Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 417 of 438
Found at i:129340903 original size:18 final size:17
Alignment explanation
Indices: 129340861--129340905 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
129340851 GAAAAATGAG
129340861 AAATTTT-AAAACACGA
1 AAATTTTGAAAACACGA
129340877 AAATTTTGAAAACACGA
1 AAATTTTGAAAACACGA
129340894 AAATTTTTGAAA
1 AAA-TTTTGAAA
129340906 CCTGAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 7 0.26
17 12 0.44
18 8 0.30
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (17 bp):
AAATTTTGAAAACACGA
Found at i:129343705 original size:28 final size:29
Alignment explanation
Indices: 129343642--129343710 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
129343632 TGAGGATTGG
* *
129343642 AATATTTTAATATTTGTAAATCTTGATCTT
1 AATATTTTAA-ATTTGTAAATATTGATATT
*
129343672 AGTATTTATAAA-TTGT-AATATTGATATT
1 AATATTT-TAAATTTGTAAATATTGATATT
129343700 AATATTTTAAA
1 AATATTTTAAA
129343711 ATTTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 4 0.12
28 16 0.47
29 4 0.12
30 7 0.21
31 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (29 bp):
AATATTTTAAATTTGTAAATATTGATATT
Found at i:129350204 original size:3 final size:3
Alignment explanation
Indices: 129350196--129350232 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
129350186 GGCTCATCAC
129350196 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
129350233 TGCCATCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:129380057 original size:2 final size:2
Alignment explanation
Indices: 129380050--129380141 Score: 57
Period size: 2 Copynumber: 47.5 Consensus size: 2
129380040 TCCTTTTAAG
* * * * *
129380050 TA TA TA TA TA TG TA TA TA TA TG TA CTT TA TG TA TA T- TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
129380092 TA TA TT TT TA TA AA TA T- TA TA TA TA TA TA TA TT 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
*
129380132 T- TA TG TA TA T
1 TA TA TA TA TA T
129380142 TGTGTACATA
Statistics
Matches: 67, Mismatches: 18, Indels: 10
0.71 0.19 0.11
Matches are distributed among these distances:
1 4 0.06
2 62 0.93
3 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.54
Consensus pattern (2 bp):
TA
Found at i:129380082 original size:9 final size:9
Alignment explanation
Indices: 129380052--129380147 Score: 55
Period size: 9 Copynumber: 11.2 Consensus size: 9
129380042 CTTTTAAGTA
129380052 TATATATATG
1 TATAT-TATG
129380062 TATATATATG
1 TATAT-TATG
129380072 TACT-TTATG
1 TA-TATTATG
129380081 TATATTATG
1 TATATTATG
129380090 TATA-TAT-
1 TATATTATG
*
129380097 T-T-TTATA
1 TATATTATG
* *
129380104 AATATTATA
1 TATATTATG
*
129380113 TATA-TATA
1 TATATTATG
*
129380121 TAT-TTA-A
1 TATATTATG
129380128 TATATTATG
1 TATATTATG
*
129380137 TATATTGTG
1 TATATTATG
129380146 TA
1 TA
129380148 CATACTTTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
6 4 0.05
7 5 0.07
8 17 0.23
9 33 0.45
10 13 0.18
11 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (9 bp):
TATATTATG
Found at i:129380161 original size:53 final size:53
Alignment explanation
Indices: 129380042--129380193 Score: 125
Period size: 56 Copynumber: 2.8 Consensus size: 53
129380032 ATATTTGTTC
* * *
129380042 CTTTTAAGTA-TATATATATGTATATAT-ATGTACTTTATGTATATTATGTATATAT
1 CTTTTAA-TATTATATATAT-TATATTTAATATA--TTATGTATATTATGTACATAT
* *
129380097 TTTTATAAATATTATATATATATATATTTAATATATTATGTATATTGTGTACATA-
1 CTTT-T-AATATTATATATAT-TATATTTAATATATTATGTATATTATGTACATAT
* *
129380152 CTTTTAATATTATCATGTATTCA-CTTTAATATA-TATGTATAT
1 CTTTTAATATTAT-ATATATT-ATATTTAATATATTATGTATAT
129380194 ATCTATGTAA
Statistics
Matches: 82, Mismatches: 9, Indels: 15
0.77 0.08 0.14
Matches are distributed among these distances:
52 9 0.11
53 18 0.22
54 7 0.09
55 6 0.07
56 21 0.26
57 17 0.21
58 4 0.05
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.53
Consensus pattern (53 bp):
CTTTTAATATTATATATATTATATTTAATATATTATGTATATTATGTACATAT
Found at i:129384292 original size:33 final size:36
Alignment explanation
Indices: 129384212--129384295 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
129384202 TTAAATAGTT
*
129384212 AAAAGAAAAAAGAAAAAATTGAAAAGAAGGGAAAGAG
1 AAAAGAAAAAAGAAAAAATT-AAAAGAAAGGAAAGAG
*
129384249 TAAACGAGAAAAAAGAACAAATT-AAAGAAAGGAAA-A-
1 -AAA--AGAAAAAAGAAAAAATTAAAAGAAAGGAAAGAG
129384285 AAAAGAAAAAA
1 AAAAGAAAAAA
129384296 AGAGAGGAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
33 8 0.19
35 3 0.07
37 1 0.02
38 14 0.33
40 16 0.38
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (36 bp):
AAAAGAAAAAAGAAAAAATTAAAAGAAAGGAAAGAG
Found at i:129388536 original size:30 final size:32
Alignment explanation
Indices: 129388486--129388556 Score: 103
Period size: 30 Copynumber: 2.3 Consensus size: 32
129388476 TAATAAAGAT
*
129388486 AAAATTATATTTTAAATTTTTTAAAAATAATA
1 AAAATTATAATTTAAATTTTTTAAAAATAATA
*
129388518 AAAATT-TAATTT-AATTTTTTAAAAATTATA
1 AAAATTATAATTTAAATTTTTTAAAAATAATA
129388548 AAAA-TATAA
1 AAAATTATAA
129388557 ACTATTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 1 0.03
30 24 0.67
31 5 0.14
32 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (32 bp):
AAAATTATAATTTAAATTTTTTAAAAATAATA
Found at i:129394455 original size:18 final size:17
Alignment explanation
Indices: 129394432--129394465 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
129394422 TTCATAAGCA
*
129394432 TATATCATTCATTTCATT
1 TATATCAAT-ATTTCATT
129394450 TATATCAATATTTCAT
1 TATATCAATATTTCAT
129394466 GCTCCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATCAATATTTCATT
Found at i:129394746 original size:46 final size:46
Alignment explanation
Indices: 129394686--129395327 Score: 1070
Period size: 46 Copynumber: 14.0 Consensus size: 46
129394676 TTTGACATGA
* * * * * * *
129394686 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGCCTTACACA-TTTCATATCAGGT
*
129394732 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
129394778 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
*
129394824 TGCCATGGTGTCTTTCAACCATGGCCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
129394870 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
*
129394916 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
* *
129394962 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
* *
129395008 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
*
129395054 TGCCATGGTGTCTTTCAACCATGGCCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
129395100 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
*
129395146 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
*
129395192 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
* *
129395238 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
* * *
129395284 TGCCATGGTATCTTTCAACCATTGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAG
129395328 AGAGCACACT
Statistics
Matches: 576, Mismatches: 19, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
45 4 0.01
46 572 0.99
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGCCTTACACATTTCATATCAGGT
Found at i:129397389 original size:3 final size:3
Alignment explanation
Indices: 129397381--129397405 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
129397371 AAAACTTTAT
129397381 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
129397406 CACGTTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:129397822 original size:30 final size:30
Alignment explanation
Indices: 129397757--129397814 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
129397747 CACCCTTAAA
* * *
129397757 ATATTTGCACTATTAGTCCTTCAATTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
129397787 ATATTTACACT-TTAATCCTTCAAATTTT
1 ATATTTACACTATTAATCCTTCAAATTTT
129397815 GAGTATTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.28, C:0.19, G:0.03, T:0.50
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:129401306 original size:23 final size:22
Alignment explanation
Indices: 129401272--129401329 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 22
129401262 ATATTTTTTG
*
129401272 TTATAACTTAATATTTATTAG-TT
1 TTATAA-TTAATATTT-TTAGAAT
129401295 TTATAATGTAAT-TTTTTAGAAT
1 TTATAAT-TAATATTTTTAGAAT
129401317 TTATAATATAATA
1 TTATAAT-TAATA
129401330 AATCTTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.13
22 16 0.53
23 10 0.33
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
TTATAATTAATATTTTTAGAAT
Found at i:129401765 original size:3 final size:3
Alignment explanation
Indices: 129401757--129401810 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
129401747 TGAGTTTTGA
129401757 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
129401805 TAT TAT
1 TAT TAT
129401811 AACATTAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:129402062 original size:23 final size:23
Alignment explanation
Indices: 129402036--129402117 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 23
129402026 TTGCGAGCTT
*
129402036 TATTGTGAAAATATTGTAAATTG
1 TATTGTAAAAATATTGTAAATTG
* * **
129402059 TATTGTAAAAATAATGTGAACAG
1 TATTGTAAAAATATTGTAAATTG
* * *
129402082 TGTTGCAAAAATATTGTAGATTG
1 TATTGTAAAAATATTGTAAATTG
*
129402105 CATTGTAAAAATA
1 TATTGTAAAAATA
129402118 CTGCTAACTG
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.37
Consensus pattern (23 bp):
TATTGTAAAAATATTGTAAATTG
Found at i:129402138 original size:46 final size:46
Alignment explanation
Indices: 129402043--129402141 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 46
129402033 CTTTATTGTG
* ** *
129402043 AAAATATTGTAAATTGTATTGTAAAAATAATGTGAACAGTGTTGCA
1 AAAATATTGTAAATTGCATTGTAAAAATAATGTGAACAGTACTGAA
* * *
129402089 AAAATATTGTAGATTGCATTGTAAAAATACTGCT-AACTGTACTGAA
1 AAAATATTGTAAATTGCATTGTAAAAATAATG-TGAACAGTACTGAA
129402135 AAAATAT
1 AAAATAT
129402142 GTCAATTTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (46 bp):
AAAATATTGTAAATTGCATTGTAAAAATAATGTGAACAGTACTGAA
Found at i:129402329 original size:54 final size:54
Alignment explanation
Indices: 129402205--129402666 Score: 442
Period size: 54 Copynumber: 8.6 Consensus size: 54
129402195 AGGATTCTAG
* * * ** *
129402205 AAATCTTGTAAGTATAAGGCTGGGATCTTAATTTAACAAGCCGCAAGATTC-AA
