Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 21
Found at i:3900341 original size:81 final size:81
Alignment explanation
Indices: 3900165--3900549 Score: 380
Period size: 81 Copynumber: 4.8 Consensus size: 81
3900155 TACCTAAAGC
* * * * * * * * * *
3900165 TATTTAGCCTTTCATCTAACTTGCATATTTGACACTTTTCTGTCAATTTCACAACTAGTCCATT-
1 TATTTAGTCGTTCATCTAACTGGCATAATTAACACATTTCTGCCAAATGCACAACTAGGCCATTC
* **
3900229 ATTCTTTTACTCAACAG
66 A-TATTTTACTCAATGG
* * * * ** * * *
3900246 TGTTTA-ACTATTCATCTATCTGGCATAATTGTCACATTTCTTCCAAATGCACAGCTAGGTCATT
1 TATTTAGTC-GTTCATCTAACTGGCATAATTAACACATTTCTGCCAAATGCACAACTAGGCCATT
3900310 CATATTTTACTCAATGG
65 CATATTTTACTCAATGG
* * *
3900327 TATTTAGTCGTTCATCTAACTGGCATAATTAACATATTTCAGCCAAATGCACAGCTAGGCCATTC
1 TATTTAGTCGTTCATCTAACTGGCATAATTAACACATTTCTGCCAAATGCACAACTAGGCCATTC
* * ***
3900392 ATCTTTTACTCCACAA
66 ATATTTTACTCAATGG
* *
3900408 TATTTAGTCGTTCATCTAACTGGCATAATTAACACATTTTTGCCTAATGCACAACTAGGCCATTC
1 TATTTAGTCGTTCATCTAACTGGCATAATTAACACATTTCTGCCAAATGCACAACTAGGCCATTC
*
3900473 ATTTTTTACTCAATGG
66 ATATTTTACTCAATGG
* * * * *
3900489 TATTCA-ACTGTTTATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCC
1 TATTTAGTC-GTTCATCTAACTGGCATAATTAACACATTTCTGCCAAATGCACAACTAGGCC
3900550 TCAAGGCATT
Statistics
Matches: 250, Mismatches: 50, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
80 2 0.01
81 246 0.98
82 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (81 bp):
TATTTAGTCGTTCATCTAACTGGCATAATTAACACATTTCTGCCAAATGCACAACTAGGCCATTC
ATATTTTACTCAATGG
Found at i:3900433 original size:162 final size:162
Alignment explanation
Indices: 3900175--3900549 Score: 425
Period size: 162 Copynumber: 2.3 Consensus size: 162
3900165 TATTTAGCCT
* * * * * * * * *
3900175 TTCATCTAACTTGCATATTTGACACTTTTCTGTCAATTTCACAACTAGTCCATT-ATTCTTTTAC
1 TTCATCTAACTGGCATAATTAACACATTTCAGCCAAATGCACAACTAGGCCATTCA-TCTTTTAC
* * * * * * ** *
3900239 TCAACAGTGTTTA-ACTATTCATCTATCTGGCATAATTGTCACATTTCTT-CCAAATGCACAGCT
65 TCCACAATATTTAGTC-GTTCATCTAACTGGCATAATTAACACATTT-TTGCCAAATGCACAACT
* * *
3900302 AGGTCATTCATATTTTACTCAATGGTATT-TAGTCG
128 AGGCCATTCATATTTTACTCAATGGTATTCAACT-G
* *
3900337 TTCATCTAACTGGCATAATTAACATATTTCAGCCAAATGCACAGCTAGGCCATTCATCTTTTACT
1 TTCATCTAACTGGCATAATTAACACATTTCAGCCAAATGCACAACTAGGCCATTCATCTTTTACT
*
3900402 CCACAATATTTAGTCGTTCATCTAACTGGCATAATTAACACATTTTTGCCTAATGCACAACTAGG
66 CCACAATATTTAGTCGTTCATCTAACTGGCATAATTAACACATTTTTGCCAAATGCACAACTAGG
*
3900467 CCATTCATTTTTTACTCAATGGTATTCAACTG
131 CCATTCATATTTTACTCAATGGTATTCAACTG
* * * *
3900499 TTTATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCC
1 TTCATCTAACTGGCATAATTAACACATTTCAGCCAAATGCACAACTAGGCC
3900550 TCAAGGCATT
Statistics
Matches: 178, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
161 2 0.01
162 172 0.97
163 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (162 bp):
TTCATCTAACTGGCATAATTAACACATTTCAGCCAAATGCACAACTAGGCCATTCATCTTTTACT
CCACAATATTTAGTCGTTCATCTAACTGGCATAATTAACACATTTTTGCCAAATGCACAACTAGG
CCATTCATATTTTACTCAATGGTATTCAACTG
Found at i:3900739 original size:134 final size:134
Alignment explanation
Indices: 3900499--3900809 Score: 453
Period size: 134 Copynumber: 2.3 Consensus size: 134
3900489 TATTCAACTG
* * *
3900499 TTTATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCTCAAGGCATTTAGC
1 TTTATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTAAAGGCACTTAGC
* * * * * *
3900564 CTTTCATCTAACTGGCATAATTGACTCCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTT
66 CTTTCATCTAACTGACATAACTGACACATTTATGTCAAATGCATAGTTAGGCCTCAAAGACACTT
3900629 AGCC
131 AGCC
* **
3900633 TTTATCTAACT-GCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTTAAAGGCACTTAG
1 TTTATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCC-TAAAGGCACTTAG
* *
3900697 CCTTTCATGTAACTGACATAACTGACACATTTATGTCAAATGCATAGTTAGGCCTCAAAGACATT
65 CCTTTCATCTAACTGACATAACTGACACATTTATGTCAAATGCATAGTTAGGCCTCAAAGACACT
3900762 TAGCC
130 TAGCC
* *
3900767 TTTCATCTAACTGGCATAATTGACACATTTCTGTCAAAGGCAC
1 TTT-ATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
3900810 TTGGATTACT
Statistics
Matches: 157, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
133 35 0.22
134 87 0.55
135 8 0.05
136 27 0.17
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (134 bp):
TTTATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTAAAGGCACTTAGC
CTTTCATCTAACTGACATAACTGACACATTTATGTCAAATGCATAGTTAGGCCTCAAAGACACTT
AGCC
Found at i:3900746 original size:68 final size:68
Alignment explanation
Indices: 3900502--3900809 Score: 433
Period size: 68 Copynumber: 4.6 Consensus size: 68
3900492 TCAACTGTTT
* ** *
3900502 ATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAACTAGGCCTC-AAGGCATTTAGCCT
1 ATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
3900566 TTC
66 TTC
* *
3900569 ATCTAACTGGCATAATTGACTCCTTTCTGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAGCCT
1 ATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
3900634 TT-
66 TTC
* *
3900636 ATCTAACT-GCATAATTGACACCTTTATGTCAAATGCACAGTTAGGCCTTAAAGGCACTTAGCCT
1 ATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
3900700 TTC
66 TTC
* * * * * * * *
3900703 ATGTAACTGACATAACTGACACATTTATGTCAAATGCATAGTTAGGCCTCAAAGACATTTAGCCT
1 ATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
3900768 TTC
66 TTC
* *
3900771 ATCTAACTGGCATAATTGACACATTTCTGTCAAAGGCAC
1 ATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCAC
3900810 TTGGATTACT
Statistics
Matches: 214, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
66 54 0.25
67 60 0.28
68 100 0.47
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
ATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
TTC
Found at i:3901011 original size:55 final size:54
Alignment explanation
Indices: 3900895--3901040 Score: 179
Period size: 55 Copynumber: 2.7 Consensus size: 54
3900885 CATCCAGAAC
* * * * * *
3900895 TTCATACACATAGTATGAATTT-TGAG-TTCGCACATATAGTACCTATACGAAA
1 TTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTACCCATACGAAA
* *
3900947 TTCATACACTTAGTATAAATTTCTTAGTTTTGCACACAAAGTGCCCATACGAAAA
1 TTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTACCCATACG-AAA
3901002 TTCATACACTTAGTATGAATTTCTTAGGTTTTTGCACAC
1 TTCATACACTTAGTATGAATTTCTTA-G-TTTTGCACAC
3901041 TTAGTGCCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
52 20 0.25
53 3 0.04
54 18 0.22
55 28 0.35
56 1 0.01
57 10 0.12
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (54 bp):
TTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTACCCATACGAAA
Found at i:3901935 original size:11 final size:11
Alignment explanation
Indices: 3901900--3901929 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3901890 CATAACTTAG
3901900 TTTTAATCCCA
1 TTTTAATCCCA
3901911 TTTTAATCCCA
1 TTTTAATCCCA
3901922 TTTTAATC
1 TTTTAATC
3901930 ATATTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (11 bp):
TTTTAATCCCA
Found at i:3902126 original size:23 final size:24
Alignment explanation
Indices: 3902100--3902145 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
3902090 TTACCCTTTT
* *
3902100 CCTTATTTAAATACA-TTTAAATA
1 CCTTATTAAAATAAATTTTAAATA
3902123 CCTTATTAAAATAAATTTTAAAT
1 CCTTATTAAAATAAATTTTAAAT
3902146 TCATTTTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (24 bp):
CCTTATTAAAATAAATTTTAAATA
Found at i:3902968 original size:22 final size:22
Alignment explanation
Indices: 3902923--3902972 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3902913 TCGGATTTAT
* *
3902923 GAAGATATTGATGGCCTTGGTG
1 GAAGATGTTGATGGCCTTGATG
**
3902945 GAAGATGTTGATGGTGTTGATG
1 GAAGATGTTGATGGCCTTGATG
3902967 G-AGATG
1 GAAGATG
3902973 GTGGTGATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.24, C:0.04, G:0.40, T:0.32
Consensus pattern (22 bp):
GAAGATGTTGATGGCCTTGATG
Found at i:3907044 original size:22 final size:23
Alignment explanation
Indices: 3907004--3907046 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3906994 AAAGATAAAA
*
3907004 AAAACAAATATGATTAATAAGGG
1 AAAACAAATATGATAAATAAGGG
*
3907027 AAAATAAATA-GATAAATAAG
1 AAAACAAATATGATAAATAAG
3907047 ATAAGTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.63, C:0.02, G:0.14, T:0.21
Consensus pattern (23 bp):
AAAACAAATATGATAAATAAGGG
Found at i:3911035 original size:21 final size:21
Alignment explanation
Indices: 3911002--3911043 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3910992 AATATGAAAA
*
3911002 CATCCTGCCCGAAGGACTTAT
1 CATCCTGCCCGAAAGACTTAT
* *
3911023 CATCTTGCTCGAAAGACTTAT
1 CATCCTGCCCGAAAGACTTAT
3911044 AGATGACCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (21 bp):
CATCCTGCCCGAAAGACTTAT
Found at i:3911316 original size:115 final size:115
Alignment explanation
Indices: 3911162--3911651 Score: 612
Period size: 115 Copynumber: 4.3 Consensus size: 115
3911152 GTTTACAGTT
* * * * * * *
3911162 ATCATTAAGAAACCCCTAAAAATTAGGCTTAG-CTATTTTAAAAATTCATGGGAAATAATCATCA
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGGAAATCATCATCA
* *
3911226 AGAAACCCTTAAAAATTAGGCTTAGCTTCTTTAAAAATTTATTGGAAATA
66 AGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTGGAAATA
3911276 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGGAAATCATCATCA
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGGAAATCATCATCA
* * *
3911341 ATAAACCCCTAAAAATTAGACTTAGCTTCTTTAAAAATTTATTGGAAATA
