Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 100 of 199
Found at i:30575293 original size:50 final size:50
Alignment explanation
Indices: 30575236--30575368 Score: 133
Period size: 50 Copynumber: 2.7 Consensus size: 50
30575226 TTAAACATAA
* *
30575236 TTAACATATAAGATGCATAAATGCATGGCTTAA-TTAAAATGCAAACTTAT
1 TTAACATATAAGATGCAT-AATGCATGACATAATTTAAAATGCAAACTTAT
* * * * * *
30575286 TTAACATATGAGTTTCATAATGCATGACATAATTTAATATGCAAACTGAA
1 TTAACATATAAGATGCATAATGCATGACATAATTTAAAATGCAAACTTAT
* * * * *
30575336 TTAATATATGAGTTACATAATGCATGAAATAAT
1 TTAACATATAAGATGCATAATGCATGACATAAT
30575369 CAAATGCAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 12 0.17
50 59 0.83
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.34
Consensus pattern (50 bp):
TTAACATATAAGATGCATAATGCATGACATAATTTAAAATGCAAACTTAT
Found at i:30576307 original size:13 final size:12
Alignment explanation
Indices: 30576277--30576319 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
30576267 ATATTTATAT
30576277 AATAAATTATTC
1 AATAAATTATTC
*
30576289 ATATAACTTACTTC
1 A-ATAAATTA-TTC
30576303 AATAAAATTATTC
1 AAT-AAATTATTC
30576316 AATA
1 AATA
30576320 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 2 0.08
13 15 0.58
14 9 0.35
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAAATTATTC
Found at i:30576674 original size:21 final size:20
Alignment explanation
Indices: 30576650--30576707 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 20
30576640 AGATATTTAT
30576650 TATTATTAATTCTATATAATA
1 TATTATT-ATTCTATATAATA
30576671 TATTATT-TAT-TATA-AA-A
1 TATTATTAT-TCTATATAATA
30576688 TATTA-TATTCT-TATAATA
1 TATTATTATTCTATATAATA
30576706 TA
1 TA
30576708 AACTTTGACT
Statistics
Matches: 32, Mismatches: 0, Indels: 13
0.71 0.00 0.29
Matches are distributed among these distances:
16 4 0.12
17 10 0.31
18 5 0.16
19 5 0.16
20 1 0.03
21 7 0.22
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTATTATTCTATATAATA
Found at i:30576703 original size:18 final size:18
Alignment explanation
Indices: 30576653--30576703 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
30576643 TATTTATTAT
*
30576653 TATTA-ATTCTATATAATA
1 TATTATATTCT-TATAAAA
*
30576671 TATTAT-TTATTATAAAA
1 TATTATATTCTTATAAAA
30576688 TATTATATTCTTATAA
1 TATTATATTCTTATAA
30576704 TATAAACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTATATTCTTATAAAA
Found at i:30584982 original size:19 final size:20
Alignment explanation
Indices: 30584958--30585011 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
30584948 GATACCAACT
*
30584958 TAAAAATATCGATACT-TTA
1 TAAAAATATCGATACTCGTA
*
30584977 TAAAAATATCGATACTCGTG
1 TAAAAATATCGATACTCGTA
*
30584997 GAAAAATATCGATAC
1 TAAAAATATCGATAC
30585012 CACTGGGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (20 bp):
TAAAAATATCGATACTCGTA
Found at i:30587149 original size:20 final size:20
Alignment explanation
Indices: 30587104--30587162 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
30587094 AACAATTTTA
*
30587104 AATCAAGTGC-AAATGATTTT
1 AATCAAGT-CAAAATGATTTC
*
30587124 AGTCAAGTCAAAATGATTTC
1 AATCAAGTCAAAATGATTTC
* *
30587144 AATCAAGTTAAAATAATTT
1 AATCAAGTCAAAATGATTT
30587163 TAAAATGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (20 bp):
AATCAAGTCAAAATGATTTC
Found at i:30593169 original size:14 final size:14
Alignment explanation
Indices: 30593150--30593186 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
30593140 TTCTCAATCA
*
30593150 CTTATCCCCTTATC
1 CTTATCCCATTATC
30593164 CTTATCCCATTATC
1 CTTATCCCATTATC
30593178 CTTATCCCA
1 CTTATCCCA
30593187 GCTCTCGGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTATCCCATTATC
Found at i:30594700 original size:21 final size:21
Alignment explanation
Indices: 30594675--30594715 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30594665 TGTTAATACA
*
30594675 AATTTCAATTTCTTTTCTAAT
1 AATTTCAATCTCTTTTCTAAT
*
30594696 AATTTCAATCTGTTTTCTAA
1 AATTTCAATCTCTTTTCTAA
30594716 ATTCCTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.15, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTTCAATCTCTTTTCTAAT
Found at i:30595245 original size:12 final size:12
Alignment explanation
Indices: 30595228--30595252 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30595218 CCATAATTTT
30595228 TACCTTTAATTC
1 TACCTTTAATTC
30595240 TACCTTTAATTC
1 TACCTTTAATTC
30595252 T
1 T
30595253 CTCTTACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (12 bp):
TACCTTTAATTC
Found at i:30596192 original size:27 final size:27
Alignment explanation
Indices: 30596157--30596223 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
30596147 CCCAATTTTA
* *
30596157 CTTCAGTAAATTTTTGACGATTTTACC
1 CTTCAGTAAAATTTTGAAGATTTTACC
* *
30596184 CTTCGGTAAAATTTTGAAGATTTTACT
1 CTTCAGTAAAATTTTGAAGATTTTACC
*
30596211 CAT-AGTAAAATTT
1 CTTCAGTAAAATTT
30596224 CGAGAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.43
Consensus pattern (27 bp):
CTTCAGTAAAATTTTGAAGATTTTACC
Found at i:30596495 original size:9 final size:9
Alignment explanation
Indices: 30596481--30596506 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30596471 TCTTTTTCTA
30596481 TTCATTTCG
1 TTCATTTCG
30596490 TTCATTTCG
1 TTCATTTCG
30596499 TTCATTTC
1 TTCATTTC
30596507 TATTCAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.23, G:0.08, T:0.58
Consensus pattern (9 bp):
TTCATTTCG
Found at i:30597735 original size:16 final size:16
Alignment explanation
Indices: 30597714--30597749 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
30597704 TTTGGTTCGC
30597714 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
30597730 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
30597746 TGTA
1 TGTA
30597750 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:30597814 original size:44 final size:45
Alignment explanation
Indices: 30597730--30597820 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
30597720 GGATTAGAGG
* * *
30597730 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
30597775 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
30597819 TG
1 TG
30597821 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:30598015 original size:21 final size:19
Alignment explanation
Indices: 30597975--30598011 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
30597965 TTAAATTTAA
30597975 TAAATATATAATTTATAAT
1 TAAATATATAATTTATAAT
30597994 TAAATATATAATTTATAA
1 TAAATATATAATTTATAA
30598012 AATTCCTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATATATAATTTATAAT
Found at i:30598345 original size:18 final size:17
Alignment explanation
Indices: 30598324--30598358 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
30598314 ATATTATTAA
*
30598324 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
30598342 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
30598359 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:30598367 original size:120 final size:120
Alignment explanation
Indices: 30598186--30598411 Score: 400
Period size: 120 Copynumber: 1.9 Consensus size: 120
30598176 ATCATATTTA
* *
30598186 AACATAATTTTTATTAAATATATTTTAATTAAAAATATATAATTTAATAAAATTCTTAATAATTA
1 AACATAAATATTATTAAATATATTTTAATTAAAAATATATAATTTAATAAAATTCTTAATAATTA
30598251 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 ATATTCTTATA-TAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
30598307 AACATAAATATTATTAAATATATTTTAATT-AAAATATATAATTTAATAAAATTCTTAATAATTC
1 AACATAAATATTATTAAATATATTTTAATTAAAAATATATAATTTAATAAAATTCTTAATAATTA
*
30598371 ATATTCTTATATAATTTATTCAAATCATAATATATGATACT
66 ATATTCTTATATAATTTACTCAAATCATAATATATGATACT
30598412 ATAATTAATA
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
119 29 0.29
120 44 0.44
121 28 0.28
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (120 bp):
AACATAAATATTATTAAATATATTTTAATTAAAAATATATAATTTAATAAAATTCTTAATAATTA
ATATTCTTATATAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:30598487 original size:26 final size:27
Alignment explanation
Indices: 30598412--30598493 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 27
30598402 ATATGATACT
* *
30598412 ATAATTAATATTAAATATATTTTAATTA
1 ATAATTATTATTAAATATAATTTAA-TA
* *
30598440 A-AATATATGATTAAATACAATTTAA-A
1 ATAAT-TATTATTAAATATAATTTAATA
*
30598466 ATAATTATTATTAAATATAATTTCATA
1 ATAATTATTATTAAATATAATTTAATA
30598493 A
1 A
30598494 AATGTTCTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 19 0.43
27 8 0.18
28 17 0.39
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
ATAATTATTATTAAATATAATTTAATA
Found at i:30601968 original size:23 final size:23
Alignment explanation
Indices: 30601941--30602013 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
30601931 TTATATTAAT
30601941 ATTATATAATCAAAATGATTTTA
1 ATTATATAATCAAAATGATTTTA
* * * ***
30601964 ATTATAT-TTC-AATTAAAAAT-
1 ATTATATAATCAAAATGATTTTA
30601984 ATTATATAATCAAAATGATTTTA
1 ATTATATAATCAAAATGATTTTA
30602007 ATTATAT
1 ATTATAT
30602014 TTTAATATAC
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 7 0.20
21 7 0.20
22 7 0.20
23 14 0.40
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (23 bp):
ATTATATAATCAAAATGATTTTA
Found at i:30605021 original size:13 final size:13
Alignment explanation
Indices: 30605003--30605029 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30604993 ATTTAATATC
30605003 AATTTATAAATTA
1 AATTTATAAATTA
30605016 AATTTATAAATTA
1 AATTTATAAATTA
30605029 A
1 A
30605030 GCCTATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTATAAATTA
Found at i:30608220 original size:15 final size:14
Alignment explanation
Indices: 30608184--30608223 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
30608174 AACTTTCAAT
**
30608184 ACTTATTTTTTTAC
1 ACTTATTTTTCGAC
30608198 ACTTATTTTTCGAC
1 ACTTATTTTTCGAC
30608212 ACTTAATTTTTC
1 ACTT-ATTTTTC
30608224 AGTTTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (14 bp):
ACTTATTTTTCGAC
Found at i:30608310 original size:42 final size:42
Alignment explanation
Indices: 30608246--30608326 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
30608236 AACACCTTAA
* * *
30608246 ACTATGATATAAATCCCCAATCTTGGAATCAGAAGATATTAG
1 ACTAAGATATAAATCCCCAATCTTCGAATCAAAAGATATTAG
30608288 ACTAAGATATAAA-CCCTCAATCTTCGAATCAAAAGATAT
1 ACTAAGATATAAATCCC-CAATCTTCGAATCAAAAGATAT
30608327 ACCCACTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (42 bp):
ACTAAGATATAAATCCCCAATCTTCGAATCAAAAGATATTAG
Found at i:30608756 original size:43 final size:43
Alignment explanation
Indices: 30608604--30608820 Score: 214
Period size: 42 Copynumber: 5.1 Consensus size: 43
30608594 TATAGAAACA
* ** * *
30608604 AAACGCCGCTAAAAGTCATGTTCTTTAGCGGCGC--AACAATAA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTC-CTAC
* * ** *
30608646 AAACGCCGCTAAAGGTCATGTTCTTTAGTGGCGC-TATAGTAG
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCTAC
30608688 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCTAC
* *
30608731 AAATGCAGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCC-AC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTTTCCTAC
** *
30608774 AAACGCCGCTAAAGAACATG-GCTTTTAGCGGCG-TTTT-CTCAC
1 AAACGCCGCTAAAGGTCATGTTC-TTTAGCGGCGCTTTTCCT-AC
30608816 AAACG
1 AAACG
30608821 TCACTATAGA
Statistics
Matches: 151, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.01
41 4 0.03
42 75 0.50
43 65 0.43
44 6 0.04
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCTAC
Found at i:30608818 original size:85 final size:85
Alignment explanation
Indices: 30608653--30608811 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 85
30608643 TAAAAACGCC
* * ** *
30608653 GCTAAAGGTCATGTTCTTTAGTGGCGCTATAGTAGAAACGCCGCTAAAGGTCATGTTCTTTAGCG
1 GCTAAAGGTCATGTTCTTTAGCGGCGCTATAGTACAAACGCCGCTAAAGAACATGCTCTTTAGCG
30608718 GCGCTTTTCCTACAAATGCA
66 GCGCTTTTCCTACAAATGCA
**
30608738 GCTAAAGGTCATGTTCTTTAGCGGCGCT-TTTTCCACAAACGCCGCTAAAGAACATGGCT-TTTA
1 GCTAAAGGTCATGTTCTTTAGCGGCGCTATAGT--ACAAACGCCGCTAAAGAACAT-GCTCTTTA
30608801 GCGGCG-TTTTC
63 GCGGCGCTTTTC
30608812 TCACAAACGT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 2 0.03
85 32 0.50
86 28 0.44
87 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (85 bp):
GCTAAAGGTCATGTTCTTTAGCGGCGCTATAGTACAAACGCCGCTAAAGAACATGCTCTTTAGCG
GCGCTTTTCCTACAAATGCA
Found at i:30608832 original size:42 final size:43
Alignment explanation
Indices: 30608754--30608855 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 43
30608744 GGTCATGTTC
* *
30608754 TTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGAACATGG-CT
1 TTTAGCGGCGCTTTTTCCACAAACGCCACTAAAGAAC-CGGACT
* *
30608797 TTTAGCGGCG--TTTTCTCACAAACGTCACTATAGAACCGGACT
1 TTTAGCGGCGCTTTTTC-CACAAACGCCACTAAAGAACCGGACT
30608839 TTTAGCGGCGCTTTTTC
1 TTTAGCGGCGCTTTTTC
30608856 AATCAAATGC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
41 7 0.14
42 29 0.57
43 10 0.20
44 5 0.10
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTTCCACAAACGCCACTAAAGAACCGGACT
Found at i:30609323 original size:21 final size:21
Alignment explanation
Indices: 30609299--30609349 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
30609289 TTCTTTTGAA
*
30609299 CCTCTGCTTCTCTCGCTG-TAG
1 CCTCTGCTTCCCTCGCTGCT-G
30609320 CCTCTGCTTCCCTCGCTGCTG
1 CCTCTGCTTCCCTCGCTGCTG
30609341 CCTCTGCTT
1 CCTCTGCTT
30609350 TAAGTTGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.02, C:0.43, G:0.18, T:0.37
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCTG
Found at i:30609364 original size:87 final size:86
Alignment explanation
Indices: 30609214--30609389 Score: 253
Period size: 87 Copynumber: 2.0 Consensus size: 86
30609204 TTCTGCTCTG
* *
30609214 CTCTGCTTCCCTCACTGCATCCTCTGCTTCTTCGATGCCGCATCTGCTTCAAGTTGTAGCTGGAG
1 CTCTGCTTCCCTCACTGCAGCCTCTGCTTCCTCGATGCCGCATCTGCTTCAAGTTGTAGCTGGAG
30609279 CTCTTCATATTTCTTTTGAAC
66 CTCTTCATATTTCTTTTGAAC
* * * * * * *
30609300 CTCTGCTTCTCTCGCTGTAGCCTCTGCTTCCCTCGCTGCTGCCTCTGCTTTAAGTTGTAGCTGGA
1 CTCTGCTTCCCTCACTGCAGCCTCTGCTT-CCTCGATGCCGCATCTGCTTCAAGTTGTAGCTGGA
*
30609365 GTTCTTCATATTTCTTTTGAAC
65 GCTCTTCATATTTCTTTTGAAC
30609387 CTC
1 CTC
30609390 AACTGTGGTC
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 25 0.32
87 54 0.68
ACGTcount: A:0.12, C:0.31, G:0.17, T:0.40
Consensus pattern (86 bp):
CTCTGCTTCCCTCACTGCAGCCTCTGCTTCCTCGATGCCGCATCTGCTTCAAGTTGTAGCTGGAG
CTCTTCATATTTCTTTTGAAC
Found at i:30614832 original size:25 final size:25
Alignment explanation
Indices: 30614813--30614982 Score: 95
Period size: 25 Copynumber: 7.0 Consensus size: 25
30614803 ATGTATTTGG
*
30614813 TAAATTATGTAGGTTATGTATTATA
1 TAAATTATGTAAGTTATGTATTATA
* * *
30614838 TAAGTTATGTAAGTTATGTATTCTG
1 TAAATTATGTAAGTTATGTATTATA
** * *
30614863 TAAGCTATGTAAGTTGTGTATTATG
1 TAAATTATGTAAGTTATGTATTATA
* * * *
30614888 TAAGTTGTGT-A-TTATGTTAGTTGTG
1 TAAATTATGTAAGTTATG-TA-TTATA
* *
30614913 T--ACTATGTAAGTTATGTATTATG
1 TAAATTATGTAAGTTATGTATTATA
* *
30614936 TAAGTTATGT-A-TTATGTTAGTTATG
1 TAAATTATGTAAGTTATG-TA-TTATA
*
30614961 T--ACTATGTAAGTTATGTATTAT
1 TAAATTATGTAAGTTATGTATTAT
30614983 GTATGTTATG
Statistics
Matches: 116, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
23 27 0.23
24 12 0.10
25 77 0.66
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (25 bp):
TAAATTATGTAAGTTATGTATTATA
Found at i:30614835 original size:16 final size:16
Alignment explanation
Indices: 30614816--30615197 Score: 235
Period size: 16 Copynumber: 22.9 Consensus size: 16
30614806 TATTTGGTAA
*
30614816 ATTATGTAGGTTATGT
1 ATTATGTAAGTTATGT
*
30614832 ATTATATAAGTTATGT
1 ATTATGTAAGTTATGT
*
30614848 AAGTTATGT-A-TTCTGT
1 -A-TTATGTAAGTTATGT
* *
30614864 AAGCTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGT
*
30614882 ATTATGTAAGTTGTGT
1 ATTATGTAAGTTATGT
* *
30614898 ATTATGTTAGTTGTGT
1 ATTATGTAAGTTATGT
*
30614914 ACTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
30614930 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
30614946 ATTATGTTAGTTATGT
1 ATTATGTAAGTTATGT
*
30614962 ACTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
30614978 ATTATGTATGTTATGT
1 ATTATGTAAGTTATGT
*
30614994 ATAATATTAATTAAGTTATGT
1 AT--TA-T--GTAAGTTATGT
* * *
30615015 ATAATATTAATTAAGTTGTGC
1 AT--TA-T--GTAAGTTATGT
* *
30615036 ATAATGTAAGTTCTGT
1 ATTATGTAAGTTATGT
30615052 ATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT
*
30615068 ATTATGT-A-TTATGC
1 ATTATGTAAGTTATGT
* *
30615082 ATTATGTATGATATGT
1 ATTATGTAAGTTATGT
*
30615098 ATAATAT-TAA-TTAAG-
1 AT--TATGTAAGTTATGT
*
30615113 -TTGT-TAA-TTATGT
1 ATTATGTAAGTTATGT
*
30615126 ATTATGTATGTTATGTAT
1 ATTATGTAAGTTATG--T
* *
30615144 ATTATTAATTAAGTTGTGT
1 ATTA-T--GTAAGTTATGT
30615163 ATTATGTAAGTTATTATGTT
1 ATTATGTAAG---TTATG-T
30615183 ATTATGTAAGTTATG
1 ATTATGTAAGTTATG
30615198 CAAGTTTATA
Statistics
Matches: 297, Mismatches: 43, Indels: 51
0.76 0.11 0.13
Matches are distributed among these distances:
12 9 0.03
14 16 0.05
15 3 0.01
16 176 0.59
17 11 0.04
18 22 0.07
19 12 0.04
20 11 0.04
21 37 0.12
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (16 bp):
ATTATGTAAGTTATGT
Found at i:30615011 original size:21 final size:21
Alignment explanation
Indices: 30614987--30615040 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
30614977 TATTATGTAT
30614987 GTTATGTATAATATTAATTAA
1 GTTATGTATAATATTAATTAA
30615008 GTTATGTATAATATTAATTAA
1 GTTATGTATAATATTAATTAA
* *
30615029 GTTGTGCATAAT
1 GTTATGTATAAT
30615041 GTAAGTTCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (21 bp):
GTTATGTATAATATTAATTAA
Found at i:30615053 original size:74 final size:70
Alignment explanation
Indices: 30614965--30615164 Score: 194
Period size: 74 Copynumber: 2.7 Consensus size: 70
30614955 GTTATGTACT
30614965 ATGTAAGTTATGTATTATGTATGTTATGTATAATATTAATTAAGTTATGTATAATATTAATTAAG
1 ATGTAAGTT-TGTATTATGTATGTTATGTATAATATTAATTAAGTTATGTATAATATTAATTAAG
30615030 TTGTGCATA
65 TTGT---TA
* * *
30615039 ATGTAAGTTCTGTATTATGTAAGTTATGTATTATGTATTATGCATTATGTATGATATGTATAATA
1 ATGTAAGTT-TGTATTATGTATGTTATGTA-TA-ATATTA---ATTA---A-GTTATGTATAATA
30615104 TTAATTAAGTTGTTA
56 TTAATTAAGTTGTTA
* *
30615119 AT-T-A---TGTATTATGTATGTTATGTATATTATTAATTAAGTTGTGTAT
1 ATGTAAGTTTGTATTATGTATGTTATGTATAATATTAATTAAGTTATGTAT
30615165 TATGTAAGTT
Statistics
Matches: 109, Mismatches: 8, Indels: 27
0.76 0.06 0.19
Matches are distributed among these distances:
65 7 0.06
66 1 0.01
69 4 0.04
72 5 0.05
73 2 0.02
74 47 0.43
75 2 0.02
76 5 0.05
78 1 0.01
79 5 0.05
80 4 0.04
82 1 0.01
83 25 0.23
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.49
Consensus pattern (70 bp):
ATGTAAGTTTGTATTATGTATGTTATGTATAATATTAATTAAGTTATGTATAATATTAATTAAGT
TGTTA
Found at i:30615072 original size:7 final size:7
Alignment explanation
Indices: 30615049--30615090 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
30615039 ATGTAAGTTC
30615049 TGTATTA
1 TGTATTA
30615056 TGTAAGTTA
1 TGT-A-TTA
30615065 TGTATTA
1 TGTATTA
30615072 TGTATTA
1 TGTATTA
*
30615079 TGCATTA
1 TGTATTA
30615086 TGTAT
1 TGTAT
