GAAACCAAAATCG
1 GAAATGAAAATCG
35792 AAGTGTTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
GAAATGAAAATCGTAACGAGAGAATAGCAACGC
Found at i:39229 original size:14 final size:14
Alignment explanation
Indices: 39210--39244 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
39200 ATTGTTTAAT
39210 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
39224 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
39238 TGATTTG
1 TGATTTG
39245 CTTAATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:39431 original size:33 final size:33
Alignment explanation
Indices: 39352--39441 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 33
39342 AAAAATGACT
* * *
39352 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
* * *
39385 ATCACAATACGAAATTAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
* * *
39418 ATCGCAACGCGAAACTAAATTCGC
1 ATCGCAATGCGAAATTAAAATCGC
39442 GTTGCGATTT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.21, G:0.17, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATTAAAATCGCAACGACAAA
Found at i:39483 original size:33 final size:33
Alignment explanation
Indices: 39441--39534 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
39431 ACTAAATTCG
*
39441 CGTTGCGATTTTAATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
39474 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
39507 CGTTGTGATTTTCATTTTGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
39535 AGTCATTTCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:39557 original size:33 final size:32
Alignment explanation
Indices: 39520--39621 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 32
39510 TGTGATTTTC
39520 ATTTTGCATTGCGATAGTCATTTCCGCGTTGCG
1 ATTTT-CATTGCGATAGTCATTTCCGCGTTGCG
** *
39553 ATTTTCACGTTGCGATTTTCATTT-CGCATTGCG
1 ATTTTCA--TTGCGATAGTCATTTCCGCGTTGCG
* *
39586 ATTCTCTCGTTGCGATAGTAATTTCCGCGTTGCG
1 ATT-T-TCATTGCGATAGTCATTTCCGCGTTGCG
39620 AT
1 AT
39622 AGACATTAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
32 2 0.04
33 28 0.50
34 24 0.43
35 2 0.04
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (32 bp):
ATTTTCATTGCGATAGTCATTTCCGCGTTGCG
Found at i:39563 original size:14 final size:14
Alignment explanation
Indices: 39546--39573 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39536 GTCATTTCCG
39546 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
39560 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
39574 TTTCGCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:39570 original size:53 final size:52
Alignment explanation
Indices: 39476--39587 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 52
39466 GATTCCCTCG
** * * *
39476 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTTGCA
1 TTGCGATAGTCATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCA
* *
39528 TTGCGATAGTCATTTCCGCGTTGCGATTTTCACGTTGCGATTTTCATTTCGCA
1 TTGCGATAGTCATTT-CGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCA
39581 TTGCGAT
1 TTGCGAT
39588 TCTCTCGTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
52 13 0.25
53 39 0.75
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.46
Consensus pattern (52 bp):
TTGCGATAGTCATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCA
Found at i:39667 original size:20 final size:20
Alignment explanation
Indices: 39594--39667 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
39584 CGATTCTCTC
* * *
39594 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTACGT
* *
39614 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTACG-T
*
39634 GATTGCGA-ACGTCATTTTCGT
1 G-TTGCGATA-GTCATTTACGT
39655 GTTGCGATAGTCA
1 GTTGCGATAGTCA
39668 AATGAATGCC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGTCATTTACGT
Found at i:42176 original size:24 final size:24
Alignment explanation
Indices: 42139--42192 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
42129 CTGAAAAATC
*
42139 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
42163 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
42187 ATCAAA
1 ATCAAA
42193 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:42206 original size:24 final size:24
Alignment explanation
Indices: 42155--42206 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42145 ATCTGAGTAT
* *
42155 TGACCAAGATCAAAGTCCGAGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
42179 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
42203 TGAC
1 TGAC
42207 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:43137 original size:20 final size:20
Alignment explanation
Indices: 43049--43235 Score: 138
Period size: 20 Copynumber: 9.6 Consensus size: 20
43039 ATAGTCAGAA
43049 TCTCGTTGCGATTTACAG-AT
1 TCTCGTTGCGATTTAC-GTAT
* *
43069 TCGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGTAT
* * * * *
43089 TCGCATTGTGATTTATGGAT
1 TCTCGTTGCGATTTACGTAT
* * *
43109 ACGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGTAT
43129 TCTCGTTGCGATTT-C----
1 TCTCGTTGCGATTTACGTAT
* *
43144 -CGCGTTGCGATTTACATAT
1 TCTCGTTGCGATTTACGTAT
*
43163 TCTCGTTGCGATTTACGGAT
1 TCTCGTTGCGATTTACGTAT
* *
43183 ACGT-GTTGCAATTTTACGTAT
1 TC-TCGTTGCGA-TTTACGTAT
*
43204 TCTCGTTGCGATTTACGGAT
1 TCTCGTTGCGATTTACGTAT
*
43224 ACTCGTTGCGAT
1 TCTCGTTGCGAT
43236 AGTCAGAATC
Statistics
Matches: 134, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
14 12 0.09
15 1 0.01
19 2 0.01
20 103 0.77
21 16 0.12
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
TCTCGTTGCGATTTACGTAT
Found at i:43142 original size:40 final size:40
Alignment explanation
Indices: 43049--43235 Score: 215
Period size: 40 Copynumber: 4.8 Consensus size: 40
43039 ATAGTCAGAA
* * *
43049 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
* * * * *
43089 TCGCATTGTGATTTATGGATACGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
*
43129 TCTCGTTGCGATTT-C-----CGCGTTGCGATTTACATAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
* *
43163 TCTCGTTGCGATTTACGGATACGTGTTGCAATTTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTAT
*
43204 TCTCGTTGCGATTTACGGATACTCGTTGCGAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGAT
43236 AGTCAGAATC
Statistics
Matches: 122, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
34 31 0.25
35 1 0.01
40 54 0.44
41 36 0.30
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (40 bp):
TCTCGTTGCGATTTACGGATACGCGTTGCGATTTACGTAT
Found at i:43177 original size:74 final size:75
Alignment explanation
Indices: 43074--43217 Score: 209
Period size: 74 Copynumber: 1.9 Consensus size: 75
43064 CAGATTCGCA
* * * *
43074 TTGCGATTTACGTATTCGCATTGTGATTTATGGATACGCATTGCGA-TTTACGTATTCTCGTTGC
