Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 2 of 15
Found at i:103342 original size:68 final size:69
Alignment explanation
Indices: 103227--103385 Score: 205
Period size: 68 Copynumber: 2.3 Consensus size: 69
103217 TAAAGATAAG
* * * * * * * *
103227 GGTGCCACGGACTCGTGGACTTAGAAGGAAAAAGAGTGCAACGGAGTTGTGGGC-TTAGAAGGAA
1 GGTGCCACAGAATTGTGGGCTTAAAAGGAAAAAGAGTGCAACAGAGTTGTGGGCTTTAAAAAGAA
103291 AAA-
66 AAAC
*
103294 GAGTGCCACAGAATTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGA
1 G-GTGCCACAGAATTGTGGGCTTAAAAGGAAAAAGAGTGCAACAGAGTTGTGGGCTTTAAAAAGA
103359 AAAAC
65 AAAAC
*
103364 GGTGCCACGGAATTGTGGGCTT
1 GGTGCCACAGAATTGTGGGCTT
103386 CGGAAAAGGG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
67 1 0.01
68 46 0.58
69 31 0.39
70 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (69 bp):
GGTGCCACAGAATTGTGGGCTTAAAAGGAAAAAGAGTGCAACAGAGTTGTGGGCTTTAAAAAGAA
AAAC
Found at i:103361 original size:35 final size:34
Alignment explanation
Indices: 103241--103385 Score: 184
Period size: 34 Copynumber: 4.2 Consensus size: 34
103231 CCACGGACTC
* * * * *
103241 GTGGACTTAGAAGGAAAAAGAGTGCAACGGAGTT
1 GTGGGCTTAAAAGGAAAAAGAGTGCCACAGAATT
*
103275 GTGGGCTTAGAAGGAAAAAGAGTGCCACAGAATT
1 GTGGGCTTAAAAGGAAAAAGAGTGCCACAGAATT
*
103309 GTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTT
1 GTGGGCTTAAAAGGAAAAAGAGTGCCACAGAATT
* *
103343 GTGGGCTTTAAAAAGAAAAACG-GTGCCACGGAATT
1 GTGGGC-TTAAAAGGAAAAA-GAGTGCCACAGAATT
103378 GTGGGCTT
1 GTGGGCTT
103386 CGGAAAAGGG
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
34 70 0.70
35 29 0.29
36 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.19
Consensus pattern (34 bp):
GTGGGCTTAAAAGGAAAAAGAGTGCCACAGAATT
Found at i:103398 original size:30 final size:30
Alignment explanation
Indices: 103359--103513 Score: 174
Period size: 30 Copynumber: 5.3 Consensus size: 30
103349 TTTAAAAAGA
* * * *
103359 AAAACGGTGCCACGGAATTGTGGGCTTCGG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTGG
*
103389 AAAAGGGTGCCACTGACTTGTGGGCTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTGG
* * * *
103419 --AAGGTTGCCACTGATTTATGGGCTTTGA
1 AAAAGGGTGCCACTGACTTGTGGGCTTTGG
*
103447 AAAAGGGTGCCACTGACTTGTGGGCTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTGG
* *
103477 --AAGGTTGCCACTGACTTATGGGCTTTGG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTGG
103505 AAAAGGGTG
1 AAAAGGGTG
103514 AAGGATGTCT
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
28 48 0.47
30 54 0.53
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (30 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTGG
Found at i:103431 original size:28 final size:28
Alignment explanation
Indices: 103391--103502 Score: 145
Period size: 28 Copynumber: 3.9 Consensus size: 28
103381 GGCTTCGGAA
*
103391 AAGGGTGCCACTGACTTGTGGGCTTTTG
1 AAGGGTGCCACTGACTTATGGGCTTTTG
* *
103419 AAGGTTGCCACTGATTTATGGGC-TTTG
1 AAGGGTGCCACTGACTTATGGGCTTTTG
*
103446 AAAAAGGGTGCCACTGACTTGTGGGCTTTTG
1 ---AAGGGTGCCACTGACTTATGGGCTTTTG
*
103477 AAGGTTGCCACTGACTTATGGGCTTT
1 AAGGGTGCCACTGACTTATGGGCTTT
103503 GGAAAAGGGT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.06
28 44 0.61
30 20 0.28
31 4 0.06
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (28 bp):
AAGGGTGCCACTGACTTATGGGCTTTTG
Found at i:103456 original size:58 final size:58