1 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGACAAACCGCAAGATTCGAA
* * * **** * *
129402258 AAATCTTGAAAGTATAAGGATGTGATCTTAAATCGACAAATTAAAATATTCGTA
1 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGACAAACCGCAAGATTCGAA
* * * * *
129402312 AAATCTTGTAAGTATAAGGTTACGATCTTAAATCGGCGAGCTGCAAGATTCGAA
1 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGACAAACCGCAAGATTCGAA
* * * * *
129402366 AAATCTTGTAAGTATAAGGTTGCGTTCTTAAATTGAAAAACCACAAGATTCAAA
1 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGACAAACCGCAAGATTCGAA
* * * *
129402420 AAATCATGTAAATATAAGGTTGCGATCTTAAATCGACAAAACGCAAGATTTGAA
1 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGACAAACCGCAAGATTCGAA
* * * * * * * * *
129402474 AAATCCTATAAGTATAAGGTTGTGATCTTAATTAGGCGAGCCCCAAGATT-GAA
1 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGACAAACCGCAAGATTCGAA
* ** * *
129402527 AAATCTTGAAAGTATAAGACTGTGATCTTAAATCGACAAACCGCAAGATTTGAA
1 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGACAAACCGCAAGATTCGAA
* * *** * * * *
129402581 AAATCTTGTAAGTGTAAGGCTGCGATCTTAAATCGGTGAGCCACAAGATTTGGA
1 AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGACAAACCGCAAGATTCGAA
129402635 AAATCTTGTAAGTATAAGGTTGCGATCTTAAA
1 AAATCTTGTAAGTATAAGGTTGCGATCTTAAA
129402667 CTGGTTAAGA
Statistics
Matches: 329, Mismatches: 78, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
53 81 0.25
54 248 0.75
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (54 bp):
AAATCTTGTAAGTATAAGGTTGCGATCTTAAATCGACAAACCGCAAGATTCGAA
Found at i:129402380 original size:161 final size:161
Alignment explanation
Indices: 129402170--129402666 Score: 527
Period size: 161 Copynumber: 3.1 Consensus size: 161
129402160 GCATGAGAAA
* * * *
129402170 GTTGCGATCTTAAATCGGTGA-CTG-AAGGATTCTAGAAATCTTGTAAGTATAAGGCTGGGATCT
1 GTTGCGATCTTAAATCGGCGAGCTGCAA-GATTCGAAAAATCTTGTAAGTATAAGGCTGCGATCT
* * *
129402233 TAATTTAACAAGCCGCAAGATTCAAAAATCTTGAAAGTATAAGGATGTGATCTTAAATCGACAAA
65 TAATTCAACAAACCGCAAGATTCAAAAATCTTGAAAGTATAAGGATGCGATCTTAAATCGACAAA
** * * * *
129402298 TTAAAATATTCGTAAAATCTTGTAAGTATAAG
130 ACACAAGATTTGAAAAATCTTGTAAGTATAAG
* * *
129402330 GTTACGATCTTAAATCGGCGAGCTGCAAGATTCGAAAAATCTTGTAAGTATAAGGTTGCGTTCTT
1 GTTGCGATCTTAAATCGGCGAGCTGCAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCGATCTT
* * * *
129402395 AAATTGAA-AAACCACAAGATTCAAAAAATCATGTAAA-TATAAGGTTGCGATCTTAAATCGACA
66 -AATTCAACAAACCGCAAGATTC-AAAAATCTTG-AAAGTATAAGGATGCGATCTTAAATCGACA
* * *
129402458 AAACGCAAGATTTGAAAAATCCTATAAGTATAAG
128 AAACACAAGATTTGAAAAATCTTGTAAGTATAAG
* * * ** * * *
129402492 GTTGTGATCTTAATTAGGCGAGCCCCAAGATT-GAAAAATCTTGAAAGTATAAGACTGTGATCTT
1 GTTGCGATCTTAAATCGGCGAGCTGCAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCGATCTT
* * * * * * *** *
129402556 AAATCGACAAACCGCAAGATTTGAAAAATCTTGTAAGTGTAAGGCTGCGATCTTAAATCGGTGAG
66 AATTCAACAAACCGCAAGA-TTCAAAAATCTTGAAAGTATAAGGATGCGATCTTAAATCGACAAA
* *
129402621 CCACAAGATTTGGAAAATCTTGTAAGTATAAG
130 ACACAAGATTTGAAAAATCTTGTAAGTATAAG
129402653 GTTGCGATCTTAAA
1 GTTGCGATCTTAAA
129402667 CTGGTTAAGA
Statistics
Matches: 276, Mismatches: 53, Indels: 15
0.80 0.15 0.04
Matches are distributed among these distances:
160 25 0.09
161 154 0.56
162 94 0.34
163 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (161 bp):
GTTGCGATCTTAAATCGGCGAGCTGCAAGATTCGAAAAATCTTGTAAGTATAAGGCTGCGATCTT
AATTCAACAAACCGCAAGATTCAAAAATCTTGAAAGTATAAGGATGCGATCTTAAATCGACAAAA
CACAAGATTTGAAAAATCTTGTAAGTATAAG
Found at i:129406361 original size:16 final size:16
Alignment explanation
Indices: 129406342--129406386 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
129406332 GAGTGGCAAG
129406342 CTAGTGAAGTGGTGAA
1 CTAGTGAAGTGGTGAA
* * *
129406358 CTAGCGGAGTGGTGAG
1 CTAGTGAAGTGGTGAA
129406374 CTAGTGAAAGTGG
1 CTAGTG-AAGTGG
129406387 CGAGTAAGCG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.27, C:0.09, G:0.42, T:0.22
Consensus pattern (16 bp):
CTAGTGAAGTGGTGAA
Found at i:129407865 original size:8 final size:9
Alignment explanation
Indices: 129407844--129407873 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
129407834 TGAACATTTG
129407844 TTTTAATAA
1 TTTTAATAA
129407853 TTTTAAT-A
1 TTTTAATAA
129407861 TTTTAATAA
1 TTTTAATAA
129407870 TTTT
1 TTTT
129407874 TTTATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTAATAA
Found at i:129409615 original size:28 final size:28
Alignment explanation
Indices: 129409553--129409637 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 28
129409543 ATTTTAGCCC
*
129409553 TATTATTGTTATTATTATTTAGAT-TAAATA
1 TATT-TTG-TATTATTATTTA-ATACAAATA
129409583 TATTTT-TAATTATTATTTAATACAACATA
1 TATTTTGT-ATTATTATTTAATACAA-ATA
* *
129409612 -ATTTTGTATTATCATTTAATATAAAT
1 TATTTTGTATTATTATTTAATACAAAT
129409638 CTAATATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
27 5 0.10
28 33 0.69
29 6 0.12
30 4 0.08
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (28 bp):
TATTTTGTATTATTATTTAATACAAATA
Found at i:129411155 original size:29 final size:29
Alignment explanation
Indices: 129411121--129411178 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
129411111 ATAAGTTAAG
129411121 ACATAATTGTACAATTTAATAAATCTATC
1 ACATAATTGTACAATTTAATAAATCTATC
129411150 ACATAATTGTACAATTTAATAAATCTATC
1 ACATAATTGTACAATTTAATAAATCTATC
129411179 TTTTACCTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (29 bp):
ACATAATTGTACAATTTAATAAATCTATC
Found at i:129416905 original size:85 final size:85
Alignment explanation
Indices: 129416811--129416997 Score: 356
Period size: 85 Copynumber: 2.2 Consensus size: 85
129416801 TATTTAAAAT
129416811 AATATTTACATAATATAAAAATATAATATTAAAAGGTATATGTACATACGTAATATATACAAATA
1 AATATTTACATAATATAAAAATATAATATTAAAAGGTATATGTACATACGTAATATATACAAATA
129416876 CATATATAATATAATGTTAA
66 CATATATAATATAATGTTAA
* *
129416896 AATATTTACATAATATAAAAATATAATTTTAAAAGGTATATGTACATACGTAATATATATAAATA
1 AATATTTACATAATATAAAAATATAATATTAAAAGGTATATGTACATACGTAATATATACAAATA
129416961 CATATATAATATAATGTTAA
66 CATATATAATATAATGTTAA
129416981 AATATTTACATAATATA
1 AATATTTACATAATATA
129416998 TATATCATAA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 100 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.37
Consensus pattern (85 bp):
AATATTTACATAATATAAAAATATAATATTAAAAGGTATATGTACATACGTAATATATACAAATA
CATATATAATATAATGTTAA
Found at i:129417045 original size:85 final size:85
Alignment explanation
Indices: 129416811--129417026 Score: 254
Period size: 85 Copynumber: 2.5 Consensus size: 85
129416801 TATTTAAAAT
* * * * * *
129416811 AATATTTACATAATATAAAAATATAATAT-TAAAAGGTATATGTACATACGTAATATATACAAAT
1 AATATTTACATAATATAAAAATATAAT-TGGAAAACGAATATGTACATACATAATATACATAAAT
129416875 ACATATATAATATAATGTTAA
65 ACATATATAATATAATGTTAA
** * * * *
129416896 AATATTTACATAATATAAAAATATAATTTTAAAAGGTATATGTACATACGTAATATATATAAATA
1 AATATTTACATAATATAAAAATATAATTGGAAAACGAATATGTACATACATAATATACATAAATA
129416961 CATATATAATATAATGTTAA
66 CATATATAATATAATGTTAA
*
129416981 AATATTTACATAATATATATATCATAATAATGTGGAAAACGAATAT
1 AATATTTACATAATATA-A-A-AAT-ATAAT-TGGAAAACGAATAT
129417027 TAATAATGTT
Statistics
Matches: 119, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
84 1 0.01
85 99 0.83
86 1 0.01
87 1 0.01
88 2 0.02
89 5 0.04
90 10 0.08
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (85 bp):
AATATTTACATAATATAAAAATATAATTGGAAAACGAATATGTACATACATAATATACATAAATA
CATATATAATATAATGTTAA
Found at i:129417079 original size:15 final size:14
Alignment explanation
Indices: 129417052--129417092 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
129417042 AATATATGCC
*
129417052 TATATACATATATA
1 TATAAACATATATA
*
129417066 TATTAAAGATATATA
1 TA-TAAACATATATA
129417081 TATAAACATATA
1 TATAAACATATA
129417093 CTAATATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (14 bp):
TATAAACATATATA
Found at i:129417289 original size:20 final size:19
Alignment explanation
Indices: 129417244--129417305 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
129417234 GACATTAAAA
*
129417244 ATATATATAATA-ATATACAC
1 ATATATATAATATA-ATA-AT
*
129417264 AAATATATAATATAATATAT
1 ATATATATAATATAATA-AT
*
129417284 ATATATATTAAAATAATAAT
1 ATATATA-TAATATAATAAT
129417304 AT
1 AT
129417306 GAAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 25 0.71
21 10 0.29
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATATATAATATAATAAT
Found at i:129417291 original size:22 final size:21
Alignment explanation
Indices: 129417244--129417305 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
129417234 GACATTAAAA
* *
129417244 ATATATAT-AATAATATACAC
1 ATATATATAAATAATATATAT
*
129417264 AAATATATAATATAATATATAT
1 ATATATATAA-ATAATATATAT
129417286 ATATAT-TAAAATAATA-ATAT
1 ATATATAT-AAATAATATATAT
129417306 GAAAAAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 11 0.31
21 8 0.23
22 16 0.46
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATATATAAATAATATATAT
Found at i:129418712 original size:24 final size:23
Alignment explanation
Indices: 129418685--129418742 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
129418675 TTGGGCCTCT
*
129418685 GTTGGGTTAGTTTAGGTGGGGTGG
1 GTTGGGTTAGTTTAGGT-GAGTGG
* *
129418709 GTTGGGTTGGTTTAGGTTAGTGG
1 GTTGGGTTAGTTTAGGTGAGTGG
129418732 GTATGGGTTAG
1 GT-TGGGTTAG
129418743 CATTTAAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.10, C:0.00, G:0.50, T:0.40
Consensus pattern (23 bp):
GTTGGGTTAGTTTAGGTGAGTGG
Found at i:129419610 original size:142 final size:140
Alignment explanation
Indices: 129419343--129419750 Score: 570
Period size: 142 Copynumber: 2.9 Consensus size: 140
129419333 ATATGAGTTG
* * * *
129419343 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTGAAA-ACAGAAATTGAAAATACCTCAGCGTG-ACCGAGGCTCAACTCACCTCTCGCAATA
* *
129419408 TGAGCTGA-TTTTGAAAGAGTAGAAATTAAAAGGTTCAACCCACCTCTCGTAATATAAGTTGATT
64 TGAGTTGATTTTTGAAAGAGTAGAAATTAAAAGGTTCAACCCACCTCTCGTAATATGAGTTGATT
129419472 CTTGAACAACAT
129 CTTGAACAACAT
* *
129419484 AAATTGAAAACAGAAATTGACAATACCTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGAC-CGAGGCTCAACTCACCTCTCGCAATAT
129419549 GAGTTGATTTTTTGAAAGAGTAGAAATTAAAAGGTTCAACCCACCTCTCGTAATATGAGTTGATT