66 AGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTGGAAATA
* * * * *
3911391 ATCATCAAGACACCCTTGAAAATCAGGCTTAGCTTCTTTTAAAAATTAATTGGAAATCATCATTA
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGGAAATCATCATCA
* * * *
3911456 AGAAACCCCTGAAAATCT-GGATTAGCTTCTTTTAAAAAATCATTGGAAATC
66 AGAAACCCCTAAAAAT-TAGGCTTAGCTTC-TTTAAAAATTCATTGGAAATA
* *
3911507 ATCATCAAGAAACCCCTGAAAACCAGGCTTAGTTTCTTTTAAAAAAATCATTGGAAATCATCATC
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTT-AAAAATTCATTGGAAATCATCATC
* * * * ** * *
3911572 AAGAAATCCTTAAAAATCAGGCTTAGTTTCTAAAAAAACTCATTTG-AA-A
65 AAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTGGAAATA
* * *
3911621 A-CATCAAGAAATCCCTAAAAATTAGGCTTAG
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAG
3911652 CATTTTTCAA
Statistics
Matches: 327, Mismatches: 44, Indels: 11
0.86 0.12 0.03
Matches are distributed among these distances:
113 26 0.08
114 30 0.09
115 160 0.49
116 67 0.20
117 44 0.13
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (115 bp):
ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGGAAATCATCATCA
AGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTCATTGGAAATA
Found at i:3911347 original size:58 final size:58
Alignment explanation
Indices: 3911162--3911703 Score: 589
Period size: 58 Copynumber: 9.4 Consensus size: 58
3911152 GTTTACAGTT
* * * * *
3911162 ATCATTAAGAAACCCCTAAAAATTAGGCTTAGC-TATTTTAAAAATTCATGGGAAATA
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
* * * *
3911219 ATCATCAAGAAACCCTTAAAAATTAGGCTTAGCTTC-TTTAAAAATTTATTGGAAATA
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
* *
3911276 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGGAAATC
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
* * * * *
3911334 ATCATCAATAAACCCCTAAAAATTAGACTTAGCTTC-TTTAAAAATTTATTGGAAATA
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
* * * *
3911391 ATCATCAAGACACCCTTGAAAATCAGGCTTAGCTTCTTTTAAAAATTAATTGGAAATC
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
* * * * *
3911449 ATCATTAAGAAACCCCTGAAAATCTGGATTAGCTTCTTTTAAAAAATCATTGGAAATC
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
* * * *
3911507 ATCATCAAGAAACCCCTGAAAACCAGGCTTAGTTTCTTTTAAAAAAATCATTGGAAATC
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTT-AAAAATTCATTGGAAATC
* * * ** * *
3911566 ATCATCAAGAAATCCTTAAAAATCAGGCTTAGTTTC-TAAAAAAACTCATTTGAAA--
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
* * * * * *
3911621 A-CATCAAGAAATCCCTAAAAATTAGGCTTAGCAT-TTTTCAAAA-TCATTTGAAAAC
1 ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
* * *
3911676 ATCATATCAAGGAACCTCTGAAAATCAG
1 ATC--ATCAAGAAACCCCTAAAAATCAG
3911704 ACCTGATTTC
Statistics
Matches: 417, Mismatches: 58, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
53 10 0.02
54 34 0.08
55 2 0.00
56 1 0.00
57 145 0.35
58 175 0.42
59 50 0.12
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (58 bp):
ATCATCAAGAAACCCCTAAAAATCAGGCTTAGCTTCTTTTAAAAATTCATTGGAAATC
Found at i:3923375 original size:13 final size:13
Alignment explanation
Indices: 3923357--3923391 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3923347 CTTAAGCCTA
* *
3923357 AAAATAACATGTT
1 AAAATAAAATATT
3923370 AAAATAAAATATT
1 AAAATAAAATATT
3923383 AAAATAAAA
1 AAAATAAAA
3923392 ACGAAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (13 bp):
AAAATAAAATATT
Found at i:3936225 original size:2 final size:2
Alignment explanation
Indices: 3936216--3936276 Score: 54
Period size: 2 Copynumber: 31.0 Consensus size: 2
3936206 TAAAATAATT
* * *
3936216 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA AA GTA TA TA AA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
3936258 AA AA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
3936277 GTTTACATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.04
2 47 0.94
3 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (2 bp):
TA
Found at i:3936230 original size:23 final size:23
Alignment explanation
Indices: 3936202--3936276 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
3936192 AATCGAATTT
*
3936202 TATATAAAATAATTTATAATATA
1 TATATAAAATAATATATAATATA
*
3936225 TATATATATATATATATATAA-AGTA
1 TATATA-AAATA-ATATATAATA-TA
*
3936250 TATA-AAGAAAAATATATAATATA
1 TATATAA-AATAATATATAATATA
3936273 TATA
1 TATA
3936277 GTTTACATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
23 21 0.49
24 9 0.21
25 13 0.30
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (23 bp):
TATATAAAATAATATATAATATA
Found at i:3936312 original size:20 final size:22
Alignment explanation
Indices: 3936283--3936325 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
3936273 TATAGTTTAC
*
3936283 ATGTAGTTTAT-TA-ATAAATT
1 ATGTAATTTATATATATAAATT
3936303 ATGTAATTTATATATATAAATT
1 ATGTAATTTATATATATAAATT
3936325 A
1 A
3936326 CATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 2 0.10
22 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
ATGTAATTTATATATATAAATT
Found at i:3936351 original size:24 final size:24
Alignment explanation
Indices: 3936312--3936358 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3936302 TATGTAATTT
*
3936312 ATATATATAAATTACATATATATA
1 ATATATATAAAGTACATATATATA
*
3936336 ATATATATTAAGTACATATATAT
1 ATATATATAAAGTACATATATAT
3936359 TACTACATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATATATAAAGTACATATATATA
Found at i:3936438 original size:9 final size:9
Alignment explanation
Indices: 3936424--3936456 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3936414 GTGTTAACAA
*
3936424 TATATAAAC
1 TATATAAAG
3936433 TATATAAAG
1 TATATAAAG
3936442 TAT-TAAAG
1 TATATAAAG
3936450 TATATAA
1 TATATAA
3936457 TTTATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (9 bp):
TATATAAAG
Found at i:3936464 original size:19 final size:19
Alignment explanation
Indices: 3936442--3936495 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 19
3936432 CTATATAAAG
3936442 TATTAAAGTATATAA-TTTA
1 TATTAAA-TATATAAGTTTA
3936461 TATTAATATAATATAAGTTTA
1 TATTAA-AT-ATATAAGTTTA
3936482 TATATAAACTATAT
1 TAT-TAAA-TATAT
3936496 TTATATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.23
20 7 0.23
21 12 0.40
22 4 0.13
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
TATTAAATATATAAGTTTA
Found at i:3936500 original size:15 final size:15
Alignment explanation
Indices: 3936482--3936598 Score: 66
Period size: 15 Copynumber: 7.9 Consensus size: 15
3936472 TATAAGTTTA
3936482 TATATAAACTATATTT
1 TATATAAACTATA-TT
3936498 ATATTATAAACTATATAAT
1 -TA-TATAAACTATAT--T
* * * *
3936517 TTTATGAGCTACA--
1 TATATAAACTATATT
*
3936530 TATATAAACTATGTT
1 TATATAAACTATATT
*
3936545 TATATGAACTATA--
1 TATATAAACTATATT
*
3936558 TATATAAAC--TATG
1 TATATAAACTATATT
*
3936571 TATATAAACTATATA
1 TATATAAACTATATT
*
3936586 TGTATAAACTATA
1 TATATAAACTATA
3936599 AAAAGTATAT
Statistics
Matches: 77, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
11 2 0.03
13 25 0.32
15 26 0.34
17 11 0.14
18 12 0.16
19 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (15 bp):
TATATAAACTATATT
Found at i:3936507 original size:18 final size:18
Alignment explanation
Indices: 3936456--3936513 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 18
3936446 AAAGTATATA
3936456 ATTTATATTAATATAA-TAT
1 ATTTATATT-ATA-AACTAT
3936475 AAGTTTATA-TATAAACTAT
1 -A-TTTATATTATAAACTAT
3936494 ATTTATATTATAAACTAT
1 ATTTATATTATAAACTAT
3936512 AT
1 AT
3936514 AATTTTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.17
18 15 0.43
19 6 0.17
20 2 0.06
21 6 0.17
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTTATATTATAAACTAT
Found at i:3936551 original size:28 final size:28
Alignment explanation
Indices: 3936519--3936597 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 28
3936509 TATATAATTT
* *
3936519 TATGAGCTACATATATAAACTATGTTTA
1 TATGAACTACATATATAAACTATGTATA
*
3936547 TATGAACTATATATATAAACTATGTATA
1 TATGAACTACATATATAAACTATGTATA
*
3936575 TA--AACTATATATGTATAAACTAT
1 TATGAACTACATA--TATAAACTAT
3936598 AAAAAGTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 9 0.20
28 37 0.80
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (28 bp):
TATGAACTACATATATAAACTATGTATA
Found at i:3936561 original size:13 final size:13
Alignment explanation
Indices: 3936529--3936598 Score: 77
Period size: 13 Copynumber: 5.1 Consensus size: 13
3936519 TATGAGCTAC
3936529 ATATATAAACTATGT
1 ATATATAAACTA--T
* *
3936544 TTATATGAACTAT
1 ATATATAAACTAT
3936557 ATATATAAACTAT
1 ATATATAAACTAT
*
3936570 GTATATAAACTAT
1 ATATATAAACTAT
3936583 ATATGTATAAACTAT
1 ATA--TATAAACTAT
3936598 A
1 A
3936599 AAAAGTATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
13 26 0.55
15 21 0.45
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (13 bp):
ATATATAAACTAT
Found at i:3937241 original size:9 final size:9
Alignment explanation
Indices: 3937227--3937259 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3937217 TAATAGTATT
3937227 TAATATTAA
1 TAATATTAA
3937236 TAATATTAA
1 TAATATTAA
*
3937245 TACTATT-A
1 TAATATTAA
3937253 TAATATT
1 TAATATT
3937260 GAAAATTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (9 bp):
TAATATTAA
Found at i:3951631 original size:20 final size:20
Alignment explanation
Indices: 3951606--3951704 Score: 87
Period size: 20 Copynumber: 4.8 Consensus size: 20
3951596 TGTATAAAGT
*
3951606 TATAAACTATGTATAGTATA
1 TATAAACTATATATAGTATA
