Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014813.1 Kokia drynarioides strain JFW-HI SEQ_129855, 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: 228131
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:26167 original size:23 final size:23
Alignment explanation
Indices: 26141--26564 Score: 557
Period size: 23 Copynumber: 18.5 Consensus size: 23
26131 TTCATGGGTT
26141 TATTTACA-CATAAATCACATTAA
1 TATTTA-AGCATAAATCACATTAA
*
26164 TATTTAAACATAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
* *
26187 TATTTAAGCGTAAATCTCATTAA
1 TATTTAAGCATAAATCACATTAA
**
26210 TATTTAAGCATAAATCGTATTAA
1 TATTTAAGCATAAATCACATTAA
*
26233 CATTTAAGCATAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
*
26256 TATTTAAGCACAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
*
26279 TATTTAAGCTTAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
*
26302 TATTTAAGCACAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
* *
26325 TATTTAACCACAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
*
26348 TATTTAAGCACAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
*
26371 TATTTAAGCATAAATCACATTAG
1 TATTTAAGCATAAATCACATTAA
* * *
26394 CATTTAAGCATAAATCATATTAG
1 TATTTAAGCATAAATCACATTAA
*
26417 CATTTAAGCATAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
* * *
26440 TATTTAAGAATATATCATATTAA
1 TATTTAAGCATAAATCACATTAA
* * *
26463 CATTTAAGCACAAAACACATTAA
1 TATTTAAGCATAAATCACATTAA
*
26486 TATTTAAGCACAAATCACATTAA
1 TATTTAAGCATAAATCACATTAA
* *
26509 TATTTAAACATAAATCATATTAA
1 TATTTAAGCATAAATCACATTAA
* * *
26532 -AATTATGCATAAATCACGTTAA
1 TATTTAAGCATAAATCACATTAA
26554 TATTTAA-CATA
1 TATTTAAGCATA
26565 TTTAATGATA
Statistics
Matches: 354, Mismatches: 45, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
22 22 0.06
23 332 0.94
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (23 bp):
TATTTAAGCATAAATCACATTAA
Found at i:27012 original size:36 final size:36
Alignment explanation
Indices: 26954--27178 Score: 290
Period size: 36 Copynumber: 6.2 Consensus size: 36
26944 TTAGCACAAT
* * * *
26954 ATATTCACTGTCACATTACATGAATAACTTACCCAC
1 ATATTTACTGTCTCATGACATGAATAACATACCCAC
* *
26990 ATATTTATTGTCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGACATGAATAACATACCCAC
**
27026 ATATTTACTGTCAAATGACATGAATAACATACCCAC
1 ATATTTACTGTCTCATGACATGAATAACATACCCAC
* *
27062 ATATTTACTGTCTCATAACAAGAATAACATACCCAC
1 ATATTTACTGTCTCATGACATGAATAACATACCCAC
* * * *
27098 ACATTTACTATCACATGACATGAATGACATACCCAC
1 ATATTTACTGTCTCATGACATGAATAACATACCCAC
* *
27134 ATATTTACTATCTCAT-AGCATGAATAACATACCCAT
1 ATATTTACTGTCTCATGA-CATGAATAACATACCCAC
27170 ATATTTACT
1 ATATTTACT
27179 TTCACAGCAG
Statistics
Matches: 164, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
35 1 0.01
36 163 0.99
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (36 bp):
ATATTTACTGTCTCATGACATGAATAACATACCCAC
Found at i:27036 original size:72 final size:72
Alignment explanation
Indices: 26954--27184 Score: 336
Period size: 72 Copynumber: 3.2 Consensus size: 72
26944 TTAGCACAAT
* * * * *
26954 ATATTCACTGTCACATTACATGAATAACTTACCCACATATTTATTGTCTCATGGCATGAATAACA
1 ATATTTACTGTCACATGACATGAATAACATACCCACATATTTACTGTCTCATAGCATGAATAACA
27019 TACCCAC
66 TACCCAC
* * *
27026 ATATTTACTGTCAAATGACATGAATAACATACCCACATATTTACTGTCTCATAACAAGAATAACA
1 ATATTTACTGTCACATGACATGAATAACATACCCACATATTTACTGTCTCATAGCATGAATAACA
27091 TACCCAC
66 TACCCAC
* * * *
27098 ACATTTACTATCACATGACATGAATGACATACCCACATATTTACTATCTCATAGCATGAATAACA
1 ATATTTACTGTCACATGACATGAATAACATACCCACATATTTACTGTCTCATAGCATGAATAACA
*
27163 TACCCAT
66 TACCCAC
*
27170 ATATTTACTTTCACA
1 ATATTTACTGTCACA
27185 GCAGTCATCA
Statistics
Matches: 141, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 141 1.00
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (72 bp):
ATATTTACTGTCACATGACATGAATAACATACCCACATATTTACTGTCTCATAGCATGAATAACA
TACCCAC
Found at i:30938 original size:17 final size:17
Alignment explanation
Indices: 30913--30950 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
30903 AAAACAATCA
*
30913 AATACAATTAATAA-TAC
1 AATAAAATT-ATAATTAC
30930 AATAAAATTATAATTAC
1 AATAAAATTATAATTAC
30947 AATA
1 AATA
30951 TTAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAAAATTATAATTAC
Found at i:39521 original size:14 final size:15
Alignment explanation
Indices: 39502--39534 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39492 ACGCATTTCT
39502 TTATTT-ACTTTCAG
1 TTATTTCACTTTCAG
*
39516 TTATTTCACTTTTAG
1 TTATTTCACTTTCAG
39531 TTAT
1 TTAT
39535 GTTGTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (15 bp):
TTATTTCACTTTCAG
Found at i:41393 original size:18 final size:18
Alignment explanation
Indices: 41366--41400 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41356 ATATGAACAA
41366 GAGAAGGAGGAAGAAGAT
1 GAGAAGGAGGAAGAAGAT
* *
41384 GAGAATGAGGAGGAAGA
1 GAGAAGGAGGAAGAAGA
41401 AACAGAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.46, T:0.06
Consensus pattern (18 bp):
GAGAAGGAGGAAGAAGAT
Found at i:43771 original size:81 final size:81
Alignment explanation
Indices: 43660--44125 Score: 616
Period size: 81 Copynumber: 5.8 Consensus size: 81
43650 TAACAAGTGG
* * *
43660 GTTAGGGTAAAAGATTGGATGGCTTTAATCTGCCCTATGGTCATGGTAAGAGATTGGATGGTGTC
1 GTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGTC
*
43725 TTCAATCTACCTTCTA
66 TTCAATCTGCCTTCTA
* * *
43741 GTTAGGGTAAAAGATCGGATGCCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTAGATGGTGTC
1 GTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGTC
* *
43806 TTCAATTTGCCCTCT-
66 TTCAATCTGCCTTCTA
*** * * *
43821 GATTAGGGTAAAAGATTGGATTATTTCAATCTACCCCATGGTTAGGGTAAGAAATTGGATGGTGT
1 G-TTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGT
*
43886 CTTCAATCTGCCTTCTG
65 CTTCAATCTGCCTTCTA
* **