Alignment explanation
Indices: 103379--103513 Score: 243
Period size: 58 Copynumber: 2.3 Consensus size: 58
103369 CACGGAATTG
* *
103379 TGGGCTTCGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGATTTA
1 TGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTA
*
103437 TGGGCTTTGAAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTA
1 TGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTA
103495 TGGGCTTTGGAAAAGGGTG
1 TGGGCTTTGGAAAAGGGTG
103514 AAGGATGTCT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 73 1.00
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.30
Consensus pattern (58 bp):
TGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTA
Found at i:105087 original size:55 final size:55
Alignment explanation
Indices: 104937--105619 Score: 708
Period size: 55 Copynumber: 11.9 Consensus size: 55
104927 TGCCTTTTTT
**
104937 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAATAGGACGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGC
* *
104993 CTTTTCCTTTCAAACCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGC
1 C---T--TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC
105054 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGACGC
* *
105110 CTTCGCCTTTCATAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCCCAAAGAGCAGGACGC
1 C-T----TTT-AAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGC
* * * * *
105171 CTTTCAAAGCCCACATAAGTTGGTGACACCTTTCAATCCTCAAAGAGCAGGACGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC
* ** *
105226 CTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC
* * * * *
105281 CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGTAGGACTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC
** *
105336 CTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGATGC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC
* * * * * *
105391 CTTTCAAAGCCCACACGAGTTGGTGGCA-TCTTCTAATCCTCAAAGAGCATGACACC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAAGAGCAGGAC-GC
* *
105447 TTTTCTTTTTAAAACCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGC
1 ----C-TTTTAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGC
* * ** * *
105507 CTCTTAAAGCCCACATAAGTTAATGGCA-TTTTCCAATCCTCAAAGAGCAGGACACCTTTC
1 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGG--A-C--GC
* * *
105567 CTTTTAAAAGCCCACACAAGTTTGTGGCACTTTTTAGTCCTCAAAGAGTAGGA
1 CTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGA
105620 TGCACTTTAT
Statistics
Matches: 528, Mismatches: 69, Indels: 57
0.81 0.11 0.09
Matches are distributed among these distances:
54 2 0.00
55 296 0.56
56 33 0.06
57 2 0.00
58 1 0.00
59 2 0.00
60 8 0.02
61 129 0.24
62 55 0.10
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (55 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGC
Found at i:105183 original size:26 final size:26
Alignment explanation
Indices: 105154--105238 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
105144 TTTTCCAGTC
105154 CCCAAAGAGCAGGACGCCTTTCAAAG
1 CCCAAAGAGCAGGACGCCTTTCAAAG
** * *
105180 CCCACATA-AGTTGGTGACACCTTTC-AAT
1 CCCA-A-AGAG-CAG-GACGCCTTTCAAAG
*
105208 CCTCAAAGAGCAGGACGCCTTTTAAAG
1 CC-CAAAGAGCAGGACGCCTTTCAAAG
105235 CCCA
1 CCCA
105239 CACGAGTTGG
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
26 14 0.33
27 9 0.21