3951626 TATAAACTATATATA-TA-A
1 TATAAACTATATATAGTATA
*
3951644 CATATAA-TATATGCATTATGTATA
1 TATA-AACTATAT--A-TA-GTATA
*
3951668 TATACAATCTATATATAGTTTA
1 TATA-AA-CTATATATAGTATA
3951690 TATAAACTATATATA
1 TATAAACTATATATA
3951705 TAACCTATAG
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
18 9 0.14
19 4 0.06
20 24 0.37
21 4 0.06
22 8 0.12
23 4 0.06
24 7 0.11
26 5 0.08
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (20 bp):
TATAAACTATATATAGTATA
Found at i:3951640 original size:13 final size:13
Alignment explanation
Indices: 3951622--3951749 Score: 64
Period size: 13 Copynumber: 9.7 Consensus size: 13
3951612 CTATGTATAG
3951622 TATATATAAACTA
1 TATATATAAACTA
3951635 TATATAT-AACATA
1 TATATATAAAC-TA
** *
3951648 TAATATATGCATTA
1 T-ATATATAAACTA
* * *
3951662 TGTATATATACAA
1 TATATATAAACTA
* * *
3951675 TCTATATATAGT-
1 TATATATAAACTA
3951687 T-TATATAAACTA
1 TATATATAAACTA
*
3951699 TATATATAACCTA
1 TATATATAAACTA
* *
3951712 TAGTTTATAAACAA
1 TA-TATATAAACTA
* *
3951726 TAGTTTATAACCTA
1 TA-TATATAAACTA
3951740 TAGTATATAA
1 TA-TATATAA
3951750 TTTATAAACT
Statistics
Matches: 90, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
11 8 0.09
12 5 0.06
13 38 0.42
14 38 0.42
15 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:3951728 original size:14 final size:14
Alignment explanation
Indices: 3951711--3951749 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3951701 TATATAACCT
3951711 ATAGTTTATAAACA
1 ATAGTTTATAAACA
* *
3951725 ATAGTTTATAACCT
1 ATAGTTTATAAACA
*
3951739 ATAGTATATAA
1 ATAGTTTATAA
3951750 TTTATAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (14 bp):
ATAGTTTATAAACA
Found at i:3951741 original size:28 final size:27
Alignment explanation
Indices: 3951681--3951749 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
3951671 ACAATCTATA
*
3951681 TATAGTTTATATAAACTATATATATAACC
1 TATAG-TT-TATAAACAATATATATAACC
*
3951710 TATAGTTTATAAACAATAGTTTATAACC
1 TATAGTTTATAAACAATA-TATATAACC
*
3951738 TATAGTATATAA
1 TATAGTTTATAA
3951750 TTTATAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.28
28 21 0.58
29 5 0.14
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.41
Consensus pattern (27 bp):
TATAGTTTATAAACAATATATATAACC
Found at i:3951753 original size:21 final size:21
Alignment explanation
Indices: 3951729--3951769 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3951719 TAAACAATAG
*
3951729 TTTATAACCTATAGTATATAA
1 TTTATAAACTATAGTATATAA
*
3951750 TTTATAAACTATAGTTTATA
1 TTTATAAACTATAGTATATA
3951770 TTAATGTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTATAAACTATAGTATATAA
Found at i:3951849 original size:36 final size:36
Alignment explanation
Indices: 3951809--3951910 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 36
3951799 TAATAATCTT
*
3951809 AACTATAATTTATATTAATATAGCATATTGTTTATA
1 AACTATAATTTATATTAATATAGCATATTGTTTAAA
* * * *
3951845 AACTATAATTTGTATTAATGTAGTATATAGTTTAAA
1 AACTATAATTTATATTAATATAGCATATTGTTTAAA
* * *
3951881 AACTATAGTTTACATTAATATTAACATATT
1 AACTATAATTTATATTAATA-TAGCATATT
3951911 AACTATAGTT
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
36 47 0.89
37 6 0.11
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (36 bp):
AACTATAATTTATATTAATATAGCATATTGTTTAAA
Found at i:3951944 original size:17 final size:16
Alignment explanation
Indices: 3951906--3952002 Score: 71
Period size: 16 Copynumber: 6.2 Consensus size: 16
3951896 TAATATTAAC
3951906 ATATTAACTATAGTTT
1 ATATTAACTATAGTTT
3951922 ATATTAA-TATAGTATT
1 ATATTAACTATAGT-TT
* *
3951938 AATATTAATTATAGTCT
1 -ATATTAACTATAGTTT
* *
3951955 ATA--AACCATA-TACT
1 ATATTAACTATAGT-TT
*
3951969 ATATTAA-TATTA-ATT
1 ATATTAACTA-TAGTTT
3951984 ATATTAACTATAGTTT
1 ATATTAACTATAGTTT
3952000 ATA
1 ATA
3952003 AACTATACTA
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
13 1 0.02
14 10 0.15
15 17 0.26
16 23 0.35
17 8 0.12
18 6 0.09
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (16 bp):
ATATTAACTATAGTTT
Found at i:3951996 original size:45 final size:44
Alignment explanation
Indices: 3951921--3952015 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 44
3951911 AACTATAGTT
*
3951921 TATATTAATATAGTATTAATATTAATTATAGTCTATAAACCATATAC
1 TATATTAATATAG-ATTAATATTAACTATAGTCTATAAA-C-TATAC
*
3951968 TATATTAATATTA-ATT-ATATTAACTATAGTTTATAAACTATAC
1 TATATTAATA-TAGATTAATATTAACTATAGTCTATAAACTATAC
3952011 TATAT
1 TATAT
3952016 AATTTATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
43 10 0.22
44 1 0.02
45 19 0.42
46 3 0.07
47 10 0.22
48 2 0.04
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (44 bp):
TATATTAATATAGATTAATATTAACTATAGTCTATAAACTATAC
Found at i:3952035 original size:45 final size:45
Alignment explanation
Indices: 3951921--3952035 Score: 110
Period size: 45 Copynumber: 2.5 Consensus size: 45
3951911 AACTATAGTT
* * *
3951921 TATATTAATATAGTATTAATATTAATTATAGTCTATAAACCATATAC
1 TATATTAATATA-AAAT-ATATTAACTATAGTCTATAAACCATATAC
* * *
3951968 TATATTAATATTAATTATATTAACTATAGTTTATAAA-C-TATAC
1 TATATTAATATAAAATATATTAACTATAGTCTATAAACCATATAC
3952011 TATA-TAATTTATAAAATATAATTAA
1 TATATTAA--TATAAAATAT-ATTAA
3952036 TATTAATATT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
42 3 0.05
43 9 0.15
44 9 0.15
45 24 0.41
46 3 0.05
47 11 0.19
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (45 bp):
TATATTAATATAAAATATATTAACTATAGTCTATAAACCATATAC
Found at i:3952042 original size:6 final size:6
Alignment explanation
Indices: 3952031--3952144 Score: 51
Period size: 6 Copynumber: 19.0 Consensus size: 6
3952021 ATAAAATATA
* * * *
3952031 ATTAAT ATTAAT ATTAAT TTTATAG ACT-AT ATTTTAT ATTAAT ATTAATT
1 ATTAAT ATTAAT ATTAAT ATTA-AT ATTAAT A-TTAAT ATTAAT ATTAA-T
** * * *
3952081 ACAAATT ATAAACT ATATTAT ATTAAT A-TAA- GTTAAT ATTAAT ATT-A-
1 ATTAA-T ATTAA-T AT-TAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
3952128 ATT-AT ATTAAT ATTAAT
1 ATTAAT ATTAAT ATTAAT
3952145 TATAAATGAT
Statistics
Matches: 83, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
4 4 0.05
5 12 0.14
6 45 0.54
7 21 0.25
8 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (6 bp):
ATTAAT
Found at i:3952054 original size:31 final size:30
Alignment explanation
Indices: 3952018--3952145 Score: 98
Period size: 31 Copynumber: 4.0 Consensus size: 30
3952008 TACTATATAA
3952018 TTTATAAAATATAATTAATATTAATATTAAT
1 TTTATAAAATATAATT-ATATTAATATTAAT
* * *
3952049 TTTATAGACTATATTTTATATTAATATTAAT
1 TTTATAAAATATA-ATTATATTAATATTAAT
* *
3952080 TACAAATTATAAACTAT-ATTATATTAATA-TAAG
1 T-----TTATAAAATATAATTATATTAATATTAAT
* *
3952113 TTAATATTAATATTAATTATATTAATATTAAT
1 TTTATA-AAATA-TAATTATATTAATATTAAT
3952145 T
1 T
3952146 ATAAATGATA
Statistics
Matches: 77, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
28 4 0.05
29 3 0.04
30 1 0.01
31 38 0.49
32 6 0.08
33 4 0.05
34 11 0.14
36 10 0.13
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
TTTATAAAATATAATTATATTAATATTAAT
Found at i:3952121 original size:21 final size:20
Alignment explanation
Indices: 3952095--3952146 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
3952085 ATTATAAACT
3952095 ATATTATATTAA-TATAAGTTA
1 ATATTATATTAATTAT-A-TTA
3952116 ATATTAATATTAATTATATTA
1 ATATT-ATATTAATTATATTA
3952137 ATATTA-ATTA
1 ATATTATATTA
3952147 TAAATGATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.14
20 1 0.03
21 13 0.45
22 8 0.28
23 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATTATATTAATTATATTA
Found at i:3958018 original size:23 final size:23
Alignment explanation
Indices: 3957987--3958040 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
3957977 ATTATTTTTC
3957987 TTTACATAAATTAAACTATATCA
1 TTTACATAAATTAAACTATATCA
* *
3958010 TTTATATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATA-TCA
3958034 TTTACAT
1 TTTACAT
3958041 TTAATCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTACATAAATTAAACTATATCA
Found at i:3958718 original size:16 final size:16
Alignment explanation
Indices: 3958697--3958728 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3958687 ACTTCACAAC
*
3958697 CAAAAAGTTAACCATA
1 CAAAAAGTAAACCATA
3958713 CAAAAAGTAAACCATA
1 CAAAAAGTAAACCATA
3958729 AAAGAACCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.19, G:0.06, T:0.16
Consensus pattern (16 bp):
CAAAAAGTAAACCATA
Found at i:3966925 original size:22 final size:21
Alignment explanation
Indices: 3966898--3966942 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
3966888 TTAACTGGTA
*
3966898 TTTTTCAACTTCTAGTTTCTCT
1 TTTTTCAACATCTAG-TTCTCT
**
3966920 TTTTTCCCCATCTAGTTCTCT
1 TTTTTCAACATCTAGTTCTCT
3966941 TT
1 TT
3966943 GGTTCAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.11, C:0.27, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTTCAACATCTAGTTCTCT
Found at i:3978745 original size:7 final size:7
Alignment explanation
Indices: 3978733--3978832 Score: 75
Period size: 7 Copynumber: 14.3 Consensus size: 7
3978723 ATGTAGAGTT
3978733 TATATTA
1 TATATTA
*
3978740 TATATTG
1 TATATTA
3978747 TATA-TA
1 TATATTA
* *
3978753 TTTAATA
1 TATATTA
3978760 TATATATA
1 TATAT-TA
3978768 TATATATA
1 TATAT-TA
3978776 TTATATTA
1 -TATATTA
*
3978784 TATATAA
1 TATATTA
3978791 TAT-TTA
1 TATATTA
3978797 TATATATAA
1 TATAT-T-A
3978806 TATATTA
1 TATATTA
3978813 TATA--A
1 TATATTA
3978818 TAT-TTA
1 TATATTA
*
3978824 TATAGTA
1 TATATTA
3978831 TA
1 TA
3978833 GCATGGTATA
