Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006497.1 Hibiscus syriacus cultivar Beakdansim tig00015808_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: 126740
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4346 original size:20 final size:20
Alignment explanation
Indices: 4321--4485 Score: 90
Period size: 20 Copynumber: 9.0 Consensus size: 20
4311 TAAATTAAAT
4321 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGGATCAGTTTTA
* * *
4341 ATTAGATAGAATCAATTTTT
1 ATTAGATAGGATCAGTTTTA
* *
4361 ATT--CT---ATTAG--TT-
1 ATTAGATAGGATCAGTTTTA
*
4373 ATTAGATAGGATCATTTTTA
1 ATTAGATAGGATCAGTTTTA
*
4393 ATTAGATAGAATCAGTTTT-
1 ATTAGATAGGATCAGTTTTA
*** *
4412 -TT--ATTCTATTAG--TT-
1 ATTAGATAGGATCAGTTTTA
*
4426 ATTAGATAGGATCATTTTTA
1 ATTAGATAGGATCAGTTTTA
*
4446 ATTAGATAGGATCATTTTTA
1 ATTAGATAGGATCAGTTTTA
* *
4466 ATTAGATAGAATCATTTTTA
1 ATTAGATAGGATCAGTTTTA
4486 TTCTGTTGCT
Statistics
Matches: 110, Mismatches: 21, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
12 3 0.03
13 2 0.02
14 3 0.03
15 5 0.05
16 6 0.05
17 8 0.07
18 3 0.03
19 4 0.04
20 76 0.69
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (20 bp):
ATTAGATAGGATCAGTTTTA
Found at i:4436 original size:53 final size:52
Alignment explanation
Indices: 4320--4464 Score: 254
Period size: 53 Copynumber: 2.8 Consensus size: 52
4310 CTAAATTAAA
* *
4320 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAATTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTTATTCTATTAGT
4372 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTTATTCTATTAGT
*
4425 TATTAGATAGGATCATTTTTAATTAGATAGGATCATTTTT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTT
4465 AATTAGATAG
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
52 39 0.44
53 50 0.56
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCATTTTTTATTCTATTAGT
Found at i:12136 original size:2 final size:2
Alignment explanation
Indices: 12129--12178 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
12119 TATTTACCAA
12129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12171 AT AT AT AT
1 AT AT AT AT
12179 TGCCTATTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17525 original size:63 final size:62
Alignment explanation
Indices: 17447--17582 Score: 200
Period size: 63 Copynumber: 2.2 Consensus size: 62
17437 TTAGTAAAAC
*
17447 TGATAATTTAGATATTAAATAAATAATTTACTCAAAAATAAATGTGAATTCAAACAAATTATA
1 TGAT-ATTTAGATATTAAATAAATAATTTACCCAAAAATAAATGTGAATTCAAACAAATTATA
* ** *
17510 TGATAGTTTATATATTAAATACGTAATTTACCCCAAAATAAATGTGAATTCAAACAAATTATA
1 TGATA-TTTAGATATTAAATAAATAATTTACCCAAAAATAAATGTGAATTCAAACAAATTATA
*
17573 TAATATTTAG
1 TGATATTTAG
17583 GTTCAATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
62 5 0.08
63 60 0.92
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (62 bp):
TGATATTTAGATATTAAATAAATAATTTACCCAAAAATAAATGTGAATTCAAACAAATTATA
Found at i:25191 original size:22 final size:22
Alignment explanation
Indices: 25163--25209 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
25153 AATCAATTAC
25163 TTTTATAAAATAT-AAATTTATT
1 TTTTATAAAATATGAAA-TTATT
* *
25185 TTTTATATAATTTGAAATTATT
1 TTTTATAAAATATGAAATTATT
25207 TTT
1 TTT
25210 GTCAGAAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTATAAAATATGAAATTATT
Found at i:30510 original size:3 final size:3
Alignment explanation
Indices: 30504--30529 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30494 TGCTGTTGGT
30504 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
30530 TGTTAACTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:32526 original size:21 final size:21
Alignment explanation
Indices: 32494--32537 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32484 TGCTTCTTTA
32494 ATTGAGAGTGCATCGATACAC
1 ATTGAGAGTGCATCGATACAC
*