30615091 GATATGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 23 0.74
8 2 0.06
9 6 0.19
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (7 bp):
TGTATTA
Found at i:30615130 original size:44 final size:44
Alignment explanation
Indices: 30615072--30615170 Score: 155
Period size: 44 Copynumber: 2.2 Consensus size: 44
30615062 TTATGTATTA
*
30615072 TGTATTATGCATTATGTATGATATGTATAATATTAATTAAGTTG
1 TGTATTATGTATTATGTATGATATGTATAATATTAATTAAGTTG
* *
30615116 T-TAATTATGTATTATGTATGTTATGTATATTATTAATTAAGTTG
1 TGT-ATTATGTATTATGTATGATATGTATAATATTAATTAAGTTG
30615160 TGTATTATGTA
1 TGTATTATGTA
30615171 AGTTATTATG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 1 0.02
44 48 0.96
45 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (44 bp):
TGTATTATGTATTATGTATGATATGTATAATATTAATTAAGTTG
Found at i:30615140 original size:83 final size:80
Alignment explanation
Indices: 30614950--30615148 Score: 199
Period size: 83 Copynumber: 2.4 Consensus size: 80
30614940 TTATGTATTA
* * *
30614950 TGTTAGTTATGTACTATGTAAGTTATGT-ATTATGTATGTTATGTATAATATTAATTAAGTTATG
1 TGTTAATTATGTATTATGT-AGTTATGTAATTATGTA-GTTATGTATAATATTAATTAAGATATG
30615014 TATAATATTAATTAAGT
64 TATAATATTAATTAAGT
** * * * *
30615031 TGTGCATAATGTAAGTTCTGTA-TTATGTAAGTTATGTA-TTATGTATTATGCATT-ATGTATGA
1 TGTTAATTATGT-A-TTATGTAGTTATGTAA-TTATGTAGTTATGTATAAT--ATTAAT-TAAGA
30615093 TATGTATAATATTAATTAAGT
60 TATGTATAATATTAATTAAGT
30615114 TGTTAATTATGTATTATGTATGTTATGTATATTAT
1 TGTTAATTATGTATTATGTA-GTTATGTA-ATTAT
30615149 TAATTAAGTT
Statistics
Matches: 95, Mismatches: 13, Indels: 18
0.75 0.10 0.14
Matches are distributed among these distances:
81 30 0.32
82 6 0.06
83 58 0.61
84 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (80 bp):
TGTTAATTATGTATTATGTAGTTATGTAATTATGTAGTTATGTATAATATTAATTAAGATATGTA
TAATATTAATTAAGT
Found at i:30615369 original size:21 final size:22
Alignment explanation
Indices: 30615327--30615369 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
30615317 ATATAGGGTG
***
30615327 ATATATTAAAAAATAGGTTTTA
1 ATATATTAAAAAATAACATTTA
30615349 ATAT-TTAAAAAATAACATTTA
1 ATATATTAAAAAATAACATTTA
30615370 CAATTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
ATATATTAAAAAATAACATTTA
Found at i:30615456 original size:17 final size:17
Alignment explanation
Indices: 30615436--30615469 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30615426 TATCCATACC
30615436 ATATATAAAAATTTTAA
1 ATATATAAAAATTTTAA
*
30615453 ATATATATAAATTTTAA
1 ATATATAAAAATTTTAA
30615470 GTAATGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATAAAAATTTTAA
Found at i:30615492 original size:18 final size:18
Alignment explanation
Indices: 30615465--30615548 Score: 89
Period size: 18 Copynumber: 4.5 Consensus size: 18
30615455 ATATATAAAT
30615465 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
30615483 TTTAATTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
*
30615505 TTTTAGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
*
30615522 TTTAAGTAATGAAATATA
1 TTTAAGTAATGTAATATA
*
30615540 TTTTAGTAA
1 TTTAAGTAA
30615549 GTAGTGTAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
17 9 0.16
18 28 0.51
19 3 0.05
20 3 0.05
21 4 0.07
22 8 0.15
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:30615513 original size:17 final size:17
Alignment explanation
Indices: 30615493--30615551 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
30615483 TTTAATTAAT
* *
30615493 GTAAGTTATAAATTTTA
1 GTAAGTAATATATTTTA
*
30615510 GTAAGTAATATATTTAA
1 GTAAGTAATATATTTTA
*
30615527 GTAATGAAATATATTTTA
1 GTAA-GTAATATATTTTA
30615545 GTAAGTA
1 GTAAGTA
30615552 GTGTAAGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 20 0.57
18 15 0.43
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (17 bp):
GTAAGTAATATATTTTA
Found at i:30615524 original size:39 final size:36
Alignment explanation
Indices: 30615457--30615600 Score: 121
Period size: 39 Copynumber: 3.8 Consensus size: 36
30615447 TTTTAAATAT
*
30615457 ATATAAATTTTAAGTAATGTAATATATTTAATTAATGTA
1 ATATAAATTTT-AGTAA-GTAATATATTTAAGTAATG-A
30615496 AGTTATAAATTTTAGTAAGTAATATATTTAAGTAATGA
1 A--TATAAATTTTAGTAAGTAATATATTTAAGTAATGA
* * * **
30615534 A-ATATATTTTAGTAAGTAGTGTAAGTAATGTAAT-A
1 ATATAAATTTTAGTAAGTAATATATTTAA-GTAATGA
* *
30615569 TATACTTAAATTTTAGTAAGTCATGTATTTAA
1 -ATA--TAAATTTTAGTAAGTAATATATTTAA
30615601 CATTCTGTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
35 23 0.26
36 6 0.07
37 1 0.01
38 2 0.02
39 40 0.46
40 5 0.06
41 10 0.11
ACGTcount: A:0.43, C:0.01, G:0.12, T:0.44
Consensus pattern (36 bp):
ATATAAATTTTAGTAAGTAATATATTTAAGTAATGA
Found at i:30616308 original size:12 final size:14
Alignment explanation
Indices: 30616288--30616319 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
30616278 TTCAACAATT
30616288 AGAAGAACAAAC-C
1 AGAAGAACAAACAC
30616301 AGAA-AACAAACAC
1 AGAAGAACAAACAC
30616314 AGAAGA
1 AGAAGA
30616320 TCGGTACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 9 0.53
14 1 0.06
ACGTcount: A:0.66, C:0.19, G:0.16, T:0.00
Consensus pattern (14 bp):
AGAAGAACAAACAC
Found at i:30617598 original size:337 final size:335
Alignment explanation
Indices: 30616977--30617964 Score: 1550
Period size: 337 Copynumber: 2.9 Consensus size: 335
30616967 TAACAAAAAC
*
30616977 AGAAAATGCTAAGTTAAAATTCGTGTACAGAAACGGCA-TCGTTTAGCCAAAATTTTAAGACACT
1 AGAAAATACTAAGTTAAAATTCGTGTACAGAAACGG-AGTCGTTTAGCCAAAATTTTAAGACACT
* * * * *
30617041 TTTGCGGCATTTCTAAAAAAACGCCGCTATTTCTTGTACATTTGTGGTGCTTCTAGAAAAGCGCC
65 TTTGCGGCATTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCGGCGTTTCTA-AAAAGCGCC
* * *
30617106 ACTAAAAATTAAAGTTCTAATCCGAAACGACGCTGTTTAATAAAGCTTTAATGCACATTTCTGGC
129 ACTAAAAATTAAAGTTCTAATCCGAAACGGCACCGTTTAATAAAGCTTTAATGCACATTTCTGGC
*
30617171 ATTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAACCAATAT
194 ATTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATAT
* *
30617236 TTTAAGTCGCTTTTGCGGA-GTTTCCTGAATGAAATGCCACTATAAATTAACAGAAATGGCGCCA
259 TTTAAGTCGCTTTTGC-GACGTTTCCTGAA-AAAATGCCACTATAAATTAACAGAAACGGCGCCA
30617300 TTGGATTAATATAG
322 TTGGATTAATATAG
*
30617314 AGAAAATTCTAAGTTAAAATTCGTGTACAGAAACGGAGTCGTTTAGCCAAAATTTTAAGACACTT
1 AGAAAATACTAAGTTAAAATTCGTGTACAGAAACGGAGTCGTTTAGCCAAAATTTTAAGACACTT
*
30617379 TTGCGGCATTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCGGCGTTTCTTAAAAATCGCCA
66 TTGCGGCATTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCGGCGTTTC-TAAAAAGCGCCA
**
30617444 CTAAAAATTAAAGTTCTAATCCGAAACGGCACCGTTTAATAAAGCTTTAATGCACATTTCTGGTG
130 CTAAAAATTAAAGTTCTAATCCGAAACGGCACCGTTTAATAAAGCTTTAATGCACATTTCTGGCA
* * *
30617509 TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACAGTGTCGTTTAGCCGATATT
195 TTTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATT
*
30617574 TTAAGTCGCTTTTGCGACGTTTCCTGAACAAAATGCCACTATAAATTAACAGAAACGGCGCCGTT
260 TTAAGTCGCTTTTGCGACGTTTCCTGAA-AAAATGCCACTATAAATTAACAGAAACGGCGCCATT
30617639 GGATTAATATAG
324 GGATTAATATAG
* * * *
30617651 AGAAAATACTAAGTTAAATTTCGTGTACAGAAACGGTGTTGTTTAGCCAAAATTTTATGACACTT
1 AGAAAATACTAAGTTAAAATTCGTGTACAGAAACGGAGTCGTTTAGCCAAAATTTTAAGACACTT
* * *
30617716 TTGCGGCGTTTCTAGAAAAACGCTGCTATTGCTTGTACATTTGCGGCGTTTCTAAGAAGCGCCAC
66 TTGCGGCATTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCGGCGTTTCTAAAAAGCGCCAC
** * *
30617781 TAAAAATTAAAGTTCTTGTCCGAAACAGCACCGTTTAATAAAGCTTTAATGCACATTTGTGGCAT
131 TAAAAATTAAAGTTCTAATCCGAAACGGCACCGTTTAATAAAGCTTTAATGCACATTTCTGGCAT
*
30617846 TTTCTTTAAAAACGCCACTAACAA-TTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATT
196 TTTCTGTAAAAACGCCACTAA-AATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATT
* * * * * *
30617910 TTAAGTCGCTGTTGCGGCGTTTCATGAACAAACGCCACTAAAAATTAACAGAAAC
260 TTAAGTCGCTTTTGCGACGTTTCCTGAAAAAATGCCACTATAAATTAACAGAAAC
30617965 AACGTCGTTT
Statistics
Matches: 602, Mismatches: 45, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
335 24 0.04
336 155 0.26
337 421 0.70
338 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (335 bp):
AGAAAATACTAAGTTAAAATTCGTGTACAGAAACGGAGTCGTTTAGCCAAAATTTTAAGACACTT
TTGCGGCATTTCTAGAAAAACGCCGCTATTGCTTGTACATTTGCGGCGTTTCTAAAAAGCGCCAC
TAAAAATTAAAGTTCTAATCCGAAACGGCACCGTTTAATAAAGCTTTAATGCACATTTCTGGCAT
TTTCTGTAAAAACGCCACTAAAATTTAATTTGCTTAAGCTAAACGGCGTCGTTTAGCCAATATTT
TAAGTCGCTTTTGCGACGTTTCCTGAAAAAATGCCACTATAAATTAACAGAAACGGCGCCATTGG
ATTAATATAG
Found at i:30618403 original size:7 final size:7
Alignment explanation
Indices: 30618393--30618424 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
30618383 CTTTCAACTT
30618393 CTAACCC
1 CTAACCC
30618400 CTAACCC
1 CTAACCC
30618407 CTAACCC
1 CTAACCC
30618414 CTAACCC
1 CTAACCC
30618421 CTAA
1 CTAA
30618425 ACCTTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.53, G:0.00, T:0.16
Consensus pattern (7 bp):
CTAACCC
Found at i:30618726 original size:7 final size:7
Alignment explanation
Indices: 30618687--30618747 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
30618677 TAATTAAGAT
*
30618687 CTAAACC
1 CTAACCC
30618694 CTAACTCC
1 CTAAC-CC
*
30618702 CTAACTC
1 CTAACCC
* **
30618709 TTAACTT
1 CTAACCC
30618716 CTAACCC
1 CTAACCC
30618723 CTAACCC
1 CTAACCC
30618730 CTAACCC
1 CTAACCC
*
30618737 CTAACCT
1 CTAACCC
30618744 CTAA
1 CTAA
30618748 ACCTTAAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
7 38 0.84
8 7 0.16
ACGTcount: A:0.31, C:0.44, G:0.00, T:0.25
Consensus pattern (7 bp):
CTAACCC
Found at i:30619454 original size:41 final size:40
Alignment explanation
Indices: 30619385--30619508 Score: 133