43903 GTTAGGGTAAAAGATTGGATGGCTTTAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGTGTC
1 GTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGTC
* *
43968 TTCAATCTGCCTTTTT
66 TTCAATCTGCCTTCTA
* *
43984 TTTAAGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTC-GAGGTAAGAGATTGGATGGTGT
1 GTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTCAG-GGTAAGAGATTGGATGGTGT
*
44048 CTTCAATCTGCCCTCTA
65 CTTCAATCTGCCTTCTA
* * * *
44065 GCTA-GGTAAAATATTGGATGTTCTTCAATTTGCCCCATGGTC-GAGGTAAGAGATTGGATGG
1 GTTAGGGTAAAAGATTGGATG-GCTTCAATCTGCCCCATGGTCAG-GGTAAGAGATTGGATGG
44126 GATGATGTAA
Statistics
Matches: 341, Mismatches: 40, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
80 17 0.05
81 323 0.95
82 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (81 bp):
GTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGTC
TTCAATCTGCCTTCTA
Found at i:44103 original size:243 final size:243
Alignment explanation
Indices: 43659--44125 Score: 683
Period size: 243 Copynumber: 1.9 Consensus size: 243
43649 TTAACAAGTG
* *
43659 GGTTAGGGTAAAAGATTGGATGGCTTTAATCTGCCCTATGGTCATGGTAAGAGATTGGATGGTGT
1 GGTTAGGGTAAAAGATTGGATGGCTTTAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGT
*
43724 CTTCAATCTACCTTCTAGTTAGGGTAAAAGATCGGATGCCTTCAATCTGCCCCATGGTCAGGGTA
66 CTTCAATCTACCTTCTAGTTAAGGTAAAAGATCGGATGCCTTCAATCTGCCCCATGGTCAGGGTA
* *
43789 AGAGATTAGATGGTGTCTTCAATTTGCCCTCTGATTAGGGTAAAAGATTGGATTATTTCAATCTA
131 AGAGATTAGATGGTGTCTTCAATCTGCCCTCTGACTAGGGTAAAAGATTGGATTATTTCAATCTA
43854 CCCCATGGTTAG-GGTAAGAAATTGGATGGTGTCTTCAATCTGCCTTCT
196 CCCCATGG-TAGAGGTAAGAAATTGGATGGTGTCTTCAATCTGCCTTCT
**
43902 GGTTAGGGTAAAAGATTGGATGGCTTTAATCTGCCCCATGGTTGGGGTAAGAGATTGGATGGTGT
1 GGTTAGGGTAAAAGATTGGATGGCTTTAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGT
* * ** * *
43967 CTTCAATCTGCCTTTTTTTTAAGGTAAAAGATTGGATGGCTTCAATCTGCCCCATGGTC-GAGGT
66 CTTCAATCTACCTTCTAGTTAAGGTAAAAGATCGGATGCCTTCAATCTGCCCCATGGTCAG-GGT
* *
44031 AAGAGATTGGATGGTGTCTTCAATCTGCCCTCT-AGCTA-GGTAAAATATTGGATGT-TCTTCAA
130 AAGAGATTAGATGGTGTCTTCAATCTGCCCTCTGA-CTAGGGTAAAAGATTGGAT-TAT-TTCAA
* * * *
44093 TTTGCCCCATGGTCGAGGTAAGAGATTGGATGG
192 TCTACCCCATGGTAGAGGTAAGAAATTGGATGG
44126 GATGATGTAA
Statistics
Matches: 200, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
242 19 0.09
243 181 0.90
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (243 bp):
GGTTAGGGTAAAAGATTGGATGGCTTTAATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGT
CTTCAATCTACCTTCTAGTTAAGGTAAAAGATCGGATGCCTTCAATCTGCCCCATGGTCAGGGTA
AGAGATTAGATGGTGTCTTCAATCTGCCCTCTGACTAGGGTAAAAGATTGGATTATTTCAATCTA
CCCCATGGTAGAGGTAAGAAATTGGATGGTGTCTTCAATCTGCCTTCT
Found at i:44464 original size:49 final size:49
Alignment explanation
Indices: 44404--44909 Score: 330
Period size: 49 Copynumber: 10.3 Consensus size: 49
44394 CGTTCTTTAG
* * *
44404 TTTTAAGGTGTTAGATCTGCTATTACGGCTTTAATCTATCCCTCTTCAA
1 TTTTAAGGTGTTAGATCTACTGTTACGGCTTCAATCTATCCCTCTTCAA
* * * * * ***
44453 TTTTAAGGTGTTA-AGTCTACCGTAACGACTTTAACCTATCCCTCTTTGG
1 TTTTAAGGTGTTAGA-TCTACTGTTACGGCTTCAATCTATCCCTCTTCAA
* * * * * *
44502 TTTTAAGGTGTAAGAT-T-CATCATTACGACTTCAATCTTTCTCTCTTCGA
1 TTTTAAGGTGTTAGATCTAC-T-GTTACGGCTTCAATCTATCCCTCTTCAA
* * * * * *
44551 TTTTAA-GTGTTAGGT-T-CGTCGTTGCGGCTTTAACCTATCCCTCTTTAG
1 TTTTAAGGTGTTAGATCTAC-T-GTTACGGCTTCAATCTATCCCTCTTCAA
** * * * * *
44599 TTTTAAGGTGGAAAATCTACCGTTGCGGCTTCAATCTTTCCCTCCTCAA
1 TTTTAAGGTGTTAGATCTACTGTTACGGCTTCAATCTATCCCTCTTCAA
* * *
44648 TTTTAGGGTGTTAAATCTA-TCGTTACGGCTTCAATCAATCCCTCTTCAA
1 TTTTAAGGTGTTAGATCTACT-GTTACGGCTTCAATCTATCCCTCTTCAA
* * * * * * * *
44697 TTTTAAGGTGTAAGATCCATTGTTACAGCTTTAATCTTTCCCTCTCCAG
1 TTTTAAGGTGTTAGATCTACTGTTACGGCTTCAATCTATCCCTCTTCAA
* * ** *
44746 TTTTAGGGTGTTAGATCCAC-GATTATAGATTCAATCTATCCCTCTTCAA
1 TTTTAAGGTGTTAGATCTACTG-TTACGGCTTCAATCTATCCCTCTTCAA
** * * ** *
44795 TTTTTGGGTGTTAGGTCT-GTCGTTGTGGCTTCAATCTATCCCTCTTCGA
1 TTTTAAGGTGTTAGATCTACT-GTTACGGCTTCAATCTATCCCTCTTCAA
* * ** *
44844 TTTAAAGGTGTTAGGTCCGCTGTTACGGCTTTAA-CTTATCCCTCTTCAA
1 TTTTAAGGTGTTAGATCTACTGTTACGGCTTCAATC-TATCCCTCTTCAA
*
44893 TTTTAAGGTGTAAGATC
1 TTTTAAGGTGTTAGATC
44910 CGTCGTTGCA
Statistics
Matches: 353, Mismatches: 90, Indels: 28
0.75 0.19 0.06
Matches are distributed among these distances:
47 1 0.00
48 39 0.11
49 307 0.87
50 5 0.01
51 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (49 bp):
TTTTAAGGTGTTAGATCTACTGTTACGGCTTCAATCTATCCCTCTTCAA
Found at i:44926 original size:147 final size:145
Alignment explanation
Indices: 44404--44988 Score: 462
Period size: 147 Copynumber: 4.0 Consensus size: 145
44394 CGTTCTTTAG
* * * *
44404 TTTTAAGGTGTTAGATCTGCTATTACGGCTTTAA-TCTATCCCTCTTCAATTTTAAGGTGTTAAG
1 TTTTAAGGTGTTAGGTCCG-TGTTACGGCTTTAACT-TATCCCTCTTCAGTTTTAAGGTG-TAAG
* ** * * * * *** * * * * * *
44468 -TCTACCGTAACGACTTTAACCTATCCCTCTTTGGTTTTAAGGTGTAAGAT-TCATCATTACGAC
63 ATCCA-CGTTGCAACTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCT-GTCGTTACGGC
* *
44531 TTCAATCTTTCTCTCTTCGA
126 TTCAATCTATCCCTCTTCGA
* * * * * *
44551 TTTTAA-GTGTTAGGTTCGTCGTTGCGGCTTTAACCTATCCCTCTTTAGTTTTAAGGTGGAAAAT
1 TTTTAAGGTGTTAGGTCCGT-GTTACGGCTTTAACTTATCCCTCTTCAGTTTTAAGGTGTAAGAT
* ** * ** *
44615 CTACCGTTGCGGCTTCAATCTTTCCCTCCTCAATTTTAGGGTGTTAAATCTATCGTTACGGCTTC
65 CCA-CGTTGCAACTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCTGTCGTTACGGCTTC
* *
44680 AATCAATCCCTCTTCAA
129 AATCTATCCCTCTTCGA
* * * * * * *
44697 TTTTAAGGTGTAAGATCCATTGTTACAGCTTTAATCTT-TCCCTCTCCAGTTTTAGGGTGTTAGA
1 TTTTAAGGTGTTAGGTCC-GTGTTACGGCTTTAA-CTTATCCCTCTTCAGTTTTAAGGTGTAAGA
** * * **
44761 TCCACGATTATAGA-TTCAATCTATCCCTCTTCAATTTTTGGGTGTTAGGTCTGTCGTTGTGGCT
64 TCCACG-TTGCA-ACTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCTGTCGTTACGGCT
44825 TCAATCTATCCCTCTTCGA
127 TCAATCTATCCCTCTTCGA
* *
