Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011374.1 Kokia drynarioides strain JFW-HI SEQ_126355, 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: 191179
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 107 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--34 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35 TTTTGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7500 original size:16 final size:17
Alignment explanation
Indices: 7479--7524 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
7469 CACAACCCCA
7479 TAAAAGGATATCT-TAT
1 TAAAAGGATATCTATAT
*
7495 TAAAAGATATATCTATAT
1 TAAAAG-GATATCTATAT
*
7513 GAAAA-GATATCT
1 TAAAAGGATATCT
7525 CATAAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 12 0.48
17 6 0.24
18 7 0.28
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (17 bp):
TAAAAGGATATCTATAT
Found at i:7508 original size:17 final size:18
Alignment explanation
Indices: 7486--7522 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
7476 CCATAAAAGG
*
7486 ATATCT-TATTAAAAGAT
1 ATATCTATATGAAAAGAT
7503 ATATCTATATGAAAAGAT
1 ATATCTATATGAAAAGAT
7521 AT
1 AT
7523 CTCATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
ATATCTATATGAAAAGAT
Found at i:13527 original size:19 final size:19
Alignment explanation
Indices: 13468--13531 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 19
13458 TTTATATACA
* *
13468 TTATTTAGAATTTT-TAAT
1 TTATTTTGAATTTTAAAAT
*
13486 TT-TTTTAAAATTTTAAAA-
1 TTATTTT-GAATTTTAAAAT
*
13504 ATATTTTGAATTTTAAAAT
1 TTATTTTGAATTTTAAAAT
13523 TTATTTTGA
1 TTATTTTGA
13532 TTATTTTGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
17 3 0.08
18 19 0.53
19 14 0.39
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (19 bp):
TTATTTTGAATTTTAAAAT
Found at i:18795 original size:28 final size:29
Alignment explanation
Indices: 18752--18806 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
18742 ACAAATTGAT
* *
18752 AGTTTAGGTACTACA-TAAATATTTTAGA
1 AGTTTAAGTACCACATTAAATATTTTAGA
18780 AGTTTAAGTACCACATTAAATATTTTA
1 AGTTTAAGTACCACATTAAATATTTTA
18807 TAAATGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (29 bp):
AGTTTAAGTACCACATTAAATATTTTAGA
Found at i:20223 original size:3 final size:3
Alignment explanation
Indices: 20215--20251 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
20205 TGACATCGGT
*
20215 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAC GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
20252 GAACGCCGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:25254 original size:30 final size:31
Alignment explanation
Indices: 25185--25286 Score: 92
Period size: 30 Copynumber: 3.5 Consensus size: 31
25175 ATAAAAGTTA
* * *
25185 TTATATTAAAAATTA-AATTATATTTTATTTT
1 TTATATTAAAAATTAGAAATA-AATTAATTTT
*
25216 TTAT-TTAAAAATT-G-AGTAAATTAATTTT
1 TTATATTAAAAATTAGAAATAAATTAATTTT
*
25244 TATATATT--AAATTAGAAATAAATTAATATT
1 T-TATATTAAAAATTAGAAATAAATTAATTTT
25274 TT-TATTAAAAATT
1 TTATATTAAAAATT
25287 TCATACGTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
28 18 0.31
29 8 0.14
30 29 0.49
31 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (31 bp):
TTATATTAAAAATTAGAAATAAATTAATTTT
Found at i:26966 original size:15 final size:14
Alignment explanation
Indices: 26946--26984 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
26936 GATTTAGATC
26946 ATATTTTAATTATTT
1 ATATTTTAATTA-TT
* *
26961 ATATTTAAAATATT
1 ATATTTTAATTATT
26975 ATATTTTAAT
1 ATATTTTAAT
26985 CAGCTATGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTTTAATTATT
Found at i:27161 original size:18 final size:18
Alignment explanation
Indices: 27138--27182 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
27128 GAATAGGTTT
27138 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
27156 TTAATTAAAAAATTTAAA
1 TTAATTAAAAAATTTAAA
27174 TTAATTAAA
1 TTAATTAAA
27183 CTTTGAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:27231 original size:18 final size:18
Alignment explanation
Indices: 27208--27242 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27198 ATTGTTTATC
*
27208 TTTTTTTCCTTTTAATTT
1 TTTTTTTCATTTTAATTT
27226 TTTTTTTCATTTTAATT
1 TTTTTTTCATTTTAATT
27243 AAAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTTCATTTTAATTT
Found at i:27432 original size:20 final size:20
Alignment explanation
Indices: 27407--27447 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
27397 TTATAATTTA
27407 ATTTTT-TTAAGAAAAACAAT
1 ATTTTTATTAA-AAAAACAAT
27427 ATTTTTATTAAAAAAACAAT
1 ATTTTTATTAAAAAAACAAT
27447 A
1 A
27448 AAGTAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTTTTATTAAAAAAACAAT
Found at i:27775 original size:23 final size:23
Alignment explanation
Indices: 27742--27791 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
27732 TATTTTTTAC
*
27742 AAAAATGAAAAACAAAAAAATAT
1 AAAAATGAAAAACAAAAAAAGAT
* **
27765 AAAAATTAAAATTAAAAAAAGAT
1 AAAAATGAAAAACAAAAAAAGAT
27788 AAAA
1 AAAA
27792 TGGGCCACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAAATGAAAAACAAAAAAAGAT
Found at i:28471 original size:2 final size:2
Alignment explanation
Indices: 28464--28500 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28454 GTATACTATC
28464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28501 ATAAACAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39554 original size:26 final size:27
Alignment explanation
Indices: 39506--39557 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
39496 ATTATTTCAA
* *
39506 TTTTTATTTATCAATTAAAATTAAATG
1 TTTTTATTTATAAACTAAAATTAAATG
*
39533 TTTTTATTT-TAAACTAACATTAAAT
1 TTTTTATTTATAAACTAAAATTAAAT
39558 TGATTCTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTTTATTTATAAACTAAAATTAAATG
Found at i:42595 original size:13 final size:13
Alignment explanation
Indices: 42577--42603 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42567 GTAACTGTGT
42577 GTGCATTGTCAAA
1 GTGCATTGTCAAA
42590 GTGCATTGTCAAA
1 GTGCATTGTCAAA
42603 G
1 G
42604 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (13 bp):
GTGCATTGTCAAA
Found at i:43767 original size:29 final size:30
Alignment explanation
Indices: 43724--43782 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
43714 TAATTGGATC
*
43724 AAATCGAAATTTCATATATAAAATTGCACA
