Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014154.1 Kokia drynarioides strain JFW-HI SEQ_129187, 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: 160074
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:2689 original size:90 final size:91
Alignment explanation
Indices: 2530--2737 Score: 251
Period size: 90 Copynumber: 2.3 Consensus size: 91
2520 AATTGCTTTT
** * ** * * *
2530 TTTTTTTGAAAATGTTTGAGGGAC-TTTTTGATGCATTTTGAATGTTCAAGTACCTAATTGAGTG
1 TTTTTTTGAAAAAATTTGAGAGACTTTTTTGATGCATTTTGAAAATTCAAATACCTAAGTGAATG
* *
2594 CAAAATAAAAGCAGAGGCTTAATTGC
66 CAAAATAAAAGCAGAGACTTAATTAC
* * *
2620 TTTTTTTGAAAAAATTTGAGAG-CTTTTTTTATGCATTTTGAAAATTTAAATATCTAAGTGAATG
1 TTTTTTTGAAAAAATTTGAGAGACTTTTTTGATGCATTTTGAAAATTCAAATACCTAAGTGAATG
* *
2684 TAAAATAAAAGCATAGACTTAATTAC
66 CAAAATAAAAGCAGAGACTTAATTAC
*
2710 TTTTTTTAAAAAAATTTGA-AGACTTTTT
1 TTTTTTTGAAAAAATTTGAGAGACTTTTT
2738 ACACTTTTAA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
89 3 0.03
90 97 0.97
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (91 bp):
TTTTTTTGAAAAAATTTGAGAGACTTTTTTGATGCATTTTGAAAATTCAAATACCTAAGTGAATG
CAAAATAAAAGCAGAGACTTAATTAC
Found at i:5299 original size:18 final size:18
Alignment explanation
Indices: 5276--5316 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
5266 GTATAAACTT
*
5276 AAATTTATTTTGAATTTA
1 AAATTTATTTTCAATTTA
5294 AAATTTATTTTCAATTTA
1 AAATTTATTTTCAATTTA
5312 AAATT
1 AAATT
5317 AAAAAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
AAATTTATTTTCAATTTA
Found at i:13317 original size:18 final size:18
Alignment explanation
Indices: 13290--13345 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
13280 GTATAAACTT
*
13290 AAATTTATTTTGAATTTA
1 AAATTCATTTTGAATTTA
13308 AAATTCATTTTGAATTTA
1 AAATTCATTTTGAATTTA
*
13326 AAATTCATTTTAAATTTA
1 AAATTCATTTTGAATTTA
13344 AA
1 AA
13346 TTTAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (18 bp):
AAATTCATTTTGAATTTA
Found at i:15121 original size:58 final size:58
Alignment explanation
Indices: 15058--15431 Score: 289
Period size: 58 Copynumber: 6.4 Consensus size: 58
15048 TAAAACCACG
* **
15058 TTTTAACCCCCAAACTTTTTAAAAATTACA-TTTGACCCTAAACTTTCAAAAAATTACA
1 TTTTAACCCCCGAACTTTCCAAAAATTACATTTTGACCCTAAACTTTC-AAAAATTACA
** * * *
15116 TTTTAACCTTCGAACTTTCTAAAAATTACA-TTTGACCCCTGAACTACTCAAAAATTACA
1 TTTTAACCCCCGAACTTTCCAAAAATTACATTTTGA-CCCTAAACT-TTCAAAAATTACA
* * * * *
15175 TTTTTGACCTCCGAAC-TTCTCAAAAATCACATATTGACCTCTAAACTTCTCAAAAATCACA
1 -TTTTAACCCCCGAACTTTC-CAAAAATTACATTTTGACC-CTAAACTT-TCAAAAATTACA
* * * * *
15236 TATTGA-TCCCGAAC-TTCCAAAAATTACATTTTTACACCTAAGCTTCTCAAAAATTACA
1 TTTTAACCCCCGAACTTTCCAAAAATTACATTTTGAC-CCTAAACTT-TCAAAAATTACA
* * * * *** *
15294 TTTTTACCCTCGAAC-ATCCAAAAATTACATTTTTACCCCGTACTTTCAAAAATCACA
1 TTTTAACCCCCGAACTTTCCAAAAATTACATTTTGACCCTAAACTTTCAAAAATTACA
* * * * *
15351 TTTTTACTCCCGAACTTTTCAAAAATTACATTTTG-CCTTCAAACTTTCAAAAATCACCA
1 TTTTAACCCCCGAACTTTCCAAAAATTACATTTTGACCCT-AAACTTTCAAAAATTA-CA
* *
15410 TTTT-A-CCCCTAATTTTCCAAAA
1 TTTTAACCCCCGAACTTTCCAAAA
15432 GTTCGACTTT
Statistics
Matches: 259, Mismatches: 45, Indels: 25
0.79 0.14 0.08
Matches are distributed among these distances:
57 39 0.15
58 105 0.41
59 63 0.24
60 31 0.12
61 21 0.08
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (58 bp):
TTTTAACCCCCGAACTTTCCAAAAATTACATTTTGACCCTAAACTTTCAAAAATTACA
Found at i:15384 original size:29 final size:28
Alignment explanation
Indices: 15065--15431 Score: 217
Period size: 30 Copynumber: 12.6 Consensus size: 28
15055 ACGTTTTAAC
* * *
15065 CCCCAAACTTTTTAAAAATTACATTTGA
1 CCCCGAACTTTTCAAAAATTACATTTTA
**
15093 CCCTAAAC-TTTCAAAAAATTACATTTTAA
1 CCCCGAACTTTTC-AAAAATTACATTTT-A
* *
15122 CCTTCGAAC-TTTCTAAAAATTACATTTGA
1 CC-CCGAACTTTTC-AAAAATTACATTTTA
**
15151 CCCCTGAACTACTCAAAAATTACATTTTTGA
1 CCCC-GAACTTTTCAAAAATTACA-TTTT-A
* * *
15182 CCTCCGAACTTCTCAAAAATCACATATTGA
1 CC-CCGAACTTTTCAAAAATTACAT-TTTA
** * * *
15212 CCTCTAAACTTCTCAAAAATCACATATTGA
1 CC-CCGAACTTTTCAAAAATTACAT-TTTA
* *
15242 TCCCGAAC-TTCCAAAAATTACATTTTTA
1 CCCCGAACTTTTCAAAAATTACA-TTTTA
* * *
15270 CACCTAAGCTTCTCAAAAATTACATTTTTA
1 CCCCGAA-CTTTTCAAAAATTACA-TTTTA
* *
15300 CCCTCGAAC-ATCCAAAAATTACATTTTTA
1 CCC-CGAACTTTTCAAAAATTACA-TTTTA
* *
15329 CCCCGTAC-TTTCAAAAATCACATTTTTA
1 CCCCGAACTTTTCAAAAATTACA-TTTTA
*
15357 CTCCCGAACTTTTCAAAAATTACATTTTG
1 C-CCCGAACTTTTCAAAAATTACATTTTA
* * *
15386 CCTTCAAAC-TTTCAAAAATCACCATTTTA
1 CC-CCGAACTTTTCAAAAATTA-CATTTTA
* *
15415 CCCCTAA-TTTTCCAAAA
1 CCCCGAACTTTTCAAAAA
15432 GTTCGACTTT
Statistics
Matches: 273, Mismatches: 48, Indels: 36
0.76 0.13 0.10
Matches are distributed among these distances:
27 3 0.01
28 84 0.31
29 69 0.25
30 90 0.33
31 25 0.09
32 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.34
Consensus pattern (28 bp):
CCCCGAACTTTTCAAAAATTACATTTTA
Found at i:21319 original size:42 final size:42
Alignment explanation
Indices: 21255--21343 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
21245 CGCTACTGTG
21255 AGTTCCACAATAACGAAGAGCATGAGATTCAGGAATGCGATA
1 AGTTCCACAATAACGAAGAGCATGAGATTCAGGAATGCGATA
* * * *
21297 AGTTTCACAATAATGAAGAGCATGAGATTCAGGAATGCAATG
1 AGTTCCACAATAACGAAGAGCATGAGATTCAGGAATGCGATA
21339 AGTTC
1 AGTTC
21344 AAAGCTATGG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (42 bp):
AGTTCCACAATAACGAAGAGCATGAGATTCAGGAATGCGATA
Found at i:27915 original size:78 final size:78
Alignment explanation
Indices: 27826--28087 Score: 267
Period size: 78 Copynumber: 3.4 Consensus size: 78
27816 TTGATGATTC
* * ** * * *
27826 CGATCTTTTACCCCGAGCCTAAGGTAGATCACCATCAGTTAATCTCTTACCCCGATCAAGGGGCA
1 CGATCTCTTACCCCGAGCCTAGGGTAGATCACCATCAGCAAATCTCTTACCCAGACCTAGGGGCA
27891 GATTGCAGTCATT
66 GATTGCAGTCATT
* * *
27904 CGATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCAATCTCTTACCCTAAACCTA-GGGC
1 CGATCTCTTACCCCGAGCCTAGGGTAGATCACCATCAGCAAATCTCTTACCC-AGACCTAGGGGC
* *
27968 AGATTACAGTCGTT
65 AGATTGCAGTCATT
* * * * * * * * * *
27982 CGATCTCTTACCTCAAGCCTGGGGTAGATCATCATCAGCAAATTTCTTACCCTGAGCTTGGAGTA
1 CGATCTCTTACCCCGAGCCTAGGGTAGATCACCATCAGCAAATCTCTTACCCAGACCTAGGGGCA
* *
28047 GATTGCAGCCATC
66 GATTGCAGTCATT
* *
28060 CAATCTCTTACCCCGAGCC-AGGGCAGAT
1 CGATCTCTTACCCCGAGCCTAGGGTAGAT
28088 TGCAACCACT
Statistics
Matches: 149, Mismatches: 33, Indels: 5
0.80 0.18 0.03
Matches are distributed among these distances:
77 10 0.07
78 136 0.91
79 3 0.02
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (78 bp):
CGATCTCTTACCCCGAGCCTAGGGTAGATCACCATCAGCAAATCTCTTACCCAGACCTAGGGGCA
GATTGCAGTCATT
Found at i:27949 original size:39 final size:39
Alignment explanation
Indices: 27828--28165 Score: 124
Period size: 39 Copynumber: 8.7 Consensus size: 39
27818 GATGATTCCG
* * **
27828 ATCTTTTACCCCGAGCCTAAGGTAGATCACCATCAGTTA
1 ATCTCTTACCCCGAGCCTAGGGTAGATCACCATCAGCCA
* * * ** ** *
