Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004609.1 Hibiscus syriacus cultivar Beakdansim tig00010303_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: 71670
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:9042 original size:1 final size:1
Alignment explanation
Indices: 9031--9120 Score: 72
Period size: 1 Copynumber: 90.0 Consensus size: 1
9021 ATGCTTGAAG
* * * * * * ** * *
9031 AAAAAAGAAAAAAGAAAAAAAAGAAAAAAAAAGAAAAAAAAGAGAAAAAAAAGGAAAAAAAGAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
9096 AAAAAAAAGAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
9121 TGGGGGGTCA
Statistics
Matches: 67, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:9058 original size:10 final size:10
Alignment explanation
Indices: 9038--9120 Score: 123
Period size: 10 Copynumber: 8.2 Consensus size: 10
9028 AAGAAAAAAG
9038 AAAAAAG-AA
1 AAAAAAGAAA
9047 AAAAAAGAAA
1 AAAAAAGAAA
9057 AAAAAAGAAA
1 AAAAAAGAAA
9067 AAAAAGAGAAA
1 AAAAA-AGAAA
*
9078 AAAAAGGAAA
1 AAAAAAGAAA
*
9088 AAAAGAGAAA
1 AAAAAAGAAA
9098 AAAAAAGAAAA
1 AAAAAAG-AAA
9109 AAAAAAGAAA
1 AAAAAAGAAA
9119 AA
1 AA
9121 TGGGGGGTCA
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
9 7 0.10
10 40 0.60
11 20 0.30
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:9059 original size:11 final size:11
Alignment explanation
Indices: 9028--9120 Score: 106
Period size: 11 Copynumber: 8.7 Consensus size: 11
9018 ATTATGCTTG
9028 AAGAAAAAAGAA
1 AAGAAAAAA-AA
9040 AA-AAGAAAAAA
1 AAGAA-AAAAAA
9051 AAG-AAAAAAA
1 AAGAAAAAAAA
9061 AAG--AAAAAA
1 AAGAAAAAAAA
*
9070 AAGAGAAAAAA
1 AAGAAAAAAAA
*
9081 AAGGAAAAAAA
1 AAGAAAAAAAA
*
9092 GAG-AAAAAAA
1 AAGAAAAAAAA
9102 AAGAAAAAAAA
1 AAGAAAAAAAA
9113 AAGAAAAA
1 AAGAAAAA
9121 TGGGGGGTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
9 9 0.12
10 18 0.25
11 39 0.54
12 6 0.08
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:10487 original size:85 final size:83
Alignment explanation
Indices: 10264--10491 Score: 357
Period size: 83 Copynumber: 2.7 Consensus size: 83
10254 ACTGGAACAA
* *
10264 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
10329 AGTTATTGAATTTGAAAG
66 AGTTATTGAATTTGAAAG
* *
10347 ATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACT
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
10412 AGTTATTGAATTTGGAAAG
66 AGTTATTGAATTT-GAAAG
* * * * *
10431 ATTAATGTGCCCAATAGCATCTTCTGGAAGTGTTATTTGAGATATATGATCTGGTTTGGTA
1 ATGAATGTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
10492 TGAACCCCAA
Statistics
Matches: 133, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
83 74 0.56
84 14 0.11
85 45 0.34
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACC
AGTTATTGAATTTGAAAG
Found at i:11525 original size:113 final size:113
Alignment explanation
Indices: 11330--11998 Score: 811
Period size: 113 Copynumber: 6.0 Consensus size: 113
11320 GCAAAGATTT
* * *
11330 AAATCCATCA-TTCAATGGATC-GACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGA
1 AAATCCATCACTT-GATGGATCAG-CTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
* * * * *
11393 AGGAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTATATTT
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTACTC
*
11443 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
11508 AAGGATGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTACTC
* * * **
11556 AAATCTATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AAGAAGTTCATAATGAGAAGAACTCATCTGAA
* * *
11620 GAAGGATGAAGAAGATCATAATGAGAAGAATTTGTTCAACC-TTTAGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTA-CTC
* * * **
11669 AAATCTATCACTTGATAGATTAGCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AAGAAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
11733 GAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTACTC
* * * * *
11782 AAATCCATCACTTGATGGATCAACTTTTCTAGAAAAAGTTCTTAATGAGAAAAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