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
5 4 0.05
6 13 0.17
7 34 0.45
8 14 0.18
9 11 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (7 bp):
TATATTA
Found at i:3978752 original size:2 final size:2
Alignment explanation
Indices: 3978733--3978855 Score: 93
Period size: 2 Copynumber: 64.0 Consensus size: 2
3978723 ATGTAGAGTT
* *
3978733 TA TA T- TA TA TA T- TG TA TA TA TT TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3978772 TA TA T- TA TA T- TA TA TA TA -A TA TT TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
3978810 T- TA TA TA -A TA TT TA TA TA GTA TA GCA TGG TA TA GTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA -TA T-A TA TA -TA TA TA TA
3978852 TA TA
1 TA TA
3978856 GTCTAAGACT
Statistics
Matches: 97, Mismatches: 11, Indels: 26
0.72 0.08 0.19
Matches are distributed among these distances:
1 9 0.09
2 82 0.85
3 6 0.06
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3978752 original size:9 final size:8
Alignment explanation
Indices: 3978733--3978827 Score: 79
Period size: 9 Copynumber: 11.5 Consensus size: 8
3978723 ATGTAGAGTT
3978733 TATA-TTA
1 TATATTTA
3978740 TATATTGTA
1 TATATT-TA
3978749 TATATTTA
1 TATATTTA
*
3978757 -ATATATA
1 TATATTTA
*
3978764 TATATATA
1 TATATTTA
3978772 TATA-TTA
1 TATATTTA
*
3978779 TATTATATA
1 TA-TATTTA
3978788 TAATATTTA
1 T-ATATTTA
*
3978797 TATATATAA
1 TATAT-TTA
3978806 TATATTATA
1 TATATT-TA
3978815 TAATATTTA
1 T-ATATTTA
3978824 TATA
1 TATA
3978828 GTATAGCATG
Statistics
Matches: 73, Mismatches: 6, Indels: 17
0.76 0.06 0.18
Matches are distributed among these distances:
7 14 0.19
8 24 0.33
9 29 0.40
10 6 0.08
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (8 bp):
TATATTTA
Found at i:3978774 original size:37 final size:36
Alignment explanation
Indices: 3978734--3978825 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 36
3978724 TGTAGAGTTT
* *
3978734 ATATTATATATTGTATAT-AT-TTAATATATATATAT
1 ATATTATATATTATATATAATATTTATATATATA-AT
3978769 ATATATATTATATTATATATAATATTTATATATATAAT
1 ATAT-TA-TATATTATATATAATATTTATATATATAAT
* *
3978807 ATATTATATAATATTTATA
1 ATATTATATATTATATATA
3978826 TAGTATAGCA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
35 4 0.08
36 13 0.27
37 13 0.27
38 8 0.16
39 11 0.22
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (36 bp):
ATATTATATATTATATATAATATTTATATATATAAT
Found at i:3978801 original size:27 final size:26
Alignment explanation
Indices: 3978733--3978832 Score: 113
Period size: 27 Copynumber: 4.0 Consensus size: 26
3978723 ATGTAGAGTT
*
3978733 TATAT-TAT-ATATTGTATATATTTAA
1 TATATATATAATATT-TATATATATAA
*
3978758 TATATATAT-ATATATATAT-TAT-A
1 TATATATATAATATTTATATATATAA
3978781 T-TATATATAATATTTATATATATAA
1 TATATATATAATATTTATATATATAA
3978806 TATATTATATAATATTTATATAGTATA
1 TATA-TATATAATATTTATATA-TATA
3978833 GCATGGTATA
Statistics
Matches: 65, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
22 7 0.11
23 11 0.17
24 5 0.08
25 12 0.18
26 9 0.14
27 17 0.26
28 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TATATATATAATATTTATATATATAA
Found at i:3980390 original size:31 final size:31
Alignment explanation
Indices: 3980346--3980432 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
3980336 TGGACTATGT
*
3980346 ATCCTCACA-ATTGGGTATCGAGATGATATTG
1 ATCCTCA-ATATTGGGTATCAAGATGATATTG
3980377 ATCCTCAATATTGGGTATCAAGATGATATTG
1 ATCCTCAATATTGGGTATCAAGATGATATTG
3980408 ATCCTCAATATTGGGTATCAAGATG
1 ATCCTCAATATTGGGTATCAAGATG
3980433 TTATCATTCT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
30 1 0.02
31 53 0.98
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (31 bp):
ATCCTCAATATTGGGTATCAAGATGATATTG
Found at i:3982572 original size:19 final size:19
Alignment explanation
Indices: 3982548--3982596 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
3982538 AATTTAAATT
3982548 AAATTACAAATCAGTGATC
1 AAATTACAAATCAGTGATC
3982567 AAATTACAAATCAGTGATC
1 AAATTACAAATCAGTGATC
3982586 AAATTACAAAT
1 AAATTACAAAT
3982597 AATTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (19 bp):
AAATTACAAATCAGTGATC
Found at i:3983647 original size:18 final size:19
Alignment explanation
Indices: 3983629--3983804 Score: 70
Period size: 20 Copynumber: 8.8 Consensus size: 19
3983619 AATGACCAAC
*
3983629 AAAATCGCAATGCGAAACA
1 AAAATCGCAACGCGAAACA
***
3983648 AAAATCGCAACGCGATTTA
1 AAAATCGCAACGCGAAACA
* *
3983667 GAAAATCGCAATGTTGAAA-A
1 -AAAATCGCAACG-CGAAACA
3983687 GAAAATCGCAACG-GTCAAA-A
1 -AAAATCGCAACGCG--AAACA
**
3983707 GAAAATCGCAACGCGATCTTCCA
1 -AAAATCGCAACGCGA---AACA
* **
3983730 AGAATCGCAACGCGATTCA
1 AAAATCGCAACGCGAAACA
***
3983749 AAGAATCGCAACGCGATTGA
1 AA-AATCGCAACGCGAAACA
***
3983769 GAAAATCGCAACGCGATTGA
1 -AAAATCGCAACGCGAAACA
3983789 GAAAATCGCAACGCGA
1 -AAAATCGCAACGCGA
3983805 TTCCAGGAAT
Statistics
Matches: 131, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
18 1 0.01
19 20 0.15
20 90 0.69
21 5 0.04
22 14 0.11
23 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:3983673 original size:20 final size:20
Alignment explanation
Indices: 3983648--3983846 Score: 174
Period size: 20 Copynumber: 9.8 Consensus size: 20
3983638 ATGCGAAACA
*
3983648 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
* * **
3983668 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTGAG
**
3983688 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TGAG
***
3983708 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TGAG
*
3983729 AAGAATCGCAACGCGATTCA-
1 AA-AATCGCAACGCGATTGAG
3983749 AAGAATCGCAACGCGATTGAG
1 AA-AATCGCAACGCGATTGAG
3983770 AAAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTGAG
*
3983790 AAAATCGCAACGCGATTCCAG
1 AAAATCGCAACGCGATT-GAG
* *
3983811 -GAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
3983830 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
3983847 CCAAGAATCG
Statistics
Matches: 150, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
18 1 0.01
19 2 0.01
20 122 0.81
21 10 0.07
22 15 0.10
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTGAG
Found at i:3983825 original size:60 final size:61
Alignment explanation
Indices: 3983706--3983859 Score: 222
Period size: 60 Copynumber: 2.5 Consensus size: 61
3983696 AACGGTCAAA
**
3983706 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGAT-TGACAAGAATCGCAACGCGATTCAAAGAATCGCAACGCGATTG
* * * *
3983768 AGAAAATCGCAACGCGATTGAGAA-AATCGCAACGCGATTCCAGGAATCGCAATGCGATTG
1 AGAAAATCGCAACGCGATTGACAAGAATCGCAACGCGATTCAAAGAATCGCAACGCGATTG
*
3983828 AGAAAATCGCAACGCGATT-CCAAGAATCGCAA
1 AGAAAATCGCAACGCGATTGACAAGAATCGCAA
3983860 AACGGCAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
59 2 0.02
60 60 0.72
61 3 0.04
62 18 0.22
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (61 bp):
AGAAAATCGCAACGCGATTGACAAGAATCGCAACGCGATTCAAAGAATCGCAACGCGATTG
Found at i:3983981 original size:6 final size:6
Alignment explanation
Indices: 3983970--3983996 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3983960 GACACGTATT
3983970 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
3983997 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3984761 original size:6 final size:6
Alignment explanation
Indices: 3984750--3984812 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
3984740 TCTCGTCTCG
3984750 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3984798 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
3984813 AATACGTGTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:3984879 original size:16 final size:16
Alignment explanation
Indices: 3984858--3984890 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3984848 CTTTTTAGAG
3984858 AAAATTTTTAAGAAAC
1 AAAATTTTTAAGAAAC
3984874 AAAATTTTTAAGAAAC
1 AAAATTTTTAAGAAAC
3984890 A
1 A
3984891 CAATACGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (16 bp):
AAAATTTTTAAGAAAC
Found at i:3984960 original size:20 final size:20
Alignment explanation
Indices: 3984935--3985223 Score: 224
Period size: 20 Copynumber: 14.4 Consensus size: 20
3984925 TTTTGCCGTT
* *
3984935 TTGCGATTCTTAGAATCGCA
1 TTGCGATTCTTTGAATCGCG
*
3984955 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-TGAATCGCG
*
3984975 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTTGAATCGCG
*
3984995 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-TGAATCGCG
* *
3985015 TTGCGATTATTGGAATCGCG
1 TTGCGATTCTTTGAATCGCG
3985035 TTGCGATT-TTCTCG-ATCGCG
1 TTGCGATTCTT-T-GAATCGCG
*
3985055 TTGCGATTCTTTGAATCGCA
1 TTGCGATTCTTTGAATCGCG
** *
3985075 TTGCGATTCTTTGGCTCGCA
1 TTGCGATTCTTTGAATCGCG
* *
3985095 TTGCGATTCTTTGGATCGCA
1 TTGCGATTCTTTGAATCGCG
*
3985115 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTTG-A-ATCGCG
3985137 TTGCGATTTTCTTTTG-A-C-CG
1 TTGCGA--TTC-TTTGAATCGCG
*
3985157 TTGCGATTTTCTTT---TCAACG
1 TTGCGA--TTCTTTGAATC-GCG
* *
3985177 TTGCGATTTTTTAAATCGCG
1 TTGCGATTCTTTGAATCGCG
3985197 TTGCGA-T-TTTGATATCGCG
1 TTGCGATTCTTTGA-ATCGCG
3985216 TTGCGATT
1 TTGCGATT
3985224 TTGTTGGTCA
Statistics
Matches: 227, Mismatches: 21, Indels: 42
0.78 0.07 0.14
Matches are distributed among these distances:
18 10 0.04
19 23 0.10
20 166 0.73
21 10 0.04
22 12 0.05
24 3 0.01
25 3 0.01
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGCGATTCTTTGAATCGCG
Found at i:3984982 original size:40 final size:40
Alignment explanation
Indices: 3984935--3985122 Score: 254