44844 TTTAAAGGTGTTAGGTCCGCTGTTACGGCTTTAACTTATCCCTCTTCAATTTTAAGGTGTAAGAT
1 TTTTAAGGTGTTAGGTCCG-TGTTACGGCTTTAACTTATCCCTCTTCAGTTTTAAGGTGTAAGAT
* * * ** * * *
44909 CCGTCGTTGCAACTTCAATCTTTTCATCTTTGATTTTAGGGTGTTAGGTCCGCCATTACGGCTTC
65 CC-ACGTTGCAACTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCTGTCGTTACGGCTTC
*
44974 AACCTATCCCTCTTC
129 AATCTATCCCTCTTC
44989 AACTCTAGGA
Statistics
Matches: 344, Mismatches: 81, Indels: 26
0.76 0.18 0.06
Matches are distributed among these distances:
145 3 0.01
146 115 0.33
147 221 0.64
148 5 0.01
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (145 bp):
TTTTAAGGTGTTAGGTCCGTGTTACGGCTTTAACTTATCCCTCTTCAGTTTTAAGGTGTAAGATC
CACGTTGCAACTTCAATCTTTCCCTCTTCAATTTTAGGGTGTTAGGTCTGTCGTTACGGCTTCAA
TCTATCCCTCTTCGA
Found at i:44988 original size:98 final size:98
Alignment explanation
Indices: 44429--44990 Score: 464
Period size: 98 Copynumber: 5.7 Consensus size: 98
44419 TCTGCTATTA
* * * * * ** * * *
44429 CGGCTTTAATCTATCCCTCTTCAATTTTAAGGTGTTAAGTCTACCGTAACGACTTTAACCTATCC
1 CGGCTTCAATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGCCGTTACGGCTTCAACCTATCC
*** * * *
44494 CTCTTTGGTTTTAAGGTGTAAGATTCATCATTA
66 CTCTTCAATTTTAAGGTGTAAGATCCATCGTTG
* * * * * * *
44527 CGACTTCAATCTTTCTCTCTTCGATTTTA-AGTGTTAGGTTCGTCGTTGCGGCTTTAACCTATCC
1 CGGCTTCAATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGCCGTTACGGCTTCAACCTATCC
* * * * * *
44591 CTCTTTAGTTTTAAGGTGGAAAATCTACCGTTG
66 CTCTTCAATTTTAAGGTGTAAGATCCATCGTTG
* * ** *** * *
44624 CGGCTTCAATCTTTCCCTCCTCAATTTTAGGGTGTTAAATCTATCGTTACGGCTTCAATCAATCC
1 CGGCTTCAATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGCCGTTACGGCTTCAACCTATCC
* *
44689 CTCTTCAATTTTAAGGTGTAAGATCCATTGTTA
66 CTCTTCAATTTTAAGGTGTAAGATCCATCGTTG
* * * * * ** * *
44722 CAGCTTTAATCTTTCCCTC-TCCAGTTTTAGGGTGTTAGATCC-ACGATTATAGATTCAATCTAT
1 CGGCTTCAATCTTTCCCTCTTCGA-TTTTAGGGTGTTAGGTCCGCCG-TTACGGCTTCAACCTAT
** * * **
44785 CCCTCTTCAATTTTTGGGTGTTAGGTCTGTCGTTG
64 CCCTCTTCAATTTTAAGGTGTAAGATCCATCGTTG
* * * * * * *
44820 TGGCTTCAATCTATCCCTCTTCGATTTAAAGGTGTTAGGTCCGCTGTTACGGCTTTAACTTATCC
1 CGGCTTCAATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGCCGTTACGGCTTCAACCTATCC
*
44885 CTCTTCAATTTTAAGGTGTAAGATCCGTCGTTG
66 CTCTTCAATTTTAAGGTGTAAGATCCATCGTTG
** * * * *
44918 CAACTTCAATCTTTTCATCTTTGATTTTAGGGTGTTAGGTCCGCCATTACGGCTTCAACCTATCC
1 CGGCTTCAATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGCCGTTACGGCTTCAACCTATCC
44983 CTCTTCAA
66 CTCTTCAA
44991 CTCTAGGATT
Statistics
Matches: 363, Mismatches: 96, Indels: 10
0.77 0.20 0.02
Matches are distributed among these distances:
97 81 0.22
98 278 0.77
99 4 0.01
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (98 bp):
CGGCTTCAATCTTTCCCTCTTCGATTTTAGGGTGTTAGGTCCGCCGTTACGGCTTCAACCTATCC
CTCTTCAATTTTAAGGTGTAAGATCCATCGTTG
Found at i:46048 original size:6 final size:6
Alignment explanation
Indices: 46037--46103 Score: 63
Period size: 6 Copynumber: 11.8 Consensus size: 6
46027 ACCCCTTCTT
* *
46037 TTTTTC TTTTTC TTTTT- TCTCTC TTTTTC TTTTTC -TTTTC -TTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
46082 TTTTAT- TTTAT- TTTTTC TTTTT
1 TTTT-TC TTTTTC TTTTTC TTTTT
46104 GCAAGTTTGA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 18 0.35
6 32 0.63
7 1 0.02
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:46078 original size:17 final size:16
Alignment explanation
Indices: 46035--46103 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 16
46025 CGACCCCTTC
46035 TTTTTTTCTTTTTCTT
1 TTTTTTTCTTTTTCTT
*
46051 TTTTCTCTCTTTTTCTT
1 TTTT-TTTCTTTTTCTT
46068 TTTCTTTTC-TTTTCTT
1 TTT-TTTTCTTTTTCTT
46084 TTATTTTAT-TTTTTCTT
1 TT-TTTT-TCTTTTTCTT
46101 TTT
1 TTT
46104 GCAAGTTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
16 17 0.37
17 28 0.61
18 1 0.02
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTCTTTTTCTT
Found at i:70238 original size:17 final size:17
Alignment explanation
Indices: 70166--70238 Score: 56
Period size: 17 Copynumber: 4.3 Consensus size: 17
70156 CTGTTAGTAA
*
70166 TCATTGTCACTACATTC
1 TCATTGTCACTACATTT
* * * *
70183 CCTTTGTCATTGCATTT
1 TCATTGTCACTACATTT
* * *
70200 TAATTGTCACAACATAT
1 TCATTGTCACTACATTT
* *
70217 GCATTGTCATTACATTT
1 TCATTGTCACTACATTT
70234 TCATT
1 TCATT
70239 TGTTATTGTA
Statistics
Matches: 38, Mismatches: 18, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (17 bp):
TCATTGTCACTACATTT
Found at i:74073 original size:22 final size:22
Alignment explanation
Indices: 74045--74090 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
74035 TAACATCGAG
74045 TAAATATGATAGATCCCCATAC
1 TAAATATGATAGATCCCCATAC
74067 TAAATATGATAGATCCCCATAC
1 TAAATATGATAGATCCCCATAC
74089 TA
1 TA
74091 CAGTAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (22 bp):
TAAATATGATAGATCCCCATAC
Found at i:75703 original size:18 final size:18
Alignment explanation
Indices: 75672--75706 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
75662 AACACAATAA
* *
75672 AAATATAATTACAATATT
1 AAATAAAATAACAATATT
75690 AAATAAAATAACAATAT
1 AAATAAAATAACAATAT
75707 AATCATAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAAAATAACAATATT
Found at i:76425 original size:23 final size:25
Alignment explanation
Indices: 76391--76445 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
76381 CTCAAACAAA
*
76391 AAAAAAATTCTCTAAAT-GTATTTT
1 AAAAAAATTCTCTAAATCGTATTTC
* *
76415 AAAAAAA-TCTCTGAATCTTATTTC
1 AAAAAAATTCTCTAAATCGTATTTC
76439 AAAAAAA
1 AAAAAAA
76446 AAAATCCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.35
Consensus pattern (25 bp):
AAAAAAATTCTCTAAATCGTATTTC
Found at i:82417 original size:38 final size:38
Alignment explanation
Indices: 82374--82711 Score: 354
Period size: 38 Copynumber: 8.9 Consensus size: 38
82364 ACACTGACAA
