Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003344.1 Hibiscus syriacus cultivar Beakdansim tig00007042_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: 118094
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1606 original size:19 final size:19
Alignment explanation
Indices: 1582--1620 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1572 GTAAATATTT
*
1582 TTATTTTTTATAAGTATAA
1 TTATTTTTTATAAGCATAA
1601 TTATTTTTTATAAGCATAA
1 TTATTTTTTATAAGCATAA
1620 T
1 T
1621 AAGTATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
TTATTTTTTATAAGCATAA
Found at i:3949 original size:42 final size:43
Alignment explanation
Indices: 3828--3995 Score: 157
Period size: 43 Copynumber: 3.9 Consensus size: 43
3818 ACAATTATGG
* *
3828 CCCCTAATTTTTTTAATC-CTACCTTTTA-TATTTATAATTGACG-
1 CCCCTAATTTTTTCAATCTC-ACTTTTTACT-TTTATAATTGA-GA
* * * *
3871 CCCTTAATTTTTTCAACCTTATTTTTTACTTTTATAATTGAGA
1 CCCCTAATTTTTTCAATCTCACTTTTTACTTTTATAATTGAGA
* *
3914 CCCCTAATTTTTTAAATCTCACTTTTTA-TCTTATAATTGA-A
1 CCCCTAATTTTTTCAATCTCACTTTTTACTTTTATAATTGAGA
* * *
3955 TTCCCTAATTTTTTTCAATTTTACTTTTTACTTTTATAATT
1 -CCCCTAA-TTTTTTCAATCTCACTTTTTACTTTTATAATT
3996 AAAGCATCTA
Statistics
Matches: 102, Mismatches: 17, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 18 0.18
43 73 0.72
44 10 0.10
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.54
Consensus pattern (43 bp):
CCCCTAATTTTTTCAATCTCACTTTTTACTTTTATAATTGAGA
Found at i:3983 original size:86 final size:86
Alignment explanation
Indices: 3828--3995 Score: 218
Period size: 86 Copynumber: 2.0 Consensus size: 86
3818 ACAATTATGG
* *
3828 CCCCTAATTTTTTTAATCCTACCTTTTATATTTATAATTGACGCCCTTAATTTTTTCAACCTTAT
1 CCCCTAATTTTTTAAATCCTACCTTTTATATTTATAATTGACGCCCTTAATTTTTTCAACCTTAC
3893 TTTTTACTTTTATAATTGAGA
66 TTTTTACTTTTATAATTGAGA
** **
3914 CCCCTAATTTTTTAAAT-CT-CACTTTT-TATCTTATAATTGAATTCCC-TAATTTTTTTCAATT
1 CCCCTAATTTTTTAAATCCTAC-CTTTTATAT-TTATAATTG-ACGCCCTTAA-TTTTTTCAACC
3975 TTACTTTTTACTTTTATAATT
62 TTACTTTTTACTTTTATAATT
3996 AAAGCATCTA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
84 4 0.06
85 19 0.26
86 49 0.68
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.54
Consensus pattern (86 bp):
CCCCTAATTTTTTAAATCCTACCTTTTATATTTATAATTGACGCCCTTAATTTTTTCAACCTTAC
TTTTTACTTTTATAATTGAGA
Found at i:7495 original size:49 final size:49
Alignment explanation
Indices: 7434--7598 Score: 285
Period size: 49 Copynumber: 3.4 Consensus size: 49
7424 TACATCTGTA
7434 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAG
*
7483 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACGAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAG
* **
7532 ACGTCAGACGTGCTAAATCATCATCAATCGTAGCACCATAGTCACAAAG
1 ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAG
*
7581 ACGTCAGACGTGTTAAAT
1 ACGTCAGACGTGCTAAAT
7599 GCTCCACCTC
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 110 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (49 bp):
ACGTCAGACGTGCTAAATCATCATCAATCATAGCACCACCGTCACAAAG
Found at i:7753 original size:52 final size:53
Alignment explanation
Indices: 7661--7766 Score: 137
Period size: 52 Copynumber: 2.0 Consensus size: 53
7651 TAAATCATTT
* * *
7661 ATCATTCACCTATCAGAATCTTTTTCAAATATCATCAAAATCAAGTATCATAC
1 ATCATTCACCTATCAGAATCTTTTTCAAACATCAACAAAATCAAGTATAATAC
*
7714 ATCATTCA-CTCATCA-AATCTTTTT-AAACATTAACAAAAATCAAGTATAATAC
1 ATCATTCACCT-ATCAGAATCTTTTTCAAACATCAAC-AAAATCAAGTATAATAC
7766 A
1 A
7767 ATATAAATCT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
51 7 0.15
52 28 0.60
53 12 0.26
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (53 bp):
ATCATTCACCTATCAGAATCTTTTTCAAACATCAACAAAATCAAGTATAATAC
Found at i:9657 original size:30 final size:28
Alignment explanation
Indices: 9623--9682 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
9613 TTTTGGTCCT
*
9623 TAAACTTTTCAAAGATTATACTTTAGCCAC
1 TAAACCTTT-AAA-ATTATACTTTAGCCAC
* * *
9653 TAAACCTTTAAACTTATATTTTAGTCAC
1 TAAACCTTTAAAATTATACTTTAGCCAC
9681 TA
1 TA
9683 GACAAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 15 0.58
29 3 0.12
30 8 0.31
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (28 bp):
TAAACCTTTAAAATTATACTTTAGCCAC
Found at i:13701 original size:2 final size:2
Alignment explanation
Indices: 13694--13719 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13684 TATTATTCAA
13694 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
13720 CTAAAGTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19768 original size:18 final size:19
Alignment explanation
Indices: 19737--19776 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
19727 TTTCAATAAA
19737 AAAATCATAAAAAAAAATT
1 AAAATCATAAAAAAAAATT
* *
19756 AAAA-CATACAAAAAATTT
1 AAAATCATAAAAAAAAATT
19774 AAA
1 AAA
19777 TTTTCAGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (19 bp):
AAAATCATAAAAAAAAATT
Found at i:30189 original size:16 final size:16
Alignment explanation
Indices: 30164--30194 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30154 CTTCTAAATT
*
30164 TTTTTTAGTTCAAGTC
1 TTTTTGAGTTCAAGTC
30180 TTTTTGAGTTCAAGT
1 TTTTTGAGTTCAAGT
30195 TTCAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTC
Found at i:30794 original size:18 final size:19
Alignment explanation
Indices: 30748--30795 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