11847 AAAGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAGA-TTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCA-ACCTTTTACTC
* *
11895 AAATCCATCACTTGATGGGTCAGTTTTTCCAG-AGAAGTTCATAATGAGAAGAACTCATC---AG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
* ** *
11956 GA-GAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACTTTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTT
11999 GAATGACTCT
Statistics
Matches: 499, Mismatches: 49, Indels: 21
0.88 0.09 0.04
Matches are distributed among these distances:
107 1 0.00
108 37 0.07
109 3 0.01
112 27 0.05
113 423 0.85
114 8 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTACTC
Found at i:11982 original size:17 final size:17
Alignment explanation
Indices: 11927--11982 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
11917 GTTTTTCCAG
11927 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
11944 AGAA-CTCATCAGGA-GAAGA
1 AGAAGTTCAT-A--ATG-AGA
11963 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
11980 AGA
1 AGA
11983 GCTTATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 2 0.06
19 9 0.29
20 4 0.13
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:12239 original size:3 final size:3
Alignment explanation
Indices: 12231--12307 Score: 91
Period size: 3 Copynumber: 24.7 Consensus size: 3
12221 ATTTTATTTA
* *
12231 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT AAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
12279 TAA TAT ATAT TATT TATT TAT TAA TAT TA
1 TAT TAT -TAT TA-T TA-T TAT TAT TAT TA
12308 CAAAACCCGG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 54 0.84
4 10 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:13681 original size:16 final size:16
Alignment explanation
Indices: 13660--13705 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
13650 ATATAATAAA
13660 TAATAATTTATTTTTT
1 TAATAATTTATTTTTT
** *
13676 TAATAATAAATTATTT
1 TAATAATTTATTTTTT
13692 TAAT-ATTTATTTTT
1 TAATAATTTATTTTT
13706 CAATATCGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATAATTTATTTTTT
Found at i:15489 original size:13 final size:15
Alignment explanation
Indices: 15471--15504 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
15461 TTGTATCAAA
15471 TTGAATTT-T-AAGT
1 TTGAATTTGTAAAGT
15484 TTGAATTTGTAAAGT
1 TTGAATTTGTAAAGT
15499 TTGAAT
1 TTGAAT
15505 AATAAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 1 0.05
15 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (15 bp):
TTGAATTTGTAAAGT
Found at i:29677 original size:21 final size:21
Alignment explanation
Indices: 29651--29726 Score: 134
Period size: 21 Copynumber: 3.6 Consensus size: 21
29641 GTTCACCGAG
29651 GACATGAAGACCATTCATAAA
1 GACATGAAGACCATTCATAAA
*
29672 GACATGAATACCATTCATAAA
1 GACATGAAGACCATTCATAAA
*
29693 GACATGAAGACCCTTCATAAA
1 GACATGAAGACCATTCATAAA
29714 GACATGAAGACCA
1 GACATGAAGACCA
29727 CTTTGCATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.18
Consensus pattern (21 bp):
GACATGAAGACCATTCATAAA
Found at i:31169 original size:11 final size:11
Alignment explanation
Indices: 31153--31177 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31143 AAAAAAACAT
31153 GGGCTGCTAAG
1 GGGCTGCTAAG
31164 GGGCTGCTAAG
1 GGGCTGCTAAG
31175 GGG
1 GGG
31178 TATTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (11 bp):
GGGCTGCTAAG
Found at i:39762 original size:14 final size:14
Alignment explanation
Indices: 39743--39770 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39733 TGTTAATTGA
39743 ACTTACGTCATTTT
1 ACTTACGTCATTTT
39757 ACTTACGTCATTTT
1 ACTTACGTCATTTT
39771 CTAAGCTTAT
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:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
ACTTACGTCATTTT
Found at i:40471 original size:6 final size:6
Alignment explanation
Indices: 40446--40719 Score: 368
