Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009308.1 Hibiscus syriacus cultivar Beakdansim tig00113044_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: 172755
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:4387 original size:29 final size:29
Alignment explanation
Indices: 4344--4426 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
4334 CTCACCTAAC
4344 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
4374 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
4403 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
4427 ATTTAGTTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:7041 original size:31 final size:31
Alignment explanation
Indices: 7006--7066 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
6996 ATTCGTAATC
* *
7006 ACTTTTGTTTCGTTTTAATTAATATGTGGTA
1 ACTTTCGTTTCGTTTTAATTAAGATGTGGTA
7037 ACTTTCGTTTCGTTTTAATTAAGATGTGGT
1 ACTTTCGTTTCGTTTTAATTAAGATGTGGT
7067 CACGATGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.21, C:0.08, G:0.18, T:0.52
Consensus pattern (31 bp):
ACTTTCGTTTCGTTTTAATTAAGATGTGGTA
Found at i:13117 original size:82 final size:81
Alignment explanation
Indices: 13000--13262 Score: 364
Period size: 81 Copynumber: 3.2 Consensus size: 81
12990 TCGGGTGGTA
* ** *
13000 TTTCACCAGCAAACGGACTATCGCGTTGAATGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
1 TTTCACCAGCGAACGGACTATCTTGTTGAACGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
*
13065 TCGTCACTAGGTGATTT
66 TCATCACTAGGTGA-TT
* * * * *
13082 TTTTACCAGCGAACGGACCATCTTGTTGGACGTCATCTCCCATTGATATTTCCGGCTCCCCTGCC
1 TTTCACCAGCGAACGGACTATCTTGTTGAACGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
* *
13147 TCATCACTAGTTGATA
66 TCATCACTAGGTGATT
* * *
13163 TTTCACCAGCGAACGGACTATCTTGTTGAACGTCTTCTTCCATCGATATTTCCGGCTCTCCTACC
1 TTTCACCAGCGAACGGACTATCTTGTTGAACGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
*
13228 TCATCACCAGGTGATT
66 TCATCACTAGGTGATT
*
13244 TTTCACCGGCGAACGGACT
1 TTTCACCAGCGAACGGACT
13263 CGCTGCTTGA
Statistics
Matches: 157, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 89 0.57
82 68 0.43
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.31
Consensus pattern (81 bp):
TTTCACCAGCGAACGGACTATCTTGTTGAACGTCATCTCCCATCGATATTTCCGGCTCCCCTACC
TCATCACTAGGTGATT
Found at i:14849 original size:14 final size:14
Alignment explanation
Indices: 14830--14859 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14820 CTCTTTTGCC
14830 TGCCTTTATCTTCT
1 TGCCTTTATCTTCT
*
14844 TGCCTTTCTCTTCT
1 TGCCTTTATCTTCT
14858 TG
1 TG
14860 TTGTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.30, G:0.10, T:0.57
Consensus pattern (14 bp):
TGCCTTTATCTTCT
Found at i:23993 original size:8 final size:8
Alignment explanation
Indices: 23980--24020 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
23970 CTCATTTTCA
23980 GAGAATTT
1 GAGAATTT
23988 GAGAATTT
1 GAGAATTT
*
23996 -AGAGTTT
1 GAGAATTT
*
24003 GGGAATTT
1 GAGAATTT
24011 GAGAATTT
1 GAGAATTT
24019 GA
1 GA
24021 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:24328 original size:128 final size:128
Alignment explanation
Indices: 24091--24846 Score: 1388
Period size: 128 Copynumber: 5.9 Consensus size: 128
24081 TAATCGGAGT
* *
24091 ACTATTCATATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCA-AGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* * * * *
24155 AATTACCCTATTATGTCACTCATGTCCCTCGGGAACACTAAATATATCAGTAACTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
24218 ACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAAAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
24283 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
24346 ACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* * *
24411 CATTGCCCTATTATATCACTTATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
24474 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
24539 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
24602 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
24667 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
24730 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
24795 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
24847 AATCAGGTAA
Statistics
Matches: 611, Mismatches: 17, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
127 49 0.08
128 562 0.92
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:25121 original size:14 final size:14
Alignment explanation
Indices: 25102--25131 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25092 CATAAGTTAA
*
25102 TTTTAATGTATATG
1 TTTTAATATATATG
25116 TTTTAATATATATG
1 TTTTAATATATATG
25130 TT
1 TT
25132 AATGATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (14 bp):
TTTTAATATATATG
Found at i:25285 original size:34 final size:34
Alignment explanation
Indices: 25247--25347 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
25237 AAATTTAATG
*
25247 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * * *
25281 TTAAATTTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
25315 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
25348 AACATTTATC
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:25896 original size:21 final size:21
Alignment explanation
Indices: 25866--25956 Score: 130
Period size: 21 Copynumber: 4.3 Consensus size: 21
25856 TATGGTATAA
*
25866 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
25887 AA-CCTAGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
25908 AATCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
25929 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
25950 AACCCTG
1 AACCCTG
25957 TGGAGATGGC
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.05
21 59 0.91
22 3 0.05
ACGTcount: A:0.22, C:0.26, G:0.32, T:0.20
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:25987 original size:21 final size:21
Alignment explanation
Indices: 25963--26010 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
25953 CCTGTGGAGA
*
25963 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
25984 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
26005 GGGCAT
1 TGGCAT
26011 GTATCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:27768 original size:16 final size:18
Alignment explanation
Indices: 27749--27794 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
27739 TAATAATTAT
27749 ATAAAATATTAT-TTTA-
1 ATAAAATATTATATTTAC
* *
27765 ATAAAAAATAATATTTAC
1 ATAAAATATTATATTTAC
27783 ATAAATATATTA
1 ATAAA-ATATTA
27795 ATATAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 10 0.43
17 4 0.17
18 5 0.22
19 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAAATATTATATTTAC
Found at i:27786 original size:18 final size:17
Alignment explanation
Indices: 27731--27787 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
27721 TTAATAATTC
*
27731 TAAATAAATAATAATT-A
1 TAAA-AAATAATATTTAA
* *
27748 TATAAAATATTATTTTAA
1 TAAAAAATAATA-TTTAA
27766 TAAAAAATAATATTTACA
1 TAAAAAATAATATTTA-A
27784 TAAA
1 TAAA
27788 TATATTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 16 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAAATAATATTTAA
Found at i:32566 original size:97 final size:99
Alignment explanation
Indices: 32429--32633 Score: 265
Period size: 97 Copynumber: 2.1 Consensus size: 99
32419 GGGTGTATTT
* * ** * *
32429 GGTTCGA-TTTTCACTAAAATCTAAATTAAACCGCGCATTGTGGGTTTTGAAAAATTGAAACTGA
1 GGTTCGATTTTTAACTAAAATATAAACCAAACCACGCATTGTGGGTTTTGAAAAATTAAAACTGA
**
32493 AACTGAATGACAT-AAAAC-AC-GATTTTCGGTTC
66 AACCAAATGACATAAAAACTACAG-TTTTCGGTTC
* *
32525 GGTTCGATTTTTAACTAAAATATAAACCGAACCACGCATTGTGTGTTTTGAAAAATTAAAACTGA
1 GGTTCGATTTTTAACTAAAATATAAACCAAACCACGCATTGTGGGTTTTGAAAAATTAAAACTGA
*
32590 AACCAAATGATATAAAAACTACAGTTTTCGGTTC
66 AACCAAATGACATAAAAACTACAGTTTTCGGTTC
*
32624 GATTCGATTT
1 GGTTCGATTT
32634 AAAGGTTTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
96 7 0.08
97 59 0.63
98 5 0.05
99 21 0.23
100 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (99 bp):
GGTTCGATTTTTAACTAAAATATAAACCAAACCACGCATTGTGGGTTTTGAAAAATTAAAACTGA
AACCAAATGACATAAAAACTACAGTTTTCGGTTC
Found at i:36474 original size:10 final size:10
Alignment explanation
Indices: 36458--36518 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
36448 CGGGTCTGGA
36458 GAACATAAAC
1 GAACATAAAC
*
36468 AAACATAAAC
1 GAACATAAAC
*
36478 GATCATAAAC
1 GAACATAAAC
36488 GAACA-AATA-
1 GAACATAA-AC
* *
36497 TAA-ATGAAC
1 GAACATAAAC
36506 GAACATAAAC
1 GAACATAAAC
36516 GAA
1 GAA
36519 TGGGTTATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
8 2 0.05
9 7 0.18
10 30 0.77
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.13
Consensus pattern (10 bp):
GAACATAAAC
Found at i:36513 original size:14 final size:14
Alignment explanation
Indices: 36475--36518 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
36465 AACAAACATA
*
36475 AACGATCATAAACG
1 AACGAACATAAACG
* * *
36489 AACAAATATAAATG
1 AACGAACATAAACG
36503 AACGAACATAAACG
1 AACGAACATAAACG
36517 AA
1 AA