Period size: 41 Copynumber: 3.0 Consensus size: 40
30619375 GCTAATACAG
* **
30619385 CGAGCATTAGCGGCGCAACACAAAAAACGCCACTAAAGCCC
1 CGAGCATTAGCGGCGC-ATATTAAAAACGCCACTAAAGCCC
* * * *
30619426 CGAGCATTAGCGGCGCATTATTATAAACGCCGCTAAAACCT
1 CGAGCATTAGCGGCGCA-TATTAAAAACGCCACTAAAGCCC
*
30619467 CAAGCATTAGCGGCG-ATATTCTAAAAACGCCACTAAAGCCC
1 CGAGCATTAGCGGCGCATA-T-TAAAAACGCCACTAAAGCCC
30619508 C
1 C
30619509 CGAAAGGTCA
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
39 2 0.03
40 3 0.04
41 63 0.93
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (40 bp):
CGAGCATTAGCGGCGCATATTAAAAACGCCACTAAAGCCC
Found at i:30619493 original size:82 final size:82
Alignment explanation
Indices: 30619353--30619508 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 82
30619343 TATTTTTTTT
* * *
30619353 GCGGCGCTTTATCAAAAACGCCGCTAATACAGCGAGCATTAGCGGCGCAACACAAAAAACGCCAC
1 GCGGCGCATTATCAAAAACGCCGCTAAAACAGCAAGCATTAGCGGCGCAACACAAAAAACGCCAC
30619418 TAAAGCCCCGAGCATTA
66 TAAAGCCCCGAGCATTA
* * ** ** *
30619435 GCGGCGCATTATTATAAACGCCGCTAAAACCTCAAGCATTAGCGGCG-ATATTCTAAAAACGCCA
1 GCGGCGCATTATCAAAAACGCCGCTAAAACAGCAAGCATTAGCGGCGCA-ACACAAAAAACGCCA
30619499 CTAAAGCCCC
65 CTAAAGCCCC
30619509 CGAAAGGTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
81 1 0.02
82 62 0.98
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (82 bp):
GCGGCGCATTATCAAAAACGCCGCTAAAACAGCAAGCATTAGCGGCGCAACACAAAAAACGCCAC
TAAAGCCCCGAGCATTA
Found at i:30623464 original size:17 final size:18
Alignment explanation
Indices: 30623438--30623471 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30623428 TTCTTTTCTC
*
30623438 CTTTTCTTTTT-TTCTTT
1 CTTTTATTTTTCTTCTTT
30623455 CTTTTATTTTTCTTCTT
1 CTTTTATTTTTCTTCTT
30623472 CGTCGTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
CTTTTATTTTTCTTCTTT
Found at i:30628749 original size:16 final size:15
Alignment explanation
Indices: 30628725--30628771 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
30628715 CTAAGATGTG
30628725 AATTGAATTGAATTT
1 AATTGAATTGAATTT
* *
30628740 AATATGAATTGTATTA
1 AAT-TGAATTGAATTT
*
30628756 AATTGAATTAAATTT
1 AATTGAATTGAATTT
30628771 A
1 A
30628772 CTCGTATAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (15 bp):
AATTGAATTGAATTT
Found at i:30631363 original size:21 final size:21
Alignment explanation
Indices: 30631339--30631379 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30631329 TAAGATAAAT
30631339 AAATATTTATC-TTAATATTTA
1 AAATATTTATCATT-ATATTTA
*
30631360 AAATTTTTATCATTATATTT
1 AAATATTTATCATTATATTT
30631380 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATATTTATCATTATATTTA
Found at i:30639840 original size:22 final size:23
Alignment explanation
Indices: 30639812--30639854 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
30639802 AAATGCCCTC
30639812 TTTTATTATTCA-ATTTATTGGA
1 TTTTATTATTCATATTTATTGGA
*
30639834 TTTTATTATTCATTTTTATTG
1 TTTTATTATTCATATTTATTG
30639855 AAAATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (23 bp):
TTTTATTATTCATATTTATTGGA
Found at i:30643372 original size:11 final size:11
Alignment explanation
Indices: 30643344--30643400 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
30643334 AATAAAAAAA
30643344 TTAAAAAGTATT
1 TTAAAAA-TATT
30643356 TT-AAAATATT
1 TTAAAAATATT
30643366 TTAAAAATA--
1 TTAAAAATATT
30643375 --AAAAAGTATT
1 TTAAAAA-TATT
30643385 TTAAAAATATT
1 TTAAAAATATT
30643396 TTAAA
1 TTAAA
30643401 TTTAAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
7 5 0.13
8 2 0.05
10 6 0.15
11 19 0.49
12 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:30643372 original size:29 final size:30
Alignment explanation
Indices: 30643339--30643408 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
30643329 TTAAAAATAA
30643339 AAAAATTAAAAAGTATTTT-AAAATATTTT
1 AAAAATTAAAAAGTATTTTAAAAATATTTT
*
30643368 AAAAATAAAAAAGTATTTTAAAAATATTTT
1 AAAAATTAAAAAGTATTTTAAAAATATTTT
*
30643398 -AAATTTAAAAA
1 AAAAATTAAAAA
30643409 TTTAAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAAATTAAAAAGTATTTTAAAAATATTTT
Found at i:30643379 original size:18 final size:19
Alignment explanation
Indices: 30643358--30643393 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30643348 AAAGTATTTT
30643358 AAAA-TATTTTAAAAATAA
1 AAAAGTATTTTAAAAATAA
30643376 AAAAGTATTTTAAAAATA
1 AAAAGTATTTTAAAAATA
30643394 TTTTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAAGTATTTTAAAAATAA
Found at i:30643415 original size:7 final size:8
Alignment explanation
Indices: 30643384--30643424 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
30643374 AAAAAAGTAT
30643384 TTTAAAAA
1 TTTAAAAA
**
30643392 TATTTTAAA
1 T-TTAAAAA
30643401 TTTAAAAA
1 TTTAAAAA
30643409 TTTAAAAA
1 TTTAAAAA
30643417 TTTAAAAA
1 TTTAAAAA
30643425 AGATTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 22 0.79
9 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTTAAAAA
Found at i:30643417 original size:16 final size:17
Alignment explanation
Indices: 30643328--30643424 Score: 58
Period size: 16 Copynumber: 5.5 Consensus size: 17
30643318 AAAAATTTAT
30643328 TTTAAAAATA--AAAAA
1 TTTAAAAATATTAAAAA
*
30643343 ATTAAAAAGTATTTTAAAATA
1 TTTAAAAA-TA--TTAAAA-A
*
30643364 TTTTAAAAATA-AAAAAGTA
1 -TTTAAAAATATTAAAA--A
**
30643383 TTTTAAAAATATTTTAAA
1 -TTTAAAAATATTAAAAA
30643401 TTTAAAAAT-TTAAAAA
1 TTTAAAAATATTAAAAA
30643417 TTTAAAAA
1 TTTAAAAA
30643425 AGATTTTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
15 7 0.11
16 15 0.23
17 9 0.14
18 5 0.08
19 13 0.20
20 6 0.09
21 3 0.05
22 7 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TTTAAAAATATTAAAAA
Found at i:30644224 original size:2 final size:2
Alignment explanation
Indices: 30644217--30644252 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
30644207 TGCCATGATT
30644217 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
30644253 GTATTACTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30645420 original size:48 final size:48
Alignment explanation
Indices: 30645368--30645463 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
30645358 ATAGTAATAA
30645368 ATCTTAAATTGAATTATTATCTGTGCTTTGTGCAAGCGGTCTAAATCG
1 ATCTTAAATTGAATTATTATCTGTGCTTTGTGCAAGCGGTCTAAATCG
30645416 ATCTTAAATTGAATTATTATCTGTGCTTTGTGCAAGCGGTCTAAATCG
1 ATCTTAAATTGAATTATTATCTGTGCTTTGTGCAAGCGGTCTAAATCG
30645464 TTTCTCGACT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (48 bp):
ATCTTAAATTGAATTATTATCTGTGCTTTGTGCAAGCGGTCTAAATCG
Found at i:30650033 original size:16 final size:15
Alignment explanation
Indices: 30650012--30650050 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
30650002 TTAAATTATG
*
30650012 GATATGTGTGTATTGT
1 GATATGTGTGTA-TAT
*
30650028 GATATGTGTTTATAT
1 GATATGTGTGTATAT
30650043 GATATGTG
1 GATATGTG
30650051 ACCATTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (15 bp):
GATATGTGTGTATAT
Found at i:30650128 original size:39 final size:39
Alignment explanation
Indices: 30650085--30650220 Score: 236
Period size: 39 Copynumber: 3.5 Consensus size: 39
30650075 CATGTTTTTA
30650085 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
30650124 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
30650163 AGTATTGTGATATATGCTTAAATGTTATGTGCTTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
30650202 TGTAATGTGATATATGCTT
1 AGTATTGTGATATATGCTT
30650221 AAAAGTGAAT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
Found at i:30650134 original size:17 final size:17
Alignment explanation
Indices: 30650112--30650178 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
30650102 TTGAATGTTA
30650112 TGTGATTATATGAGTAT
1 TGTGATTATATGAGTAT
*
30650129 TGTGATATATGCTTGAATGT-T
1 TGTGAT-TAT--ATG-A-GTAT
30650150 ATGTGATTATATGAGTAT
1 -TGTGATTATATGAGTAT
30650168 TGTGA-TATATG
1 TGTGATTATATG
30650179 CTTAAATGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
16 6 0.15
17 13 0.32
18 5 0.12
19 2 0.05
20 2 0.05
21 5 0.12
22 8 0.20
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.46
Consensus pattern (17 bp):
TGTGATTATATGAGTAT
Found at i:30650221 original size:39 final size:39
Alignment explanation
Indices: 30650085--30650237 Score: 234
Period size: 39 Copynumber: 3.9 Consensus size: 39
30650075 CATGTTTTTA
*
30650085 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG
*
30650124 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG
*
30650163 AGTATTGTGATATATGCTTAAATGTTATGTGCTTATATG
1 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG
* * * *
30650202 TGTAATGTGATATATGCTTAAAAGTGAATGTGATTA
1 AGTATTGTGATATATGCTTAAATGT-TATGTGATTA
30650238 CCATGTAAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 98 0.92
40 8 0.08
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.44
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG
Found at i:30656030 original size:15 final size:16
Alignment explanation
Indices: 30656004--30656033 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30655994 TATTTACACG
30656004 GAAAAGGAAAAAAAAA
1 GAAAAGGAAAAAAAAA
30656020 GAAAA-GAAAAAAAA
1 GAAAAGGAAAAAAAA
30656034 GTTGGGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
GAAAAGGAAAAAAAAA
Found at i:30656126 original size:2 final size:2
Alignment explanation
Indices: 30656119--30656160 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
30656109 TATAGGTTGA
30656119 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30656161 GTTTATCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30656469 original size:21 final size:21