27867 ATCTCTTACCCCGA-TCAAGGGGCAGAT-TGCAGTCATTCG
1 ATCTCTTACCCCGAGCCTA-GGGTAGATCACCA-TCAGCCA
*
27906 ATCTCTTACCCCGAGCTTAGGGTAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATCACCATCAGCCA
** * * * * *
27945 ATCTCTTACCCTAAACCTAGGGCAGATTA-CAGTC-GTTCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATCACCA-TCAG-CCA
* * * * *
27984 ATCTCTTACCTCAAGCCTGGGGTAGATCATCATCAGCAA
1 ATCTCTTACCCCGAGCCTAGGGTAGATCACCATCAGCCA
* * *
28023 ATTTCTTACCCTGAG-CTTGGAGTAGATTGCAGCCAT---CCA
1 ATCTCTTACCCCGAGCCTAGG-GTAGA-T-CA-CCATCAGCCA
* ** * *
28062 ATCTCTTACCCCGAGCC-AGGGCAGATTGCAACCA-CTCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATCACCATCAGC-CA
* * * *** **
28100 ATCTCTTACCTCAAG-CTTGCGGTAGATCGTTATCAGTAA
1 ATCTCTTACCCCGAGCCTAG-GGTAGATCACCATCAGCCA
28139 ATCTCTTACCCCGAGCCT-GGTGTAGAT
1 ATCTCTTACCCCGAGCCTAGG-GTAGAT
28166 TGCGACTATT
Statistics
Matches: 215, Mismatches: 63, Indels: 42
0.67 0.20 0.13
Matches are distributed among these distances:
35 2 0.01
37 3 0.01
38 32 0.15
39 163 0.76
40 10 0.05
41 2 0.01
42 3 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTAGGGTAGATCACCATCAGCCA
Found at i:28212 original size:77 final size:77
Alignment explanation
Indices: 28061--28247 Score: 173
Period size: 77 Copynumber: 2.4 Consensus size: 77
28051 GCAGCCATCC
*
28061 AATCTCTTACCCCGAGCCAGGGCAGATTGCAACCACTCAATCTCTTACCTCAAGCTTGCGGTAGA
1 AATCTCTTACCCCGAGCCAGGGCAGATTGCAACCACTCAATCTCTTACCTCAAGCTTGCGGCAGA
*** *
28126 TCGTTATCAGTA
66 TCACCATCAGCA
* * * * * * * *
28138 AATCTCTTACCCCGAGCCTGGTGTAGATTGCGACTATTCGATCTTTTACC-CTGAGCTTG-GGCA
1 AATCTCTTACCCCGAGCCAGG-GCAGATTGCAACCACTCAATCTCTTACCTC-AAGCTTGCGGCA
28201 GATCACCATCAGCA
64 GATCACCATCAGCA
* * *
28215 ATTATCTTACCCCGA-TCATGAGGCAGATTGCAA
1 AATCTCTTACCCCGAGCCA-G-GGCAGATTGCAA
28248 TCATTCGAAG
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
76 1 0.01
77 57 0.66
78 29 0.33
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (77 bp):
AATCTCTTACCCCGAGCCAGGGCAGATTGCAACCACTCAATCTCTTACCTCAAGCTTGCGGCAGA
TCACCATCAGCA
Found at i:30590 original size:29 final size:29
Alignment explanation
Indices: 30544--30875 Score: 269
Period size: 29 Copynumber: 11.3 Consensus size: 29
30534 TTCCTGAGTT
* * * *
30544 TTTCTAAAATCACGTTTTGACCCTCAAAC
1 TTTCAAAAATTACATTTTTACCCTCAAAC
* * *
30573 TTTCCAAAATTACATTTTAACCCTTAAAC
1 TTTCAAAAATTACATTTTTACCCTCAAAC
* * *
30602 TTTCCAAACA-TACATTTTAACCCTTAAAC
1 TTT-CAAAAATTACATTTTTACCCTCAAAC
* *
30631 TTTCCAAAATTTACATTTTAACCC-CAAAAC
1 TTT-CAAAAATTACATTTTTACCCTC-AAAC
* *
30661 TACTCAAAAATTACATTTTTGACCCTCGAAC
1 T-TTCAAAAATTACATTTTT-ACCCTCAAAC
* *
30692 TAATCAAAAATTACATTTTTA-CCTCGAAC
1 T-TTCAAAAATTACATTTTTACCCTCAAAC
* * *
30721 TTCCAAAAGTTACATTTTTACAGC-CAAAC
1 TTTCAAAAATTACATTTTTAC-CCTCAAAC
*
30750 TTCTCAAAAATTACATTTTTACCCTCGAAC
1 TT-TCAAAAATTACATTTTTACCCTCAAAC
* **
30780 TTCCAAAAATTACATTTTTACCCTCGTAC
1 TTTCAAAAATTACATTTTTACCCTCAAAC
* * *
30809 TTTCAAAAATCACGTTTTTACCCTCGAAC
1 TTTCAAAAATTACATTTTTACCCTCAAAC
* * * * *
30838 TTCTCAAAAAATACAATTTTGCCCCCGAAC
1 TT-TCAAAAATTACATTTTTACCCTCAAAC
30868 -TTCAAAAA
1 TTTCAAAAA
30876 ATCACCATTT
Statistics
Matches: 256, Mismatches: 36, Indels: 23
0.81 0.11 0.07
Matches are distributed among these distances:
28 23 0.09
29 123 0.48
30 82 0.32
31 27 0.11
32 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTCAAAAATTACATTTTTACCCTCAAAC
Found at i:30776 original size:59 final size:58
Alignment explanation
Indices: 30549--30875 Score: 295
Period size: 59 Copynumber: 5.6 Consensus size: 58
30539 GAGTTTTTCT
* * * * * **
30549 AAAATCACGTTTTGACCCTCAAACTTTCCAAAATTACATTTTAACCCTTAAACTTTCCA
1 AAAATTACATTTTTACCCTCAAACTTTCAAAAATTACATTTTTACCCTCGAAC-TTCCA
* * * * * * *
30608 AACA-TACATTTTAACCCTTAAACTTTCCAAAATTTACATTTTAACCC-CAAAACTACTCA
1 AAAATTACATTTTTACCCTCAAACTTT-CAAAAATTACATTTTTACCCTC-GAACTTC-CA
* *
30667 AAAATTACATTTTTGACCCTCGAACTAATCAAAAATTACATTTTTA-CCTCGAACTTCCA
1 AAAATTACATTTTT-ACCCTCAAACT-TTCAAAAATTACATTTTTACCCTCGAACTTCCA
* *
30726 AAAGTTACATTTTTACAGC-CAAACTTCTCAAAAATTACATTTTTACCCTCGAACTTCCA
1 AAAATTACATTTTTAC-CCTCAAACTT-TCAAAAATTACATTTTTACCCTCGAACTTCCA
** * *
30785 AAAATTACATTTTTACCCTCGTACTTTCAAAAATCACGTTTTTACCCTCGAACTTCTCA
1 AAAATTACATTTTTACCCTCAAACTTTCAAAAATTACATTTTTACCCTCGAACTTC-CA
* * * * *
30844 AAAAATACAATTTTGCCCCCGAAC-TTCAAAAA
1 AAAATTACATTTTTACCCTCAAACTTTCAAAAA
30876 ATCACCATTT
Statistics
Matches: 223, Mismatches: 33, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
58 82 0.37
59 100 0.45
60 15 0.07
61 25 0.11
62 1 0.00
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAATTACATTTTTACCCTCAAACTTTCAAAAATTACATTTTTACCCTCGAACTTCCA
Found at i:30952 original size:30 final size:29
Alignment explanation
Indices: 30893--30954 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
30883 TTTTACACCC
* *
30893 AATTTTTCAAAAGTTTGACTTTAATCCCA
1 AATTTTTCAAAAATTTAACTTTAATCCCA
* *
30922 AATTTTTCAAAAATTTCAATTTTGATCCCA
1 AATTTTTCAAAAATTT-AACTTTAATCCCA
30952 AAT
1 AAT
30955 CCCTCAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (29 bp):
AATTTTTCAAAAATTTAACTTTAATCCCA
Found at i:39320 original size:26 final size:26
Alignment explanation
Indices: 39286--39341 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
39276 AAAATTAACC
39286 AAAATTATGCACATAATAAAAATATA
1 AAAATTATGCACATAATAAAAATATA
*
39312 AAAATTATGCACGTAATAAAAATATA
1 AAAATTATGCACATAATAAAAATATA
39338 AAAA
1 AAAA
39342 AATCCAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (26 bp):
AAAATTATGCACATAATAAAAATATA
Found at i:42847 original size:31 final size:31
Alignment explanation
Indices: 42804--42871 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
42794 AAATTTTAAA
* *
42804 TTAATAAAAAT-AAAATTACATTTTATCTTT
1 TTAAAAAAAATAAAAATTACATTTAATCTTT
**
42834 CTTAAAAAAAATAAAAATTTGATTTAATCTTT
1 -TTAAAAAAAATAAAAATTACATTTAATCTTT
42866 TTAAAA
1 TTAAAA
42872 TTATAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 16 0.50
32 16 0.50
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAAAAAATAAAAATTACATTTAATCTTT
Found at i:45462 original size:17 final size:18
Alignment explanation
Indices: 45442--45478 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
45432 AAGTTTTATT
*
45442 TTTTTAATT-TTTTTGAA
1 TTTTTAATTATTTTTAAA
45459 TTTTTAATTATTTTTAAA
1 TTTTTAATTATTTTTAAA
45477 TT
1 TT
45479 AAATTAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTTAATTATTTTTAAA
Found at i:47487 original size:18 final size:17
Alignment explanation
Indices: 47464--47505 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
47454 TTTTTTGTGT
47464 AATTATATAAT-ATATGGA
1 AATTATATAATGATAT--A
47482 AATTATA-AATGATATA
1 AATTATATAATGATATA
47498 AATTATAT
1 AATTATAT
47506 GCAATTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.36
17 3 0.14
18 11 0.50
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
AATTATATAATGATATA