30738 TCTGAGCTCG
*
30748 ATTC-AAGCTCCAAACTCA
1 ATTCAAAGCTCGAAACTCA
30766 ATTCAAA-CTCGAAACTCA
1 ATTCAAAGCTCGAAACTCA
30784 ATT-AAAGCTCGA
1 ATTCAAAGCTCGA
30796 TTTTGAGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 3 0.11
18 22 0.81
19 2 0.07
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (19 bp):
ATTCAAAGCTCGAAACTCA
Found at i:32100 original size:7 final size:7
Alignment explanation
Indices: 32081--32127 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
32071 AATCAAATTA
*
32081 AGGGCTT
1 AGGGTTT
32088 AGGGTTT
1 AGGGTTT
*
32095 ATGGTTT
1 AGGGTTT
32102 AGGGTTT
1 AGGGTTT
*
32109 AAGGTTT
1 AGGGTTT
32116 AGGGTTT
1 AGGGTTT
32123 AGGGT
1 AGGGT
32128 GTAATCTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.17, C:0.02, G:0.40, T:0.40
Consensus pattern (7 bp):
AGGGTTT
Found at i:37049 original size:28 final size:28
Alignment explanation
Indices: 37009--37064 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
36999 GATACATTGT
37009 AATGAATGCAATCTTTTGTATGCTATGG
1 AATGAATGCAATCTTTTGTATGCTATGG
37037 AATGAATGCAATCTTTTGTATGCTATGG
1 AATGAATGCAATCTTTTGTATGCTATGG
37065 TTGATTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (28 bp):
AATGAATGCAATCTTTTGTATGCTATGG
Found at i:45411 original size:12 final size:12
Alignment explanation
Indices: 45390--45443 Score: 72
Period size: 12 Copynumber: 4.4 Consensus size: 12
45380 AAAAGGACAG
45390 ATAATATTTTTT
1 ATAATATTTTTT
*
45402 ATAATTTTTTTT
1 ATAATATTTTTT
*
45414 ATAATAATCTTTT
1 ATAAT-ATTTTTT
*
45427 ATAATTTTTTTT
1 ATAATATTTTTT
45439 ATAAT
1 ATAAT
45444 GTTTGAACAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
12 26 0.72
13 10 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
ATAATATTTTTT
Found at i:45431 original size:25 final size:24
Alignment explanation
Indices: 45390--45443 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 24
45380 AAAAGGACAG
*
45390 ATAATATTTTTTATAATTTTTTTT
1 ATAATATCTTTTATAATTTTTTTT
45414 ATAATAATCTTTTATAATTTTTTTT
1 ATAAT-ATCTTTTATAATTTTTTTT
45439 ATAAT
1 ATAAT
45444 GTTTGAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 5 0.18
25 23 0.82
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATAATATCTTTTATAATTTTTTTT
Found at i:46249 original size:20 final size:20
Alignment explanation
Indices: 46226--46277 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
46216 AACGCGATCC
46226 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
46246 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
46266 CCAAAATCGCAA
1 CCAGAATCGCAA
46278 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:46358 original size:20 final size:20
Alignment explanation
Indices: 46333--46526 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
46323 GATTTTCCAT
* *
46333 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
46353 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
46373 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
46393 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
46413 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
46433 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
46453 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
46473 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
46494 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
46514 AATCGCAACGCGA
1 AATCGCAACGCGA
46527 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:46378 original size:40 final size:39
Alignment explanation
Indices: 46329--46526 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
46319 TTGCGATTTT
* ** *
46329 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
46367 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
46408 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
46448 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
46487 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
46527 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:46416 original size:60 final size:60
Alignment explanation
Indices: 46333--46525 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
46323 GATTTTCCAT
* ** * *
46333 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
46393 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
46453 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
46514 AATCGCAACGCG
1 AATCGCAACGCG
46526 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:46946 original size:33 final size:33
Alignment explanation
Indices: 46907--46977 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
46897 TTCACTTAGA
*
46907 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
46940 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
46973 TTTCA
1 TTTCA
46978 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:47117 original size:14 final size:14
Alignment explanation
Indices: 47098--47152 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
47088 AGAATGACTG
47098 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
47112 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
47131 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
47145 TCGCAACG
1 TCGCAACG
47153 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:47135 original size:33 final size:33
Alignment explanation
Indices: 47098--47168 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