Period size: 40 Copynumber: 4.7 Consensus size: 40
3984925 TTTTGCCGTT
*
3984935 TTGCGATTCTTAGAATCGCATTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
*
3984975 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
* * *
3985015 TTGCGATTATTGGAATCGCGTTGCGATTTTCTCGATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
* *** *
3985055 TTGCGATTCTTTGAATCGCATTGCGATTCTT-TGGCTCGCA
1 TTGCGATTCTTGGAATCGCATTGCGATT-TTCTCAATCGCG
3985095 TTGCGATTCTTTGG-ATCGCATTGCGATT
1 TTGCGATTC-TTGGAATCGCATTGCGATT
3985123 CTTGGAAGAT
Statistics
Matches: 135, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 130 0.96
41 5 0.04
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCATTGCGATTTTCTCAATCGCG
Found at i:3985365 original size:5 final size:5
Alignment explanation
Indices: 3985331--3985482 Score: 50
Period size: 5 Copynumber: 29.6 Consensus size: 5
3985321 ATCATAAATA
* *
3985331 ATAAT AT-AT ACTTAT ATAGT ATAAT AATAAT ATAAT ATAAT ATAA- ATACACT
1 ATAAT ATAAT A-TAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATA-A-T
* * ** * * *
3985383 AATAAT ATTTAT ATACT ATAA- ATGCT ATGATAT ATACT ATACT ATATGT
1 -ATAAT A-TAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATA-AT
*
3985432 ATAAT -T-AT ACTAA- ATAA- AGTAAT AT-AT ATAAT ATAAT ATTAT ATATAT
1 ATAAT ATAAT A-TAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
3985480 ATA
1 ATA
3985483 TTGTACATAA
Statistics
Matches: 112, Mismatches: 16, Indels: 37
0.68 0.10 0.22
Matches are distributed among these distances:
3 2 0.02
4 17 0.15
5 61 0.54
6 25 0.22
7 4 0.04
8 3 0.03
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:3985378 original size:16 final size:16
Alignment explanation
Indices: 3985331--3985372 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
3985321 ATCATAAATA
* *
3985331 ATAATAT-ATACTTAT
1 ATAATATAATAATAAT
*
3985346 ATAGTATAATAATAAT
1 ATAATATAATAATAAT
3985362 ATAATATAATA
1 ATAATATAATA
3985373 TAAATACACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
ATAATATAATAATAAT
Found at i:3985460 original size:2 final size:2
Alignment explanation
Indices: 3985453--3985551 Score: 56
Period size: 2 Copynumber: 53.5 Consensus size: 2
3985443 AAATAAAGTA
* *
3985453 AT AT AT AT A- AT AT A- AT AT -T AT AT AT AT AT AT -T GT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
3985491 A- AT AA AA AT AT AG AT AT -T AT AT AT AT -T A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3985528 AT AG ACT AT AT AT -T AT ACT AT AT A
1 AT AT A-T AT AT AT AT AT A-T AT AT A
3985552 CCATTTAAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
1 10 0.13
2 63 0.83
3 3 0.04
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3985467 original size:19 final size:19
Alignment explanation
Indices: 3985433--3985482 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
3985423 ACTATATGTA
3985433 TAAT-TATACTAAATAA-AG
1 TAATATATA-TAAATAATAG
*
3985451 TAATATATATAATATAATAT
1 TAATATATATAA-ATAATAG
3985471 TATATATATATA
1 TA-ATATATATA
3985483 TTGTACATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.26
19 8 0.30
20 3 0.11
21 9 0.33
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
TAATATATATAAATAATAG
Found at i:3985526 original size:15 final size:16
Alignment explanation
Indices: 3985459--3985530 Score: 55
Period size: 15 Copynumber: 4.8 Consensus size: 16
3985449 AGTAATATAT
*
3985459 ATAATATA-ATATTAT
1 ATAATATATATATTAC
3985474 AT-ATATATAT-TGTAC
1 ATAATATATATAT-TAC
* * *
3985489 ATAATAAAAATA-TAG
1 ATAATATATATATTAC
*
3985504 ATATTATATATATTA-
1 ATAATATATATATTAC
3985519 ATAATATATATA
1 ATAATATATATA
3985531 GACTATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
14 6 0.14
15 30 0.68
16 8 0.18
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (16 bp):
ATAATATATATATTAC
Found at i:3989639 original size:3 final size:3
Alignment explanation
Indices: 3989626--3989656 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3989616 TTAATCCGAG
*
3989626 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3989657 ATATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:3990024 original size:13 final size:13
Alignment explanation
Indices: 3990008--3990032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3989998 GAATTGTGTC
3990008 TCAAAGTTGTCTA
1 TCAAAGTTGTCTA
3990021 TCAAAGTTGTCT
1 TCAAAGTTGTCT
3990033 CTAAGATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TCAAAGTTGTCTA
Found at i:3991063 original size:29 final size:29
Alignment explanation
Indices: 3991021--3991077 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
3991011 CTAAAGAGTT
3991021 AAGCTTGGTCCCAGATTTAATCATGCCTG
1 AAGCTTGGTCCCAGATTTAATCATGCCTG
3991050 AAGCTTGGTCCCAGATTTAATCATGCCT
1 AAGCTTGGTCCCAGATTTAATCATGCCT
3991078 CCAAAGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (29 bp):
AAGCTTGGTCCCAGATTTAATCATGCCTG
Found at i:3992712 original size:14 final size:14
Alignment explanation
Indices: 3992693--3992721 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3992683 ATAGACACAA
3992693 ATATAGTAGTCCAC
1 ATATAGTAGTCCAC
3992707 ATATAGTAGTCCAC
1 ATATAGTAGTCCAC
3992721 A
1 A
3992722 AGCTGCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (14 bp):
ATATAGTAGTCCAC
Found at i:3994025 original size:83 final size:83
Alignment explanation
Indices: 3993895--3994361 Score: 490
Period size: 83 Copynumber: 5.6 Consensus size: 83
3993885 CAATATGGTA
* * ** *
3993895 ACTTTAGTGGTGTTTTTATATAAATAATATAATATGGTTCATCTATAGTGGCATTTTTTCAACAA
1 ACTTTAGCGGTGTTTTTATAAAAATGCTATAATAGGGTTCATCTATAGTGGCATTTTTTCAACAA
** * *
3993960 ACGCATCTATAGAGTAGT
66 ACGCCGCAACAGAGTAGT
* * * * * *
3993978 ACTTTACCGGTGTCTTTACAAAAATGCCATAATAGGGTTAATTTATAGTGGCATTTTTTCAACAA
1 ACTTTAGCGGTGTTTTTATAAAAATGCTATAATAGGGTTCATCTATAGTGGCATTTTTTCAACAA
3994043 ACGCCGCAACAGAGTAGT
66 ACGCCGCAACAGAGTAGT
* ** * * * * *
3994061 ACATTT-GTGGCATTTTTATACAAATGTTGTAATAGGGTTCATCTATAGTGGTATTTTCTCAACA
1 AC-TTTAGCGGTGTTTTTATAAAAATGCTATAATAGGGTTCATCTATAGTGGCATTTTTTCAACA
3994125 AACGCCGCAA-AGGAGTAGT
65 AACGCCGCAACA-GAGTAGT
* * ** ** *
3994144 ACTTTAGCAGTGTTTTTACAAAAATATTGCAATAGGGTTTATCTATAGTGGCATTTTTTCAACAA
1 ACTTTAGCGGTGTTTTTATAAAAATGCTATAATAGGGTTCATCTATAGTGGCATTTTTTCAACAA
*
3994209 ACGCCGCAACAGAGTAAT
66 ACGCCGCAACAGAGTAGT
* * ** * *
3994227 A-TGCTAGCGGTGTTTTTATATAAATGCTGCAATAGGGTTCATATATAGTGTCATTTTTTCAACA
1 ACT-TTAGCGGTGTTTTTATAAAAATGCTATAATAGGGTTCATCTATAGTGGCATTTTTTCAACA
*
3994291 AATGCCGCAACAGAGTAGT
65 AACGCCGCAACAGAGTAGT
* ** * * *
3994310 ACATTAGCAATGTTTTTATACAAATACCATAATAGGGTTCATCTATAGTGGC
1 ACTTTAGCGGTGTTTTTATAAAAATGCTATAATAGGGTTCATCTATAGTGGC
3994362 GTTTATTATA
Statistics
Matches: 315, Mismatches: 63, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
82 5 0.02
83 306 0.97
84 4 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (83 bp):
ACTTTAGCGGTGTTTTTATAAAAATGCTATAATAGGGTTCATCTATAGTGGCATTTTTTCAACAA
ACGCCGCAACAGAGTAGT
Found at i:4001203 original size:21 final size:21
Alignment explanation
Indices: 4001147--4001191 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
4001137 ATTTATTATA
* *
4001147 ATGGATTTAAAGTTGGTTGTT
1 ATGGAATTAAAGTTTGTTGTT
4001168 ATGGAATTAAAGTTTGTTGTT
1 ATGGAATTAAAGTTTGTTGTT
4001189 ATG
1 ATG
4001192 AATGTCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (21 bp):
ATGGAATTAAAGTTTGTTGTT
Found at i:4003782 original size:14 final size:15
Alignment explanation
Indices: 4003755--4003785 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4003745 CAACCAAACC
4003755 TTAATTACATATTAT
1 TTAATTACATATTAT
4003770 TTAATTA-ATATTAT
1 TTAATTACATATTAT
4003784 TT
1 TT
4003786 TTGAATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTACATATTAT
Found at i:4004789 original size:6 final size:6
Alignment explanation
Indices: 4004778--4004854 Score: 154
Period size: 6 Copynumber: 12.8 Consensus size: 6
4004768 GTTCCAAGAA
4004778 TCAAAC TCAAAC TCAAAC TCAAAC TCAAAC TCAAAC TCAAAC TCAAAC
1 TCAAAC TCAAAC TCAAAC TCAAAC TCAAAC TCAAAC TCAAAC TCAAAC
4004826 TCAAAC TCAAAC TCAAAC TCAAAC TCAAA
1 TCAAAC TCAAAC TCAAAC TCAAAC TCAAA
4004855 AAAATCATGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (6 bp):
TCAAAC
Found at i:4005515 original size:31 final size:31
Alignment explanation
Indices: 4005480--4005588 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 31
4005470 ATATTAATCG
4005480 AGTGACCAAAACATAAATTATATAATATATA
1 AGTGACCAAAACATAAATTATATAATATATA
** **
4005511 AGTGACCAAATAGGTAGTTTACCCTA-AATAATAATA
1 AGTGACCAAA-ACATAAATTA---TATAAT-AT-ATA
* *
4005547 GAGTGACCAAAATATAAATTAGATAATATATA
1 -AGTGACCAAAACATAAATTATATAATATATA
4005579 AGTGACCAAA
1 AGTGACCAAA
4005589 TAGGTAGTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
31 20 0.33
32 9 0.15
33 3 0.05
34 6 0.10
35 4 0.07
36 9 0.15
37 10 0.16
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (31 bp):
AGTGACCAAAACATAAATTATATAATATATA
Found at i:4005552 original size:37 final size:36
Alignment explanation
Indices: 4005501--4005681 Score: 125
Period size: 37 Copynumber: 5.2 Consensus size: 36
4005491 CATAAATTAT
4005501 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATA-ATAAGTGACCAAATAGGTAGTTTACCCTAA
*** *
4005538 ATAATAATAGAGTGACCAAA-A--TA---TAAATTAG
1 ATAATAATA-AGTGACCAAATAGGTAGTTTACCCTAA
4005569 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATA-ATAAGTGACCAAATAGGTAGTTTACCCTAA
* * * ** **