36519 TGGGTTATCA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:38133 original size:30 final size:29
Alignment explanation
Indices: 38098--38165 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 29
38088 CCTAAATTTC
38098 TTTGTTTATTGGGACTTCATTGTCCTTAGA
1 TTTGTTTATTGGGACTTCA-TGTCCTTAGA
* *
38128 TTTG-TT-TT-GTAGTTCATGTCCTTAGA
1 TTTGTTTATTGGGACTTCATGTCCTTAGA
38154 TTTGTTTATTGG
1 TTTGTTTATTGG
38166 CAGAATCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 14 0.42
27 8 0.24
28 4 0.12
29 3 0.09
30 4 0.12
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (29 bp):
TTTGTTTATTGGGACTTCATGTCCTTAGA
Found at i:45539 original size:15 final size:15
Alignment explanation
Indices: 45519--45550 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
45509 TATGATAGTC
45519 TGGGAAATCTGGAAA
1 TGGGAAATCTGGAAA
45534 TGGGAAATCTGGAAA
1 TGGGAAATCTGGAAA
45549 TG
1 TG
45551 AGTAGTACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.34, T:0.22
Consensus pattern (15 bp):
TGGGAAATCTGGAAA
Found at i:47365 original size:24 final size:24
Alignment explanation
Indices: 47337--47388 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
47327 TATATGATTT
*
47337 TAAAATAAAA-AATAGTTAAGTGAC
1 TAAAATAAAATAATAATT-AGTGAC
*
47361 TAAAATAAAATAATAATTAGTTAC
1 TAAAATAAAATAATAATTAGTGAC
47385 TAAA
1 TAAA
47389 CGTGTAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.29
Consensus pattern (24 bp):
TAAAATAAAATAATAATTAGTGAC
Found at i:52125 original size:57 final size:58
Alignment explanation
Indices: 52017--52126 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
52007 AACAAATAAG
* *
52017 TACTTAAAATATATCATTTTTCATTTAAGTACGTAAAGTATTTTTTTATTAAAATAGA
1 TACTTAAAATATATCATTTTTCATTCAAGTACGTAAAGTATTTTTTAATTAAAATAGA
* *
52075 TACTTAAAGTAT-TCATTTTTTTATTCAAGTAAC-TAAAGTA-TTTTTAATTAAA
1 TACTTAAAATATATCA-TTTTTCATTCAAGT-ACGTAAAGTATTTTTTAATTAAA
52127 GTTAAATATC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 14 0.30
58 30 0.65
59 2 0.04
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.47
Consensus pattern (58 bp):
TACTTAAAATATATCATTTTTCATTCAAGTACGTAAAGTATTTTTTAATTAAAATAGA
Found at i:53240 original size:31 final size:31
Alignment explanation
Indices: 53182--53265 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
53172 TCAATAAAAT
* *
53182 TTAAAAAATTATAAAA-TACTTATTAAATTTA
1 TTAAAAAATTATAAAATTA-TTAATAAATTAA
*
53213 TTAAAAGATTATAAAATTATTAATAAATTAA
1 TTAAAAAATTATAAAATTATTAATAAATTAA
* *
53244 TCT-AAATACTATAAAATTATTA
1 T-TAAAAAATTATAAAATTATTA
53266 TTATATTATC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
31 43 0.93
32 3 0.07
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
TTAAAAAATTATAAAATTATTAATAAATTAA
Found at i:53242 original size:19 final size:19
Alignment explanation
Indices: 53186--53235 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
53176 TAAAATTTAA
*
53186 AAAATTA-TAAAATACTTATT
1 AAAATTATTAAAAGA-TTA-T
*
53206 AAATTTATTAAAAGATTAT
1 AAAATTATTAAAAGATTAT
53225 AAAATTATTAA
1 AAAATTATTAA
53236 TAAATTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.42
20 9 0.35
21 6 0.23
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATTATTAAAAGATTAT
Found at i:53798 original size:26 final size:28
Alignment explanation
Indices: 53738--53799 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
53728 GAGTATTGTT
*
53738 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
53769 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
53795 GAGCT
1 GAGCT
53800 TAAAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:55239 original size:20 final size:20
Alignment explanation
Indices: 55214--55287 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
55204 CGATTTTTCA
*
55214 AAATCGCAATGCGAATATGT
1 AAATCGCAACGCGAATATGT
* *
55234 AAATCGTAACACGAATATGT
1 AAATCGCAACGCGAATATGT
* *
55254 AAATCGAAATGCGAATATGT
1 AAATCGCAACGCGAATATGT
55274 AAATCGCAACGCGA
1 AAATCGCAACGCGA
55288 TTCTGACTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:55320 original size:21 final size:21
Alignment explanation
Indices: 55296--55341 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
55286 GATTCTGACT
*
55296 ATCGTAATACGATAATACAAA
1 ATCGTAACACGATAATACAAA
*
55317 ATCGTAACATGATAATACAAA
1 ATCGTAACACGATAATACAAA
55338 ATCG
1 ATCG
55342 CAACGCGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (21 bp):
ATCGTAACACGATAATACAAA
Found at i:55488 original size:21 final size:20
Alignment explanation
Indices: 55462--55528 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
55452 TAATAGGAAA
55462 ATCGCAACGTGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
* * **
55483 ATCGCAAC-GAATTTGGAAA
1 ATCGCAACGGAACTTCGACT
*
55502 ATCTCAACGCGAACTTCGACT
1 ATCGCAACG-GAACTTCGACT
55523 ATCGCA
1 ATCGCA
55529 TTGCGATAAT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 14 0.41
21 20 0.59
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGGAACTTCGACT
Found at i:55593 original size:41 final size:38
Alignment explanation
Indices: 55522--55635 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 38
55512 GAACTTCGAC
* * * **
55522 TATCGCATTGCGATAATGGAGATCGCGTTGCGATTTTGTA
1 TATCGCATTGCGATAGTAGA-ATCGTGTTGCGA-TTTACA
55562 TTATCGCATTGCGATAGTCAGAATCGTGTTGCGATTTACA
1 -TATCGCATTGCGATAGT-AGAATCGTGTTGCGATTTACA
* *
55602 TATTCGCAATGCGATAGTAAAAATCGTGTTGCGA
1 TA-TCGCATTGCGATAGT-AGAATCGTGTTGCGA
55636 ATCTGGAAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.03
40 32 0.51
41 27 0.43
42 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (38 bp):
TATCGCATTGCGATAGTAGAATCGTGTTGCGATTTACA
Found at i:55673 original size:20 final size:19
Alignment explanation
Indices: 55650--55695 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
55640 GGAAACTGAT
* *
55650 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
55670 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
55689 TTGCGAT
1 TTGCGAT
55696 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:55685 original size:19 final size:19
Alignment explanation
Indices: 55661--55697 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
55651 TGCGATACTG
*
55661 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
55680 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
55698 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:56317 original size:21 final size:21
Alignment explanation
Indices: 56202--56317 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
56192 GCGAAATAAA
**
56202 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
56222 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
56242 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
56263 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
56283 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
56305 AATCGCAACGCGA
1 AATCGCAACGCGA
56318 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:56368 original size:40 final size:40
Alignment explanation
Indices: 56305--56533 Score: 239
Period size: 40 Copynumber: 5.7 Consensus size: 40
56295 GATTTTCCAG
* ** * * *
56305 AATCGCAACGCGAATATGAAAATCGCAACGCGGA-CACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATC-CGTA
* *
56345 AATCGCAACGCGTATCCATAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
56385 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* *
56425 TATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTA
* * * *
56465 AATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTA
* * * *
56505 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
56534 ACTGAAATTT
Statistics
Matches: 168, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 166 0.99
41 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
Found at i:56520 original size:20 final size:20
Alignment explanation
Indices: 56343--56533 Score: 233
Period size: 20 Copynumber: 9.6 Consensus size: 20
56333 CGCGGACACA
* *
56343 TAAATCGCAACGCGTATCCA
1 TAAATCGCAACGAGTATCCG
*
56363 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGAGTATCCG
*
56383 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
56403 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
56423 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
56443 TAAATCGCAACGA-TAATCCG
1 TAAATCGCAACGAGT-ATCCG
* *
56463 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGAGTATCCG
56483 TAAATCGCAACGA-TAATCCG
1 TAAATCGCAACGAGT-ATCCG
* *
56503 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGAGTATCCG
*
56523 TAAATCACAAC
1 TAAATCGCAAC
56534 ACTGAAATTT
Statistics
Matches: 152, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 151 0.99
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGAGTATCCG
Found at i:57265 original size:24 final size:24
Alignment explanation
Indices: 57226--57272 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
57216 AAATTTGGTC
57226 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
57250 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
57273 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:57464 original size:12 final size:12