1 TTGCGATTTACATATTCGCATTGCGATTTACGGATACGCATTGCAATTTTACGTATTCTCGTTGC
43138 GATTTCCGCG
66 GATTTCCGCG
* * **
43148 TTGCGATTTACATATTCTCGTTGCGATTTACGGATACGTGTTGCAATTTTACGTATTCTCGTTGC
1 TTGCGATTTACATATTCGCATTGCGATTTACGGATACGCATTGCAATTTTACGTATTCTCGTTGC
43213 GATTT
66 GATTT
43218 ACGGATACTC
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
74 38 0.62
75 23 0.38
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (75 bp):
TTGCGATTTACATATTCGCATTGCGATTTACGGATACGCATTGCAATTTTACGTATTCTCGTTGC
GATTTCCGCG
Found at i:43286 original size:20 final size:20
Alignment explanation
Indices: 43052--43296 Score: 135
Period size: 20 Copynumber: 12.5 Consensus size: 20
43042 GTCAGAATCT
*
43052 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACATATTCG
* *
43072 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACATATTCG
* * *** *
43092 CATTGTGATTTATGGATACG
1 CGTTGCGATTTACATATTCG
* * *
43112 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACATATTCG
43132 CGTTGCGATTT-C-----CG
1 CGTTGCGATTTACATATTCG
*
43146 CGTTGCGATTTACATATTCT
1 CGTTGCGATTTACATATTCG
** *
43166 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACATATTCG
* * * *
43186 TGTTGCAATTTTACGTATTCT
1 CGTTGCGA-TTTACATATTCG
** * *
43207 CGTTGCGATTTACGGATACT
1 CGTTGCGATTTACATATTCG
* * *
43227 CGTTGCGATAGT-CAGAATCG
1 CGTTGCGAT-TTACATATTCG
* * *
43247 CGTTGTGATTTATATGTTCG
1 CGTTGCGATTTACATATTCG
*
43267 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACATATTCG
*
43287 TGTTGCGATT
1 CGTTGCGATT
43297 ATAGAAAATC
Statistics
Matches: 172, Mismatches: 44, Indels: 18
0.74 0.19 0.08
Matches are distributed among these distances:
14 12 0.07
15 1 0.01
19 2 0.01
20 141 0.82
21 16 0.09
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTACATATTCG
Found at i:44928 original size:34 final size:32
Alignment explanation
Indices: 44875--44944 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
44865 CCTTACAAAC
* *
44875 TCCCTAGTTTTTCCGGGCTAAATTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
44907 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
44941 TCCC
1 TCCC
44945 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:47421 original size:18 final size:18
Alignment explanation
Indices: 47398--47453 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
47388 GCACTTAAAA
47398 TTTGTCCCGAATGACCAC
1 TTTGTCCCGAATGACCAC
47416 TTTGTCCCGAATGACCAC
1 TTTGTCCCGAATGACCAC
*
47434 TATGTCCCGAATGACCAC
1 TTTGTCCCGAATGACCAC
47452 TT
1 TT
47454 ATAACCCTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (18 bp):
TTTGTCCCGAATGACCAC
Found at i:49903 original size:36 final size:36
Alignment explanation
Indices: 49839--49907 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
49829 AATGCTTTAT
*
49839 GTTTCAAAAGAAACTGTCTCGAGCAAGATAAAATTA
1 GTTTCAAAAGAAACTATCTCGAGCAAGATAAAATTA
* *
49875 GTTTCAAAAGAAATTATCTC-ATGTAAGATAAAA
1 GTTTCAAAAGAAACTATCTCGA-GCAAGATAAAA
49908 AAAATTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.03
36 28 0.97
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (36 bp):
GTTTCAAAAGAAACTATCTCGAGCAAGATAAAATTA
Found at i:51678 original size:13 final size:13
Alignment explanation
Indices: 51670--51696 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51660 AATATCGTTA
51670 GAACTTATCTAAG
1 GAACTTATCTAAG
51683 GAACTTATCTAAG
1 GAACTTATCTAAG
51696 G
1 G
51697 TCTGATCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (13 bp):
GAACTTATCTAAG
Found at i:52697 original size:17 final size:16
Alignment explanation
Indices: 52675--52721 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
52665 ACTTCTTTTA
52675 TTTAAAAATAATAATTT
1 TTTAAAAA-AATAATTT
*
52692 TTTAAAGAAATAAATTT
1 TTTAAAAAAAT-AATTT
52709 TTTAGAAAAAATA
1 TTTA-AAAAAATA
52722 TAAACGTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 3 0.12
17 17 0.65
18 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (16 bp):
TTTAAAAAAATAATTT
Found at i:55846 original size:2 final size:2
Alignment explanation
Indices: 55841--55877 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
55831 AAAAAATCAA
55841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55878 AATAAAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57391 original size:3 final size:3
Alignment explanation
Indices: 57383--57443 Score: 74
Period size: 3 Copynumber: 20.3 Consensus size: 3
57373 AATAAGAAAC
57383 AAT AAT AAT AA- AAT AATT AAT AAT AA- AGAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT A-AT AAT -AAT AAT AAT AAT
57429 AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
57444 GTATAATATA
Statistics
Matches: 52, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
2 5 0.10
3 40 0.77
4 7 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:57391 original size:21 final size:20
Alignment explanation
Indices: 57359--57398 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
57349 ACCCTAAAAA
*
57359 AAACAAAATAATTAAATAAG
1 AAACAAAATAATAAAATAAG
57379 AAACAATAATAATAAAATAA
1 AAACAA-AATAATAAAATAA
57399 TTAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (20 bp):
AAACAAAATAATAAAATAAG
Found at i:57449 original size:19 final size:19
Alignment explanation
Indices: 57383--57463 Score: 76
Period size: 19 Copynumber: 4.1 Consensus size: 19
57373 AATAAGAAAC
*
57383 AATAATAATAAAATAAT-T
1 AATAATAATATAATAATAT
*
57401 AATAATAAAGATAATAA-AT
1 AATAAT-AATATAATAATAT
57420 AATAATAATAATAATAATAT
1 AATAATAAT-ATAATAATAT
57440 AATAGTATAATATATATATATAT
1 AATA--ATAATATA-ATA-ATAT
57463 A
1 A
57464 TTTTAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 8 0.15
19 22 0.42
20 6 0.12
21 3 0.06
22 8 0.15
23 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AATAATAATATAATAATAT
Found at i:57460 original size:8 final size:7
Alignment explanation
Indices: 57411--57488 Score: 62
Period size: 7 Copynumber: 11.7 Consensus size: 7
57401 AATAATAAAG
*
57411 ATAATAA
1 ATAATAT
57418 ATAATA-
1 ATAATAT
57424 ATAATA-
1 ATAATAT
57430 ATAATAAT
1 ATAAT-AT
57438 ATAATAGT
1 ATAATA-T
57446 ATAATAT
1 ATAATAT
57453 AT-ATAT
1 ATAATAT
57459 AT-ATATT
1 ATAATA-T
*
57466 TTAA-A-
1 ATAATAT
57471 A-AATAT
1 ATAATAT
57477 ATAATAT
1 ATAATAT
57484 ATAAT
1 ATAAT
57489 TTCCAAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
4 2 0.03
5 1 0.02
6 21 0.34
7 24 0.39
8 13 0.21
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:57496 original size:24 final size:24
Alignment explanation
Indices: 57448--57498 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
57438 ATAATAGTAT
*
57448 AATATATATATATATATTTTAAAA
1 AATATATATATATATATTTCAAAA
*
57472 AATATATA-ATATATAATTTCCAAA
1 AATATATATATATAT-ATTTCAAAA
57496 AAT
1 AAT