4005606 ATAATAATCGAGTGATCAAACCA--TAAATTA-GAT-A
1 ATAATAAT-AAGTGACCAAA-TAGGTAGTTTACCCTAA
*
4005640 AT-AT-ATAAGAGACCAAATAGGTAGTTTACCCTAA
1 ATAATAATAAGTGACCAAATAGGTAGTTTACCCTAA
4005674 ATAATAAT
1 ATAATAAT
4005682 CGAGTGACTA
Statistics
Matches: 105, Mismatches: 23, Indels: 33
0.65 0.14 0.20
Matches are distributed among these distances:
30 1 0.01
31 28 0.27
32 11 0.10
33 3 0.03
34 10 0.10
35 3 0.03
36 13 0.12
37 35 0.33
38 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.28
Consensus pattern (36 bp):
ATAATAATAAGTGACCAAATAGGTAGTTTACCCTAA
Found at i:4005577 original size:68 final size:68
Alignment explanation
Indices: 4005468--4005742 Score: 469
Period size: 68 Copynumber: 4.0 Consensus size: 68
4005458 ATTTTGAAAA
* *
4005468 AAATATTAATCGAGTGACCAAAACATAAATTATATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
4005533 CCT
66 CCT
* *
4005536 AAATAATAATAGAGTGACCAAAATATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
4005601 CCT
66 CCT
* * *
4005604 AAATAATAATCGAGTGATCAAACCATAAATTAGATAATATATAAGAGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
4005669 CCT
66 CCT
* *
4005672 AAATAATAATCGAGTGACTAAAACATAAATTAGATAATATATAAGTAACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
4005737 CCT
66 CCT
4005740 AAA
1 AAA
4005743 AAATCCCTAA
Statistics
Matches: 193, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 193 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (68 bp):
AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
CCT
Found at i:4006866 original size:53 final size:53
Alignment explanation
Indices: 4006790--4006903 Score: 156
Period size: 53 Copynumber: 2.2 Consensus size: 53
4006780 TGCACCTAAG
* * *
4006790 TGTCAAAATGGTAATCCACAAACTCATTATGAATTCCATGGATGCACATATAA
1 TGTCGAAATGGTAATCCACAAACTCATTATGAATACCATGGATGCACACATAA
* * * * *
4006843 TGTCGAAATGGTCATTCATAAACTCATTATGAATACCATGGGTGCACACATAG
1 TGTCGAAATGGTAATCCACAAACTCATTATGAATACCATGGATGCACACATAA
4006896 TGTCGAAA
1 TGTCGAAA
4006904 GTACACATAG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (53 bp):
TGTCGAAATGGTAATCCACAAACTCATTATGAATACCATGGATGCACACATAA
Found at i:4006951 original size:23 final size:23
Alignment explanation
Indices: 4006924--4006999 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 23
4006914 TATAGATACG
4006924 AAAATGCAACATATGCATTAAAC
1 AAAATGCAACATATGCATTAAAC
* * ** * *
4006947 AAAATGGATCGATAACCATCATAC
1 AAAATGCAAC-ATATGCATTAAAC
*
4006971 GAAAATGCAACTTATGCATTAAAC
1 -AAAATGCAACATATGCATTAAAC
4006995 AAAAT
1 AAAAT
4007000 CAATAGATAA
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
23 13 0.34
24 17 0.45
25 8 0.21
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (23 bp):
AAAATGCAACATATGCATTAAAC
Found at i:4006990 original size:48 final size:48
Alignment explanation
Indices: 4006919--4007018 Score: 164
Period size: 48 Copynumber: 2.1 Consensus size: 48
4006909 CATAGTATAG
** *
4006919 ATACGAAAATGCAACATATGCATTAAACAAAATGGATCGATAACCATC
1 ATACGAAAATGCAACATATGCATTAAACAAAATCAATAGATAACCATC
*
4006967 ATACGAAAATGCAACTTATGCATTAAACAAAATCAATAGATAACCATC
1 ATACGAAAATGCAACATATGCATTAAACAAAATCAATAGATAACCATC
4007015 ATAC
1 ATAC
4007019 ACAAAGTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.49, C:0.19, G:0.10, T:0.22
Consensus pattern (48 bp):
ATACGAAAATGCAACATATGCATTAAACAAAATCAATAGATAACCATC
Found at i:4007586 original size:22 final size:20
Alignment explanation
Indices: 4007543--4007580 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4007533 TTTAGACTGA
4007543 ATAGTATCGATACCTCTCCT
1 ATAGTATCGATACCTCTCCT
*
4007563 ATAGTATCGATACTTCTC
1 ATAGTATCGATACCTCTC
4007581 TTCTATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (20 bp):
ATAGTATCGATACCTCTCCT
Found at i:4007942 original size:20 final size:21
Alignment explanation
Indices: 4007899--4007942 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
4007889 AAACTAACTT
** *
4007899 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
4007920 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
4007940 ACA
1 ACA
4007943 CTTAAGACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:4008957 original size:20 final size:20
Alignment explanation
Indices: 4008934--4008971 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4008924 TGAACCGGTC
4008934 CGAGTCAA-CTCGAACCGAAT
1 CGAGTCAACCT-GAACCGAAT
4008954 CGAGTCAACCTGAACCGA
1 CGAGTCAACCTGAACCGA
4008972 GTCAACCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.34, C:0.32, G:0.21, T:0.13
Consensus pattern (20 bp):
CGAGTCAACCTGAACCGAAT
Found at i:4012707 original size:17 final size:17
Alignment explanation
Indices: 4012685--4012718 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4012675 TCCTCAAAAC
4012685 TTCCATATAAGTCTTTT
1 TTCCATATAAGTCTTTT
4012702 TTCCATATAAGTCTTTT
1 TTCCATATAAGTCTTTT
4012719 CAACGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (17 bp):
TTCCATATAAGTCTTTT
Found at i:4013258 original size:43 final size:43
Alignment explanation
Indices: 4013183--4013521 Score: 394
Period size: 43 Copynumber: 7.9 Consensus size: 43
4013173 TTTTAACAAA
* * * * * * *
4013183 AAACACCGCTAAACATCATA-ACATATTACGGCGTTTGTCTGAG
1 AAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTTTATGAC
* *
4013226 AAACGCTGCTAAATATTAACACCTATTGCGGCGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* * * * *
4013269 AAACGCCACTAAATATCAACACCTTTTGCGGTGTTTTTATAAAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTAT-GAC
* * *
4013313 AAACGCCACTAAATATCAACACCTATTGCGGCGTTTGT-TGAA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* *
4013355 AAACGCTGCTAAATATCAACACCTATAGCGGCGTTTTTATGAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* * *
4013398 AAACGACGCTAAATATCAACATCTATTGCGGCGTTTTTATAAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* * **
4013441 AAACGCCACTAAATATCAACACCTATTGCGACGTTTTTAACAC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
* *
4013484 AAACGCCGCTAAATATCAATACTTATTGCGGCGTTTTT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT
4013522 CACAAAAAAC
Statistics
Matches: 253, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
42 37 0.15
43 180 0.71
44 36 0.14
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAC
Found at i:4013401 original size:129 final size:128
Alignment explanation
Indices: 4013180--4013521 Score: 454
Period size: 129 Copynumber: 2.6 Consensus size: 128
4013170 TTGTTTTAAC
* * * * * * *
4013180 AAAAAACACCGCTAAACATCATA-ACATATTACGGCGTTTGTCTGAGAAACGCTGCTAAATATTA
1 AAAAAACGCCACTAAATATCA-ACACCTATTGCGGCGTTTGT-TGAAAAACGCTGCTAAATATCA
* * *
4013244 ACACCTATTGCGGCGTTTTTATGACAAACGCCACTAAATATCAACACCTTTTGCGGTGTTTTTAT
64 ACACCTATTGCGGCGTTTTTATGACAAACGACACTAAATATCAACACCTATTGCGGCGTTTTTAT
4013309 AAAAAAACGCCACTAAATATCAACACCTATTGCGGCGTTTGTTGAAAAACGCTGCTAAATATCAA
1 -AAAAAACGCCACTAAATATCAACACCTATTGCGGCGTTTGTTGAAAAACGCTGCTAAATATCAA
* * *
4013374 CACCTATAGCGGCGTTTTTATGACAAACGACGCTAAATATCAACATCTATTGCGGCGTTTTTAT
65 CACCTATTGCGGCGTTTTTATGACAAACGACACTAAATATCAACACCTATTGCGGCGTTTTTAT
* * * *
4013438 AACAAACGCCACTAAATATCAACACCTATTGCGACGTTT-TTAACACAAACGCCGCTAAATATCA
1 AAAAAACGCCACTAAATATCAACACCTATTGCGGCGTTTGTTGA-A-AAACGCTGCTAAATATCA
* *
4013502 ATACTTATTGCGGCGTTTTT
64 ACACCTATTGCGGCGTTTTT
4013522 CACAAAAAAC
Statistics
Matches: 189, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
127 3 0.02
128 38 0.20
129 114 0.60
130 34 0.18
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (128 bp):
AAAAAACGCCACTAAATATCAACACCTATTGCGGCGTTTGTTGAAAAACGCTGCTAAATATCAAC
ACCTATTGCGGCGTTTTTATGACAAACGACACTAAATATCAACACCTATTGCGGCGTTTTTAT
Found at i:4023194 original size:36 final size:37
Alignment explanation
Indices: 4023152--4023231 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 37
4023142 ATCGAATTAA
* *
4023152 ACGGGGACAGGGAAAAACT-GTTTATGCTAAACGGGG
1 ACGGGGACAGGAAAAAAATCGTTTATGCTAAACGGGG
* *
4023188 ACGGGGA-TGGAAAAAAATCGTTTATGTTAAACGGGG
1 ACGGGGACAGGAAAAAAATCGTTTATGCTAAACGGGG
*
4023224 ACAGGGAC
1 ACGGGGAC
4023232 GGGTTTAGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 8 0.22
36 29 0.78
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.17
Consensus pattern (37 bp):
ACGGGGACAGGAAAAAAATCGTTTATGCTAAACGGGG
Found at i:4024172 original size:10 final size:10
Alignment explanation
Indices: 4024157--4024181 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4024147 TTGAATATTG
4024157 TTTTTATATA
1 TTTTTATATA
4024167 TTTTTATATA
1 TTTTTATATA
4024177 TTTTT
1 TTTTT
4024182 TTAATTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTATATA
Found at i:4024276 original size:22 final size:23
Alignment explanation
Indices: 4024251--4024305 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
4024241 TTATTTTATA
* *
4024251 TATTTATTTACTATTGTTTAG-T
1 TATTTATTTACTACTATTTAGTT
* *
4024273 TATTTACTTATTACTATTTAGTTT
1 TATTTATTTACTACTATTTAG-TT
4024297 TATTTATTT
1 TATTTATTT
4024306 GTCATGATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.65
24 9 0.35
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (23 bp):
TATTTATTTACTACTATTTAGTT
Found at i:4034109 original size:75 final size:75
Alignment explanation
Indices: 4033979--4034182 Score: 259
Period size: 75 Copynumber: 2.7 Consensus size: 75
4033969 CAAAGCCAAA
* ** * **
4033979 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
4034043 TTGGCTCCGAG
65 TTGGCTCCGAG
*