47088 AGAATGACTG
**
47098 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
47131 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
47164 TCGCA
1 TCGCA
47169 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:47186 original size:19 final size:19
Alignment explanation
Indices: 47164--47261 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
47154 GAAACCAAAA
*
47164 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
47183 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
47197 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
47216 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
47230 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
47249 TCGCGTTGCGATT
1 TCGCGTTGCGATT
47262 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:47205 original size:14 final size:14
Alignment explanation
Indices: 47186--47275 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
47176 TTTCATTTCG
47186 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
47200 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
47219 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
47233 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
47250 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
47266 CGTTGCGATT
1 CGTTGCGATT
47276 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:47211 original size:33 final size:33
Alignment explanation
Indices: 47169--47283 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
47159 CAAAATCGCA
47169 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
47202 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
47235 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
47268 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
47284 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:49186 original size:92 final size:93
Alignment explanation
Indices: 48981--49267 Score: 549
Period size: 93 Copynumber: 3.1 Consensus size: 93
48971 TAGATTGCTT
*
48981 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
49046 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
49074 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
49138 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
49166 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
49231 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
49259 AGTAAATTT
1 AGTAAATTT
49268 ATCCATTCAA
Statistics
Matches: 190, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 91 0.48
93 99 0.52
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:49409 original size:33 final size:32
Alignment explanation
Indices: 49328--49458 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 32
49318 ACGAAACTTA
49328 AAATCGCAACGCGAAACCAAAATCGCAACGCGAAACC
1 AAATCGCAACGCGAAACCAAAATCGCAA--CG--A-C
**
49365 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 -AAATCGCAACGCGAAACCAAAATCGCAACGAC
49398 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
49431 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
49459 TTGCGATTTT
Statistics
Matches: 87, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
32 2 0.02
33 56 0.64
34 1 0.01
36 2 0.02
38 26 0.30
ACGTcount: A:0.47, C:0.29, G:0.18, T:0.07
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:49456 original size:52 final size:51
Alignment explanation
Indices: 49328--49458 Score: 167
Period size: 52 Copynumber: 2.5 Consensus size: 51
49318 ACGAAACTTA
49328 AAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCG
1 AAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCG
* ** * *
49379 AAAT-GAAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-
1 AAATCGCAACGCGAAAC--CAAAATCGCAACGCGAAACCAAAATCGCAACG-CG
49431 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
49459 TTGCGATTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 42 0.65
53 3 0.05
54 8 0.12
ACGTcount: A:0.47, C:0.29, G:0.18, T:0.07
Consensus pattern (51 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCG
Found at i:49464 original size:19 final size:19
Alignment explanation
Indices: 49311--49458 Score: 163
Period size: 19 Copynumber: 8.3 Consensus size: 19
49301 TAGTTTACTT
* *
49311 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
49331 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
49350 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
49369 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
49388 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
49402 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
49421 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
49435 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
49454 TCGCA
1 TCGCA
49459 TTGCGATTTT
Statistics
Matches: 109, Mismatches: 9, Indels: 21
0.78 0.06 0.15
Matches are distributed among these distances:
14 19 0.17
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 65 0.60
20 13 0.12
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.08
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:49476 original size:19 final size:19
Alignment explanation
Indices: 49454--49588 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
49444 GAAACCAAAA
*
49454 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
49473 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