Found at i:48205 original size:15 final size:13
Alignment explanation
Indices: 48177--48201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48167 CACATATAAA
48177 AAAAAATATTAAT
1 AAAAAATATTAAT
48190 AAAAAATATTAA
1 AAAAAATATTAA
48202 AATATTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAATATTAAT
Found at i:53266 original size:29 final size:29
Alignment explanation
Indices: 53243--53310 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
53233 TAATATTATT
53243 TTATATTTATATATTGCATAAATAAATAA
1 TTATATTTATATATTGCATAAATAAATAA
53272 TTATATTTATATATTGCATAAATAAATAA
1 TTATATTTATATATTGCATAAATAAATAA
53301 TTATATTTAT
1 TTATATTTAT
53311 CCAATATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATATTTATATATTGCATAAATAAATAA
Found at i:53323 original size:29 final size:29
Alignment explanation
Indices: 53243--53327 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
53233 TAATATTATT
* * * *
53243 TTATATTTATATATTGCATAAATAAATAA
1 TTATATTTATACAATACAAAAATAAATAA
* * * *
53272 TTATATTTATATATTGCATAAATAAATAA
1 TTATATTTATACAATACAAAAATAAATAA
* *
53301 TTATATTTATCCAATATAAAAATAAAT
1 TTATATTTATACAATACAAAAATAAAT
53328 TGATGTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (29 bp):
TTATATTTATACAATACAAAAATAAATAA
Found at i:59271 original size:414 final size:414
Alignment explanation
Indices: 58501--59332 Score: 1301
Period size: 414 Copynumber: 2.0 Consensus size: 414
58491 GTTCGTTCTC
* *
58501 TAAACAAGTGCTGCAGAGTGTTGGAGTAGCATACTCAACCAACAGTATGGATCAAAGATGGAAAG
1 TAAACAAGTGCTGAAGAGTGTTGGAGTAGCATACTCAACCAACAGTATGGAACAAAGATGGAAAG
58566 ATTAGTTAGCAACAGAACTAGTAACAACCAACACATTATCTATAAGAAAACTTGTAGTAACATTC
66 ATTAGTTAGCAACAGAACTAGTAACAACCAACACATTATCTATAAGAAAACTTGTAGTAACATTC
* * * * *
58631 TTGACACTTTGGCATAATCGCAGCAAGGTGTATCATATTGAACCAAGTCAAAACATATTCAGAGT
131 TGGACACTTTGGCATAATCACAACAAGGTGTATCATACTGAACCAAGTCAAAACAAATTCAGAGT
** * * * *
58696 AATTTTGTTCACAAATGCCTTCATCTTTGAATTAGATAGCCTAAGTGCTATTTCAAATAGTGTGC
196 AATTTCATTCACAAATGCCTTCATCTCTAAAATAGATAGCCTAAGTGCTATTTCAAATAATGTGC
* * *
58761 CAGAAAGAAAAATCACTAGATGGCAACAGTCGACAAAGGACACTATCTAAATAAATTTCGACTCA
261 CAGAAAGAAAAATCACTAGATGGCAACAGCCGACAAAGGACACTATCAAAATAAATTTCGACGCA
*
58826 TGTTATGATAGCCATACAAACAACTCAATTTCAAGGATTATTGCAAGAGACAATGAAGGGTATAT
326 TGTTATGATAGCCATACAAACAACTCAATTTCAAGGATTATTGCAAGAGACAATGAAAGGTATAT
*
58891 CTTGGCAGCATGTGTTTACCCTAA
391 CTTGGCAGCATGTGCTTACCCTAA
*
58915 TAAACAAGT-CATGAAGAGTGTTGGAGTAGCATACTCGACCAACAGTATGGAACAAAGATGGAAA
1 TAAACAAGTGC-TGAAGAGTGTTGGAGTAGCATACTCAACCAACAGTATGGAACAAAGATGGAAA
* *
58979 GATTAGTTAGCAATAGAACTAGTAACAACCAACACATTATCTATAAGAAAACTTTTAGTAACATT
65 GATTAGTTAGCAACAGAACTAGTAACAACCAACACATTATCTATAAGAAAACTTGTAGTAACATT
* * ** *
59044 CTGGGCACTTTGGCATAATCACAACAAGGTGTATCATACTGGAGTAGGTCAAAACAAATTCAGAG
130 CTGGACACTTTGGCATAATCACAACAAGGTGTATCATACTGAACCAAGTCAAAACAAATTCAGAG
* * *
59109 TAATTTCATTCATAAATGCCTTCATCTCTAAAATAGATAGCTTAAGTGTTATTTC-AATCAATGT
195 TAATTTCATTCACAAATGCCTTCATCTCTAAAATAGATAGCCTAAGTGCTATTTCAAAT-AATGT
* * *
59173 GCCAGAAAGACAAATCACTAGATGGCAATC-GCCGACAGAGGACATTATCAAAATAAATTTCGAC
259 GCCAGAAAGAAAAATCACTAGATGGCAA-CAGCCGACAAAGGACACTATCAAAATAAATTTCGAC
* *
59237 GCATGTTATGATAGCCATACAAACAACTCAATTTCAAGGATTATTGCAAGAGATAGTGAAAGGTA
323 GCATGTTATGATAGCCATACAAACAACTCAATTTCAAGGATTATTGCAAGAGACAATGAAAGGTA
*
59302 TATCTTGGCAGCGTGTGCTTACCCTAA
388 TATCTTGGCAGCATGTGCTTACCCTAA
59329 TAAA
1 TAAA
59333 TGTATGCGAG
Statistics
Matches: 380, Mismatches: 35, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
413 4 0.01
414 375 0.99
415 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (414 bp):
TAAACAAGTGCTGAAGAGTGTTGGAGTAGCATACTCAACCAACAGTATGGAACAAAGATGGAAAG
ATTAGTTAGCAACAGAACTAGTAACAACCAACACATTATCTATAAGAAAACTTGTAGTAACATTC
TGGACACTTTGGCATAATCACAACAAGGTGTATCATACTGAACCAAGTCAAAACAAATTCAGAGT
AATTTCATTCACAAATGCCTTCATCTCTAAAATAGATAGCCTAAGTGCTATTTCAAATAATGTGC
CAGAAAGAAAAATCACTAGATGGCAACAGCCGACAAAGGACACTATCAAAATAAATTTCGACGCA
TGTTATGATAGCCATACAAACAACTCAATTTCAAGGATTATTGCAAGAGACAATGAAAGGTATAT
CTTGGCAGCATGTGCTTACCCTAA
Found at i:61298 original size:25 final size:25
Alignment explanation
Indices: 61244--61290 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
61234 AATATTCATG
* *
61244 AAATAATCATTGTTTAATTGGGAAA
1 AAATAATCATAGTTTAAATGGGAAA
61269 AAATAA-CATAGTTTAAATGGGA
1 AAATAATCATAGTTTAAATGGGA
61291 GAAGAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.32
Consensus pattern (25 bp):
AAATAATCATAGTTTAAATGGGAAA
Found at i:65547 original size:192 final size:191
Alignment explanation
Indices: 65149--65590 Score: 466
Period size: 192 Copynumber: 2.3 Consensus size: 191
65139 TTACCAGTAC
* * * * *
65149 CGATGCTGCTCATACGAGCTGTCGATGACTCGTAACATATGCGGTACCCTAGCCATCGGTACGAT
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCTAGCCATCGATACGAT
* * ** * *
65214 GTTTGTCTGTAAACTGTCCCTTAACGATGCTGCTCACATGAGCTGTCGAGAATATGCAGTGAAGC
66 GTTTGTCTATAAACTGTCCCCTAACGATGCTGCTCACACAAGCTATCGAGAATATGCACTGAAGC
** *
65279 ATAAATCCCAGCCATCGTAGAGTTTGTAATCCATTTTAGGATTTCATCTCTTTTCCAACTCA
131 ATAAATCCCAGCCATCGTAGAGCCTATAATCCATTTTAGGATTTCATCTCTTTT-CAACTCA
* * * *
65341 TGATGCTACTCACACGAGTTGTCGAGGACTCGCAACAAATGCGGTA-CCTAGCTATCGATAC-A-
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCTAGCCATCGATACGAT
* *
65403 GTATCTGTGC-ATATAATTGTCCCCTAACGATGCTGCTCACACAAGCTATCGAGAATATGCACTT
66 GT-T-TGT-CTATA-AACTGTCCCCTAACGATGCTGCTCACACAAGCTATCGAGAATATGCACTG
* * * * * *
65467 ATGCATAAATCCTAGCTATTGTAGTGCCTATAATCCATTCTT-GGA-TTCATTTCTCATTTT-GA
127 AAGCATAAATCCCAGCCATCGTAGAGCCTATAATCCATT-TTAGGATTTCA--TCTC-TTTTCAA
65529 CTCA
188 CTCA
* * ** * *
65533 CGATGTTGCTCACACGAGCTGTCGAGAACTCGCAACGTATGTGGTACCTTAGCCATCG
1 CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCTAGCCATCG
65591 TGTCGGTTTC
Statistics
Matches: 205, Mismatches: 36, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
189 2 0.01
190 2 0.01
191 22 0.11
192 160 0.78
193 15 0.07
194 4 0.02
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (191 bp):
CGATGCTGCTCACACGAGCTGTCGAGGACTCGCAACAAATGCGGTACCCTAGCCATCGATACGAT
GTTTGTCTATAAACTGTCCCCTAACGATGCTGCTCACACAAGCTATCGAGAATATGCACTGAAGC
ATAAATCCCAGCCATCGTAGAGCCTATAATCCATTTTAGGATTTCATCTCTTTTCAACTCA
Found at i:67926 original size:29 final size:29
Alignment explanation
Indices: 67863--67928 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
67853 ATTTAATAAC
* *
67863 ACAATAAAAATATAATTATAGTATTAAAT
1 ACAATAAAAATATAATCATAGTAATAAAT
* *
67892 AAAATAACAATATAATCATAGTAAT-AAT
1 ACAATAAAAATATAATCATAGTAATAAAT
67920 GACAATAAA
1 -ACAATAAA
67929 TATTAATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.61, C:0.06, G:0.05, T:0.29
Consensus pattern (29 bp):
ACAATAAAAATATAATCATAGTAATAAAT
Found at i:68388 original size:96 final size:99
Alignment explanation
Indices: 68262--68439 Score: 251
Period size: 99 Copynumber: 1.8 Consensus size: 99