4034054 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
4034119 TTGTTCCGAG
66 TGGCTCCGAG
* ** * *
4034129 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCCAGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCC
4034183 TTGTACAACG
Statistics
Matches: 113, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
74 44 0.39
75 69 0.61
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:4040359 original size:19 final size:19
Alignment explanation
Indices: 4040328--4040368 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4040318 GTTATTTTTC
4040328 AAATTATTGTGTT-TTGATT
1 AAATTATTGTGTTGTT-ATT
4040347 AAATTA-TGTTGTTGTTATT
1 AAATTATTG-TGTTGTTATT
4040366 AAA
1 AAA
4040369 AACTATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.10
19 16 0.80
20 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
AAATTATTGTGTTGTTATT
Found at i:4042608 original size:75 final size:74
Alignment explanation
Indices: 4042455--4042664 Score: 242
Period size: 75 Copynumber: 2.8 Consensus size: 74
4042445 CAAAGCCAAA
* ** * **
4042455 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATG
1 AATTCCAGAATGCTCGGAGGGAACCGATT---CCCCCATAGGAGG-ACCGATTCCCCCCTAAACA
4042520 GTTTGGCTCCGAG
62 GTTTGGCTCCGAG
*
4042533 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAGCCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGA-CCGATTCCCCCCTAAACAGTT
* *
4042598 TTGTTCCGAG
65 TGGCTCCGAG
* * *
4042608 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGG-ACCGATTCCCCCCT
4042665 TGTACAACGG
Statistics
Matches: 116, Mismatches: 13, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
74 1 0.01
75 83 0.72
76 7 0.06
78 25 0.22
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGACCGATTCCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:4044505 original size:13 final size:13
Alignment explanation
Indices: 4044489--4044523 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
4044479 CTTGAATGAA
4044489 AAAATAAAAAAAT
1 AAAATAAAAAAAT
*
4044502 AAAAAAAAAAAAT
1 AAAATAAAAAAAT
4044515 AAAATAAAA
1 AAAATAAAA
4044524 GGGGGTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:4044510 original size:18 final size:18
Alignment explanation
Indices: 4044487--4044523 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
4044477 AACTTGAATG
*
4044487 AAAAAATAAA-AAAATAA
1 AAAAAAAAAATAAAATAA
4044504 AAAAAAAAAATAAAATAA
1 AAAAAAAAAATAAAATAA
4044522 AA
1 AA
4044524 GGGGGTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (18 bp):
AAAAAAAAAATAAAATAA
Found at i:4045056 original size:24 final size:24
Alignment explanation
Indices: 4045029--4045099 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
4045019 ATGGGCAGAG
*
4045029 TGATAGCCAAATAGTACATGGACT
1 TGATAGCCAAATAGTACAAGGACT
*
4045053 TGATAGCCAAATAGTACAGGGACT
1 TGATAGCCAAATAGTACAAGGACT
* *
4045077 TGATTGCCAAATAATACAAGGAC
1 TGATAGCCAAATAGTACAAGGAC
4045100 CTGACCGCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (24 bp):
TGATAGCCAAATAGTACAAGGACT
Found at i:4046178 original size:12 final size:12
Alignment explanation
Indices: 4046161--4046186 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4046151 ATTAGATTAC
4046161 TATAACTATATA
1 TATAACTATATA
4046173 TATAACTATATA
1 TATAACTATATA
4046185 TA
1 TA
4046187 ATAGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATAACTATATA
Found at i:4050415 original size:21 final size:21
Alignment explanation
Indices: 4050389--4050464 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
4050379 GCAAATAAGT
4050389 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
4050410 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
4050430 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
4050451 AAATCGCAATGCGA
1 AAATCGCAACGCGA
4050465 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:4050429 original size:41 final size:41
Alignment explanation
Indices: 4050372--4050464 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
4050362 TTTTCGCAAT
*
4050372 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
4050413 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
4050454 TCGCAATGCGA
1 TCGCAATGCGA
4050465 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:4050443 original size:20 final size:20
Alignment explanation
Indices: 4050372--4050445 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
4050362 TTTTCGCAAT
* *
4050372 TCGCAATGCAAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
4050392 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
4050413 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
4050433 TCGCAACGCGAAT
1 TCGCAACGCGAAT
4050446 TGGGAAAATC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:4050477 original size:41 final size:41
Alignment explanation
Indices: 4050391--4050525 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
4050381 AAATAAGTAA
* *
4050391 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
4050432 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
4050473 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
4050514 TTCGCAACGCGA
1 ATCGCAACGCGA
4050526 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:4050478 original size:20 final size:20
Alignment explanation
Indices: 4050453--4050547 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
4050443 AATTGGGAAA
*
4050453 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
4050473 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
4050494 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
4050514 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
4050534 TTCGCAACGCGATA
1 ATCGCAACGCGATA
4050548 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:4050763 original size:22 final size:22
Alignment explanation
Indices: 4050735--4050778 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4050725 CACTCTCTCA
*
4050735 CCCATCTCCGACGAAATTCGTC
1 CCCATCTCCGACGAAATCCGTC
4050757 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
4050779 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.43, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:4051671 original size:53 final size:53
Alignment explanation
Indices: 4051591--4051696 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
4051581 CGGTACTTTA
4051591 CGCAAAGACGATGGTGCATGGCGTGTTGAGGTGTCTACATTACGCGGTGAGGT
1 CGCAAAGACGATGGTGCATGGCGTGTTGAGGTGTCTACATTACGCGGTGAGGT
4051644 CGCAAAGACGATGGTGCATGGCGTGTTGAGGTGTCTACATTACGCGGTGAGGT
1 CGCAAAGACGATGGTGCATGGCGTGTTGAGGTGTCTACATTACGCGGTGAGGT
4051697 AGCCGCTCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.25
Consensus pattern (53 bp):
CGCAAAGACGATGGTGCATGGCGTGTTGAGGTGTCTACATTACGCGGTGAGGT
Found at i:4051843 original size:12 final size:13
Alignment explanation
Indices: 4051816--4051849 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
4051806 ACTGCTAAAC
4051816 TGTTTTTGTAGTTT
1 TGTTTTTG-AGTTT
4051830 TGTTTTTG-GTTT
1 TGTTTTTGAGTTT
4051842 TGTTTTTG
1 TGTTTTTG
4051850 TCTTTTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.03, C:0.00, G:0.24, T:0.74
Consensus pattern (13 bp):
TGTTTTTGAGTTT
Found at i:4051967 original size:19 final size:20
Alignment explanation
Indices: 4051924--4051979 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
4051914 TGCAACACGA
4051924 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
4051944 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
4051963 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
4051980 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:4051987 original size:14 final size:14
Alignment explanation
Indices: 4051968--4052025 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4051958 ATGCGAAATG
4051968 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
4051982 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
4051998 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
4052014 AAAATCGCAACG
1 AAAATCGCAACG
4052026 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:4052010 original size:32 final size:33
Alignment explanation
Indices: 4051952--4052042 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
4051942 GGAAATGGCT
4051952 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
4051985 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
4052017 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
4052043 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:4052036 original size:19 final size:19
Alignment explanation
Indices: 4051952--4052047 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
4051942 GGAAATGGCT
4051952 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4051971 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
4051985 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
4052003 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
4052017 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4052036 ATCGCAATGCGA
1 ATCGCAATGCGA
4052048 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
14 20 0.33
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.18
19 21 0.34
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4052093 original size:32 final size:33
Alignment explanation
Indices: 4052054--4052131 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
4052044 GCGATTTGTG
4052054 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