32515 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATACAC
32536 AT
1 AT
32538 AACCCATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATACAC
Found at i:33954 original size:60 final size:60
Alignment explanation
Indices: 33861--33975 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
33851 CTCCACGATG
* * **
33861 TTGATATTTAGGTCGAGCAAGCTAGTAGTTGAATGCCTTCCCCTTTAACTTGAAGGCATT
1 TTGATATTGAGGTCGAGCAAGCTAGTAGTTGAATGCCTCCCCCTGGAACTTGAAGGCATT
*
33921 TTGATATTGAGGTCGAAG-AAGCTCGTAGTTGAATGCCTCCCCCTGGAACTTGAAG
1 TTGATATTGAGGTCG-AGCAAGCTAGTAGTTGAATGCCTCCCCCTGGAACTTGAAG
33976 ACACCGTGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 47 0.96
61 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (60 bp):
TTGATATTGAGGTCGAGCAAGCTAGTAGTTGAATGCCTCCCCCTGGAACTTGAAGGCATT
Found at i:34858 original size:20 final size:20
Alignment explanation
Indices: 34830--35041 Score: 174
Period size: 20 Copynumber: 10.5 Consensus size: 20
34820 GATTTTCCAG
* ** *
34830 AATCTCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
* *
34850 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
34869 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
* *
34891 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
34911 AATCGCAACGCTAATACGTAA
1 AATCGCAACGCGAATCCGT-A
* * *
34932 AATCACAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
34952 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
34972 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
34992 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
35012 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATCCGTA
35032 AATCGCAACG
1 AATCGCAACG
35042 AGATTCTGAC
Statistics
Matches: 154, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
19 1 0.01
20 121 0.79
21 31 0.20
22 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:34893 original size:41 final size:41
Alignment explanation
Indices: 34848--35043 Score: 222
Period size: 41 Copynumber: 4.8 Consensus size: 41
34838 CGCGAATATG
* *
34848 AAAATCGCAACGCG-ATTCTG-ACTATCGCAACGAGTATCCGT
1 AAAATCGCAACGCGTA-TCTGTA-AATCGCAACGAGTATACGT
*
34889 AAAATCGCAACGCGTATCTGTAAATCGCAACG-CTAATACGT
1 AAAATCGCAACGCGTATCTGTAAATCGCAACGAGT-ATACGT
* *
34930 AAAATCACAACGCGTATCTGTAAATCGCAACGAGAATACGT
1 AAAATCGCAACGCGTATCTGTAAATCGCAACGAGTATACGT
* * * * *
34971 -AAATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGT
1 AAAATCGCAACGCGTATCTGTAAATCGCAACGAGTATACGT
* *
35011 -AAATCGCAATGCGAATCTGTAAATCGCAACGAG
1 AAAATCGCAACGCGTATCTGTAAATCGCAACGAG
35044 ATTCTGACTA
Statistics
Matches: 136, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
40 65 0.48
41 69 0.51
42 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGTATCTGTAAATCGCAACGAGTATACGT
Found at i:34986 original size:40 final size:41
Alignment explanation
Indices: 34830--35044 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 41
34820 GATTTTCCAG
* * *
34830 AATCTCAACGCGAATATG-AAAATCGCAACGCG-ATTCTG-A
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTA-TCTGTA
* * *
34869 CTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCTGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTA
** *
34911 AATCGCAACGCTAATACGTAAAATCACAACGCGTATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTA
* *
34952 AATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTA
* * * *
34992 AATCGCAATGCGAATACGT-AAATCGCAATGCGAATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTA
35032 AATCGCAACGAGA
1 AATCGCAACGAGA
35045 TTCTGACTAT
Statistics
Matches: 149, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
40 77 0.52
41 70 0.47
42 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTA
Found at i:35872 original size:19 final size:19
Alignment explanation
Indices: 35808--35906 Score: 117
Period size: 19 Copynumber: 5.1 Consensus size: 19
35798 TCTTTTAGTT