65 GAGTTGA-TTTTTGAAAGAGTAGAAATTAAAAGGTTCAACCCACCTCTCGTAATATGAGTTGATT
129419614 CTTGAACAACAT
129 CTTGAACAACAT
* * *
129419626 AAATTGAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCATCTCTCGCAAT
1 AAATTGAAAACAGAAATTGAAAATACCTCAG--CGTGA-CCGAGGCTCAACTCACCTCTCGCAAT
** * * * *
129419691 ATGAGTTGATTTTTG-AAGAACAGAAATTAAAAGGCTT-AACTCACCTTTCGCAAGATGAGT
63 ATGAGTTGATTTTTGAAAGAGTAGAAATTAAAAGG-TTCAACCCACCTCTCGTAATATGAGT
129419751 CAATTTTCTA
Statistics
Matches: 241, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
139 1 0.00
140 55 0.23
141 8 0.03
142 132 0.55
143 8 0.03
144 36 0.15
145 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (140 bp):
AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTGAAAGAGTAGAAATTAAAAGGTTCAACCCACCTCTCGTAATATGAGTTGATTCT
TGAACAACAT
Found at i:129419642 original size:13 final size:13
Alignment explanation
Indices: 129419615--129419648 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
129419605 GAGTTGATTC
*
129419615 TTGAACAACATAAA
1 TTGAA-AACAGAAA
129419629 TTGAAAACAGAAA
1 TTGAAAACAGAAA
129419642 TTGAAAA
1 TTGAAAA
129419649 TAGCTCAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:129419944 original size:74 final size:71
Alignment explanation
Indices: 129419767--129420066 Score: 293
Period size: 74 Copynumber: 4.2 Consensus size: 71
129419757 TCTAAACTAA
* * * * *
129419767 AAATACCTTAGCGTGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGA-TTTTGGAACATA
1 AAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATA
129419831 AATT-G
66 AATTAG
* * * * * *
129419836 AAATTACCTCAACGTGTCTTAAGGCTCAAATCACCTCTCGCAATATGAGCTGATTTTTGAAACAA
1 AAA-TACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAC-A
*
129419901 CAAGAATTAG
64 -TA-AATTAG
** **
129419911 AAATACCTCAGCGTGACCTGAGGCTTGACTCACCTCTCGCAATATGAGTCAATTTTTGAAACATA
1 AAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATA
*
129419976 AACTA-
66 AATTAG
** *
129419981 ACAATACCTCAGCGTGTGACCTGAGGCTCAACTCATTTCTTGCAATATGAGTTGATTTTTGAAAA
1 A-AATACCTCAGC--GTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAA
* *
129420046 CATGAGTTA-
62 CATAAATTAG
129420055 AAGATACCTCAG
1 AA-ATACCTCAG
129420067 AGTACCCAAA
Statistics
Matches: 187, Mismatches: 33, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
69 3 0.02
70 41 0.22
71 23 0.12
72 2 0.01
73 42 0.22
74 72 0.39
75 4 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (71 bp):
AAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATA
AATTAG
Found at i:129431556 original size:55 final size:55
Alignment explanation
Indices: 129431472--129431581 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
129431462 GTGTGGTCGG
129431472 ACACCTATTAGATTTTTCTTTAAAAACGAGGAAAAGGCCGAGTTAAGGTCTACGT
1 ACACCTATTAGATTTTTCTTTAAAAACGAGGAAAAGGCCGAGTTAAGGTCTACGT
129431527 ACACCTATTAGATTTTTCTTTAAAAACGAGGAAAAGGCCGAGTTAAGGTCTACGT
1 ACACCTATTAGATTTTTCTTTAAAAACGAGGAAAAGGCCGAGTTAAGGTCTACGT
129431582 TAAAAGTCAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (55 bp):
ACACCTATTAGATTTTTCTTTAAAAACGAGGAAAAGGCCGAGTTAAGGTCTACGT
Found at i:129432481 original size:85 final size:85
Alignment explanation
Indices: 129432390--129432576 Score: 356
Period size: 85 Copynumber: 2.2 Consensus size: 85
129432380 TATTTAAAAT
129432390 AATATTTACATAATATAAAAATATAATATTAAAAGGTATATGTACATACGTAATATATACAAATA
1 AATATTTACATAATATAAAAATATAATATTAAAAGGTATATGTACATACGTAATATATACAAATA
129432455 CATATATAATATAATGTTAA
66 CATATATAATATAATGTTAA
* *
129432475 AATATTTACATAATATAAAAATATAATTTTAAAAGGTATATGTACATACGTAATATATATAAATA
1 AATATTTACATAATATAAAAATATAATATTAAAAGGTATATGTACATACGTAATATATACAAATA
129432540 CATATATAATATAATGTTAA
66 CATATATAATATAATGTTAA
129432560 AATATTTACATAATATA
1 AATATTTACATAATATA
129432577 TATATCATAA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 100 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.37
Consensus pattern (85 bp):
AATATTTACATAATATAAAAATATAATATTAAAAGGTATATGTACATACGTAATATATACAAATA
CATATATAATATAATGTTAA
Found at i:129432624 original size:85 final size:85
Alignment explanation
Indices: 129432390--129432605 Score: 254
Period size: 85 Copynumber: 2.5 Consensus size: 85
129432380 TATTTAAAAT
* * * * * *
129432390 AATATTTACATAATATAAAAATATAATAT-TAAAAGGTATATGTACATACGTAATATATACAAAT
1 AATATTTACATAATATAAAAATATAAT-TGGAAAACGAATATGTACATACATAATATACATAAAT
129432454 ACATATATAATATAATGTTAA
65 ACATATATAATATAATGTTAA
** * * * *
129432475 AATATTTACATAATATAAAAATATAATTTTAAAAGGTATATGTACATACGTAATATATATAAATA
1 AATATTTACATAATATAAAAATATAATTGGAAAACGAATATGTACATACATAATATACATAAATA
129432540 CATATATAATATAATGTTAA
66 CATATATAATATAATGTTAA
*
129432560 AATATTTACATAATATATATATCATAATAATGTGGAAAACGAATAT
1 AATATTTACATAATATA-A-A-AAT-ATAAT-TGGAAAACGAATAT
129432606 TAATAATGTT
Statistics
Matches: 119, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
84 1 0.01
85 99 0.83
86 1 0.01
87 1 0.01
88 2 0.02
89 5 0.04
90 10 0.08
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (85 bp):
AATATTTACATAATATAAAAATATAATTGGAAAACGAATATGTACATACATAATATACATAAATA
CATATATAATATAATGTTAA
Found at i:129432866 original size:20 final size:19
Alignment explanation
Indices: 129432821--129432880 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
129432811 GACATTAAAA
*
129432821 ATATATATAATA-ATATACAC
1 ATATATATAATATA-ATA-AT
*
129432841 AAATATATAATATAAT-AT
1 ATATATATAATATAATAAT
*
129432859 ATATATATTAAAATAATAAT
1 ATATATA-TAATATAATAAT
129432879 AT
1 AT
129432881 GAAAAAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 17 0.52
21 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATATATAATATAATAAT
Found at i:129434013 original size:24 final size:24
Alignment explanation
Indices: 129433986--129434036 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
129433976 TTGGGCCTCT
*
129433986 GTTGGGTTAGTTTAGGTGGGT-TGG
1 GTTGGGTTAGGTTA-GTGGGTATGG
*
129434010 GTTGGTTTAGGTTAGTGGGTATGG
1 GTTGGGTTAGGTTAGTGGGTATGG
129434034 GTT
1 GTT
129434037 AGCATTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.10, C:0.00, G:0.47, T:0.43
Consensus pattern (24 bp):
GTTGGGTTAGGTTAGTGGGTATGG
Found at i:129435639 original size:16 final size:17
Alignment explanation
Indices: 129435611--129435642 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
129435601 CTCTTAGGAA
129435611 GTTGTTGGAATGATAGG
1 GTTGTTGGAATGATAGG
129435628 GTTGTT-GAATGATAG
1 GTTGTTGGAATGATAG
129435643 CTTTAGTTGC
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:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (17 bp):
GTTGTTGGAATGATAGG
Found at i:129436596 original size:24 final size:25
Alignment explanation
Indices: 129436564--129436611 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
129436554 TATTAAAATT
129436564 TATTAATTAT-TTTAAAATTTTAAC
1 TATTAATTATATTTAAAATTTTAAC
* *
129436588 TATTCATTATATTTTAAATTTTAA
1 TATTAATTATATTTAAAATTTTAA
129436612 ATTTAATAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTAATTATATTTAAAATTTTAAC
Found at i:129436685 original size:12 final size:12
Alignment explanation
Indices: 129436668--129436713 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
129436658 TTTTCTTACT
129436668 TTAAAATAATTA
1 TTAAAATAATTA
*
129436680 TTAAAATATTCTA
1 TTAAAATAAT-TA
* *
129436693 TAAAAATATTTA
1 TTAAAATAATTA
129436705 TTAAAATAA
1 TTAAAATAA
129436714 AAATATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAAAATAATTA
Found at i:129436723 original size:25 final size:24
Alignment explanation
Indices: 129436669--129436724 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
129436659 TTTCTTACTT
***
129436669 TAAAATAATTATTAAAATATTCTA
1 TAAAATAATTATTAAAATAAAATA
*
129436693 TAAAAATATTTATTAAAATAAAAATA
1 T-AAAATAATTATTAAAAT-AAAATA
129436719 TAAAAT
1 TAAAAT
129436725 TATCCTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 21 0.81
26 4 0.15
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TAAAATAATTATTAAAATAAAATA
Found at i:129436912 original size:30 final size:29
Alignment explanation
Indices: 129436851--129436919 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
129436841 AAATAATTAT
*
129436851 TTAAAATTATTTAAAAAATAAAAATACTG
1 TTAAAATTATTTAAAAAATAAAAATAATG
** * *
129436880 TTAAAATATATTTAAAATTTTAAGATAATG
1 TTAAAAT-TATTTAAAAAATAAAAATAATG
129436910 TTAAGAATTA
1 TTAA-AATTA
129436920 ATAAATTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 7 0.21
30 23 0.70
31 3 0.09
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (29 bp):
TTAAAATTATTTAAAAAATAAAAATAATG
Found at i:129439099 original size:25 final size:27
Alignment explanation
Indices: 129439071--129439143 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 27
129439061 TTGAAATTTT
*
129439071 TTTCTTATATCTT-TTTATTTT-AAAC
1 TTTCTTATATATTATTTATTTTAAAAC
*
129439096 TTTCATATGTATATATTATTTATTTTAAAAT
1 TTTC---T-TATATATTATTTATTTTAAAAC
*
129439127 TTTCTTATATGTTATTT
1 TTTCTTATATATTATTT
129439144 TGTTATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
25 4 0.10
27 11 0.28
28 2 0.05
29 7 0.18
30 8 0.21
31 7 0.18
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (27 bp):
TTTCTTATATATTATTTATTTTAAAAC
Found at i:129439264 original size:13 final size:13
Alignment explanation
Indices: 129439246--129439297 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 13
129439236 CTTATATTAA
129439246 ATTGTTTTTTTAT
1 ATTGTTTTTTTAT
129439259 ATTGTTTTTATATAT
1 ATTGTTTTT-T-TAT
* *
129439274 ATTATTTATTTTAA
1 ATTGTTT-TTTTAT
129439288 ATTTGTTTTT
1 A-TTGTTTTT
129439298 CACGTGTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 9 0.28
14 6 0.19
15 15 0.47
16 2 0.06
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (13 bp):
ATTGTTTTTTTAT
Found at i:129439506 original size:22 final size:22
Alignment explanation
Indices: 129439476--129439532 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
129439466 TTTTTTATGT
* *
129439476 ATTACTTATTTAAAATTGTTTC
1 ATTATTTATTTAAAATGGTTTC
* *
129439498 ATTATTTATTTTAAATGGTTTT
1 ATTATTTATTTAAAATGGTTTC
129439520 ATGTTATTTATTT
1 A--TTATTTATTT
129439533 CGTTCTCTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 19 0.66
24 10 0.34
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTATTTATTTAAAATGGTTTC
Found at i:129442200 original size:58 final size:60
Alignment explanation
Indices: 129442125--129442264 Score: 151
Period size: 58 Copynumber: 2.4 Consensus size: 60
129442115 GTTTGATCCT
* * ** *
129442125 AAATCTAAAAAATTCAATAAATTTAGCCCTTAATGTTTACAAAATTTGTCATTTTAGTTC
1 AAATCTAAAAAATTCAATAAAATTAGCCCTCAACATTTACAAAATTTGTCAATTTAGTTC
* * **
129442185 AAAT-TAAAAAA-TCAATAAAATTATCCCTCAACATTTACAAAATTTTTCAATTTAACTC
1 AAATCTAAAAAATTCAATAAAATTAGCCCTCAACATTTACAAAATTTGTCAATTTAGTTC
* *
129442243 TAATTCTAAAAATTTCAA-AAAA
1 -AAATCTAAAAAATTCAATAAAA
129442265 CTTATTTAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
58 38 0.58
59 10 0.15
60 14 0.21
61 4 0.06
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.36
Consensus pattern (60 bp):
AAATCTAAAAAATTCAATAAAATTAGCCCTCAACATTTACAAAATTTGTCAATTTAGTTC
Found at i:129443553 original size:15 final size:15
Alignment explanation
Indices: 129443533--129443563 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
129443523 ATCAATGCCT
*
129443533 TCATTTTTTTTCAAA
1 TCATTTTTTTACAAA
129443548 TCATTTTTTTACAAA
1 TCATTTTTTTACAAA
129443563 T
1 T
129443564 TAATTTATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (15 bp):
TCATTTTTTTACAAA
Found at i:129446957 original size:3 final size:3
Alignment explanation
Indices: 129446949--129447214 Score: 98
Period size: 3 Copynumber: 87.7 Consensus size: 3
129446939 GAATTAAATA
*
129446949 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
129446996 TGT TGT TGT TGT TGT TGT TAT CT-T TAT TAC TAT TAC TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
129447041 TAC TAT T-T CCAT TAT TTT TAT T-T CTAAC TAT TAT TTT TAT GTAT ATAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT -T-AT TAT TAT TAT TAT -TAT -TAT
* ** * *
129447089 TAT TAT T-T ATAT CAT CGT TAT TAT TAC TAT TAT TAAA TAT CT-T TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT -TAT TAT
* * * * * * *
129447135 TAT TAC TAT TAT TTT TGT TCCT T-T TAT TAT TGTT TAT CAT CAT TA-
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T-AT TAT TAT TAT TAT
* ** *
129447180 TAT TAT TAT TAT TAC TCC TAT TAT TAT TAT CAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
129447215 CTTCTTTTTT
Statistics
Matches: 203, Mismatches: 42, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
2 11 0.05
3 175 0.86
4 17 0.08
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:129451671 original size:8 final size:8
Alignment explanation
Indices: 129451649--129451678 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
129451639 AACGCTTTTT
129451649 TGCATTCA
1 TGCATTCA
129451657 TTGCATTCA
1 -TGCATTCA
129451666 TGCATTCA
1 TGCATTCA
129451674 TGCAT
1 TGCAT
129451679 CGGCATTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (8 bp):
TGCATTCA
Found at i:129454014 original size:93 final size:93
Alignment explanation
Indices: 129453855--129454025 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
129453845 GCCCATAAGT
* *
129453855 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
129453920 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
129453948 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
129454013 CGAGTTCGGATGC
66 CGAGTTCGGATGC
129454026 TCCCATCCTA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:129454022 original size:46 final size:46
Alignment explanation
Indices: 129453847--129454033 Score: 236
Period size: 46 Copynumber: 4.0 Consensus size: 46
129453837 TAGCANCCGC
* * *
129453847 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
129453893 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
129453943 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
129453986 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCCCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
129454032 CC
1 CC
129454034 TAGTGACATG
Statistics
Matches: 121, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
43 3 0.02
44 1 0.01
45 2 0.02
46 77 0.64
47 32 0.26
48 2 0.02
49 1 0.01
50 3 0.02
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:129456430 original size:30 final size:30
Alignment explanation
Indices: 129456386--129456474 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
129456376 CAAAGATAAC
129456386 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
129456415 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
129456445 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
129456475 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:129456434 original size:15 final size:15
Alignment explanation
Indices: 129456386--129456465 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
129456376 CAAAGATAAC
*
129456386 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
129456400 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
129456415 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
129456430 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
129456445 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
129456460 AAGAAA
1 AAGAAA
129456466 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:129456474 original size:15 final size:15
Alignment explanation
Indices: 129456397--129456474 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
129456387 AGAAAACCGA
129456397 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
129456412 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
129456426 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
129456441 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
129456457 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
129456472 ATA
1 ATA
129456475 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:129459529 original size:93 final size:93
Alignment explanation
Indices: 129459417--129459587 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
129459407 GCCCATAAGT
* *
129459417 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
129459482 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
129459510 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
129459575 CGAGTTCGGATGC
66 CGAGTTCGGATGC
129459588 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:129459603 original size:46 final size:46
Alignment explanation
Indices: 129459409--129459589 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
129459399 TGTAACCCGC
* * *
129459409 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
129459455 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
129459505 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
129459548 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
129459590 AACCATCCTA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 72 0.62
47 32 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:129461462 original size:9 final size:9
Alignment explanation
Indices: 129461448--129461522 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
129461438 TGTGGTTAAA
129461448 AATTAACCG
1 AATTAACCG
*
129461457 AATTAAACG
1 AATTAACCG
*
129461466 AGTTAACCG
1 AATTAACCG
129461475 AATTAACCG
1 AATTAACCG
*
129461484 AATTAACCA
1 AATTAACCG
129461493 AATTAACCG
1 AATTAACCG
129461502 AATTAACC-
1 AATTAACCG
* *
129461510 AAATACCCG
1 AATTAACCG
129461519 AATT
1 AATT
129461523 GAATCACTAC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
8 6 0.11
9 50 0.89
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:129461651 original size:72 final size:72
Alignment explanation
Indices: 129461521--129461670 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
129461511 AATACCCGAA
*
129461521 TTGAATCACTACATAATTAAAAACATTACATAAGTCTTTGAATCACTACATAATTAAAAATATTA
1 TTGAATCACTACATAATTAAAAACATTACA-AAGTCTTTGAATCACTACATAATTAAAAACATTA
129461586 CATAAGTC
65 CATAAGTC
*
129461594 TATGAATCACTACATAATTTAAAACATTAC-AAGTCTTTGAATCACTACATAATTAAAAACATTA
1 T-TGAATCACTACATAATTAAAAACATTACAAAGTCTTTGAATCACTACATAATTAAAAACATTA
129461658 CATAAGTC
65 CATAAGTC
129461666 TTGAA
1 TTGAA
129461671 ATTAACACAT
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
71 4 0.05
72 42 0.57
73 1 0.01
74 27 0.36
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.33
Consensus pattern (72 bp):
TTGAATCACTACATAATTAAAAACATTACAAAGTCTTTGAATCACTACATAATTAAAAACATTAC
ATAAGTC
Found at i:129461684 original size:37 final size:37
Alignment explanation
Indices: 129461521--129461667 Score: 253
Period size: 37 Copynumber: 4.0 Consensus size: 37
129461511 AATACCCGAA
129461521 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
129461558 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
* *
129461595 ATGAATCACTACATAATTTAAAACATTAC--AAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
129461630 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
129461667 T
1 T
129461668 GAAATTAACA
Statistics
Matches: 102, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
35 33 0.32
37 69 0.68
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:129464117 original size:19 final size:20
Alignment explanation
Indices: 129464091--129464140 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
129464081 AAATTATATA
129464091 ATAA-ATTAAA-ACACATTT
1 ATAATATTAAATACACATTT
*
129464109 ATAATATTAAAATACATATTT
1 ATAATATT-AAATACACATTT
129464130 ATAATATTAAA
1 ATAATATTAAA
129464141 CAATTTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
20 6 0.21
21 15 0.54
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAATATTAAATACACATTT
Found at i:129464208 original size:12 final size:11
Alignment explanation
Indices: 129464188--129464221 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
129464178 AGAATACTTG
129464188 TTAAATAAAAT
1 TTAAATAAAAT
*
129464199 TTATAATAAAAA
1 TTA-AATAAAAT
129464211 TTAAATAAAAT
1 TTAAATAAAAT
129464222 ATTGGTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TTAAATAAAAT
Found at i:129465773 original size:18 final size:19
Alignment explanation
Indices: 129465738--129465787 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
129465728 AACCGACCGA
129465738 TTAACCGAATTGGGTCGG-
1 TTAACCGAATTGGGTCGGT
***
129465756 TTAACCGAATTTTTTCGGTT
1 TTAACCGAATTGGGTCGG-T
129465776 TTAACCGAATTG
1 TTAACCGAATTG