**
82374 GAAGCCTATTAGGCA-TAAAGCCCGATAAACACCGGCAC
1 GAAGCCTGCTAGGCACT-AAGCCCGATAAACACCGGCAC
* * * * *
82412 AAAGCCTGTTAGGCACTAAGCCCGATGAACACCGACAT
1 GAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCAC
* * *
82450 GAAGCTTGCTAGGCACTAAGCCCAATAAACACTGGCAC
1 GAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCAC
* * * *
82488 GAAGCCTGTTAGGCATTAAGCCCGATAAACAACGACAC
1 GAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCAC
* * * *
82526 GAAGTCTGCTAGGCACTAAGCTCGATAAACATCGACAC
1 GAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCAC
* * * ** *
82564 CAAGCCTTCTAGGCACTAAGCTCGATAAACATTGGCAT
1 GAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCAC
* * * *
82602 GAAGCCCGCTAGGCACTAAGCTCGATAAAAACCAGCAC
1 GAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCAC
* * *
82640 GAACCCTGCTAGGCATTAAGCCTGATAAACACCGGCAC
1 GAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCAC
* * *
82678 AAAGCTTGCTAGGCACTAAGCCTGATAAACACCG
1 GAAGCCTGCTAGGCACTAAGCCCGATAAACACCG
82712 CATACAACTA
Statistics
Matches: 249, Mismatches: 50, Indels: 2
0.83 0.17 0.01
Matches are distributed among these distances:
38 248 1.00
39 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (38 bp):
GAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCAC
Found at i:83275 original size:18 final size:18
Alignment explanation
Indices: 83252--83288 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
83242 ACCATCACCT
83252 ACATGAATACATCAACTA
1 ACATGAATACATCAACTA
*
83270 ACATGAATATATCAACTA
1 ACATGAATACATCAACTA
83288 A
1 A
83289 GAACAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.24
Consensus pattern (18 bp):
ACATGAATACATCAACTA
Found at i:100217 original size:4 final size:4
Alignment explanation
Indices: 100202--100247 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
100192 AAGCATGATT
100202 TGTA TG-A TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
100248 CATATGACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.07
4 38 0.93
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:104052 original size:165 final size:165
Alignment explanation
Indices: 103857--104187 Score: 644
Period size: 165 Copynumber: 2.0 Consensus size: 165
103847 AATAAATCTA
103857 AATAAAAAACTTAATTAAACTAGAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
1 AATAAAAAACTTAATTAAACTAGAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
103922 TTCTTGTTGACATAAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
66 TTCTTGTTGACATAAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
103987 AATAACAATAAAATAATAAGAGCTGATAATACAAT
131 AATAACAATAAAATAATAAGAGCTGATAATACAAT
**
104022 AATAAAACTCTTAATTAAACTAGAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
1 AATAAAAAACTTAATTAAACTAGAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
104087 TTCTTGTTGACATAAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
66 TTCTTGTTGACATAAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
104152 AATAACAATAAAATAATAAGAGCTGATAATACAAT
131 AATAACAATAAAATAATAAGAGCTGATAATACAAT
104187 A
1 A
104188 TTGGGCTCAT
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 164 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (165 bp):
AATAAAAAACTTAATTAAACTAGAACTCTAACTAATCTAAACAAGAAGTAGTTTTAAACTAAACT
TTCTTGTTGACATAAAACTCCTAAAAACTTAAACTACTTAATAATTATTCAAAATTCGGAATAAA
AATAACAATAAAATAATAAGAGCTGATAATACAAT
Found at i:105139 original size:13 final size:14
Alignment explanation
Indices: 105110--105139 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
105100 TTCAATACAT
105110 TGACATTTAACCTC
1 TGACATTTAACCTC
105124 TGACATTTAA-CTC
1 TGACATTTAACCTC
105137 TGA
1 TGA
105140 TTGTGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:110613 original size:172 final size:173
Alignment explanation
Indices: 110282--110624 Score: 607
Period size: 172 Copynumber: 2.0 Consensus size: 173
110272 TTGCAGTCAG
*
110282 ATTTAGCATTACGACTTGTGAAGTCAGTGATCCTCTCCACTTCTTTACACTTAATCCATTTATTT
1 ATTTAGCATTACGACTTGTAAAGTCAGTGATCCTCTCCACTTCTTTACACTTAATCCATTTATTT
*
110347 TAAGTTTTTGAATTTACTTTTCAACATCTCAACAAACCATTCATTTTCTATATTTTGCTCTGACA
66 TAAGTTTTTAAATTTACTTTTCAACATCTCAACAAACCATTCATTTTCTATATTTTGCTCTGACA
* * *
110412 TTTAACATTCTGATTGCATTGATAGATTTACTTCTTAACTTAT
131 TTTAACATTCTAATTGCACTGACAGATTTACTTCTTAACTTAT
* *
110455 ATTTAGCATTGCGACTTGTAAAGTCAGTGATCCTCTCCACTTCTTTACACTTGATCCATTTATTT
1 ATTTAGCATTACGACTTGTAAAGTCAGTGATCCTCTCCACTTCTTTACACTTAATCCATTTATTT
110520 TAAG-TTTTAAATTTACTTTTCAACATCTCAACAAACCATTCATTTTCTATATTTTGCTCTGACA
66 TAAGTTTTTAAATTTACTTTTCAACATCTCAACAAACCATTCATTTTCTATATTTTGCTCTGACA
*
110584 TTTAACATTCTAATTGCGCTGACAGATTTACTTCTTAACTT
131 TTTAACATTCTAATTGCACTGACAGATTTACTTCTTAACTT
110625 GTATAATTTT
Statistics
Matches: 162, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
172 96 0.59
173 66 0.41
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (173 bp):
ATTTAGCATTACGACTTGTAAAGTCAGTGATCCTCTCCACTTCTTTACACTTAATCCATTTATTT
TAAGTTTTTAAATTTACTTTTCAACATCTCAACAAACCATTCATTTTCTATATTTTGCTCTGACA
TTTAACATTCTAATTGCACTGACAGATTTACTTCTTAACTTAT
Found at i:128369 original size:12 final size:12
Alignment explanation
Indices: 128352--128391 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
128342 CTCTTCAACT
*
128352 TCTTTTCCTTCC
1 TCTTTTTCTTCC
128364 TCTTTTTCTTCC
1 TCTTTTTCTTCC
*
128376 TCTTTTTCTTTC
1 TCTTTTTCTTCC
128388 TCTT
1 TCTT
128392 CTTTTACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTTTTTCTTCC
Found at i:136999 original size:26 final size:26
Alignment explanation
Indices: 136970--137048 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
136960 AGACATGCTT
136970 ATGCAGCGACAATTCTGGACATATTC
1 ATGCAGCGACAATTCTGGACATATTC
* * * *
136996 ATGCAGTGATAATT-TTGA-GTAGGTTC
1 ATGCAGCGACAATTCTGGACATA--TTC
* *
137022 TTGCAGCGACAATTCTGTACATATTC