68252 ATAAAACAAT
*
68262 ATGAAAATAAATAAAAACAAGATAAATAAAC-AAAAA-TAA-AAATTAAATG-CTAAAACAAACA
1 ATGAAAACAAATAAAAACAAGATAAATAAACAAAAAATTAATAAATTAAATGTC-AAAACAAAC-
68323 AAC-AAATATAAACAATAAAAATAATTGGATTATGC
64 AACTAAATATAAACAATAAAAATAATTGGATTATGC
* *
68358 ATGAAAACAAATGAAAAATAA-ATAAATAAACAAAAAATTAATAAATTAAATGTCAAAATAAACA
1 ATGAAAACAAAT-AAAAACAAGATAAATAAACAAAAAATTAATAAATTAAATGTCAAAACAAACA
*
68422 ACTAAATATAAATAATAA
65 ACTAAATATAAACAATAA
68440 TAAAAAAGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
96 21 0.29
97 12 0.17
98 6 0.08
99 32 0.44
100 1 0.01
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (99 bp):
ATGAAAACAAATAAAAACAAGATAAATAAACAAAAAATTAATAAATTAAATGTCAAAACAAACAA
CTAAATATAAACAATAAAAATAATTGGATTATGC
Found at i:72008 original size:52 final size:52
Alignment explanation
Indices: 71941--72186 Score: 313
Period size: 52 Copynumber: 4.8 Consensus size: 52
71931 GCCATAAACG
71941 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGAATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGAATT
* * * *
71993 AAGGGGTCCGATGACTAAATGTCATCATGAGTATATGAATCCTTTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGAATT
*
72045 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGAATT
* ** *
72097 AAAAGGTCCGATGACT--GTGTCATTATGAGTATATGAATCGC-TTGC-AGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATC-CTTTACGA-ATT
* ** *
72147 ATAG-GGTCCGGTGGTTATGTGTCATCGTGAGTATATGAAT
1 A-AGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAAT
72187 GAAGTGAAAT
Statistics
Matches: 171, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
50 37 0.22
51 2 0.01
52 132 0.77
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (52 bp):
AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGAATT
Found at i:72793 original size:21 final size:21
Alignment explanation
Indices: 72768--72845 Score: 102
Period size: 21 Copynumber: 3.6 Consensus size: 21
72758 GACTTGAGTT
72768 GTATCGGTAGTTGTATTGTGA
1 GTATCGGTAGTTGTATTGTGA
*
72789 GTATCAGTAGTTGTATTGTGA
1 GTATCGGTAGTTGTATTGTGA
* *
72810 GTATCGGTAGTTATATGTATAGA
1 GTATCGGTAGTTGTAT-TGT-GA
72833 TGTATCGGTAGTT
1 -GTATCGGTAGTT
72846 TGCATACTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 34 0.68
22 2 0.04
23 2 0.04
24 12 0.24
ACGTcount: A:0.23, C:0.05, G:0.29, T:0.42
Consensus pattern (21 bp):
GTATCGGTAGTTGTATTGTGA
Found at i:72948 original size:21 final size:22
Alignment explanation
Indices: 72921--72981 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
72911 TAGATGCATG
*
72921 ACATGTACCGGTAGAAATTA-T
1 ACATGTACCGGTAGAAATTAGC
* * *
72942 ACTTGTATCGGTA-AAACTAGC
1 ACATGTACCGGTAGAAATTAGC
*
72963 ACAGGTACCGGTAGAAATT
1 ACATGTACCGGTAGAAATT
72982 TGCATCGTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 5 0.17
21 21 0.70
22 4 0.13
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.26
Consensus pattern (22 bp):
ACATGTACCGGTAGAAATTAGC
Found at i:79047 original size:49 final size:49
Alignment explanation
Indices: 78974--79087 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 49
78964 TCTCTTCGGG
* ** * *
78974 TTTAGGGGTGCAAGATTCGTTGTTGTGGCTTTAATATGTCCCTCTTCATT
1 TTTA-GGGTGTAAGATTCACTGTTGTAGCTTTAATATGTCCCTCTTCAAT
* *
79024 TTTAGGGTGTAAGATTCACTGTTGTAGCTTTAATCTGTCCCTTTTCAAT
1 TTTAGGGTGTAAGATTCACTGTTGTAGCTTTAATATGTCCCTCTTCAAT
* *
79073 TTTAAGGTGTTAGAT
1 TTTAGGGTGTAAGAT
79088 CCATCATTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
49 51 0.93
50 4 0.07
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.45
Consensus pattern (49 bp):
TTTAGGGTGTAAGATTCACTGTTGTAGCTTTAATATGTCCCTCTTCAAT
Found at i:79257 original size:48 final size:49
Alignment explanation
Indices: 79002--79558 Score: 268
Period size: 49 Copynumber: 11.4 Consensus size: 49
78992 GTTGTTGTGG
* * * *
79002 CTTTAATATGTCCCTCTTC-ATTTTTAGGGTGTAAGATTCACTGTT--GTA
1 CTTTAATCTTTCCCTCTTCGA-TTTTAGGGTGTAAGATCCACCGTTACG-A
* * * * * * *
79050 GCTTTAATCTGTCCCTTTTCAATTTTAAGGTGTTAGATCCATCATTACGA
1 -CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGATCCACCGTTACGA
* * * * * ** * * *
79100 TTTTAAT-TTATCTCTCTT-TAGTTTTAAGGTATAAGATCTTCCATTATGG
1 CTTTAATCTT-TCCCTCTTCGA-TTTTAGGGTGTAAGATCCACCGTTACGA
* *
79149 CTTTAATCTTTCCCTCTTTGATTTTAGGGTGTAAGATCCACCGTTATGA
1 CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGATCCACCGTTACGA
*
79198 CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGA-CCACCTTTACGA
1 CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGATCCACCGTTACGA
* * * *** *
79246 CTTTAATCTTTCCCTCTTCGATTTTAAGGTGTTAGGTCTGTCGTTACGG
1 CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGATCCACCGTTACGA
* * ** * * **
79295 CTCTAATCTATCCCT-TTTTAGTTTTAGGGTGTAAGATCTACTGTTGTGA
1 CTTTAATCTTTCCCTCTTCGA-TTTTAGGGTGTAAGATCCACCGTTACGA
* * * * * **** * *
79344 CTTTATTCTTCCCCTCTTTGATTTTAGGGTGTTAGGTTTGTCGATACAA
1 CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGATCCACCGTTACGA
* ** * * * **** * *
79393 CTTTAACCTATTCATTTTTAG-TTCTAGGGTGTAAGATCTGTTGTTAAGG
1 CTTTAATCT-TTCCCTCTTCGATTTTAGGGTGTAAGATCCACCGTTACGA
* * * * * * * *
79442 GTTTAATCTTTCCCTTTTCAATTTTAGAGTGTTAGGTCCACCATTACGG
1 CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGATCCACCGTTACGA
* * * * ** * *
79491 CTTTAACCTATCCCTATT-TAGTTTTAGGGTGTAAGATCCATTGTTGCGG
1 CTTTAATCTTTCCCTCTTCGA-TTTTAGGGTGTAAGATCCACCGTTACGA
*
79540 CTTTAATATTTCCCTCTTC
1 CTTTAATCTTTCCCTCTTC
79559 AACTCTAGGG
Statistics
Matches: 378, Mismatches: 116, Indels: 27
0.73 0.22 0.05
Matches are distributed among these distances:
48 56 0.15
49 306 0.81
50 15 0.04
51 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.45
Consensus pattern (49 bp):
CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGATCCACCGTTACGA
Found at i:79320 original size:146 final size:147
Alignment explanation
Indices: 79023--79375 Score: 394
Period size: 146 Copynumber: 2.4 Consensus size: 147
79013 CCCTCTTCAT
* * * * * *
79023 TTTTAGGGTGTAAGATTCACTGTTGT-AGCTTTAATCTGTCCCTTTTCAATTTTAAGGTGTTAGA
1 TTTTAGGGTGTAAGATCCACTGTTGTGA-CTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGA
* * * * * *
79087 TCCATCATTACGATTTTAATTTATCTCTCTTTAGTTTTAAGGTATAAGATCTTCCATTATGGCTT
65 TCCACCATTACGACTTTAATTTATCCCTCTTGAGTTTTAAGGTATAAGATCTTCCATTACGGCTC
*
79152 TAATCTTTCCCTCTTTGA
130 TAATCTATCCCTCTTTGA
* *
79170 TTTTAGGGTGTAAGATCCACCGTTATGACTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGA-
1 TTTTAGGGTGTAAGATCCACTGTTGTGACTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGAT
* * * * *
79234 CCACCTTTACGACTTTAATCTT-TCCCTCTTCGA-TTTTAAGGTGTTAGGTCTGT-CGTTACGGC
66 CCACCATTACGACTTTAAT-TTATCCCTCTT-GAGTTTTAAGGTATAAGATCT-TCCATTACGGC
*
79296 TCTAATCTATCCCT-TTTTA
128 TCTAATCTATCCCTCTTTGA
* * * *
79315 GTTTTAGGGTGTAAGATCTACTGTTGTGACTTTATTCTTCCCCTCTTTGATTTTAGGGTGT
1 -TTTTAGGGTGTAAGATCCACTGTTGTGACTTTAATCTTTCCCTCTTCGATTTTAGGGTGT
79376 TAGGTTTGTC
Statistics