28 9 0.21
29 11 0.26
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.19
Consensus pattern (26 bp):
CCCAAAGAGCAGGACGCCTTTCAAAG
Found at i:105683 original size:42 final size:41
Alignment explanation
Indices: 105630--105777 Score: 128
Period size: 42 Copynumber: 3.6 Consensus size: 41
105620 TGCACTTTAT
*
105630 TTTCC-TCTTTCTTTCATCCTCAAAGAGCAGGACATATTTC
1 TTTCCTTCTTTCTTTCGTCCTCAAAGAGCAGGACATATTTC
*
105670 GTTTCCCTT-TTTCTTTTGTCCTC-AAGAAGCAGGACACT-TTTC
1 -TTT-CCTTCTTTCTTTCGTCCTCAAAG-AGCAGGACA-TATTTC
* * * *
105712 TTTCCTTCTCTTCCTTCGTCCTCAAGGAGCAAGACCTATTTC
1 TTTCCTTCT-TTCTTTCGTCCTCAAAGAGCAGGACATATTTC
* *
105754 ATTCTCTT-TTCCTTT-GTCCTCAAA
1 TTTC-CTTCTTTCTTTCGTCCTCAAA
105778 AAGTGGGACA
Statistics
Matches: 87, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
40 12 0.14
41 15 0.17
42 53 0.61
43 7 0.08
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (41 bp):
TTTCCTTCTTTCTTTCGTCCTCAAAGAGCAGGACATATTTC
Found at i:105716 original size:82 final size:82
Alignment explanation
Indices: 105622--105776 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 82
105612 GAGTAGGATG
* * * *
105622 CACTTTATTTTCC-TCT-TTCTTTCATCCTCAAAGAGCAGGACATATTTCGTTTCCCTTTTTCTT
1 CACTTTATTTTCCTTCTCTTCCTTCATCCTCAAAGAGCAAGACATATTTC-ATTCCC-TTTTCCT
105685 TTGTCCTCAAGAAGCAGGA
64 TTGTCCTCAAGAAGCAGGA
* * * *
105704 CACTTT-TCTTTCCTTCTCTTCCTTCGTCCTCAAGGAGCAAGACCTATTTCATTCTCTTTTCCTT
1 CACTTTAT-TTTCCTTCTCTTCCTTCATCCTCAAAGAGCAAGACATATTTCATTCCCTTTTCCTT
105768 TGTCCTCAA
65 TGTCCTCAA
105777 AAAGTGGGAC
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
81 1 0.02
82 27 0.44
83 7 0.11
84 27 0.44
ACGTcount: A:0.18, C:0.29, G:0.10, T:0.43
Consensus pattern (82 bp):
CACTTTATTTTCCTTCTCTTCCTTCATCCTCAAAGAGCAAGACATATTTCATTCCCTTTTCCTTT
GTCCTCAAGAAGCAGGA
Found at i:107508 original size:51 final size:51
Alignment explanation
Indices: 107359--107579 Score: 207
Period size: 51 Copynumber: 4.3 Consensus size: 51
107349 GAAAATAACG
* * *
107359 GGGTTGGAGTATCCATGGTTGTG-AAAATTAGTGTTTTTGGAAATAAAATC-
1 GGGTTGGAGTATCCCTGATTGTGAAAAATTAGTG-TTTTGGAAATAAAACCA
* * ** * *
107409 GGAGTTAGAGTATCCCCGATT-AAAAGAAAATCGATGTTTT-GAAGATAAAACCA
1 GG-GTTGGAGTATCCCTGATTGTGAA-AAATTAG-TGTTTTGGAA-ATAAAACCA
* *
107462 GGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCG
1 GGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCA
* * * * * * *
107513 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCA
1 GGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCA
107564 GGGTTGGAGTATCCCT
1 GGGTTGGAGTATCCCT
107580 TCGGAGGTAA
Statistics
Matches: 137, Mismatches: 26, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
50 2 0.01
51 89 0.65
52 40 0.29
53 6 0.04
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (51 bp):
GGGTTGGAGTATCCCTGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCA
Found at i:107540 original size:103 final size:102
Alignment explanation
Indices: 107359--107579 Score: 302
Period size: 103 Copynumber: 2.2 Consensus size: 102
107349 GAAAATAACG
* * * *
107359 GGGTTGGAGTATCCATGGTTGTGAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTAGAGTATCC
1 GGGTTGGAGTATCCCTGATTGTGAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTAGAGTATCC
* *
107424 CCGATTAAAAGAAAATCGATGTTTT-GAAGATAAAACCA
66 CCGATTAAAAG-AAATCAATATTTTGGAA-ATAAAACCA