1 AAATCGAAAATTCATATATAAAATTGCACA
* *
43754 AAATC-AAAATTCATGTATACAATTGCACA
1 AAATCGAAAATTCATATATAAAATTGCACA
43783 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCGAAAATTCATATATAAAATTGCACA
Found at i:46341 original size:17 final size:16
Alignment explanation
Indices: 46319--46360 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
46309 ATAACCAAAT
46319 AAAATAATTAAATGAAA
1 AAAATAATTAAAT-AAA
*
46336 AAAATAATAAAATAAA
1 AAAATAATTAAATAAA
*
46352 TAAATAATT
1 AAAATAATT
46361 CATGAACTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAATAATTAAATAAA
Found at i:47340 original size:15 final size:15
Alignment explanation
Indices: 47299--47340 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 15
47289 AAATATAATA
47299 TAATATA-ATATTTT
1 TAATATATATATTTT
47313 TAAT-TATA-A-TTT
1 TAATATATATATTTT
47325 TAATATATATATTTT
1 TAATATATATATTTT
47340 T
1 T
47341 TTTCATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 7 0.29
13 7 0.29
14 6 0.25
15 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATATATATATTTT
Found at i:47368 original size:13 final size:13
Alignment explanation
Indices: 47308--47369 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
47298 ATAATATAAT
*
47308 ATTTTTAATTATA
1 ATTTTTATTTATA
* *
47321 ATTTTAATATATA
1 ATTTTTATTTATA
47334 TATTTTT-TTTCATA
1 -ATTTTTATTT-ATA
*
47348 A-ATTTATTTATA
1 ATTTTTATTTATA
47360 ATTTTTATTT
1 ATTTTTATTT
47370 CTTAATAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
12 7 0.18
13 23 0.61
14 8 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTTATTTATA
Found at i:47665 original size:24 final size:22
Alignment explanation
Indices: 47618--47660 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
47608 TATATATATA
47618 TATATATCATTATTTTATAATT
1 TATATATCATTATTTTATAATT
47640 TATATATCATTATTTTA-AATT
1 TATATATCATTATTTTATAATT
47661 ATTTAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATATCATTATTTTATAATT
Found at i:51590 original size:3 final size:3
Alignment explanation
Indices: 51577--51632 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
51567 AATGTCAATG
* * *
51577 TTC TCC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTCC TCC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC
*
51623 TCC TTC TTC T
1 TTC TTC TTC T
51633 GTAATTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (3 bp):
TTC
Found at i:54852 original size:15 final size:14
Alignment explanation
Indices: 54827--54857 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
54817 TTTTAAAATT
54827 ATTTTATTTTTTTA
1 ATTTTATTTTTTTA
54841 ATTTTGATTTTTTTA
1 ATTTT-ATTTTTTTA
54856 AT
1 AT
54858 ATTTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
ATTTTATTTTTTTA
Found at i:54863 original size:18 final size:17
Alignment explanation
Indices: 54814--54863 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 17
54804 CTGCATGCTA
* *
54814 ATTTTTTAAAATTATTTT
1 ATTTTTTTAAATT-TTTG
54832 ATTTTTTT-AA-TTTTG
1 ATTTTTTTAAATTTTTG
54847 ATTTTTTTAATATTTTT
1 ATTTTTTTAA-ATTTTT
54864 ATAAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 11 0.41
16 2 0.07
17 3 0.11
18 11 0.41
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
ATTTTTTTAAATTTTTG
Found at i:61990 original size:27 final size:27
Alignment explanation
Indices: 61932--61990 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
61922 AATTTGCTTC
* * *
61932 GACTCAATTTAATTATAAAAAATTTCA
1 GACTCAATTAAAATATAAAAAATCTCA
*
61959 AACTCAATTAAAATATAAAATAA-CTCA
1 GACTCAATTAAAATATAAAA-AATCTCA
61986 GACTC
1 GACTC
61991 GATCATTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (27 bp):
GACTCAATTAAAATATAAAAAATCTCA
Found at i:66205 original size:19 final size:20
Alignment explanation
Indices: 66168--66207 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
66158 ACCCCTTAAA
* *
66168 TTTTGGGAAATTATGATTTT
1 TTTTGGGAAAATATCATTTT
66188 TTTTGGGAAAAT-TCATTTT
1 TTTTGGGAAAATATCATTTT
66207 T
1 T
66208 CCCTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.55
Consensus pattern (20 bp):
TTTTGGGAAAATATCATTTT
Found at i:69059 original size:136 final size:136
Alignment explanation
Indices: 68668--69059 Score: 527
Period size: 136 Copynumber: 2.9 Consensus size: 136
68658 TTCAACACTA
* * * * *
68668 AAAATTACTTCATTTCATCCAACTCTATTCATATTAATTAGCTCATGGTTAGAGAACTATTTACG
1 AAAATTACTTCATTTCATCCAATTCTATTCATATTAACTAGCTCATGCTTTGAGAACTATTTACA
** * * * *
68733 CATTGCTTTACAC-ATAGTATCAG-AAATTATCAGTAAACTAAGAGGGATGTCATTCGTTTATTC
66 CACAGTTTTACACAATACTATTAGCAGATTATCAGTAAACTAAGAGGGATGTCATTCGTTTATTC
*
68796 GGGTCT
131 AGGTCT
* * * *
68802 AAAATTACTTCATTTCATCCAATTCTATTTATATTTACTAGCTCATGCTTTGAAAACTATTCACA
1 AAAATTACTTCATTTCATCCAATTCTATTCATATTAACTAGCTCATGCTTTGAGAACTATTTACA
* * *
68867 CACAGTTTTACACATTACTATTAGCAGTTTATCAGTAAACTAAGAGGGACGTCATTCGTTTATTC
66 CACAGTTTTACACAATACTATTAGCAGATTATCAGTAAACTAAGAGGGATGTCATTCGTTTATTC
68932 AGGTCT
131 AGGTCT
* * *
68938 AAAATTACTTCATTTCATCTAGTTCTATTCATATTAACTAGCTCATGCTTTGAGAACCATTTACA
1 AAAATTACTTCATTTCATCCAATTCTATTCATATTAACTAGCTCATGCTTTGAGAACTATTTACA
* * * * *
69003 CACGGTTTTACACAATACTATTAGCAGCTTATCAGTAAAGTATGAGGGATGCCATTC
66 CACAGTTTTACACAATACTATTAGCAGATTATCAGTAAACTAAGAGGGATGTCATTC
69060 ATTCTCATTT
Statistics
Matches: 223, Mismatches: 33, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
134 66 0.30
135 7 0.03
136 150 0.67
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (136 bp):
AAAATTACTTCATTTCATCCAATTCTATTCATATTAACTAGCTCATGCTTTGAGAACTATTTACA
CACAGTTTTACACAATACTATTAGCAGATTATCAGTAAACTAAGAGGGATGTCATTCGTTTATTC
AGGTCT
Found at i:71073 original size:319 final size:319
Alignment explanation
Indices: 70445--71362 Score: 1086
Period size: 319 Copynumber: 2.9 Consensus size: 319
70435 AATGACGAAA
* *
70445 AACTGAAAAGCGAAAAACTAAAATACGTTTTTTCAAGTCAATGGTTTTTCAGAATTTGTGTA---
1 AACTG-AAAGCCAAAAACAAAAATACG-TTTTTCAAGTCAATGGTTTTTCAGAATTTGTGTAGTT
*
70507 -G-TTCGTAGCAACGGTTATAGGAAACAAAACGACATGCGTTTTGGGTTCTTTTTTCAACAATAA
64 CGATTCGTAGCAACGGTTTTAGGAAACAAAACGACATGCGTTTTGGGTTCTTTTTTCAACAATAA
* * *
70570 GTAGGCCCAAAGGAACAGA-GCATAAAAACAGAGGTTGTGAAAATGAAGGAAAAAATATAT-ACT
129 GTAGGCCCAAAGGAACAGATCCA-AAAAACAGAGGTTGCGAAAATGAAGGAAAAAATAT-TCTCT
* * *
70633 TAATGTGGCTGCTAGGATTTGAGCCCAGGTCTACACTGCCACAACGTGGAATTCTTACCACTAAA