Period size: 6 Copynumber: 45.7 Consensus size: 6
40436 CTTTTAAAAA
* * * * * *
40446 ATATGT ATATGT ATATAT ATACAT ATATAC ATATAC ATATAT ACATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * * * *
40494 ATATAT ATACAT ATATAT GTATAT GTATAT GTATAT ACATAT ACATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
40542 ATATAT ATATAT ATATAT ATATGT ATATGT ATATAC ATATAC ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
40590 ATATAT ATATAT ATATGT ATATGT ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
40638 ATGTAT ATATAT ATATAC ATATAT ATATAT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
40686 ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
40720 CCCTTGTTGT
Statistics
Matches: 245, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 245 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (6 bp):
ATATAT
Found at i:40471 original size:8 final size:8
Alignment explanation
Indices: 40446--40719 Score: 368
Period size: 8 Copynumber: 34.2 Consensus size: 8
40436 CTTTTAAAAA
*
40446 ATATGTAT
1 ATATATAT
*
40454 ATGTATAT
1 ATATATAT
*
40462 ATATACAT
1 ATATATAT
*
40470 ATATACAT
1 ATATATAT
*
40478 ATACATAT
1 ATATATAT
*
40486 ATACATAT
1 ATATATAT
40494 ATATATAT
1 ATATATAT
*
40502 ACATATAT
1 ATATATAT
*
40510 ATGTATAT
1 ATATATAT
* *
40518 GTATATGT
1 ATATATAT
*
40526 ATATACAT
1 ATATATAT
*
40534 ATACATAT
1 ATATATAT
40542 ATATATAT
1 ATATATAT
40550 ATATATAT
1 ATATATAT
*
40558 ATATATGT
1 ATATATAT
*
40566 ATATGTAT
1 ATATATAT
*
40574 ATACATAT
1 ATATATAT
*
40582 ACATATAT
1 ATATATAT
40590 ATATATAT
1 ATATATAT
40598 ATATATAT
1 ATATATAT
* *
40606 GTATATGT
1 ATATATAT
40614 ATATATAT
1 ATATATAT
40622 ATATATAT
1 ATATATAT
40630 ATATATAT
1 ATATATAT
*
40638 ATGTATAT
1 ATATATAT
40646 ATATATAT
1 ATATATAT
*
40654 ACATATAT
1 ATATATAT
40662 ATATATAT
1 ATATATAT
40670 ATATATAT
1 ATATATAT
40678 ATATATAT
1 ATATATAT
40686 ATATATAT
1 ATATATAT
40694 ATATATAT
1 ATATATAT
40702 ATATATAT
1 ATATATAT
40710 ATATATAT
1 ATATATAT
40718 AT
1 AT
40720 CCCTTGTTGT
Statistics
Matches: 231, Mismatches: 35, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 231 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (8 bp):
ATATATAT
Found at i:40474 original size:14 final size:14
Alignment explanation
Indices: 40446--40719 Score: 368
Period size: 14 Copynumber: 19.6 Consensus size: 14
40436 CTTTTAAAAA
* *
40446 ATATGTATATGTAT
1 ATATATATATATAT
*
40460 ATATATACATATAT
1 ATATATATATATAT
* *
40474 ACATATACATATAT
1 ATATATATATATAT
*
40488 ACATATATATATAT
1 ATATATATATATAT
* *
40502 ACATATATATGTAT
1 ATATATATATATAT
* *
40516 ATGTATATGTATAT
1 ATATATATATATAT
* *
40530 ACATATACATATAT
1 ATATATATATATAT
40544 ATATATATATATAT
1 ATATATATATATAT
* *
40558 ATATATGTATATGT
1 ATATATATATATAT
* *
40572 ATATACATATACAT
1 ATATATATATATAT
40586 ATATATATATATAT
1 ATATATATATATAT
* *
40600 ATATATGTATATGT
1 ATATATATATATAT
40614 ATATATATATATAT
1 ATATATATATATAT
*
40628 ATATATATATATGT
1 ATATATATATATAT
*
40642 ATATATATATATAC
1 ATATATATATATAT
40656 ATATATATATATAT
1 ATATATATATATAT
40670 ATATATATATATAT
1 ATATATATATATAT
40684 ATATATATATATAT
1 ATATATATATATAT
40698 ATATATATATATAT
1 ATATATATATATAT
40712 ATATATAT
1 ATATATAT
40720 CCCTTGTTGT
Statistics
Matches: 228, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 228 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:41005 original size:9 final size:9
Alignment explanation
Indices: 40987--41093 Score: 100
Period size: 9 Copynumber: 12.3 Consensus size: 9
40977 AAAGGAAAGT
*
40987 AAAAACAGA
1 AAAAAGAGA
40996 AAAAAGAGA
1 AAAAAGAGA
*
41005 AAAAAAAG-
1 AAAAAGAGA
*
41013 AAAAACAGA
1 AAAAAGAGA
41022 AAAAAGAG-
1 AAAAAGAGA
41030 AAAAA-AGA
1 AAAAAGAGA
*
41038 AGAAAGAGA
1 AAAAAGAGA
*
41047 AAACAGA-A
1 AAAAAGAGA
41055 GAAAAAGAG-
1 -AAAAAGAGA
*
41064 AAAAAGAAA
1 AAAAAGAGA
41073 AAAAAGA-A
1 AAAAAGAGA
41081 AAAAAGAAGA
1 AAAAAG-AGA
41091 AAA
1 AAA
41094 TAGAAAATAG