Alignment explanation
Indices: 57447--57471 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57437 ATATAATCCT
57447 GAAGAAGAAAAA
1 GAAGAAGAAAAA
57459 GAAGAAGAAAAA
1 GAAGAAGAAAAA
57471 G
1 G
57472 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:59823 original size:34 final size:33
Alignment explanation
Indices: 59755--59934 Score: 261
Period size: 33 Copynumber: 5.2 Consensus size: 33
59745 CGGAAATTAC
59755 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * *
59788 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAA
*
59822 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
59860 AATCGCAACGAGAGAATCGCAATGCGAAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCG-AAATGAA
59894 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
59927 AATCGCAA
1 AATCGCAA
59935 TGCGAAATGA
Statistics
Matches: 134, Mismatches: 6, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
33 51 0.38
34 49 0.37
36 3 0.02
38 17 0.13
39 14 0.10
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:59832 original size:53 final size:52
Alignment explanation
Indices: 59769--60006 Score: 315
Period size: 53 Copynumber: 4.5 Consensus size: 52
59759 GCAACGAGAG
*
59769 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGC-GAAATGAA
*
59822 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AA-GAAAATCGCAATGCGAAATGAA
* *
59874 AATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AAATGAAAATCGCAACAAGAAAATCGCAATGCGAAATGAA
* *
59927 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGC-GAAATGAA
59980 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
60007 TGCGATTCTC
Statistics
Matches: 168, Mismatches: 5, Indels: 24
0.85 0.03 0.12
Matches are distributed among these distances:
48 10 0.06
49 1 0.01
50 2 0.01
51 1 0.01
52 47 0.28
53 91 0.54
55 2 0.01
56 1 0.01
57 2 0.01
58 11 0.07
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:59862 original size:72 final size:72
Alignment explanation
Indices: 59769--60006 Score: 291
Period size: 72 Copynumber: 3.4 Consensus size: 72
59759 GCAACGAGAG
*
59769 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
59834 AAATGAA
66 AAATGAA
* * *
59841 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAA--CG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
*
59904 --A-GAG
66 AAATGAA
*
59908 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAGAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AA-GAAAATCGCAATGCGGAAATGAAAATCGCA
59967 ATGCGGAAATGAA
61 ATGC-GAAATGAA
59980 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
60007 TGCGATTCTC
Statistics
Matches: 145, Mismatches: 10, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
66 10 0.07
67 30 0.21
68 2 0.01
69 2 0.01
70 3 0.02
71 2 0.01
72 96 0.66
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:59883 original size:105 final size:105
Alignment explanation
Indices: 59755--59953 Score: 355
Period size: 105 Copynumber: 1.9 Consensus size: 105
59745 CGGAAATTAC
59755 AATCGCAACGAGAGAATCGCAATGCG-AAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCCCAACAAGAAAATCGCAATGC-GAAAT
59819 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
65 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * *
59860 AATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCCCAACAAGAAAATCGCAATGCGAAATG
59925 AAAATCGCAATGCGAAATGAAAATCGCAA
66 AAAATCGCAATGCGAAATGAAAATCGCAA
59954 CGAGAGAATC
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
105 61 0.68
106 29 0.32
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (105 bp):
AATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCCCAACAAGAAAATCGCAATGCGAAATG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:60025 original size:86 final size:88
Alignment explanation
Indices: 59799--60011 Score: 310
Period size: 86 Copynumber: 2.4 Consensus size: 88
59789 ATCCCAACAA
59799 GAAAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATC
1 GAAAATCGCAATGC-GAAATGAAAATCGCAATGCG-AAT--AAATCGCAATGCGAAATGAAAATC
59864 GCAACGAGAGAATCGCAATGCGAAAAT
62 GCAACGAGAGAATCGCAATGCGAAAAT
*
59891 GAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCG-AAT--AAATCGCAATGCGAAATGAAAATCG
*
59951 CAACGAGAGAATCGCAATGCGGAAAT
63 CAACGAGAGAATCGCAATGCGAAAAT
59977 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
60012 TTCTCTCGTT
Statistics
Matches: 113, Mismatches: 3, Indels: 12
0.88 0.02 0.09
Matches are distributed among these distances:
86 81 0.72
87 1 0.01
88 2 0.02
89 1 0.01
90 3 0.03
91 14 0.12
92 11 0.10
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (88 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAATAAATCGCAATGCGAAATGAAAATCGCAA
CGAGAGAATCGCAATGCGAAAAT
Found at i:60045 original size:53 final size:52
Alignment explanation
Indices: 59982--60097 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
59972 GAAATGAAAA
*
59982 TCGCAATGCGAAATGAAAATCGCAATGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCAATGCGATTCTCTCGTTGCGATTTTCATT
** ** ** *
60034 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCAATGCGATTCTCTCGTTGCGATTTTCATT
60087 TCGCATTGCGA
1 TCGCATTGCGA
60098 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCAATGCGATTCTCTCGTTGCGATTTTCATT
Found at i:60060 original size:19 final size:19
Alignment explanation
Indices: 60020--60107 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
60010 GATTCTCTCG
60020 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
60040 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
60059 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
60073 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
60092 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
60108 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:60217 original size:14 final size:14
Alignment explanation
Indices: 60198--60234 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
60188 CATCAATTAC
60198 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
60212 ACAAATCATCTTTT
1 ACAAATCAACTTTT
60226 ACAAATCAA
1 ACAAATCAA
60235 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:61668 original size:21 final size:21
Alignment explanation
Indices: 61638--61698 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
61628 GTGAATCGGG
61638 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * ** *
61659 CTCTTCAATGATGACAGTGAC
1 CTCTTGAATGGTGGGAGGGAC
*
61680 CTCTTGAACGGTGGGAGGG
1 CTCTTGAATGGTGGGAGGG
61699 GACTCTCGAG
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:62199 original size:19 final size:19
Alignment explanation
Indices: 62157--62329 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
62147 TAGTTTACTT
* *
62157 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
62177 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
62196 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
* **
62215 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
62234 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
62253 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
62267 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
62286 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
62300 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
62319 TCGCAATGCGA
1 TCGCAACGCGA
62330 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 80 0.63
20 12 0.10
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:62270 original size:14 final size:14
Alignment explanation
Indices: 62251--62307 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
62241 GCGAAATGAA
*
62251 AATCGCAACGACAG
1 AATCGCAACGAAAG
62265 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
62282 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
62298 AATCGCAACG
1 AATCGCAACG
62308 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:62278 original size:33 final size:33
Alignment explanation
Indices: 62232--62324 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
62222 GCGAAACCAA
62232 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
62265 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
62298 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
62325 TGCGATTTTG
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:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:62321 original size:52 final size:52
Alignment explanation
Indices: 62191--62329 Score: 156
Period size: 52 Copynumber: 2.7 Consensus size: 52
62181 AACGCGAAAT
* * *
62191 GAGAATCGCAACGAGAAACCAAAATCGCAATGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
62243 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
62295 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
62330 TTTTGGTTTC
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 44 0.64
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:62360 original size:14 final size:14
Alignment explanation
Indices: 62341--62399 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
62331 TTTGGTTTCG
62341 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