192 TAATGTGGCTGCTGGGATTCGAGCCCAGGTC--CACAGCCACAACGTGGAATTCTTACCACTAAA
* * * *
70698 CTACAGCCACAAGATATTCGTTGTGACCATAGAGAAATATTATTGAGTAAATCTCAA-GGG-AT-
255 CTACAGCCACAAGATATTCGCTGTGACCATAGACAAATA-TAATCAGTAAATCTCAAGGGGAATA
70760 G
319 G
* * *
70761 -AC-G-AAGCCAAGAACAAAAATACGTTTATTCAAGTCGATGGTTTTTTAGAATTTGTGTAGTTC
1 AACTGAAAGCCAAAAACAAAAATACGTTT-TTCAAGTCAATGGTTTTTCAGAATTTGTGTAGTTC
*
70823 GTACTTCGTAGCAACGATTTTAGGAAACAAAACGACATGCGTTTTGGGTTCTTTTTTCAACAATA
65 G-A-TTCGTAGCAACGGTTTTAGGAAACAAAACGACATGCGTTTTGGGTTCTTTTTTCAACAATA
*
70888 AGTAGGCCCAAATGAACAGATCCAAAAAACAGAGGTTGCGAAAATGAAGGAAAAAATATTCTCTT
128 AGTAGGCCCAAAGGAACAGATCCAAAAAACAGAGGTTGCGAAAATGAAGGAAAAAATATTCTCTT
* * * *
70953 AATGTGGCTGCTGGGATTCGAGCCCAAGTCCACGGCCACAACGTGGATTTCTTACCGCTAAACTA
193 AATGTGGCTGCTGGGATTCGAGCCCAGGTCCACAGCCACAACGTGGAATTCTTACCACTAAACTA
* * * *
71018 CAGCCACAAGATGTTCGCTGTGGCCAAATTATTTACAAA-A-AATCAGTAGATCTCAAGGGGGAA
258 CAGCCACAAGATATTCGCTGTGACC--A-TA--GACAAATATAATCAGTAAATCTCAA-GGGG--
71081 AAATGACG
315 -AAT-A-G
*
71089 AAAAACTGAAAAGCGAAAAACAAAAATACGTTTTATCAAGTCAATGGTTTTTCAGAATTTGTGTA
1 ---AACTG-AAAGCCAAAAACAAAAATACGTTTT-TCAAGTCAATGGTTTTTCAGAATTTGTGTA
*
71154 GTTC-A----TAGCAACGGTTTTAGGAAACAAAAGGACATGCGTTTTGGGTTCTTTTTTCAACAA
61 GTTCGATTCGTAGCAACGGTTTTAGGAAACAAAACGACATGCGTTTTGGGTTCTTTTTTCAACAA
* * ** * *
71214 TAAGTTGGCCCAAAGGAACAGATCCTAAAAACAGAGGTTGCGAAAATGAAAAAAAAAACACTCTC
126 TAAGTAGGCCCAAAGGAACAGATCCAAAAAACAGAGGTTGCGAAAATGAAGGAAAAAATATTCTC
* * * *
71279 TTAATGTGGCTGCTGGGATTCTA-CCCAGGTCTCCACAGTCACTACGTGGAATTCTTACCACCAA
191 TTAATGTGGCTGCTGGGATTCGAGCCCAGG--TCCACAGCCACAACGTGGAATTCTTACCACTAA
*
71343 ACTACAGCCACAAGTTATTC
254 ACTACAGCCACAAGATATTC
71363 AGTAATTTAA
Statistics
Matches: 520, Mismatches: 48, Indels: 55
0.83 0.08 0.09
Matches are distributed among these distances:
311 3 0.01
312 46 0.09
314 1 0.00
315 2 0.00
316 1 0.00
317 54 0.10
318 1 0.00
319 156 0.30
320 4 0.01
321 4 0.01
322 4 0.01
325 2 0.00
327 5 0.01
328 134 0.26
329 45 0.09
332 2 0.00
333 2 0.00
334 1 0.00
335 53 0.10
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (319 bp):
AACTGAAAGCCAAAAACAAAAATACGTTTTTCAAGTCAATGGTTTTTCAGAATTTGTGTAGTTCG
ATTCGTAGCAACGGTTTTAGGAAACAAAACGACATGCGTTTTGGGTTCTTTTTTCAACAATAAGT
AGGCCCAAAGGAACAGATCCAAAAAACAGAGGTTGCGAAAATGAAGGAAAAAATATTCTCTTAAT
GTGGCTGCTGGGATTCGAGCCCAGGTCCACAGCCACAACGTGGAATTCTTACCACTAAACTACAG
CCACAAGATATTCGCTGTGACCATAGACAAATATAATCAGTAAATCTCAAGGGGAATAG
Found at i:72056 original size:20 final size:21
Alignment explanation
Indices: 72018--72069 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
72008 GTTCAGAATT
*
72018 TTTTTTAGATTTTAAATAA-TA
1 TTTTTTAGA-ATTAAATAACTA
*
72039 TTTTTTAGAATTACATAACTA
1 TTTTTTAGAATTAAATAACTA
*
72060 TGTTTTAGAA
1 TTTTTTAGAA
72070 AATTTTCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (21 bp):
TTTTTTAGAATTAAATAACTA
Found at i:73493 original size:32 final size:32
Alignment explanation
Indices: 73455--73522 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
73445 TTAGAGGTTG
* * *
73455 ATTAATACAAATCCTTGAATATATTAGGATTA
1 ATTAATACAAATCCTCGAAAAAATTAGGATTA
73487 ATTAATACAAATCCTCGAAAAAATTAGGATTA
1 ATTAATACAAATCCTCGAAAAAATTAGGATTA
73519 ATTA
1 ATTA
73523 GAAATTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (32 bp):
ATTAATACAAATCCTCGAAAAAATTAGGATTA
Found at i:74859 original size:22 final size:21
Alignment explanation
Indices: 74811--74903 Score: 77
Period size: 22 Copynumber: 4.5 Consensus size: 21
74801 AATTATATTG
*
74811 TTGTTTTGGTGCTATTTTTTTTA
1 TTGTTTTGGTGC--TGTTTTTTA
*
74834 TTGTTTTGGTTGCTGTTTTTTG
1 TTGTTTTGG-TGCTGTTTTTTA
* *
74856 TTGTTTTAGTGTTGTTTTTTA
1 TTGTTTTGGTGCTGTTTTTTA
* *
74877 CTG-TTT--TGAT-TTTTTTA
1 TTGTTTTGGTGCTGTTTTTTA
74894 TTGTTTTGGT
1 TTGTTTTGGT
74904 TGTTGTTTGG
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
17 9 0.16
18 6 0.10
20 4 0.07
21 12 0.21
22 15 0.26
23 9 0.16
24 3 0.05
ACGTcount: A:0.06, C:0.03, G:0.20, T:0.70
Consensus pattern (21 bp):
TTGTTTTGGTGCTGTTTTTTA
Found at i:74881 original size:21 final size:22
Alignment explanation
Indices: 74827--74883 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
74817 TGGTGCTATT
*
74827 TTTTTTATTGTTTTGGTTGCTG
1 TTTTTTATTGTTTTAGTTGCTG
* *
74849 TTTTTTGTTGTTTTAG-TGTTG
1 TTTTTTATTGTTTTAGTTGCTG
*
74870 TTTTTTACTGTTTT
1 TTTTTTATTGTTTT
74884 GATTTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 16 0.53
22 14 0.47
ACGTcount: A:0.05, C:0.04, G:0.19, T:0.72
Consensus pattern (22 bp):
TTTTTTATTGTTTTAGTTGCTG
Found at i:75009 original size:12 final size:12
Alignment explanation
Indices: 74939--75012 Score: 87
Period size: 12 Copynumber: 6.2 Consensus size: 12
74929 GTTTTGATGC
74939 TGCTATTTTT-T
1 TGCTATTTTTGT
74950 ATGCTATTTTTGT
1 -TGCTATTTTTGT
* **
74963 TGTTATTTTTAC
1 TGCTATTTTTGT
*
74975 TGCTATATTTGT
1 TGCTATTTTTGT
*
74987 TGCTGTTTTTGT
1 TGCTATTTTTGT
74999 TGCTATTTTTGT
1 TGCTATTTTTGT
75011 TG
1 TG
75013 TTTTTGTTAA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
12 50 0.98
13 1 0.02
ACGTcount: A:0.11, C:0.08, G:0.16, T:0.65
Consensus pattern (12 bp):
TGCTATTTTTGT
Found at i:75063 original size:12 final size:12
Alignment explanation
Indices: 75048--75072 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75038 TTTTTGCTGC
75048 TATTTTGATTGT
1 TATTTTGATTGT
75060 TATTTTGATTGT
1 TATTTTGATTGT
75072 T
1 T
75073 TAGATATTAT
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:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TATTTTGATTGT
Found at i:75073 original size:46 final size:46
Alignment explanation
Indices: 74992--75085 Score: 111
Period size: 46 Copynumber: 2.0 Consensus size: 46
74982 TTTGTTGCTG
* * * *
74992 TTTTTGTTGCTATTTTTGTTGTTTTTGTTAATGTTTTGCTATTATT
1 TTTTTGCTGCTATTTTTGTTGTTTTTGTGAATGTTTAGATATTATT
*
75038 TTTTTGCTGCTA-TTTTGATTGTTATTT-TGATTGTTTAGATATTATT
1 TTTTTGCTGCTATTTTTG-TTGTT-TTTGTGAATGTTTAGATATTATT
75084 TT
1 TT
75086 ATGCGTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 5 0.12
46 33 0.80
47 3 0.07
ACGTcount: A:0.14, C:0.04, G:0.15, T:0.67
Consensus pattern (46 bp):
TTTTTGCTGCTATTTTTGTTGTTTTTGTGAATGTTTAGATATTATT
Found at i:77290 original size:2 final size:2
Alignment explanation
Indices: 77283--77308 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
77273 TAAATAAGTT