Statistics
Matches: 81, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
7 2 0.02
8 31 0.38
9 44 0.54
10 4 0.05
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:41007 original size:16 final size:16
Alignment explanation
Indices: 40988--41082 Score: 96
Period size: 16 Copynumber: 6.2 Consensus size: 16
40978 AAGGAAAGTA
40988 AAAACAGAAAAAAGAG
1 AAAACAGAAAAAAGAG
41004 ---A-A-AAAAAAGA-
1 AAAACAGAAAAAAGAG
41014 AAAACAGAAAAAAGAG
1 AAAACAGAAAAAAGAG
* *
41030 AAAAAAGAAGAAAGAG
1 AAAACAGAAAAAAGAG
41046 AAAACAGAAGAAAAAGAG
1 AAAACAG-A-AAAAAGAG
*
41064 AAAA-AGAAAAAAAAG
1 AAAACAGAAAAAAGAG
41079 AAAA
1 AAAA
41083 AAAGAAGAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
11 8 0.12
12 1 0.02
13 2 0.03
14 1 0.02
15 19 0.29
16 21 0.32
17 3 0.05
18 11 0.17
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAACAGAAAAAAGAG
Found at i:41016 original size:26 final size:25
Alignment explanation
Indices: 40982--41100 Score: 116
Period size: 26 Copynumber: 4.6 Consensus size: 25
40972 ACACAAAAGG
40982 AAAGTAAAAACAGAAAAAAGAGAAAAA
1 AAAG-AAAAA-AGAAAAAAGAGAAAAA
41009 AAAGAAAAACAGAAAAAAGAG--AAA
1 AAAGAAAAA-AGAAAAAAGAGAAAAA
* * * *
41033 AAAGAAGAAAGAGAAAACAGAAGAA
1 AAAGAAAAAAGAAAAAAGAGAAAAA
*
41058 AAAGAGAAAAAGAAAAAAAAGAAAAAA
1 AAAGA-AAAAAGAAAAAAGAG-AAAAA
*
41085 AGAAGAAAATAGAAAA
1 A-AAGAAAAAAGAAAA
41101 TAGACATATC
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
23 9 0.12
24 11 0.14
25 7 0.09
26 29 0.37
27 18 0.23
28 4 0.05
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.02
Consensus pattern (25 bp):
AAAGAAAAAAGAAAAAAGAGAAAAA
Found at i:41023 original size:58 final size:57
Alignment explanation
Indices: 40961--41084 Score: 139
Period size: 58 Copynumber: 2.1 Consensus size: 57
40951 GAAGAGATAT
40961 AGAAAAAACACACACAAAAG-GAAAGTA-AAAACAG-A-AAAAAGAGAAAAAAAAGAAAAA
1 AGAAAAAACACA-A-AAAAGAGAAAG-AGAAAACAGAAGAAAAAGAGAAAAAAAA-AAAAA
* * *
41018 CAGAAAAAAGAGAAAAAAGAAGAAAGAGAAAACAGAAGAAAAAGAGAAAAAGAAAAAAA
1 -AGAAAAAACACAAAAAAG-AGAAAGAGAAAACAGAAGAAAAAGAGAAAAAAAAAAAAA
41077 AGAAAAAA
1 AGAAAAAA
41085 AGAAGAAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
56 5 0.09
57 2 0.03
58 30 0.52
59 6 0.10
60 15 0.26
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.01
Consensus pattern (57 bp):
AGAAAAAACACAAAAAAGAGAAAGAGAAAACAGAAGAAAAAGAGAAAAAAAAAAAAA
Found at i:41074 original size:7 final size:7
Alignment explanation
Indices: 41006--41100 Score: 68
Period size: 7 Copynumber: 12.6 Consensus size: 7
40996 AAAAAGAGAA
41006 AAAAAAG
1 AAAAAAG
41013 AAAAACAG
1 AAAAA-AG
41021 AAAAAAGAG
1 -AAAAA-AG
41030 AAAAAAG
1 AAAAAAG
41037 AAGAAAGAG
1 AA-AAA-AG
*
41046 AAAACAG
1 AAAAAAG
41053 AAGAAAAAG
1 -A-AAAAAG
41062 AGAAAAAG
1 A-AAAAAG
41070 AAAAAA-
1 AAAAAAG
41076 AAGAAAA-
1 AA-AAAAG
*
41083 AAAGAAG
1 AAAAAAG
*
41090 AAAATAG
1 AAAAAAG
41097 AAAA
1 AAAA
41101 TAGACATATC
Statistics
Matches: 74, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
6 5 0.07
7 31 0.42
8 22 0.30
9 16 0.22
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:41083 original size:16 final size:16
Alignment explanation
Indices: 40982--41100 Score: 112
Period size: 17 Copynumber: 7.1 Consensus size: 16
40972 ACACAAAAGG
* *
40982 AAAGTAAAAACAGAAAA
1 AAAGAAAAAAAAG-AAA
40999 AAGAGAAAAAAAAGAAA
1 AA-AGAAAAAAAAGAAA
*
41016 AACAGAAAAAAGAGAAA
1 AA-AGAAAAAAAAGAAA
* *
41033 AAAGAAGAAAGAGAAA
1 AAAGAAAAAAAAGAAA
* *
41049 ACAGAAGAAAAAGAGAA
1 AAAGAAAAAAAAGA-AA
41066 AAAGAAAAAAAAGAAAA
1 AAAGAAAAAAAAG-AAA
*
41083 AAAGAAGAAAATAGAAA
1 AAAGAA-AAAAAAGAAA
41100 A
1 A
41101 TAGACATATC
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
16 25 0.28
17 47 0.53
18 16 0.18
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAGAAAAAAAAGAAA
Found at i:41093 original size:8 final size:8
Alignment explanation
Indices: 41008--41093 Score: 54
Period size: 8 Copynumber: 10.5 Consensus size: 8