* *
35808 GAAATGAAAATCGCAATGA
1 GAAATGAAAATCGCAACGC
35827 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
35847 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
*
35867 GAAATGAAAATCGCAACGG
1 GAAATGAAAATCGCAACGC
* *
35886 GAAATTAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
35905 GA
1 GA
35907 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 36 0.53
20 30 0.44
21 2 0.03
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:35950 original size:33 final size:33
Alignment explanation
Indices: 35913--35994 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
35903 GCGATTTTGG
* **
35913 TTTCGCGTTGCGATTATCTCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTATCACGTTGCAATGGTCA
* *
35946 TTTCGCGTTGCGATTCTCACGTTGCGATGGTCA
1 TTTCGCGTTGCGATTATCACGTTGCAATGGTCA
35979 TTTCCGCGTTGCGATT
1 TTT-CGCGTTGCGATT
35995 TTCATTCTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 31 0.72
34 12 0.28
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.41
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCACGTTGCAATGGTCA
Found at i:35999 original size:20 final size:20
Alignment explanation
Indices: 35958--36016 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
35948 TCGCGTTGCG
* **
35958 ATTCTCACGTTGCGATGGTC
1 ATTCTCGCGTTGCGATTTTC
35978 ATT-TCCGCGTTGCGATTTTC
1 ATTCT-CGCGTTGCGATTTTC
*
35998 ATTCTCTCGTTGCGATTTT
1 ATTCTCGCGTTGCGATTTT
36017 AAGTTTAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (20 bp):
ATTCTCGCGTTGCGATTTTC
Found at i:36582 original size:20 final size:20
Alignment explanation
Indices: 36557--36771 Score: 168
Period size: 20 Copynumber: 10.7 Consensus size: 20
36547 GCTTTAAAAA
36557 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
36577 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
* * *
36597 TCGCATTGTGATTTACGGAT
1 TCGCGTTGCGATTTACGTAT
* * *
36617 ACGCATTGCGATTTATGTAT
1 TCGCGTTGCGATTTACGTAT
* * *
36637 TCTCGTTGCGATTTATAG-AA
1 TCGCGTTGCGATTTA-CGTAT
*
36657 TCTCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAT
* *
36677 T-GTCATTGCGATTTACGGAT
1 TCG-CGTTGCGATTTACGTAT
* *
36697 ACGCGTTGCGATTTTACGGAT
1 TCGCGTTGCGA-TTTACGTAT
* * * *
36718 ACTCGTTGCGATAGT-CAG-AA
1 TCGCGTTGCGAT-TTAC-GTAT
** *
36738 TCGCGTTGCGATTTATATGT
1 TCGCGTTGCGATTTACGTAT
36758 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
36772 TCCAGTTGCG
Statistics
Matches: 157, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.01
20 132 0.84
21 23 0.15
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGTAT
Found at i:36903 original size:20 final size:19
Alignment explanation
Indices: 36853--36907 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
36843 TATTCTTCAT
36853 AATCGCGTTGCGATTCTGG
1 AATCGCGTTGCGATTCTGG
* **
36872 AAACTGATTTGCGATTCTGG
1 AATC-GCGTTGCGATTCTGG
36892 AGATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
36908 TTTATTTCGC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (19 bp):
AATCGCGTTGCGATTCTGG
Found at i:37419 original size:20 final size:21
Alignment explanation
Indices: 37394--37432 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
37384 ATTAATTTTT
37394 AATG-AAATCTACTTAAAATC
1 AATGAAAATCTACTTAAAATC
*
37414 AATGAAAATCTATTTAAAA
1 AATGAAAATCTACTTAAAA
37433 ATTAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (21 bp):
AATGAAAATCTACTTAAAATC
Found at i:56138 original size:3 final size:3
Alignment explanation
Indices: 56130--56173 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
56120 TTTTTATCCA
56130 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
56174 AATATATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56185 original size:11 final size:11
Alignment explanation
Indices: 56169--56200 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
56159 TTATTATTAT
56169 TATTAAATATA