Alignment explanation
Indices: 30656427--30656470 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
30656417 TATAGGTATT
* * *
30656427 ATTTTGATAAATATATATTAA
1 ATTTTAATAAACATATAATAA
*
30656448 ATTTTAATAAACATCTAATAA
1 ATTTTAATAAACATATAATAA
30656469 AT
1 AT
30656471 AATTATTGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTTTAATAAACATATAATAA
Found at i:30661084 original size:15 final size:15
Alignment explanation
Indices: 30661061--30661091 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30661051 TTACACTAAC
*
30661061 TATAGTATTTAAAAA
1 TATAATATTTAAAAA
30661076 TATAATATTTAAAAA
1 TATAATATTTAAAAA
30661091 T
1 T
30661092 GAAAGGTGTG
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
TATAATATTTAAAAA
Found at i:30665346 original size:109 final size:106
Alignment explanation
Indices: 30665182--30665494 Score: 417
Period size: 109 Copynumber: 3.0 Consensus size: 106
30665172 GATTAAGATA
*
30665182 TAAAAGGATATTTGGCTATTTGGTCCAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTC
1 TAAAAGGATATTTGGCTA-TTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTT-
*
30665247 CTCGAATTTCCAAGCGCAAAACATTGCCTTATTTTGAAATTTTT
64 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA-TTTT
* *
30665291 TAAAAGGATATTCGGTTATCTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCA------
1 TAAAAGGATATTTGGCTAT-TGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTC
30665350 -C-AATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTT
65 TCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTT
* *
30665390 TAAAAGGATATTTGGCTATTAGGTCGAACGAAAAAAATCGAAACCCAACACATTAGGGCACGCTT
1 TAAAAGGATATTTGGCTATT-GGTCGAACG-AGAAAATCGAAACCCAGCACATTAGGGCACG-TT
* * * *
30665455 TCTCGAACTTCCAAATGCAAAATATTGCCTTATTTAGAAA
63 TCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
30665495 AATTTTCTTT
Statistics
Matches: 180, Mismatches: 12, Indels: 24
0.83 0.06 0.11
Matches are distributed among these distances:
98 1 0.01
99 30 0.17
100 61 0.34
101 1 0.01
108 2 0.01
109 85 0.47
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (106 bp):
TAAAAGGATATTTGGCTATTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTCT
CGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTT
Found at i:30665427 original size:100 final size:100
Alignment explanation
Indices: 30665251--30665450 Score: 323
Period size: 100 Copynumber: 2.0 Consensus size: 100
30665241 CGTTTCCTCG
* *
30665251 AATTTCCAAGCGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTCGGTTATCTGGTC
1 AATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTCGGCTATCTGGTC
* *
30665316 GAACGAGAAAATCGAAACCCAGCACATTAGGGCAC
66 GAACGAAAAAATCGAAACCCAACACATTAGGGCAC
*
30665351 AATTTCCAAACGCAAAACATTGCCTTATTTTGAAA-TTTTTAAAAGGATATTTGGCTAT-TAGGT
1 AATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTCGGCTATCT-GGT
30665414 CGAACGAAAAAAATCGAAACCCAACACATTAGGGCAC
65 CGAACG-AAAAAATCGAAACCCAACACATTAGGGCAC
30665451 GCTTTCTCGA
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
98 1 0.01
99 30 0.32
100 62 0.67
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (100 bp):
AATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTAAAAGGATATTCGGCTATCTGGTC
GAACGAAAAAATCGAAACCCAACACATTAGGGCAC
Found at i:30665545 original size:21 final size:20
Alignment explanation
Indices: 30665521--30665565 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
30665511 GTATGGTGTT
*
30665521 AATATGCATGATG-GAATAATA
1 AATATG-ATAATGTGAATAA-A
30665542 AATATGATAATGTGAATAAA
1 AATATGATAATGTGAATAAA
30665562 AATA
1 AATA
30665566 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.29
Consensus pattern (20 bp):
AATATGATAATGTGAATAAA
Found at i:30666136 original size:3 final size:3
Alignment explanation
Indices: 30666122--30666153 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
30666112 ATAAAAGGAA
*
30666122 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
30666154 ACTAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30666586 original size:2 final size:2
Alignment explanation
Indices: 30666579--30666603 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30666569 AGATAGAAAA
30666579 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
30666604 ATAGGCCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:30668257 original size:36 final size:33
Alignment explanation
Indices: 30668204--30668308 Score: 95
Period size: 37 Copynumber: 3.0 Consensus size: 33
30668194 TAAATATATC
*
30668204 ATACAAAAATATTTAAAAATTTAAAAAATATAGAAA
1 ATACAAAAA-ATGTAAAAA-TTAAAAAATATA-AAA
*
30668240 ATACAAAAAAGTGTAAAAAATTATAAAATTATTAAAA
1 ATACAAAAAA-TGT-AAAAATTA-AAAAATA-TAAAA
* *
30668277 ATGAAAAAAAATGTTAAAA-TAAAAAATATAAA
1 AT-ACAAAAAATGTAAAAATTAAAAAATATAAA
30668309 TTATATAAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
33 4 0.07
34 6 0.10
35 3 0.05
36 18 0.31
37 19 0.32
38 9 0.15
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (33 bp):
ATACAAAAAATGTAAAAATTAAAAAATATAAAA
Found at i:30668713 original size:25 final size:25
Alignment explanation
Indices: 30668678--30668747 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 25
30668668 TTTTTCTATA
30668678 TTTTC-ATAATTTTTAAAATTTTAT
1 TTTTCTATAATTTTTAAAATTTTAT
* *
30668702 TTTTCTATAATTTCTATAATTTTTAT
1 TTTTCTATAATTTTTA-AAATTTTAT
*
30668728 TTTT-T-TAA-TTTTAATATTTT
1 TTTTCTATAATTTTTAAAATTTT
30668748 TTAATATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 5 0.13
23 4 0.10
24 8 0.21
25 10 0.26
26 12 0.31
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTCTATAATTTTTAAAATTTTAT
Found at i:30668736 original size:15 final size:16
Alignment explanation
Indices: 30668669--30668759 Score: 60
Period size: 16 Copynumber: 5.4 Consensus size: 16
30668659 GTTATAATAT
*
30668669 TTTTCTATATTTTCATAA
1 TTTT-TATATTTT-TTAA
** *
30668687 TTTTTA-AAATTTTAT
1 TTTTTATATTTTTTAA
*
30668702 TTTTCTATAATTTCTATAA
1 TTTT-TAT-ATTT-TTTAA
30668721 TTTTTAT-TTTTTTAA
1 TTTTTATATTTTTTAA
*
30668736 TTTTAATATTTTTTAA
1 TTTTTATATTTTTTAA
30668752 TATTTTAT
1 T-TTTTAT
30668760 GCAAAATTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
15 16 0.29
16 17 0.30
17 7 0.12
18 9 0.16
19 7 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTATATTTTTTAA
Found at i:30668749 original size:16 final size:15
Alignment explanation
Indices: 30668718--30668752 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30668708 ATAATTTCTA
*
30668718 TAATTTTTATTTTTT
1 TAATTTTAATTTTTT
30668733 TAATTTTAATATTTTT
1 TAATTTTAAT-TTTTT
30668749 TAAT
1 TAAT
30668753 ATTTTATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TAATTTTAATTTTTT
Found at i:30668749 original size:24 final size:26
Alignment explanation
Indices: 30668669--30668738 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
30668659 GTTATAATAT
*
30668669 TTTTCTATATTTTC-ATAATTTTTA-AA
1 TTTT-TAT-TTTTCTATAATTTCTATAA
*
30668695 ATTTTATTTTTCTATAATTTCTATAA
1 TTTTTATTTTTCTATAATTTCTATAA
30668721 TTTTTATTTTT-T-TAATTT
1 TTTTTATTTTTCTATAATTT
30668739 TAATATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 11 0.28
25 13 0.33
26 15 0.38
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTTATTTTTCTATAATTTCTATAA
Found at i:30668756 original size:18 final size:17
Alignment explanation
Indices: 30668725--30668758 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30668715 CTATAATTTT
*
30668725 TATTTTTTTAATTTTAA
1 TATTTTTTAAATTTTAA
30668742 TATTTTTTAATATTTTA
1 TATTTTTTAA-ATTTTA
30668759 TGCAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTTAAATTTTAA
Found at i:30670872 original size:51 final size:51
Alignment explanation
Indices: 30670778--30670878 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
30670768 TTCTAGGGGA
* * *
30670778 GGATGTGTAGCCTATGAGCTTGACACTTAGTGCCTAAACGTGTTTTTGGAG
1 GGATGTGTAGCCTACGAGCTTGACACTTAGTGCCCAAACGTGTTCTTGGAG
* * **
30670829 GGATGTTTAGCCTACGGGCTTGACA-TTCAGTGCCCAAGTGTGTTCTTGGA
1 GGATGTGTAGCCTACGAGCTTGACACTT-AGTGCCCAAACGTGTTCTTGGA
30670879 TGGTAAAGCT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.33
Consensus pattern (51 bp):
GGATGTGTAGCCTACGAGCTTGACACTTAGTGCCCAAACGTGTTCTTGGAG
Found at i:30673193 original size:24 final size:24
Alignment explanation
Indices: 30673166--30673213 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
30673156 TTTACTGCAA
30673166 TATTGAGTGGCTTGACCACAACGT
1 TATTGAGTGGCTTGACCACAACGT
*
30673190 TATTGAGTGGCTTGACCATAACGT
1 TATTGAGTGGCTTGACCACAACGT
30673214 GCAGCTTGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (24 bp):
TATTGAGTGGCTTGACCACAACGT
Found at i:30673296 original size:39 final size:39
Alignment explanation
Indices: 30673253--30673344 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
30673243 GCCATAACGT
* * * * * *
30673253 TATTCTGTGGTTTGACCATAATGAGTAACTTGTCTGCAA
1 TATTCAGTGGCTTGACCACAACGAGCAACTTGACTGCAA
*
30673292 TATTCAGTGGCTTGACCACAACGTGCAACTTGACTGCAA
1 TATTCAGTGGCTTGACCACAACGAGCAACTTGACTGCAA
30673331 TATAT-AGTGGCTTG
1 TAT-TCAGTGGCTTG
30673345 GCTACAACAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 44 0.98
40 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (39 bp):
TATTCAGTGGCTTGACCACAACGAGCAACTTGACTGCAA
Found at i:30673301 original size:63 final size:63
Alignment explanation
Indices: 30673160--30673315 Score: 188
Period size: 63 Copynumber: 2.5 Consensus size: 63
30673150 GGCAGTTTTA
* * *
30673160 CTGCAATATTGAGTGGCTTGACCACAACGTTATTGAGTGGCTTGACCATAACGTGCAGCTTGT
1 CTGCAATATTGAGTGGCTTGACCACAACGTTATTCAGTGGCTTGACCATAACGAGCAACTTGT