40998 AAAGAGAAAA
41008 AAAAGAA-
1 AAAAGAAG
41015 AAACAGAA-
1 AAA-AGAAG
*
41023 AAAAGAGAA
1 AAAAGA-AG
41032 AAAAGAAG
1 AAAAGAAG
41040 AAAGAGAA-
1 AAA-AGAAG
*
41048 AACAGAAG
1 AAAAGAAG
41056 AAAA-AGAG
1 AAAAGA-AG
*
41064 AAAAAGAAAA
1 -AAAAG-AAG
*
41074 AAAAGAAA
1 AAAAGAAG
41082 AAAAGAAG
1 AAAAGAAG
41090 AAAA
1 AAAA
41094 TAGAAAATAG
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
7 11 0.17
8 33 0.51
9 19 0.29
10 1 0.02
11 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:41798 original size:26 final size:28
Alignment explanation
Indices: 41736--41805 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
41726 GCCAACCCGG
* * *
41736 AACATATTACCTCCCCAAATTGACCTGA
1 AACACATTACTTCCCCAAATTGAACTGA
41764 AACACATTACTTCCCCAAATT-AAC-GA
1 AACACATTACTTCCCCAAATTGAACTGA
41790 AACACATTACCTTCCC
1 AACACATTA-CTTCCC
41806 AAGGAACCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.29
27 8 0.21
28 19 0.50
ACGTcount: A:0.37, C:0.34, G:0.04, T:0.24
Consensus pattern (28 bp):
AACACATTACTTCCCCAAATTGAACTGA
Found at i:41806 original size:26 final size:28
Alignment explanation
Indices: 41736--41807 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 28
41726 GCCAACCCGG
* * *
41736 AACATATTACCTCCCCAAATTGACCTGA
1 AACACATTACCTTCCCAAATTGAACTGA
41764 AACACATTA-CTTCCCCAAATT-AAC-GA
1 AACACATTACCTT-CCCAAATTGAACTGA
41790 AACACATTACCTTCCCAA
1 AACACATTACCTTCCCAA
41808 GGAACCCTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 16 0.41
27 7 0.18
28 16 0.41
ACGTcount: A:0.39, C:0.33, G:0.04, T:0.24
Consensus pattern (28 bp):
AACACATTACCTTCCCAAATTGAACTGA
Found at i:43112 original size:55 final size:53
Alignment explanation
Indices: 43053--43408 Score: 374
Period size: 54 Copynumber: 6.6 Consensus size: 53
43043 GTGTTTTTTT
* * ** * *
43053 AGAAATTAAGTTTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAA
1 AGAAACTAAGTCTGATTTTCAGGGGTTTCTTGA-TATTTTCAAATGA-ATTTTAA
** * * *
43108 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGACCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGGGGTTTCTTGAT-ATTTTCAAATGA-ATTTTAA
*
43163 AGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTAA
1 AGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAA
* * * * * *
43216 AGAAGCTAAGCCTAATTTTTAGGGGTTTCTGGATGTTTTCAAATGAATTTTCAA
1 AGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTT-AA
* *
43270 AGAAATTAAGTCTGAATTTT-AGGGGTTTCTTGATGTTTTCAAATGAATTTTCAA
1 AGAAACTAAGTCTG-ATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTT-AA
* * *
43324 AGAAA-TGAAGCCTAATTTTCAGTGGTTTCTTGATATTTTCAAATGAATTTTTAA
1 AGAAACT-AAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAA-TTTTAA
* * * *
43378 AGAAACTAAGCCTAATTTTTAGGAGTTTCTT
1 AGAAACTAAGTCTGATTTTCAGGGGTTTCTT
43409 TATGATAACT
Statistics
Matches: 265, Mismatches: 29, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
53 57 0.22
54 118 0.45
55 90 0.34
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (53 bp):
AGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAA
Found at i:43296 original size:54 final size:54
Alignment explanation
Indices: 43089--43408 Score: 396
Period size: 54 Copynumber: 5.9 Consensus size: 54
43079 TTCTTGACAA
* * * **
43089 TTTTCAAATGAGCTTTT-AAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
1 TTTTCAAATGA-ATTTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
* ** * *
43143 ATTTTTAAATGACCTTTCAAAGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATG
1 -TTTTCAAATGAATTTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
* * *
43198 TTTTCAAATGAATTTT-AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTGGATG
1 TTTTCAAATGAATTTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
* *
43251 TTTTCAAATGAATTTTCAAAGAAATTAAGTCTGAATTTT-AGGGGTTTCTTGATG
1 TTTTCAAATGAATTTTCAAAGAAACTAAGCCT-AATTTTCAGGGGTTTCTTGATG
* *
43305 TTTTCAAATGAATTTTCAAAGAAA-TGAAGCCTAATTTTCAGTGGTTTCTTGATA