129465788 TGCACACCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 15 0.58
20 11 0.42
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (19 bp):
TTAACCGAATTGGGTCGGT
Found at i:129466318 original size:176 final size:176
Alignment explanation
Indices: 129466013--129467167 Score: 1570
Period size: 176 Copynumber: 6.6 Consensus size: 176
129466003 GCAACATTGG
** * * * *
129466013 TGAAGATTGAAGATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATC-GAAAATGGTGAATCTTAT
1 TGAAGATTGAAGATCTTATCTCCCT-AAGCAGTAGCGGAGCAGATCAGAAGA-GGCGAATCTTAT
* * *
129466077 CTCCATGTATTGGCAATGGAGCAGATTTTA-CCACCAACCTTATCTCTCTGAGGTAGCAAGAGAG
64 CTCCATGTATCGGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGAGAG
* * * * * **
129466141 CAGATTGAAGAATAATTTTTATCTTTCTGAGGTAATAAGAAAGCAGAC
129 CAGGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGAC
*
129466189 TGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAGAAGAGGCGAATCATATCT
1 TGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAGAAGAGGCGAATCTTATCT
* * *
129466254 CCATGTATCGGCAATGGAGTAGATTTTAGCCACTAGCCTTATTTCTCTAAGGTAGCAAGAGAGCA
66 CCATGTATCGGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
*
129466319 GGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGTAGAC
131 GGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGAC
* **
129466365 TGAAGATTGAATATCTTATCTCCCTAAGCAGTAGCGGAGCAGATC-GAAAGAGGCGAATCACATC
1 TGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAG-AAGAGGCGAATCTTATC
* ** *
129466429 TCCATGTGTCAACAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTTAGGTAGCAAGAGAGC
65 TCCATGTATCGGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGAGAGC
129466494 AGGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGAC
130 AGGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGAC
* *
129466541 TGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGGAAGAGGCGAATCATATCT
1 TGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAGAAGAGGCGAATCTTATCT
* *
129466606 CCATGTGTCGGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTTAGGTAGCAAGAGAGCA
66 CCATGTATCGGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
* * *
129466671 GGTTGAAGATTGAGTATTATCCTTCTGAGGTAGCAAGAAAGCAAAC
131 GGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGAC
** *
129466717 TGAAGATTGAAGATCTTATCTCTATAAGCAGTAGCGGAGTAGATCAGAAGAGGCGAATCTTATCT
1 TGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAGAAGAGGCGAATCTTATCT
* * * * *
129466782 CCATGTATCGGTAATGGAGCAGATTTAAGTCC-CAAGCCTTATCTCTTTGAGGTAGCAAGAGAAC
66 CCATGTATCGGCAATGGAGCAGATTTTAG-CCACTAGCCTTATCTCTCTGAGGTAGCAAGAGAGC
* *
129466846 AGGTTAAAGATTGAGTCTTATCTTTCTAAGGTAGCAAGAAAGCAGAC
130 AGGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGAC
* * *
129466893 TGAAGATTGAATATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAGAGGCGAATCTTATCT
1 TGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAGAAGAGGCGAATCTTATCT
* * *
129466958 CCATGCATCAGCAATGGAGCAGATTTTAACCACTAG-CTCTATCTCTCTGAGGTAGCAAGAGAGC
66 CCATGTATCGGCAATGGAGCAGATTTTAGCCACTAGCCT-TATCTCTCTGAGGTAGCAAGAGAGC
** * * * * *
129467022 AGGTTGGCGATTGTAATATTATCTTCCTGAGGTAACAAGGAAGCAGAC
130 AGGTTGAAGATTG-AGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGAC
* * * * * * *
129467070 TGAAGATTGAAGATC-TATTTCCCGAAACAGTTGTGGAGCAGAT-TGAGGATGGC-AGATCTTAT
1 TGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAGAAGA-GGCGA-ATCTTAT
* * *
129467132 CTCCATGTATCGGCGATGGGGCAGATTTGAGCCACT
64 CTCCATGTATCGGCAATGGAGCAGATTTTAGCCACT
129467168 GGTCCTATTT
Statistics
Matches: 878, Mismatches: 91, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
175 63 0.07
176 770 0.88
177 45 0.05
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (176 bp):
TGAAGATTGAAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAGAAGAGGCGAATCTTATCT
CCATGTATCGGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGAGAGCA
GGTTGAAGATTGAGTCTTATCTTTCTGAGGTAGCAAGAAAGCAGAC
Found at i:129466526 original size:43 final size:45
Alignment explanation
Indices: 129466467--129466562 Score: 133
Period size: 43 Copynumber: 2.2 Consensus size: 45
129466457 AGCCACTAGC
* * **
129466467 CTTATCTCTCTTAGGTAGCAAGAGAGCAGGTTGAAGATTG-AG-T
1 CTTATCTCTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
*
129466510 CTTATCTTTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
1 CTTATCTCTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
129466555 CTTATCTC
1 CTTATCTC
129466563 CCTAAGCAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 35 0.78
44 2 0.04
45 8 0.18
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (45 bp):
CTTATCTCTCTGAGGTAGCAAGAAAGCAGACTGAAGATTGAAGAT
Found at i:129467348 original size:6 final size:6
Alignment explanation
Indices: 129467306--129467342 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
129467296 GCCCGAGCCC
*
129467306 ATAAAA ATAAAA ATAAAA ACCAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA A-TAAAA ATAAAA ATAAAA
129467343 CAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (6 bp):
ATAAAA
Found at i:129467350 original size:14 final size:15
Alignment explanation
Indices: 129467309--129467361 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
129467299 CGAGCCCATA
129467309 AAAATAAAAATAAAAACC
1 AAAA-AAAAAT-AAAA-C
129467327 AAAAATAAAAATAAAAC
1 -AAAA-AAAAATAAAAC
*
129467344 AAAAAAAAATAAACC
1 AAAAAAAAATAAAAC
129467359 AAA
1 AAA
129467362 TTGTTTATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 13 0.39
16 4 0.12
17 1 0.03
18 4 0.12
19 11 0.33
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAAAAAATAAAAC
Found at i:129467350 original size:19 final size:19
Alignment explanation
Indices: 129467308--129467349 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
129467298 CCGAGCCCAT
*
129467308 AAAAATAAAAATAAAAACC
1 AAAAATAAAAATAAAAACA
129467327 AAAAATAAAAAT-AAAACA
1 AAAAATAAAAATAAAAACA
129467345 AAAAA
1 AAAAA
129467350 AAATAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (19 bp):
AAAAATAAAAATAAAAACA
Found at i:129468923 original size:18 final size:17
Alignment explanation
Indices: 129468902--129468935 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
129468892 ATATATATAT
*
129468902 ATATATATATATATTTTG
1 ATATATAAAT-TATTTTG
129468920 ATATATAAATTATTTT
1 ATATATAAATTATTTT
129468936 AATAGAGTTT
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:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATATATAAATTATTTTG
Found at i:129469435 original size:2 final size:2
Alignment explanation
Indices: 129469428--129469474 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
129469418 ACTTATATGT
129469428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
129469470 TA TA T
1 TA TA T
129469475 TGCGTTTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:129470825 original size:30 final size:30
Alignment explanation
Indices: 129470770--129470827 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
129470760 TATTTTATTA
*
129470770 TTTATCATCTTTATTTATCATTTTTCCAAT
1 TTTATCATCTTTATTTATCAATTTTCCAAT
129470800 TTTATCAT-TTTATTT-TCTTAATTTTCCA
1 TTTATCATCTTTATTTATC--AATTTTCCA
129470828 TTGATGACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 2 0.08
29 7 0.28
30 16 0.64
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTATCATCTTTATTTATCAATTTTCCAAT
Found at i:129478813 original size:120 final size:120
Alignment explanation
Indices: 129478560--129478941 Score: 522
Period size: 120 Copynumber: 3.2 Consensus size: 120
129478550 TTTTTGCGGA
* ** *
129478560 GAAGTTGCAGCAGTTTGAGATTGAGGAGCCGCCGTCGCCATTGGTGGTTTAGGCTCAGTTACAGC
1 GAAGTTACAGCAGTTTGAGCCTGAGGAGCCGCCGTCGCCATTGGTGGTTTAGGCTCAGATACAGC
*
129478625 C-TT--TGGAGGTGACGGTACTTTCTGGTCTCTTTGTTTTTCAATACTGGA-GTCT
66 CTTTGGTGGAGGTGACGGTACTTTCTGGTCTCTTTGTTTTTCAATACCGGAGGT-T
* * * * *
129478677 GAAGCTACAGCTGTTTGAGCCTGAGGAACCGCCGTCGCCATTTGTGGTTTAGGCTCAGCTACAGC
1 GAAGTTACAGCAGTTTGAGCCTGAGGAGCCGCCGTCGCCATTGGTGGTTTAGGCTCAGATACAGC
* * *
129478742 CTTTGGTGGAGGAGACGGTACTTTCTGGTCTCTTAGTTTTTCAACACCGGAGGTT
66 CTTTGGTGGAGGTGACGGTACTTTCTGGTCTCTTTGTTTTTCAATACCGGAGGTT
* *
129478797 GAAGTTACAGCAGTTTGAGCCTGAGGAGCCGTCGTCGCCATTGGTGGTTTAGGCTCAGATACAGT
1 GAAGTTACAGCAGTTTGAGCCTGAGGAGCCGCCGTCGCCATTGGTGGTTTAGGCTCAGATACAGC
* * * * *
129478862 CTTTGGTGGAGGTGACGGTTCTTTTTGGCCTCTTTGTTTTTCAATGCCGGAGGCT
66 CTTTGGTGGAGGTGACGGTACTTTCTGGTCTCTTTGTTTTTCAATACCGGAGGTT
*
129478917 GAAG-CAGCAGCAGTTTGAGCCTGAG
1 GAAGTTA-CAGCAGTTTGAGCCTGAG
129478942 CCGTTGGCAT
Statistics
Matches: 232, Mismatches: 28, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
117 58 0.25
118 2 0.01
119 1 0.00
120 169 0.73
121 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (120 bp):
GAAGTTACAGCAGTTTGAGCCTGAGGAGCCGCCGTCGCCATTGGTGGTTTAGGCTCAGATACAGC
CTTTGGTGGAGGTGACGGTACTTTCTGGTCTCTTTGTTTTTCAATACCGGAGGTT
Found at i:129489531 original size:14 final size:14
Alignment explanation
Indices: 129489508--129489558 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
129489498 AGATACTGCT
*
129489508 CTTAGGATTTAGGG
1 CTTAGTATTTAGGG
**
129489522 CTTAGTATTT-GAT
1 CTTAGTATTTAGGG
129489535 CTTTAG-ATTTAGGG
1 C-TTAGTATTTAGGG
129489549 CTTAGTATTT
1 CTTAGTATTT
129489559 GCAGTTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.47
Consensus pattern (14 bp):
CTTAGTATTTAGGG
Found at i:129493779 original size:12 final size:12
Alignment explanation
Indices: 129493762--129493787 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
129493752 AAGTTACCCA
129493762 TTGGCTAAAGTT
1 TTGGCTAAAGTT
129493774 TTGGCTAAAGTT
1 TTGGCTAAAGTT
129493786 TT
1 TT
129493788 CGATTCATGT
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (12 bp):
TTGGCTAAAGTT
Found at i:129498458 original size:15 final size:15
Alignment explanation
Indices: 129498438--129498468 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
129498428 CTGATTTGGC
129498438 TCAAATTGGCTTGTT
1 TCAAATTGGCTTGTT
129498453 TCAAATTGGCTTGTT
1 TCAAATTGGCTTGTT
129498468 T
1 T
129498469 GTTTAAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (15 bp):
TCAAATTGGCTTGTT
Found at i:129500545 original size:408 final size:408
Alignment explanation