1 ATGCAGCGACAATTCTGGACATATTC
137048 A
1 A
137049 CACAACGATA
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
24 2 0.05
25 3 0.08
26 29 0.76
27 2 0.05
28 2 0.05
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (26 bp):
ATGCAGCGACAATTCTGGACATATTC
Found at i:137027 original size:52 final size:52
Alignment explanation
Indices: 136971--137091 Score: 161
Period size: 52 Copynumber: 2.3 Consensus size: 52
136961 GACATGCTTA
** ** *
136971 TGCAGCGACAATTCTGGACATATTCATGCAGTGATAATTTTGAGTAGGTTCT
1 TGCAGCGACAATTCTGGACATATTCACACAACGATAATTCTGAGTAGGTTCT
*
137023 TGCAGCGACAATTCTGTACATATTCACACAACGATAATTCTGAGTAGGTTCT
1 TGCAGCGACAATTCTGGACATATTCACACAACGATAATTCTGAGTAGGTTCT
** *
137075 TGTGGCAACAATTCTGG
1 TGCAGCGACAATTCTGG
137092 GTGCAATGCT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (52 bp):
TGCAGCGACAATTCTGGACATATTCACACAACGATAATTCTGAGTAGGTTCT
Found at i:142363 original size:14 final size:15
Alignment explanation
Indices: 142332--142365 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
142322 TACATTTTTC
*
142332 TTTATTTGTTTCACT
1 TTTACTTGTTTCACT
*
142347 TTTACTTGTTTCATT
1 TTTACTTGTTTCACT
142362 TTTA
1 TTTA
142366 AATTTTATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTACTTGTTTCACT
Found at i:148628 original size:24 final size:26
Alignment explanation
Indices: 148600--148657 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 26
148590 CATTACAATT
* *
148600 TTTTATATTTACTTT-TTGTCTTTTG
1 TTTTATATTTAATTTGTTGTCTTTAG
* *
148625 -TTTATTTTTAATTTGTTTTCTTTAG
1 TTTTATATTTAATTTGTTGTCTTTAG
148650 TTTTATAT
1 TTTTATAT
148658 AAGAATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 12 0.46
25 8 0.31
26 6 0.23
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (26 bp):
TTTTATATTTAATTTGTTGTCTTTAG
Found at i:150427 original size:21 final size:18
Alignment explanation
Indices: 150401--150451 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
150391 TGAGGCAGAG
150401 GAAAAAGTAAGAAAAGAAGAA
1 GAAAAAG-AAGAAAAG--GAA
*
150422 GAAAAAGAAGAGAAGGAA
1 GAAAAAGAAGAAAAGGAA
150440 GAAAAAGAAGAA
1 GAAAAAGAAGAA
150452 GATGTTGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 14 0.50
20 7 0.25
21 7 0.25
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAGAAAAGGAA
Found at i:150429 original size:9 final size:9
Alignment explanation
Indices: 150401--150451 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
150391 TGAGGCAGAG
150401 GAAAAAGTAA
1 GAAAAAG-AA
150411 GAAAAGAAGAA
1 G-AAA-AAGAA
150422 GAAAAAGAA
1 GAAAAAGAA
* *
150431 GAGAAGGAA
1 GAAAAAGAA
150440 GAAAAAGAA
1 GAAAAAGAA
150449 GAA
1 GAA
150452 GATGTTGCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 22 0.63
10 4 0.11
11 6 0.17
12 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (9 bp):
GAAAAAGAA
Found at i:153124 original size:24 final size:24
Alignment explanation
Indices: 153079--153133 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
153069 ACAATCAATT
*
153079 CATTTTATATTACAGTTGCACTAA
1 CATTTTATATTACAGTTACACTAA
* * *
153103 CATTTTGTATTACATTTACACTGA
1 CATTTTATATTACAGTTACACTAA
153127 CAGTTTT
1 CA-TTTT
153134 TACTCTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 22 0.85
25 4 0.15
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.45
Consensus pattern (24 bp):
CATTTTATATTACAGTTACACTAA
Found at i:156589 original size:9 final size:9
Alignment explanation
Indices: 156575--156607 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
156565 ACCTGCTCTA
156575 AATGTTTCT
1 AATGTTTCT
156584 AATGTTTCT
1 AATGTTTCT
156593 AATGTTTCT
1 AATGTTTCT
156602 AATGTT
1 AATGTT
156608 AATGCTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (9 bp):
AATGTTTCT
Found at i:156986 original size:11 final size:12
Alignment explanation
Indices: 156970--156998 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
156960 AAAGCTCAAT
156970 TGGATGATACA-
1 TGGATGATACAG
156981 TGGATGATACAG
1 TGGATGATACAG
156993 TGGATG
1 TGGATG
156999 CAAGAATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.31, C:0.07, G:0.34, T:0.28
Consensus pattern (12 bp):
TGGATGATACAG
Found at i:165550 original size:31 final size:27
Alignment explanation
Indices: 165485--165552 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 27
165475 AAATTTCAAT
165485 AAATAAAAAATATATAAAATTATTAAA
1 AAATAAAAAATATATAAAATTATTAAA
* * *
165512 TATTAAAATAATATAATATAAATATTTTAAA
1 AAATAAAA-AATAT-ATA-AAAT-TATTAAA
165543 AAATAAAAAA
1 AAATAAAAAA
165553 AAATATGAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 6 0.19
28 5 0.16
29 3 0.09
30 6 0.19
31 12 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATAAAAAATATATAAAATTATTAAA
Found at i:165963 original size:5 final size:5
Alignment explanation
Indices: 165949--165982 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
165939 AACAACTAGA
* *
165949 TTTTC CTTTC TTTTC TTTTT TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
165983 TAAAGTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:165973 original size:15 final size:15
Alignment explanation
Indices: 165955--165983 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
165945 TAGATTTTCC
165955 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
165970 TTTCTTTTCTTTTT
1 TTTCTTTTCTTTTT
165984 AAAGTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:167150 original size:29 final size:29
Alignment explanation
Indices: 167090--167151 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
167080 TTAAATTTTA
*
167090 AAAATATAGAAACTAAAATCCTAAAATTT
1 AAAATATAGAAACTAAAATCCTAAAATAT
* *
167119 AAAATATAGAAA-TTAAATTCTAAACATAT
1 AAAATATAGAAACTAAAATCCTAAA-ATAT
167148 AAAA
1 AAAA
167152 AGTTTTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.27
Consensus pattern (29 bp):
AAAATATAGAAACTAAAATCCTAAAATAT