62355 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
62372 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
62388 CGTTGCGATTTT
1 CGTTGCGATTTT
62400 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:62367 original size:33 final size:33
Alignment explanation
Indices: 62325--62418 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
62315 AAAATCGCAA
62325 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
*
62358 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
**
62391 TGCGATTTTCATTTCGCGTTGCGATTTT
1 TGCGATTTTGGTTTCGCGTTGCGATTTT
62419 AAGTTTCGTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:62379 original size:19 final size:18
Alignment explanation
Indices: 62325--62434 Score: 92
Period size: 19 Copynumber: 6.3 Consensus size: 18
62315 AAAATCGCAA
62325 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
62344 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
62358 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
62377 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
62391 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
62410 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
62430 TGCGA
1 TGCGA
62435 AAGTAAACTA
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
14 23 0.31
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 32 0.43
20 12 0.16
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:62691 original size:93 final size:93
Alignment explanation
Indices: 62532--62847 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
62522 TCAGGGTATT
62532 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
62597 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
62625 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
62690 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
62718 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
62783 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
62811 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
62848 AAGCAATCTA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:64565 original size:20 final size:20
Alignment explanation
Indices: 64534--64597 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
64524 TTTTGGTTGA
64534 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
64554 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
64574 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
64595 AAT
1 AAT
64598 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:64586 original size:21 final size:21
Alignment explanation
Indices: 64532--64596 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
64522 TCTTTTGGTT
64532 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
64553 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
64573 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
64594 GAA
1 GAA
64597 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:64680 original size:21 final size:20
Alignment explanation
Indices: 64621--64684 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 20
64611 GAAAATCGCA
64621 ATTTTCATTTTTCTCGTTGCAG
1 ATTTTCA-TTTTCTCGTTGC-G
** *
64643 ATAGTCATTTTCACGTTGCG
1 ATTTTCATTTTCTCGTTGCG
64663 ATTTTCATTTATCTCGTTGCG
1 ATTTTCATTT-TCTCGTTGCG
64684 A
1 A
64685 CTCTTCTGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
20 9 0.26
21 21 0.60
22 5 0.14
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (20 bp):
ATTTTCATTTTCTCGTTGCG
Found at i:64806 original size:33 final size:33
Alignment explanation
Indices: 64764--64834 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
64754 AATACTAACT
64764 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
***
64797 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAACAACGCGAAA
64830 TGAAA
1 TGAAA
64835 TCTAAGTGAA
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:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAACAACGCGAAA
Found at i:65239 original size:20 final size:20
Alignment explanation
Indices: 65214--65406 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
65204 CTTTAAAAAT
65214 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
65234 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
65254 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
65275 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
65295 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
65315 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
65335 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
65355 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
65375 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
65395 CGCGTTGCGATT
1 CGCGTTGCGATT
65407 CTGGAAAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 134 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:66086 original size:63 final size:64
Alignment explanation
Indices: 65965--66088 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 64
65955 TCTTTCGAAA
* *
65965 TTTTCTGGTTTAATTATTTGTTAAGACATTATCAGTTTTAAAGTTTAATAAAATTAAGTCCTTTC
1 TTTTCTGGTCTAATTATTTGTTAAGACATGATCAGTTTTAAAG-TTAATAAAATTAAGTCCTTTC
* * * *
66030 TTTTTTGGTCTAATTATTTTTTAGGACATGAT-AGTTTTGAAA-TTAATGAAATTAAGTCC
1 TTTTCTGGTCTAATTATTTGTTAAGACATGATCAGTTTT-AAAGTTAATAAAATTAAGTCC
66089 CAATCCTCTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 16 0.31
64 6 0.12
65 30 0.58
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (64 bp):
TTTTCTGGTCTAATTATTTGTTAAGACATGATCAGTTTTAAAGTTAATAAAATTAAGTCCTTTC
Found at i:68608 original size:15 final size:17
Alignment explanation
Indices: 68584--68619 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
68574 CTGGAAACTC
68584 AATA-AAATATT-AA-T
1 AATATAAATATTCAATT
68598 AATATAAATATTCAATT
1 AATATAAATATTCAATT
68615 AATAT
1 AATAT
68620 TGAACAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 7 0.37
16 2 0.11
17 6 0.32
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATAAATATTCAATT
Found at i:69220 original size:26 final size:26
Alignment explanation
Indices: 69191--69241 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
69181 CAAAGAAAAC
69191 AAAAGAATAAAATATAAATATATTAT
1 AAAAGAATAAAATATAAATATATTAT
** *
69217 AAAAGTGTAAAATATAATTATATTA
1 AAAAGAATAAAATATAAATATATTA
69242 CATAAGATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (26 bp):
AAAAGAATAAAATATAAATATATTAT
Found at i:70469 original size:18 final size:19
Alignment explanation
Indices: 70423--70471 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
70413 GAATTAAATA
*
70423 AATAAATAAATAACTATTG
1 AATAAATAAATAACTAATG
70442 AATAAA-AAATAA-TAATG
1 AATAAATAAATAACTAATG
70459 AGA-AAATAAATAA
1 A-ATAAATAAATAA
70472 AGTAGAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 8 0.30
18 13 0.48
19 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.24
Consensus pattern (19 bp):
AATAAATAAATAACTAATG
Found at i:71240 original size:12 final size:12
Alignment explanation
Indices: 71225--71259 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
71215 AATAATAGTT
71225 CTAATAAAATAA
1 CTAATAAAATAA
71237 CTAATAAAATAA
1 CTAATAAAATAA
*
71249 -TAATAGAATAA
1 CTAATAAAATAA
71260 TCAAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (12 bp):
CTAATAAAATAA
Found at i:72229 original size:31 final size:31
Alignment explanation
Indices: 72193--72251 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
72183 AACTTAAAAG
* *
72193 AGTTTTGTAATATTGAAATTTAAATAATTTT
1 AGTTTTATAATAATGAAATTTAAATAATTTT
72224 AGTTTTATAATAATGAAATTTAAATAAT
1 AGTTTTATAATAATGAAATTTAAATAAT
72252 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (31 bp):
AGTTTTATAATAATGAAATTTAAATAATTTT
Found at i:72300 original size:22 final size:22
Alignment explanation
Indices: 72275--72507 Score: 324
Period size: 22 Copynumber: 10.6 Consensus size: 22
72265 ATAATAAATT
*
72275 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
72297 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
72319 TTTTAAAATATAAT-TTTTCATA
1 TTTTAAAATA-AATCAATCCATA
*
72341 TTTTAAAATAAACCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
72363 TTTTTAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
72385 TTTTAAAATAAACCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
72407 TTTTTAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
72429 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATCCATA
*
72451 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
72473 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
72495 TTTTAAAATAAAT
1 TTTTAAAATAAAT
72508 AAAAAATAAA
Statistics
Matches: 187, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
21 2 0.01
22 182 0.97
23 3 0.02
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:72342 original size:44 final size:43
Alignment explanation
Indices: 72275--72584 Score: 361
Period size: 44 Copynumber: 7.3 Consensus size: 43
72265 ATAATAAATT
*
72275 TTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAAT-AATCCATATTTTAAAATAAATCAATCCATA
** * *
72319 TTTTAAAATATAATTTTTCATATTTTAAAATAAACCAATCCATA