1 TATTAAATATA
56180 TATTAAATATA
1 TATTAAATATA
56191 TATATAAATA
1 TAT-TAAATA
56201 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:56661 original size:19 final size:19
Alignment explanation
Indices: 56637--56675 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
56627 CCCCAACCTG
56637 AAAAAAAGACG-GAGACAGA
1 AAAAAAAGA-GAGAGACAGA
56656 AAAAAAAGAGAGAGACAGA
1 AAAAAAAGAGAGAGACAGA
56675 A
1 A
56676 CCGGAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.67, C:0.08, G:0.26, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAGAGAGACAGA
Found at i:56698 original size:16 final size:16
Alignment explanation
Indices: 56638--56708 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 16
56628 CCCAACCTGA
* *
56638 AAAAAAGACGGAGACAG
1 AAAAAA-ACAGAGAAAG
*
56655 AAAAAAA-AGAGAGAG
1 AAAAAAACAGAGAAAG
* * * *
56670 ACAGAACCGGAGAAAG
1 AAAAAAACAGAGAAAG
56686 AAAAAAACAGAGAAA-
1 AAAAAAACAGAGAAAG
56701 AAAAAAAC
1 AAAAAAAC
56709 TACTAACCAA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
15 18 0.43
16 18 0.43
17 6 0.14
ACGTcount: A:0.68, C:0.10, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAAACAGAGAAAG
Found at i:57648 original size:13 final size:13
Alignment explanation
Indices: 57632--57678 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
57622 ATATAATAAA
57632 TAAATATTTATTT
1 TAAATATTTATTT
*
57645 TAAATAAATTATTT
1 TAAAT-ATTTATTT
57659 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
57672 TCAATAT
1 TAAATAT
57679 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:58354 original size:19 final size:19
Alignment explanation
Indices: 58314--58357 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
58304 TCTTTTCAAA
*
58314 ATTTTTATATATACTTATT
1 ATTTTCATATATACTTATT
*
58333 ATTTTCATA-ATATTTATAT
1 ATTTTCATATATACTTAT-T
58352 ATTTTC
1 ATTTTC
58358 TTATTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTCATATATACTTATT
Found at i:58361 original size:30 final size:30
Alignment explanation
Indices: 58306--58372 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
58296 TAATTCTTTC
*
58306 TTTTCA-AAATTTTTATATATACTTATT-A
1 TTTTCATAAATTTATATATATACTTATTAA
* *
58334 TTTTCATAATATTTATATATTTTCTTATTAA
1 TTTTCATAA-ATTTATATATATACTTATTAA
58365 TATTTCAT
1 T-TTTCAT
58373 TTTATTTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.19
29 2 0.06
30 16 0.50
31 2 0.06
32 6 0.19
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTCATAAATTTATATATATACTTATTAA
Found at i:65525 original size:83 final size:83
Alignment explanation
Indices: 65386--65799 Score: 785
Period size: 83 Copynumber: 5.0 Consensus size: 83
65376 GAAAGAGACT
65386 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
65451 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
65469 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
*
65534 TTTAGAAGGTGAATTTGC
66 TTTAGAAGATGAATTTGC
*
65552 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCCAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
65617 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
65635 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
65700 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
*
65718 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGGCAG-ACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
*
65782 TTTGGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
65800 TCATAGTAAA
Statistics
Matches: 325, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
82 30 0.09
83 295 0.91
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (83 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
TTTAGAAGATGAATTTGC
Found at i:67022 original size:230 final size:227
Alignment explanation
Indices: 66634--67849 Score: 1798
Period size: 230 Copynumber: 5.3 Consensus size: 227
66624 TCCAGAAAAG