Matches: 174, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
145 4 0.02
146 111 0.64
147 58 0.33
148 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45
Consensus pattern (147 bp):
TTTTAGGGTGTAAGATCCACTGTTGTGACTTTAATCTTTCCCTCTTCGATTTTAGGGTGTAAGAT
CCACCATTACGACTTTAATTTATCCCTCTTGAGTTTTAAGGTATAAGATCTTCCATTACGGCTCT
AATCTATCCCTCTTTGA
Found at i:79386 original size:98 final size:98
Alignment explanation
Indices: 79023--79557 Score: 400
Period size: 98 Copynumber: 5.5 Consensus size: 98
79013 CCCTCTTCAT
* * * *
79023 TTTTAGGGTGTAAGAT-TCACTGTTGT-AGCTTTAATCTGTCCCT-TTTCAATTTTAAGGTGTTA
1 TTTTAGGGTGTAAGATCT-ACTGTTATGA-CTTTAATCTTTCCCTCTTT-GATTTTAGGGTGTTA
* * * * ** * *
79085 GATCCATCATTACGATTTTAATTTATCTCTCTTTAG
63 GGTCCACCGTTACGACTTTAACCTATCCCTTTTTAG
* * * ** * * *
79121 TTTTAAGGTATAAGATCTTCCATTATGGCTTTAATCTTTCCCTCTTTGATTTTAGGGTGTAAGAT
1 TTTTAGGGTGTAAGATCTACTGTTATGACTTTAATCTTTCCCTCTTTGATTTTAGGGTGTTAGGT
* * * * *
79186 CCACCGTTATGACTTTAATCTTTCCC-TCTTCG
66 CCACCGTTACGACTTTAACCTATCCCTTTTTAG
* * * *
79218 ATTTTAGGGTGTAAGA-CCACCT-TTACGACTTTAATCTTTCCCTCTTCGATTTTAAGGTGTTAG
1 -TTTTAGGGTGTAAGATCTA-CTGTTATGACTTTAATCTTTCCCTCTTTGATTTTAGGGTGTTAG
*** * * *
79281 GTCTGTCGTTACGGCTCTAATCTATCCCTTTTTAG
64 GTCCACCGTTACGACTTTAACCTATCCCTTTTTAG
* * *
79316 TTTTAGGGTGTAAGATCTACTGTTGTGACTTTATTCTTCCCCTCTTTGATTTTAGGGTGTTAGGT
1 TTTTAGGGTGTAAGATCTACTGTTATGACTTTAATCTTTCCCTCTTTGATTTTAGGGTGTTAGGT
**** * * * *
79381 TTGTCGATACAACTTTAACCTATTCATTTTTAG
66 CCACCGTTACGACTTTAACCTATCCCTTTTTAG
* ** * ** * *
79414 TTCTAGGGTGTAAGATCTGTTGTTAAGGGTTTAATCTTTCCCT-TTTCAATTTTAGAGTGTTAGG
1 TTTTAGGGTGTAAGATCTACTGTTATGACTTTAATCTTTCCCTCTTT-GATTTTAGGGTGTTAGG
* * *
79478 TCCACCATTACGGCTTTAACCTATCCCTATTTAG
65 TCCACCGTTACGACTTTAACCTATCCCTTTTTAG
* * ** * *
79512 TTTTAGGGTGTAAGATCCATTGTTGCGGCTTTAATATTTCCCTCTT
1 TTTTAGGGTGTAAGATCTACTGTTATGACTTTAATCTTTCCCTCTT
79558 CAACTCTAGG
Statistics
Matches: 342, Mismatches: 85, Indels: 19
0.77 0.19 0.04
Matches are distributed among these distances:
97 80 0.23
98 256 0.75
99 6 0.02
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.44
Consensus pattern (98 bp):
TTTTAGGGTGTAAGATCTACTGTTATGACTTTAATCTTTCCCTCTTTGATTTTAGGGTGTTAGGT
CCACCGTTACGACTTTAACCTATCCCTTTTTAG
Found at i:90932 original size:18 final size:18
Alignment explanation
Indices: 90888--90946 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
90878 AGAAGAAGAT
90888 AATAATAATAAT-AATAATA
1 AATAATAA-AATAAATAA-A
* *
90907 AAT-GTAAATTAAATAAA
1 AATAATAAAATAAATAAA
* *
90924 AATAATAAAATAGATAAG
1 AATAATAAAATAAATAAA
90942 AATAA
1 AATAA
90947 AATGGCATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 6 0.19
18 23 0.72
19 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AATAATAAAATAAATAAA
Found at i:91098 original size:92 final size:93
Alignment explanation
Indices: 90952--91127 Score: 234
Period size: 92 Copynumber: 1.9 Consensus size: 93
90942 AATAAAATGG
*
90952 CATGAAAATAAATACCAAGATAAATAAACAAAAAATAAAAATTAAATGCTAAAATAAACAAAC-A
1 CATGAAAATAAATACCAAGATAAATAAACAAAAAAT-AAAATTAAATGCCAAAATAAAC-AACTA
91016 AATACAAACAATAAAAATAATTGGATTAGA
64 AATACAAACAATAAAAATAATTGGATTAGA
* *
91046 CATGAAAATAAATGA-CAA-ATAAATAAATAAATTAAT-AAATTAAATGCCAAAATAAACAACTA
1 CATGAAAATAAAT-ACCAAGATAAATAAACAAA-AAATAAAATTAAATGCCAAAATAAACAACTA
* * *
91108 AATATAAATAATAATAATAA
64 AATACAAACAATAAAAATAA
91128 AAAAGAACAC
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
91 3 0.04
92 38 0.52
93 12 0.16
94 19 0.26
95 1 0.01
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.22
Consensus pattern (93 bp):
CATGAAAATAAATACCAAGATAAATAAACAAAAAATAAAATTAAATGCCAAAATAAACAACTAAA
TACAAACAATAAAAATAATTGGATTAGA
Found at i:92292 original size:7 final size:7
Alignment explanation
Indices: 92280--92307 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
92270 TAAATCAAAT
92280 GTGTTGA
1 GTGTTGA
92287 GTGTTGA
1 GTGTTGA
92294 GTGTTGA
1 GTGTTGA
92301 GTGTTGA
1 GTGTTGA
92308 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTGTTGA
Found at i:93802 original size:14 final size:15
Alignment explanation
Indices: 93783--93817 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
93773 ATAAAAAATT
93783 TCTTTCTT-TTTTTC
1 TCTTTCTTATTTTTC
93797 TCTTTCTTCATTTTTC
1 TCTTTCTT-ATTTTTC
93813 TCTTT
1 TCTTT
93818 TTGTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
16 11 0.58
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTTTCTTATTTTTC
Found at i:93804 original size:18 final size:18
Alignment explanation
Indices: 93781--93830 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
93771 TTATAAAAAA
*
93781 TTTCTTTCTTTTTTTCTC
1 TTTCTTTCTTTTTCTCTC
*
93799 TTTC-TTCATTTTTCTCTT
1 TTTCTTTC-TTTTTCTCTC
*
93817 TTTGTTTCTTTTTC
1 TTTCTTTCTTTTTC
93831 AAATGACTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTCTTTCTTTTTCTCTC
Found at i:96515 original size:17 final size:17
Alignment explanation
Indices: 96495--96529 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
96485 AGAAATCTGC
*
96495 AGGAAAGAGGATTTATA
1 AGGAAAAAGGATTTATA
96512 AGGAAAAAGGATTTATA
1 AGGAAAAAGGATTTATA
96529 A
1 A
96530 CCTAGGCGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (17 bp):
AGGAAAAAGGATTTATA
Found at i:96780 original size:20 final size:21
Alignment explanation
Indices: 96755--96793 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
96745 GCAAGGAATT
96755 TGAAAC-AATAAAAGTAAAAG
1 TGAAACAAATAAAAGTAAAAG
96775 TGAAACAAATAAAAGTAAA
1 TGAAACAAATAAAAGTAAA
96794 TAAACAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.67, C:0.05, G:0.13, T:0.15
Consensus pattern (21 bp):
TGAAACAAATAAAAGTAAAAG
Found at i:103760 original size:2 final size:2
Alignment explanation
Indices: 103753--103779 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
103743 TATTAATGAA
103753 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 A
103780 AATTAAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:106113 original size:37 final size:38
Alignment explanation
Indices: 106063--106134 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
106053 ATTAAGTGAC
* *
106063 ACCCAGTGTCTCATCG-GCCTAGCCGAAGTAAAATGAT
1 ACCCAGTATCTCATCGAACCTAGCCGAAGTAAAATGAT
* *
106100 ACCCAGTATCTCATCGAATCTATCCGAAGTAAAAT
1 ACCCAGTATCTCATCGAACCTAGCCGAAGTAAAAT
106135 AATGACACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 15 0.50
38 15 0.50
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (38 bp):
ACCCAGTATCTCATCGAACCTAGCCGAAGTAAAATGAT
Found at i:106153 original size:41 final size:38
Alignment explanation
Indices: 106059--106157 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 38
106049 TCCAATTAAG
*
106059 TGACACCCAGTGTCTCATCG-GCCTAGCCGAAGTAAAA
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAA
* * * *
106096 TGATACCCAGTATCTCATCGAATCTATCCGAAGTAAAATAA
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGT--AA-AA