1 TTTTAAAATA-AATAATCCATATTTTAAAATAAATCAATCCATA
* *
72363 TTTTTAAATAAATCAATCCATATTTTAAAATAAACCAATCCATA
1 TTTTAAAATAAAT-AATCCATATTTTAAAATAAATCAATCCATA
* **
72407 TTTTTAAATAAATCAATCCATATTTTAAAATAAATCAATATATA
1 TTTTAAAATAAAT-AATCCATATTTTAAAATAAATCAATCCATA
* ***
72451 TTTTAAAATAAATCAATCTATATTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAAT-AATCCATATTTTAAAATAAATCAATCCATA
72495 TTTTAAAAT--A-AAT--A-A----AAAATAAATCAATCCATA
1 TTTTAAAATAAATAATCCATATTTTAAAATAAATCAATCCATA
*
72528 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAAT-AATCCATATTTTAAAATAAATCAATCCATA
72572 TTTTAAAATAAAT
1 TTTTAAAATAAAT
72585 TTTAAAATAG
Statistics
Matches: 230, Mismatches: 23, Indels: 26
0.82 0.08 0.09
Matches are distributed among these distances:
33 24 0.10
35 1 0.00
37 4 0.02
38 1 0.00
39 1 0.00
40 4 0.02
42 1 0.00
43 3 0.01
44 188 0.82
45 3 0.01
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (43 bp):
TTTTAAAATAAATAATCCATATTTTAAAATAAATCAATCCATA
Found at i:72345 original size:66 final size:65
Alignment explanation
Indices: 72275--72584 Score: 345
Period size: 66 Copynumber: 4.9 Consensus size: 65
72265 ATAATAAATT
** *
72275 TTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATATTTTAAAATATAATTTTTCAT
1 TTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATATTTTAAAATA-AATAATCCAT
72340 A
65 A
* * * *
72341 TTTTAAAATAAACCAATCCATATTTTTAAATAAATCAATCCATATTTTAAAATAAACCAATCCAT
1 TTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATATTTTAAAATAAA-TAATCCAT
72406 A
65 A
* * ** *
72407 TTTTTAAATAAATCAATCCATATTTTAAAATAAATCAATATATATTTTAAAATAAATCAATCTAT
1 TTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT-AATCCAT
72472 A
65 A
*** *
72473 TTTTAAAATAAATTTTTCCATATTTTAAAAT--A--AAT--A-A----AAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT-AATCCAT
72527 A
65 A
* *
72528 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAT
1 TTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT
72585 TTTAAAATAG
Statistics
Matches: 209, Mismatches: 22, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
55 45 0.22
57 1 0.00
59 4 0.02
60 1 0.00
61 1 0.00
62 4 0.02
64 1 0.00
65 2 0.01
66 150 0.72
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (65 bp):
TTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATATTTTAAAATAAATAATCCATA
Found at i:72516 original size:55 final size:55
Alignment explanation
Indices: 72455--72562 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
72445 TATATATTTT
* ***
72455 AAAATAAATCAATCTATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATAA
1 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATAA
72510 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT
1 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAAT
72563 CAATCTATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (55 bp):
AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATAA
Found at i:72537 original size:22 final size:22
Alignment explanation
Indices: 72510--72584 Score: 141
Period size: 22 Copynumber: 3.4 Consensus size: 22
72500 AAATAAATAA
72510 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
72532 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATCCATATTTT
*
72554 AAAATAAATCAATCTATATTTT
1 AAAATAAATCAATCCATATTTT
72576 AAAATAAAT
1 AAAATAAAT
72585 TTTAAAATAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATAAATCAATCCATATTTT
Found at i:72560 original size:77 final size:77
Alignment explanation
Indices: 72433--72584 Score: 241
Period size: 77 Copynumber: 2.0 Consensus size: 77
72423 TCCATATTTT
* * ***
72433 AAAATAAATCAATATATATTTTAAAATAAATCAATCTATATTTTAAAATAAATTTTTCCATATTT
1 AAAATAAATCAATACATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTT
72498 TAAAATAAATAA
66 TAAAATAAATAA
* *
72510 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTT
1 AAAATAAATCAATACATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTT
72575 TAAAATAAAT
66 TAAAATAAAT
72585 TTTAAAATAG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 68 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (77 bp):
AAAATAAATCAATACATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTT
TAAAATAAATAA
Found at i:72601 original size:11 final size:12
Alignment explanation
Indices: 72571--72610 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
72561 ATCAATCTAT
72571 ATTTTAAAATAA
1 ATTTTAAAATAA
*
72583 ATTTTAAAATAG
1 ATTTTAAAATAA
72595 A-TTT-AAAT-A
1 ATTTTAAAATAA
72604 ATTTTAA
1 ATTTTAA
72611 TTTATTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:72603 original size:121 final size:120
Alignment explanation
Indices: 72389--72608 Score: 336
Period size: 121 Copynumber: 1.8 Consensus size: 120
72379 TCCATATTTT
*
72389 AAAATAAACCAATCCATATTTTTAAATAAATCAATCCATATTTTAAAATAAATCAATATATATTT
1 AAAATAAACCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATATTT
** *
72454 TAAAATAAATCAATCTATATTTTAAAATAAATTTTTCCATATTTTAAAATAAATAA
66 TAAAATAAATCAAAATAGATTTTAAAAT-AATTTTTCCATATTTTAAAATAAATAA
* *
72510 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTT
1 AAAATAAACCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATATTT
*
72575 TAAAATAAATTTTAAAATAGA-TTT-AAATAATTTT
66 TAAAATAAA--TCAAAATAGATTTTAAAATAATTTT
72609 AATTTATTTG
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
120 6 0.07
121 75 0.83
122 3 0.03
123 6 0.07
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.39
Consensus pattern (120 bp):
AAAATAAACCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATATTT
TAAAATAAATCAAAATAGATTTTAAAATAATTTTTCCATATTTTAAAATAAATAA
Found at i:72604 original size:99 final size:99
Alignment explanation
Indices: 72412--72601 Score: 317
Period size: 99 Copynumber: 1.9 Consensus size: 99
72402 CCATATTTTT
*
72412 AAATAAATCAATCCATATTTTAAAATAAATCAATATATATTTTAAAATAAATCAATCTATATTTT
1 AAATAAATCAATCCATATTTTAAAATAAATCAATACATATTTTAAAATAAATCAATCTATATTTT
*** *
72477 AAAATAAATTTTTCCATATTTTAAAATAAATAAA
66 AAAATAAATTTTAAAATAATTTAAAATAAATAAA
*
72511 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTT
1 AAATAAATCAATCCATATTTTAAAATAAATCAATACATATTTTAAAATAAATCAATCTATATTTT
72576 AAAATAAATTTTAAAATAGATTTAAA
66 AAAATAAATTTTAAAATA-ATTTAAA
72602 TAATTTTAAT
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 78 0.93
100 6 0.07
ACGTcount: A:0.53, C:0.08, G:0.01, T:0.38
Consensus pattern (99 bp):
AAATAAATCAATCCATATTTTAAAATAAATCAATACATATTTTAAAATAAATCAATCTATATTTT
AAAATAAATTTTAAAATAATTTAAAATAAATAAA
Found at i:72608 original size:77 final size:76
Alignment explanation
Indices: 72428--72610 Score: 208
Period size: 77 Copynumber: 2.4 Consensus size: 76
72418 ATCAATCCAT
* * ***
72428 ATTTTAAAATAAATCAATATATATTTTAAAATAAATCAATCTATATTTTAAAATAAATTTTTCCA
1 ATTTTAAAAT-AATTAA-ATATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCA
72493 TATTTTAAAATAA
64 TATTTTAAAATAA
** * * *
72506 A-TAAAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTA
1 ATTTTAAAATAATTAAAT--ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCA
72570 TATTTTAAAATAA
64 TATTTTAAAATAA
72583 ATTTTAAAATAGATTTAAATA-ATTTTAA
1 ATTTTAAAATA-A-TTAAATATATTTTAA
72611 TTTATTTGAA
Statistics
Matches: 86, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
75 2 0.02
76 3 0.03
77 67 0.78
78 9 0.10
79 1 0.01
80 4 0.05
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (76 bp):
ATTTTAAAATAATTAAATATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
TTTTAAAATAA
Found at i:78648 original size:19 final size:19
Alignment explanation
Indices: 78624--78677 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
78614 CCGAAACCGG
78624 TTTTTTCGGTTCGGTTCGA
1 TTTTTTCGGTTCGGTTCGA
*
78643 TTTTTT---TAACGGTTCGA
1 TTTTTTCGGT-TCGGTTCGA
*
78660 GTTTTTCGGTTCGGTTCG
1 TTTTTTCGGTTCGGTTCG
78678 GTTCGGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
19 13 0.46
20 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (19 bp):
TTTTTTCGGTTCGGTTCGA
Found at i:84775 original size:30 final size:31
Alignment explanation
Indices: 84731--84789 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
84721 CCCAGAATAT
*
84731 TTAACTGTAACTGTTACAT-TTAATAGGTTAA
1 TTAACTGTAACTGTTA-ATATTAAAAGGTTAA
84762 TTAACTG-AACTGTTAATATTAAAAGGTT
1 TTAACTGTAACTGTTAATATTAAAAGGTT
84790 TCAGTTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 2 0.08
30 17 0.65
31 7 0.27
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (31 bp):
TTAACTGTAACTGTTAATATTAAAAGGTTAA
Found at i:89714 original size:4 final size:4
Alignment explanation
Indices: 89715--90709 Score: 1360
Period size: 4 Copynumber: 247.2 Consensus size: 4
89705 GCATGCATGC
* * *
89715 ATGT ATGT ATGC ATGC ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
89763 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
89811 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
89859 ATGT ATGT ATGT ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
89907 ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * *
89955 ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGC ATGC ATGCAC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG--T ATGT