49489 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
49506 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
49522 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
49539 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
49558 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
49578 TCGTGTTGCGA
1 TCGCGTTGCGA
49589 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:49495 original size:14 final size:14
Alignment explanation
Indices: 49476--49532 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
49466 TTTCATTTCG
49476 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
49490 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
49507 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
49523 CGTTGCGATT
1 CGTTGCGATT
49533 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:49501 original size:33 final size:33
Alignment explanation
Indices: 49459--49551 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
49449 CAAAATCGCA
*
49459 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
49492 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
49525 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
49552 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:51511 original size:14 final size:14
Alignment explanation
Indices: 51492--51527 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
51482 ATTGTTTAAT
51492 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
51506 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
51520 TGATTTGT
1 TGATTTGT
51528 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:51650 original size:19 final size:19
Alignment explanation
Indices: 51634--51735 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
51624 AAAAATGACT
51634 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
51653 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
51672 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
51686 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
51705 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
51725 ATCGCAATGCG
1 ATCGCAATGCG
51736 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:51788 original size:19 final size:19
Alignment explanation
Indices: 51764--52036 Score: 336
Period size: 19 Copynumber: 15.4 Consensus size: 19
51754 GATTATCTCG
51764 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
51783 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
51802 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
51816 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
51835 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
51854 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
51873 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
51892 TTGCGATTTTAATTTCACA
1 TTGCGATTTTCATTTCGCA
*
51911 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
51925 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
51944 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
51963 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
51977 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
51997 TTGCGA-TTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
52010 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
52029 TTGCGATT
1 TTGCGATT
52037 GTATTTTCCG
Statistics
Matches: 222, Mismatches: 10, Indels: 44
0.80 0.04 0.16
Matches are distributed among these distances:
13 5 0.02
14 23 0.10
15 1 0.00
16 22 0.10
17 21 0.09
18 2 0.01
19 142 0.64
20 6 0.03
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:51893 original size:109 final size:102
Alignment explanation
Indices: 51764--52004 Score: 167
Period size: 109 Copynumber: 2.3 Consensus size: 102
51754 GATTATCTCG
51764 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
51826 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
51873 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCACATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTTT--CGTTGCGATTTCATTTCGATTGCGATTTT
* * * * *
51935 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
51977 TTGCGATTTTCATTTCCGCATTGCGATT
1 TTGCGATTTTCATTT-CGCATTGCGATT
52005 TCATGTTGGG
Statistics
Matches: 117, Mismatches: 8, Indels: 20
0.81 0.06 0.14
Matches are distributed among these distances:
102 7 0.06
103 6 0.05
104 20 0.17
105 11 0.09
107 2 0.02
109 70 0.60
111 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (102 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:52008 original size:52 final size:52
Alignment explanation
Indices: 51742--52005 Score: 420
Period size: 52 Copynumber: 5.0 Consensus size: 52
51732 TGCGTTTATA
*
51742 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
51794 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
51846 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
51903 ATTTCACATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
51955 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTT
52006 CATGTTGGGA
Statistics
Matches: 198, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
52 128 0.65
53 13 0.07
54 7 0.04
55 8 0.04
57 42 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:52031 original size:52 final size:51
Alignment explanation
Indices: 51742--52036 Score: 353
Period size: 52 Copynumber: 5.6 Consensus size: 51
51732 TGCGTTTATA
*