1 TTTTCAAATGAATTTTCAAAGAAACT-AAGCCTAATTTTCAGGGGTTTCTTGATG
* * *
43359 TTTTCAAATGAATTTTTAAAGAAACTAAGCCTAATTTTTAGGAGTTTCTT
1 TTTTCAAATGAATTTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTT
43409 TATGATAACT
Statistics
Matches: 236, Mismatches: 23, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
53 55 0.23
54 129 0.55
55 52 0.22
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (54 bp):
TTTTCAAATGAATTTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
Found at i:43378 original size:162 final size:162
Alignment explanation
Indices: 43089--43407 Score: 457
Period size: 162 Copynumber: 2.0 Consensus size: 162
43079 TTCTTGACAA
* *
43089 TTTTCAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATG
1 TTTTCAAATGAGATTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATG
* * * *
43154 ACCTTTCAAAGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTAAAGA
66 AACTTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAAAGA
* *
43219 AGCTAAGCCTAATTTTTAGGGGTTTCTGGATG
131 AACTAAGCCTAATTTTTAGGAGTTTCTGGATG
* **
43251 TTTTCAAATGA-ATTTTCAAAGAAATTAAGTCTGAATTTT-AGGGGTTTCTTGATG-TTTTCAAA
1 TTTTCAAATGAGATTTT-AAAGAAACTAAGTCTG-ATTTTCAGAAGTTTCTTGATGATTTTCAAA
* *
43313 TGAATTTTCAAAGAAA-TGAAGCCTAATTTTCAGTGGTTTCTTGATATTTTCAAATGAATTTTTA
64 TGAACTTTCAAAGAAACT-AAGCCTAATTTTCAGGGGTTTCTTGATATTTTCAAATGAA-TTTTA
43377 AAGAAACTAAGCCTAATTTTTAGGAGTTTCT
127 AAGAAACTAAGCCTAATTTTTAGGAGTTTCT
43408 TTATGATAAC
Statistics
Matches: 140, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
160 1 0.01
161 61 0.44
162 73 0.52
163 5 0.04
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (162 bp):
TTTTCAAATGAGATTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATG
AACTTTCAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATATTTTCAAATGAATTTTAAAGA
AACTAAGCCTAATTTTTAGGAGTTTCTGGATG
Found at i:43855 original size:41 final size:40
Alignment explanation
Indices: 43742--43871 Score: 100
Period size: 41 Copynumber: 3.1 Consensus size: 40
43732 AGGGTTTCTT
**
43742 GATGAGTAAGTCCTTCGGGGACATC-AGTAAGTCTTTCGAGCGT
1 GATGA-TAAGTCCTTC--GGACATCTA-TAAGTCTTTCGAGCAA
* * * * *
43785 GATGCTTAAATCTTTCGGGTCAACTATAAGTCTTTCGAGCAA
1 GATG-ATAAGTCCTTC-GGACATCTATAAGTCTTTCGAGCAA
* * *
43827 GATGATAAGTCCTTCGGACCATCTATAAGACCTTCGAGCAG
1 GATGATAAGTCCTTCGGA-CATCTATAAGTCTTTCGAGCAA
43868 GATG
1 GATG
43872 TTTTCAAATG
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
40 2 0.03
41 30 0.43
42 24 0.35
43 13 0.19
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (40 bp):
GATGATAAGTCCTTCGGACATCTATAAGTCTTTCGAGCAA
Found at i:43929 original size:275 final size:274
Alignment explanation
Indices: 43435--43977 Score: 867
Period size: 275 Copynumber: 2.0 Consensus size: 274
43425 TGAAAGATTT
*
43435 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTCCGGGCCATCAATAAGTC
1 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTCCGGGACATCAATAAGTC
*
43500 TTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCT
66 TTTCGAGCATGATGCTTAAATCCTTCGGGTCAACTATAAGTCTTTCAAGCAAGATGATAAGTCCT
* * * * *
43565 TCGTGACATCCATATGACTTTCGGGCAGGATGTTTTCAAATGAGTTTTTAGAAATTAAGCTAGAT
131 TCGTGACATCCATAAGACCTTCGAGCAGGATGTTTTCAAATGAGTTTATAGAAACTAAGCTAGAT
* *
43630 TTTCAGGGGTTTCTTGATGATTATCTCCAAAGAGTTTTTTAAAGGAAGCTAAGCCT-ATTTTTAG
196 TTTCAGGGGTTTCTTGACGATTATCTCCAAAGA-ATTTTTAAAGGAAGCTAAGCCTAATTTTTAG
43694 GGGTTCCTTAACAAC
260 GGGTTCCTTAACAAC
* * *
43709 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGGACATCAGTAAGT
1 TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGT-CTTCCGGGACATCAATAAGT
* * *
43774 CTTTCGAGCGTGATGCTTAAATCTTTCGGGTCAACTATAAGTCTTTCGAGCAAGATGATAAGTCC
65 CTTTCGAGCATGATGCTTAAATCCTTCGGGTCAACTATAAGTCTTTCAAGCAAGATGATAAGTCC
*
43839 TTCG-GACCATCTATAAGACCTTCGAGCAGGATGTTTTCAAATGAGTTTATAGAAACTAAGCCT-
130 TTCGTGA-CATCCATAAGACCTTCGAGCAGGATGTTTTCAAATGAGTTTATAGAAACTAAG-CTA