* * * *
90005 ATGC ATGC ATGT ATGT ATGT ATGC ATGT ATGT ATGT ATGC ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * *
90053 ATGC ATGT ATGA ATGT ATGC ATGC ATGCAC ATGC ATGC ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATG--T ATGT ATGT ATGT ATGT ATGT
* * * * *
90103 ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * * *
90151 ATGC ATGC ATGT ATGC ATGC ATGC ATGC ATGC ATGT ATGT ATGC ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
90199 ATGC ATGC ATGC ATGC ATGT ATGT ATGT ATGT ATGC ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
90247 ATGT ATGC ATGT ATGT ATGT ATGT ATGC ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
90295 ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
90343 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
90391 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
90439 ATGT ATGT ATGT ATGT ATGC ATGT ATGC ATGT ATGT ATGC ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
90487 ATGT ATGC ATGC ATGCAC ATGC ATGC ATGT ATGT ATGT ATGT ATGT AAGT
1 ATGT ATGT ATGT ATG--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * *
90537 ATGT ATGT ATGC ATGC ATGC ATGC ATGC ATGC ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
90585 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
90633 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
90681 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
90710 ATATTCAATA
Statistics
Matches: 927, Mismatches: 58, Indels: 12
0.93 0.06 0.01
Matches are distributed among these distances:
4 915 0.99
6 12 0.01
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (4 bp):
ATGT
Found at i:90006 original size:14 final size:14
Alignment explanation
Indices: 89987--90013 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89977 GTATGCATGT
89987 ATGCATGCATGCAC
1 ATGCATGCATGCAC
90001 ATGCATGCATGCA
1 ATGCATGCATGCA
90014 TGTATGTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (14 bp):
ATGCATGCATGCAC
Found at i:91154 original size:29 final size:30
Alignment explanation
Indices: 91117--91177 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
91107 ATAAAAAAAT
* *
91117 TAAATTATT-ATTAAATTTATCACTTTTTA
1 TAAAATATTAATTAAATTTATCAATTTTTA
91146 TAAAATATTAATTAAATTTATCAATTTTTA
1 TAAAATATTAATTAAATTTATCAATTTTTA
91176 TA
1 TA
91178 TTGATTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (30 bp):
TAAAATATTAATTAAATTTATCAATTTTTA
Found at i:94751 original size:31 final size:32
Alignment explanation
Indices: 94707--94766 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
94697 AAAATGTTGC
*
94707 AAAATGAATATTAATTTTATCA-TATTTTCAT
1 AAAATGAATATTAAATTTATCATTATTTTCAT
*
94738 AAAAT-AATAATTAAATTTATTATTATTTT
1 AAAATGAAT-ATTAAATTTATCATTATTTT
94767 TACAATTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.12
31 16 0.64
32 6 0.24
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (32 bp):
AAAATGAATATTAAATTTATCATTATTTTCAT
Found at i:100304 original size:31 final size:31
Alignment explanation
Indices: 100260--100332 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
100250 GTTAACTCGT
* *
100260 AGTGACCACATCTTAAATAAATAAAAATGAA
1 AGTGATCATATCTTAAATAAATAAAAATGAA
* *
100291 AGTGATCATATCTTAATTAAATATAAATGAA
1 AGTGATCATATCTTAAATAAATAAAAATGAA
*
100322 AATGATCATAT
1 AGTGATCATAT
100333 ACTATTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (31 bp):
AGTGATCATATCTTAAATAAATAAAAATGAA
Found at i:103334 original size:13 final size:13
Alignment explanation
Indices: 103316--103343 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
103306 ATATCCTTTG
103316 ACTTCTTTTAACA
1 ACTTCTTTTAACA
103329 ACTTCTTTTAACA
1 ACTTCTTTTAACA
103342 AC
1 AC
103344 ATTACATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (13 bp):
ACTTCTTTTAACA
Found at i:106764 original size:31 final size:31
Alignment explanation
Indices: 106721--106787 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
106711 GGAACGGCAT
*
106721 CAAATGGTCGATTACGTCGGGGACCATATTG
1 CAAACGGTCGATTACGTCGGGGACCATATTG
* * *
106752 CAAACGGTCGATTACTTTGGGGGCCATATTG
1 CAAACGGTCGATTACGTCGGGGACCATATTG
106783 CAAAC
1 CAAAC
106788 AGACTAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (31 bp):
CAAACGGTCGATTACGTCGGGGACCATATTG
Found at i:107523 original size:7 final size:7
Alignment explanation
Indices: 107485--107530 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
107475 TATTAATTTT
*
107485 TAATAAA
1 TAATTAA
107492 TAATTAA
1 TAATTAA
*
107499 -AAATAA
1 TAATTAA
107505 TAAATTAA
1 T-AATTAA
107513 TAATTAA
1 TAATTAA
107520 TAATT-A
1 TAATTAA
107526 TAATT
1 TAATT
107531 TTATTACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
6 11 0.32
7 17 0.50
8 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAATTAA
Found at i:108726 original size:60 final size:60
Alignment explanation
Indices: 108574--108727 Score: 152
Period size: 60 Copynumber: 2.6 Consensus size: 60
108564 ACAACTTTAT
* *
108574 TTTTGAACATTTCATTTTCATCCCCAATCTATAACTCTCATTTAAAATTAGTCCCTAAAC
1 TTTTGAACATTTCATTTTCATCCCCAAACTATGACTCTCATTTAAAATTAGTCCCTAAAC
* ** * * * ** *
108634 TCTAAAACCTTTCAATTTCATGCTTAAACTATGAC-CATTATTCT-AAATTAGT-CCTCAAAC
1 TTTTGAACATTTCATTTTCATCCCCAAACTATGACTC-TCATT-TAAAATTAGTCCCT-AAAC
*
108694 TTTTGAACATTTCATTTTCATCCCCAAGCTATGA
1 TTTTGAACATTTCATTTTCATCCCCAAACTATGA
108728 TATAACAACA
Statistics
Matches: 71, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
59 4 0.06
60 66 0.93
61 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
TTTTGAACATTTCATTTTCATCCCCAAACTATGACTCTCATTTAAAATTAGTCCCTAAAC
Found at i:109882 original size:31 final size:31
Alignment explanation
Indices: 109847--109947 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
109837 AAGATCTAAA
*
109847 AGTTTAAGGACCAATTTAGAATGAGATTCAT
1 AGTTTAAGGACAAATTTAGAATGAGATTCAT
** * *
109878 AGTTTGGGGATGAAATTT-GAAT--G-TTCAAA
1 AGTTTAAGGA-CAAATTTAGAATGAGATTC-AT
* *
109907 AGTTTAAGGACTAATTTAGAATGAGAGTCAT
1 AGTTTAAGGACAAATTTAGAATGAGATTCAT
109938 AGTTTAAGGA
1 AGTTTAAGGA
109948 TGAATCAATT
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 8 0.15
29 14 0.26
31 24 0.45
32 7 0.13
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (31 bp):
AGTTTAAGGACAAATTTAGAATGAGATTCAT
Found at i:109913 original size:60 final size:60
Alignment explanation
Indices: 109820--109951 Score: 194
Period size: 60 Copynumber: 2.2 Consensus size: 60
109810 TTTCAATGAA
*
109820 TTTGGGGATGAAATTGAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGATTCATAG
1 TTTGGGGATGAAATTGAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAG
* * *
109880 TTTGGGGATGAAATTTGAATGTTC-AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
1 TTTGGGGATGAAA-TTGAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAG
**
109940 TTTAAGGATGAA
1 TTTGGGGATGAA
109952 TCAATTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 57 0.88
61 8 0.12
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (60 bp):
TTTGGGGATGAAATTGAAAGATCTAAAAGTTTAAGGACCAATTTAGAATGAGAGTCATAG
Found at i:110022 original size:77 final size:77
Alignment explanation
Indices: 109885--110028 Score: 225
Period size: 77 Copynumber: 1.9 Consensus size: 77
109875 CATAGTTTGG
* * * * *
109885 GGATGAAATTTGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAAGGATG
1 GGATAAAATCTGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAAGGATG
109950 AATCAATTTTTT
66 AATCAATTTTTT
**
109962 GGATAAAATCTGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAAAATTGTAGTTTAAGGATG
1 GGATAAAATCTGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAAGGATG
110027 AA
66 AA
110029 ATTAAAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 60 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (77 bp):
GGATAAAATCTGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAAAATCATAGTTTAAGGATG
AATCAATTTTTT
Found at i:110042 original size:31 final size:31
Alignment explanation
Indices: 109984--110042 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
109974 AATGTTCAAA
* **
109984 AGTTTAAGGACTAATTTAAAATGAAAATTGT
1 AGTTTAAGGACTAAATTAAAAAAAAAATTGT
110015 AGTTTAAGGA-TGAAATTAAAAAAAAAAT
1 AGTTTAAGGACT-AAATTAAAAAAAAAAT
110043 ATTCGATTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.53, C:0.02, G:0.15, T:0.31
Consensus pattern (31 bp):
AGTTTAAGGACTAAATTAAAAAAAAAATTGT
Found at i:112610 original size:2 final size:2
Alignment explanation
Indices: 112603--112634 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
112593 GATATTTTAT
112603 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
112635 AACCTTCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:115392 original size:45 final size:45
Alignment explanation
Indices: 115313--115434 Score: 127
Period size: 45 Copynumber: 2.7 Consensus size: 45
115303 GGATTATGTG
* * * * *
115313 CCGCCATCATCTGTACCGCCAGAACTTCCCACGCCAGGAATCCCT
1 CCGCCACCGTCTGAACCGCCAGAACTTCCAACGCCAGGAATCCCA
* * * *
115358 CCGTCACCGTCTGAACCGCCGGTACTTCCAACGCCGGGAATCCCA
1 CCGCCACCGTCTGAACCGCCAGAACTTCCAACGCCAGGAATCCCA
* * * *