* * * * * * * *
30673223 CTGCGATAGTGAGTGG-TTTAGCCATAACGTTATTCTGTGGTTTGACCATAATGAGTAACTTGT
1 CTGCAATATTGAGTGGCTTGA-CCACAACGTTATTCAGTGGCTTGACCATAACGAGCAACTTGT
*
30673286 CTGCAATATTCAGTGGCTTGACCACAACGT
1 CTGCAATATTGAGTGGCTTGACCACAACGT
30673316 GCAACTTGAC
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
62 3 0.04
63 69 0.92
64 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (63 bp):
CTGCAATATTGAGTGGCTTGACCACAACGTTATTCAGTGGCTTGACCATAACGAGCAACTTGT
Found at i:30689892 original size:49 final size:47
Alignment explanation
Indices: 30689794--30689914 Score: 152
Period size: 49 Copynumber: 2.5 Consensus size: 47
30689784 AATCTCCGTA
* * * *
30689794 TAAGACCATATCTGGAATATGGCATCATTGTGATATGTGATTCCGTG
1 TAAGACCATAGCTGGACTATGGCATCATTGTGATATGTGATTACATG
* * *
30689841 TAAGACCATAGCTGGGCTATGGCATCGGTATGTGATATGTGATTATATG
1 TAAGACCATAGCTGGACTATGGCATC-AT-TGTGATATGTGATTACATG
*
30689890 TAAGACCATAGTTGGACTATGGCAT
1 TAAGACCATAGCTGGACTATGGCAT
30689915 GTGAAAACGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 23 0.37
48 1 0.02
49 39 0.62
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (47 bp):
TAAGACCATAGCTGGACTATGGCATCATTGTGATATGTGATTACATG
Found at i:30692716 original size:23 final size:23
Alignment explanation
Indices: 30692689--30692792 Score: 129
Period size: 23 Copynumber: 4.3 Consensus size: 23
30692679 AGTGTTATTG
30692689 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
30692712 TTCAGTGGTAGCTTCGGCTTCGGCTACAT
1 ATCAGTGGTA------GCTTCGGCTACAT
*
30692741 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
30692764 -TCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
30692786 ATCAGTG
1 ATCAGTG
30692793 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
22 21 0.30
23 27 0.39
29 22 0.31
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:30692745 original size:29 final size:28
Alignment explanation
Indices: 30692699--30692781 Score: 106
Period size: 29 Copynumber: 3.1 Consensus size: 28
30692689 ATCAGTGGTA
30692699 GCTTCGGCTACATTTCAGTGGTAGCTTCG
1 GCTTCGGCTACA-TTCAGTGGTAGCTTCG
30692728 GCTTCGGCTACATATCAGTGGTAGC-T--
1 GCTTCGGCTACAT-TCAGTGGTAGCTTCG
30692754 --TT-GGCTACATTCAGTGGTAGCTTCG
1 GCTTCGGCTACATTCAGTGGTAGCTTCG
30692779 GCT
1 GCT
30692782 ACATATCAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
22 11 0.23
23 9 0.19
24 2 0.04
27 1 0.02
28 2 0.04
29 23 0.48
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.34
Consensus pattern (28 bp):
GCTTCGGCTACATTCAGTGGTAGCTTCG
Found at i:30692964 original size:38 final size:37
Alignment explanation
Indices: 30692922--30692994 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
30692912 ACGTGTGGAA
* *
30692922 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
30692960 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
30692995 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:30697743 original size:25 final size:23
Alignment explanation
Indices: 30697688--30697746 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
30697678 ATGAATTTTC
30697688 TCAAAATTTTATCGGGTAAAATCG
1 TCAAAA-TTTATCGGGTAAAATCG
* *
30697712 TAAAAAATTTATCAGCGGTGAAATCG
1 T-CAAAATTTATC-G-GGTAAAATCG
30697738 TCAAAATTT
1 TCAAAATTT
30697747 TACTGGAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 7 0.24
25 12 0.41
26 10 0.34
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (23 bp):
TCAAAATTTATCGGGTAAAATCG
Found at i:30697743 original size:26 final size:24
Alignment explanation
Indices: 30697688--30697748 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 24
30697678 ATGAATTTTC
30697688 TCAAAATTTTATCGGGTAAAATCG
1 TCAAAATTTTATCGGGTAAAATCG
* * *
30697712 TAAAAAATTTATCAGCGGTGAAATCG
1 TCAAAATTTTATC-G-GGTAAAATCG
30697738 TCAAAATTTTA
1 TCAAAATTTTA
30697749 CTGGAGTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 11 0.37
25 1 0.03
26 18 0.60
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (24 bp):
TCAAAATTTTATCGGGTAAAATCG
Found at i:30697760 original size:25 final size:24
Alignment explanation
Indices: 30697688--30697760 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 24
30697678 ATGAATTTTC
30697688 TCAAAATTTTA-TCGGGTAAAATCG
1 TCAAAATTTTACT-GGGTAAAATCG
* * * *
30697712 TAAAAAATTTATCAGCGGTGAAATCG
1 TCAAAATTTTA-CTG-GGTAAAATCG
30697738 TCAAAATTTTACTGGAGTAAAAT
1 TCAAAATTTTACTGG-GTAAAAT
30697761 TGGGATGAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
24 10 0.27
25 9 0.24
26 18 0.49
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (24 bp):
TCAAAATTTTACTGGGTAAAATCG
Found at i:30699466 original size:7 final size:7
Alignment explanation
Indices: 30699454--30699486 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
30699444 CAAAACTCGG
30699454 AATAATA
1 AATAATA
30699461 AATAATAA
1 AATAAT-A
30699469 AATAATA
1 AATAATA
30699476 AATAATA
1 AATAATA
30699483 AATA
1 AATA
30699487 CAATATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AATAATA
Found at i:30699474 original size:15 final size:15
Alignment explanation
Indices: 30699454--30699484 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30699444 CAAAACTCGG
30699454 AATAATAAATAATAA
1 AATAATAAATAATAA
30699469 AATAATAAATAATAA
1 AATAATAAATAATAA
30699484 A
1 A
30699485 TACAATATTT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAATAAATAATAA
Found at i:30701194 original size:12 final size:12
Alignment explanation
Indices: 30701177--30701201 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30701167 ATTTTATAAC
30701177 ATAAATATTGTT
1 ATAAATATTGTT
30701189 ATAAATATTGTT
1 ATAAATATTGTT
30701201 A
1 A
30701202 ATATCCTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATAAATATTGTT
Found at i:30707301 original size:24 final size:24
Alignment explanation
Indices: 30707269--30707315 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
30707259 AGTGTTTTTG
*
30707269 AAAAGTACTTTTGAATTCAAAAAT
1 AAAAGTACTTTTGAATTAAAAAAT
* *
30707293 AAAATTACTTTTGCATTAAAAAA
1 AAAAGTACTTTTGAATTAAAAAA
30707316 AGAACACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (24 bp):
AAAAGTACTTTTGAATTAAAAAAT
Found at i:30709951 original size:20 final size:20
Alignment explanation
Indices: 30709926--30709978 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
30709916 AAACTATAAT
30709926 TGCAAAAAAG-TTCAAGCATG
1 TGCAAAAAAGATT-AAGCATG
**
30709946 TGCAAAAAAGATTGGGCATG
1 TGCAAAAAAGATTAAGCATG
30709966 TGC-AAAAAGATTA
1 TGCAAAAAAGATTA
30709979 TCGTCTCAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.31
20 18 0.62
21 2 0.07
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (20 bp):
TGCAAAAAAGATTAAGCATG
Found at i:30714306 original size:16 final size:16
Alignment explanation
Indices: 30714287--30714348 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
30714277 ATTTTAATAA
30714287 AATTTAATATTAAATT
1 AATTTAATATTAAATT
* **
30714303 AATTTGATATTTATCTT
1 AATTTAATA-TTAAATT
* * *
30714320 GA-TAAATATTATATT
1 AATTTAATATTAAATT
30714335 AATTTAATATTAAA
1 AATTTAATATTAAA
30714349 ATGATTAAGT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
15 7 0.21
16 21 0.62
17 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (16 bp):
AATTTAATATTAAATT
Found at i:30716936 original size:22 final size:21
Alignment explanation
Indices: 30716910--30716952 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
30716900 GGGTAGAATT
*
30716910 GTAAATTAATAATAAAACTAAA
1 GTAAATTAATAAGAAAA-TAAA
30716932 GTAAATTAATAAGAAAATAAA
1 GTAAATTAATAAGAAAATAAA
30716953 CATTGTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (21 bp):
GTAAATTAATAAGAAAATAAA
Found at i:30717967 original size:20 final size:19
Alignment explanation
Indices: 30717942--30718005 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
30717932 GCTTGTACAG
30717942 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTTT-GTGCCTCT
*
30717962 GTTTGCACTTCAGTGCCTCT
1 GTTTGCACTT-TGTGCCTCT
* *
30717982 GATCGCACATTTGTGCCTCT
1 GTTTGCAC-TTTGTGCCTCT
30718002 GTTT
1 GTTT
30718006 CGCATATATG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 34 0.94
21 2 0.06
ACGTcount: A:0.09, C:0.27, G:0.22, T:0.42
Consensus pattern (19 bp):
GTTTGCACTTTGTGCCTCT
Found at i:30723215 original size:327 final size:327
Alignment explanation
Indices: 30722608--30723257 Score: 949
Period size: 327 Copynumber: 2.0 Consensus size: 327
30722598 AGAGCTTCGC
* * *
30722608 TAACTTTTGCAGAGAGTAGTCCATCCAAACCAGAGTAAAATAGGCAAACTTGGTCAATCGACCCA
1 TAACGTTTCCAGAGAGTAGTCCATCCAAACCAGAATAAAATAGGCAAACTTGGTCAATCGACCCA
* * * *
30722673 CGATGACCCAAACAAAACCCTTTTTAGTGGGTGTCAAGGGCAACCCATTAACAAAGTCCATTGTC
66 CGATAACCCAAACAAAACCCTTTTTAGTGGGTGTCAAGGGCAACCCACTAACAAAGTCCATCGCC
* * *
30722738 ACTTGTTCTCATATCCATAAAAGAATCTCAACATGTTGTAGAAAACCAAAAGGCAAATGGTGCTC
131 ACTCGTTCTCATATCCATAAAAGAATCTCAACAGGTTGTAGAAAACCAAAAGGAAAATGGTGCTC
* * * * *
30722803 AGCCTTAACTTACTGGCACGTTAGACAATGAGCAATAAAATCTGTTCCCTCTCGTTTCAACCTCG
196 AGCCTTAACTTACTGACACGTTAGACAATGAGCAACAAAATCTGTTACCTCTCGTTTAAAACTCG
* **
30722868 GCCACCAATACAATTCACTGAGATCCCGATACATCTTATTACCACCGGGATGTATAACATAAGGC
261 GCCACCAATACAACTCACTGAGATCCCGATACATCTTATTACCACCGAAATGTATAACATAAGGC
30722933 CT
326 CT
* *** * * *
30722935 TAACGTTTCCAGAGAGTAGTCCATCCAAACCGGAATAAAATAGGTGGACTTGGTTAGTTGACCCA
1 TAACGTTTCCAGAGAGTAGTCCATCCAAACCAGAATAAAATAGGCAAACTTGGTCAATCGACCCA
*
30723000 CGATAACCCAAACAGAACCCTTTTTAGTGGGTGTCAAGGGCAACCCACTAACAAAGTCCATCGCC
66 CGATAACCCAAACAAAACCCTTTTTAGTGGGTGTCAAGGGCAACCCACTAACAAAGTCCATCGCC
* * * ***