77283 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
77309 AATTTTATTT
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):
TA
Found at i:78373 original size:17 final size:17
Alignment explanation
Indices: 78351--78383 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
78341 GTTTGGTCAA
78351 TAATTTT-CTATTTTTTT
1 TAATTTTGCT-TTTTTTT
78368 TAATTTTGCTTTTTTT
1 TAATTTTGCTTTTTTT
78384 AGTATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (17 bp):
TAATTTTGCTTTTTTTT
Found at i:108148 original size:19 final size:19
Alignment explanation
Indices: 108124--108162 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
108114 CTTTGTCAAT
108124 ATTTATACACATCAGAAAA
1 ATTTATACACATCAGAAAA
108143 ATTTATACACATCAGAAAA
1 ATTTATACACATCAGAAAA
108162 A
1 A
108163 CATTCATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (19 bp):
ATTTATACACATCAGAAAA
Found at i:113192 original size:12 final size:12
Alignment explanation
Indices: 113177--113201 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
113167 AAAAAAACCC
113177 AAAAATAATAAA
1 AAAAATAATAAA
113189 AAAAATAATAAA
1 AAAAATAATAAA
113201 A
1 A
113202 TTCTCAAATT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATAATAAA
Found at i:116243 original size:22 final size:22
Alignment explanation
Indices: 116204--116249 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
116194 GTCACTCAAC
*
116204 TAAAGCTTCATTTAAATATTTT
1 TAAAGCTTCATTTAAATACTTT
116226 TAAAGCTTCA-TTATAATACTTT
1 TAAAGCTTCATTTA-AATACTTT
116248 TA
1 TA
116250 TATATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (22 bp):
TAAAGCTTCATTTAAATACTTT
Found at i:120309 original size:26 final size:27
Alignment explanation
Indices: 120280--120358 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
120270 TATTTATTTG
120280 ATATTTGTAAATATT-T-TAAAATATAT
1 ATATTT-TAAATATTATATAAAATATAT
* *
120306 ATATTTTACATATTCATATATAATATAT
1 ATATTTTAAATATT-ATATAAAATATAT
*
120334 ATATTTTAAA-ATATATATTAAATAT
1 ATATTTTAAATAT-TATATAAAATAT
120359 TTTTAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
25 7 0.16
26 6 0.14
27 12 0.27
28 19 0.43
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (27 bp):
ATATTTTAAATATTATATAAAATATAT
Found at i:120347 original size:21 final size:22
Alignment explanation
Indices: 120290--120368 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 22
120280 ATATTTGTAA
*
120290 ATATTTTAAAATATATATATTTT
1 ATATTTTAAAATATA-ATATTAT
* * * *
120313 ACATATTCATATATAATA-TAT
1 ATATTTTAAAATATAATATTAT
*
120334 ATATTTTAAAATAT-ATATTAA
1 ATATTTTAAAATATAATATTAT
*
120355 ATATTTTTAAATAT
1 ATATTTTAAAATAT
120369 CAATCAATTC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
20 3 0.07
21 27 0.61
22 3 0.07
23 11 0.25
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTTAAAATATAATATTAT
Found at i:120347 original size:23 final size:22
Alignment explanation
Indices: 120321--120365 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
120311 TTACATATTC
*
120321 ATATATAATATATATATTTTAAA
1 ATATATAATAAATAT-TTTTAAA
*
120344 ATATATATTAAATATTTTTAAA
1 ATATATAATAAATATTTTTAAA
120366 TATCAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATATAATAAATATTTTTAAA
Found at i:122659 original size:23 final size:21
Alignment explanation
Indices: 122624--122666 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
122614 TTTTAATTCT
122624 TTAAAAAAATAAAATTATAAA
1 TTAAAAAAATAAAATTATAAA
122645 TTAATAAATAATAAAATTATAA
1 TTAA-AAA-AATAAAATTATAA
122667 TTTTCACTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 3 0.15
23 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAAAAAATAAAATTATAAA
Found at i:125354 original size:22 final size:22
Alignment explanation
Indices: 125290--125355 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
125280 TGTTTAAAAA
* *
125290 AATACAAATTTATTTAAAT-TT
1 AATATAAAATTATTTAAATATT
* * *
125311 AATGATAAAAATATATACATATT
1 AAT-ATAAAATTATTTAAATATT
*
125334 AATATAAAATTATTTATATATT
1 AATATAAAATTATTTAAATATT
125356 TTCTAAAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 3 0.09
22 27 0.77
23 5 0.14
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (22 bp):
AATATAAAATTATTTAAATATT
Found at i:130233 original size:22 final size:22
Alignment explanation
Indices: 130189--130229 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
130179 TTAAATTGGG
* *
130189 TTTAAATTCGTTTAAATTTATT
1 TTTAAATTCGTTAAAATTAATT
130211 TTTAAATTC-TTAAAATTAA
1 TTTAAATTCGTTAAAATTAA
130230 ATTTATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTAAATTCGTTAAAATTAATT
Found at i:130234 original size:20 final size:20
Alignment explanation
Indices: 130211--130253 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
130201 TAAATTTATT
130211 TTTAAATTCTTAAAATTAAA
1 TTTAAATTCTTAAAATTAAA
** * *
130231 TTTATCTTTTTAAATTTAAA
1 TTTAAATTCTTAAAATTAAA
130251 TTT
1 TTT
130254 CATTAAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAAATTCTTAAAATTAAA
Found at i:132313 original size:28 final size:28
Alignment explanation
Indices: 132207--132611 Score: 241
Period size: 29 Copynumber: 13.9 Consensus size: 28
132197 CACTGGAGGT
* * *
132207 CCCTAAACTATCTAGAAATTATATTTTAAC
1 CCCTAAACTTTCCA-AAATTACATTTT-AC
* * * *
132237 TCCTAAACTTCTCTAAAAATATATTTTAAC
1 CCCTAAACTT-TCCAAAATTACATTTT-AC
* *
132267 CCCCAAACCTTCCAAAAATTACATTTTAC
1 CCCTAAACTTTCC-AAAATTACATTTTAC
132296 CCCTAAACTTTCCAAAATT-CTATTTTTGA-
1 CCCTAAACTTTCCAAAATTAC-A-TTTT-AC
** *
132325 CATTAAACTTTCTAAAAATTACATTTTTAC
1 CCCTAAACTTTC-CAAAATTACA-TTTTAC
* *
132355 CCCTAAACTTTCCAAAATTCCATTTTTAA
1 CCCTAAACTTTCCAAAATTACA-TTTTAC
* *
132384 CCCTAAAATTTTCAAAAATTACATTTTAC
1 CCCT-AAACTTTCCAAAATTACATTTTAC
* *
132413 CCTTAAACTTTCCAAAATTCCATTTTGA-
1 CCCTAAACTTTCCAAAATTACATTTT-AC
* * *
132441 CCTTGAATTTTCCAAAATTACCATTTTA-
1 CCCTAAACTTTCCAAAATTA-CATTTTAC
* ** *
132469 CCCTCGAACTTTTGAAAATTCCATTTTGA-
1 CCCT-AAACTTTCCAAAATTACATTTT-AC
** *
132498 CCCT-ATTTTTCAAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAATTA-CATTTTAC
* *
132526 CCCCAAACTTTCCAAAATTCCATATTTGAC
1 CCCTAAACTTTCCAAAATTACAT-TTT-AC
**
132556 CCC-AATTTTTTCCAAAAATTACCATTTTAC
1 CCCTAA-ACTTTCC-AAAATTA-CATTTTAC
* *
132586 CCCCAAAC-TTCCAAAAATTCCATTTT
1 CCCTAAACTTTCC-AAAATTACATTTT
132612 TAAATCTAAT
Statistics
Matches: 302, Mismatches: 51, Indels: 46