115403 CCGCCACCATCGGTACCGCCAGAAATTCCAAC
1 CCGCCACCGTCTGAACCGCCAGAACTTCCAAC
115435 ACCCGGATTC
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.23, C:0.43, G:0.18, T:0.16
Consensus pattern (45 bp):
CCGCCACCGTCTGAACCGCCAGAACTTCCAACGCCAGGAATCCCA
Found at i:115734 original size:22 final size:22
Alignment explanation
Indices: 115709--115779 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
115699 AGTTTTTATT
115709 TATTTTAGTATTTATCCTAAAA
1 TATTTTAGTATTTATCCTAAAA
** ** * **
115731 TA-TTTAACATTTAGTTTTTATT
1 TATTTTAGTATTTA-TCCTAAAA
*
115753 TATTTTAGTATTTATCGTAAAA
1 TATTTTAGTATTTATCCTAAAA
115775 TATTT
1 TATTT
115780 AACGTGTTAA
Statistics
Matches: 33, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
21 9 0.27
22 15 0.45
23 9 0.27
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (22 bp):
TATTTTAGTATTTATCCTAAAA
Found at i:115744 original size:44 final size:44
Alignment explanation
Indices: 115696--115782 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
115686 ATACTTAAAG
115696 TTTAGTTTTTATTTATTTTAGTATTTATCCTAAAATATTTAACA
1 TTTAGTTTTTATTTATTTTAGTATTTATCCTAAAATATTTAACA
*
115740 TTTAGTTTTTATTTATTTTAGTATTTATCGTAAAATATTTAAC
1 TTTAGTTTTTATTTATTTTAGTATTTATCCTAAAATATTTAAC
115783 GTGTTAATAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (44 bp):
TTTAGTTTTTATTTATTTTAGTATTTATCCTAAAATATTTAACA
Found at i:115958 original size:44 final size:45
Alignment explanation
Indices: 115875--115969 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
115865 GAACATATAC
115875 TAAAATGAAACAAAAATTAAATTTTAGGTATAATTTTGAAAATTT
1 TAAAATGAAACAAAAATTAAATTTTAGGTATAATTTTGAAAATTT
* * *
115920 TAAAATGAAACAAAATTTGAATTTTAGGTATGA-TTTGAAAATTT
1 TAAAATGAAACAAAAATTAAATTTTAGGTATAATTTTGAAAATTT
115964 TAAAAT
1 TAAAAT
115970 TTAGATATGA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 17 0.36
45 30 0.64
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (45 bp):
TAAAATGAAACAAAAATTAAATTTTAGGTATAATTTTGAAAATTT
Found at i:117603 original size:12 final size:12
Alignment explanation
Indices: 117586--117610 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
117576 CTTTACCTAT
117586 AAATAAATAAAC
1 AAATAAATAAAC
117598 AAATAAATAAAC
1 AAATAAATAAAC
117610 A
1 A
117611 GAAAATATGT
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATAAATAAAC
Found at i:122133 original size:27 final size:26
Alignment explanation
Indices: 122081--122151 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 26
122071 CTCTTCTTAC
122081 TGCTAATTTGAGCC-TTTTTTCATTT
1 TGCTAATTTGAGCCTTTTTTTCATTT
* *
122106 TGCTAATGTGAGCCTTTTTTTCCTTTT
1 TGCTAATTTGAGCCTTTTTTT-CATTT
*
122133 TGCTAATTTGAGTCTTTTT
1 TGCTAATTTGAGCCTTTTT
122152 CTTTGGTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 13 0.32
26 6 0.15
27 21 0.52
ACGTcount: A:0.14, C:0.15, G:0.14, T:0.56
Consensus pattern (26 bp):
TGCTAATTTGAGCCTTTTTTTCATTT
Found at i:122473 original size:21 final size:20
Alignment explanation
Indices: 122448--122546 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
122438 AATCAGTTTC
122448 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
122469 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
122490 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
122510 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
122531 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
122547 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:122575 original size:20 final size:20
Alignment explanation
Indices: 122514--122742 Score: 248
Period size: 20 Copynumber: 11.4 Consensus size: 20
122504 GATTTTCAAG
* ** *
122514 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
122534 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
122554 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
122574 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
122594 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
122614 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
122634 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
122654 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* *
122674 AATCGCAACGCGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
122694 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
122714 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
122734 AATCACAAC
1 AATCGCAAC
122743 ACTGAAATTT
Statistics
Matches: 177, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 173 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:123479 original size:24 final size:24
Alignment explanation
Indices: 123435--123481 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
123425 AAATTTGGTC
*
123435 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCAGACTTTGATA
*
123459 TTGGTCAATA-CACAGATTTTGAT
1 TTGGTCAATATC-CAGACTTTGAT
123482 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCAGACTTTGATA
Found at i:126069 original size:72 final size:72
Alignment explanation
Indices: 125976--126209 Score: 288
Period size: 72 Copynumber: 3.3 Consensus size: 72
125966 GCAACGAGAG
125976 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
126041 AAATGAA
66 AAATGAA
* *
126048 AATCGCAATGCGAAATGAAAATCGCAACGAT-AGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
126112 GAAATGAA
65 GAAATGAA
* * * * * *
126120 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATTAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
126180 CG--A-GAG
64 CGAAATGAA
126186 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
126210 GCAATGCGAA
Statistics
Matches: 141, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 17 0.12
72 90 0.64
73 10 0.07
74 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:126097 original size:53 final size:52
Alignment explanation
Indices: 125962--126231 Score: 397
Period size: 53 Copynumber: 5.1 Consensus size: 52
125952 CGGAAATTAC
*
125962 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
126009 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
126067 AATCGCAACGATAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
*
126120 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
126172 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
126225 AATCGCA
1 AATCGCA
126232 TTGCGATTCT
Statistics
Matches: 203, Mismatches: 7, Indels: 20
0.88 0.03 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 64 0.32
53 113 0.56
55 2 0.01
56 1 0.00
58 13 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:126237 original size:72 final size:68
Alignment explanation
Indices: 125943--126236 Score: 267
Period size: 72 Copynumber: 4.2 Consensus size: 68
125933 GCATTTGACT
** * * *
125943 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATG
126007 AAA
66 AAA
*
126010 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
126075 CGAT-AGA
61 CGATGAAA
* * * * *
126082 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
126144 CGAAATGAAA
61 CG--ATGAAA
*
126154 ATCGCAATGC-GAAATTAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
126218 AAATGAAA
63 --ATGAAA
*
126226 ATCGCATTGCG
1 ATCGCAATGCG
126237 ATTCTCTCGT
Statistics
Matches: 188, Mismatches: 20, Indels: 32
0.78 0.08 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 33 0.18
69 4 0.02
70 1 0.01
71 21 0.11
72 105 0.56
73 5 0.03
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATG
AAA
Found at i:126251 original size:105 final size:105
Alignment explanation
Indices: 125962--126231 Score: 408
Period size: 105 Copynumber: 2.6 Consensus size: 105
125952 CGGAAATTAC
*
125962 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--C-
*
126021 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
126067 AATCGCAACGATAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
*
126132 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
126172 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
126232 TTGCGATTCT
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
105 122 0.79
106 16 0.10
108 2 0.01
109 1 0.01
111 13 0.08
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (105 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:126295 original size:54 final size:52
Alignment explanation
Indices: 126227--126344 Score: 209
Period size: 54 Copynumber: 2.2 Consensus size: 52
126217 GAAATGAAAA
126227 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
126280 TCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
126333 TCGCATTTCGAT
1 TCGCATTGCGAT
126345 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
52 10 0.16
53 20 0.32
54 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:126324 original size:19 final size:19
Alignment explanation
Indices: 126246--126344 Score: 127
Period size: 20 Copynumber: 5.4 Consensus size: 19
126236 GATTCTCTCG
126246 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
126266 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
126286 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
126300 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