30723065 ACTCGTTCTCATTTCCATAAAAGAATCTTAACAGGTTGTAGCAAACTGGAAGGAAAATGGTGCTC
131 ACTCGTTCTCATATCCATAAAAGAATCTCAACAGGTTGTAGAAAACCAAAAGGAAAATGGTGCTC
* * *
30723130 AGCCTTAACTTGCTGACAGGTTAGACAATGAGCAACAAAATCTGTTACCTCTCGTTTAAAATTCG
196 AGCCTTAACTTACTGACACGTTAGACAATGAGCAACAAAATCTGTTACCTCTCGTTTAAAACTCG
* ** *
30723195 GCCACTAATACAACTCACTGAGATCTTGATACATCTTATTACCACCGAAATGTATAGCATAAG
261 GCCACCAATACAACTCACTGAGATCCCGATACATCTTATTACCACCGAAATGTATAACATAAG
30723258 CGCTACCATG
Statistics
Matches: 284, Mismatches: 39, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
327 284 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (327 bp):
TAACGTTTCCAGAGAGTAGTCCATCCAAACCAGAATAAAATAGGCAAACTTGGTCAATCGACCCA
CGATAACCCAAACAAAACCCTTTTTAGTGGGTGTCAAGGGCAACCCACTAACAAAGTCCATCGCC
ACTCGTTCTCATATCCATAAAAGAATCTCAACAGGTTGTAGAAAACCAAAAGGAAAATGGTGCTC
AGCCTTAACTTACTGACACGTTAGACAATGAGCAACAAAATCTGTTACCTCTCGTTTAAAACTCG
GCCACCAATACAACTCACTGAGATCCCGATACATCTTATTACCACCGAAATGTATAACATAAGGC
CT
Found at i:30723609 original size:62 final size:62
Alignment explanation
Indices: 30723533--30723652 Score: 222
Period size: 62 Copynumber: 1.9 Consensus size: 62
30723523 ACTAACAAAC
30723533 CGCTCTACGACTGAGAGCATCGGCCACCACATTGGCCATACCAGGATGATACTCTATCGTGT
1 CGCTCTACGACTGAGAGCATCGGCCACCACATTGGCCATACCAGGATGATACTCTATCGTGT
* *
30723595 CGCTCTACGACTGAGAGCATCGGCCACCACATTGGGCTTACCAGGATGATACTCTATC
1 CGCTCTACGACTGAGAGCATCGGCCACCACATTGGCCATACCAGGATGATACTCTATC
30723653 ATGTAGTCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.23
Consensus pattern (62 bp):
CGCTCTACGACTGAGAGCATCGGCCACCACATTGGCCATACCAGGATGATACTCTATCGTGT
Found at i:30727450 original size:15 final size:14
Alignment explanation
Indices: 30727406--30727452 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
30727396 TGTTAATAAT
30727406 AATTTTTA-TATTG
1 AATTTTTATTATTG
30727419 AATTTTTATT-TGATG
1 AATTTTTATTAT--TG
30727434 AATTTTTATTAATTG
1 AATTTTTATT-ATTG
30727449 AATT
1 AATT
30727453 AATGGTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.31
14 1 0.03
15 18 0.62
17 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (14 bp):
AATTTTTATTATTG
Found at i:30738545 original size:22 final size:22
Alignment explanation
Indices: 30738520--30738601 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
30738510 TTACCAGTCA
30738520 CCATGAGAGCTTAGTACGTTAG
1 CCATGAGAGCTTAGTACGTTAG
30738542 CCATGAGAGCTTAGTACGTTAG
1 CCATGAGAGCTTAGTACGTTAG
* * * *
30738564 CCATGAGGGTTTAGTTCGTTAA
1 CCATGAGAGCTTAGTACGTTAG
*
30738586 ACATGAGAGCTTAGTA
1 CCATGAGAGCTTAGTA
30738602 ACTGATAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (22 bp):
CCATGAGAGCTTAGTACGTTAG
Found at i:30741730 original size:69 final size:68
Alignment explanation
Indices: 30741565--30741742 Score: 232
Period size: 70 Copynumber: 2.6 Consensus size: 68
30741555 AAAGGTTAAT
* * * *
30741565 GAGAGCTAAAAGCTCCCAACTGTCATTCTAAGGCTCGTAGGTTCAATACCACAGCCCTTAAACAG
1 GAGAGTTAAAAGCTCCC-ACTGTCATTCTAAGGCTCGCAAGTTCAATACCAAAGCCC-TAAACAG
30741630 TTAGC
64 TTAGC
* *
30741635 GAGAGTTAAAAGCTCCCTACTATCATTCTAATGCTCGCAAGTTCAATACCAAAGCTCC-AAACAG
1 GAGAGTTAAAAGCTCCC-ACTGTCATTCTAAGGCTCGCAAGTTCAATACCAAAGC-CCTAAACAG
30741699 TTAGC
64 TTAGC
* *
30741704 GATAGTTAAAAGCTCCCAGCTGTCATTTTAAGGCTCGCA
1 GAGAGTTAAAAGCTCCCA-CTGTCATTCTAAGGCTCGCA
30741743 GGTTTAACAT
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
68 1 0.01
69 44 0.46
70 48 0.51
71 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (68 bp):
GAGAGTTAAAAGCTCCCACTGTCATTCTAAGGCTCGCAAGTTCAATACCAAAGCCCTAAACAGTT
AGC
Found at i:30741922 original size:58 final size:58
Alignment explanation
Indices: 30741769--30741931 Score: 188
Period size: 58 Copynumber: 2.8 Consensus size: 58
30741759 CTCCAAACAG
* * *
30741769 CTCACGAATTTACATTCCCGAATAATTATTTCAAAAAA-ATGCCTAAGTTCAAAAAAA
1 CTCACGGATTTACATTCCCTACTAATTATTTCAAAAAATATGCCTAAGTTCAAAAAAA
* * * * * *
30741826 CTCACGGATTTACATT-CCTAGCTGAGTATTTCAGAAAATATGCCTAAGTTGAAAATAG
1 CTCACGGATTTACATTCCCTA-CTAATTATTTCAAAAAATATGCCTAAGTTCAAAAAAA
* *
30741884 CTCGA-GGATTTACATTCCCTACTAATTATATCAAAAAATAAGCCTAAG
1 CTC-ACGGATTTACATTCCCTACTAATTATTTCAAAAAATATGCCTAAG
30741932 CTTAAAACAA
Statistics
Matches: 88, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
56 3 0.03
57 28 0.32
58 52 0.59
59 5 0.06
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (58 bp):
CTCACGGATTTACATTCCCTACTAATTATTTCAAAAAATATGCCTAAGTTCAAAAAAA
Found at i:30741949 original size:58 final size:58
Alignment explanation
Indices: 30741776--30741951 Score: 180
Period size: 58 Copynumber: 3.1 Consensus size: 58
30741766 CAGCTCACGA
* * *
30741776 ATTTACATTCCCGAATAATTATTTCAAAAAA-ATGCCTAAGTTCAAAAAAAC-TCACGG
1 ATTTACATTCCCTACTAATTATTTCAAAAAATATGCCTAAGTTCAAAAAAACTTGA-GG
* * * * * * *
30741833 ATTTACATT-CCTAGCTGAGTATTTCAGAAAATATGCCTAAGTTGAAAATAGCTCGAGG
1 ATTTACATTCCCTA-CTAATTATTTCAAAAAATATGCCTAAGTTCAAAAAAACTTGAGG
* * *
30741891 ATTTACATTCCCTACTAATTATATCAAAAAATAAGCCTAAGCTT-AAAACAACTTGAGG
1 ATTTACATTCCCTACTAATTATTTCAAAAAATATGCCTAAG-TTCAAAAAAACTTGAGG
30741949 ATT
1 ATT
30741952 CACAATCGAT
Statistics
Matches: 96, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
56 3 0.03
57 22 0.23
58 64 0.67
59 7 0.07
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (58 bp):
ATTTACATTCCCTACTAATTATTTCAAAAAATATGCCTAAGTTCAAAAAAACTTGAGG
Found at i:30743964 original size:51 final size:51
Alignment explanation
Indices: 30743834--30743986 Score: 193
Period size: 51 Copynumber: 3.0 Consensus size: 51
30743824 ATGTGAAAGT
** *
30743834 GAAAGTGATGGTCAGGTGTGTAGTACTATGTTCAGGCTACTACGTGTA-C-
1 GAAAGTGATGGTCACATGTGTAGTACTATGTACAGGCTACTACGTGTATCG
* * * *
30743883 TAAAATGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTACGTGTATCG
1 GAAAGTGAT-GGTCACATGTGTAGTACTATGTACAGGCTACTACGTGTATCG
* * *
30743935 GATAGTGATGGTCACATGTGTAGTACTATGTACAGGCTACTATGTGAATCG
1 GAAAGTGATGGTCACATGTGTAGTACTATGTACAGGCTACTACGTGTATCG
30743986 G
1 G
30743987 TATCATTAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 7 0.08
50 35 0.40
51 40 0.45
52 6 0.07
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (51 bp):
GAAAGTGATGGTCACATGTGTAGTACTATGTACAGGCTACTACGTGTATCG
Found at i:30751199 original size:19 final size:19
Alignment explanation
Indices: 30751177--30751213 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30751167 TTATTAAAAT
* *
30751177 TTAAAAATATATAAAATTA
1 TTAAAAAAACATAAAATTA
30751196 TTAAAAAAACATAAAATT
1 TTAAAAAAACATAAAATT
30751214 CAATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAAAAACATAAAATTA
Found at i:30759087 original size:7 final size:7
Alignment explanation
Indices: 30759075--30759172 Score: 151
Period size: 7 Copynumber: 13.9 Consensus size: 7
30759065 GAGGATTGGG
30759075 AATTGAA
1 AATTGAA
*
30759082 ATTTGAA
1 AATTGAA
*
30759089 ATTTGAA
1 AATTGAA
30759096 AATTGAA
1 AATTGAA
30759103 AATTGAA
1 AATTGAA
30759110 AATTGAA
1 AATTGAA
30759117 AATTGAA
1 AATTGAA
30759124 AATTGAA
1 AATTGAA
30759131 AATTGAA
1 AATTGAA
*
30759138 AATTGAT
1 AATTGAA
*
30759145 GATTGAAA
1 AATTG-AA
30759153 AATTGAA
1 AATTGAA
30759160 AATTGAA
1 AATTGAA
30759167 AATTGA
1 AATTGA
30759173 GGATTGAGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
7 79 0.94
8 5 0.06
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (7 bp):
AATTGAA
Found at i:30759564 original size:18 final size:19
Alignment explanation
Indices: 30759534--30759575 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
30759524 TTTTTATAAT
30759534 ATTTTATTAATATTTTAAC
1 ATTTTATTAATATTTTAAC
*
30759553 ATTTTA-TAATATTTTAAG
1 ATTTTATTAATATTTTAAC
30759571 ATTTT
1 ATTTT
30759576 TTTATTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTATTAATATTTTAAC
Found at i:30759645 original size:10 final size:10
Alignment explanation
Indices: 30759525--30759568 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
30759515 TTTTTTTTAT
30759525 TTTTATAATA
1 TTTTATAATA
30759535 TTTTATTAATA
1 TTTTA-TAATA
*
30759546 -TTT-TAACA
1 TTTTATAATA
30759554 TTTTATAATA
1 TTTTATAATA
30759564 TTTTA
1 TTTTA
30759569 AGATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 4 0.14
9 3 0.10
10 17 0.59
11 5 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTATAATA
Found at i:30769034 original size:19 final size:19
Alignment explanation
Indices: 30769010--30769059 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
30769000 CAACAACTAG
30769010 AAATAAATATTTA-TAAAAA
1 AAATAAA-ATTTATTAAAAA
*
30769029 AAATAAAATTTATTAAAAT
1 AAATAAAATTTATTAAAAA
*
30769048 GAA-AAAATTTAT
1 AAATAAAATTTAT
30769060 AACCATACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATAAAATTTATTAAAAA
Found at i:30769041 original size:18 final size:18
Alignment explanation
Indices: 30769010--30769061 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
30769000 CAACAACTAG
30769010 AAATAAATATTTATAAAAA
1 AAATAAA-ATTTATAAAAA
*
30769029 AAATAAAATTTATTAAAAT
1 AAATAAAATTTA-TAAAAA
*
30769048 GAA-AAAATTTATAA
1 AAATAAAATTTATAA
30769062 CCATACTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 3 0.10
18 13 0.43
19 14 0.47
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATAAAATTTATAAAAA
Found at i:30770769 original size:166 final size:166
Alignment explanation
Indices: 30770474--30771030 Score: 826
Period size: 166 Copynumber: 3.4 Consensus size: 166
30770464 GGAAAGTGCC
30770474 GCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTATCT
1 GCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTATCT
* * * * * *
30770539 GGAAATGCCGATAAAGATATAGCATTTGCGGTGCTTATAAAACAACGCCGCTAATGACCGGTACA