51742 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTC
**
51794 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATT-TCGCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
51846 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTA
1 ATTTCGCATTGCG------ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
51903 ATTTCACATTGCGA-TTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTC-G-CGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
51955 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGA-TTTC
1 ATTTCGCATTGCGATT-TCGCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
* * *
52007 ATGTTGGGATTTTC-ATTTCGCGTTGCGATT
1 AT-TTCGCA-TTGCGATTTCGCGTTGCGATT
52037 GTATTTTCCG
Statistics
Matches: 215, Mismatches: 15, Indels: 26
0.84 0.06 0.10
Matches are distributed among these distances:
50 3 0.01
51 2 0.01
52 141 0.66
53 18 0.08
54 5 0.02
57 43 0.20
58 3 0.01
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (51 bp):
ATTTCGCATTGCGATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:54336 original size:12 final size:12
Alignment explanation
Indices: 54319--54343 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54309 TCTTCGGGGA
54319 CTTTTTCTTCTT
1 CTTTTTCTTCTT
54331 CTTTTTCTTCTT
1 CTTTTTCTTCTT
54343 C
1 C
54344 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:54552 original size:24 final size:24
Alignment explanation
Indices: 54518--54564 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
54508 CTGAAACATC
54518 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
54542 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
54565 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:55275 original size:20 final size:20
Alignment explanation
Indices: 55247--55615 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
55237 AAATTTAAGT
* * * *
55247 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
55267 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
55287 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
55307 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
55327 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
55347 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
55367 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
55387 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
55407 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
55427 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
55447 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
55467 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
55487 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
55507 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
55527 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
55547 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
55567 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
55587 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
55607 GTTGCGATT
1 GTTGCGATT
55616 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:62052 original size:2 final size:2
Alignment explanation
Indices: 62040--62072 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
62030 TTTCCATTTT
*
62040 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62073 TAAAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:64016 original size:83 final size:83
Alignment explanation
Indices: 63778--64024 Score: 269
Period size: 83 Copynumber: 3.0 Consensus size: 83
63768 TTAGCATCTA
* * * * *
63778 TATAGATGACCCCTATTACGGCGTTTTTATAAAAACGCCGCTAAAGTATTACTTTATTGCTGCCT
1 TATAGATGAACCCTATTGCGGCGTTTTTATAAAAACGCCGCTAAAGTACTACTTTATTGCAGCAT
* *
63843 TTGTTAAAAAAAAGCCAC
66 TTGTTGAAAAAACGCCAC
* * * * * * *
63861 CATAGATGAATCCTATTGCGACATTTGTATAAAAACGCCGCTAAAGTACTATTTTATTGCAGTAT
1 TATAGATGAACCCTATTGCGGCGTTTTTATAAAAACGCCGCTAAAGTACTACTTTATTGCAGCAT
*
63926 TTGTTGAAAAAACGTCAC
66 TTGTTGAAAAAACGCCAC
* * * * * ** * *
63944 TATAGATTAACCCTATTGCGGCGTTTTTACACAAACGCCGCTAAAATACTACTCTATCACGGCGT
1 TATAGATGAACCCTATTGCGGCGTTTTTATAAAAACGCCGCTAAAGTACTACTTTATTGCAGCAT
*
64009 TTATTGAAAAAACGCC
66 TTGTTGAAAAAACGCC
64025 GCTAAGGTAC
Statistics
Matches: 131, Mismatches: 33, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
83 131 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (83 bp):
TATAGATGAACCCTATTGCGGCGTTTTTATAAAAACGCCGCTAAAGTACTACTTTATTGCAGCAT
TTGTTGAAAAAACGCCAC
Found at i:64866 original size:2 final size:2
Alignment explanation
Indices: 64859--64892 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
64849 TAAAATACTA
64859 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
64893 TGATTAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68810 original size:34 final size:35
Alignment explanation
Indices: 68766--69104 Score: 120
Period size: 36 Copynumber: 9.5 Consensus size: 35
68756 ACAATTTTCA
68766 AAAACCTATATAATATATATTTTCAAAAAT-ATTTT
1 AAAA-CTATATAATATATATTTTCAAAAATGATTTT
* * * *
68801 AAAATTATATATATATACTTTTTTTAAAAAACG-TTTT
1 AAAACTATATA-ATATA--TATTTTCAAAAATGATTTT
* * *
68838 CAAA--AT-T-ATATA-GTTTTCAAAAATGTTTTT
1 AAAACTATATAATATATATTTTCAAAAATGATTTT
* * *
68868 AAAACTATATATTATA-AGTTTT-TAAAATGATTTC
1 AAAACTATATAATATATA-TTTTCAAAAATGATTTT
* *
68902 AAAACTATATAATATATATATGTTTTC-AAACTGTTTCTTTTT
1 AAAACTATAT-A-ATATATA--TTTTCAAAAATG----ATTTT