Found at i:167965 original size:116 final size:117
Alignment explanation
Indices: 167826--168057 Score: 412
Period size: 117 Copynumber: 2.0 Consensus size: 117
167816 TTTAAATAAA
* *
167826 AGTAAAGTTGAACAAATTGATAAAATCAAGTTAAAATGGTTTCAATT-GGTCAAATATTTTTAAA
1 AGTAAAGTTGAACAAATTGATAAAATCAAGTTAAAATGGTTTCAATTGGGGCAAATATTCTTAAA
*
167890 TATGTTTTAACCATTTTCAAATAAGTTAAAATTACTCCAGGACAAAAAGTAC
66 TATGTTTTAACCATTTTCAAACAAGTTAAAATTACTCCAGGACAAAAAGTAC
*
167942 AGTAAAGTTGAACAAATTGATAAAATCAATTTAAAATGGTTTCAATTGGGGCAAATATTCTTAAA
1 AGTAAAGTTGAACAAATTGATAAAATCAAGTTAAAATGGTTTCAATTGGGGCAAATATTCTTAAA
*
168007 TATGTTTTAACCATTTTCAAACAAGTTAGAATTACTCCAGGACAAAAAGTA
66 TATGTTTTAACCATTTTCAAACAAGTTAAAATTACTCCAGGACAAAAAGTA
168058 TCGGTACTTT
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
116 46 0.42
117 64 0.58
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (117 bp):
AGTAAAGTTGAACAAATTGATAAAATCAAGTTAAAATGGTTTCAATTGGGGCAAATATTCTTAAA
TATGTTTTAACCATTTTCAAACAAGTTAAAATTACTCCAGGACAAAAAGTAC
Found at i:176141 original size:21 final size:21
Alignment explanation
Indices: 176115--176160 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
176105 AGAGTTTTTA
* * *
176115 GTATCGGTAGTATCATGGCTT
1 GTATCGGTAGAAGCATGACTT
176136 GTATCGGTAGAAGCATGACTT
1 GTATCGGTAGAAGCATGACTT
176157 GTAT
1 GTAT
176161 TAGTAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACTT
Found at i:176166 original size:21 final size:21
Alignment explanation
Indices: 176128--176168 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
176118 TCGGTAGTAT
* *
176128 CATGGCTTGTATCGGTAGAAG
1 CATGACTTGTATCAGTAGAAG
*
176149 CATGACTTGTATTAGTAGAA
1 CATGACTTGTATCAGTAGAA
176169 TTACCTCAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (21 bp):
CATGACTTGTATCAGTAGAAG
Found at i:178588 original size:25 final size:25
Alignment explanation
Indices: 178554--178608 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
178544 AGAAATGTGA
* *
178554 GGTGATTTTTAGTAGGCTTCGAGAC
1 GGTGATTTTTAGCAAGCTTCGAGAC
* *
178579 GGTGATTTTTAGCAAGCTTTGAGCC
1 GGTGATTTTTAGCAAGCTTCGAGAC
178604 GGTGA
1 GGTGA
178609 ATGTTTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.35
Consensus pattern (25 bp):
GGTGATTTTTAGCAAGCTTCGAGAC
Found at i:185729 original size:198 final size:197
Alignment explanation
Indices: 185390--185979 Score: 957
Period size: 198 Copynumber: 3.0 Consensus size: 197
185380 AATGTAGAAT
*
185390 ACCTTTGTATTGGTCAGAGTTGAGCGAGCCTAAGTTGGTTGGAACTGACTTGATTCATGAGACCG
1 ACCTTTGTATTGGTCAGAGTTGAGCGAGCCTAAGTTGGTTGGAACCGACTTGATTCATGAGACCG
* * *
185455 AAGACAAAGTGCGGGTGATCCGCGATTGCTTGAAAGCAGCGTCTGACCGGTAAAAGTTGGTAGAA
66 AAGACAAAGTGC-GGTGATCCGCGACTGCTTGAAAGCAGCGTCTGACCGGCAAAAGTTGGAAGAA
* * *
185520 AGTGCTAAGGTTTGGTAAAAAAGGAAAGTTGAGTCCACGGTTTATCGAGCCGTATGAGATCATTA
130 GGTGCTAAGGTTTGGTAGAAAAGGAAAGTTGAGTCCACGGTTTATCGGGCCGTATGAGATCATTA
185585 AAC
195 AAC
185588 ACCTTTGTATTGGTCAGAGTTGAGCGAGCCTAAGTTGGTTGGAACCGACTTGATTCATGAGACCG
1 ACCTTTGTATTGGTCAGAGTTGAGCGAGCCTAAGTTGGTTGGAACCGACTTGATTCATGAGACCG
* * *
185653 AAGACAAAGTGCAGGTGATCCGCGACTGATTGAAAGCAACGTCTGACCGGCAAAAGTTGGCAGAA
66 AAGACAAAGTGC-GGTGATCCGCGACTGCTTGAAAGCAGCGTCTGACCGGCAAAAGTTGGAAGAA
* * *
185718 GGTGATAAGGTTTGGTAGAAAAGGAAAGCTT-AGTCAACAGTTTATCGGGCCGTATGAGATCATT
130 GGTGCTAAGGTTTGGTAGAAAAGGAAAG-TTGAGTCCACGGTTTATCGGGCCGTATGAGATCATT
185782 AAAC
194 AAAC
*
185786 ACCTTTGTATTGGTCAGAGTTGAGCGAGCCTAAGTTGATTGGAACCGACTTGATTCATGAGACCG
1 ACCTTTGTATTGGTCAGAGTTGAGCGAGCCTAAGTTGGTTGGAACCGACTTGATTCATGAGACCG
* * * * *
185851 AAGATAAAGTGCGAGTTATCTGCGACTGCTTGAAAGTAGCGTCTGACCGACAAAAGTTGGAAGAA
66 AAGACAAAGTGCG-GTGATCCGCGACTGCTTGAAAGCAGCGTCTGACCGGCAAAAGTTGGAAGAA
*
185916 GGTGCTAAGGTTTGGTAGAAAAGGAAAGTTGAGTCCATGGTTTATCGGGCCGTATGAGATCATT
130 GGTGCTAAGGTTTGGTAGAAAAGGAAAGTTGAGTCCACGGTTTATCGGGCCGTATGAGATCATT
185980 GAATAGGTTG
Statistics
Matches: 363, Mismatches: 26, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
197 3 0.01
198 358 0.99
199 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (197 bp):
ACCTTTGTATTGGTCAGAGTTGAGCGAGCCTAAGTTGGTTGGAACCGACTTGATTCATGAGACCG
AAGACAAAGTGCGGTGATCCGCGACTGCTTGAAAGCAGCGTCTGACCGGCAAAAGTTGGAAGAAG
GTGCTAAGGTTTGGTAGAAAAGGAAAGTTGAGTCCACGGTTTATCGGGCCGTATGAGATCATTAA
AC
Found at i:192729 original size:3 final size:3
Alignment explanation
Indices: 192721--192764 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
192711 TATAAAGTAA
192721 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
192765 CTTTTATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:195782 original size:19 final size:21
Alignment explanation
Indices: 195746--195787 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
195736 AAAAATAAAA
*
195746 AATAAAAACAATCCAA-TTAT
1 AATAAAAACAATCAAATTTAT
*
195766 AATAAAAA-AATTAAATTTAT
1 AATAAAAACAATCAAATTTAT
195786 AA
1 AA
195788 CTTTATATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAAAAACAATCAAATTTAT
Found at i:196876 original size:24 final size:25
Alignment explanation
Indices: 196848--196894 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
196838 ATACACACAC
196848 AAAAT-ATAATAAAAAG-TGAAAATA
1 AAAATGATAA-AAAAAGTTGAAAATA
*
196872 AAAATGGTAAAAAAAGTTGAAAA
1 AAAATGATAAAAAAAGTTGAAAA
196895 CCTTGATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (25 bp):
AAAATGATAAAAAAAGTTGAAAATA
Found at i:206985 original size:15 final size:15
Alignment explanation
Indices: 206939--206985 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
206929 TTAAATTTTA
* *
206939 AAAAATATAGAGATA
1 AAAAATATAAAGATT
206954 AAAAATGATAAA-A-T
1 AAAAAT-ATAAAGATT
206968 AAAAATATAAAGATT
1 AAAAATATAAAGATT
206983 AAA
1 AAA
206986 TTTTTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
15 11 0.41
16 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAAATATAAAGATT
Found at i:208366 original size:16 final size:17
Alignment explanation
Indices: 208345--208378 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
208335 TTTGGACATA
*
208345 ATAATTAA-ATAAAAGT
1 ATAATTAATAGAAAAGT
208361 ATAATTAATAGAAAAGT
1 ATAATTAATAGAAAAGT
208378 A
1 A
208379 ACTAAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (17 bp):
ATAATTAATAGAAAAGT
Found at i:209790 original size:30 final size:31
Alignment explanation
Indices: 209756--209827 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
209746 GTTGGATTTA
*
209756 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTAAACTTATCGAAAA-GTG
*
209786 ACAAAACAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
209817 ACAAAACAGTC
1 ACAAAACAGTC
209828 CTCTTGGCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 18 0.47
31 15 0.39
32 5 0.13
ACGTcount: A:0.47, C:0.19, G:0.14, T:0.19
Consensus pattern (31 bp):
ACAAAACAGTCACTAAACTTATCGAAAAGTG
Found at i:210695 original size:30 final size:31
Alignment explanation
Indices: 210623--210702 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
210613 ATTAAATAGG
*
210623 AAGTAGAG-GACTGTTTTGTCACTTTTCGAT
1 AAGTTGAGTGACTGTTTTGTCACTTTTCGAT
* *
210653 AATTTTAGTGACTGTTTTGTCACATTTTC-A-
1 AAGTTGAGTGACTGTTTTGTCAC-TTTTCGAT
*
210683 AAGTTGAGTGACTATTTTGT
1 AAGTTGAGTGACTGTTTTGT
210703 TAAATGTAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
30 22 0.52
31 15 0.36
32 5 0.12
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (31 bp):
AAGTTGAGTGACTGTTTTGTCACTTTTCGAT
Found at i:217641 original size:23 final size:23
Alignment explanation
Indices: 217571--217630 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
217561 ATATCCAAAT
*
217571 AATATTAAAAACGACAACGAAAC
1 AATAGTAAAAACGACAACGAAAC
* * *
217594 AATAGTAAAAATGGCAATGAAAC
1 AATAGTAAAAACGACAACGAAAC
217617 AATAGTAAAAACGA
1 AATAGTAAAAACGA
217631 ACAAAAAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.60, C:0.12, G:0.13, T:0.15
Consensus pattern (23 bp):
AATAGTAAAAACGACAACGAAAC
Found at i:219231 original size:32 final size:32
Alignment explanation
Indices: 219195--219295 Score: 75
Period size: 32 Copynumber: 3.2 Consensus size: 32
219185 CATACATACT
219195 CCATAATGATTCAATTATATTTTCACCATTAA
1 CCATAATGATTCAATTATATTTTCACCATTAA
* * ** * * *
219227 CCAT-ATAAATTC--TGCATACATACATACA-TACT
1 CCATAAT-GATTCAAT-TATATTTTCA-CCATTA-A
219259 CCATAATGATTCAATTATATTTTCACCATTAA
1 CCATAATGATTCAATTATATTTTCACCATTAA
219291 CCATA
1 CCATA
219296 TAAATTCTGC
Statistics
Matches: 47, Mismatches: 14, Indels: 16
0.61 0.18 0.21
Matches are distributed among these distances:
30 1 0.02
31 10 0.21
32 25 0.53
33 10 0.21
34 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.37
Consensus pattern (32 bp):
CCATAATGATTCAATTATATTTTCACCATTAA
Found at i:219257 original size:64 final size:64
Alignment explanation
Indices: 219183--219307 Score: 250
Period size: 64 Copynumber: 2.0 Consensus size: 64
219173 GTGTAACACC
219183 TACATACATACTCCATAATGATTCAATTATATTTTCACCATTAACCATATAAATTCTGCATACA
1 TACATACATACTCCATAATGATTCAATTATATTTTCACCATTAACCATATAAATTCTGCATACA
219247 TACATACATACTCCATAATGATTCAATTATATTTTCACCATTAACCATATAAATTCTGCAT
1 TACATACATACTCCATAATGATTCAATTATATTTTCACCATTAACCATATAAATTCTGCAT
219308 GAATGAATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (64 bp):
TACATACATACTCCATAATGATTCAATTATATTTTCACCATTAACCATATAAATTCTGCATACA
Found at i:223740 original size:283 final size:282
Alignment explanation
Indices: 223228--223797 Score: 942
Period size: 283 Copynumber: 2.0 Consensus size: 282
223218 TTATCTATGC
*
223228 ATAAACAAAGCTTGGTTGCGCATAAATGTTAGAACTTTTACTCTAATTGTTGGAAAAGGAAGTGT
1 ATAAACAAAGCTTGGTTACGCATAAATGTTAGAACTTTTACTCTAATTGTTGGAAAAGGAAGTGT
*
223293 AGTGAAGGTATGCTGCAGGTGCAAGACGAAGAGGAGAAGGATTAGGATTGAGAATCTTGCCCTGA
66 AGTGAAGGTATGCTGCAGGTGCAAGACGAAGAGGAGAAGAATTAGGATTGAGAATCTTGCCCTGA
* * * *
223358 CAAAATAAAAATGCCATGGCAATCCTAAGAGAGCTCACTCAACAAATGTAGCTTGTTTTAGAAAC
131 CAAAATAAAAAAGCCATGGCAATCCCAAGAGAGCTCACTCAACAAATGCAGCTTGTTCTAGAAAC
*
223423 AGCTAGTTGGATTGTACCTCCTTGGAGAATATACCAGAAACAAGTGCACAAGGTGTGAGTTGTGA
196 AGCTAGTTGGATTGTACCTCCTTGGAGAATATACCAGAAACAAGTGCACAAGGTGTGAGTTATGA
*
223488 AGTACTAGCTTGAGGAAGATCT
261 AGCACTAGCTTGAGGAAGATCT
* *
223510 ATAAACAAAGCTTGGTTATGCATAAATGTTAGAATTTTTACTCTAATTGTTGGAAAAGGAAGTGT
1 ATAAACAAAGCTTGGTTACGCATAAATGTTAGAACTTTTACTCTAATTGTTGGAAAAGGAAGTGT
* * *
223575 AGTGAAGGTATGTTGCAGTTGCAAGACGAAGAGGAGAAGAATTAAGGATTGAGAATCTTGCCTTG
66 AGTGAAGGTATGCTGCAGGTGCAAGACGAAGAGGAGAAGAATT-AGGATTGAGAATCTTGCCCTG
* * * *
223640 GCAAAATAAAAAAGCCATGGCAATCCCAAGAGAGCTGACTCAGCAGATGCAGCTTGTTCTAGAAA
130 ACAAAATAAAAAAGCCATGGCAATCCCAAGAGAGCTCACTCAACAAATGCAGCTTGTTCTAGAAA
* ** *
223705 TAGCTAGTTGGATTGTACCTCCTTGGAGAATATACCAGAAGTAGGTGCACAAGGTGTGAGTTATG
195 CAGCTAGTTGGATTGTACCTCCTTGGAGAATATACCAGAAACAAGTGCACAAGGTGTGAGTTATG
223770 AAGCACTAGCTTGAGGAAGATCT
260 AAGCACTAGCTTGAGGAAGATCT
223793 ATAAA
1 ATAAA
223798 TACTCGTGCA
Statistics
Matches: 266, Mismatches: 21, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
282 102 0.38
283 164 0.62
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (282 bp):
ATAAACAAAGCTTGGTTACGCATAAATGTTAGAACTTTTACTCTAATTGTTGGAAAAGGAAGTGT
AGTGAAGGTATGCTGCAGGTGCAAGACGAAGAGGAGAAGAATTAGGATTGAGAATCTTGCCCTGA
CAAAATAAAAAAGCCATGGCAATCCCAAGAGAGCTCACTCAACAAATGCAGCTTGTTCTAGAAAC
AGCTAGTTGGATTGTACCTCCTTGGAGAATATACCAGAAACAAGTGCACAAGGTGTGAGTTATGA
AGCACTAGCTTGAGGAAGATCT
Found at i:225278 original size:36 final size:36
Alignment explanation
Indices: 225226--225329 Score: 131
Period size: 36 Copynumber: 2.9 Consensus size: 36
225216 TGATCGTTAT
*
225226 TCATTTTACTCTCTGTTGACCTAAAGGTCATGATGC
1 TCATTTTACTCCCTGTTGACCTAAAGGTCATGATGC
* * * *
225262 TCGTTTTACTCCCTGTTGACCCAAAGGTCATTATGT
1 TCATTTTACTCCCTGTTGACCTAAAGGTCATGATGC