*
106137 TGACACCCGGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
106158 CTCAAGGTCG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 18 0.36
38 10 0.20
40 2 0.04
41 20 0.40
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (38 bp):
TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAA
Found at i:108843 original size:19 final size:19
Alignment explanation
Indices: 108819--108875 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
108809 ATATTTGATT
108819 TTCACATCAATTTCACATA
1 TTCACATCAATTTCACATA
* *
108838 TTCACATCAATGTCACATG
1 TTCACATCAATTTCACATA
*
108857 TTCACA--AATTCCACATA
1 TTCACATCAATTTCACATA
108874 TT
1 TT
108876 TTCATATCTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
17 10 0.30
19 23 0.70
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (19 bp):
TTCACATCAATTTCACATA
Found at i:109235 original size:45 final size:45
Alignment explanation
Indices: 109164--109289 Score: 164
Period size: 45 Copynumber: 2.8 Consensus size: 45
109154 ACTCGCCACT
* *
109164 TCGGGTTGCCCGACAATGATAACTCACTTATATTGAATTGCTAACC
1 TCGGGTTACCCGACAATGATAGCTCACTTATATTGAATTGCT-ACC
* *
109210 -CGGGTTACCTGACAACGATAGCTCACTTATATTGAATTGCTACC
1 TCGGGTTACCCGACAATGATAGCTCACTTATATTGAATTGCTACC
* * * *
109254 TCGAGTTACCCAAAAATGATAGCTCACTTATGTTGA
1 TCGGGTTACCCGACAATGATAGCTCACTTATATTGA
109290 TATGCAGTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 3 0.04
45 66 0.96
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (45 bp):
TCGGGTTACCCGACAATGATAGCTCACTTATATTGAATTGCTACC
Found at i:112047 original size:27 final size:27
Alignment explanation
Indices: 112017--112137 Score: 89
Period size: 27 Copynumber: 4.4 Consensus size: 27
112007 TCTAATTTTG
*
112017 GCTCGAAAGAGCGTTAATATGATTCTA
1 GCTCGAAAGAGCGTTAATCTGATTCTA
* * * *
112044 GCTCGAAAGAGCATAAATCTGATTATG
1 GCTCGAAAGAGCGTTAATCTGATTCTA
* * * *
112071 GCTTGAAAGAGAGTTATTCTGATTCTG
1 GCTCGAAAGAGCGTTAATCTGATTCTA
* * * * * *
112098 GGTTGAAAGAGCATTATTCTAATTCTGG
1 GCTCGAAAGAGCGTTAATCTGATTCT-A
*
112126 GCTCGTAAGAGC
1 GCTCGAAAGAGC
112138 TAACCATTCT
Statistics
Matches: 75, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
27 65 0.87
28 10 0.13
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (27 bp):
GCTCGAAAGAGCGTTAATCTGATTCTA
Found at i:112094 original size:54 final size:54
Alignment explanation
Indices: 112005--112136 Score: 138
Period size: 54 Copynumber: 2.4 Consensus size: 54
111995 TTTGAGGAGT
* *
112005 AATCTAATTTTGGCTCGAAAGAGCGTTAATATGATTCTAGCTCGAAAGAGCATA
1 AATCTAATTATGGCTCGAAAGAGAGTTAATATGATTCTAGCTCGAAAGAGCATA
* * * * * * * *
112059 AATCTGATTATGGCTTGAAAGAGAGTTATTCTGATTCTGGGTTGAAAGAGCATT
1 AATCTAATTATGGCTCGAAAGAGAGTTAATATGATTCTAGCTCGAAAGAGCATA
* * *
112113 ATTCTAATTCTGGGCTCGTAAGAG
1 AATCTAATTAT-GGCTCGAAAGAG
112137 CTAACCATTC
Statistics
Matches: 62, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
54 52 0.84
55 10 0.16
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (54 bp):
AATCTAATTATGGCTCGAAAGAGAGTTAATATGATTCTAGCTCGAAAGAGCATA
Found at i:112172 original size:23 final size:23
Alignment explanation
Indices: 112119--112202 Score: 141
Period size: 23 Copynumber: 3.6 Consensus size: 23
112109 CATTATTCTA
112119 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAA-C
*
112143 ATTCTGGGCTCGTAAGGGCTAAC
1 ATTCTGGGCTCGTAAGAGCTAAC
*
112166 ATTCTGGGCTTGTAAGAGCTAAC
1 ATTCTGGGCTCGTAAGAGCTAAC
112189 ATTCTGGGCTCGTA
1 ATTCTGGGCTCGTA
112203 TGAGTTAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
23 35 0.62
24 21 0.38
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (23 bp):
ATTCTGGGCTCGTAAGAGCTAAC
Found at i:119418 original size:178 final size:178
Alignment explanation
Indices: 119112--119469 Score: 680
Period size: 178 Copynumber: 2.0 Consensus size: 178
119102 TGGTTGCAGG
*
119112 TTATCCCTAGTAATCATTGGAATAGATTCTTCTCAATTAATTTTTAGGAGTGGTCGGTATCTAAT
1 TTATCCCTAGTAATCATTGGAATAGATTCTTCTCAATTAATTTTTAAGAGTGGTCGGTATCTAAT
*
119177 TTACAGATTAACTCAAAGACGGGTTTAGAAGGGATTCCTTGGTCTTGTATTTTTGGTTTGTTGGC
66 TTACAGATTAACTCAAAGACGCGTTTAGAAGGGATTCCTTGGTCTTGTATTTTTGGTTTGTTGGC
119242 ATGCCGTATTTGGAAGAACATGAATCTTCTCACATTTCGTGGAATTTT
131 ATGCCGTATTTGGAAGAACATGAATCTTCTCACATTTCGTGGAATTTT
*
119290 TTATCCTTAGTAATCATTGGAATAGATTCTTCTCAATTAATTTTTAAGAGTGGTCGGTATCTAAT
1 TTATCCCTAGTAATCATTGGAATAGATTCTTCTCAATTAATTTTTAAGAGTGGTCGGTATCTAAT
*
119355 TTACAGATTAACTCAACGACGCGTTTAGAAGGGATTCCTTGGTCTTGTATTTTTGGTTTGTTGGC
66 TTACAGATTAACTCAAAGACGCGTTTAGAAGGGATTCCTTGGTCTTGTATTTTTGGTTTGTTGGC
119420 ATGCCGTATTTGGAAGAACATGAATCTTCTCACATTTCGTGGAATTTT
131 ATGCCGTATTTGGAAGAACATGAATCTTCTCACATTTCGTGGAATTTT
119468 TT
1 TT
119470 GGAGCCCTGT
Statistics
Matches: 176, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
178 176 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (178 bp):
TTATCCCTAGTAATCATTGGAATAGATTCTTCTCAATTAATTTTTAAGAGTGGTCGGTATCTAAT
TTACAGATTAACTCAAAGACGCGTTTAGAAGGGATTCCTTGGTCTTGTATTTTTGGTTTGTTGGC
ATGCCGTATTTGGAAGAACATGAATCTTCTCACATTTCGTGGAATTTT
Found at i:126428 original size:12 final size:12
Alignment explanation
Indices: 126411--126451 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
126401 TCCATTATTA
126411 ATATAATGCAAT
1 ATATAATGCAAT
*
126423 ATATAAAT--AAA
1 ATAT-AATGCAAT
126434 ATATAATGCAAT
1 ATATAATGCAAT
126446 ATATAA
1 ATATAA
126452 ATAAATTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.12
11 6 0.25
12 12 0.50
13 3 0.12
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (12 bp):
ATATAATGCAAT
Found at i:126466 original size:21 final size:23
Alignment explanation
Indices: 126410--126456 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
126400 ATCCATTATT
126410 AATATAATGCAATATATAAATAA
1 AATATAATGCAATATATAAATAA
126433 AATATAATGCAATATATAAATAA
1 AATATAATGCAATATATAAATAA
126456 A
1 A
126457 TTAACTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (23 bp):
AATATAATGCAATATATAAATAA
Found at i:127049 original size:21 final size:22
Alignment explanation
Indices: 127023--127064 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
127013 TTTACAACCT
127023 TTCAATCAAT-CAAGAA-TTAAA
1 TTCAATC-ATGCAAGAACTTAAA
127044 TTCAATCATGCAAGAACTTAA
1 TTCAATCATGCAAGAACTTAA
127065 GAATCACGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 13 0.68
22 4 0.21
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.29
Consensus pattern (22 bp):
TTCAATCATGCAAGAACTTAAA
Found at i:127539 original size:39 final size:39
Alignment explanation
Indices: 127481--127619 Score: 163
Period size: 39 Copynumber: 3.6 Consensus size: 39
127471 TAATTTTGAA
127481 CTCGGGGTAAGAGATCGAATGGTTGTAATCTGCCCCAGG
1 CTCGGGGTAAGAGATCGAATGGTTGTAATCTGCCCCAGG
* ** *
127520 CTCAGGGTAAGAGATCGAATGGTTACAATCTGCCCTAGG
1 CTCGGGGTAAGAGATCGAATGGTTGTAATCTGCCCCAGG
* * * * * *
127559 CTCGGGGTAAGAGATTTG-CTGATGGTGATCTGCCCCAAG
