Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 39 of 39
Found at i:7671837 original size:50 final size:51
Alignment explanation
Indices: 7671774--7671889 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
7671764 TATAGCGCGC
* **
7671774 TGCAGGGGCCGCGCTATA-CCCACGTGGCGCCAGCTCACCGTATAGCAAGA
1 TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACCGTATAGCAAGA
* * **
7671824 TTCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCATCGTATAGCGCGA
1 TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACCGTATAGCAAGA
*
7671875 TGCAGAGGGCGCGCT
1 TGCAGGGGGCGCGCT
7671890 TTACTGCTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
50 16 0.29
51 40 0.71
ACGTcount: A:0.21, C:0.32, G:0.32, T:0.16
Consensus pattern (51 bp):
TGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACCGTATAGCAAGA
Found at i:7691220 original size:28 final size:28
Alignment explanation
Indices: 7691170--7691226 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
7691160 CTCTCCATTT
*
7691170 ACATTATGTTGTCTAGCGAGTGCTTGAA
1 ACATTATGTCGTCTAGCGAGTGCTTGAA
*
7691198 ACATTATGTCGTTTAGTCG-GTGCTTGAA
1 ACATTATGTCGTCTAG-CGAGTGCTTGAA
7691226 A
1 A
7691227 GCAACGACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.37
Consensus pattern (28 bp):
ACATTATGTCGTCTAGCGAGTGCTTGAA
Found at i:7695768 original size:3 final size:3
Alignment explanation
Indices: 7695760--7695785 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7695750 GGACCTCAAA
7695760 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
7695786 GAAACTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:7702864 original size:21 final size:21
Alignment explanation
Indices: 7702840--7702881 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
7702830 TAGTTTATTT
7702840 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
7702861 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
7702882 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:7702929 original size:33 final size:33
Alignment explanation
Indices: 7702876--7702973 Score: 164
Period size: 32 Copynumber: 3.0 Consensus size: 33
7702866 TTTGTTTCAA
7702876 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
7702908 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
7702941 TTATC-AACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
7702973 T
1 T
7702974 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 37 0.59
33 26 0.41
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:7704181 original size:26 final size:26
Alignment explanation
Indices: 7704145--7704205 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
7704135 AACCGGTTAC
7704145 ACCGGTTAGGATATCCGGCCCTCCAA
1 ACCGGTTAGGATATCCGGCCCTCCAA
7704171 ACCGGTTAGGATATCCGGCCCTCCAA
1 ACCGGTTAGGATATCCGGCCCTCCAA
7704197 ACCGGTTAG
1 ACCGGTTAG
7704206 AAACCGAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (26 bp):
ACCGGTTAGGATATCCGGCCCTCCAA
Found at i:7706706 original size:15 final size:15
Alignment explanation
Indices: 7706676--7706709 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7706666 AAATATAAAA
**
7706676 TATAAAATTATTTTT
1 TATAAAATTAAATTT
7706691 TATAAAATTAAATTT
1 TATAAAATTAAATTT
7706706 TATA
1 TATA
7706710 TTCGAATTCA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATAAAATTAAATTT
Found at i:7716050 original size:2 final size:2
Alignment explanation
Indices: 7716001--7716030 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7715991 ATATCCATTC
7716001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7716031 CAAATCCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7716389 original size:20 final size:21
Alignment explanation
Indices: 7716339--7716395 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
7716329 TATGAAATTT
7716339 TGTCCCGAAGGACCACTATGAAA
1 TGTCCCGAAGGACCACTAT--AA
* *
7716362 TATCCCGAAGGATCACTAT-A
1 TGTCCCGAAGGACCACTATAA
7716382 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
7716396 GCGTAGACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 13 0.43
23 17 0.57
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTATAA
Found at i:7719251 original size:14 final size:14
Alignment explanation
Indices: 7719232--7719262 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
7719222 TTTCTTTGCC
7719232 TAATGTATTAAATT
1 TAATGTATTAAATT
7719246 TAATGTATTAAATT
1 TAATGTATTAAATT
7719260 TAA
1 TAA
7719263 GTGAAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
TAATGTATTAAATT
Found at i:7720385 original size:22 final size:22
Alignment explanation
Indices: 7720355--7720405 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
7720345 CTTCAGCCCT
7720355 TTGCTCCAACACCTTCAACGATG
1 TTGC-CCAACACCTTCAACGATG
7720378 TTGCCCAACACCTTCAACGATG
1 TTGCCCAACACCTTCAACGATG
7720400 TTGCCC
1 TTGCCC
7720406 TTCTGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.24, C:0.37, G:0.14, T:0.25
Consensus pattern (22 bp):
TTGCCCAACACCTTCAACGATG
Found at i:7721240 original size:21 final size:21
Alignment explanation
Indices: 7721216--7721257 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
7721206 TTCTGCACGT
7721216 CCCGCTCTATGGATGCAACGC
1 CCCGCTCTATGGATGCAACGC
*
7721237 CCCGCTTTATGGATGCAACGC
1 CCCGCTCTATGGATGCAACGC
7721258 ATGCATGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.36, G:0.24, T:0.21
Consensus pattern (21 bp):
CCCGCTCTATGGATGCAACGC
Found at i:7729235 original size:81 final size:82
Alignment explanation
Indices: 7729133--7729288 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 82
7729123 AATGATACTT
* * * * * *
7729133 TAATGGCGTTTCTTAAACAAACGCCGCTATAGAGTAGTACTATAGCGGCATTTTTATATAAACGC
1 TAATGACGTTTCTTAAACAAACGCCACAACAAAGTAGTACTATAGCGGCATTTTTATACAAACGC
7729198 CGCAATAGGTACATATG
66 CGCAATAGGTACATATG
* * * *
7729215 TAATGACGTTT-TTCAACAAACGCCACAACAAAGTAGTACTTTAGCGGCGTTTTTATACAAACTC
1 TAATGACGTTTCTTAAACAAACGCCACAACAAAGTAGTACTATAGCGGCATTTTTATACAAACGC
*
7729279 TGCAATAGGT
66 CGCAATAGGT
7729289 CCATCTATAG
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
81 53 0.84
82 10 0.16
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (82 bp):
TAATGACGTTTCTTAAACAAACGCCACAACAAAGTAGTACTATAGCGGCATTTTTATACAAACGC
CGCAATAGGTACATATG
Found at i:7729308 original size:81 final size:82
Alignment explanation
Indices: 7729148--7729444 Score: 251
Period size: 84 Copynumber: 3.6 Consensus size: 82
7729138 GCGTTTCTTA
* * * * * * * *
7729148 AACAAACGCCGCTATAGAGTAGTACTATAGCGGCATTTTTATATAAACGCCGCAATAGGTACATA
1 AACAAACGCCGCAACAAAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTACATC
* * * *
7729213 TGTAATGACGTTTTTC-
66 TATAGTGGCATTTTTCT
* * *
7729229 AACAAACGCCACAACAAAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAATAGGTCCATC
1 AACAAACGCCGCAACAAAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTACATC
7729294 TATAGTGGCATTTTTTTCT
66 TATAGTGGCA--TTTTTCT
* * * * * *
7729313 GACAAACGCCGCAA-AAGATTTGTACTTTAGCGGCGTTTTTATA-AAAATGCCACAATAGAGTTC
1 AACAAACGCCGCAACAA-AGTAGTACTTTAGCGGCGTTTTTATACAAACT-CCGCAATAG-GTAC
*
7729376 -TCCTATAGTGGCTTTTTTTCT
63 AT-CTATAGTGGC-ATTTTTCT
* * * * * *
7729397 AATAAACGCTGCAACATATTAGAACTTTAGCGGCGTTTTTACACAAAC
1 AACAAACGCCGCAACAAAGTAGTACTTTAGCGGCGTTTTTATACAAAC
7729445 GCCATAAAAA
Statistics
Matches: 174, Mismatches: 32, Indels: 16
0.78 0.14 0.07
Matches are distributed among these distances:
81 60 0.34
83 12 0.07
84 85 0.49
85 17 0.10
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (82 bp):
AACAAACGCCGCAACAAAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTACATC
TATAGTGGCATTTTTCT
Found at i:7734119 original size:43 final size:42
Alignment explanation
Indices: 7734058--7734319 Score: 335
Period size: 43 Copynumber: 6.1 Consensus size: 42
7734048 CTTTTACGGT
*
7734058 GTTTGTGGGAAAAACGCCGCTAAATCTCAAGACCTATTGCGGC
1 GTTTGT-GGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
*
7734101 GTTTGTGGAAAAAACGCCGCTAAATCTCAACACCTATTGCGGA
1 GTTTGTGG-AAAAACGCCGCTAAATCTCAACACCTATTGCGGC
7734144 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
1 GTTTGT-GGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* * * * *
7734187 GTTTGTTGAAAAAACGCCGCTAAATATCAAAACATATTGCGGT
1 GTTTG-TGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* *
7734230 GTTTGTTGGACAAACGCCGCTAAATATCAACACCTATTGCGGC
1 GTTTG-TGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* * * ***
7734273 GTTTGTTGGACAAACGCCGCTATATATCGTTACCTATTGCGGC
1 GTTTG-TGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
7734316 GTTT
1 GTTT
7734320 TTTGTTACCA
Statistics
Matches: 199, Mismatches: 17, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
42 2 0.01
43 194 0.97
44 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (42 bp):
GTTTGTGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
Found at i:7734311 original size:86 final size:85
Alignment explanation
Indices: 7734004--7734319 Score: 391
Period size: 86 Copynumber: 3.7 Consensus size: 85
7733994 TATAGATATG
* ** * * * * * *
7734004 ACCTTTTGCGGCGTTTGTTCTAAAAACGCCGCTATATACCAGATCTTTTACGGTGTTTGTGGGAA
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAAACCTATTGCGGTGTTTGTGGGAA
*
7734069 AAACGCCGCTAAATCTCAAG
66 AAACGCCGCTAAATCTCAAC
* *
7734089 ACCTATTGCGGCGTTTG-TGGAAAAAACGCCGCTAAATCTCAACACCTATTGCGGAGTTTGTGGG
1 ACCTATTGCGGCGTTTGTTGG-AAAAACGCCGCTAAATATCAA-ACCTATTGCGGTGTTTGTGGG
7734153 AAAAACGCCGCTAAATCTCAAC
64 AAAAACGCCGCTAAATCTCAAC
* * *
7734175 ACCTATTGCGGCGTTTGTTGAAAAAACGCCGCTAAATATCAAAACATATTGCGGTGTTTGTTGGA
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATC-AAACCTATTGCGGTGTTTGTGGGA
* *
7734240 CAAACGCCGCTAAATATCAAC
65 AAAACGCCGCTAAATCTCAAC
* * ** *
7734261 ACCTATTGCGGCGTTTGTTGGACAAACGCCGCTATATATCGTTACCTATTGCGGCGTTT
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATC-AAACCTATTGCGGTGTTT
7734320 TTTGTTACCA
Statistics
Matches: 200, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
84 1 0.00
85 33 0.17
86 162 0.81
87 4 0.02
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (85 bp):
ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAAACCTATTGCGGTGTTTGTGGGAA
AAACGCCGCTAAATCTCAAC
Found at i:7744549 original size:24 final size:24
Alignment explanation
Indices: 7744522--7744571 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
7744512 TTCTTATGCT
7744522 ATACACACATTATCTTGAGGTTAA
1 ATACACACATTATCTTGAGGTTAA
7744546 ATACACACATTATCTTGAGGTTAA
1 ATACACACATTATCTTGAGGTTAA
7744570 AT
1 AT
7744572 CGACCATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (24 bp):
ATACACACATTATCTTGAGGTTAA
Found at i:7755523 original size:19 final size:19
Alignment explanation
Indices: 7755467--7755529 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
7755457 CTATTTAAAC
**
7755467 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
7755487 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
7755507 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
7755526 TAAA
1 TAAA
7755530 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:7755574 original size:75 final size:76
Alignment explanation
Indices: 7755487--7755651 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 76
7755477 AAAAAATAAT
*
7755487 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGATAAAGAT
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
7755551 AAAAT-ATAAAA
65 AAAATGATAAAA
* * *
7755562 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACATAGATAAAATA
1 ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
* * *
7755627 TAATGTTTAAA
66 AAATGATAAAA
*
7755638 ATATTATCCTAAAT
1 ATAATATCCTAAAT
7755652 TTGAGTTTAA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 32 0.41
76 47 0.59
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (76 bp):
ATAATATCCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
AAATGATAAAA
Found at i:7757225 original size:14 final size:13
Alignment explanation
Indices: 7757194--7757221 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7757184 CCGATGACTG
7757194 TTCTGTTCGAACT
1 TTCTGTTCGAACT
7757207 TTCTGTTCGAACT
1 TTCTGTTCGAACT
7757220 TT
1 TT
7757222 TCTGCACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (13 bp):
TTCTGTTCGAACT
Found at i:7757261 original size:28 final size:27
Alignment explanation
Indices: 7757219--7757308 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 27
7757209 CTGTTCGAAC
7757219 TTTTCTGCACAGTTCGAACCAAATCAGT
1 TTTTCTGCACAGTTCGAACCAAATCA-T
* ** *
7757247 TTTTCTGCACTGTTCTG-TTC-GA--AT
1 TTTTCTGCACAGTTC-GAACCAAATCAT
*
7757271 TTTTCTGCACAGTTCGAACCAAGTCAAT
1 TTTTCTGCACAGTTCGAACCAAATC-AT
7757299 TTTTCTGCAC
1 TTTTCTGCAC
7757309 TGTTTTTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
23 1 0.02
24 16 0.34
25 1 0.02
27 1 0.02
28 27 0.57
29 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (27 bp):
TTTTCTGCACAGTTCGAACCAAATCAT
Found at i:7757275 original size:52 final size:52
Alignment explanation
Indices: 7757207--7757312 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
7757197 TGTTCGAACT
*
7757207 TTCTGTTCGAACTTTTCTGCACAGTTCGAACCAAATCAGTTTTTCTGCACTG
1 TTCTGTTCGAACTTTTCTGCACAGTTCGAACCAAATCAATTTTTCTGCACTG
* *