* *
68944 AAAA--AT-T-ATATTTATTTT-AAAAATGTTTTTT
1 AAAACTATATAATATATATTTTCAAAAATG-ATTTT
** * *
68975 AAAACCGTATAATATATATTTTTTAAAAAACG-TTTT
1 AAAACTATATAATATATA--TTTTCAAAAATGATTTT
* * * **
69011 AAAAACTATATATTATATTTATTTCCAAAGCG-TTTT
1 -AAAACTATATAATATATAT-TTTCAAAAATGATTTT
*
69047 AAAAACTATATAATATATAATTGTTTCAAATATG-TTTT
1 -AAAACTATATAATATAT-A-T-TTTCAAAAATGATTTT
*
69085 CAAAACTATATTATATATAT
1 -AAAACTATATAATATATAT
69105 ATATATATAT
Statistics
Matches: 233, Mismatches: 40, Indels: 61
0.70 0.12 0.18
Matches are distributed among these distances:
29 10 0.04
30 7 0.03
31 9 0.04
32 7 0.03
33 2 0.01
34 40 0.17
35 23 0.10
36 44 0.19
37 37 0.16
38 44 0.19
39 1 0.00
40 2 0.01
42 7 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (35 bp):
AAAACTATATAATATATATTTTCAAAAATGATTTT
Found at i:68813 original size:36 final size:37
Alignment explanation
Indices: 68772--68849 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 37
68762 TTCAAAAACC
68772 TATATA-ATATA-TATTTTCAAAAATA-TTTT-AAAAT
1 TATATATATATACTATTTTCAAAAA-ACTTTTCAAAAT
* *
68806 TATATATATATACTTTTTTTAAAAAACGTTTTCAAAAT
1 TATATATATATACTATTTTCAAAAAAC-TTTTCAAAAT
68844 TATATA
1 TATATA
68850 GTTTTCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 6 0.16
35 6 0.16
36 10 0.27
37 4 0.11
38 11 0.30
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (37 bp):
TATATATATATACTATTTTCAAAAAACTTTTCAAAAT
Found at i:68815 original size:38 final size:38
Alignment explanation
Indices: 68772--68849 Score: 60
Period size: 37 Copynumber: 2.2 Consensus size: 38
68762 TTCAAAAACC
* *
68772 TATATA-ATATA--TATTTTCAAAAATATTTT-AAAATT
1 TATATATATATACTTATTTTAAAAAACATTTTCAAAA-T
* *
68807 ATATAT--ATATACTTTTTTTAAAAAACGTTTTCAAAAT
1 -TATATATATATACTTATTTTAAAAAACATTTTCAAAAT
68844 TATATA
1 TATATA
68850 GTTTTCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
35 5 0.15
36 10 0.29
37 15 0.44
38 4 0.12
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (38 bp):
TATATATATATACTTATTTTAAAAAACATTTTCAAAAT
Found at i:68859 original size:29 final size:29
Alignment explanation
Indices: 68822--68878 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
68812 TATATACTTT
*
68822 TTTTAAAAAACGTTTTCAAAATTATATAG
1 TTTTAAAAAACGTTTTCAAAACTATATAG
* * *
68851 TTTTCAAAAATGTTTTTAAAACTATATA
1 TTTTAAAAAACGTTTTCAAAACTATATA
68879 TTATAAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (29 bp):
TTTTAAAAAACGTTTTCAAAACTATATAG
Found at i:68882 original size:36 final size:36
Alignment explanation
Indices: 68842--69105 Score: 143
Period size: 36 Copynumber: 7.2 Consensus size: 36
68832 CGTTTTCAAA
68842 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
* * *
68878 ATTATA-AGTTTT-TAAAATGATTTCAAAACTATAT
1 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
*
68912 AATATATATATGTTTTC-AAACTGTTTCTTTTTAAAA--AT-T
1 -AT-TATATA-GTTTTCAAAAATG----TTTTTAAAACTATAT
* **
68951 A-TATTTA-TTTT-AAAAATGTTTTTTAAAACCGTAT
1 ATTATATAGTTTTCAAAAATG-TTTTTAAAACTATAT
* * * * *
68985 AATATATATTTTTTAAAAAACGTTTTAAAAACTATAT
1 ATTATATA-GTTTTCAAAAATGTTTTTAAAACTATAT
* * ** *
69022 ATTATAT-TTATTTCCAAAGCGTTTTAAAAACTATAT
1 ATTATATAGT-TTTCAAAAATGTTTTTAAAACTATAT
* * * *
69058 AATATATAATTGTTTCAAATATGTTTTCAAAACTATATT
1 ATTATAT-AGT-TTTCAAAAATGTTTTTAAAACTATA-T
69097 ATATATATA
1 AT-TATATA
69106 TATATATATA
Statistics
Matches: 179, Mismatches: 27, Indels: 41
0.72 0.11 0.17
Matches are distributed among these distances:
31 9 0.05
33 1 0.01
34 30 0.17
35 15 0.08
36 44 0.25
37 23 0.13
38 39 0.22
39 4 0.02
40 7 0.04
42 7 0.04
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (36 bp):
ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
Found at i:69016 original size:37 final size:37
Alignment explanation
Indices: 68950--69102 Score: 116
Period size: 38 Copynumber: 4.1 Consensus size: 37
68940 TTTTAAAAAT
* * *
68950 TATATTTATTTTAAAAATGTTTTTTAAAACCGTATAATA
1 TATATTTATTTAAAAAACG-TTTTAAAAACC-TATAATA
68989 TATATTT-TTTAAAAAACGTTTTAAAAA-CTAT-ATA
1 TATATTTATTTAAAAAACGTTTTAAAAACCTATAATA
** * *
69023 TTATATTTATTTCCAAAGCGTTTTAAAAACTATATAATA
1 -TATATTTATTTAAAAAACGTTTTAAAAAC-CTATAATA
* * * * * * *
69062 TATAATTGTTTCAAATATGTTTTCAAAA-CTATATTA
1 TATATTTATTTAAAAAACGTTTTAAAAACCTATAATA
69098 TATAT
1 TATAT
69103 ATATATATAT
Statistics
Matches: 92, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
34 3 0.03
35 10 0.11
36 28 0.30
37 8 0.09
38 33 0.36
39 10 0.11
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATTTATTTAAAAAACGTTTTAAAAACCTATAATA
Found at i:69103 original size:2 final size:2
Alignment explanation
Indices: 69091--69129 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
69081 TTTTCAAAAC
*
69091 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69130 AAAAATGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69881 original size:84 final size:82
Alignment explanation
Indices: 69740--70675 Score: 962
Period size: 84 Copynumber: 11.3 Consensus size: 82
69730 ACCCCGCAGT
* * *
69740 TGAGTGTAATCGAACTCG-GGAGTC-TTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
1 TGAGTGTAATCGAACTCGAAG-GTCTTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGCA
*
69802 TATGATGTGCCTTGGAGC
65 AATGATGTGCCTTGGAGC
* * * * * *
69820 TGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGGT--CAGATAACCCTTCTCGACTTAAGTTATGCTGC
* *
69885 AAATGATGTGCCCTCGAAGC