126319 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
126338 TTTCGAT
1 TTGCGAT
126345 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 11
0.84 0.04 0.13
Matches are distributed among these distances:
14 6 0.08
16 5 0.07
17 6 0.08
18 3 0.04
19 25 0.35
20 26 0.37
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:126350 original size:19 final size:19
Alignment explanation
Indices: 126255--126352 Score: 71
Period size: 19 Copynumber: 5.3 Consensus size: 19
126245 GTTGCGATTT
**
126255 TCATTTCCGCATTGCGATTT
1 TCATTT-CGCATTGCGATAG
126275 TCATTTCCGCATTGCGAT--
1 TCATTT-CGCATTGCGATAG
* **
126293 TC-TCTCG--TTGCGATTT
1 TCATTTCGCATTGCGATAG
**
126309 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
*
126328 TCATTTCGCATTTCGATAG
1 TCATTTCGCATTGCGATAG
126347 TCATTT
1 TCATTT
126353 TTGCCTTCAA
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
14 7 0.10
16 4 0.06
17 6 0.09
18 2 0.03
19 31 0.46
20 18 0.26
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:126470 original size:14 final size:14
Alignment explanation
Indices: 126451--126487 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
126441 CATCAATTAC
126451 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
126465 ACAAATCATCTTTT
1 ACAAATCAACTTTT
126479 ACAAATCAA
1 ACAAATCAA
126488 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:127367 original size:20 final size:20
Alignment explanation
Indices: 127336--127432 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
127326 TTTTGGTTGA
127336 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
127356 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
127376 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
127395 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
127410 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
127430 AAT
1 AAT
127433 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:127388 original size:21 final size:21
Alignment explanation
Indices: 127334--127398 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
127324 TCTTTTGGTT
127334 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
127355 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
127375 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
127396 GAA
1 GAA
127399 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:127402 original size:14 final size:14
Alignment explanation
Indices: 127383--127439 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
127373 GAGAAATGAA
127383 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
127397 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
127416 AATCGCAACGAGAG
1 AATCGCAACGAGAG
127430 AATCGCAACG
1 AATCGCAACG
127440 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:127415 original size:33 final size:33
Alignment explanation
Indices: 127334--127456 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
127324 TCTTTTGGTT
*
127334 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
127375 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
127408 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
127441 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
127457 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:127490 original size:19 final size:19
Alignment explanation
Indices: 127457--127564 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 19
127447 AAAATCGCAA
**
127457 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
127476 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
127495 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
127509 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGT
** *
127530 TGCAGATAGTCATTTTCACGT
1 TGC-GATTTTCA-TTTCGCGT
127551 TGCGATTTTCATTT
1 TGCGATTTTCATTT
127565 ATCTCGTTGC
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 25 0.34
20 6 0.08
21 17 0.23
22 9 0.12
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:127526 original size:21 final size:21
Alignment explanation
Indices: 127500--127576 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
127490 CGCGTTGCGA
127500 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
127521 TTCTCTCGTTGCAGATAGTCAT
1 TTCTCTCGTTGC-GATTTTCAT
*
127543 TT-TCACGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
127563 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
127577 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.19
21 30 0.62
22 9 0.19
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:127693 original size:33 final size:33
Alignment explanation
Indices: 127656--127726 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
127646 AATACTAACT
127656 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
* * * *
127689 TGAAAATCGCAACGAGAGAATCGTAACTCGAAA
1 TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
127722 TGAAA
1 TGAAA
127727 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACAAGAGAATAGCAACGCGAAA
Found at i:128131 original size:20 final size:20
Alignment explanation
Indices: 128106--128197 Score: 114
Period size: 20 Copynumber: 4.6 Consensus size: 20
128096 CTTTAAAAAT
128106 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
128126 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
128146 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
128166 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
128186 CGCGTTGCGATT
1 CGCGTTGCGATT
128198 CTGGAAAATC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
20 63 0.98
21 1 0.02
ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:132028 original size:55 final size:55
Alignment explanation
Indices: 131952--132063 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
131942 ATGCTCCCAT
**
131952 TGTTCTTCTATTTAGTGTGCCTGAGCTAAAAATGTCACTGCACTTTCGCTTGATA
1 TGTTCTTCTATTTAGCATGCCTGAGCTAAAAATGTCACTGCACTTTCGCTTGATA
* **
132007 TGTTTTTCTATTTAGCATGCCTGAGCTGCAAATGTCACTGCACTTTCGCTTGATA
1 TGTTCTTCTATTTAGCATGCCTGAGCTAAAAATGTCACTGCACTTTCGCTTGATA
132062 TG
1 TG
132064 CTCTCTGTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (55 bp):
TGTTCTTCTATTTAGCATGCCTGAGCTAAAAATGTCACTGCACTTTCGCTTGATA
Found at i:135097 original size:11 final size:11
Alignment explanation
Indices: 135081--135107 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
135071 CACGGTTAAT
135081 GACATTAACGC
1 GACATTAACGC
135092 GACATTAACGC
1 GACATTAACGC
135103 GACAT
1 GACAT
135108 AACACGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (11 bp):
GACATTAACGC
Found at i:136551 original size:21 final size:21
Alignment explanation
Indices: 136521--136571 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
136511 TATTTCAGTT
136521 GGGAC-AAATTGACAAATCTA
1 GGGACTAAATTGACAAATCTA
* *
136541 GGGACTAAATTGATAAATTTA
1 GGGACTAAATTGACAAATCTA
136562 GGGACTAAAT
1 GGGACTAAAT
136572 GTTATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (21 bp):
GGGACTAAATTGACAAATCTA
Found at i:136903 original size:31 final size:32
Alignment explanation
Indices: 136868--136939 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
136858 ACGATTATTG
*
136868 AACTT-TCCAAACAATTACAAAATTATCATTA
1 AACTTATCCAAACAATTACAAAATGATCATTA
* * *
136899 AACTTAT-CAAACTATTACAAAATGGTCCTTA
1 AACTTATCCAAACAATTACAAAATGATCATTA
136930 AACTTATCCA
1 AACTTATCCA
136940 GCTTTATCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (32 bp):
AACTTATCCAAACAATTACAAAATGATCATTA
Found at i:140824 original size:18 final size:17
Alignment explanation
Indices: 140771--140825 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
140761 GTTTACTTTA
*
140771 GAATGATT-AAGCG-CT
1 GAATGATTCAAACGTCT
140786 GAATGATTCAAACGT-T
1 GAATGATTCAAACGTCT
* *
140802 GAATGATTTAAAGGCTCT
1 GAATGATTCAAACG-TCT
140820 GAATGA
1 GAATGA
140826 ATTAGCTCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 8 0.24
16 17 0.52
17 1 0.03
18 7 0.21
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (17 bp):
GAATGATTCAAACGTCT
Found at i:152538 original size:2 final size:2
Alignment explanation
Indices: 152533--152572 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
152523 ACCTTCCCCC
* *
152533 CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
152573 ATATATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:161226 original size:29 final size:29
Alignment explanation
Indices: 161193--161248 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
161183 ACCAATATCT
* *
161193 AAATATAAAATTTAAAAATTCAAAATACA
1 AAATACAAAATCTAAAAATTCAAAATACA
* *
161222 AAATACAAAATCTAATAATTCATAATA
1 AAATACAAAATCTAAAAATTCAAAATA
161249 TAAATAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (29 bp):
AAATACAAAATCTAAAAATTCAAAATACA
Found at i:166336 original size:21 final size:21
Alignment explanation
Indices: 166312--166360 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
166302 GAATCCGAAA
*
166312 TATTTAAAAATAATAATTATT
1 TATTTAAAAATAATAATCATT
166333 TATTTAAAAATAATAATCATT
1 TATTTAAAAATAATAATCATT
166354 TATTTAA
1 TATTTAA
166361 CTACTGTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTTAAAAATAATAATCATT
Done.