* *
107462 GGGTTGGAGTATCCCTGATTGTGAAAAATTAGTG-TTTTAGAAATAAAACCGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCTGATTGTG-AAAATTAGTGTTTTTAGAAATAAAACCGGAGTTAGAGTATC
** *
107526 CCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCA
65 CCCGATTAAAAGAAATCAATATTTTGGAAATAAAACCA
107564 GGGTTGGAGTATCCCT
1 GGGTTGGAGTATCCCT
107580 TCGGAGGTAA
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
102 35 0.33
103 60 0.57
104 10 0.10
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.30
Consensus pattern (102 bp):
GGGTTGGAGTATCCCTGATTGTGAAAATTAGTGTTTTTAGAAATAAAACCGGAGTTAGAGTATCC
CCGATTAAAAGAAATCAATATTTTGGAAATAAAACCA
Found at i:107691 original size:52 final size:51
Alignment explanation
Indices: 107622--107754 Score: 169
Period size: 52 Copynumber: 2.6 Consensus size: 51
107612 AAATAACGAG
* * * *
107622 GTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAA-ATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTGGTG-TTTT-GAAGATAAAACCGGA
* * *
107674 GTTGAAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACCGGG
1 GTTGGAGTATCCCCGATT-ATGGAAAATTGGTGTTTTGAAGATAAAACCGGA
107726 GTTGGAGTATCCCCGATTATGGAAAATTG
1 GTTGGAGTATCCCCGATTATGGAAAATTG
107755 AGAAAGTTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
51 13 0.19
52 46 0.66
53 11 0.16
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGAAGATAAAACCGGA
Found at i:121520 original size:52 final size:52
Alignment explanation
Indices: 121462--122113 Score: 359
Period size: 52 Copynumber: 12.5 Consensus size: 52
121452 TTAATTGTTC
121462 ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCT
* ** *
121514 TTAATCGGGGATACTCCAACTTCGATTTT-TTTTCTAAAAACACCAATTTTTC-
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTTC--AAAACACCAATTTTCCT
* * * * *** ** *** *
121566 ACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGCATACTCTAACCCCGTTACCT
1 ATAATCGGGGATACTCCAACCCCG--ATTTTAT-TTTCA-AAAC--ACCAATTTTCCT
** * * ***
121624 CCAA--GGGGATACTCCAACCCCGACTTT-TTTTCTAAAATATTGA-TTT-CT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCCT
* *
121672 CATAATCGGGGATACTCCAACCCCGATTTTA-TTTCTAAAACACTAATTTTTC-
1 -ATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCCT
* * *
121724 ACAATCGGGGATACTCCAACCCCGGTTTTATCTTCAAAACACCAATTTTCCT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCT
* * * * *
121776 TTAATCGGGGATACTTCAACTCCGATTTTATTTCCAAAAGCACCAATTTTTC-
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAA-CACCAATTTTCCT
* * * * * ***** * * **
121828 ACAATCGAGGATACTCCAATCTCGTTATTTCATCGGGGATACTCCAA--CCCCGT
1 ATAATCGGGGATACTCCAACCCCG--ATTTTATTTTCAAAACACCAATTTTCC-T
* ** * * ***
121881 -TACCTCCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTT-CT
1 ATA-AT-C--GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCT
* * *
121934 CATAATCGGGGATACTCTAACCCCGGTTTTA-TTTCTAAAACACTAATTTTCC-
1 -ATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCCT
* * *
121986 ACAATCGGGGATACTCCAACCCCGATTTTATCTTCAAAACACCGATTTTCCT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCT
* * * *
122038 TTAATCGGGGATACTCCAACTCTGATTTTATTTTCAAAAACACCAATTTTTC-
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCCT
* * *
122090 ACAACCGGGGATACTCTAACCCCG
1 ATAATCGGGGATACTCCAACCCCG
122114 TTATTTTCAA
Statistics
Matches: 444, Mismatches: 119, Indels: 74
0.70 0.19 0.12