0.76 0.13 0.12
Matches are distributed among these distances:
27 12 0.04
28 71 0.24
29 107 0.35
30 93 0.31
31 16 0.05
32 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAATTACATTTTAC
Found at i:132343 original size:58 final size:58
Alignment explanation
Indices: 132279--132708 Score: 412
Period size: 59 Copynumber: 7.3 Consensus size: 58
132269 CCAAACCTTC
* ** *
132279 CAAAAATTA-CATTTTACCCCTAAACTTTCCAAAATTCTATTTTTGACATTAAACTTT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTT
*
132336 CTAAAAATTA-CATTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTAAAATTTT
1 C-AAAAATTACCA-TTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCT-AAATTTT
* * *
132396 CAAAAATTA-CATTTTACCCTTAAACTTTCCAAAATTCCA-TTTTGACCTTGAATTTT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTT
* * ** *
132452 CCAAAATTACCATTTTA-CCCTCGAACTTTTGAAAATTCCA-TTTTGACCCT-ATTTTT
1 CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTGACCCTAAATTTT
* * * *
132508 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATATTTGACCCCAATTTTTT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAA-ATTTT
* * ** *
132567 CCAAAAATTACCATTTTACCCCCAAAC-TTCCAAAAATTCCATTTTTAAATCTAATTTTTTTT
1 -CAAAAATTACCATTTTACCCCTAAACTTTCC-AAAATTCCATTTTTGACCCTAA---ATTTT
* * * * * *
132629 CAAAAAATTACCATTTTA-CCCTCGAAC-TTCTAAAAATTTCATTTTTTACCCCAAACTTT
1 C-AAAAATTACCATTTTACCCCT-AAACTTTC-CAAAATTCCATTTTTGACCCTAAATTTT
132688 CACAAAATTACCATTTTACCC
1 CA-AAAATTACCATTTTACCC
132709 TTAAGTATCC
Statistics
Matches: 317, Mismatches: 38, Indels: 33
0.82 0.10 0.09
Matches are distributed among these distances:
56 53 0.17
57 51 0.16
58 39 0.12
59 73 0.23
60 52 0.16
61 4 0.01
62 45 0.14
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.39
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCTAAATTTT
Found at i:132365 original size:30 final size:29
Alignment explanation
Indices: 132207--132708 Score: 230
Period size: 29 Copynumber: 17.1 Consensus size: 29
132197 CACTGGAGGT
* * * *
132207 CCCTAAACTATCTAGAAATTATATTTTAAC
1 CCCTAAACTTTC-AAAAATTACATTTTTAC
* * *
132237 TCCTAAACTTCTCTAAAAA-TATATTTTAAC
1 CCCTAAACTT-TC-AAAAATTACATTTTTAC
* *
132267 CCCCAAACCTTCCAAAAATTACA-TTTTAC
1 CCCTAAA-CTTTCAAAAATTACATTTTTAC
*
132296 CCCTAAACTTTCCAAAATT-CTATTTTTGA-
1 CCCTAAACTTTCAAAAATTAC-ATTTTT-AC
**
132325 CATTAAACTTTCTAAAAATTACATTTTTAC
1 CCCTAAACTTTC-AAAAATTACATTTTTAC
* * *
132355 CCCTAAACTTTCCAAAATTCCATTTTTAA
1 CCCTAAACTTTCAAAAATTACATTTTTAC
*
132384 CCCTAAAATTTTCAAAAATTACA-TTTTAC
1 CCCT-AAACTTTCAAAAATTACATTTTTAC
* * * *
132413 CCTTAAACTTTCCAAAATTCCATTTTGA-
1 CCCTAAACTTTCAAAAATTACATTTTTAC
* * * *
132441 CCTTGAATTTTCCAAAATTACCA-TTTTA-
1 CCCTAAACTTTCAAAAATTA-CATTTTTAC
* ** * *
132469 CCCTCGAACTTTTGAAAATTCCATTTTGA-
1 CCCT-AAACTTTCAAAAATTACATTTTTAC
**
132498 CCCT-ATTTTTCAAAAATTACCA-TTTTAC
1 CCCTAAACTTTCAAAAATTA-CATTTTTAC
* * * *
132526 CCCCAAACTTTCCAAAATTCCATATTTGAC
1 CCCTAAACTTTCAAAAATTACAT-TTTTAC
**
132556 CCC-AATTTTTTCCAAAAATTACCA-TTTTAC
1 CCCTAA-ACTTT-CAAAAATTA-CATTTTTAC
* * * *
132586 CCCCAAACTTCCAAAAATTCCATTTTTAA
1 CCCTAAACTTTCAAAAATTACATTTTTAC
** **
132615 ATCTAATTTTTTTTCAAAAAATTACCA-TTTTA-
1 CCCTAA---ACTTTC-AAAAATTA-CATTTTTAC
* *
132647 CCCTCGAAC-TTCTAAAAATTTCATTTTTTAC
1 CCCT-AAACTTTC-AAAAATTACA-TTTTTAC
132678 CCC-AAACTTTCACAAAATTACCA-TTTTAC
1 CCCTAAACTTTCA-AAAATTA-CATTTTTAC
132707 CC
1 CC
132709 TTAAGTATCC
Statistics
Matches: 360, Mismatches: 76, Indels: 73
0.71 0.15 0.14
Matches are distributed among these distances:
27 15 0.04
28 63 0.17
29 134 0.37
30 101 0.28
31 25 0.07
32 7 0.02
33 13 0.04
34 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTCAAAAATTACATTTTTAC
Found at i:133835 original size:31 final size:31
Alignment explanation
Indices: 133770--133835 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
133760 TTTAGGCACT
* * *
133770 AAATTGAACATTGAAGCCAAACTTAAGTATC
1 AAATTAAACATTGAAGCCAAACTTAAGAACC
*
133801 AAATTAAACATTGAAGTCAAA-TTAAGAAACC
1 AAATTAAACATTGAAGCCAAACTTAAG-AACC
133832 AAAT
1 AAAT
133836 AGTATATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.24
Consensus pattern (31 bp):
AAATTAAACATTGAAGCCAAACTTAAGAACC
Found at i:133855 original size:1 final size:1
Alignment explanation
Indices: 133849--133911 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
133839 ATATTATTTC
* * * * * * * *
133849 AAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
133912 GAAACCAAAT
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:133862 original size:7 final size:7
Alignment explanation
Indices: 133850--133915 Score: 132
Period size: 7 Copynumber: 9.4 Consensus size: 7
133840 TATTATTTCA
133850 AAAAAAG
1 AAAAAAG
133857 AAAAAAG
1 AAAAAAG
133864 AAAAAAG
1 AAAAAAG
133871 AAAAAAG
1 AAAAAAG
133878 AAAAAAG
1 AAAAAAG
133885 AAAAAAG
1 AAAAAAG
133892 AAAAAAG
1 AAAAAAG
133899 AAAAAAG
1 AAAAAAG
133906 AAAAAAG
1 AAAAAAG
133913 AAA
1 AAA
133916 CCAAATAGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 59 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:137287 original size:21 final size:21
Alignment explanation
Indices: 137261--137319 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
137251 ATTGCCTCGA
137261 TTTTAAAGTAAAA-AAA-AACAG
1 TTTTAAA--AAAACAAACAACAG
*
137282 TTTTAAAAAAACAAACATCAG
1 TTTTAAAAAAACAAACAACAG
137303 TTTTAAAAAAACAAACA
1 TTTTAAAAAAACAAACA
137320 TGCGAGTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 4 0.11
20 3 0.09
21 28 0.80
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (21 bp):
TTTTAAAAAAACAAACAACAG
Found at i:137330 original size:22 final size:21
Alignment explanation
Indices: 137279--137320 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
137269 TAAAAAAAAA
137279 CAGTTTTAAAAAAACAAACAT
1 CAGTTTTAAAAAAACAAACAT
137300 CAGTTTTAAAAAAACAAACAT
1 CAGTTTTAAAAAAACAAACAT
137321 GCGAGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (21 bp):
CAGTTTTAAAAAAACAAACAT
Found at i:137589 original size:59 final size:57
Alignment explanation
Indices: 137512--137898 Score: 316
Period size: 59 Copynumber: 6.5 Consensus size: 57
137502 CGGATACCCG
* * **
137512 GGGGT-AAAATGGTAATTTTGGGAAAATTAGGGGTTAAAAATGGAATTCTTGGAAGTTC
1 GGGGTAAAAATGG-GATTTTTGGAAGTTTAGGGGTTAAAAATGGAATT-TTGGAAGTTC
* * *