**
43902 GATTTTCAGGGGTTTCTTGACGATTATCTTTAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTT
193 GATTTTCAGGGGTTTCTTGACGATTATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTT
43967 AGGGGTTCCTT
258 AGGGGTTCCTT
43978 GATGACAACT
Statistics
Matches: 247, Mismatches: 18, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
274 66 0.27
275 179 0.72
276 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (274 bp):
TAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAATAAGTCTTCCGGGACATCAATAAGTC
TTTCGAGCATGATGCTTAAATCCTTCGGGTCAACTATAAGTCTTTCAAGCAAGATGATAAGTCCT
TCGTGACATCCATAAGACCTTCGAGCAGGATGTTTTCAAATGAGTTTATAGAAACTAAGCTAGAT
TTTCAGGGGTTTCTTGACGATTATCTCCAAAGAATTTTTAAAGGAAGCTAAGCCTAATTTTTAGG
GGTTCCTTAACAAC
Found at i:44737 original size:139 final size:138
Alignment explanation
Indices: 44490--44888 Score: 563
Period size: 139 Copynumber: 2.9 Consensus size: 138
44480 AGATGAACCA
* * *
44490 ATCAACATTTCAAATGGAGAATTCATAAT-G-AGAACTCATCCGATGAAGTAGAAGAAGTTCATA
1 ATCAACATTTCTAATGGAGAGTTCATAATAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATA
* * *
44553 ATGAGAAG-ATCTTGTTCGACCTTAGCTTGATTCATCGCATATGGAGTTGAATCAGCAACACCTC
66 ATGAGAAGAAT-TTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
44617 ACTCGAGGG
130 ACTCGAGGG
*
44626 ATCAACATTTCTAATGGAGAGTTCATAATAAGAAGAACTCATCCGATGAAGGAGAAGAAGTTTAT
1 ATCAACATTTCTAATGGAGAGTTCATAAT-AGAAGAACTCATCCGATGAAGGAGAAGAAGTTCAT
* *
44691 AATGAGAAGAATTTGTTCAACCTTAGCTCGATTCGTCACATATGGAGTTGAATCAGCAATACCTC
65 AATGAGAAGAATTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTC
44756 ACTCGAGGG
130 ACTCGAGGG
* * *
44765 ATCAACATTACTAGTGGAGAGTTCATAATGAGAAGAACTCATTCGAT-AAGGGAGAAGAAGTTCA
1 ATCAACATTTCTAATGGAGAGTTCATAAT-AGAAGAACTCATCCGATGAA-GGAGAAGAAGTTCA
* * * * * *
44829 TAATGAGAAGAACTTGTTCAACCTTAGCTTGTTTCCATCGCATAAGGAGTTGGATCAGCA
64 TAATGAGAAGAATTTGTTCAACCTTAGCTCGATT-CATCACATATGGAGTTGAATCAGCA
44889 TCATCGTTTC
Statistics
Matches: 236, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
136 27 0.11
138 3 0.01
139 183 0.78
140 23 0.10
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (138 bp):
ATCAACATTTCTAATGGAGAGTTCATAATAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATA
ATGAGAAGAATTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
CTCGAGGG
Found at i:44847 original size:20 final size:19
Alignment explanation
Indices: 44785--44848 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 19
44775 CTAGTGGAGA
44785 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* *
44804 CATTCGATAAGGGAGAAGAA--
1 -GTTC-ATAA-TGAGAAGAACT
44824 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
44844 GTTCA
1 GTTCA
44849 ACCTTAGCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 8 0.23
18 4 0.11
19 3 0.09
20 8 0.23
21 4 0.11
22 8 0.23
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:56736 original size:14 final size:15
Alignment explanation
Indices: 56717--56753 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
56707 ACAATAGATC
56717 AAAAGAAAGAAAGA-
1 AAAAGAAAGAAAGAG
*
56731 AAAAGAAAAAAAGAG
1 AAAAGAAAGAAAGAG
56746 AAAA-AAAG
1 AAAAGAAAG
56754 TTGTTCGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAGAG
Found at i:58942 original size:43 final size:43
Alignment explanation
Indices: 58892--58973 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
58882 TGATTATATA
58892 TATATATATAATATTTTATATTTTTTATATTAATTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAATTATATTAAT
58935 TATATATATAATATTTTATATTTTTTATATTAATTATAT
1 TATATATATAATATTTTATATTTTTTATATTAATTATAT
58974 ATAAAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (43 bp):
TATATATATAATATTTTATATTTTTTATATTAATTATATTAAT
Found at i:58952 original size:34 final size:34
Alignment explanation
Indices: 58914--58985 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
58904 ATTTTATATT
*
58914 TTTTATATTAATTATATTAATTATATATATAATA
1 TTTTATATTAATTATATTAATTATATATAAAATA