66634 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* *
66699 ACCTTTTACCTGAATTCATCAAATTGATGGATTATTTTTTTCAGAGAAAGTTCATAATGAGAAGA
66 ACCTTTTATCTGAATTCATC-AATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGA
*
66764 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAAT
130 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGTTTGAAT
66829 TCATCATTTGATGGATCAACATTGCCAGGAAGA
195 TCATCATTTGATGGATCAACATTGCCAGGAAGA
66862 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * *
66927 TCAACCTTTTATCTGAATTCATCACTGGATGGATTATTTTTTCCAGAGAAGGTTCATAATGAGAA
63 TCAACCTTTTATCTGAATTCATCAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAA
* ***
66992 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-ACCTGA
128 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGTTTGA
* * *** **
67056 ATTCATCAAATTGATGGATTATTTTTTTCAGAGAA-A
193 ATTCATC-ATTTGATGGATCAACATTGCCAG-GAAGA
** * *
67092 GTTCATAATGAGAAGAACTCATCTGAAGAAATAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* * * * * *** *
67157 ACATTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GAAGAGTTCATAATGAGAAG
66 ACCTTTT-ATCTGAATTCATCAATTGATGGATTATTTTTTCCAGAGAA-AGTTCATAATGAGAAG
* * *
67221 AACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-ATCT
129 AA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGTTT
* * * *** *
67285 GAATTCATCACTGGATGGATTATTTTTTCCAGAGAAG-
191 GAATTCATCATTTGATGGATCAACATTGCCAG-GAAGA
67322 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
*
67387 ACCTTTTACCTGAATTCATCAAATTGATGGATTA-TTTTT-CAGAGAAAGTTCATAATGAGAAGA
66 ACCTTTTATCTGAATTCATC-AATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGA
*
67450 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGGTTTGAAT
130 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGTTTGAAT
67515 TCATCATTTGATGGATCAACATTGCCAGGAAGA
195 TCATCATTTGATGGATCAACATTGCCAGGAAGA
67548 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* *
67613 TCAACCTTTTATCTGAATTCATCACTGGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAA
63 TCAACCTTTTATCTGAATTCATCAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAA
*
67678 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGGTTTGA
128 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGTTTGA
67743 ATTCATCATTTGATGGATCAACATTGCCAGGAAGA
193 ATTCATCATTTGATGGATCAACATTGCCAGGAAGA
* * *
67778 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
*
67843 ACTTTTT
66 ACCTTTT
67850 GCATAATTCT
Statistics
Matches: 899, Mismatches: 69, Indels: 41
0.89 0.07 0.04
Matches are distributed among these distances:
225 56 0.06
226 45 0.05
227 102 0.11
228 96 0.11
229 96 0.11
230 369 0.41
231 135 0.15
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (227 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
ACCTTTTATCTGAATTCATCAATTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGGTTTGAATT
CATCATTTGATGGATCAACATTGCCAGGAAGA
Found at i:67248 original size:344 final size:344
Alignment explanation
Indices: 66621--67850 Score: 2227
Period size: 344 Copynumber: 3.6 Consensus size: 344
66611 ATAGATTAGC
*
66621 TTTTCCAGAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
66686 AAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATTTTTTTCAGAGAAAGTT
66 AAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATTTTTTTCAGAGAAAGTT
*
66751 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACC
131 CATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACC
66816 TTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACT
196 TTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACT
66881 CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATT
261 CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATT
66946 CATCACTGGATGGATTATT
326 CATCACTGGATGGATTATT
66965 TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