66 GGAAACGCCGGTAAAGATCTAGCATTTGCGGTGCTTATAAAAAAACGCCGCTAAAGATCGGTACA
*
30770604 TTAGCGGCGCTACCACAAAAATGCCACTAATGCTCA
131 TTAGCGGCGCTACTACAAAAATGCCACTAATGCTCA
* * * *
30770640 GCAAATAATTAAACAGAACGCCATCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTTTCC
1 GCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTATCT
* * * *
30770705 GTAAACGCCGGTAAAGATCTAGTATTTGCGGCGCTTATAAAAAAACGCCACTAAAGATCGGTACA
66 GGAAACGCCGGTAAAGATCTAGCATTTGCGGTGCTTATAAAAAAACGCCGCTAAAGATCGGTACA
* *
30770770 TTACCGGCGCTACTACAAAAATGCCACTAATGCTCT
131 TTAGCGGCGCTACTACAAAAATGCCACTAATGCTCA
* *
30770806 GCAAATAATTAAGCAGAACACCGTCGTTTAACTTTGACCTGTAGTGGCACTAACGGCGTTTATCT
1 GCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTATCT
* * * * **
30770871 GGAAACACCGGTAAAGATCAAGCAGTTACGGTGCTTATATTAAAACGCCGCTAAAGATCGGTACA
66 GGAAACGCCGGTAAAGATCTAGCATTTGCGGTGCTTATAAAAAAACGCCGCTAAAGATCGGTACA
* * * * * *
30770936 TTAGCGACCCTGCTATAAAAACGCCACTAATGCTCC
131 TTAGCGGCGCTACTACAAAAATGCCACTAATGCTCA
*
30770972 GTAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGT
1 GCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGT
30771031 CTTTATACAA
Statistics
Matches: 348, Mismatches: 43, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
166 348 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (166 bp):
GCAAATAATTAAGCAGAACGCCGTCGTTTAACTTTGACCTGTAGTGGCACTAGCGGCGTTTATCT
GGAAACGCCGGTAAAGATCTAGCATTTGCGGTGCTTATAAAAAAACGCCGCTAAAGATCGGTACA
TTAGCGGCGCTACTACAAAAATGCCACTAATGCTCA
Found at i:30771441 original size:23 final size:24
Alignment explanation
Indices: 30771390--30771435 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
30771380 GTTTTAGTTA
30771390 CTATTCATGGTTTAACAGGTTAGG
1 CTATTCATGGTTTAACAGGTTAGG
*
30771414 CTATT-ATGGTTTAA-GGGTTAGG
1 CTATTCATGGTTTAACAGGTTAGG
30771436 GTTATTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 9 0.43
24 5 0.24
ACGTcount: A:0.24, C:0.09, G:0.28, T:0.39
Consensus pattern (24 bp):
CTATTCATGGTTTAACAGGTTAGG
Found at i:30771645 original size:22 final size:22
Alignment explanation
Indices: 30771587--30771646 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
30771577 GTTGAGTGTT
* *
30771587 TAGGGGTGAG-GGCTTAGGGTT
1 TAGGGGTTAGTGGCTTAGGGTC
*
30771608 TAGGGGTTA-TAAGCTTAGGGTC
1 TAGGGGTTAGT-GGCTTAGGGTC
30771630 TAGGGGTTAGTGGCTTA
1 TAGGGGTTAGTGGCTTA
30771647 AGGTTACGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 8 0.25
22 23 0.72
23 1 0.03
ACGTcount: A:0.18, C:0.07, G:0.43, T:0.32
Consensus pattern (22 bp):
TAGGGGTTAGTGGCTTAGGGTC
Found at i:30771911 original size:21 final size:21
Alignment explanation
Indices: 30771887--30771939 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
30771877 GGCTAAGGGC
30771887 TTATGGTTTAGGGTTTAAAT-T
1 TTATGGTTTAGGGTTT-AATGT
** *
30771908 TTATATTTTAAGGTTTAATGT
1 TTATGGTTTAGGGTTTAATGT
*
30771929 TTAGGGTTTAG
1 TTATGGTTTAG
30771940 CTAAAAACAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.53
Consensus pattern (21 bp):
TTATGGTTTAGGGTTTAATGT
Found at i:30772456 original size:83 final size:83
Alignment explanation
Indices: 30772328--30772575 Score: 252
Period size: 83 Copynumber: 3.0 Consensus size: 83
30772318 GCTGAAAGCG
* * * *
30772328 CCGCAAGGGTTT-TTAACAATTTGCCAATGCGGCGTCGTTTTTGTACTGGAATAAAAATAGTAGT
1 CCGCAAGGATTTATTAA-AATTTCCCAATGCGGCGCCGTTTCTGTACTGGAATAAAAATAGTAGT
30772392 GGCGTTTTTTAGGAAAACA
65 GGCGTTTTTTAGGAAAACA
* * * * * *
30772411 CCGCAAGGATTTATTAAACTTTCCCAATGTGGCACCGTTTCTGTACTGGGA-AAAATTTGATAGT
1 CCGCAAGGATTTATTAAAATTTCCCAATGCGGCGCCGTTTCTGTACTGGAATAAAAATAG-TAGT
**
30772475 GGCGTTTTTTAGGAAAATG
65 GGCGTTTTTTAGGAAAACA
* * * * *** *
30772494 CTGCAATGATTTATTAAAATTTTCCAATGCGGCGCCGTTTCTAT-CTTTCATAAAAATCTAATA-
1 CCGCAAGGATTTATTAAAATTTCCCAATGCGGCGCCGTTTCTGTACTGGAATAAAAA--TAGTAG
30772557 TGGCGTTTTTTAGGAAAAC
64 TGGCGTTTTTTAGGAAAAC
30772576 GTCGTAAAAA
Statistics
Matches: 134, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
82 9 0.07
83 118 0.88
84 6 0.04
85 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (83 bp):
CCGCAAGGATTTATTAAAATTTCCCAATGCGGCGCCGTTTCTGTACTGGAATAAAAATAGTAGTG
GCGTTTTTTAGGAAAACA
Found at i:30774410 original size:17 final size:17
Alignment explanation
Indices: 30774388--30774422 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
30774378 AACTTATTAA
30774388 TATATATATTTTAAAAT
1 TATATATATTTTAAAAT
*
30774405 TATATATATTTTTAAAT
1 TATATATATTTTAAAAT
30774422 T
1 T
30774423 TAATTTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATATATTTTAAAAT
Found at i:30774462 original size:22 final size:21
Alignment explanation
Indices: 30774382--30774480 Score: 80
Period size: 22 Copynumber: 4.6 Consensus size: 21
30774372 GTACATAACT
*
30774382 TATTAATATATATATTTTAAA
1 TATTAATATATATAATTTAAA
*
30774403 -ATT-ATATATAT-TTTTAAA
1 TATTAATATATATAATTTAAA
*
30774421 T-TTAATTTAGCTTATTAATTTAACA
1 TATTAATATA---TA-TAATTTAA-A
*
30774446 TATTAATATATATAATTTAATG
1 TATTAATATATATAATTTAA-A
30774468 TATTAATATATAT
1 TATTAATATATAT
30774481 TTTAAAAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
18 9 0.14
19 12 0.19
20 3 0.05
22 23 0.36
23 3 0.05
24 5 0.08
25 2 0.03
26 7 0.11
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTAATATATATAATTTAAA
Found at i:30774521 original size:13 final size:13
Alignment explanation
Indices: 30774498--30774579 Score: 64
Period size: 12 Copynumber: 6.3 Consensus size: 13
30774488 ATTTATCAAT
30774498 CATATCATAACTTA
1 CATA-CATAACTTA
30774512 CATACATAACTTA
1 CATACATAACTTA
* *
30774525 AATA-A-AATTTA
1 CATACATAACTTA
* *
30774536 TATATA-AACTTACA
1 CATACATAACTT--A
30774550 CAATACATAACTTA
1 C-ATACATAACTTA
30774564 CATA-ATAACTTA
1 CATACATAACTTA
30774576 CATA
1 CATA
30774580 ACTTATATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
11 8 0.14
12 18 0.32
13 15 0.26
14 7 0.12
15 4 0.07
16 5 0.09
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (13 bp):
CATACATAACTTA
Found at i:30774749 original size:42 final size:43
Alignment explanation
Indices: 30774698--30774850 Score: 193
Period size: 43 Copynumber: 3.6 Consensus size: 43
30774688 TTTTTTCTAT
* *
30774698 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-CTTACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTACCAC
* * * *
30774740 AAACGCCGCTAAAGACCATGACCTTTAGTGATGCTTTTTCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTACCAC
* * * *
30774783 TAACGCCGCTAAAGATCATGACCTTTAGCGGTGCTTTTATCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTACCAC
*
30774826 AAACGCCGCTAAAGAACAA-ACCTTT
1 AAACGCCGCTAAAGACCAAGACCTTT
30774851 TAAAAAAATT
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 36 0.38
43 59 0.62
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTTACCAC
Found at i:30775583 original size:23 final size:23
Alignment explanation
Indices: 30775534--30775584 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
30775524 TTAGGTGTCC
* * *
30775534 GTATAAAGACATGTCAGATATGG
1 GTATGAAGACATGTCAGAGATGA
* *
30775557 GTATGAAGGCATGTCTGAGATGA
1 GTATGAAGACATGTCAGAGATGA
30775580 GTATG
1 GTATG
30775585 TTCAATTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
GTATGAAGACATGTCAGAGATGA
Found at i:30775720 original size:26 final size:29
Alignment explanation
Indices: 30775682--30775744 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
30775672 ATAATAAAAA
30775682 ATAA-AAAAAATAGA-G-GAACTCTTATC
1 ATAATAAAAAATAGAGGAGAACTCTTATC
30775708 AT-ATAAAAAATAGAGGAAGAACTCTTATC
1 ATAATAAAAAATAGAGG-AGAACTCTTATC
30775737 ATAATAAA
1 ATAATAAA
30775745 TCAACAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 1 0.03
26 12 0.38
27 1 0.03
29 13 0.41
30 5 0.16
ACGTcount: A:0.56, C:0.10, G:0.11, T:0.24
Consensus pattern (29 bp):
ATAATAAAAAATAGAGGAGAACTCTTATC
Found at i:30775940 original size:18 final size:18
Alignment explanation
Indices: 30775917--30775953 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30775907 ATATAATAAC
30775917 TTAAACTTTTAGGTTCAA
1 TTAAACTTTTAGGTTCAA
30775935 TTAAACTTTTAGGTTCAA
1 TTAAACTTTTAGGTTCAA
30775953 T
1 T
30775954 GATTCTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAAACTTTTAGGTTCAA
Found at i:30780157 original size:146 final size:147
Alignment explanation
Indices: 30779848--30780138 Score: 496
Period size: 146 Copynumber: 2.0 Consensus size: 147
30779838 GGAATTTTTT
*
30779848 TAAAATGGCGCTATTTTTGTAAAAGTAAATTTTATTTTGTGGCTTTTTTTATAAAAACGCCGCTA
1 TAAAATGGCGCTATTTTTGTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAAAAACGCCGCTA
* * *
30779913 TTGCTTATCTATTGCGGCGTTTTTCATAAAAACGTCGCAAAAAAATATTTTATTTGGAATAAAAC
66 TTGCTTATCTATTGCGGCGTTTTTCATAAAAACGCCGCAAAAAAACATTTCATTTGGAATAAAAC
30779978 GACACTGTTTTGCTATA
131 GACACTGTTTTGCTATA
* * *
30779995 TAGAATGGCGCAATTTTT-TAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAAAAACGCTGCTA
1 TAAAATGGCGCTATTTTTGTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAAAAACGCCGCTA
*
30780059 TTGCTTATCTATTGCGGCGTTTTTCATAAAAACGCCGC-AAAAAGCATTTCATTTGGAATAAAAC
66 TTGCTTATCTATTGCGGCGTTTTTCATAAAAACGCCGCAAAAAAACATTTCATTTGGAATAAAAC
30780123 GACACTGTTTTGCTAT
131 GACACTGTTTTGCTAT
30780139 GCTAAAATTT
Statistics
Matches: 136, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
145 39 0.29
146 81 0.60
147 16 0.12
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (147 bp):
TAAAATGGCGCTATTTTTGTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAAAAACGCCGCTA
TTGCTTATCTATTGCGGCGTTTTTCATAAAAACGCCGCAAAAAAACATTTCATTTGGAATAAAAC
GACACTGTTTTGCTATA
Done.