Indices: 129499790--129501009 Score: 2440
Period size: 408 Copynumber: 3.0 Consensus size: 408
129499780 AAGATAAATG
129499790 AATGACATATAAATGAAAAACACCGGCTATAGATTATAGTAATGGGATCACCTGTAGATGAAAAA
1 AATGACATATAAATGAAAAACACCGGCTATAGATTATAGTAATGGGATCACCTGTAGATGAAAAA
129499855 AAAGTATTCAAAGGGTCATGAATATTCCTACTAATGATTATCAAGATCCAGATGACAATCGAGCT
66 AAAGTATTCAAAGGGTCATGAATATTCCTACTAATGATTATCAAGATCCAGATGACAATCGAGCT
129499920 TAACTAAGACACACTCCAAACGAGGCATTTCAAGTAATGTGGTATGTGCATTTTAAAGATTAAGG
131 TAACTAAGACACACTCCAAACGAGGCATTTCAAGTAATGTGGTATGTGCATTTTAAAGATTAAGG
129499985 AGTAGGTGCAGTTTGGTTTAGGTACATAGAGAAAAAACTAATTCTAGATGCATATTTTGAGAAAG
196 AGTAGGTGCAGTTTGGTTTAGGTACATAGAGAAAAAACTAATTCTAGATGCATATTTTGAGAAAG
129500050 AGCTTAAATGAGAAGGTACAAGTTAGGTGAAAATTTTCTTATAGTATCATATGAACTTTTTTTTT
261 AGCTTAAATGAGAAGGTACAAGTTAGGTGAAAATTTTCTTATAGTATCATATGAACTTTTTTTTT
129500115 TTCTCTTTTTAGGAACTATAATTTATATATTTGTTAGGCCCTAGAGAATTATAAAAAAAATATTT
326 TTCTCTTTTTAGGAACTATAATTTATATATTTGTTAGGCCCTAGAGAATTATAAAAAAAATATTT
129500180 TTGTATTTAGTGAGCTTA
391 TTGTATTTAGTGAGCTTA
129500198 AATGACATATAAATGAAAAACACCGGCTATAGATTATAGTAATGGGATCACCTGTAGATGAAAAA
1 AATGACATATAAATGAAAAACACCGGCTATAGATTATAGTAATGGGATCACCTGTAGATGAAAAA
129500263 AAAGTATTCAAAGGGTCATGAATATTCCTACTAATGATTATCAAGATCCAGATGACAATCGAGCT
66 AAAGTATTCAAAGGGTCATGAATATTCCTACTAATGATTATCAAGATCCAGATGACAATCGAGCT
129500328 TAACTAAGACACACTCCAAACGAGGCATTTCAAGTAATGTGGTATGTGCATTTTAAAGATTAAGG
131 TAACTAAGACACACTCCAAACGAGGCATTTCAAGTAATGTGGTATGTGCATTTTAAAGATTAAGG
129500393 AGTAGGTGCAGTTTGGTTTAGGTACATAGAGAAAAAACTAATTCTAGATGCATATTTTGAGAAAG
196 AGTAGGTGCAGTTTGGTTTAGGTACATAGAGAAAAAACTAATTCTAGATGCATATTTTGAGAAAG
129500458 AGCTTAAATGAGAAGGTACAAGTTAGGTGAAAATTTTCTTATAGTATCATATGAACTTTTTTTTT
261 AGCTTAAATGAGAAGGTACAAGTTAGGTGAAAATTTTCTTATAGTATCATATGAACTTTTTTTTT
129500523 TTCTCTTTTTAGGAACTATAATTTATATATTTGTTAGGCCCTAGAGAATTATAAAAAAAATATTT
326 TTCTCTTTTTAGGAACTATAATTTATATATTTGTTAGGCCCTAGAGAATTATAAAAAAAATATTT
129500588 TTGTATTTAGTGAGCTTA
391 TTGTATTTAGTGAGCTTA
129500606 AATGACATATAAATGAAAAACACCGGCTATAGATTATAGTAATGGGATCACCTGTAGATGAAAAA
1 AATGACATATAAATGAAAAACACCGGCTATAGATTATAGTAATGGGATCACCTGTAGATGAAAAA
129500671 AAAGTATTCAAAGGGTCATGAATATTCCTACTAATGATTATCAAGATCCAGATGACAATCGAGCT
66 AAAGTATTCAAAGGGTCATGAATATTCCTACTAATGATTATCAAGATCCAGATGACAATCGAGCT
129500736 TAACTAAGACACACTCCAAACGAGGCATTTCAAGTAATGTGGTATGTGCATTTTAAAGATTAAGG
131 TAACTAAGACACACTCCAAACGAGGCATTTCAAGTAATGTGGTATGTGCATTTTAAAGATTAAGG
129500801 AGTAGGTGCAGTTTGGTTTAGGTACATAGAGAAAAAACTAATTCTAGATGCATATTTTGAGAAAG
196 AGTAGGTGCAGTTTGGTTTAGGTACATAGAGAAAAAACTAATTCTAGATGCATATTTTGAGAAAG
129500866 AGCTTAAATGAGAAGGTACAAGTTAGGTGAAAATTTTCTTATAGTATCATATGAACTTTTTTTTT
261 AGCTTAAATGAGAAGGTACAAGTTAGGTGAAAATTTTCTTATAGTATCATATGAACTTTTTTTTT
129500931 TTCTCTTTTTAGGAACTATAATTTATATATTTGTTAGGCCCTAGAGAATTATAAAAAAAATATTT
326 TTCTCTTTTTAGGAACTATAATTTATATATTTGTTAGGCCCTAGAGAATTATAAAAAAAATATTT
129500996 TTGTATTTAGTGAG
391 TTGTATTTAGTGAG
129501010 GTTATTATCT
Statistics
Matches: 812, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
408 812 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (408 bp):
AATGACATATAAATGAAAAACACCGGCTATAGATTATAGTAATGGGATCACCTGTAGATGAAAAA
AAAGTATTCAAAGGGTCATGAATATTCCTACTAATGATTATCAAGATCCAGATGACAATCGAGCT
TAACTAAGACACACTCCAAACGAGGCATTTCAAGTAATGTGGTATGTGCATTTTAAAGATTAAGG
AGTAGGTGCAGTTTGGTTTAGGTACATAGAGAAAAAACTAATTCTAGATGCATATTTTGAGAAAG
AGCTTAAATGAGAAGGTACAAGTTAGGTGAAAATTTTCTTATAGTATCATATGAACTTTTTTTTT
TTCTCTTTTTAGGAACTATAATTTATATATTTGTTAGGCCCTAGAGAATTATAAAAAAAATATTT
TTGTATTTAGTGAGCTTA
Found at i:129504517 original size:15 final size:15
Alignment explanation
Indices: 129504497--129504527 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
129504487 CTTTTTCATT
129504497 ATCCATAAACTTTAA
1 ATCCATAAACTTTAA
129504512 ATCCATAAACTTTAA
1 ATCCATAAACTTTAA
129504527 A
1 A
129504528 CTACTACAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (15 bp):
ATCCATAAACTTTAA
Found at i:129505016 original size:77 final size:77
Alignment explanation
Indices: 129504883--129505035 Score: 229
Period size: 77 Copynumber: 2.0 Consensus size: 77
129504873 CCACTTAATT
* * * *
129504883 AAGAATTTTCAAGTTAAAAATCAATTTAAGGAAAAATAAGTTTTTTTAGTTGCATTTGTCTCACA
1 AAGAATTTTCAAGTTAAAAATCAATTTAAGGAAAAATAAGTTTTTGTAATTACATTTGTCTCAAA
129504948 TATTTTCCTTTTC
66 TA-TTTCCTTTTC
*
129504961 AAGAATTTTCAAGTT-AAAATCAATTTAAGGAAAGATATA-TTTTTGTAATTACATTTGTCTCAA
1 AAGAATTTTCAAGTTAAAAATCAATTTAAGGAAAAATA-AGTTTTTGTAATTACATTTGTCTCAA
129505024 ATATTTCCTTTT
65 ATATTTCCTTTT
129505036 TAAATTTTAC
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
76 9 0.13
77 44 0.64
78 16 0.23
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (77 bp):
AAGAATTTTCAAGTTAAAAATCAATTTAAGGAAAAATAAGTTTTTGTAATTACATTTGTCTCAAA
TATTTCCTTTTC
Found at i:129508000 original size:17 final size:17
Alignment explanation
Indices: 129507946--129508005 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 17
129507936 ATTTACGTGT
*
129507946 TTAATT-ATTTTAATCAA
1 TTAATTAATTTT-ATGAA
129507963 TTAATTATATATTCTATTGAA
1 TTAATTA-AT-TT-TA-TGAA
129507984 TTAATTAATTTTATGAA
1 TTAATTAATTTTATGAA
*
129508001 ATAAT
1 TTAAT
129508006 CAAAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 14 0.39
18 2 0.06
19 4 0.11
20 5 0.14
21 11 0.31
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAATTAATTTTATGAA
Found at i:129508329 original size:17 final size:17
Alignment explanation
Indices: 129508307--129508345 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
129508297 TTCTTTTTTT
129508307 TCTTTTATTT-TCCATTC
1 TCTTTTATTTCTCC-TTC
*
129508324 TCTTTTGTTTCTCCTTC
1 TCTTTTATTTCTCCTTC
129508341 TCTTT
1 TCTTT
129508346 GATTGATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.05, C:0.26, G:0.03, T:0.67
Consensus pattern (17 bp):
TCTTTTATTTCTCCTTC
Found at i:129511734 original size:13 final size:13
Alignment explanation
Indices: 129511718--129511747 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
129511708 TAATTGAATG
129511718 ACATAAATCTACT
1 ACATAAATCTACT
129511731 ACATAAATCTACT
1 ACATAAATCTACT
129511744 ACAT
1 ACAT
129511748 TAGAGCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (13 bp):
ACATAAATCTACT
Found at i:129520024 original size:74 final size:74
Alignment explanation
Indices: 129519903--129520051 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
129519893 ACAACTTAGG
129519903 CAATATCAGGTCGAGTCAGGGCCACATATTGTAAAACACCGGCAAGACTCCTATATTCAGTTAGA
1 CAATATCAGGTCGAGTCAGGGCCACATATTGTAAAACACCGGCAAGACTCCTATATTCAGTTAGA
129519968 TCACTGAGA
66 TCACTGAGA
129519977 CAATATCAGGTCGAGTCAGGGCCACATATTGTAAAACACCGGCAAGACTCCTATATTCAGTTAGA
1 CAATATCAGGTCGAGTCAGGGCCACATATTGTAAAACACCGGCAAGACTCCTATATTCAGTTAGA
129520042 TCACTGAGA
66 TCACTGAGA
129520051 C
1 C
129520052 GATTTCTTTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (74 bp):
CAATATCAGGTCGAGTCAGGGCCACATATTGTAAAACACCGGCAAGACTCCTATATTCAGTTAGA
TCACTGAGA
Found at i:129527337 original size:44 final size:43
Alignment explanation
Indices: 129527251--129527339 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 43
129527241 ATTAATAATT
* * *
129527251 TTAATTTTAATTATTTTTAAATGTGTAATTATCACAATTTCTA
1 TTAATTTTAATTATATTTAAATGTATAATTATCACAACTTCTA
* *
129527294 TTAATTTATAATTATATTTAAATGTATAATTATGATAACTTCTA
1 TTAATTT-TAATTATATTTAAATGTATAATTATCACAACTTCTA
129527338 TT
1 TT
129527340 GTATTTCAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 7 0.17
44 33 0.82
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (43 bp):
TTAATTTTAATTATATTTAAATGTATAATTATCACAACTTCTA
Found at i:129534004 original size:69 final size:69
Alignment explanation
Indices: 129533893--129534031 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
129533883 GATAGGAAAA
*
129533893 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
129533958 GCTG
66 GCTG
129533962 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
129534027 GCTG
66 GCTG
129534031 A
1 A
129534032 TAGAGTCTTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (69 bp):
ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
GCTG
Found at i:129537431 original size:22 final size:22
Alignment explanation
Indices: 129537401--129537442 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
129537391 AGGTTCCGTT
* *
129537401 TTTTCTTTTTTCTTTTTTTTCC
1 TTTTATTTTTTATTTTTTTTCC
129537423 TTTTATTTTTTATTTTTTTT
1 TTTTATTTTTTATTTTTTTT
129537443 ATTTTTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTATTTTTTATTTTTTTTCC
Found at i:129537448 original size:22 final size:22
Alignment explanation
Indices: 129537400--129537448 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
129537390 GAGGTTCCGT
* * *
129537400 TTTTTCTTTTTTCTTTTTTTTC
1 TTTTTATTTTTTATTTTTTTTA
*
129537422 CTTTTATTTTTTATTTTTTTTA
1 TTTTTATTTTTTATTTTTTTTA
129537444 TTTTT
1 TTTTT
129537449 TTTGGTTGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.06, C:0.08, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTATTTTTTATTTTTTTTA
Found at i:129548371 original size:33 final size:33
Alignment explanation
Indices: 129548274--129548372 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
129548264 TTTCTTCTTG
*
129548274 ACATTCCAGCTCCTGTCCAGCAACAAAACACCC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
*
129548307 ACATTCCAGCTCCTGTCCAGCAGCAAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
*
129548340 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
129548373 CCACTCAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.31, C:0.41, G:0.10, T:0.17
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACAAAACACTC
Found at i:129554206 original size:25 final size:25
Alignment explanation
Indices: 129554159--129554206 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
129554149 CCTGCGAAGC
129554159 CAAAAGATAAAAGAAAGAAAGAATT
1 CAAAAGATAAAAGAAAGAAAGAATT
129554184 CAAAAGA-AAATA-AAAGAACAGAA
1 CAAAAGATAAA-AGAAAGAA-AGAA
129554207 ATGAAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.71, C:0.06, G:0.15, T:0.08
Consensus pattern (25 bp):
CAAAAGATAAAAGAAAGAAAGAATT
Found at i:129555475 original size:17 final size:16
Alignment explanation