4052086 TTTCGCGTTGCGA-TTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
4052118 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
4052132 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
31 13 0.30
32 30 0.70
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:4052128 original size:19 final size:19
Alignment explanation
Indices: 4052104--4052170 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4052094 TGCGATTTGT
**
4052104 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
4052123 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
4052143 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
4052162 CGTTGCGAT
1 CGTTGCGAT
4052171 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:4052150 original size:20 final size:19
Alignment explanation
Indices: 4052116--4052170 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
4052106 TTGCGATTTT
*
4052116 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4052135 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
4052155 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
4052171 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:4054053 original size:14 final size:14
Alignment explanation
Indices: 4054034--4054069 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
4054024 ATTGTTTAAT
4054034 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
4054048 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
4054062 TGATTTGT
1 TGATTTGT
4054070 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:4054241 original size:19 final size:19
Alignment explanation
Indices: 4054184--4054234 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
4054174 CTATCGCAAC
4054184 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
4054203 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
4054222 ATGAAAATCGCAA
1 ATGAAAATCGCAA
4054235 CGAGAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.16
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:4054329 original size:20 final size:20
Alignment explanation
Indices: 4054272--4054329 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
4054262 TCGCATTGCG
* *
4054272 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
4054292 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
4054312 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
4054330 TCAAATGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:4058084 original size:20 final size:18
Alignment explanation
Indices: 4058052--4058229 Score: 102
Period size: 20 Copynumber: 9.8 Consensus size: 18
4058042 GTCTTTGGTT
4058052 GAAATGAAATCGCAACGA
1 GAAATGAAATCGCAACGA
*
4058070 GATAATGAGAATCGCAACGCG
1 GA-AATGA-AATCGCAACG-A
*
4058091 GAAATGACTATCGCAACGA
1 GAAATGA-AATCGCAACGA
*
4058110 G--A-G-AATCGCAACGC
1 GAAATGAAATCGCAACGA
* * *
4058124 GAAATGACTATCGCGACCA
1 GAAATGA-AATCGCAACGA
* *
4058143 G--A--CAATCGCAACGC
1 GAAATGAAATCGCAACGA
* *
4058157 GAAATGAAAATTGCAACCGC
1 GAAATG-AAATCGCAA-CGA
* *
4058177 GAAATAAAAATCGCAACGC
1 GAAAT-GAAATCGCAACGA
*
4058196 GAAATGAAATCGCAACGC
1 GAAATGAAATCGCAACGA
4058214 GAAATGAAAATCGCAA
1 GAAATG-AAATCGCAA
4058230 TGCGATTTTG
Statistics
Matches: 124, Mismatches: 20, Indels: 31
0.71 0.11 0.18
Matches are distributed among these distances:
14 18 0.15
16 3 0.02
17 3 0.02
18 20 0.16
19 38 0.31
20 40 0.32
21 2 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
GAAATGAAATCGCAACGA
Found at i:4058133 original size:33 final size:33
Alignment explanation
Indices: 4058076--4058163 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
4058066 ACGAGATAAT
*
4058076 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
4058110 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
4058143 GACAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
4058164 AAATTGCAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:4058172 original size:19 final size:19
Alignment explanation
Indices: 4058052--4058234 Score: 147
Period size: 19 Copynumber: 10.1 Consensus size: 19
4058042 GTCTTTGGTT
*
4058052 GAAATG-AAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
4058070 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
4058090 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
4058108 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
4058124 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
4058142 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
4058157 GAAATGAAAATTGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
4058177 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
4058196 GAAATG-AAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
4058214 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
4058233 GA
1 GA
4058235 TTTTGGTTTC
Statistics
Matches: 133, Mismatches: 17, Indels: 29
0.74 0.09 0.16
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.02
17 1 0.01
18 24 0.18
19 43 0.32
20 39 0.29
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:4058263 original size:19 final size:19
Alignment explanation
Indices: 4058230--4058274 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
4058220 AAAATCGCAA
*
4058230 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
4058249 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
4058268 TGCGATT
1 TGCGATT
4058275 ATCTCATTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:4058855 original size:20 final size:20
Alignment explanation
Indices: 4058830--4058882 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
4058820 GGCGCTATGT
4058830 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
4058850 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
4058870 TATCTCGTTGCGA
1 AATCGCGTTGCGA
4058883 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:4058914 original size:20 final size:20
Alignment explanation
Indices: 4058889--4058944 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
4058879 GCGATTTTGT
4058889 ATTATCGCATTGCGATAGTA
1 ATTATCGCATTGCGATAGTA
*
4058909 ATTATCGCATTGCGATAGTC
1 ATTATCGCATTGCGATAGTA
*
4058929 AGTATCGCATTGCGAT
1 ATTATCGCATTGCGAT
4058945 TTCCCAATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
ATTATCGCATTGCGATAGTA
Found at i:4058956 original size:20 final size:20
Alignment explanation
Indices: 4058933--4058983 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
4058923 ATAGTCAGTA
*
4058933 TCGCATTGCGATTTCCCAAT
1 TCGCATTGCGATTTACCAAT
* **
4058953 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
4058973 TCGCATTGCGA
1 TCGCATTGCGA
4058984 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:4059054 original size:21 final size:21
Alignment explanation
Indices: 4059014--4059054 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4059004 ATTGTATACC
**
4059014 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
4059035 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
4059055 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:4059231 original size:2 final size:2
Alignment explanation
Indices: 4059224--4059255 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4059214 GTTTATTTAG
4059224 AT 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 AT
4059256 GAAAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4059606 original size:16 final size:16
Alignment explanation
Indices: 4059586--4059628 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
4059576 AAAGTCCATT
4059586 AAAAATAAAACTTT-A
1 AAAAATAAAACTTTCA
4059601 ACAAAATAAAA-TTTCA
1 A-AAAATAAAACTTTCA
4059617 AAATAATAAAAC
1 AAA-AATAAAAC
4059629 AATTTCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATAAAACTTTCA
Found at i:4069526 original size:20 final size:20
Alignment explanation
Indices: 4069503--4069545 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4069493 AATCCACCAC
*
4069503 ATGCAACTATAT-GTTCCTAA
1 ATGCAACTAAATGGTT-CTAA
*
4069523 ATGCATCTAAATGGTTCTAA
1 ATGCAACTAAATGGTTCTAA
4069543 ATG
1 ATG
4069546 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGGTTCTAA
Found at i:4092150 original size:19 final size:19
Alignment explanation
Indices: 4092128--4092165 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4092118 AACTTGTTCC
*
4092128 AAGTTTGCACACTTCTTCT
1 AAGTCTGCACACTTCTTCT
*
4092147 AAGTCTGCATACTTCTTCT
1 AAGTCTGCACACTTCTTCT
4092166 CTAGACTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (19 bp):
AAGTCTGCACACTTCTTCT
Found at i:4093713 original size:95 final size:95
Alignment explanation
Indices: 4093540--4093745 Score: 288
Period size: 95 Copynumber: 2.2 Consensus size: 95
4093530 GAATTAGCTG
* * * *
4093540 AGTAGTATCAATACCATCGTAAGGGTATTGATACCATGCAACATCGAATCTAAATTTGGTATCGA
1 AGTAGTATCGATACCATCGTAAGGGTATCGATACCAGGAAACATCGAATCTAAATTTGGTATCGA
*
4093605 TACCGAAATGGGGTATCAGTACCATAGTAT
66 TACCGAAAGGGGGTATCAGTACCATAGTAT
* * *
4093635 TGTAGTATCGATACCATGGTAAGGGTATCGATACTAGGAAACATCGAA-CGTAAATTTGGTATCG
1 AGTAGTATCGATACCATCGTAAGGGTATCGATACCAGGAAACATCGAATC-TAAATTTGGTATCG
* *
4093699 ATACTGGAAGGGGGTATCAGTACCATAGTAT
65 ATACCGAAAGGGGGTATCAGTACCATAGTAT
* *
4093730 AGAAGTATCGGTACCA
1 AGTAGTATCGATACCA
4093746 GAGTAGAAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
94 1 0.01
95 96 0.99
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (95 bp):
AGTAGTATCGATACCATCGTAAGGGTATCGATACCAGGAAACATCGAATCTAAATTTGGTATCGA
TACCGAAAGGGGGTATCAGTACCATAGTAT
Done.