137570 GTGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTTTAAAATGGGATTTTGGAAGTTC
1 G-GGGTAAAAATGGGATTTTTGGAAGTTTAGGGGTTAAAAATGGAATTTTGGAAGTTC
* * * *
137628 GGGGGTAAAAATGGGATTTTTGGATG-TTCGAGGG-TAAAAATAGAATTTTTGAAAGTTTC
1 -GGGGTAAAAATGGGATTTTTGGAAGTTTAG-GGGTTAAAAATGGAA-TTTTGGAAG-TTC
* * ** *
137687 GGGAGTAAAAATGGGATTTTTGGAAGTTTTA-GGGTTATAAACGGAATTTTCAAAAGTTTT
1 GGG-GTAAAAATGGGATTTTTGGAAG-TTTAGGGGTTAAAAATGGAATTTT-GGAAG-TTC
* * * * *
137747 GGGGTCAAAAATGGGATTTTTGGAAGTTTCGGTG-TGAAAACGAAATTTTTGGAAGTTCC
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTAGGGGTTAAAAATGGAA-TTTTGGAAGTT-C
* * **
137806 AGGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATAGAATTTTTAAAAGTTTC
1 -GGGGTAAAAATGGGATTTTTGGAAGTTTAGGGGTTAAAAATGGAA-TTTTGGAAG-TTC
** *
137866 AAGGTCAAAAATGGGATTTTTGAACAGTTTAGG
1 GGGGT-AAAAATGGGATTTTTGGA-AGTTTAGG
137899 AACCTCCAAG
Statistics
Matches: 269, Mismatches: 40, Indels: 37
0.78 0.12 0.11
Matches are distributed among these distances:
57 11 0.04
58 50 0.19
59 108 0.40
60 89 0.33
61 11 0.04
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (57 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTAGGGGTTAAAAATGGAATTTTGGAAGTTC
Found at i:137814 original size:119 final size:116
Alignment explanation
Indices: 137546--137887 Score: 390
Period size: 119 Copynumber: 2.9 Consensus size: 116
137536 AATTAGGGGT
*
137546 TAAAAATG-GAATTCTTGGAAGTTCGTGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTT-TAA
1 TAAAAA-GAGAATTTTTGGAAGTTCG-GGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTTAT-A
* ** *
137609 AATGGGATTTTGGAAG-TTCGGGGGT-AAAAATGGGATTTTTGGATGTTCGAGGG
63 AATGGAATTTTAAAAGTTTC-GGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG
* * *
137662 TAAAAATAGAATTTTTGAAAGTTTCGGGAGTAAAAATGGGATTTTTGGAAGTTTTAGGGTTATAA
1 TAAAAAGAGAATTTTTGGAAG-TTCGGG-GTAAAAATGGGATTTTTGGAAGTTTTGGGGTTATAA
* * *
137727 ACGGAATTTTCAAAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTCG-GTG
64 ATGGAATTTT-AAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGAGGG
* *
137781 TGAAAACGA-AATTTTTGGAAGTTCCAGGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTTAAA
1 T-AAAAAGAGAATTTTTGGAAGTT-C-GGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTTATA
* **
137845 AATAGAATTTTTAAAAGTTTCAAGGTCAAAAATGGGATTTTTG
63 AATGGAA-TTTTAAAAGTTTCGGGGTCAAAAATGGGATTTTTG
137888 AACAGTTTAG
Statistics
Matches: 193, Mismatches: 21, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
116 19 0.10
117 45 0.23
118 11 0.06
119 102 0.53
120 16 0.08
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (116 bp):
TAAAAAGAGAATTTTTGGAAGTTCGGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTTATAAAT
GGAATTTTAAAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG
Found at i:137839 original size:29 final size:29
Alignment explanation
Indices: 137541--137887 Score: 297
Period size: 30 Copynumber: 11.7 Consensus size: 29
137531 GGGAAAATTA
* *
137541 GGGGTTAAAAATGGAATTCTTGGAAG-TTC
1 GGGG-TAAAAATGGGATTTTTGGAAGTTTC
*
137570 GTGGGTAAAAATGGGATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGGATTTTTGGAAGTTTC
*
137600 GGGGTTTAAAATGGGA-TTTTGGAAG-TTC
1 GGGG-TAAAAATGGGATTTTTGGAAGTTTC
*
137628 GGGGGTAAAAATGGGATTTTTGGATG-TTC
1 -GGGGTAAAAATGGGATTTTTGGAAGTTTC
* * *
137657 GAGGGTAAAAATAGAATTTTTGAAAGTTTC
1 G-GGGTAAAAATGGGATTTTTGGAAGTTTC
*
137687 GGGAGTAAAAATGGGATTTTTGGAAGTTTTA
1 GGG-GTAAAAATGGGATTTTTGGAAG-TTTC
* * * * *** *
137718 GGGTTATAAACGGAATTTTCAAAAGTTTT
1 GGGGTAAAAATGGGATTTTTGGAAGTTTC
137747 GGGGTCAAAAATGGGATTTTTGGAAGTTTC
1 GGGGT-AAAAATGGGATTTTTGGAAGTTTC
* * * ** *
137777 GGTGTGAAAACGAAATTTTTGGAAGTTCC
1 GGGGTAAAAATGGGATTTTTGGAAGTTTC
*
137806 AGGGGTAAAAATGGGATTTTTGGAAGTTTT
1 -GGGGTAAAAATGGGATTTTTGGAAGTTTC
* * **
137836 GGGGTTAAAAATAGAATTTTTAAAAGTTTC
1 GGGG-TAAAAATGGGATTTTTGGAAGTTTC
**
137866 AAGGTCAAAAATGGGATTTTTG
1 GGGGT-AAAAATGGGATTTTTG
137888 AACAGTTTAG
Statistics
Matches: 251, Mismatches: 54, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
28 13 0.05
29 100 0.40
30 132 0.53
31 6 0.02
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGGATTTTTGGAAGTTTC
Found at i:139016 original size:12 final size:13
Alignment explanation
Indices: 138999--139031 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
138989 TATTAACCAA
138999 TAATAATATT-TT
1 TAATAATATTCTT
139011 TAATAATATTCTT
1 TAATAATATTCTT
139024 TAATAATA
1 TAATAATA
139032 ATAAATCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATAATATTCTT
Found at i:139708 original size:22 final size:23
Alignment explanation
Indices: 139670--139717 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
139660 AACAAAAATA
*
139670 AAATTTAAAGTTAAATTTATGAT
1 AAATTTAAAGTTAAATTTATAAT
*
139693 AAATTTTAA-TTAAATTTATAAT
1 AAATTTAAAGTTAAATTTATAAT
139715 AAA
1 AAA
139718 CTCAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
AAATTTAAAGTTAAATTTATAAT
Found at i:139714 original size:12 final size:12
Alignment explanation
Indices: 139670--139714 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
139660 AACAAAAATA
139670 AAATTTA-AAGTT
1 AAATTTATAA-TT
*
139682 AAATTTATGA-T
1 AAATTTATAATT
139693 AAATTT-TAATT
1 AAATTTATAATT
139704 AAATTTATAAT
1 AAATTTATAAT
139715 AAACTCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 2 0.07
11 14 0.50
12 11 0.39
13 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (12 bp):
AAATTTATAATT
Found at i:141719 original size:31 final size:31
Alignment explanation
Indices: 141661--141719 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
141651 TTTTAATTTT
*
141661 TTTAAAACTTTTATATTATTTTAATTTAATA
1 TTTAAAACTTTTATATAATTTTAATTTAATA
141692 TTTAATAA-TTTTATATAAATTTT-ATTTA
1 TTTAA-AACTTTTATAT-AATTTTAATTTA
141720 TTGAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTAAAACTTTTATATAATTTTAATTTAATA
Found at i:144210 original size:24 final size:23
Alignment explanation
Indices: 144179--144223 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
144169 GTTATCATTA
144179 AATTTTAAATTTATAGATTTAAT
1 AATTTTAAATTTATAGATTTAAT
* *
144202 AATTATTAATTTTATATATTTA
1 AATT-TTAAATTTATAGATTTA
144224 TTATACATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AATTTTAAATTTATAGATTTAAT
Found at i:146252 original size:18 final size:17
Alignment explanation