1 CTCGGGGTAAGAGA-TCGAATGGTTGTAATCTGCCCCAGG
*
127598 CTCGGGGTAAAAGATCGAATGG
1 CTCGGGGTAAGAGATCGAATGG
127620 CTGCAATTTA
Statistics
Matches: 80, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
38 2 0.03
39 76 0.95
40 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.23
Consensus pattern (39 bp):
CTCGGGGTAAGAGATCGAATGGTTGTAATCTGCCCCAGG
Found at i:127634 original size:39 final size:39
Alignment explanation
Indices: 127481--127636 Score: 158
Period size: 39 Copynumber: 4.0 Consensus size: 39
127471 TAATTTTGAA
* *
127481 CTCGGGGTAAGAGATCGAATGGTTGTAATCTGCCCCAGG
1 CTCGGGGTAAGAGATCGAATGGTTGCAATCTGCCCCAAG
* * * *
127520 CTCAGGGTAAGAGATCGAATGGTTACAATCTGCCCTAGG
1 CTCGGGGTAAGAGATCGAATGGTTGCAATCTGCCCCAAG
127559 CTCGGGGTAAGAGATTTGCTG-ATGG-TG--ATCTGCCCCAAG
1 CTCGGGGTAAGAGA--T-C-GAATGGTTGCAATCTGCCCCAAG
* * * *
127598 CTCGGGGTAAAAGATCGAATGGCTGCAATTTACCCCAAG
1 CTCGGGGTAAGAGATCGAATGGTTGCAATCTGCCCCAAG
127637 ATTGAACAGT
Statistics
Matches: 98, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
35 1 0.01
36 5 0.05
37 3 0.03
39 81 0.83
41 2 0.02
42 5 0.05
43 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
CTCGGGGTAAGAGATCGAATGGTTGCAATCTGCCCCAAG
Found at i:127694 original size:39 final size:39
Alignment explanation
Indices: 127651--128028 Score: 254
Period size: 39 Copynumber: 9.7 Consensus size: 39
127641 AACAGTTGCA
** *
127651 ATCTGCCTTAGGCTCAGGGTAAGAGATTGACTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* **
127690 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * * * * * ** *
127729 ATCTGTCCTAGGCTCGGGGTAAAAGATCGAATGGTTATA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * *
127768 ATCTACCCCAGGCTCGGGGTAAGAGATTTACTAATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * * * * * *
127807 ATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTGTA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * * * * * ***
127846 ATCTGCCTCAAGCTTGGGGTAAGAGATCGGACAGCT-ACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT-TGACTGATGGTG
** * *
127885 ATCCACCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * * * * **
127924 ATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * ** **
127963 ATCTGTCTCAGGCTCAAGGTAAGAGATTGGTTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
* * *
128002 ATCTGCCCCAAGCTTGGGGTAAAAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
128029 CGAATCTTCG
Statistics
Matches: 248, Mismatches: 89, Indels: 4
0.73 0.26 0.01
Matches are distributed among these distances:
38 4 0.02
39 240 0.97
40 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTG
Found at i:127775 original size:143 final size:143
Alignment explanation
Indices: 127502--127777 Score: 363
Period size: 143 Copynumber: 1.9 Consensus size: 143
127492 AGATCGAATG
* * * * *
127502 GTTGTAATCTGCCCCAGGCTCAGGGTAAGAGATCGAATGGTTACAATCTGCCCTAGGCTCGGGGT
1 GTTGCAATCTGCCCCAGGCTCAGGGTAAGAGATCGAATGATGACAATCTGCCCCAAGCTCGGGGT
* * *
127567 AAGAGATTTGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTGCAATTTACC
66 AAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTACAATCTACC
127632 CCAAGATTGAACA
131 CCAAGATTGAACA
** * * ***
127645 GTTGCAATCTGCCTTAGGCTCAGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGT
1 GTTGCAATCTGCCCCAGGCTCAGGGTAAGAGATCGAATGATGACAATCTGCCCCAAGCTCGGGGT
* * * * * *
127710 AAGAGATTGGTTGATGGTGATCTGTCCTAGGCTCGGGGTAAAAGATCGAATGGTTATAATCTACC
66 AAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTACAATCTACC
127775 CCA
131 CCA
127778 GGCTCGGGGT
Statistics
Matches: 112, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
143 112 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (143 bp):
GTTGCAATCTGCCCCAGGCTCAGGGTAAGAGATCGAATGATGACAATCTGCCCCAAGCTCGGGGT
AAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTACAATCTACC
CCAAGATTGAACA
Found at i:127850 original size:117 final size:118
Alignment explanation
Indices: 127660--127977 Score: 408
Period size: 117 Copynumber: 2.7 Consensus size: 118
127650 AATCTGCCTT
* * * ** *
127660 AGGCTCAGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGAT
1 AGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGT
* * ** * * *
127725 GGTGATCTGTCCT-AGGCTCGGGGTAAAAGATCGAATGGTTATAATCTACCCC
66 TGTAATCTGTCCTCAGGCTCGGGGTAAAAGATCGAACAGCTACAATCCACCCC
* *
127777 AGGCTCGGGGTAAGAGATTTACTAATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGT
1 AGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGT
* * * *
127842 TGTAATCTG-CCTCAAGCTTGGGGTAAGAGATCGGACAGCTACAATCCACCCC
66 TGTAATCTGTCCTCAGGCTCGGGGTAAAAGATCGAACAGCTACAATCCACCCC
* * *
127894 AAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGT
1 AGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGT
*
127959 TGCAATCTGT-CTCAGGCTC
66 TGTAATCTGTCCTCAGGCTC
127978 AAGGTAAGAG
Statistics
Matches: 172, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
116 3 0.02
117 169 0.98
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (118 bp):
AGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGT
TGTAATCTGTCCTCAGGCTCGGGGTAAAAGATCGAACAGCTACAATCCACCCC
Found at i:128011 original size:117 final size:116
Alignment explanation
Indices: 127662--128028 Score: 378
Period size: 117 Copynumber: 3.1 Consensus size: 116
127652 TCTGCCTTAG
* * * ** * *
127662 GCTCAGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGATGG
1 GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* * * * * *
127727 TGATCTGTC-CTAGGCTCGGGGTAAAAGATCGAATGGTTATAATCTACCCCAG
66 TAATCTGTCTC-AGGCTCGGGGTAAGAGATCG-GTGATGATAATCTACCCCAA
* *
127779 GCTCGGGGTAAGAGATTTACTAATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
1 GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* * * ** * *
127844 TAATCTGCCTCAAGCTTGGGGTAAGAGATCGGACA-GCTACAATCCACCCCAA
66 TAATCTGTCTCAGGCTCGGGGTAAGAGATCGGTGATG--ATAATCTACCCCAA
* *
127896 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGTTG
1 GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
* ** * * * *
127961 CAATCTGTCTCAGGCTCAAGGTAAGAGATTGGTTGATGGTGATCTGCCCCAA
66 TAATCTGTCTCAGGCTCGGGGTAAGAGATCGG-TGATGATAATCTACCCCAA
* *
128013 GCTTGGGGTAAAAGAT
1 GCTCGGGGTAAGAGAT
128029 CGAATCTTCG
Statistics
Matches: 203, Mismatches: 42, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
117 200 0.99
118 2 0.01
119 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (116 bp):
GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGGTTG
TAATCTGTCTCAGGCTCGGGGTAAGAGATCGGTGATGATAATCTACCCCAA
Found at i:139888 original size:28 final size:28
Alignment explanation
Indices: 139857--140236 Score: 163
Period size: 30 Copynumber: 13.1 Consensus size: 28
139847 TTTCAGAGAA
*
139857 TTTAGGGTTAAAACGTAATTTTGGAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAG
* * *
139885 TTTAAAGAGTAAAAAAT-TTATTTTGGGAAAG
1 TTT--AGGGT-TAAAATGTAATTTT-GGAAAG
* *