57499 GCTTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
AATATATATATATATATTTCAAAA
Found at i:57562 original size:36 final size:37
Alignment explanation
Indices: 57464--57648 Score: 180
Period size: 38 Copynumber: 4.9 Consensus size: 37
57454 TATATATATA
* * *
57464 TTTTAAAAAATATATAATATATAATTTCCAAAAAT-GCT
1 TTTTAAAAATTATATATTATATAATTTTC-AAAATCG-T
* *
57502 TTTAAAAAAATTATATATTATATATATTTTCAAAATGGT
1 TTT-TAAAAATTATATATTATATA-ATTTTCAAAATCGT
*
57541 TTTTAAAAATTATATATTATATAAATGTTTTCATAA-CG-
1 TTTTAAAAATTATATATTATAT-AA--TTTTCAAAATCGT
* * *
57579 TTTTCAAAAGTATATATTATATATATTTT-AAAAACGT
1 TTTTAAAAATTATATATTATATA-ATTTTCAAAATCGT
*
57616 TTTCAAAAATTATATATTATATAATTTTCAAAA
1 TTTTAAAAATTATATATTATATAATTTTCAAAA
57649 AATATATTTT
Statistics
Matches: 124, Mismatches: 13, Indels: 21
0.78 0.08 0.13
Matches are distributed among these distances:
35 3 0.02
36 11 0.09
37 25 0.20
38 43 0.35
39 28 0.23
40 14 0.11
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTTAAAAATTATATATTATATAATTTTCAAAATCGT
Found at i:57657 original size:15 final size:16
Alignment explanation
Indices: 57634--57663 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
57624 ATTATATATT
57634 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
57650 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
57664 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:57676 original size:52 final size:53
Alignment explanation
Indices: 57599--57710 Score: 156
Period size: 52 Copynumber: 2.1 Consensus size: 53
57589 TATATATTAT
57599 ATATATTTTAAAAACGTTTTCAAAAATTATATATTATAT-AA-TTTTCAAAAA
1 ATATATTTTAAAAACGTTTTCAAAAATTATATATTATATAAACTTTTCAAAAA
** *
57650 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAACGTTTTCAAAAA
1 ATATATTTT-AAAAACGTTTTCAAAAATTATATATTATATAAAC-TTTTCAAAAA
*
57705 CTATAT
1 ATATAT
57711 ATTATATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
51 9 0.17
52 27 0.51
53 2 0.04
55 15 0.28
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (53 bp):
ATATATTTTAAAAACGTTTTCAAAAATTATATATTATATAAACTTTTCAAAAA
Found at i:57697 original size:28 final size:28
Alignment explanation
Indices: 57598--57730 Score: 131
Period size: 28 Copynumber: 5.0 Consensus size: 28
57588 GTATATATTA
* *
57598 TATATATTTTAAAAACGTTTTCAAAAAT
1 TATATATTATATAAACGTTTTCAAAAAT
57626 TATATATTATAT-AA--TTTTCAAAAA-
1 TATATATTATATAAACGTTTTCAAAAAT
* * *
57650 -ATATATTTTCA-AAATGGTTTTTAAAAAT
1 TATATATTAT-ATAAA-CGTTTTCAAAAAT
*
57678 TATATATTATATAAACGTTTTCAAAAAC
1 TATATATTATATAAACGTTTTCAAAAAT
57706 TATATATTATAT-AA--TTTTCAAAAAT
1 TATATATTATATAAACGTTTTCAAAAAT
57731 ATTTTAAAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
23 8 0.09
24 3 0.03
25 20 0.23
27 13 0.15
28 33 0.38
29 11 0.12
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (28 bp):
TATATATTATATAAACGTTTTCAAAAAT
Found at i:57797 original size:38 final size:37
Alignment explanation
Indices: 57461--57830 Score: 184
Period size: 36 Copynumber: 9.7 Consensus size: 37
57451 ATATATATAT
* * *
57461 ATATTTTAAAAAATATATAATATATA-ATTTCCAAAA
1 ATATTTTAAAAACTATATATTATATATATTTTCAAAA
* *
57497 ATGCTTTTAAAAAAATTATATATTATATATATTTTC-AAA
1 AT-ATTTT--AAAAACTATATATTATATATATTTTCAAAA
* * * *
57536 ATGGTTTTTAAAAATTATATATTATATAAATGTTTTC-ATA
1 AT--ATTTTAAAAACTATATATTATAT--ATATTTTCAAAA
** * *
57576 ACGTTTTCAAAAGTATATATTATATATATTTT-AAAA
1 ATATTTTAAAAACTATATATTATATATATTTTCAAAA
** *
57612 ACGTTTTCAAAAATTATATATTATATA-ATTTTCAAAAAA
1 ATATTTT-AAAAACTATATATTATATATATTTTC--AAAA
** * * ** * *
57651 TATATTTTCAAAATGGTTTTTAAAAATTATATATTAT-ATAA
1 -ATATTTT-AAAA-ACTATAT-ATTA-TATATATTTTCAAAA
**
57692 ACGTTTTCAAAAACTATATATTATATA-ATTTTCAAAA
1 ATATTTT-AAAAACTATATATTATATATATTTTCAAAA
* * *
57729 ATATTTTAAAAACTATATAATACACATATTTTCAAAA
1 ATATTTTAAAAACTATATATTATATATATTTTCAAAA
*
57766 A-ATGTTT-TAAACTATATATTATATATGTATTTTCAAAA
1 ATAT-TTTAAAAACTATATATTATATA--TATTTTCAAAA
* * **
57804 ACAATTTGCAAACTATATGA-TATATAT
1 ATATTTTAAAAACTATAT-ATTATATAT
57831 GTGTATATAT
Statistics
Matches: 263, Mismatches: 46, Indels: 49
0.73 0.13 0.14
Matches are distributed among these distances:
36 58 0.22
37 48 0.18
38 55 0.21
39 45 0.17
40 41 0.16
41 6 0.02
42 2 0.01
43 4 0.02
44 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATTTTAAAAACTATATATTATATATATTTTCAAAA
Found at i:58680 original size:84 final size:84
Alignment explanation
Indices: 58461--59182 Score: 932
Period size: 84 Copynumber: 8.7 Consensus size: 84
58451 AAGGTCTTTA
* * *
58461 GCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATG--ATGCCTTGGAGCTGAGCGGAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
* *
58524 ACTCGAA-GTCTTTTGGTC
66 ACTCGAAGGTCTTTTGTTG
* * * * * * * *
58542 ACAGATAACCTTTCTAGCCTTGAGTTATGCTGTAAACGATGTGCCGTT-GAGCTGAGCGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCG
*
58606 AACTCAAAGGTCTTTTGTTG
65 AACTCGAAGGTCTTTTGTTG
* * * *
58626 GCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
*
58691 ACTCGAAGGTCTTTGGTTG
66 ACTCGAAGGTCTTTTGTTG
58710 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
*
58775 ACTCGAAGGTCTTTGGTTG
66 ACTCGAAGGTCTTTTGTTG
* * * * * *
58794 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTTCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT-ATGCCTTGGAGCTGAGCGTAGTCG
**
58859 AACTCGGGGGTC---T-TTG
65 AACTCGAAGGTCTTTTGTTG
* * * * *
58875 GCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
* * *
58940 ACTCGAAAGTCTTTTGGTC
66 ACTCGAAGGTCTTTTGTTG
* * *
58959 ACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAACTGAGCGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCG
*
59023 AACTCAAAGGTCTTTTGTTG
65 AACTCGAAGGTCTTTTGTTG
*
59043 GCAGATAACCCTTCTCGACTTAAGTTGTGCTGCAAATG--ATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
*
59106 ACTCGAAGGTCTTTGGTTG
66 ACTCGAAGGTCTTTTGTTG
59125 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAGTA--CC-TGGAGCTGAGCGTA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA-TATGCCTTGGAGCTGAGCGTA
59183 TAACCCTTCT
Statistics
Matches: 557, Mismatches: 69, Indels: 29
0.85 0.11 0.04
Matches are distributed among these distances:
80 27 0.05
81 72 0.13
82 88 0.16
83 31 0.06
84 308 0.55
85 31 0.06
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (84 bp):
GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTTGTTG
Found at i:58878 original size:249 final size:248
Alignment explanation
Indices: 58461--59182 Score: 928
Period size: 249 Copynumber: 2.9 Consensus size: 248
58451 AAGGTCTTTA
* * *
58461 GCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATG--ATGCCTTGGAGCTGAGCGGAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
** * * * * * *
58524 ACTCGAA-GTCTTTTGG-TCACAGATAACCTTTCTAGCCTTGAGTTATGCTGTAAACGATGTGCC