67030 AAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATTTTTTTCAGAGAAAGTT
66 AAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATTTTTTTCAGAGAAAGTT
* *
67095 CATAATGAGAAGAACTCATCTGAAGAAATAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACA
131 CATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACC
67160 TTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACT
196 TTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACT
67225 CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATT
261 CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATT
67290 CATCACTGGATGGATTATT
326 CATCACTGGATGGATTATT
67309 TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
67374 AAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTA--TTTTTCAGAGAAAGTT
66 AAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATTTTTTTCAGAGAAAGTT
*
67437 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACC
131 CATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACC
67502 TTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACT
196 TTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACT
67567 CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATT
261 CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATT
67632 CATCACTGGATGGATTATT
326 CATCACTGGATGGATTATT
*
67651 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * *** * * *** **
67716 AAGAACTTGTTCAACTTTTTGGTTTGAATTCATC-ATTTGATGGATCAACATTGCCAG-GAAGAG
66 AAGAATTTGTTCAACCTTTT-ACCTGAATTCATCAAATTGATGGATTATTTTTTTCAGAGAA-AG
67779 TTCATAATGAGAAGAACTCATCTGAAG-AAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
129 TTCATAATGAGAAGAACTCATCTGAAGAAAG-AAGAAGAAGTTCATAATAAGAAGAACTTGTTCA
*
67843 ACTTTTTG
193 ACCTTTTG
67851 CATAATTCTA
Statistics
Matches: 861, Mismatches: 20, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
342 320 0.37
343 15 0.02
344 526 0.61
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (344 bp):
TTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATTTTTTTCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACC
TTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACT
CGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATT
CATCACTGGATGGATTATT
Found at i:68175 original size:3 final size:3
Alignment explanation
Indices: 68167--68207 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
68157 TTTTTATCCA
68167 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
68208 AATATATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:68219 original size:11 final size:11
Alignment explanation
Indices: 68203--68232 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
68193 TTATTATTAT
68203 TATTAAATATA
1 TATTAAATATA
68214 TATTAAATATA
1 TATTAAATATA
68225 TA-TAAATA
1 TATTAAATA
68233 ATTAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAAATATA
Found at i:68690 original size:18 final size:18
Alignment explanation
Indices: 68667--68705 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
68657 ACCCCAACCT
68667 GAAAAAAAGACG-GAGACA
1 GAAAAAAAGA-GAGAGACA
68685 GAAAAAAAGAGAGAGACA
1 GAAAAAAAGAGAGAGACA
68703 GAA
1 GAA
68706 CCGGAGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (18 bp):
GAAAAAAAGAGAGAGACA
Found at i:68993 original size:10 final size:10
Alignment explanation
Indices: 68978--69003 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
68968 GCCACCGGAT
68978 GCGGTGGCCG
1 GCGGTGGCCG
68988 GCGGTGGCCG
1 GCGGTGGCCG
68998 GCGGTG
1 GCGGTG
69004 ACAGTCACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.62, T:0.12
Consensus pattern (10 bp):
GCGGTGGCCG
Found at i:74705 original size:22 final size:22
Alignment explanation
Indices: 74664--74704 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
74654 GAAAAATAGA
74664 TAATTAATATAATTTATTTTCT