7757259 TTCTGTTCGAATTTTTCTGCACAGTTCGAACCAAGTCAATTTTTCTGCACTG
1 TTCTGTTCGAACTTTTCTGCACAGTTCGAACCAAATCAATTTTTCTGCACTG
7757311 TT
1 TT
7757313 TTTTTTCCCG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41
Consensus pattern (52 bp):
TTCTGTTCGAACTTTTCTGCACAGTTCGAACCAAATCAATTTTTCTGCACTG
Found at i:7757433 original size:21 final size:21
Alignment explanation
Indices: 7757409--7757456 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
7757399 AATTCGCTAA
7757409 AAAAATAAAAAAAAT-AAAAC
1 AAAAATAAAAAAAATAAAAAC
7757429 GAAAAAT-AAAAAAATAAAAAC
1 -AAAAATAAAAAAAATAAAAAC
7757450 AAAAATA
1 AAAAATA
7757457 TAACGAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.10
Consensus pattern (21 bp):
AAAAATAAAAAAAATAAAAAC
Found at i:7767042 original size:15 final size:14
Alignment explanation
Indices: 7767003--7767056 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
7766993 ACCCATTTCG
* *
7767003 TTATATTTTTGTTT
1 TTATTTTTTTATTT
7767017 TTATTTTTTTATTT
1 TTATTTTTTTATTT
*
7767031 TCATTTTATTTATTT
1 TTATTTT-TTTATTT
7767046 TTATTTTTTTA
1 TTATTTTTTTA
7767057 GCGAACTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 22 0.63
15 13 0.37
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.80
Consensus pattern (14 bp):
TTATTTTTTTATTT
Found at i:7767295 original size:16 final size:17
Alignment explanation
Indices: 7767267--7767298 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
7767257 CAAACATAGA
7767267 AGTGCAGGAAAAAAAAT
1 AGTGCAGGAAAAAAAAT
7767284 AGTGCA-GAAAAAAAA
1 AGTGCAGGAAAAAAAA
7767299 ACAGATTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.62, C:0.06, G:0.22, T:0.09
Consensus pattern (17 bp):
AGTGCAGGAAAAAAAAT
Found at i:7767299 original size:17 final size:17
Alignment explanation
Indices: 7767267--7767299 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7767257 CAAACATAGA
*
7767267 AGTGCAGGAAAAAAAAT
1 AGTGCAGAAAAAAAAAT
7767284 AGTGCAGAAAAAAAAA
1 AGTGCAGAAAAAAAAA
7767300 CAGATTTGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.06, G:0.21, T:0.09
Consensus pattern (17 bp):
AGTGCAGAAAAAAAAAT
Found at i:7769005 original size:76 final size:75
Alignment explanation
Indices: 7768914--7769078 Score: 242
Period size: 76 Copynumber: 2.2 Consensus size: 75
7768904 TTAAACTCAA
*
7768914 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
7768978 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
7768990 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
7769055 TTTAATTAGG
66 TTTAATTAAG
*
7769065 ATTTAGAATATTAT
1 ATTTAGGATATTAT
7769079 ATAATTTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 37 0.46
76 43 0.54
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:7769747 original size:17 final size:18
Alignment explanation
Indices: 7769720--7769766 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
7769710 AATCTCTTTA
7769720 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
*
7769739 A-TTTTTATTTAATTCTT
1 ATTTTTTATTTAATTATT
7769756 ATTTTTTATTT
1 ATTTTTTATTT
7769767 TAACCACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.54
18 11 0.42
19 1 0.04
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:7771150 original size:73 final size:73
Alignment explanation
Indices: 7771030--7771195 Score: 219
Period size: 73 Copynumber: 2.2 Consensus size: 73
7771020 AAATACCTAA
*
7771030 AAAATATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAA
1 AAAA-ATAATATCCTAAATCCTAATTAAAATAC-AAAACCTATTTAAACTAAAATACAAAGATAA
7771095 AGATAAAATAT
64 A-ATAAAATAT
*
7771106 AAAAATAATATCCTAAA-CTTAATTAAAACTA-AAAACCTATTTAAACTAAAATACAAAGATAAA
1 AAAAATAATATCCTAAATCCTAATTAAAA-TACAAAACCTATTTAAACTAAAATACAAAGATAAA
* *
7771169 ATATAATGT
65 ATAAAATAT
** *
7771178 TCAAATATTATCCTAAAT
1 AAAAATAATATCCTAAAT
7771196 TTGAGTTTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
72 21 0.26
73 32 0.40
74 10 0.12
75 14 0.17
76 4 0.05
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (73 bp):
AAAAATAATATCCTAAATCCTAATTAAAATACAAAACCTATTTAAACTAAAATACAAAGATAAAA
TAAAATAT
Found at i:7776392 original size:38 final size:38
Alignment explanation
Indices: 7776316--7776389 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 38
7776306 ACTTGAAGAT
*
7776316 TAAATTATTCTCTCAGTCTCATTAAAAACATATTTTTA
1 TAAATTATTCCCTCAGTCTCATTAAAAACATATTTTTA
*
7776354 TAAATTATTCCCT-TGTCTCATTAAAAACATATTTTT
1 TAAATTATTCCCTCAGTCTCATTAAAAACATATTTTT
7776390 TATTAACTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 22 0.65
38 12 0.35
ACGTcount: A:0.35, C:0.16, G:0.03, T:0.46
Consensus pattern (38 bp):
TAAATTATTCCCTCAGTCTCATTAAAAACATATTTTTA
Found at i:7779871 original size:18 final size:18
Alignment explanation
Indices: 7779848--7779883 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7779838 CACCAGAGGA
7779848 ATCAAATGAGACATTGGT
1 ATCAAATGAGACATTGGT
7779866 ATCAAATGAGACATTGGT
1 ATCAAATGAGACATTGGT
7779884 TCAGGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
ATCAAATGAGACATTGGT
Found at i:7781636 original size:17 final size:18
Alignment explanation
Indices: 7781614--7781647 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7781604 TAACCACGAT
7781614 AAACGC-AACGCAATCAA
1 AAACGCGAACGCAATCAA
*
7781631 AAACGCGACCGCAATCA
1 AAACGCGAACGCAATCA
7781648 GGATAAACGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.32, G:0.15, T:0.06
Consensus pattern (18 bp):
AAACGCGAACGCAATCAA
Found at i:7798734 original size:14 final size:14
Alignment explanation
Indices: 7798682--7798734 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
7798672 TTGAATGTTA
*
7798682 TTAATAATT-TAAT
1 TTAAAAATTATAAT
*
7798695 TTAAAAATTAAAAT
1 TTAAAAATTATAAT
* *
7798709 TTAACATATTATATT
1 TTAA-AAATTATAAT
7798724 TTAAAAATTAT
1 TTAAAAATTAT
7798735 TCATGAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
13 8 0.25
14 13 0.41
15 11 0.34
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAAAAATTATAAT
Found at i:7806954 original size:52 final size:51
Alignment explanation
Indices: 7806884--7806985 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 51
7806874 AATTAGCAAC
*
7806884 AGAATAAAATTGATTCTATCTAATTAAAACAT-ATCCTATCTAATAACTAAT
1 AGAATAAAACTGATTCTATCTAATTAAAAC-TGATCCTATCTAATAACTAAT
*
7806935 AGAATAAAAACTGATTCTATCTAATTAAAACTGATCTTATCTAATAACTAA
1 AGAAT-AAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACTAA
7806986 CATAAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
51 6 0.13
52 41 0.87
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (51 bp):
AGAATAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACTAAT
Found at i:7806966 original size:20 final size:20
Alignment explanation
Indices: 7806941--7806979 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
7806931 TAATAGAATA
7806941 AAAACTGAT-TCTATCTAATT
1 AAAACTGATCT-TATCTAATT
7806961 AAAACTGATCTTATCTAAT
1 AAAACTGATCTTATCTAAT
7806980 AACTAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCTTATCTAATT
Found at i:7806996 original size:52 final size:52
Alignment explanation
Indices: 7806881--7806996 Score: 155
Period size: 52 Copynumber: 2.2 Consensus size: 52
7806871 TAAAATTAGC
* *
7806881 AACAG-AATAAAATTGATTCTATCTAATTAAAACATATCCTATCTAATAACT
1 AACAGAAAAAAAACTGATTCTATCTAATTAAAACATATCCTATCTAATAACT
* * *
7806932 AATAGAATAAAAACTGATTCTATCTAATTAAAAC-TGATCTTATCTAATAACT
1 AACAGAAAAAAAACTGATTCTATCTAATTAAAACAT-ATCCTATCTAATAACT
*
7806984 AACATAAAAAAAA
1 AACAGAAAAAAAA
7806997 ACTAGTTAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 5 0.09
52 50 0.91
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (52 bp):
AACAGAAAAAAAACTGATTCTATCTAATTAAAACATATCCTATCTAATAACT
Found at i:7811617 original size:3 final size:3
Alignment explanation
Indices: 7811611--7811646 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
7811601 TATGTAACAT
7811611 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
7811647 TTTAATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:7811998 original size:55 final size:55
Alignment explanation
Indices: 7811938--7812144 Score: 206
Period size: 55 Copynumber: 3.8 Consensus size: 55
7811928 CAATGGGTTC
* * * *
7811938 GTTCCCTCTTTCTTTCAGGGAGTAT-AGAACTCAAAC-ATCTTCAACACTCGTGTCT
1 GTTCCCT-TTTCTTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCATGTCT
* * *
7811993 GTTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCATGTCT
1 GTTCCCTTTTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCT
* * * *
7812048 -TCTCCCTATTCCTTT-AGAGAGTATAAGACTCGAACAATCTTCAACTATCATTTAT
1 GT-TCCCT-TTTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCT
* * * * *
7812103 GCTCCCTATTCCTTCAGAGAGTATGAGACTCGAATAATCTTC
1 GTTCCCTTTTCTTTCAGAGAGTATAAGACTCGAACAATCTTC
7812145 TTCTTACGGG
Statistics
Matches: 126, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
54 25 0.20
55 97 0.77
56 4 0.03
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (55 bp):
GTTCCCTTTTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCT
Found at i:7812162 original size:55 final size:53
Alignment explanation
Indices: 7812103--7812310 Score: 204
Period size: 55 Copynumber: 3.8 Consensus size: 53
7812093 TATCATTTAT
* * *
7812103 GCTCCCTATTCCTTCAGAGAGTATGAGACTCGAATAATCTTCTTCTTACGGGTTC
1 GCTCCCTCTTTCTTCAGAGAGTAT-AGACTCGAA-AATCTTCTTCATACGGGTTC
* * * *
7812158 GCTCCCTCTTTCTTCAGAGAGTATAGAACTCGAATATCTTTTTTCAAACGGGTTT
1 GCTCCCTCTTTCTTCAGAGAGTATAG-ACTCGAAAATC-TTCTTCATACGGGTTC
* * * * *
7812213 GCTCCCTCTTTC-TCTAGGGAGTATAAAACTCGGACATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGAGAGTAT-AGACTCGAAAATCTTCTTCATACGGGTTC
* *
7812267 GCTCCCTCTTTC-TCTAGGGAGTATAGAACTCGAACATCTTCTTC
1 GCTCCCTCTTTCTTC-AGAGAGTATAG-ACTCGAAAATCTTCTTC
7812311 TTCTTCACTA
Statistics
Matches: 133, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
53 1 0.01
54 61 0.46
55 70 0.53
56 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (53 bp):
GCTCCCTCTTTCTTCAGAGAGTATAGACTCGAAAATCTTCTTCATACGGGTTC
Found at i:7812280 original size:54 final size:54
Alignment explanation
Indices: 7812121--7812310 Score: 249
Period size: 54 Copynumber: 3.5 Consensus size: 54
7812111 TTCCTTCAGA
* ** *
7812121 GAGTAT-GAGACTCGAATAATCTTCTTCTTACGGGTTCGCTCCCTCTTTCT-TCAGA
1 GAGTATAGA-ACTCGAA-CATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * *
7812176 GAGTATAGAACTCGAATATCTTTTTTCAAACGGGTTTGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATC-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* *
7812231 GAGTATAAAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
1 GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
7812285 GAGTATAGAACTCGAACATCTTCTTC
1 GAGTATAGAACTCGAACATCTTCTTC
7812311 TTCTTCACTA
Statistics
Matches: 119, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
54 59 0.50
55 57 0.48
56 3 0.03
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (54 bp):
GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:7813411 original size:18 final size:17
Alignment explanation
Indices: 7813379--7813417 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
7813369 GAACCCTCCC
7813379 TTTTCTTTTTCTTCCTT
1 TTTTCTTTTTCTTCCTT
*
7813396 TTTTCATTTTTTTTCCTT
1 TTTTC-TTTTTCTTCCTT
7813414 TTTT
1 TTTT
7813418 AATCCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTTCTTCCTT
Found at i:7823369 original size:16 final size:17
Alignment explanation
Indices: 7823344--7823379 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
7823334 CTTTATTCAT
7823344 ATGGTATCTACCCAA-C
1 ATGGTATCTACCCAATC
*
7823360 ATGGTGTCTACCCAATC
1 ATGGTATCTACCCAATC
7823377 ATG
1 ATG
7823380 CTTTAGTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (17 bp):
ATGGTATCTACCCAATC
Found at i:7826712 original size:3 final size:3
Alignment explanation
Indices: 7826706--7826744 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
7826696 TATGTAACAT
7826706 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
7826745 TTTAATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:7827287 original size:20 final size:20
Alignment explanation
Indices: 7827262--7827301 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
7827252 AATAACAGAA
*
7827262 TAAAACTGATTATATCTAAT
1 TAAAACTGATCATATCTAAT
*
7827282 TAAAACTGATCCTATCTAAT
1 TAAAACTGATCATATCTAAT
7827302 AACTAACAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAACTGATCATATCTAAT
Found at i:7827328 original size:52 final size:52
Alignment explanation
Indices: 7827254--7827379 Score: 200
Period size: 52 Copynumber: 2.4 Consensus size: 52
7827244 ATAAAATTAA
* * *
7827254 TAACAGAAT-AAAACTGATTATATCTAATTAAAACTGATCCTATCTAATAAC
1 TAACAGAATAAAAACTAATTATATATAATTAAAACTGATCATATCTAATAAC
7827305 TAACAGAATAAAAACTAATTATATATAATTAAAACTGATCATATCTAATAAC
1 TAACAGAATAAAAACTAATTATATATAATTAAAACTGATCATATCTAATAAC
7827357 TAACAGAATAAAATATCTAATTA
1 TAACAGAATAAAA-A-CTAATTA
7827380 ACAATCTTAA
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 9 0.13
52 52 0.75
53 1 0.01
54 7 0.10
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.31
Consensus pattern (52 bp):
TAACAGAATAAAAACTAATTATATATAATTAAAACTGATCATATCTAATAAC
Found at i:7827348 original size:20 final size:20
Alignment explanation