Indices: 146221--146256 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
146211 TATTATAATC
146221 TATATTATAGTAATAGT
1 TATATTATAGTAATAGT
*
146238 TATATATATATTAATAGT
1 TATAT-TATAGTAATAGT
146256 T
1 T
146257 TTAGTAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (17 bp):
TATATTATAGTAATAGT
Found at i:146382 original size:16 final size:17
Alignment explanation
Indices: 146361--146394 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
146351 ATAATTATAG
146361 TATTAAA-AATATTTTA
1 TATTAAATAATATTTTA
146377 TATTAAATTAATATTTTA
1 TATTAAA-TAATATTTTA
146395 AATATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTAAATAATATTTTA
Found at i:155884 original size:17 final size:17
Alignment explanation
Indices: 155849--155884 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
155839 CGATATTTGG
* *
155849 ATGATTAAATTTTTTTT
1 ATGATTAAATTATTGTT
155866 ATGATTAAATTATTGTT
1 ATGATTAAATTATTGTT
155883 AT
1 AT
155885 TAAATATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (17 bp):
ATGATTAAATTATTGTT
Found at i:156047 original size:26 final size:26
Alignment explanation
Indices: 155997--156048 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
155987 AATTGACTAA
*** *
155997 TTAATTTGTTATTATTTTTTTATTGG
1 TTAATTTGTTATTATTGAATGATTGG
156023 TTAATTTGTTATTATTGAATGATTGG
1 TTAATTTGTTATTATTGAATGATTGG
156049 ATTATACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (26 bp):
TTAATTTGTTATTATTGAATGATTGG
Found at i:170692 original size:21 final size:22
Alignment explanation
Indices: 170668--170709 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
170658 ATTATTTTAG
170668 ATTTAACATATTTA-AAAATTA
1 ATTTAACATATTTATAAAATTA
* *
170689 ATTTAATATTTTTATAAAATT
1 ATTTAACATATTTATAAAATT
170710 CTAAAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTAACATATTTATAAAATTA
Found at i:170748 original size:21 final size:21
Alignment explanation
Indices: 170709--170748 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
170699 TTTATAAAAT
* **
170709 TCTAAAATTTTAGGCTCTACC
1 TCTAAAATTCTAGAATCTACC
170730 TCTAAAATTCTAGAATCTA
1 TCTAAAATTCTAGAATCTA
170749 AATTCTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (21 bp):
TCTAAAATTCTAGAATCTACC
Found at i:170996 original size:55 final size:55
Alignment explanation
Indices: 170887--171023 Score: 174
Period size: 57 Copynumber: 2.5 Consensus size: 55
170877 AAAAAAAAGC
* *
170887 AAAG-AAACGTTACTTTC-AAATAAAAAAATTAAAAATGTATGCATAAAGATATGA
1 AAAGAAAATGTTACTTTCAAAAAAAAAAAATTAAAAATGTATGCATAAAGA-ATGA
170941 AAAGAAAATGTTACTTTCAAAAAAAAAAAATTTAAAAATGTATGCATAAAG-ATGA
1 AAAGAAAATGTTACTTTCAAAAAAAAAAAA-TTAAAAATGTATGCATAAAGAATGA
*
170996 AATGAGAAACATGTTAATTT-AAAAAAAA
1 AA--AGAAA-ATGTTACTTTCAAAAAAAA
171024 TTTAATTTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
54 4 0.05
55 18 0.24
56 10 0.14
57 33 0.45
58 9 0.12
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.26
Consensus pattern (55 bp):
AAAGAAAATGTTACTTTCAAAAAAAAAAAATTAAAAATGTATGCATAAAGAATGA
Found at i:172247 original size:19 final size:18
Alignment explanation
Indices: 172225--172271 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
172215 TTTCTCACTC
172225 TTTATTTATTT-ATTTATTT
1 TTTATTT-TTTCATTT-TTT
172244 TTTATGTTTTTCATTTTTT
1 TTTAT-TTTTTCATTTTTT
*
172263 TTCATTTTT
1 TTTATTTTT
172272 AATGTTTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.16
19 15 0.60
20 6 0.24
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTATTTTTTCATTTTTT
Found at i:178527 original size:21 final size:21
Alignment explanation
Indices: 178501--178542 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
178491 TTGTCACTGT
178501 CATGAAAGTAAATTAAAATGA
1 CATGAAAGTAAATTAAAATGA
178522 CATGAAAGTAAATTAAAATGA
1 CATGAAAGTAAATTAAAATGA
178543 TACTATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (21 bp):
CATGAAAGTAAATTAAAATGA
Found at i:180538 original size:16 final size:16
Alignment explanation
Indices: 180519--180576 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 16
180509 AAAAATTAAA
*
180519 TTAAACTTTTATTATT
1 TTAAAATTTTATTATT
180535 TTAAAAATTATTA-TATT
1 TT-AAAATT-TTATTATT
* *
180552 TT--ACTTTTATTAAT
1 TTAAAATTTTATTATT
180566 TTAAAATTTTA
1 TTAAAATTTTA
180577 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
13 3 0.09
14 8 0.24
16 8 0.24
17 11 0.33
18 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAAATTTTATTATT
Found at i:186911 original size:17 final size:17
Alignment explanation
Indices: 186856--186919 Score: 76
Period size: 17 Copynumber: 3.7 Consensus size: 17
186846 AGATTTTAAT
186856 TTTAAATTTATTGTAAA
1 TTTAAATTTATTGTAAA
* * *
186873 TTTAAGACTTATT-TGGAG
1 TTTAA-ATTTATTGT-AAA
186891 TTTAAATTTATTGTAAA
1 TTTAAATTTATTGTAAA
186908 TTTAAATTTATT
1 TTTAAATTTATT
186920 TTGAAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 25 0.66
18 13 0.34
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTGTAAA
Found at i:187702 original size:3 final size:3
Alignment explanation
Indices: 187696--187732 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
187686 AGTAATAAAT
187696 ATA ATA ATTA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
187733 AAAGTTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:187705 original size:22 final size:22
Alignment explanation
Indices: 187688--187732 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
187678 TTATTAGTAG
187688 TAATAA-ATATAATAATTAATAA
1 TAATAATA-ATAATAATTAATAA
187710 TAATAATAATAATAA-TAA-AA
1 TAATAATAATAATAATTAATAA
187730 TAA
1 TAA
187733 AAAGTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.23
21 3 0.14
22 13 0.59
23 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATAATAATAATAATTAATAA
Found at i:188912 original size:29 final size:29
Alignment explanation
Indices: 188864--188941 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
188854 ACCCCTGAAC
188864 TTTTCCAAAA-TCC-TATTTTAACCCTAAA
1 TTTTCCAAAATTCCAT-TTTTAACCCTAAA
188892 TTTTCCAAAATTCCATTTTTAACCCTAAA
1 TTTTCCAAAATTCCATTTTTAACCCTAAA
* *
188921 TTCTCTAAAAATTACCATTTT
1 TTTTC-CAAAATT-CCATTTT
188942 ACCCCCGAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
28 10 0.23
29 20 0.45
30 7 0.16
31 7 0.16
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (29 bp):
TTTTCCAAAATTCCATTTTTAACCCTAAA
Found at i:188956 original size:58 final size:55