Indices: 129555442--129555494 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
129555432 ATAATTTTAT
*
129555442 TATTATTAATTTAAAA
1 TATTATAAATTTAAAA
129555458 TATTATAAATTATAAAA
1 TATTATAAATT-TAAAA
*
129555475 TA-TCTAAA-TTAAAA
1 TATTATAAATTTAAAA
*
129555489 TTTTAT
1 TATTAT
129555495 TATTTTAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 6 0.19
15 3 0.10
16 15 0.48
17 7 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTATAAATTTAAAA
Found at i:129558435 original size:10 final size:10
Alignment explanation
Indices: 129558420--129558455 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
129558410 TTTGACACGG
129558420 ATTTTTTCTT
1 ATTTTTTCTT
*
129558430 ATTTTTTCTA
1 ATTTTTTCTT
129558440 ATTTTTTCTT
1 ATTTTTTCTT
129558450 GATTTT
1 -ATTTT
129558456 CTTTTTCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (10 bp):
ATTTTTTCTT
Found at i:129568106 original size:32 final size:31
Alignment explanation
Indices: 129568046--129568113 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
129568036 AATGTAAAAA
*
129568046 AAAAAAATTATTAAAATTATAGTCAATAATAT
1 AAAAAAATTATTAAAATTATAGTAAATAAT-T
* *
129568078 AAAAAAATTATTGAAATT-TCATTAAATAATT
1 AAAAAAATTATTAAAATTAT-AGTAAATAATT
129568109 AAAAA
1 AAAAA
129568114 TAAACCATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (31 bp):
AAAAAAATTATTAAAATTATAGTAAATAATT
Found at i:129568168 original size:2 final size:2
Alignment explanation
Indices: 129568161--129568188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
129568151 TAATTTCTAA
129568161 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
129568189 TTGTCTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:129568498 original size:29 final size:30
Alignment explanation
Indices: 129568448--129568508 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
129568438 TCAGAACTAC
* *
129568448 ATATTAATTTTAGTTTAATGTGCAATGTTAT
1 ATATAAATTTTAATTT-ATGTGCAATGTTAT
* *
129568479 ATATAAATTTTAATTT-TGTGTAATTTTAT
1 ATATAAATTTTAATTTATGTGCAATGTTAT
129568508 A
1 A
129568509 CATTTAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 12 0.46
31 14 0.54
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (30 bp):
ATATAAATTTTAATTTATGTGCAATGTTAT
Found at i:129570401 original size:22 final size:22
Alignment explanation
Indices: 129570373--129570416 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
129570363 TTTTTTTTAA
129570373 AATATTTATATTATATTATTTT
1 AATATTTATATTATATTATTTT
129570395 AATATTTATATTATATTATTTT
1 AATATTTATATTATATTATTTT
129570417 TACTTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
AATATTTATATTATATTATTTT
Found at i:129570405 original size:17 final size:17
Alignment explanation
Indices: 129570383--129570516 Score: 56
Period size: 17 Copynumber: 8.3 Consensus size: 17
129570373 AATATTTATA
129570383 TTATATTATTTTAATAT
1 TTATATTATTTTAATAT
*
129570400 TTATATTATATT-AT-T
1 TTATATTATTTTAATAT
129570415 TT-TACTTA--TTAAT-T
1 TTATA-TTATTTTAATAT
** * *
129570429 TT-TA-TATAATCATCT
1 TTATATTATTTTAATAT
*
129570444 TAATATTATTTTAATAT
1 TTATATTATTTTAATAT
***
129570461 TTATATTAAAATAATA-
1 TTATATTATTTTAATAT
*
129570477 TTATA-TATTTAGAATAT
1 TTATATTATTT-TAATAT
*
129570494 GTT-TATTTTTTTAATAT
1 -TTATATTATTTTAATAT
129570511 ATTATA
1 -TTATA
129570517 AACTATATAA
Statistics
Matches: 86, Mismatches: 19, Indels: 23
0.67 0.15 0.18
Matches are distributed among these distances:
12 2 0.02
13 2 0.02
14 12 0.14
15 10 0.12
16 13 0.15
17 39 0.45
18 8 0.09
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.59
Consensus pattern (17 bp):
TTATATTATTTTAATAT
Found at i:129570587 original size:18 final size:19
Alignment explanation
Indices: 129570553--129570589 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
129570543 AATATAAAGT
*
129570553 ATTATAGACATAAAAATAA
1 ATTATAGACAAAAAAATAA
129570572 ATTATAGA-AAAAAAATAA
1 ATTATAGACAAAAAAATAA
129570590 CAATTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (19 bp):
ATTATAGACAAAAAAATAA
Found at i:129571920 original size:17 final size:18
Alignment explanation
Indices: 129571888--129571955 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
129571878 GAAAGTTGTG
*
129571888 ATAATTATATATTTAAAA
1 ATAATTATACATTTAAAA
*
129571906 ATAATTATA-ATTT-AAT
1 ATAATTATACATTTAAAA
* * *
129571922 AGAAGTACACATTTAAAA
1 ATAATTATACATTTAAAA
129571940 ATAATTATA-ATTTAAA
1 ATAATTATACATTTAAA
129571956 TTGCAATTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
16 8 0.20
17 15 0.38
18 17 0.43
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
ATAATTATACATTTAAAA
Found at i:129583411 original size:9 final size:9
Alignment explanation
Indices: 129583399--129583428 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
129583389 AATTTTTTAA
*
129583399 ATTAATCAT
1 ATTAATCCT
129583408 ATTAATCCT
1 ATTAATCCT
129583417 ATTAATCCT
1 ATTAATCCT
129583426 ATT
1 ATT
129583429 GAGTTGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (9 bp):
ATTAATCCT
Found at i:129584462 original size:35 final size:35
Alignment explanation
Indices: 129584416--129584487 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
129584406 TCTTTACTTT
*
129584416 TTGAATTAAAAATGTAAGTCCAAATATTAACATTA
1 TTGAATTAAAAATATAAGTCCAAATATTAACATTA
129584451 TTGAATTAAAAATATAAGTCCAAATATTAACATTA
1 TTGAATTAAAAATATAAGTCCAAATATTAACATTA
129584486 TT
1 TT
129584488 AAAGTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (35 bp):
TTGAATTAAAAATATAAGTCCAAATATTAACATTA
Found at i:129584624 original size:8 final size:8
Alignment explanation
Indices: 129584611--129584677 Score: 52
Period size: 8 Copynumber: 8.6 Consensus size: 8
129584601 AATTATATCT
129584611 AAAATTTA
1 AAAATTTA
129584619 AAAATTTA
1 AAAATTTA
129584627 AAAA--TA
1 AAAATTTA
129584633 AAAATATTA
1 AAAAT-TTA
* *
129584642 AATATTTG
1 AAAATTTA
129584650 AAAA--TA
1 AAAATTTA
129584656 AAAATATTA
1 AAAAT-TTA
* *
129584665 AATATTTG
1 AAAATTTA
129584673 AAAAT
1 AAAAT
129584678 AAAAATACAG
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
6 11 0.24
8 23 0.50
9 12 0.26
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (8 bp):
AAAATTTA
Found at i:129584691 original size:24 final size:23
Alignment explanation
Indices: 129584611--129584684 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
129584601 AATTATATCT
* *
129584611 AAAAT-TTAAAAATTTAAAAATA
1 AAAATATTAAATATTTGAAAATA
129584633 AAAATATTAAATATTTGAAAATA
1 AAAATATTAAATATTTGAAAATA
129584656 AAAATATTAAATATTTGAAAATA
1 AAAATATTAAATATTTGAAAATA
129584679 AAAATA
1 AAAATA
129584685 CAGAAATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 5 0.10
23 44 0.90
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
AAAATATTAAATATTTGAAAATA
Found at i:129584693 original size:29 final size:27
Alignment explanation
Indices: 129584625--129584696 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 27
129584615 TTTAAAAATT
129584625 TAAAAATAAAAATATTAAATATTTGAAAA
1 TAAAAAT-AAAA-ATTAAATATTTGAAAA
129584654 TAAAAAT----ATTAAATATTTGAAAA
1 TAAAAATAAAAATTAAATATTTGAAAA
129584677 TAAAAATACAGAAATTAAAT
1 TAAAAATA-A-AAATTAAAT
129584697 TCTAAATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
23 23 0.62
29 14 0.38
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (27 bp):
TAAAAATAAAAATTAAATATTTGAAAA
Found at i:129595953 original size:2 final size:2
Alignment explanation
Indices: 129595946--129595975 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
129595936 AACTGTCGAA
129595946 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
129595976 GTGTGTGTGT
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:129603955 original size:32 final size:31
Alignment explanation
Indices: 129603919--129604083 Score: 85
Period size: 32 Copynumber: 5.2 Consensus size: 31
129603909 TTTTATGTTT
*
129603919 CTTAAAAGTTAGAGAAAAATATTTTTAGGTCC
1 CTTAAAAGTTAGAGAAAAATATTTTT-GGCCC
* *
129603951 CTTAAAA-TTTG-GCAAAAATAATTTTTGGGCC
1 CTTAAAAGTTAGAG-AAAAAT-ATTTTTGGCCC
* *
129603982 CTTAAAAGCTA-AAATAAAAT-TTTTTGGGGCCC
1 CTTAAAAGTTAGAGA-AAAATATTTTT--GGCCC
* * *
129604014 CTTAAAAGTT-GA-TAAAAT-TTTTTTGACC
1 CTTAAAAGTTAGAGAAAAATATTTTTGGCCC
* *
129604042 TTTAAAAAGTTA-AAAAATAATAATTTTTTAGGCCC
1 CTT-AAAAGTTAGAGAAA-AAT-A-TTTTT-GGCCC
129604077 CTTAAAA
1 CTTAAAA
129604084 ACTGGAAAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 30
0.69 0.10 0.20
Matches are distributed among these distances:
28 5 0.05
29 8 0.08
30 18 0.18
31 24 0.24
32 33 0.32
34 9 0.09
35 5 0.05
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (31 bp):
CTTAAAAGTTAGAGAAAAATATTTTTGGCCC
Found at i:129604233 original size:2 final size:2
Alignment explanation
Indices: 129604226--129604256 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
129604216 GGCTCAATTG
129604226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
129604257 ATAGTGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:129604556 original size:28 final size:30
Alignment explanation
Indices: 129604510--129604565 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 30
129604500 TTTGAAGTTT
129604510 AAATATCTGACCCCAAATT-T-AAAAAATA
1 AAATATCTGACCCCAAATTGTGAAAAAATA
129604538 AAAT-TCTGACCCCAAAATTGTGAAAAAA
1 AAATATCTGACCCC-AAATTGTGAAAAAA
129604566 ATTCAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
28 9 0.36
29 1 0.04
30 6 0.24
ACGTcount: A:0.52, C:0.18, G:0.07, T:0.23
Consensus pattern (30 bp):
AAATATCTGACCCCAAATTGTGAAAAAATA
Found at i:129605313 original size:19 final size:22
Alignment explanation
Indices: 129605276--129605320 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
129605266 AATTTTTAAA
129605276 ATTTTAAAAATATATAAAAATT
1 ATTTTAAAAATATATAAAAATT
129605298 ATTTT-AAAA-ATA-AAAAATT
1 ATTTTAAAAATATATAAAAATT
129605317 ATTT
1 ATTT
129605321 AAATTGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 4 0.17
22 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTTAAAAATATATAAAAATT
Found at i:129608017 original size:27 final size:27
Alignment explanation
Indices: 129607981--129608037 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
129607971 ACATGTTGCA
* *
129607981 CCTATCTGACAGGCTCAACTAGTTGAG
1 CCTATCTGACAAGCACAACTAGTTGAG