Indices: 7827315--7827353 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7827305 TAACAGAATA
*
7827315 AAAACTAATTATATATAATT
1 AAAACTAATCATATATAATT
* *
7827335 AAAACTGATCATATCTAAT
1 AAAACTAATCATATATAAT
7827354 AACTAACAGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAACTAATCATATATAATT
Found at i:7828496 original size:3 final size:3
Alignment explanation
Indices: 7828488--7828551 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
7828478 TTTTATTAAA
* * * * *
7828488 ATT ATT ATT ATT ATT ATT ATAA AAT ATT ATT ATC ATT ATT ATA AAT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
7828534 ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
7828552 TATTTACAGC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 49 0.98
4 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:7830367 original size:146 final size:146
Alignment explanation
Indices: 7830097--7830367 Score: 345
Period size: 146 Copynumber: 1.9 Consensus size: 146
7830087 AATAATAATA
* * * * *
7830097 TTTATTTATTTTTTTAATATTAAAAAAGAACATTCTTAAAGCAACTAGATGTCTTATTCTGATAT
1 TTTATTTATTTTATTAATATTAAAAAAGAACAATCTTAAAGCAACTAGATATATTATTCTAATAT
* * * * *
7830162 TTTAAAAATAAATAAATATCCTGCTTATAAAAATATATATATATATTTACTTCATTATTTTTAGG
66 TTTAAAAATAAATAAATATCCTACTTACAAAAATAAATATATATATATACTACATTATTTTTAGG
7830227 AAAATTATTATTATTT
131 AAAATTATTATTATTT
7830243 TTTATTTA-TTTATTAATATTAAAGAAATG-ACAATCTTAAAGCAACTAGATATATT-TTCTAAT
1 TTTATTTATTTTATTAATATTAAA-AAA-GAACAATCTTAAAGCAACTAGATATATTATTCTAAT
* * *
7830305 ATTTT-TAAATAAATAAATATCTTATTTACAAAAACCTAAATATATATATATA-TACATATATTT
64 ATTTTAAAAATAAATAAATATCCTACTTACAAAAA--TAAATATATATATATACTACAT-TATTT
7830368 AGTATTTTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
144 24 0.22
145 29 0.27
146 53 0.50
147 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (146 bp):
TTTATTTATTTTATTAATATTAAAAAAGAACAATCTTAAAGCAACTAGATATATTATTCTAATAT
TTTAAAAATAAATAAATATCCTACTTACAAAAATAAATATATATATATACTACATTATTTTTAGG
AAAATTATTATTATTT
Found at i:7839387 original size:15 final size:15
Alignment explanation
Indices: 7839363--7839396 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7839353 GATTTTTTTG
*
7839363 ACATTCTAATTCCAT
1 ACATTATAATTCCAT
*
7839378 ACATTATAATTTCAT
1 ACATTATAATTCCAT
7839393 ACAT
1 ACAT
7839397 AGACATAACT
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:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (15 bp):
ACATTATAATTCCAT
Found at i:7842130 original size:18 final size:18
Alignment explanation
Indices: 7842107--7842154 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
7842097 GTTGTGGTTA
*
7842107 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAAAATT
7842125 AAATAAAAGAA-AAAAATT
1 AAATAAAA-AATAAAAATT
7842143 AAATAAACAAAT
1 AAATAAA-AAAT
7842155 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 23 0.88
19 3 0.12
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (18 bp):
AAATAAAAAATAAAAATT
Found at i:7844616 original size:53 final size:51
Alignment explanation
Indices: 7844536--7844645 Score: 157
Period size: 53 Copynumber: 2.1 Consensus size: 51
7844526 TGTCCGATGA
* *
7844536 TGCACTGTTTTGTTCAAACTTTTCTGCACAGTTCGAACCAAATCTATTTTTT
1 TGCACTGTTCTGTTCAAACTTTTCTGCACAGTTCGAACCAAATC-AGTTTTT
* * *
7844588 CTGCACTGTTCTGTTCGAATTTTTCTGCACAGTTCGAACCAAGTCAGTTTTT
1 -TGCACTGTTCTGTTCAAACTTTTCTGCACAGTTCGAACCAAATCAGTTTTT
7844640 TGCACT
1 TGCACT
7844646 ATTTTTTTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
51 6 0.12
52 6 0.12
53 40 0.77
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (51 bp):
TGCACTGTTCTGTTCAAACTTTTCTGCACAGTTCGAACCAAATCAGTTTTT
Found at i:7844754 original size:8 final size:8
Alignment explanation
Indices: 7844741--7844779 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
7844731 AAAGTTCATT
7844741 AAAAAATA
1 AAAAAATA
7844749 AAAAAATAAA
1 AAAAAAT--A
7844759 ACAAAAATA
1 A-AAAAATA
7844768 AAAAAATA
1 AAAAAATA
7844776 AAAA
1 AAAA
7844780 CAAAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 18 0.64
9 2 0.07
10 2 0.07
11 6 0.21
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:7844771 original size:20 final size:20
Alignment explanation
Indices: 7844742--7844787 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
7844732 AAGTTCATTA
7844742 AAAAATAAAAAAAT-AAAAC
1 AAAAATAAAAAAATAAAAAC
7844761 AAAAATAAAAAAATAAAAAC
1 AAAAATAAAAAAATAAAAAC
7844781 AAAAATA
1 AAAAATA
7844788 TAACGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.85, C:0.04, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAATAAAAAAATAAAAAC
Found at i:7850366 original size:3 final size:3
Alignment explanation
Indices: 7850349--7850398 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
7850339 GATATATTAA
* *
7850349 AAT AA- AAT AAAT AAT AAT AAT AAT -AT AAT AAT AAAT ATT AAT AGT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
7850394 AAT AA
1 AAT AA
7850399 ATATAAAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 4 0.10
3 29 0.74
4 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:7850390 original size:24 final size:24
Alignment explanation
Indices: 7850350--7850405 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
7850340 ATATATTAAA
7850350 ATAA-AATAAATAATAATAATAAT
1 ATAATAATAAATAATAATAATAAT
* *
7850373 ATAATAATAAATATTAATAGTAAT
1 ATAATAATAAATAATAATAATAAT
7850397 A-AAT-ATAAA
1 ATAATAATAAA
7850406 AGTGGGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 5 0.17
23 7 0.23
24 18 0.60
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
ATAATAATAAATAATAATAATAAT
Found at i:7850465 original size:21 final size:21
Alignment explanation
Indices: 7850439--7850478 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7850429 GTTAAAATAA
7850439 AAAATAAGAACTAAATAAAAG
1 AAAATAAGAACTAAATAAAAG
* *
7850460 AAAATAATAATTAAATAAA
1 AAAATAAGAACTAAATAAA
7850479 CAAATTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAATAAGAACTAAATAAAAG
Found at i:7851100 original size:19 final size:21
Alignment explanation
Indices: 7851060--7851103 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
7851050 TAAAACAAGC
*
7851060 TAAAACATCTTAAATCCTAAT
1 TAAAACATCTTAAATACTAAT
7851081 TAAAACAT-TTAAA-ACTAAT
1 TAAAACATCTTAAATACTAAT
7851100 TAAA
1 TAAA
7851104 CTAAAATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 5 0.23
21 8 0.36
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAAACATCTTAAATACTAAT
Found at i:7851191 original size:13 final size:13
Alignment explanation
Indices: 7851168--7851201 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