66 ACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT-CC
* * * * *
58587 GTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTT
129 CTTGAGCTGAGCGTAGTCGAACTCGAAGGTC--TTGTTGGCAGATAACCCTTCTCGACTTAAGTT
* * *
58652 GTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTG
192 ATGCTGCAAATGATAT-CCTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTTGG-TC
58710 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
58775 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTTCCC
66 ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG-TCCC
* * * ** * *
58840 TCGAAGCTGAGTGTAATCGAACTCGGGGGTC-T-TTGGCAGATAGCCCTTCTCGACTTAAGCTAT
130 TTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* *
58903 TCTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTTGGTC
194 GCTGCAAATGATAT-CCTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTTGGTC
* * *
58959 ACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTT-GAACTGAGCGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCG
* * *
59023 AACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTGTGCTGCAAATGATG--CC
65 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTCCC
59086 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTT
130 TT-GAGCTGAGCGTAGTCGAACTCGAAGGTC-TT-GTTGGCAGATAACCCTTCTCGACTTAAGTT
59151 ATGCTGCAAATGAGTA-CC-TGGAGCTGAGCGTA
192 ATGCTGCAAATGA-TATCCTTGGAGCTGAGCGTA
59183 TAACCCTTCT
Statistics
Matches: 415, Mismatches: 44, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
246 26 0.06
247 1 0.00
248 15 0.04
249 224 0.54
250 47 0.11
251 37 0.09
252 42 0.10
253 23 0.06
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (248 bp):
GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTCCCT
TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
TGCAAATGATATCCTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTTGGTC
Found at i:58954 original size:333 final size:323
Alignment explanation
Indices: 58461--59672 Score: 1199
Period size: 333 Copynumber: 3.8 Consensus size: 323
58451 AAGGTCTTTA
* * * *
58461 GCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATG-CCTTGGAGCTGAGCGGAGTCGAA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTCC-TGGAGCTGAGCGTAATCGAA
* * * *
58525 CTCGAAGTCTTTTGGTCACAGATAACCTTTCTAGCCTTGAGTTATGCTGTAAACGATGTGCCGTT
65 CTCG--GTC-TTTGG---CAGATAGCCCTTCT-GACTT-AG-TATTCTGTAAACGATGTGCCGTT
58590 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTG
121 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTT-GCAGACAACCCTTGTAGACTTAAGTTGTG
58655 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACC
185 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACC
58720 CTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
250 CTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
58785 CTTTGGTTG
315 CTTTGGTTG
* *
58794 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTTCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG-T-CCT-GGAGCTGAGCGTAATCG
* * *
58859 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTACC-TTG
63 AACTC---GGTCTTTGGCAGATAGCCCTTCT-GACTT-AG-TATTCTGTAAACGATGTGCCGTT-
** * * * *
58923 GAGCTGAGCGTAGTCGAACTCGAAA-GTCTTTTGGTCACAGATAACCCTTCTCGACTTAAGTTAT
121 GAGCTGAGCGTAGTCGAACTC-AAAGGTCTTTT-GTTGCAGACAACCCTTGTAGACTTAAGTTGT
* * * *
58987 GCTGCAAATGATGTGCCGTT-GAACTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAA
184 GCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
*
59051 CCCTTCTCGACTTAAGTTGTGCTGCAAATG--ATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
248 CCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
59114 GTCTTTGGTTG
313 GTCTTTGGTTG
59125 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA-GTACCTGGAGCTGAGCGT-AT--AA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT-CCTGGAGCTGAGCGTAATCGAA
* * *
59186 C-C---C-TT--C---TAG-CC-T-TGAGTTA-T-GT-TGTAAACGATGTGCCGTTGAACTGAGC
65 CTCGGTCTTTGGCAGATAGCCCTTCTGACTTAGTATTCTGTAAACGATGTGCCGTTGAGCTGAGC
59235 GTAGTCGAACTCAAAGGTCTTTTGTTGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGA
130 GTAGTCGAACTCAAAGGTCTTTTGTTGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGA
59300 TATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACT
195 TATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACT
* * * * * *
59365 TAAG-TATGCTGCAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCG--GG-----GGTTT
260 TAAGTTATGCTGCAAATGAT-ATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TT
59422 G
323 G
* * *
59423 GCAGAT-A--------GACTTAGGTTAT-CTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT-CC-TGGAGCTGAGCGTAATCGA
* * * * * * * * * *
59478 ACTCAAAGGTCTTTGCTAACAGATAACTCTTCTAGCCTGAGTTATGCTGTAAATGTTATGCCCTT
64 ACTC---GGTCTTTG---GCAGATAGCCCTTCT-GACTTAG-TATTCTGTAAACGATGTGCCGTT
* * * * * * * * * * *
59543 GAAGCTGAGTGTAATCGAACTTAAGGGTC-TTTG--GCAGATAGCCCTTCTCGACTTAAGCTATT
121 G-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGCAGACAACCCTTGTAGACTTAAGTTGTG
* * *
59605 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGG-TGGCAGGTAGCC
185 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACC
59668 CTTCT
250 CTTCT
59673 GGCCTTGAGC
Statistics
Matches: 748, Mismatches: 83, Indels: 116
0.79 0.09 0.12
Matches are distributed among these distances:
288 10 0.01
289 15 0.02
290 12 0.02
291 1 0.00
293 3 0.00
294 1 0.00
297 3 0.00
298 9 0.01
300 1 0.00
301 16 0.02
302 103 0.14
303 39 0.05
304 27 0.04
305 1 0.00
306 1 0.00
307 1 0.00
308 4 0.01
309 3 0.00
310 2 0.00
311 3 0.00
312 4 0.01
313 18 0.02
314 4 0.01
315 70 0.09
317 21 0.03
318 23 0.03
324 1 0.00
325 3 0.00
327 2 0.00
328 10 0.01
329 4 0.01
330 1 0.00
331 83 0.11
332 2 0.00
333 210 0.28
334 7 0.01
335 1 0.00
336 25 0.03
337 3 0.00
339 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (323 bp):
GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTCCTGGAGCTGAGCGTAATCGAAC
TCGGTCTTTGGCAGATAGCCCTTCTGACTTAGTATTCTGTAAACGATGTGCCGTTGAGCTGAGCG
TAGTCGAACTCAAAGGTCTTTTGTTGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGAT
ATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT
AAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
Found at i:59329 original size:83 final size:83
Alignment explanation
Indices: 59184--59383 Score: 242
Period size: 83 Copynumber: 2.4 Consensus size: 83
59174 CTGAGCGTAT
* * * * * * *
59184 AACCCTTCTAGCCTTGAGTTATGTTGTAAACGATGTGCCGTT-GAACTGAGCGTAGTCGAACTCA
1 AACCCTTCTAGACTTAAG-TATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCA
*
59248 AAGGTCTTTTGTT-GCAGAC
64 AAGGTCTTTGGTTGGCAGAC
* * *
59267 AACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGA
1 AACCCTTCTAGACTTAAG-TATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAA
*
59332 AGGTCTTTGGTTGGCAGAT
65 AGGTCTTTGGTTGGCAGAC
*
59351 AACCCTTCTCGACTTAAGTATGCTGCAAATGAT
1 AACCCTTCTAGACTTAAGTATGCTGCAAATGAT
59384 GTTCCCTCGA
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
82 2 0.02
83 77 0.77
84 21 0.21
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (83 bp):
AACCCTTCTAGACTTAAGTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAA
GGTCTTTGGTTGGCAGAC
Found at i:59375 original size:219 final size:219
Alignment explanation
Indices: 58963--59635 Score: 729
Period size: 219 Copynumber: 3.0 Consensus size: 219
58953 TTGGTCACAG
* *
58963 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGTTGAACTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGACTTAAGTTATGCTGCAAACGATGTGCCGTTGAACTGAGCGTAGTCGAACTC
* *
59028 AAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTGTGCTGCAAATGATGCCTTGGAGC
66 AAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGCCTTGGAGC
59093 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
131 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
59158 AAATGAGTACCTGGAGCTGAGCGT
196 AAATGAGTACCTGGAGCTGAGCGT
* * * *
59182 ATAACCCTTCTAGCCTTGAGTTATGTTGTAAACGATGTGCCGTTGAACTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGACTTAAGTTATGCTGCAAACGATGTGCCGTTGAACTGAGCGTAGTCGAACTC
*
59247 AAAGGTCTTTTGTT-GCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGA
66 AAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATG--ATGCCTTGGA
59311 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG-TATGCT
129 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCT
* * *
59375 GCAAATGATGTTCCCTCGAAGCTGAGTGT
194 GCAAATGA-G-TACCT-GGAGCTGAGCGT
* * * **
59404 AATCGAACTCGGGGGTTTGGCAGATAGACTTAGGTTAT-CTGCAAATGATGTGCC-TTGGAGTTG
1 -AT--AAC-C-----CTT--C---TAGACTTAAGTTATGCTGCAAACGATGTGCCGTT-GAACTG
* ** * * * * * *
59467 AGCGTAGTCGAACTCAAAGGTC-TTTGCTAACAGATAACTCTTCTAG-CCTGAGTTATGCTGTAA
51 AGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAA
* * * * *
59530 ATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC--T--TTGGCAGATAGCCCTTC
116 ATG--ATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCTTC
* * *
59590 TCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGT
177 TCGACTTAAGTTATGCTGCAAATGA-GTACC-TGGAGCTGAGCGT
59635 A
1 A
59636 GTCGAACTCG
Statistics
Matches: 389, Mismatches: 40, Indels: 39
0.83 0.09 0.08
Matches are distributed among these distances:
218 35 0.09
219 87 0.22
220 69 0.18
221 4 0.01
222 10 0.03
223 2 0.01
225 3 0.01
226 1 0.00
230 1 0.00
231 41 0.11
232 16 0.04
233 2 0.01
234 29 0.07
235 78 0.20
236 11 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (219 bp):
ATAACCCTTCTAGACTTAAGTTATGCTGCAAACGATGTGCCGTTGAACTGAGCGTAGTCGAACTC
AAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGCCTTGGAGC
TGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
AAATGAGTACCTGGAGCTGAGCGT
Found at i:59410 original size:84 final size:83
Alignment explanation
Indices: 59184--59414 Score: 241
Period size: 83 Copynumber: 2.8 Consensus size: 83
59174 CTGAGCGTAT
* * * * * * * * *
59184 AACCCTTCTAGCCTTGAGTTATGTTGTAAACGATGTGCCGTTGAA-CTGAGCGTAGTCGAACTCA
1 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATAT-CCCTCGAAGCTGAGCGTAGTCGAACTCG
*
59248 AAGGTCTTTTGTTGCAGAC
65 AAGGTCTTTGGTTGCAGAC
* * * * *
59267 AACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGA
1 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATATCCCTCGAAGCTGAGCGTAGTCGAACTCGA
*
59332 AGGTCTTTGGTTGGCAGAT
66 AGGTCTTTGGTT-GCAGAC
* * * *
59351 AACCCTTCTCGACTTAAG-TATGCTGCAAATGATGTTCCCTCGAAGCTGAGTGTAATCGAACTCG
1 AACCCTTCTAGACTTAAGTTATGCTGCAAATGAT-ATCCCTCGAAGCTGAGCGTAGTCGAACTCG
59415 GGGGTTTGGC
Statistics
Matches: 122, Mismatches: 23, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
82 5 0.04
83 72 0.59
84 45 0.37
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (83 bp):
AACCCTTCTAGACTTAAGTTATGCTGCAAATGATATCCCTCGAAGCTGAGCGTAGTCGAACTCGA
AGGTCTTTGGTTGCAGAC
Found at i:59629 original size:80 final size:78
Alignment explanation
Indices: 59441--59677 Score: 222
Period size: 80 Copynumber: 2.9 Consensus size: 78
59431 ACTTAGGTTA
* * * *
59441 TCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACT
1 TCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC-AAGGTCTTTG---GCAGATAGCC
* *
59506 CTTCTAGCCTGAGTTAT
62 CTTCTAGCCTAAGCTAT
* * * * * * * *
59523 GCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCT
1 TCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAA-GGTCTTTGGCAGATAGCCCT
* *
59588 TCTCGACTTAAGCTAT
64 TCTAG-CCTAAGCTAT
*
59604 TCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCC
1 TCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC-AAGGTCTT--TGGCAGATAGCCC
*
59669 TTCTGGCCT
63 TTCTAGCCT
59678 TGAGCTAAGC
Statistics
Matches: 122, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
80 41 0.34
81 22 0.18
82 30 0.25
83 29 0.24
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (78 bp):
TCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAGGTCTTTGGCAGATAGCCCTTC
TAGCCTAAGCTAT
Found at i:59691 original size:82 final size:81
Alignment explanation
Indices: 59442--59694 Score: 258
Period size: 82 Copynumber: 3.1 Consensus size: 81
59432 CTTAGGTTAT
* ** * *
59442 CTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACTC
1 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTG-TGGCAGATAGCCC
*
59507 TTCTAGCC-TGAGTTATG
64 TTCTAGCCTTGAGCTATG
* * * * * * * *
59524 CTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTT-TGGCAGATAGCCCT
1 CTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGTGGCAGATAGCCCT
* * * *
59588 TCTCGACTTAAGCTATT
65 TCTAGCCTTGAGCTATG
* *
59605 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCCT
1 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT-GTGGCAGATAGCCCT
* *
59670 TCTGGCCTTGAGCTAAG
65 TCTAGCCTTGAGCTATG
59687 CTGCAAAT
1 CTGCAAAT
59695 AGTTTGTTTA
Statistics
Matches: 134, Mismatches: 33, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
80 44 0.33
81 17 0.13
82 46 0.34
83 27 0.20
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (81 bp):
CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGTGGCAGATAGCCCTT
CTAGCCTTGAGCTATG
Found at i:62724 original size:18 final size:19
Alignment explanation
Indices: 62684--62728 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
62674 AGTTAATGTG
*
62684 AATGCAATGAAAATAACAA
1 AATGCAAAGAAAATAACAA
62703 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAACAA
62721 AATGCAAA
1 AATGCAAA
62729 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:63380 original size:17 final size:17