* * *
129608008 CCTATTTGACAAGCACGACTAGTTGTG
1 CCTATCTGACAAGCACAACTAGTTGAG
129608035 CCT
1 CCT
129608038 TCTTGGTAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (27 bp):
CCTATCTGACAAGCACAACTAGTTGAG
Found at i:129612306 original size:35 final size:35
Alignment explanation
Indices: 129612239--129612406 Score: 185
Period size: 35 Copynumber: 4.6 Consensus size: 35
129612229 TCCTCATTGA
*** *
129612239 AATACCATACCTACATTTTTTTAACTCGGTATGGGA-
1 AATACCATACCTACA-TTTCACAACTCAGTAT-GGAT
* **
129612275 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
129612315 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
129612350 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
129612385 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
129612407 CTTTGCCATG
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
35 74 0.63
36 14 0.12
39 3 0.03
40 27 0.23
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:129612365 original size:75 final size:73
Alignment explanation
Indices: 129612234--129612406 Score: 210
Period size: 75 Copynumber: 2.4 Consensus size: 73
129612224 GGTTTTCCTC
*** * * **
129612234 ATTGAAATACCATACCTACATTTTTTTAACTCGGTATGGGAAATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACA-TTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAAC
129612299 TCAGTATGG
65 TCAGTATGG
*
129612308 ATTTGATAATACCATACCTACATTTCACAGCTCAGTAT-GGATAATACCATACCTACATTTCACA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGGA-AATACCATACCTACATTTCACA
129612372 ACTCAGTATGG
63 ACTCAGTATGG
129612383 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
129612407 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 2 0.02
74 4 0.05
75 46 0.52
76 15 0.17
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGGAAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:129615636 original size:12 final size:12
Alignment explanation
Indices: 129615621--129615651 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
129615611 TTCTCTTTTA
129615621 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
129615633 TTTTTCTTTCTC
1 TTTTTCTTTCCC
129615645 TTTTTCT
1 TTTTTCT
129615652 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:129615696 original size:16 final size:17
Alignment explanation
Indices: 129615675--129615708 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
129615665 TTTTCAATTC
129615675 TGTTTCTAT-TCTCTTT
1 TGTTTCTATATCTCTTT
*
129615691 TGTTTCTTTATCTCTTT
1 TGTTTCTATATCTCTTT
129615708 T
1 T
129615709 ATATTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.71
Consensus pattern (17 bp):
TGTTTCTATATCTCTTT
Found at i:129616046 original size:15 final size:14
Alignment explanation
Indices: 129616028--129616058 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
129616018 TTAATTTATT
129616028 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
129616043 TAATAATAATCTAA
1 TAATAATAATCTAA
129616057 TA
1 TA
129616059 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:129616069 original size:21 final size:20
Alignment explanation
Indices: 129616045--129616113 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
129616035 AATGCTAATA
129616045 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
129616066 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
129616085 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
129616106 ATAATAAT
1 ATAATAAT
129616114 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:129619292 original size:22 final size:22
Alignment explanation
Indices: 129619258--129619321 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
129619248 TCAACATTTT
*
129619258 AATAAATCA-ATAAAAATTATCA
1 AATAAAT-ATATAAAAATTATAA
*
129619280 AATAAATATATAATAA-TATAA
1 AATAAATATATAAAAATTATAA
*
129619301 AATTACATTATATAAAAATTA
1 AA-TA-AATATATAAAAATTA
129619322 CATTAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 15 0.44
23 10 0.29
24 2 0.06
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATATATAAAAATTATAA
Found at i:129619315 original size:15 final size:16
Alignment explanation
Indices: 129619295--129619326 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
129619285 ATATATAATA
129619295 ATAT-AAAATTACATT
1 ATATAAAAATTACATT
129619310 ATATAAAAATTACATT
1 ATATAAAAATTACATT
129619326 A
1 A
129619327 AAAAATCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:129619590 original size:114 final size:114
Alignment explanation
Indices: 129619384--129619828 Score: 734
Period size: 114 Copynumber: 3.9 Consensus size: 114
129619374 ATACTAACAC
* * *
129619384 AAAATAACTATAAAATTATTTTTTT-AAATACATTACTAAAAAAAATTCACAATACACTAATACA
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACT-AAAAAAATT-ACAATACACTAAT--A
129619448 CACTAAACCACTAAACACTAACAA--TATATAACCTAATCTTAAATTACTAAT
62 CACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
*
129619499 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACACTAATGCACT
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACACTAATACACT
*
129619564 AAACCACTAAACACTAACAATTTATATAACCTAACCTTAAATTACTAAT
66 AAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
*
129619613 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATATACTAATACACT
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACACTAATACACT
129619678 AAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
66 AAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
* * *
129619727 AAAATAGCTATAAAATTATTATTTTTTAAATATATTACTAAAAAAATCACAATACACTAATACAC
1 AAAATAGCTATAAAAATATT-TTTTTAAAATATATTACTAAAAAAATTACAATACACTAATACAC
*
129619792 TAAACTACTAAACACTAACAATTTATATAACCTAATC
65 TAAACCACTAAACACTAACAATTTATATAACCTAATC
129619829 AACTATAAAA
Statistics
Matches: 313, Mismatches: 13, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
112 24 0.08
114 169 0.54
115 109 0.35
116 11 0.04
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (114 bp):
AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACACTAATACACT
AAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
Found at i:129619795 original size:229 final size:228
Alignment explanation
Indices: 129619384--129619826 Score: 739
Period size: 229 Copynumber: 1.9 Consensus size: 228
129619374 ATACTAACAC
*
129619384 AAAATAACTATAAAATTATTTTTTTAAATACATTACTAAAAAAAATTCACAATACACTAATACAC
1 AAAATAACTATAAAAATATTTTTTTAAATACATTACTAAAAAAAATTCACAATACACTAATA-AC
129619449 ACTAAACCACTAAACACTAACAATATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAA
65 ACTAAACCACTAAACACTAACAATATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAA
* *
129619514 ATATTTTTTTAAAATATATTACTAAAAAAATTACAATACACTAATGCACTAAACCACTAAACACT
130 ATATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACACTAAACCACTAAACACT
129619579 AACAATTTATATAACCTAACCTTAAATTACTAAT
195 AACAATTTATATAACCTAACCTTAAATTACTAAT
* * *
129619613 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACT-AAAAAAATT-ACAATATACTAAT-AC
1 AAAATAACTATAAAAATATTTTTTT-AAATACATTACTAAAAAAAATTCACAATACACTAATAAC
129619675 ACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAA
65 ACTAAACCACTAAACACTAACAA--TATATAACCTAATCTTAAATTACTAATAAAATAGCTATAA
* * *
129619740 AATTATTATTTTTTAAATATATTACTAAAAAAATCACAATACACTAATACACTAAACTACTAAAC
128 AAATATT-TTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACACTAAACCACTAAAC
129619805 ACTAACAATTTATATAACCTAA
192 ACTAACAATTTATATAACCTAA
129619827 TCAACTATAA
Statistics
Matches: 201, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
226 25 0.12
228 58 0.29
229 107 0.53
230 11 0.05
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.32
Consensus pattern (228 bp):
AAAATAACTATAAAAATATTTTTTTAAATACATTACTAAAAAAAATTCACAATACACTAATAACA
CTAAACCACTAAACACTAACAATATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAA
TATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACACTAAACCACTAAACACTA
ACAATTTATATAACCTAACCTTAAATTACTAAT
Found at i:129619901 original size:90 final size:94
Alignment explanation
Indices: 129619734--129619905 Score: 248
Period size: 98 Copynumber: 1.8 Consensus size: 94
129619724 AATAAAATAG
*
129619734 CTATAAAATTATTATTTTTTAAATATATTACTAAAAAAATCACAATACACTAATACACTAAACTA
1 CTATAAAATTATTATTTTTAAAATATATTACTAAAAAAATCACAATACAC--ATACACT-AACTA
129619799 CTAAACACTAACAATTTATATAACCTAATCAA
63 CTAAACACTAACAATTTATATAACCTAATCAA
129619831 CTATAAAATTATT-TTTTTAAATATATTATTACTAAAAAAATCACAATACAC-TA-A-T-AC-AC
1 CTATAAAATTATTATTTTTAAA-ATA-TATTACTAAAAAAATCACAATACACATACACTAACTAC
129619890 TAAACACTAACAATTT
64 TAAACACTAACAATTT
129619906 GTAACCTAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
90 18 0.25
91 2 0.03
93 1 0.01
94 1 0.01
95 2 0.03
96 7 0.10
97 16 0.22
98 25 0.35
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (94 bp):
CTATAAAATTATTATTTTTAAAATATATTACTAAAAAAATCACAATACACATACACTAACTACTA
AACACTAACAATTTATATAACCTAATCAA
Found at i:129620148 original size:38 final size:35
Alignment explanation
Indices: 129620074--129620143 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
129620064 TAATAAATTA
129620074 CTAAAATAATACATTACCTTTTTTTCTTCTTCTTC
1 CTAAAATAATACATTACCTTTTTTTCTTCTTCTTC
129620109 CTAAAATAATACATTACCTTTTTTTCTTCTTCTTC
1 CTAAAATAATACATTACCTTTTTTTCTTCTTCTTC
129620144 TTCCTTCTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (35 bp):
CTAAAATAATACATTACCTTTTTTTCTTCTTCTTC
Found at i:129620153 original size:16 final size:16
Alignment explanation
Indices: 129620132--129620162 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
129620122 TTACCTTTTT
*
129620132 TTCTTCTTCTTCTTCC
1 TTCTTCTTCTCCTTCC
129620148 TTCTTCTTCTCCTTC
1 TTCTTCTTCTCCTTC
129620163 TCCTTTCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCTTCTTCTCCTTCC
Found at i:129620326 original size:21 final size:22
Alignment explanation
Indices: 129620302--129620345 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
129620292 CAAGGGCAAG
129620302 GCAGCAGCAGCAGC-AGGTGGA
1 GCAGCAGCAGCAGCTAGGTGGA
129620323 GCAGCAGCAGCAGCTAGGTGGA
1 GCAGCAGCAGCAGCTAGGTGGA
129620345 G
1 G
129620346 GTGTTGTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.27, C:0.23, G:0.43, T:0.07
Consensus pattern (22 bp):
GCAGCAGCAGCAGCTAGGTGGA
Done.