1 TAATTAATATAATTTATTTTCT
*
74686 TAATTAA-ATAATTTTTTTT
1 TAATTAATATAATTTATTTT
74705 TTGTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TAATTAATATAATTTATTTTCT
Found at i:74815 original size:22 final size:19
Alignment explanation
Indices: 74792--74836 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
74782 TTAAAAATAT
74792 TATTATTATA-TATATTTAA
1 TATTATTATATTAT-TTTAA
* *
74811 TATTAATATATTATTTTAG
1 TATTATTATATTATTTTAA
74830 TATTATT
1 TATTATT
74837 TTAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTATTATATTATTTTAA
Found at i:74824 original size:30 final size:27
Alignment explanation
Indices: 74785--74866 Score: 78
Period size: 30 Copynumber: 2.9 Consensus size: 27
74775 ATAAACATTA
74785 AAAATATTATTATTATATATATTTAAT
1 AAAATATTATTATTATATATATTTAAT
74812 ATTAATATATTATT-TTAGTAT-TATTTTAAT
1 A--AA-ATATTATTATTA-TATATA-TTTAAT
*
74842 AAAATATTAATTATTAAATTATATT
1 AAAATATT-ATTATTATA-TATATT
74867 AATTGATAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 16
0.73 0.02 0.26
Matches are distributed among these distances:
27 6 0.13
28 6 0.13
29 13 0.29
30 20 0.44
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
AAAATATTATTATTATATATATTTAAT
Found at i:83895 original size:20 final size:20
Alignment explanation
Indices: 83866--83959 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
83856 CGTTAAGGAA
83866 TGTACCGATACACTATAGTG
1 TGTACCGATACACTATAGTG
* *
83886 TGTACGGATACACTATAGCG
1 TGTACCGATACACTATAGTG
83906 TGTACCGATACACTATAGTG
1 TGTACCGATACACTATAGTG
83926 -GTTACCGATACACTATAGTG
1 TG-TACCGATACACTATAGTG
83946 TGTACCGATACACT
1 TGTACCGATACACT
83960 TCAAAAGGGA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
19 1 0.01
20 66 0.97
21 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (20 bp):
TGTACCGATACACTATAGTG
Found at i:84663 original size:23 final size:23
Alignment explanation
Indices: 84633--84716 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
84623 TCCTTCGGGA
* * *
84633 CATAGTGGTCATTCAGGACATTT
1 CATAGTGGCCATTCGGGATATTT
*
84656 CATAGTGGCCCTTCGGGATATTT
1 CATAGTGGCCATTCGGGATATTT
*
84679 CATAGTGGCCCTTCGGGATATTT
1 CATAGTGGCCATTCGGGATATTT
*
84702 CATAGTGGTCATTCG
1 CATAGTGGCCATTCG
84717 AGAAAAATTC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (23 bp):
CATAGTGGCCATTCGGGATATTT
Found at i:88207 original size:20 final size:20
Alignment explanation
Indices: 88178--88249 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
88168 CGCTAAGGAA
88178 TGTATCGATACACTATAGTG
1 TGTATCGATACACTATAGTG
* *
88198 TGTATTGATACACTATAGTA
1 TGTATCGATACACTATAGTG
88218 TGTATCGATACACTATAGTG
1 TGTATCGATACACTATAGTG
88238 TGTATCGATACA
1 TGTATCGATACA
88250 TTTCAAAAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (20 bp):
TGTATCGATACACTATAGTG
Found at i:88938 original size:23 final size:24
Alignment explanation
Indices: 88912--88958 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
88902 AGGGTTCTAT
*
88912 GTGGTCCTTCGGGA-CATTTCATA
1 GTGGTCCTTCGGGACCAATTCATA
88935 GTGGTCCTTCGGGACCAATTCATA
1 GTGGTCCTTCGGGACCAATTCATA
88959 TATCCCTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (24 bp):
GTGGTCCTTCGGGACCAATTCATA
Found at i:93256 original size:3 final size:3
Alignment explanation
Indices: 93235--93273 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
93225 CCCACTTGAA
* *
93235 ATT ATT GTT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
93274 CATTTTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:111472 original size:36 final size:36
Alignment explanation
Indices: 111427--111499 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
111417 CTACGCCATC
*
111427 TCTGTTATATTTTGGTGA-A-ATGTGTTTTATTGTCA
1 TCTGTTATATTTTGGGGACACATGT-TTTTATTGTCA
111462 TCTGTGTATATTTTGGGGACACATGTTTTTATTGTCA
1 TCTGT-TATATTTTGGGGACACATGTTTTTATTGTCA
111499 T