**
58948 TTTTATATTTTTTATATTAATTATATATAAAATA
1 TTTTATATTAATTATATTAATTATATATAAAATA
58982 TTTT
1 TTTT
58986 CGAGTTCGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TTTTATATTAATTATATTAATTATATATAAAATA
Found at i:58971 original size:9 final size:9
Alignment explanation
Indices: 58916--58973 Score: 59
Period size: 9 Copynumber: 6.7 Consensus size: 9
58906 TTTATATTTT
58916 TTATATTAA
1 TTATATTAA
58925 TTATATTAA
1 TTATATTAA
58934 TTATA-TATA
1 TTATATTA-A
*
58943 TAATATT--
1 TTATATTAA
**
58950 TTATATTTT
1 TTATATTAA
58959 TTATATTAA
1 TTATATTAA
58968 TTATAT
1 TTATAT
58974 ATAAAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 6 0.15
8 2 0.05
9 32 0.78
10 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTATATTAA
Found at i:63606 original size:35 final size:37
Alignment explanation
Indices: 63539--63607 Score: 124
Period size: 35 Copynumber: 1.9 Consensus size: 37
63529 TGTACAACCT
63539 AAAATGTTAATTTTTTAACATTTTTTATTGGCAATCG
1 AAAATGTTAATTTTTTAACATTTTTTATTGGCAATCG
63576 AAAATGTTAA-TTTTTAACA-TTTTTATTGGCAA
1 AAAATGTTAATTTTTTAACATTTTTTATTGGCAA
63608 CCGTTTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 13 0.41
36 9 0.28
37 10 0.31
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (37 bp):
AAAATGTTAATTTTTTAACATTTTTTATTGGCAATCG
Found at i:64685 original size:60 final size:60
Alignment explanation
Indices: 64633--64748 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
64623 ACTATGACTC
* *
64633 TCATTCTAAATTAATC-CTCAAAC-TTTTGAATATTTCAATTTTATCCCCAAACTATAACAT
1 TCATTCTAAATTAATCTC-CAAACTTTTTGAACATTTCAATTTCAT-CCCAAACTATAACAT
* *
64693 TCATTCTAAATTAGTCTCCAAACTTTTTGAACATTTCAATTTCATCTCAAACTATA
1 TCATTCTAAATTAATCTCCAAACTTTTTGAACATTTCAATTTCATCCCAAACTATA
64749 TGTATATACT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 30 0.60
61 20 0.40
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41
Consensus pattern (60 bp):
TCATTCTAAATTAATCTCCAAACTTTTTGAACATTTCAATTTCATCCCAAACTATAACAT
Found at i:64994 original size:60 final size:58
Alignment explanation
Indices: 64866--65015 Score: 203
Period size: 60 Copynumber: 2.5 Consensus size: 58
64856 TGTTTGATGG
* *
64866 ATTTGGGGATGAAATTGGAATATTTAAAAGTTTAGGACCAATTTAGAAAGAGGGTCAT
1 ATTTGGGGATGAAATTAGAATATTTAAAAGTTTAGGACCAATTTAGAAAGAGAGTCAT
* * *
64924 ATATTAGGGATGAAATTAGATTATTTAAAAGTTTAAGGACTAATTTA-AAATGAGAGTCAT
1 AT-TTGGGGATGAAATTAGAATATTTAAAAGTTT-AGGACCAATTTAGAAA-GAGAGTCAT
*
64984 AATTTGGGGATGAAATTAGAATGTTTAAAAGT
1 -ATTTGGGGATGAAATTAGAATATTTAAAAGT
65016 AGAGTTTGAA
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
58 2 0.03
59 31 0.39
60 45 0.56
61 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (58 bp):
ATTTGGGGATGAAATTAGAATATTTAAAAGTTTAGGACCAATTTAGAAAGAGAGTCAT
Found at i:65232 original size:3 final size:3
Alignment explanation
Indices: 65224--65259 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
65214 CTCAATCCCT
65224 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65260 CAAACCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:66616 original size:23 final size:22
Alignment explanation
Indices: 66578--66625 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
66568 TTAATTACAA
*
66578 TTTAGTCCTTGATTTTATTTTAT
1 TTTAGTCCTTGATTTTA-ATTAT
66601 TTTAGTCCTT-ATTTTTAATTAT
1 TTTAGTCCTTGA-TTTTAATTAT
66623 TTT
1 TTT
66626 CCAACTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (22 bp):
TTTAGTCCTTGATTTTAATTAT
Found at i:66622 original size:22 final size:23
Alignment explanation
Indices: 66578--66625 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
66568 TTAATTACAA
*
66578 TTTAGTCCTTGATTTTATTTTAT
1 TTTAGTCCTTGATTTTATATTAT
66601 TTTAGTCCTT-ATTTT-TAATTAT
1 TTTAGTCCTTGATTTTAT-ATTAT
66623 TTT
1 TTT
66626 CCAACTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 12 0.52
23 10 0.43
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (23 bp):
TTTAGTCCTTGATTTTATATTAT
Done.