7851158 TATTTAAACT
7851168 AAAATACAAATATA
1 AAAATA-AAATATA
*
7851182 AAGATAAAATATA
1 AAAATAAAATATA
7851195 AAAATAA
1 AAAATAA
7851202 TATCCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAATAAAATATA
Found at i:7856245 original size:13 final size:13
Alignment explanation
Indices: 7856227--7856259 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
7856217 AAACTCCTGA
7856227 TTGAATTGCAACT
1 TTGAATTGCAACT
*
7856240 TTGAATTGCAGCT
1 TTGAATTGCAACT
7856253 TTGAATT
1 TTGAATT
7856260 TTTTATAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (13 bp):
TTGAATTGCAACT
Found at i:7861315 original size:7 final size:7
Alignment explanation
Indices: 7861303--7861338 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
7861293 ATATGTAAAG
7861303 CATCCAT
1 CATCCAT
7861310 CATCCAT
1 CATCCAT
*
7861317 AATCCAT
1 CATCCAT
7861324 CATCCAT
1 CATCCAT
7861331 CAT-CAT
1 CATCCAT
7861337 CA
1 CA
7861339 GCCGGGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.28
Consensus pattern (7 bp):
CATCCAT
Found at i:7867419 original size:18 final size:17
Alignment explanation
Indices: 7867398--7867432 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
7867388 TGTTTGTATA
*
7867398 TTTTAAATTTAAATATTT
1 TTTTAAA-TAAAATATTT
7867416 TTTTAAATAAAATATTT
1 TTTTAAATAAAATATTT
7867433 AACGGCCGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAAATAAAATATTT
Found at i:7871218 original size:3 final size:3
Alignment explanation
Indices: 7871177--7871234 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
7871167 GTTGCAAGAC
* * * *
7871177 TAA TAT TAA TAAA TAA TAA -AA TAT TAA CAA TCA -AA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7871221 TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA
7871235 AATCAAATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
2 5 0.12
3 35 0.81
4 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:7871229 original size:17 final size:17
Alignment explanation
Indices: 7871178--7871234 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
7871168 TTGCAAGACT
*
7871178 AATATTAATAAATAATAA
1 AATAATAAT-AATAATAA
* *
7871196 AAT-AT--TAACAATCA
1 AATAATAATAATAATAA
7871210 AATAATAATAATAATAA
1 AATAATAATAATAATAA
7871227 AATAATAA
1 AATAATAA
7871235 AATCAAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
14 9 0.29
15 3 0.10
17 16 0.52
18 3 0.10
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAATAATAATAATAA
Found at i:7871230 original size:14 final size:14
Alignment explanation
Indices: 7871183--7871237 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
7871173 AGACTAATAT
7871183 TAATAAATAATAAAA
1 TAAT-AATAATAAAA
* * *
7871198 TATTAACAATCAAA
1 TAATAATAATAAAA
7871212 TAATAATAAT--AA
1 TAATAATAATAAAA
7871224 TAA-AATAATAAAA
1 TAATAATAATAAAA
7871237 T
1 T
7871238 CAAATTATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
11 6 0.18
12 5 0.15
13 3 0.09
14 16 0.48
15 3 0.09
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:7877716 original size:96 final size:97
Alignment explanation
Indices: 7877560--7877754 Score: 349
Period size: 96 Copynumber: 2.0 Consensus size: 97
7877550 TCTATTTAAA
7877560 CTATTTAATCCGTTGATCAGCTCAATCGGTTAAAAATATCAAGTACTTATAATAAAATA-TTGAT
1 CTATTTAATCCGTTGATCAGCTCAATCGGTTAAAAATATCAAGTACTTATAATAAAATATTTGAT
7877624 TTTTCAAATCGAATACTTGGCCTACTATTTTT
66 TTTTCAAATCGAATACTTGGCCTACTATTTTT
*
7877656 CTATTTAATCCGTTGATCAGCTGAATCGGTTAAAAA-ATCAAGTACTTATAATAAAAATATTTGA
1 CTATTTAATCCGTTGATCAGCTCAATCGGTTAAAAATATCAAGTACTTATAAT-AAAATATTTGA
*
7877720 TTTTTCAAATCGAATACTTGGCCTATTATTTTT
65 TTTTTCAAATCGAATACTTGGCCTACTATTTTT
7877753 CT
1 CT
7877755 CGAGTTTCTA
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
95 16 0.17
96 41 0.43
97 38 0.40
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (97 bp):
CTATTTAATCCGTTGATCAGCTCAATCGGTTAAAAATATCAAGTACTTATAATAAAATATTTGAT
TTTTCAAATCGAATACTTGGCCTACTATTTTT
Found at i:7877850 original size:13 final size:14
Alignment explanation
Indices: 7877825--7877859 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
7877815 ACTCAATTTC
7877825 TTATATATTTTTATT
1 TTATAT-TTTTTATT
7877840 TT-TATTTTTTATT
1 TTATATTTTTTATT
7877853 TTATATT
1 TTATATT
7877860 AGATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.53
14 7 0.37
15 2 0.11
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTATATTTTTTATT
Found at i:7878772 original size:27 final size:29
Alignment explanation
Indices: 7878730--7878802 Score: 80
Period size: 32 Copynumber: 2.5 Consensus size: 29
7878720 CCGAGCCGAG
**
7878730 TCGAACTCGATTACT-AT-TAAGCTCGAC
1 TCGAACTCGAAAACTAATCTAAGCTCGAC
7878757 TCGAACTCGAAAACTATAAATCTAAGCTCGAC
1 TCGAACTCGAAAAC--T-AATCTAAGCTCGAC
7878789 TCG-ACTCGAAAACT
1 TCGAACTCGAAAACT
7878803 CGCAAGCCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 12 0.31
29 2 0.05
31 12 0.31
32 13 0.33
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.25
Consensus pattern (29 bp):
TCGAACTCGAAAACTAATCTAAGCTCGAC
Found at i:7878940 original size:23 final size:23
Alignment explanation
Indices: 7878904--7878959 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
7878894 ACTCGATTGA
* *
7878904 AGCTCGATTAAAGCTTGATTTTG
1 AGCTCGATTCAAGCTCGATTTTG
*
7878927 AGCTCAATTCAAGCTCGATTTTG
1 AGCTCGATTCAAGCTCGATTTTG
7878950 AGCTCGATTC
1 AGCTCGATTC
7878960 TGTGCTCGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGATTTTG
Found at i:7880377 original size:17 final size:19
Alignment explanation
Indices: 7880339--7880377 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
7880329 TTTGGGAAAC
*
7880339 TGTGAAGCAGATATCAAGT
1 TGTGAAGCAGATATCAAAT
7880358 TGTGAAGCAG-T-TCAAAT
1 TGTGAAGCAGATATCAAAT
7880375 TGT
1 TGT
7880378 ACATAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (19 bp):
TGTGAAGCAGATATCAAAT
Found at i:7881528 original size:21 final size:20
Alignment explanation
Indices: 7881504--7881544 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
7881494 TGGATTTAAT
7881504 ATTTAGGGTTTAGGGTTTTAG
1 ATTTAGGGTTTA-GGTTTTAG
*
7881525 ATTTATGGTTTAGGTTTTAG
1 ATTTAGGGTTTAGGTTTTAG
7881545 GGCTTAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (20 bp):
ATTTAGGGTTTAGGTTTTAG
Found at i:7881714 original size:14 final size:14
Alignment explanation
Indices: 7881695--7881724 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7881685 TATAATTATC
*
7881695 AATAATGTATTTTT
1 AATAATGTAATTTT
7881709 AATAATGTAATTTT
1 AATAATGTAATTTT
7881723 AA
1 AA
7881725 AAATCTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:7882568 original size:111 final size:111