64 AAATGATGTG-CCTTGGAGC
* ** * *
69905 TGAGTGTAATCGAACTTGGGGGTC-TTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAA
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGCAA
*
69968 ATGATATGCCTTGGAGC
66 ATGATGTGCCTTGGAGC
* * * * * *
69985 TGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGGT--CAGATAACCCTTCTCGACTTAAGTTATGCTGC
* *
70050 AAATGATGTGCCCTCGAAGC
64 AAATGATGTG-CCTTGGAGC
* ** * *
70070 TGAGTGTAATCGAACTTGGGGGTC-TTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAA
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGCAA
*
70133 ATGATATGCCTTGGAGC
66 ATGATGTGCCTTGGAGC
* * * * * *
70150 TGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGGT--CAGATAACCCTTCTCGACTTAAGTTATGCTGC
* *
70215 AAATGATGTGCCCTCGAAGC
64 AAATGATGTG-CCTTGGAGC
* ** * *
70235 TGAGTGTAATCGAACTTGGGGGTC-TTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAA
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGCAA
*
70298 ATGATATGCCTTGGAGC
66 ATGATGTGCCTTGGAGC
* * * * * *
70315 TGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
1 TGAGTGTAATCGAACTCGAAGGTCTTTTG--GTCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* *
70380 AAATGATGTGCCCTCGAAGC
64 AAATGATGTG-CCTTGGAGC
70400 TGAGTGTAATCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTG
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGG-T--CAGATAACCCTTCTCGACTTAAGTTATGCTG
*
70464 CAAATGATATGCCTTGGAGC
63 CAAATGATGTGCCTTGGAGC
* * * * * *
70484 TGAGTGTAATCGAACTCAAAGGTCTTTTGGTCACAGAGAACCCTTCTAGCCTTGAGTTATGCTGT
1 TGAGTGTAATCGAACTCGAAGGTCTTTTGGT--CAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * *
70549 AAATGTTATGCCCTTGAAGC
64 AAATGATGTG-CCTTGGAGC
* * * *
70569 TGAGTGTAATCGAACT-TAAGGGTC-TTTGG-CAGATAGCCCTTCTCGACTTTAAGCTATTCTGC
1 TGAGTGTAATCGAACTCGAA-GGTCTTTTGGTCAGATAACCCTTCTCGAC-TTAAGTTATGCTGC
70631 AAATGATGTGCCTTGGAGC
64 AAATGATGTGCCTTGGAGC
* *
70650 TGAGCGTAGTCGAACTCGAAGGTCTT
1 TGAGTGTAATCGAACTCGAAGGTCTT
70676 GGTGGTAGGT
Statistics
Matches: 697, Mismatches: 129, Indels: 58
0.79 0.15 0.07
Matches are distributed among these distances:
80 97 0.14
81 165 0.24
82 22 0.03
83 1 0.00
84 234 0.34
85 178 0.26
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (82 bp):
TGAGTGTAATCGAACTCGAAGGTCTTTTGGTCAGATAACCCTTCTCGACTTAAGTTATGCTGCAA
ATGATGTGCCTTGGAGC
Found at i:69932 original size:165 final size:165
Alignment explanation
Indices: 69695--70675 Score: 1586
Period size: 165 Copynumber: 5.9 Consensus size: 165
69685 TGACAAATAG
* * * * * * * *
69695 CCCTTCTTGCCATGAGCTATGTTGTAAATGATATGACCC-CGCAGTTGAGTGTAATCGAACTCGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCCTCGAAGCTGAGTGTAATCGAACTTGG
* * *
69759 GAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAG
65 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
69824 CGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
130 CGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
69860 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
69925 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
69990 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
131 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
70025 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
70090 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
70155 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
131 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
70190 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
70255 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
* ** *
70320 GTAGTCGAACTCGAAGGTCTTTTGTTGGCAGACAA
131 GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
* * * * * **
70355 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAA
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
* *
70420 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCT
66 GGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCT
* * * *
70485 GAGTGTAATCGAACTCAAAGGTCTTTTGGTCACAGAGAA
127 GAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
* * * **
70524 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
* *
70589 GGTCTTTGGCAGATAGCCCTTCTCGACTTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
66 GGTCTTTGGCAGATAGCCCTTCTCGAC-TTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
70654 CGTAGTCGAACTCGAAGGTCTT
130 CGTAGTCGAACTCGAAGGTCTT
70676 GGTGGTAGGT
Statistics
Matches: 762, Mismatches: 48, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
164 3 0.00
165 559 0.73
166 53 0.07
167 2 0.00
169 145 0.19
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGGG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
Found at i:77214 original size:29 final size:28
Alignment explanation
Indices: 77133--77229 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 28
77123 AACCTATATA
*
77133 ATATATTTTCAAAAATATTTTAAAATTATAT
1 ATATATTTTCAAAAATGTTTTAAAA--AT-T
* * *
77164 ATATACTTTTTTAAAAACGTTTTCAAAATT
1 ATATA--TTTTCAAAAATGTTTTAAAAATT
* *
77194 ATATAGTTTTCAAAAATGTTTTTAAAACT
1 ATATA-TTTTCAAAAATGTTTTAAAAATT
77223 ATATATT
1 ATATATT
77230 ATAAGTTTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
28 2 0.04
29 24 0.44
30 6 0.11
31 7 0.13
33 16 0.29
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (28 bp):
ATATATTTTCAAAAATGTTTTAAAAATT
Found at i:77226 original size:63 final size:61
Alignment explanation