139916 TTT-GGGGTAAAATGTAATTTT-TACAAG
1 TTTAGGGTTAAAATGTAATTTTGGA-AAG
* * *
139943 TTTGGGGATTAAAATGTATTTTTAG-AAG
1 TTTAGGG-TTAAAATGTAATTTTGGAAAG
*
139971 TTTAGGGGTTAAAATGTGAA-TTTCGAAAG
1 TTTA-GGGTTAAAATGT-AATTTTGGAAAG
* *
140000 TTCGAGGG-TAAAATGTAATTTTTGAGAAG
1 TT-TAGGGTTAAAATGTAATTTTGGA-AAG
* * * *
140029 TTAAGGG-CAAAATTTTAATTTTTGAGAAG
1 TTTAGGGTTAAAA-TGTAATTTTGGA-AAG
* * *
140058 TTCAAGGG-TCAAATGTGATTTTTGG-AAG
1 TT-TAGGGTTAAAATGT-AATTTTGGAAAG
*
140086 TTTA-GGTTCAAAATATAATTTTTAGG-AAG
1 TTTAGGGTT-AAAATGTAA-TTTT-GGAAAG
* * **
140115 TTTGAGGGTAAAAATGTATTTTTTAAGAAG
1 TTT-AGGGTTAAAATGTAATTTTGGA-AAG
* **
140145 TTTGAGGGTTAAAATGTGATTTTTAAGAAG
1 TTT-AGGGTTAAAATGTAATTTTGGA-AAG
* *
140175 TTTGAGGGTTAAAATGTGATTTTTGAAAAG
1 TTT-AGGGTTAAAATGT-AATTTTGGAAAG
* *
140205 TTTAAGGGTCAATATATG-ATTTTTGGAAAG
1 TTT-AGGGTTAA-A-ATGTAATTTTGGAAAG
140235 TT
1 TT
140237 CAAGACCTTC
Statistics
Matches: 280, Mismatches: 43, Indels: 56
0.74 0.11 0.15
Matches are distributed among these distances:
26 3 0.01
27 16 0.06
28 68 0.24
29 61 0.22
30 106 0.38
31 23 0.08
32 3 0.01
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (28 bp):
TTTAGGGTTAAAATGTAATTTTGGAAAG
Found at i:140206 original size:30 final size:30
Alignment explanation
Indices: 139912--140236 Score: 218
Period size: 30 Copynumber: 11.2 Consensus size: 30
139902 TTATTTTGGG
*
139912 AAAGTTTG-GGG-TAAAATGTAATTTTT-A
1 AAAGTTTGAGGGTTAAAATGTGATTTTTGA
*
139939 CAAGTTTG-GGGATTAAAATGT-ATTTTT-A
1 AAAGTTTGAGGG-TTAAAATGTGATTTTTGA
* * *
139967 GAAGTTT-AGGGGTTAAAATGTGAATTTCG-
1 AAAGTTTGA-GGGTTAAAATGTGATTTTTGA
* *
139996 AAAGTTCGAGGG-TAAAATGTAATTTTTGA
1 AAAGTTTGAGGGTTAAAATGTGATTTTTGA
* * * * *
140025 GAAG-TTAAGGG-CAAAATTTTAATTTTTGA
1 AAAGTTTGAGGGTTAAAA-TGTGATTTTTGA
* ** *
140054 GAAGTTCAAGGG-TCAAATGTGATTTTTG-
1 AAAGTTTGAGGGTTAAAATGTGATTTTTGA
* * *
140082 GAAGTTT-A-GGTTCAAAATATAATTTTT-A
1 AAAGTTTGAGGGTT-AAAATGTGATTTTTGA
* * *
140110 GGAAGTTTGAGGGTAAAAATGT-ATTTTTTA
1 -AAAGTTTGAGGGTTAAAATGTGATTTTTGA
140140 AGAAGTTTGAGGGTTAAAATGTGATTTTT-A
1 A-AAGTTTGAGGGTTAAAATGTGATTTTTGA
140170 AGAAGTTTGAGGGTTAAAATGTGATTTTTGA
1 A-AAGTTTGAGGGTTAAAATGTGATTTTTGA
* * * * *
140201 AAAGTTTAAGGGTCAATATATGATTTTTGG
1 AAAGTTTGAGGGTTAAAATGTGATTTTTGA
140231 AAAGTT
1 AAAGTT
140237 CAAGACCTTC
Statistics
Matches: 246, Mismatches: 32, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
26 2 0.01
27 12 0.05
28 61 0.25
29 63 0.26
30 97 0.39
31 11 0.04
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.39
Consensus pattern (30 bp):
AAAGTTTGAGGGTTAAAATGTGATTTTTGA
Found at i:141956 original size:17 final size:16
Alignment explanation
Indices: 141909--141990 Score: 51
Period size: 17 Copynumber: 5.0 Consensus size: 16
141899 TTAAAATTTA
*
141909 AATTT-AATTTAAAAGA
1 AATTTAAATTTAAAA-T
* * *
141925 AATTCAAACTCAAAAT
1 AATTTAAATTTAAAAT
141941 AAGTTTAAATTTAAAAT
1 AA-TTTAAATTTAAAAT
* *
141958 AAATTCAAACTT-AAAT
1 -AATTTAAATTTAAAAT
*
141974 AAATTAAATTTTAAAAT
1 AATTTAAA-TTTAAAAT
141991 TAGGTTCAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
15 6 0.12
16 12 0.24
17 29 0.59
18 2 0.04
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:141974 original size:33 final size:33
Alignment explanation
Indices: 141907--141990 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 33
141897 TTTTAAAATT
* *
141907 TAAATTTAATTTAAAAGAAATTCAAACTCAAAA
1 TAAATTAAATTTAAAATAAATTCAAACTCAAAA
* *
141940 TAAGTTTAAATTTAAAATAAATTCAAACT-TAAA
1 TAA-ATTAAATTTAAAATAAATTCAAACTCAAAA
141973 TAAATTAAATTTTAAAAT
1 TAAATTAAA-TTTAAAAT
141991 TAGGTTCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
32 5 0.11
33 17 0.39
34 22 0.50
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (33 bp):
TAAATTAAATTTAAAATAAATTCAAACTCAAAA
Found at i:141987 original size:16 final size:16
Alignment explanation
Indices: 141945--141988 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
141935 CAAAATAAGT
*
141945 TTAAATTTAAAATAAA
1 TTAAATTTTAAATAAA
*
141961 TTCAAA-CTTAAATAAA
1 TT-AAATTTTAAATAAA
141977 TTAAATTTTAAA
1 TTAAATTTTAAA
141989 ATTAGGTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.13
16 17 0.74
17 3 0.13
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAATTTTAAATAAA
Found at i:143560 original size:73 final size:73
Alignment explanation
Indices: 143441--143586 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
143431 AGAGGTAGGA
143441 TTTTGAATTAAACGCCACCCTTGTTTGGCCAAAAGGGCAACGTTAAATTTAGCAAACGAATAGAA
1 TTTTGAATTAAACGCCACCCTTGTTTGGCCAAAAGGGCAACGTTAAATTTAGCAAACGAATAGAA
143506 ACCTAATC
66 ACCTAATC
*
143514 TTTTGAATTAAACGCCACCCTTGTTTGGCCAAAAGGGCAACGTTAAATTTAGCGAACGAATAGAA
1 TTTTGAATTAAACGCCACCCTTGTTTGGCCAAAAGGGCAACGTTAAATTTAGCAAACGAATAGAA
143579 ACCTAATC
66 ACCTAATC
143587 CCCCTTCAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (73 bp):
TTTTGAATTAAACGCCACCCTTGTTTGGCCAAAAGGGCAACGTTAAATTTAGCAAACGAATAGAA
ACCTAATC
Found at i:148652 original size:23 final size:23
Alignment explanation
Indices: 148611--148654 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
148601 ATAATTTGAT
148611 TTTTATGATGTAAAAAATAAATA
1 TTTTATGATGTAAAAAATAAATA
*
148634 TTTTAT-ATTTAAAATAATAAA
1 TTTTATGATGTAAAA-AATAAA
148655 AAGAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TTTTATGATGTAAAAAATAAATA
Found at i:150849 original size:26 final size:24
Alignment explanation
Indices: 150819--150866 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
150809 ATAGTTTTTG
150819 AATTTACATATGCTTTTAAATTTTAT
1 AATTTACATAT--TTTTAAATTTTAT
*
150845 AATTTATATATTTTTAAATTTT
1 AATTTACATATTTTTAAATTTT
150867 TTATTTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
26 10 0.48
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (24 bp):
AATTTACATATTTTTAAATTTTAT
Found at i:155482 original size:27 final size:27
Alignment explanation
Indices: 155441--155508 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
155431 ATATTTGGAG
* *
155441 ATATT-TTTCATTAAT-TAATTAGTTAA
1 ATATTATTTTATTAATAT-ATTACTTAA
*
155467 ATATTATTTTATTAATATTTTACTTAA
1 ATATTATTTTATTAATATATTACTTAA
155494 ATATTTATTATTATT
1 ATA-TTATT-TTATT
155509 TATTTAGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 5 0.14
27 19 0.54
28 6 0.17
29 5 0.14
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (27 bp):
ATATTATTTTATTAATATATTACTTAA
Found at i:157151 original size:34 final size:35
Alignment explanation
Indices: 157088--157156 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
157078 GAAGAGAGTT
157088 CTTTCGAGAGAACAAAATGATGTTTTTGAAAAGAA
1 CTTTCGAGAGAACAAAATGATGTTTTTGAAAAGAA
* *
157123 CTTTCGAGAGAACAAAA-GTTGTTTTTGAAGAGAA
1 CTTTCGAGAGAACAAAATGATGTTTTTGAAAAGAA
157157 GGTTAAGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 15 0.47
35 17 0.53
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (35 bp):
CTTTCGAGAGAACAAAATGATGTTTTTGAAAAGAA
Done.