Alignment explanation
Indices: 7882427--7882782 Score: 552
Period size: 111 Copynumber: 3.2 Consensus size: 111
7882417 GTATTAATCC
* * **
7882427 TTTTTATTAAAAAGTATCTATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGA
1 TTTTTA-T-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGA
* * * *
7882492 ATCTGGTTTTGTCATATTTATACATGTTATATTGTAAAATATCGATCA
64 AACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATCA
*
7882540 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCTTTTTTGTCATAATGAAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAA
* *
7882605 CTGATTTTGTCATATTTTTACCTGTTATATTGTAAAATATCTATCC
66 CTGATTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATCA
*
7882651 TTTTTATAAAAGGATCGATAATTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAA
1 TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAA
7882716 CTGATTTTGTCATATTTTTTACCTGTTATATTGTAAAATATCGATACA
66 CTGATTTTGTCATA-TTTTTACCTGTTATATTGTAAAATATCGAT-CA
*
7882764 TTTTTAT-AAAGTATCGATA
1 TTTTTATAAAAGGATCGATA
7882783 TTTTATAGGC
Statistics
Matches: 226, Mismatches: 15, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
111 171 0.76
112 41 0.18
113 14 0.06
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (111 bp):
TTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCATTTTTGTCATAATGAAA
CTGATTTTGTCATATTTTTACCTGTTATATTGTAAAATATCGATCA
Found at i:7883426 original size:111 final size:111
Alignment explanation
Indices: 7883229--7883698 Score: 672
Period size: 111 Copynumber: 4.2 Consensus size: 111
7883219 AAGATCGATT
* ** *
7883229 CTTTTTATAAAAAGTATTTATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGA
1 CTTTTTAT-AAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGA
*
7883294 AACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
65 AACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
* * **
7883341 TTTTTTATAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCATTTTTGTCATAATGAA
1 CTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAA
* * *
7883406 ACTGATTTTGTCATAGTTTTACCTGTTATATTGTAAAGTATCTATC
66 ACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
* *
7883452 CTTTTTATAAAAGGATCGATACTTTCAACATATCAGATAAATTTTACCGTTTTTGTCATAATGAA
1 CTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAA
* * *
7883517 ACTAATTTTTTCATATTTTTACCTGTTATATTGTAAAGTATATATC
66 ACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
* * *
7883563 CTTTTTATAAAAGGATAGATACTTTCAACATATCAAGTAAATTTTACCGGTTTTGTCATTATGAA
1 CTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAA
* * * * **
7883628 ATTGGTTTTGTCATATTTTTACCTGTTACATTGTAAAATATCGATA
66 ACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
*
7883674 CATTTTTAT-AAAGTATCGATACTTT
1 C-TTTTTATAAAAGGATCGATACTTT
7883699 ATAAGCACTA
Statistics
Matches: 323, Mismatches: 34, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
111 309 0.96
112 14 0.04
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (111 bp):
CTTTTTATAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTTTTGTCATAATGAA
ACTGATTTTGTCATATTTTTACCTGTTATATTGTAAAGTATATATA
Found at i:7884152 original size:23 final size:23
Alignment explanation
Indices: 7884091--7884153 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
7884081 ACATATTTAA
** *
7884091 TATATAAAAGCTACCTATTACGT
1 TATATAAGTGCTACCTATTACAT
*
7884114 TATATAAGTGCAACCTATTACAT
1 TATATAAGTGCTACCTATTACAT
*
7884137 TATATAAGTGGTACCTA
1 TATATAAGTGCTACCTA
7884154 ATATAATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (23 bp):
TATATAAGTGCTACCTATTACAT
Found at i:7884225 original size:87 final size:87
Alignment explanation
Indices: 7884113--7884271 Score: 255
Period size: 87 Copynumber: 1.8 Consensus size: 87
7884103 ACCTATTACG
* * *
7884113 TTATATAAGTGCAACCTATTACATTATATAAGTGGTACCTAATATAATATTGTGCTTAATAATGT
1 TTATATAAGCGCAACCTATTACATTATATAAGCGGTACCTAATATAATATTGTACTTAATAATGT
7884178 TTCCAGTAATTAACATATTTTA
66 TTCCAGTAATTAACATATTTTA
* ** *
7884200 TTATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTATTTAATAATGT
1 TTATATAAGCGCAACCTATTACATTATATAAGCGGTACCTAATATAATATTGTACTTAATAATGT
7884265 TTCCAGT
66 TTCCAGT
7884272 TAAATGATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (87 bp):
TTATATAAGCGCAACCTATTACATTATATAAGCGGTACCTAATATAATATTGTACTTAATAATGT
TTCCAGTAATTAACATATTTTA
Found at i:7884249 original size:23 final size:23
Alignment explanation
Indices: 7884199--7884243 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
7884189 AACATATTTT
*
7884199 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
7884222 ATTATATAAGCGGTACCTAATA
1 ATTATATAAGCGCTACCTAATA
7884244 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:7887120 original size:56 final size:56
Alignment explanation
Indices: 7887049--7887165 Score: 216
Period size: 56 Copynumber: 2.1 Consensus size: 56
7887039 GACGCCTATT
* *
7887049 GCTGCGAAAGTAAGCCTCCAGCTGCTGCCAAAGCTGAAGCCGGTATCGTTCCGCTC
1 GCTGTGAAAGTAAGCCTCCAGCTGCTACCAAAGCTGAAGCCGGTATCGTTCCGCTC
7887105 GCTGTGAAAGTAAGCCTCCAGCTGCTACCAAAGCTGAAGCCGGTATCGTTCCGCTC
1 GCTGTGAAAGTAAGCCTCCAGCTGCTACCAAAGCTGAAGCCGGTATCGTTCCGCTC
7887161 GCTGT
1 GCTGT
7887166 TGCCGCAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.21
Consensus pattern (56 bp):
GCTGTGAAAGTAAGCCTCCAGCTGCTACCAAAGCTGAAGCCGGTATCGTTCCGCTC
Found at i:7891535 original size:127 final size:126
Alignment explanation
Indices: 7891309--7891958 Score: 955
Period size: 127 Copynumber: 5.2 Consensus size: 126
7891299 TACTATTCAT
* *
7891309 GTGAAGGCGCATTCCCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
7891374 ATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGAGGACC
66 ATTATGTCACTTATGTCCCCC-GGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* * *
7891436 GTGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTTTTTTGTCAGAGAATATGTTATCATTTCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
** ** *
7891501 ATTATGTCACTTATGTCCCATTGGAACTATTCATGTCAATATATATTATTCCTTAGGGGACT
66 ATTATGTCACTTATGTCCC-CCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* *
7891563 GTGAAGGCGTGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
** *
7891628 ATTATGTCACTTATGTCCCCAAGAACTATTTATGTCAATACCTATTATTCCTTAGGGGACC
66 ATTATGTCACTTATGTCCCCCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* * *
7891689 GTGAAGGTGCGTTCCCGGGGGCACGCCTTCCATTA-TTTATCAGAGAATATGTTATCATTGCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * *
7891753 ATTATGTCACGTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGAGATC
66 ATTATGTCACTTATGTCCCCCG-GAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* * * *
7891815 GTGAAGACGCGTTCCCGGTGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTTCCCT
1 GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * *
7891880 ATTATGTCACTTATGTCCCCCGAGAACTATTCATGTC-ATATCTACTATTTCTTAGGGGA-C
66 ATTATGTCACTTATGTCCCCCG-GAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
* * *
7891940 TTTAAAGCGCGTTCCCGGG
1 GTGAAGGCGCGTTCCCGGG
7891959 AACTATAGAT
Statistics
Matches: 469, Mismatches: 51, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
125 62 0.13
126 150 0.32
127 257 0.55
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (126 bp):
GTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTTATGTCCCCCGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACC
Found at i:7891840 original size:252 final size:253
Alignment explanation
Indices: 7891308--7891958 Score: 963
Period size: 252 Copynumber: 2.6 Consensus size: 253
7891298 GTACTATTCA
* *
7891308 TGTGAAGGCGCATTCCCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 TGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* *
7891373 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGAGGACCGT
65 TATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
** * * *
7891438 GAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTTTTTTGTCAGAGAATATGTTATCATTTCCCTAT
130 GAAGGCGCGTTCCCGGGGGCACGCCTTCCATTTATTTATCAGAGAATATGTTATCATTGCCCTAT
* ** * *
7891503 TATGTCACTTATGTCCCATTGGAACTATTCATGTCAATATATATTATTCCTTAGGGGAC
195 TATGTCACGTATGTCCCACCGGAACTATTCATGTCAATACATATTATTCCTTAGGAGAC
*
7891562 TGTGAAGGCGTGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 TGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* *
7891627 TATTATGTCACTTATGT-CCCCAAGAACTATTTATGTCAATACCTATTATTCCTTAGGGGACCGT
65 TATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGT
*
7891691 GAAGGTGCGTTCCCGGGGGCACGCCTTCCA-TTATTTATCAGAGAATATGTTATCATTGCCCTAT
130 GAAGGCGCGTTCCCGGGGGCACGCCTTCCATTTATTTATCAGAGAATATGTTATCATTGCCCTAT
*
7891755 TATGTCACGTATGTCCC-CCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGAGA-
195 TATGTCACGTATGTCCCACCG-GAACTATTCATGTCAATACATATTATTCCTTAGGAGAC
* * *
7891813 TCGTGAAGACGCGTTCCCGGTGGCGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTTCC
1 T-GTGAAGGCGCGTTCCCGG-GGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCC
* * * *
7891878 CTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTC-ATATCTACTATTTCTTAGGGGA-CT
64 CTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCG
* *
7891941 TTAAAGCGCGTTCCCGGG
129 TGAAGGCGCGTTCCCGGG
7891959 AACTATAGAT
Statistics
Matches: 360, Mismatches: 33, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
251 20 0.06
252 174 0.48
253 88 0.24
254 78 0.22
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (253 bp):
TGTGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTG
AAGGCGCGTTCCCGGGGGCACGCCTTCCATTTATTTATCAGAGAATATGTTATCATTGCCCTATT
ATGTCACGTATGTCCCACCGGAACTATTCATGTCAATACATATTATTCCTTAGGAGAC
Found at i:7892405 original size:34 final size:33
Alignment explanation
Indices: 7892367--7892463 Score: 124
Period size: 32 Copynumber: 2.9 Consensus size: 33
7892357 TGAATTAATG
7892367 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATACTATAATTT-TATTTTAAAT
* * *
7892401 TTAAATTTCGAATAATATTA-TTTATTTTAATT
1 TTAAATTTCGAATACTATAATTTTATTTTAAAT
* *
7892433 TTGAATTTGGAATACTATAATTTGTATTTTA
1 TTAAATTTCGAATACTATAATTT-TATTTTA
7892464 TAAACATTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 25 0.46
33 4 0.07
34 25 0.46
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (33 bp):
TTAAATTTCGAATACTATAATTTTATTTTAAAT
Found at i:7893029 original size:20 final size:20
Alignment explanation
Indices: 7892980--7893042 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
7892970 AGTATAAAAC
*
7892980 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
7893000 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
7893021 CCTGCGGGCTAGGAAAGTAA
1 CCTGCGGGCTAGGAATGTAA
7893041 CC
1 CC
7893043 CTTCGGAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 21 0.52
21 19 0.47
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.17
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:7894699 original size:19 final size:20
Alignment explanation
Indices: 7894675--7894725 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
7894665 CGGCCAAGAG
* *
7894675 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
7894694 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
7894714 CATGTATTTTCA
1 CATGTATTTTCA
7894726 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:7895480 original size:19 final size:19
Alignment explanation
Indices: 7895427--7895476 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
7895417 TTGGAGTGCA
**
7895427 AAAAGAAG-AGAAAA-ATC
1 AAAAGAAGAAGAAAAGAAG
7895444 AAAAGAAGAAGAAAAGAAG
1 AAAAGAAGAAGAAAAGAAG
7895463 AAAAGAA-AAGAAAA
1 AAAAGAAGAAGAAAA
7895477 AGAATTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
18 13 0.45
19 8 0.28
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAAGAAGAAGAAAAGAAG
Found at i:7898858 original size:19 final size:20
Alignment explanation
Indices: 7898834--7898884 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
7898824 CGGCCAAGAG
* *
7898834 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
7898853 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
7898873 CATGTATTTTCA
1 CATGTATTTTCA
7898885 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:7900743 original size:15 final size:14
Alignment explanation
Indices: 7900723--7900792 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 14
7900713 ATAAATTTAA
7900723 ATAAATAATAATTAT
1 ATAAAT-ATAATTAT
* *
7900738 ATAAATATTATTTT
1 ATAAATATAATTAT
* *
7900752 AATAAAAAATATTTAT
1 -AT-AAATATAATTAT
*
7900768 ATAATTAT-ATTAAT
1 ATAAATATAATT-AT
7900782 ATAAATATAAT
1 ATAAATATAAT
7900793 AACTATTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
13 2 0.05
14 19 0.46
15 12 0.29
16 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAATATAATTAT
Found at i:7902997 original size:29 final size:29
Alignment explanation
Indices: 7902954--7903012 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
7902944 AAAATTCTTA
*
7902954 ACAAATATTACTTTATAATCACCTCAAAC
1 ACAAATATTACTTTATAATCACATCAAAC
*
7902983 ACAAATATTATTTTATAATCACATCAAAC
1 ACAAATATTACTTTATAATCACATCAAAC
7903012 A
1 A
7903013 ATTCAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.32
Consensus pattern (29 bp):
ACAAATATTACTTTATAATCACATCAAAC
Done.