Alignment explanation
Indices: 63354--63386 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
63344 TGCAAACGAT
*
63354 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
63371 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
63387 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:66043 original size:20 final size:20
Alignment explanation
Indices: 66018--66095 Score: 63
Period size: 24 Copynumber: 3.8 Consensus size: 20
66008 CCCTGAAAAA
66018 AAACAA-AATAATTAAATAAG
1 AAACAATAATAA-TAAATAAG
*
66038 AAACAATAATAATAAATAAAAT
1 AAACAATAATAATAAAT--AAG
66060 AATTACAATAATAATAAAT--G
1 AA--ACAATAATAATAAATAAG
*
66080 ATAATAATAATAATAA
1 A-AACAATAATAATAA
66096 TAATAATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.24
20 12 0.24
21 6 0.12
22 4 0.08
24 15 0.31
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.26
Consensus pattern (20 bp):
AAACAATAATAATAAATAAG
Found at i:66050 original size:3 final size:3
Alignment explanation
Indices: 66042--66108 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
66032 AATAAGAAAC
* * *
66042 AAT AAT AAT AAAT AA- AAT AAT TAC AAT AAT AAT AAAT GAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
66088 AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
66109 GTATAATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:66084 original size:34 final size:32
Alignment explanation
Indices: 66022--66096 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 32
66012 GAAAAAAAAC
66022 AAAATAATTAAATAAGAAACAATAATAATAAAT
1 AAAATAATTAAATAAGAAACAATAATAAT-AAT
* *
66055 AAAATAATTACAATAATAATA-AATGATAATAAT
1 AAAATAATTA-AATAAGAA-ACAATAATAATAAT
66088 AATAATAAT
1 AA-AATAAT
66097 AATAATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 15 0.41
34 21 0.57
35 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (32 bp):
AAAATAATTAAATAAGAAACAATAATAATAAT
Found at i:66114 original size:19 final size:17
Alignment explanation
Indices: 66067--66129 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 17
66057 AATAATTACA
66067 ATAATA-ATAAATGATAAT
1 ATAATATAT-AAT-ATAAT
66085 AATAATA-ATAATAATAAT
1 -ATAATATATAAT-ATAAT
66103 ATAATAGTATAATATATAT
1 ATAATA-TATAATATA-AT
66122 ATAA-ATAT
1 ATAATATAT
66130 TTTTAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
17 9 0.22
18 12 0.30
19 19 0.47
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
ATAATATATAATATAAT
Found at i:66178 original size:40 final size:40
Alignment explanation
Indices: 66134--66216 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
66124 AAATATTTTT
66134 AAAAAAAATATAATATATA-ATTTCCAAAAATGCTTTTAAA
1 AAAAAAAATATAATATATATATTTCC-AAAATGCTTTTAAA
** * * * *
66174 AAAAATTATATATTATATATATTTTCAAAATGGTTTTTAA
1 AAAAAAAATATAATATATATATTTCCAAAATGCTTTTAAA
66214 AAA
1 AAA
66217 TTATATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
40 31 0.86
41 5 0.14
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (40 bp):
AAAAAAAATATAATATATATATTTCCAAAATGCTTTTAAA
Found at i:66224 original size:40 final size:38
Alignment explanation
Indices: 66129--66315 Score: 161
Period size: 38 Copynumber: 4.9 Consensus size: 38
66119 TATATAAATA
* * *
66129 TTTTTAAAAAAAATATAATATATA-ATTTCCAAAAAT-G
1 TTTTTAAAAAATATATATTATATATATTTTC-AAAATCG
* *
66166 CTTTTAAAAAAAATTATATATTATATATATTTTCAAAATGG
1 -TTTT-TAAAAAA-TATATATTATATATATTTTCAAAATCG
* * *
66207 TTTTTAAAAATTATATATTATATAAATGTTTTCATAA-CG
1 TTTTTAAAAAATATATATTATAT--ATATTTTCAAAATCG
* * *
66246 -TTTTCAAAAGTATATATTATATATATTTT-AAAAACG
1 TTTTTAAAAAATATATATTATATATATTTTCAAAATCG
* *
66282 TTTTCAAAAATTATATATTATATA-ATTTTCAAAA
1 TTTTTAAAAAATATATATTATATATATTTTCAAAA
66316 AATATATTTT
Statistics
Matches: 124, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
35 3 0.02
36 13 0.10
37 24 0.19
38 36 0.29
39 12 0.10
40 30 0.24
41 6 0.05
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (38 bp):
TTTTTAAAAAATATATATTATATATATTTTCAAAATCG
Found at i:66225 original size:38 final size:38
Alignment explanation
Indices: 66174--66315 Score: 175
Period size: 38 Copynumber: 3.8 Consensus size: 38
66164 TGCTTTTAAA
*
66174 AAAAATTATATATTATATATATTTTCAAAATGGTTTTT
1 AAAAATTATATATTATATATATTTTCAAAATCGTTTTT
* *
66212 AAAAATTATATATTATATAAATGTTTTCATAA-CG-TTTT
1 AAAAATTATATATTATAT--ATATTTTCAAAATCGTTTTT
* * * *
66250 CAAAAGTATATATTATATATATTTT-AAAAACGTTTTC
1 AAAAATTATATATTATATATATTTTCAAAATCGTTTTT
66287 AAAAATTATATATTATATA-ATTTTCAAAA
1 AAAAATTATATATTATATATATTTTCAAAA
66316 AATATATTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
35 3 0.03
36 13 0.15
37 24 0.27
38 38 0.43
39 1 0.01
40 10 0.11
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (38 bp):
AAAAATTATATATTATATATATTTTCAAAATCGTTTTT
Found at i:66314 original size:25 final size:25
Alignment explanation
Indices: 66282--66397 Score: 124
Period size: 25 Copynumber: 4.4 Consensus size: 25
66272 TTTAAAAACG
66282 TTTTCAAAAATTATATATTATATAA
1 TTTTCAAAAATTATATATTATATAA
* * * **
66307 TTTTCAAAAAATATATTTTCAAAATGG
1 TTTTCAAAAATTATATATT--ATATAA
*
66334 TTTTTAAAAATTATATATTATATAAACA
1 TTTTCAAAAATTATATATTATAT--A-A
*
66362 TTTTCAAAAACTATATATTATATAA
1 TTTTCAAAAATTATATATTATATAA
66387 TTTTCAAAAAT
1 TTTTCAAAAAT
66398 ATTTTAAAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
25 31 0.43
26 1 0.01
27 19 0.26
28 21 0.29
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTTCAAAAATTATATATTATATAA
Found at i:66324 original size:15 final size:16
Alignment explanation
Indices: 66301--66330 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
66291 ATTATATATT
66301 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
66317 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
66331 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:66343 original size:52 final size:53
Alignment explanation
Indices: 66266--66377 Score: 156
Period size: 52 Copynumber: 2.1 Consensus size: 53
66256 TATATATTAT
66266 ATATATTTTAAAAACGTTTTCAAAAATTATATATTATAT-A-ATTTTCAAAAA
1 ATATATTTTAAAAACGTTTTCAAAAATTATATATTATATAACATTTTCAAAAA
** *
66317 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAACATTTTCAAAAA
1 ATATATTTT-AAAAACGTTTTCAAAAATTATATATTATAT-AACATTTTCAAAAA
*
66372 CTATAT
1 ATATAT
66378 ATTATATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
51 9 0.17
52 27 0.51
54 1 0.02
55 16 0.30
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (53 bp):
ATATATTTTAAAAACGTTTTCAAAAATTATATATTATATAACATTTTCAAAAA
Found at i:66365 original size:28 final size:28
Alignment explanation
Indices: 66265--66397 Score: 113
Period size: 28 Copynumber: 5.0 Consensus size: 28
66255 GTATATATTA
* * *
66265 TATATATTTTAAAAACGTTTTCAAAAAT
1 TATATATTATATAAACATTTTCAAAAAT