225298 TCATGTTT-CTCCCTGTTGA-CTCAAAGGTCATG
1 TCAT-TTTACTCCCTGTTGACCT-AAAGGTCATG
225330 CCCGTTACCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.02
36 54 0.93
37 3 0.05
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.38
Consensus pattern (36 bp):
TCATTTTACTCCCTGTTGACCTAAAGGTCATGATGC
Found at i:227924 original size:22 final size:22
Alignment explanation
Indices: 227899--227960 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
227889 TTAATAAAAA
**
227899 ATTTATATTGTTGTTTTGGTTG
1 ATTTATATTACTGTTTTGGTTG
* *
227921 ATTTTTTTTACTGTTTTGGTTG
1 ATTTATATTACTGTTTTGGTTG
* *
227943 ATTTTTTTTTACTGTTTT
1 A-TTTATATTACTGTTTT
227961 TGAGTCGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 19 0.54
23 16 0.46
ACGTcount: A:0.11, C:0.03, G:0.16, T:0.69
Consensus pattern (22 bp):
ATTTATATTACTGTTTTGGTTG
Found at i:227952 original size:23 final size:22
Alignment explanation
Indices: 227910--227960 Score: 93
Period size: 23 Copynumber: 2.3 Consensus size: 22
227900 TTTATATTGT
227910 TGTTTTGGTTGATTTTTTTTAC
1 TGTTTTGGTTGATTTTTTTTAC
227932 TGTTTTGGTTGATTTTTTTTTAC
1 TGTTTTGGTTGA-TTTTTTTTAC
227955 TGTTTT
1 TGTTTT
227961 TGAGTCGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.71
Consensus pattern (22 bp):
TGTTTTGGTTGATTTTTTTTAC
Found at i:227971 original size:24 final size:23
Alignment explanation
Indices: 227910--227974 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 23
227900 TTTATATTGT
*
227910 TGTTTTGGTTGA-TTTTTTTTAC
1 TGTTTTGGTCGATTTTTTTTTAC
*
227932 TGTTTTGGTTGATTTTTTTTTAC
1 TGTTTTGGTCGATTTTTTTTTAC
227955 TGTTTTTGAGTCG-TTTTTTT
1 TG-TTTTG-GTCGATTTTTTT
227975 ATTGTTTTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 12 0.31
23 12 0.31
24 12 0.31
25 3 0.08
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (23 bp):
TGTTTTGGTCGATTTTTTTTTAC
Found at i:227994 original size:23 final size:22
Alignment explanation
Indices: 227910--227987 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
227900 TTTATATTGT
*
227910 TGTTTTGGTTGATTTTTTTTAC
1 TGTTTTGATTGATTTTTTTTAC
*
227932 TGTTTTGGTTGATTTTTTTTTAC
1 TGTTTTGATTGA-TTTTTTTTAC
* *
227955 TGTTTTTGAGTCG--TTTTTTTAT
1 TG-TTTTGA-TTGATTTTTTTTAC
227977 TGTTTTGATTG
1 TGTTTTGATTG
227988 CTATTTTCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.04
21 6 0.12
22 22 0.45
23 12 0.24
24 5 0.10
25 2 0.04
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.68
Consensus pattern (22 bp):
TGTTTTGATTGATTTTTTTTAC
Found at i:228006 original size:12 final size:12
Alignment explanation
Indices: 227997--228093 Score: 65
Period size: 12 Copynumber: 8.3 Consensus size: 12
227987 GCTATTTTCA
227997 TGTTATTTTTGC
1 TGTTATTTTTGC
*
228009 TGTTATTTTTGT
1 TGTTATTTTTGC
* * *
228021 TGCTGTTTTTGT
1 TGTTATTTTTGC
**
228033 TACTA-TTTT--
1 TGTTATTTTTGC
* *
228042 TGTTGTTTTTAC
1 TGTTATTTTTGC
228054 TGTTATTTTTGC
1 TGTTATTTTTGC
* * *
228066 TGTTGTTTTGGT
1 TGTTATTTTTGC
*
228078 TGTTATTTTTGT
1 TGTTATTTTTGC
228090 TGTT
1 TGTT
228094 TGGATGTTAT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
9 2 0.03
10 4 0.06
11 4 0.06
12 57 0.85
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:228018 original size:45 final size:42
Alignment explanation
Indices: 227968--228107 Score: 111
Period size: 45 Copynumber: 3.1 Consensus size: 42
227958 TTTTGAGTCG
*
227968 TTTTTTTATTGTTTTGATTGCTATTTTCATGTTATTTTTGCTGTTA
1 TTTTTGTATTGTTTTG-TTGCTATTTT--TGTT-TTTTTGCTGTTA
* *
228014 TTTTTGT-TGCTGTTTTTGTTACTATTTTTGTTGTTTTTACTGTTA
1 TTTTTGTAT--TG-TTTTGTTGCTATTTTTGTT-TTTTTGCTGTTA
* * * * *
228059 TTTTTGCTGTTGTTTTGGTTGTTATTTTTGTTGTTTGGATGTTA
1 TTTTTG-TATTGTTTT-GTTGCTATTTTTGTTTTTTTGCTGTTA
228103 TTTTT
1 TTTTT
228108 TATGCGTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
44 17 0.22
45 37 0.47
46 7 0.09
47 12 0.15
48 5 0.06
ACGTcount: A:0.09, C:0.05, G:0.17, T:0.69
Consensus pattern (42 bp):
TTTTTGTATTGTTTTGTTGCTATTTTTGTTTTTTTGCTGTTA
Found at i:228093 original size:24 final size:23
Alignment explanation
Indices: 228003--228093 Score: 87
Period size: 24 Copynumber: 4.0 Consensus size: 23
227993 TTCATGTTAT
* *
228003 TTTTGCTGTTATTTTTGTTGCTG
1 TTTTGTTGTTATTTTTGTTGTTG
**
228026 TTTTTGTTACTATTTTTGTTG-T-
1 -TTTTGTTGTTATTTTTGTTGTTG
** *
228048 TTTTACTGTTATTTTTGCTGTTG
1 TTTTGTTGTTATTTTTGTTGTTG
228071 TTTTGGTTGTTATTTTTGTTGTT
1 TTTT-GTTGTTATTTTTGTTGTT
228094 TGGATGTTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
21 15 0.28
22 1 0.02
23 5 0.09
24 32 0.60
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (23 bp):
TTTTGTTGTTATTTTTGTTGTTG
Found at i:228108 original size:21 final size:21
Alignment explanation
Indices: 228038--228108 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 21
228028 TTTGTTACTA
**
228038 TTTTTGTTGTTTTTACTGTTAT
1 TTTTTGTTGTTTGGA-TGTTAT
*
228060 TTTTGCTGTTGTTTTGGTTGTTA-
1 TTTT--TGTTG-TTTGGATGTTAT
228083 TTTTTGTTGTTTGGATGTTAT
1 TTTTTGTTGTTTGGATGTTAT
228104 TTTTT
1 TTTTT
228109 ATGCGTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 10 0.24
21 10 0.24
22 4 0.10
23 4 0.10
24 10 0.24
25 3 0.07
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (21 bp):
TTTTTGTTGTTTGGATGTTAT
Found at i:228108 original size:45 final size:45
Alignment explanation
Indices: 228008--228107 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
227998 GTTATTTTTG
* * **
228008 CTGTTATTTTTGTTGCTGTTTTTGTTACTATTTTTGTTGTTTTTA
1 CTGTTATTTTTGCTGCTGTTTTGGTTACTATTTTTGTTGTTTGGA
* **
228053 CTGTTATTTTTGCTGTTGTTTTGGTTGTTATTTTTGTTGTTTGGA
1 CTGTTATTTTTGCTGCTGTTTTGGTTACTATTTTTGTTGTTTGGA
228098 -TGTTATTTTT
1 CTGTTATTTTT
228108 TATGCGTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 10 0.21
45 38 0.79
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (45 bp):
CTGTTATTTTTGCTGCTGTTTTGGTTACTATTTTTGTTGTTTGGA
Done.