1 T
111500 ATGTATACCG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
35 5 0.15
36 12 0.35
37 13 0.38
38 4 0.12
ACGTcount: A:0.19, C:0.08, G:0.21, T:0.52
Consensus pattern (36 bp):
TCTGTTATATTTTGGGGACACATGTTTTTATTGTCA
Found at i:111557 original size:2 final size:2
Alignment explanation
Indices: 111550--111621 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
111540 ACTTCTGGTG
111550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
111592 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
111622 TTATTATGTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112634 original size:24 final size:23
Alignment explanation
Indices: 112584--112636 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
112574 ATTTGTCTTT
* *
112584 GTGACATGTTTTTTTCTACTCTT
1 GTGACATGATTTTTTCTACTCTC
* *
112607 GTGATATGATTTTTTCTTGCTCTC
1 GTGACATGATTTTTTC-TACTCTC
112631 GTGACA
1 GTGACA
112637 CGTTCCTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.51
Consensus pattern (23 bp):
GTGACATGATTTTTTCTACTCTC
Found at i:115387 original size:2 final size:2
Alignment explanation
Indices: 115380--115431 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
115370 ACCATATAAG
115380 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
115422 AT AT AT AT AT
1 AT AT AT AT AT
115432 TATTCTTTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115970 original size:158 final size:158
Alignment explanation
Indices: 115713--116030 Score: 417
Period size: 158 Copynumber: 2.0 Consensus size: 158
115703 TATTGTATAT
* * *
115713 GAGCATGCGATTCAAATTTGGTAAAAAACATACTTAAAATAAAGGATGAATTGAAGAAAAAAAGA
1 GAGCATGCGATTCAAATTTAGTAAAAAACAGACTTAAAATAAAGGATAAATTGAAGAAAAAAAGA
* * * *
115778 AGATATGAAAAGGTTGAGGACTAACTTAAAAAATAGAAAA-TTATTATCAAAAAGTGGAATTGAA
66 AGATATGAAAAGATTGAGGACTAAATTAAAAAATAGAAAATTTATTATCAAAAAGAGAAATTGAA
* * *
115842 AGTACATATTTATTATACGATGGTTTAA
131 AGTACACATGTATGATACGATGGTTTAA
* * * * *
115870 GAGCATGCGGTTCAATTTTAGTAAAAAA-AGGGACTTAAAGTAAAGGATAAATTGAAGAAATAAG
1 GAGCATGCGATTCAAATTTAGTAAAAAACA--GACTTAAAATAAAGGATAAATTGAAGAAAAAAA
* *
115934 GAAGATATGAAAA-ATTGAGAGATTAAATTAAGAAATAGAAAATTTATTATCAAAAAGAGAAATT
64 GAAGATATGAAAAGATTGAG-GACTAAATTAAAAAATAGAAAATTTATTATCAAAAAGAGAAATT
* *
115998 GAAAGTACACATGTATGCTATGATGGTTTAA
128 GAAAGTACACATGTATGATACGATGGTTTAA
116029 GA
1 GA
116031 CTTAAAATAA
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
156 1 0.01
157 30 0.22
158 60 0.43
159 47 0.34
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (158 bp):
GAGCATGCGATTCAAATTTAGTAAAAAACAGACTTAAAATAAAGGATAAATTGAAGAAAAAAAGA
AGATATGAAAAGATTGAGGACTAAATTAAAAAATAGAAAATTTATTATCAAAAAGAGAAATTGAA
AGTACACATGTATGATACGATGGTTTAA
Found at i:116085 original size:127 final size:129
Alignment explanation
Indices: 115901--116155 Score: 399
Period size: 128 Copynumber: 2.0 Consensus size: 129
115891 TAAAAAAAGG
* * *
115901 GACTTAAAGTAAAGGATAAATTGAAGAAATAAGGAAGATATGAAAAATTGAGAGATTAAATT-AA
1 GACTTAAAATAAAGGATAAATTGAAGAAAAAAGAAAGATATGAAAAATTGAGAGATTAAATTGAA
*
115965 GAAATAGAAAA-TTTATTATCAAAAAGAGAAATTGAAAGTACACATGTATGCTATGATGGTTTAA
66 -AAATAGAAAACTTTATTATCAAAAAGAGAAATTAAAAGTACACATGTATGCTATGATGGTTTAA
* * *
116029 GACTTAAAATAAAGGATAAATTG-AGAAAAAAGAAATATATGAAAATTTGAGGGATTAAATTGAA
1 GACTTAAAATAAAGGATAAATTGAAGAAAAAAGAAAGATATGAAAAATTGAGAGATTAAATTGAA
* *
116093 AAATAGAAAACTTTATTATCAAAAAGAGAAATTAAAAGTTCACATGTATTCTATGATGGTTTA
66 AAATAGAAAACTTTATTATCAAAAAGAGAAATTAAAAGTACACATGTATGCTATGATGGTTTA
116156 GGAGCATGTG
Statistics
Matches: 116, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
127 43 0.37
128 73 0.63
ACGTcount: A:0.51, C:0.04, G:0.17, T:0.28
Consensus pattern (129 bp):
GACTTAAAATAAAGGATAAATTGAAGAAAAAAGAAAGATATGAAAAATTGAGAGATTAAATTGAA
AAATAGAAAACTTTATTATCAAAAAGAGAAATTAAAAGTACACATGTATGCTATGATGGTTTAA
Done.