66293 TATATATTATAT--A-ATTTTCAAAAA-
1 TATATATTATATAAACATTTTCAAAAAT
* ** *
66317 -ATATATTTTCA-AAATGGTTTTTAAAAAT
1 TATATATTAT-ATAAA-CATTTTCAAAAAT
*
66345 TATATATTATATAAACATTTTCAAAAAC
1 TATATATTATATAAACATTTTCAAAAAT
66373 TATATATTATAT--A-ATTTTCAAAAAT
1 TATATATTATATAAACATTTTCAAAAAT
66398 ATTTTAAAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 19
0.73 0.10 0.16
Matches are distributed among these distances:
23 8 0.09
24 1 0.01
25 22 0.26
26 2 0.02
27 9 0.11
28 32 0.38
29 11 0.13
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (28 bp):
TATATATTATATAAACATTTTCAAAAAT
Found at i:66410 original size:36 final size:36
Alignment explanation
Indices: 66174--66496 Score: 174
Period size: 37 Copynumber: 8.6 Consensus size: 36
66164 TGCTTTTAAA
* **
66174 AAAAATTATATATTATATATATTTTCAAAATGGTTTTT
1 AAAAACTATATATTATATATATTTTCAAAA--AATTTT
* * * **
66212 AAAAATTATATATTATATAAATGTTTTCATAACGTTTT
1 AAAAACTATATATTATAT--ATATTTTCAAAAAATTTT
* * *
66250 CAAAAGTATATATTATATATATTTT-AAAAACGTTTT
1 AAAAACTATATATTATATATATTTTCAAAAA-ATTTT
*
66286 CAAAAATTATATATTATATA-ATTTTCAAAAAATATATTTT
1 -AAAAACTATATATTATATATATTTTC--AAAA-A-ATTTT
** * * ** * *
66326 CAAAATGGTTTTTAAAAATTATATATTAT-ATAAACATTTT
1 -AAAA-ACTATAT-ATTA-TATATATTTTCA-AAAAATTTT
66366 CAAAAACTATATATTATATA-ATTTTCAAAAATATTTT
1 -AAAAACTATATATTATATATATTTTCAAAAA-ATTTT
* *
66403 AAAAACTATATAATATACATATTTTCAAAAAATGTTT
1 AAAAACTATATATTATATATATTTTCAAAAAAT-TTT
*
66440 --AAACTATATATTATATATGTATTTTCAAAAACAATTT
1 AAAAACTATATATTATATA--TATTTTCAAAAA-ATTTT
**
66477 GCAAACTATATGA-TATATAT
1 AAAAACTATAT-ATTATATAT
66497 GTGTATATAT
Statistics
Matches: 228, Mismatches: 34, Indels: 47
0.74 0.11 0.15
Matches are distributed among these distances:
35 18 0.08
36 42 0.18
37 57 0.25
38 41 0.18
39 22 0.10
40 31 0.14
41 4 0.02
42 5 0.02
43 4 0.02
44 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAAACTATATATTATATATATTTTCAAAAAATTTT
Found at i:66427 original size:37 final size:36
Alignment explanation
Indices: 66130--66496 Score: 145
Period size: 37 Copynumber: 9.7 Consensus size: 36
66120 ATATAAATAT
** * *
66130 TTTTAAAAAAAATATAATATATA-ATTTCCAAAAATGC
1 TTTTAAAAACTATATAATATATATATTTTCAAAAA--A
* * **
66167 TTTTAAAAAAAATTATATATTATATATATTTTCAAAATGGT
1 TTTT---AAAAACTATATAATATATATATTTTCAAAA--AA
* * * * **
66208 TTTTAAAAATTATATATTATATAAATGTTTTCATAACG
1 TTTTAAAAACTATATA--ATATATATATTTTCAAAAAA
* * * *
66246 TTTTCAAAAGTATATATTATATATATTTT-AAAAACG
1 TTTTAAAAACTATATAATATATATATTTTCAAAAA-A
* *
66282 TTTTCAAAAATTATATATTATATA-ATTTTCAAAAAATATA
1 TTTT-AAAAACTATATAATATATATATTTTC--AAAA-A-A
** * * * * *
66322 TTTTCAAAATGGTTTTTAAAAATTATATATTAT-ATAAACA
1 TTTT-AAAA-ACTATAT-AATA-TATATATTTTCA-AAAAA
*
66362 TTTTCAAAAACTATATATTATATA-ATTTTCAAAAATA
1 TTTT-AAAAACTATATAATATATATATTTTCAAAAA-A
*
66399 TTTTAAAAACTATATAATATACATATTTTCAAAAAA
1 TTTTAAAAACTATATAATATATATATTTTCAAAAAA
*
66435 TGTTT--AAACTATATATTATATATGTATTTTCAAAAACA
1 T-TTTAAAAACTATATA--ATATATATATTTTCAAAAA-A
* ** *
66473 ATTTGCAAACTATATGATATATAT
1 TTTTAAAAACTATATAATATATAT
66497 GTGTATATAT
Statistics
Matches: 256, Mismatches: 46, Indels: 56
0.72 0.13 0.16
Matches are distributed among these distances:
35 13 0.05
36 46 0.18
37 72 0.28
38 29 0.11
39 16 0.06
40 50 0.20
41 17 0.07
42 5 0.02
43 4 0.02
44 4 0.02
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (36 bp):
TTTTAAAAACTATATAATATATATATTTTCAAAAAA
Found at i:66494 original size:39 final size:36
Alignment explanation
Indices: 66368--66498 Score: 117
Period size: 36 Copynumber: 3.6 Consensus size: 36
66358 AACATTTTCA
* *
66368 AAAACTATATAT-TATAT-AATTTTCAAAAATATTTT
1 AAAACTATATATATATATGTATTTTCAAAAA-AATTT
**
66403 AAAAACTATATA-ATATACATATTTTC-AAAAAATGTT
1 -AAAACTATATATATATATGTATTTTCAAAAAAAT-TT
*
66439 TAAACTATATATTATATATGTATTTTCAAAAACAATTT
1 AAAACTATATA-TATATATGTATTTTCAAAAA-AATTT
*
66477 GCAAACTATATGATATATATGT
1 -AAAACTATAT-ATATATATGT
66499 GTATATATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
35 12 0.15
36 21 0.27
37 18 0.23
38 6 0.08
39 21 0.27
40 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (36 bp):
AAAACTATATATATATATGTATTTTCAAAAAAATTT
Found at i:67050 original size:14 final size:14
Alignment explanation
Indices: 67031--67099 Score: 68
Period size: 14 Copynumber: 4.8 Consensus size: 14
67021 TTTGAAAACT
67031 CAAATATAATATGA
1 CAAATATAATATGA
* *
67045 CAAATAAAATAAATAAA
1 CAAATATAAT--AT-GA
* *
67062 TAAATATAATATGT
1 CAAATATAATATGA
67076 CAAATATAATATGA
1 CAAATATAATATGA
67090 CAAATA-AATA
1 CAAATATAATA
67100 AATAAATAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
13 4 0.09
14 27 0.61
15 2 0.05
16 2 0.05
17 9 0.20
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (14 bp):
CAAATATAATATGA
Found at i:67067 original size:31 final size:32
Alignment explanation
Indices: 67032--67103 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
67022 TTGAAAACTC
*
67032 AAATATAATATGACAAATAAAATA-AATAAAT
1 AAATATAATATGACAAATAAAATATAACAAAT
* * *
67063 AAATATAATATGTCAAATATAATATGACAAAT
1 AAATATAATATGACAAATAAAATATAACAAAT
67095 AAATA-AATA
1 AAATATAATA
67104 AATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 26 0.72
32 10 0.28
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (32 bp):
AAATATAATATGACAAATAAAATATAACAAAT
Found at i:67709 original size:17 final size:19
Alignment explanation
Indices: 67687--67728 Score: 70
Period size: 17 Copynumber: 2.3 Consensus size: 19
67677 AAAATATGGT
67687 ACAAAATGTATA-AAAC-A
1 ACAAAATGTATACAAACAA
67704 ACAAAATGTATACAAACAA
1 ACAAAATGTATACAAACAA
67723 ACAAAA
1 ACAAAA
67729 GACGTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 12 0.52
18 4 0.17
19 7 0.30
ACGTcount: A:0.67, C:0.14, G:0.05, T:0.14
Consensus pattern (19 bp):
ACAAAATGTATACAAACAA
Found at i:70700 original size:24 final size:20
Alignment explanation
Indices: 70673--70730 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
70663 GCATGGGTAG
70673 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
70697 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
70717 TGTATCGATGCACT
1 TGCATCGATGCACT
70731 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:71533 original size:18 final size:18
Alignment explanation
Indices: 71507--71555 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
71497 TCTACGCGGT
71507 CTTTCGGGACATAGTGGTC
1 CTTT-GGGACATAGTGGTC
71526 CTTTGGGACATAGTGGTC
1 CTTTGGGACATAGTGGTC
*
71544 CTTCGGGACATA
1 CTTTGGGACATA
71556 TGTGTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (18 bp):
CTTTGGGACATAGTGGTC
Found at i:73763 original size:24 final size:25
Alignment explanation
Indices: 73731--73789 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