Alignment explanation
Indices: 188894--189179 Score: 193
Period size: 58 Copynumber: 5.0 Consensus size: 55
188884 ACCCTAAATT
*
188894 TTCCAAAATTCCATTTTTAACCCTAAATTCTCTAAAAATTACCATTTTACCCCCGAA
1 TTCCAAAATTCCATTTTTAACCC-AAATT-TCCAAAAATTACCATTTTACCCCCGAA
* * ** * * * *
188951 CTTCCAAAAATTCCA-TTTTGACCTTGATTTTTCTAAAATTTATCATTTTACCCTCGAA
1 -TTCC-AAAATTCCATTTTTAACC--CAAATTTCCAAAAATTACCATTTTACCCCCGAA
* * * * *
189009 CTTCCTAAAATTCTA-TTTTGACACC-GATTTCCCAAAATTACCATTTTACCCCCGGA
1 -TTCC-AAAATTCCATTTTTAAC-CCAAATTTCCAAAAATTACCATTTTACCCCCGAA
* * *
189065 TGTCTAAAAATTCCATTTTTAAACCCAAACTTTCCAAAAATTGCCATTTTA-CCCTGAA
1 T-TC-CAAAATTCCATTTTT-AACCCAAA-TTTCCAAAAATTACCATTTTACCCCCGAA
* * * * *
189123 TGTCTAAAAATTCTATTTTTAACCCCAAACTTTCCCAAAATTACTATTTTGCCCCCG
1 T-TC-CAAAATTCCATTTTTAA-CCCAAA-TTTCCAAAAATTACCATTTTACCCCCG
189180 GGTATCCAAA
Statistics
Matches: 184, Mismatches: 32, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
55 1 0.01
56 33 0.18
57 8 0.04
58 106 0.58
59 36 0.20
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (55 bp):
TTCCAAAATTCCATTTTTAACCCAAATTTCCAAAAATTACCATTTTACCCCCGAA
Found at i:188968 original size:28 final size:29
Alignment explanation
Indices: 188927--189179 Score: 112
Period size: 29 Copynumber: 8.8 Consensus size: 29
188917 TAAATTCTCT
188927 AAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCC
** ** *
188956 AAAAATT-CCATTTTGA-CCTTGATTTTTCT
1 AAAAATTACCATTTT-ACCCCCGA-ACTTCC
* * *
188985 AAAATTTATCATTTTACCCTCGAACTTCC
1 AAAAATTACCATTTTACCCCCGAACTTCC
* * * *
189014 TAAAATT-CTATTTTGA-CACCG-ATTTCC
1 AAAAATTACCATTTT-ACCCCCGAACTTCC
* * *
189041 CAAAATTACCATTTTACCCCCGGA-TGTCT
1 AAAAATTACCATTTTACCCCCGAACT-TCC
** *
189070 AAAAATT-CCATTTTTAAACCCAAACTTTCC
1 AAAAATTACCA-TTTTACCCCCGAAC-TTCC
* * *
189100 AAAAATTGCCATTTTA-CCCTGAA-TGTCT
1 AAAAATTACCATTTTACCCCCGAACT-TCC
* * *
189128 AAAAATT-CTATTTTTAACCCCAAACTTTCC
1 AAAAATTACCA-TTTTACCCCCGAAC-TTCC
* * *
189158 CAAAATTACTATTTTGCCCCCG
1 AAAAATTACCATTTTACCCCCG
189180 GGTATCCAAA
Statistics
Matches: 165, Mismatches: 40, Indels: 37
0.68 0.17 0.15
Matches are distributed among these distances:
27 15 0.09
28 47 0.28
29 54 0.33
30 41 0.25
31 8 0.05
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCGAACTTCC
Found at i:189017 original size:30 final size:30
Alignment explanation
Indices: 188925--189134 Score: 101
Period size: 28 Copynumber: 7.3 Consensus size: 30
188915 CCTAAATTCT
*
188925 CTAAAAATTACCATTTTACCCCCGAACTTC
1 CTAAAAATTACCATTTTACCCTCGAACTTC
* ** *
188955 C-AAAAATT-CCATTTTGA-CCTTGATTTTT
1 CTAAAAATTACCATTTT-ACCCTCGAACTTC
* *
188983 CTAAAATTTATCATTTTACCCTCGAACTTC
1 CTAAAAATTACCATTTTACCCTCGAACTTC
* * *
189013 CT-AAAATT-CTATTTTGACAC-CG-ATTTC
1 CTAAAAATTACCATTTT-ACCCTCGAACTTC
* * *
189040 C-CAAAATTACCATTTTACCCCCGGA-TGT-
1 CTAAAAATTACCATTTTACCCTCGAACT-TC
* *
189068 CTAAAAATT-CCATTTTTAAACC-CAAACTTTC
1 CTAAAAATTACCA-TTTT-ACCCTCGAAC-TTC
*
189099 C-AAAAATTGCCATTTTACCCT-GAA-TGT-
1 CTAAAAATTACCATTTTACCCTCGAACT-TC
189126 CTAAAAATT
1 CTAAAAATT
189135 CTATTTTTAA
Statistics
Matches: 136, Mismatches: 24, Indels: 42
0.67 0.12 0.21
Matches are distributed among these distances:
27 16 0.12
28 42 0.31
29 42 0.31
30 31 0.23
31 5 0.04
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (30 bp):
CTAAAAATTACCATTTTACCCTCGAACTTC
Found at i:189115 original size:59 final size:59
Alignment explanation
Indices: 189036--189180 Score: 211
Period size: 58 Copynumber: 2.5 Consensus size: 59
189026 TTGACACCGA
189036 TTTCCCAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTTTAAACCCAAAC
1 TTTCCCAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTTTAAACCCAAAC
* * * * * *
189095 TTTCCAAAAATTGCCATTTTA-CCCTGAATGTCTAAAAATTCTATTTTTAACCCCAAAC
1 TTTCCCAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTTTAAACCCAAAC
* *
189153 TTTCCCAAAATTACTATTTTGCCCCCGG
1 TTTCCCAAAATTACCATTTTACCCCCGG
189181 GTATCCAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
58 50 0.68
59 23 0.32
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (59 bp):
TTTCCCAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTTTAAACCCAAAC
Found at i:189163 original size:30 final size:31
Alignment explanation
Indices: 188879--189172 Score: 99
Period size: 29 Copynumber: 10.1 Consensus size: 31
188869 CAAAATCCTA
* *
188879 TTTTAACCCTAAATTTTCC-AAAATT-CCAT
1 TTTTAACCCCAAACTTTCCAAAAATTACCAT
* *
188908 TTTTAACCCTAAA-TTCTCTAAAAATTACCA-
1 TTTTAACCCCAAACTT-TCCAAAAATTACCAT
* *
188938 TTTTACCCCCGAAC-TTCCAAAAATT-CCA-
1 TTTTAACCCCAAACTTTCCAAAAATTACCAT
* *** ** * * *
188966 TTTTGACCTTGATTTTTCTAAAATTTATCA-
1 TTTTAACCCCAAACTTTCCAAAAATTACCAT
* * *
188996 TTTT-ACCCTCGAAC-TTCCTAAAATT-CTA-
1 TTTTAACCC-CAAACTTTCCAAAAATTACCAT
* * * *
189024 TTTTGACACC-GA-TTTCCCAAAATTACCA-
1 TTTTAACCCCAAACTTTCCAAAAATTACCAT
* ** * *
189052 TTTTACCCCCGGA-TGTCTAAAAATT-CCAT
1 TTTTAACCCCAAACTTTCCAAAAATTACCAT
* *
189081 TTTTAAACCCAAACTTTCCAAAAATTGCCA-
1 TTTTAACCCCAAACTTTCCAAAAATTACCAT
** * * *
189111 TTTT-ACCCTGAA-TGTCTAAAAATT-CTAT
1 TTTTAACCCCAAACTTTCCAAAAATTACCAT
* *
189139 TTTTAACCCCAAACTTTCCCAAAATTACTAT
1 TTTTAACCCCAAACTTTCCAAAAATTACCAT
189170 TTT
1 TTT
189173 GCCCCCGGGT
Statistics
Matches: 197, Mismatches: 50, Indels: 34
0.70 0.18 0.12
Matches are distributed among these distances:
27 13 0.07
28 45 0.23
29 78 0.40
30 48 0.24
31 13 0.07
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (31 bp):
TTTTAACCCCAAACTTTCCAAAAATTACCAT
Found at i:189200 original size:59 final size:57
Alignment explanation
Indices: 189036--189200 Score: 195
Period size: 58 Copynumber: 2.8 Consensus size: 57
189026 TTGACACCGA
189036 TTTCCCAAAATTACCATTTTACCCCCGGATGTCTAAAAATTCCATTTTTAAACCCAAAC
1 TTTCCCAAAATTACCATTTT-CCCCCGGATGTCTAAAAATT-CATTTTTAAACCCAAAC
* * * * * *
189095 TTTCCAAAAATTGCCATTTTACCCTGAATGTCTAAAAATTCTATTTTTAACCCCAAAC
1 TTTCCCAAAATTACCATTTTCCCCCGGATGTCTAAAAATTC-ATTTTTAAACCCAAAC
* * * *
189153 TTTCCCAAAATTACTATTTTGCCCCCGGGTATCCAAAAATCTCATTTT
1 TTTCCCAAAATTACCATTTT-CCCCCGGATGTCTAAAAAT-TCATTTT
189201 CAACTCTGAT
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
57 1 0.01
58 49 0.56
59 36 0.41
60 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (57 bp):
TTTCCCAAAATTACCATTTTCCCCCGGATGTCTAAAAATTCATTTTTAAACCCAAAC
Done.