Indices: 77133--77261 Score: 161
Period size: 63 Copynumber: 2.1 Consensus size: 61
77123 AACCTATATA
* ** * *
77133 ATATATTTTCAAAAATATTTTAAAATTATATA-TATACTTTTTTAAAAACGTTTTCAAAATT
1 ATATATTTTCAAAAATATTTTAAAACTATATATTATAAGTTTTT-AAAACGATTTCAAAACT
* *
77194 ATATAGTTTTCAAAAATGTTTTTAAAACTATATATTATAAGTTTTTAAAATGATTTCAAAACT
1 ATATA-TTTTCAAAAAT-ATTTTAAAACTATATATTATAAGTTTTTAAAACGATTTCAAAACT
77257 ATATA
1 ATATA
77262 ATATATATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 5 0.09
62 11 0.19
63 33 0.57
64 9 0.16
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (61 bp):
ATATATTTTCAAAAATATTTTAAAACTATATATTATAAGTTTTTAAAACGATTTCAAAACT
Found at i:77232 original size:36 final size:36
Alignment explanation
Indices: 77191--77455 Score: 136
Period size: 36 Copynumber: 7.2 Consensus size: 36
77181 CGTTTTCAAA
77191 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
* * *
77227 ATTATA-AGTTTT-TAAAATGATTTCAAAACTATAT
1 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
*
77261 AATATATATATGTTTTC-AAACTGTTTCTTTTTAAAA--AT-T
1 -AT-TATATA-GTTTTCAAAAATG----TTTTTAAAACTATAT
* **
77300 A-TATTTA-TTTT-AAAAATGTTTTTTTAAAACCGTAT
1 ATTATATAGTTTTCAAAAATG--TTTTTAAAACTATAT
* * * * *
77335 AATATATATTTTTTTAAAAACGTTTTAAAAACTATAT
1 ATTATATA-GTTTTCAAAAATGTTTTTAAAACTATAT
* * ** *
77372 ATTATAT-TTATTTCCAAAGCGTTTTAAAAACTATAT
1 ATTATATAGT-TTTCAAAAATGTTTTTAAAACTATAT
* * * *
77408 AATATATAATTGTTTCAAATATGTTTTCAAAACTATTAT
1 ATTATAT-AGT-TTTCAAAAATGTTTTTAAAACTA-TAT
77447 ATATATATA
1 AT-TATATA
77456 TATATATATA
Statistics
Matches: 180, Mismatches: 27, Indels: 41
0.73 0.11 0.17
Matches are distributed among these distances:
32 10 0.06
34 29 0.16
35 12 0.07
36 49 0.27
37 19 0.11
38 35 0.19
39 12 0.07
40 7 0.04
42 7 0.04
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (36 bp):
ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
Found at i:77451 original size:2 final size:2
Alignment explanation
Indices: 77444--77497 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
77434 TCAAAACTAT
77444 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77486 TA TA TA TA TA TA
1 TA TA TA TA TA TA
77498 AAAAATGAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:81882 original size:23 final size:23
Alignment explanation
Indices: 81821--81875 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
81811 AACCGTAAGC
81821 TACCA-AAAGACAGAGAAAAACA
1 TACCACAAAGACAGAGAAAAACA
* *
81843 TACCACAAAGACAGAGATAAACG
1 TACCACAAAGACAGAGAAAAACA
*
81866 TACCATAAAG
1 TACCACAAAG
81876 GTAGAGAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.56, C:0.20, G:0.15, T:0.09
Consensus pattern (23 bp):
TACCACAAAGACAGAGAAAAACA
Found at i:93584 original size:38 final size:38
Alignment explanation
Indices: 93508--93584 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
93498 CAAGCATTCA
* * * *
93508 ACCAGGGAAGATAAATAGTTAAATATAAGAAGTGTTTT
1 ACCAGGGAAGAAAAATACTTAAATATAAGAAATATTTT
*
93546 ACCAGGGAAGAAAAATACTTATATATAAGAAATATTTT
1 ACCAGGGAAGAAAAATACTTAAATATAAGAAATATTTT
93584 A
1 A
93585 ACGCGAATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (38 bp):
ACCAGGGAAGAAAAATACTTAAATATAAGAAATATTTT
Found at i:98608 original size:25 final size:23
Alignment explanation
Indices: 98573--98643 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 23
98563 AAAAATTAAA
98573 TTAAGTTAATA-ATAAAATATGTT
1 TTAAGTTAATACATAAAATAT-TT
* *
98596 TAATAAGTTAATATAAAAAATATTT
1 T--TAAGTTAATACATAAAATATTT
98621 TTAAGTTATATACATAAAATATT
1 TTAAGTTA-ATACATAAAATATT
98644 ATGAATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 8 0.20
24 12 0.29
25 13 0.32
26 8 0.20
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (23 bp):
TTAAGTTAATACATAAAATATTT
Found at i:98623 original size:26 final size:25
Alignment explanation
Indices: 98574--98624 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
98564 AAAATTAAAT
*
98574 TAAGTTAATAATAAAATATGTTTAA
1 TAAGTTAATAAAAAAATATGTTTAA
*
98599 TAAGTTAATATAAAAAATATTTTTAA
1 TAAGTTAATA-AAAAAATATGTTTAA
98625 GTTATATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (25 bp):
TAAGTTAATAAAAAAATATGTTTAA
Found at i:106423 original size:30 final size:31
Alignment explanation
Indices: 106389--106480 Score: 114
Period size: 32 Copynumber: 3.0 Consensus size: 31
106379 TTTAACTCCT
*
106389 AAATTTAAAAAAAATA-CTAGTTGACCCTTA
1 AAATTTAAAAAAAATATCAAGTTGACCCTTA
* *
106419 AAATTTTAAAAAAATATCAATTTGACCCTTA
1 AAATTTAAAAAAAATATCAAGTTGACCCTTA
* * *
106450 AAACTTTAAATAAAATATCAATTTAACCCTT
1 AAA-TTTAAAAAAAATATCAAGTTGACCCTT
106481 TAATCCGACA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.28
31 15 0.28
32 24 0.44
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (31 bp):
AAATTTAAAAAAAATATCAAGTTGACCCTTA
Found at i:106470 original size:32 final size:31
Alignment explanation
Indices: 106396--106480 Score: 118
Period size: 31 Copynumber: 2.7 Consensus size: 31
106386 CCTAAATTTA
* * *
106396 AAAAAAATA-CTAGTTGACCCTTAAAATTTT
1 AAAAAAATATCAATTTGACCCTTAAAACTTT
106426 AAAAAAATATCAATTTGACCCTTAAAACTTT
1 AAAAAAATATCAATTTGACCCTTAAAACTTT
*
106457 AAATAAAATATCAATTTAACCCTT
1 AAA-AAAATATCAATTTGACCCTT
106481 TAATCCGACA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.18
31 21 0.43
32 19 0.39
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (31 bp):
AAAAAAATATCAATTTGACCCTTAAAACTTT
Done.