73721 GATGAAAAAA
*
73731 ATTTGATGAAGAAGTTTTGAA-AATG
1 ATTTGATGAAGAA-TTTTAAATAATG
73756 ATTT-ATGAAAGAATTTTAAATAATG
1 ATTTGATG-AAGAATTTTAAATAATG
73781 -TTTGATGAA
1 ATTTGATGAA
73790 TTTTTTTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (25 bp):
ATTTGATGAAGAATTTTAAATAATG
Found at i:73827 original size:24 final size:25
Alignment explanation
Indices: 73746--73829 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 25
73736 ATGAAGAAGT
*
73746 TTTG-AAAATGATTT-ATGAAAG-AA
1 TTTGAAAAATG-TTTGATGAAAGTTA
* ** *
73769 TTTTAAATAATGTTTGATGAATTTTT
1 TTTGAAA-AATGTTTGATGAAAGTTA
73795 TTTGAAAAATGTTTGAT-AAAGTTA
1 TTTGAAAAATGTTTGATGAAAGTTA
73819 TTTGAAAAATG
1 TTTGAAAAATG
73830 GTGCCCCTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
23 3 0.06
24 20 0.42
25 19 0.40
26 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.44
Consensus pattern (25 bp):
TTTGAAAAATGTTTGATGAAAGTTA
Found at i:73827 original size:25 final size:26
Alignment explanation
Indices: 73750--73827 Score: 65
Period size: 25 Copynumber: 3.1 Consensus size: 26
73740 AGAAGTTTTG
* *
73750 AAAATGATTT-ATGAAAG-AATTTTAA
1 AAAATG-TTTGATGAAAGTTATTTGAA
* ** *
73775 ATAATGTTTGATGAATTTTTTTTG-A
1 AAAATGTTTGATGAAAGTTATTTGAA
73800 AAAATGTTTGAT-AAAGTTATTTGAA
1 AAAATGTTTGATGAAAGTTATTTGAA
73825 AAA
1 AAA
73828 TGGTGCCCCT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
24 11 0.28
25 26 0.65
26 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (26 bp):
AAAATGTTTGATGAAAGTTATTTGAA
Found at i:75911 original size:17 final size:19
Alignment explanation
Indices: 75889--75930 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
75879 AAAATAAGGT
*
75889 ACAAAATGTATA-AAAC-A
1 ACAAAATGTAAACAAACAA
75906 ACAAAATGTAAACAAACAA
1 ACAAAATGTAAACAAACAA
75925 ACAAAA
1 ACAAAA
75931 GAAGGGACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 4 0.18
19 7 0.32
ACGTcount: A:0.69, C:0.14, G:0.05, T:0.12
Consensus pattern (19 bp):
ACAAAATGTAAACAAACAA
Found at i:76433 original size:18 final size:17
Alignment explanation
Indices: 76391--76437 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
76381 ATATATTAAC
*
76391 AAAATTAATAAAACACA
1 AAAAATAATAAAACACA
76408 AAATAATAATAAAATCA-A
1 AAA-AATAATAAAA-CACA
76426 TAAAAATAATAA
1 -AAAAATAATAA
76438 TCTTTTCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.12
18 18 0.69
19 5 0.19
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAATAAAACACA
Found at i:76748 original size:22 final size:22
Alignment explanation
Indices: 76722--76775 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
76712 CCCGAAGTTC
76722 AAAACCAAACCTCATTTTTACT
1 AAAACCAAACCTCATTTTTACT
76744 AAAACCAAACCTCATTTTTACT
1 AAAACCAAACCTCATTTTTACT
*
76766 AAAACTAAAC
1 AAAACCAAAC
76776 ATAAATCCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAACCAAACCTCATTTTTACT
Found at i:78941 original size:2 final size:2
Alignment explanation
Indices: 78926--78993 Score: 120
Period size: 2 Copynumber: 34.5 Consensus size: 2
78916 AATATAAAAA
*
78926 AT AT AA AT AT -T 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
78967 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 A
78994 GGGGCGGGTC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:80080 original size:20 final size:21
Alignment explanation
Indices: 80055--80106 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
80045 TTTTCCCAAT
*
80055 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
80075 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
80096 TCGCAATGCGA
1 TCGCAATGCGA
80107 TACTGACTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:80121 original size:20 final size:20
Alignment explanation
Indices: 80096--80209 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
80086 ATTGGGAAAA
*
80096 TCGCAATGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
* * *
80116 TCGCAATGCGATACTTACTA
1 TCGCAACGCGATACTGACTT
* * **
80136 TCGCAATGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
*
80157 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
80177 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
80197 TCGCAACGCGATA
1 TCGCAACGCGATA
80210 ATACATAATC
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:80126 original size:61 final size:62
Alignment explanation
Indices: 80054--80223 Score: 159
Period size: 61 Copynumber: 2.8 Consensus size: 62
80044 ATTTTCCCAA
* ** * *
80054 TTCGCAATGCGAATAAGTA-AATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
1 TTCGCAATGCGAATAAGTACAATCGCAACGCGATAAT-ACAAAATCGCAACGAGATACTGACT
** * *
80115 TTCGCAATGCG-ATACTTACTATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACT
1 TTCGCAATGCGAATAAGTACAATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACT
* * ** ** *
80176 TTCGCAACGCGATTCTG-ACTTTCGCAACGCGATAATACATAATCGCAA
1 TTCGCAATGCGAATAAGTACAATCGCAACGCGATAATACAAAATCGCAA
80224 TGCGATTTTC
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
60 5 0.06
61 81 0.91
62 3 0.03
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (62 bp):
TTCGCAATGCGAATAAGTACAATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACT
Found at i:80422 original size:22 final size:22
Alignment explanation
Indices: 80396--80439 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
80386 CACTCTCTCA
*
80396 CCCATCTTCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
80418 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
80440 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:80700 original size:20 final size:20
Alignment explanation
Indices: 80675--80727 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
80665 CGATTTTAGT
80675 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
* **
80695 TTCGCGTTGAGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
80715 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
80728 TTTCATTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:80928 original size:25 final size:24
Alignment explanation
Indices: 80874--80928 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
80864 TGTTTATTAT
* *
80874 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
80898 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
80924 TGTTT
1 TGTTT
80929 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:82060 original size:18 final size:18
Alignment explanation
Indices: 82034--82078 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
82024 TCCACTTCGG
*
82034 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
82052 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
82070 GAGCCATCA
1 GAGCCATCA
82079 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Done.