Matches are distributed among these distances:
48 2 0.00
49 4 0.01
50 4 0.01
51 152 0.34
52 158 0.36
53 52 0.12
54 26 0.06
55 5 0.01
56 32 0.07
57 6 0.01
58 3 0.01
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.32
Consensus pattern (52 bp):
ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCT
Found at i:121691 original size:51 final size:51
Alignment explanation
Indices: 121628--122113 Score: 324
Period size: 51 Copynumber: 9.4 Consensus size: 51
121618 TTACCTCCAA
* * * *
121628 GGGGATACTCCAACCCCGACTTTT-TTTCTAAAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCCGA-TTTTATTTCTAAAACACTAATTTCTCACAATC
*
121679 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTCTCACAATC
* *
121730 GGGGATACTCCAACCCCGGTTTTATCTTC-AAAACACCAATTT-TC-CTTTAATC
1 GGGGATACTCCAACCCCGATTTTAT-TTCTAAAACACTAATTTCTCAC---AATC
* * * * *
121782 GGGGATACTTCAACTCCGATTTTATTTCCAAAAGCACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAA-CACTAATTTCTCACAATC
* * * * ***** * * * *** * *
121834 GAGGATACTCCAATCTCGTTATTTCATCGGGGATACTCCAACCCCGTTAC-CTCC
1 GGGGATACTCCAACCCCG--ATTTTATTTCTAAAACACTAATTTC-TCACAAT-C
** * * * * *
121888 GAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCATAATC
1 --GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTCTCACAATC
* *
121941 GGGGATACTCTAACCCCGGTTTTATTTCTAAAACACTAATTT-TCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTCT-CACAATC
**
121992 GGGGATACTCCAACCCCGATTTTATCTTC-AAAACACCGATTT-TC-CTTTAATC
1 GGGGATACTCCAACCCCGATTTTAT-TTCTAAAACACTAATTTCTCAC---AATC
* * * * * *
122044 GGGGATACTCCAACTCTGATTTTATTTTCAAAAACACCAATTTTTCACAACC
1 GGGGATACTCCAACCCCGATTTTA-TTTCTAAAACACTAATTTCTCACAATC
*
122096 GGGGATACTCTAACCCCG
1 GGGGATACTCCAACCCCG
122114 TTATTTTCAA
Statistics
Matches: 340, Mismatches: 70, Indels: 49
0.74 0.15 0.11
Matches are distributed among these distances:
49 2 0.01
50 8 0.02
51 157 0.46
52 100 0.29
53 31 0.09
54 25 0.07
55 2 0.01
56 15 0.04
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTCTCACAATC
Found at i:121881 original size:28 final size:28
Alignment explanation
Indices: 121831--121907 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
121821 ATTTTTCACA
* * * **
121831 ATCGAGGATACTCCAATCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
121859 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGGGGATACTCCAACCCCGTTACCTC
***
121887 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
121908 GCTTTATTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACCTC
Found at i:121929 original size:262 final size:262
Alignment explanation
Indices: 121453--122144 Score: 1125
Period size: 262 Copynumber: 2.6 Consensus size: 262
121443 TTAAGTTTCT
* * *
121453 TAATTGTTCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAA
1 TAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATCTTCAAAACACCAATTTTCCTTTAA
* * *
121518 TCGGGGATACTCCAACTTCGATTTTTTTTCTAAAAACACCAATTTTTCACAATCGAGGATACTCC
66 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCC
* *
121583 AACCTCGTTATTTCATCGGGCATACTCTAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGAC
131 AACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGAC
* *
121648 TTTTTTTCTAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
196 TTTATTTCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
121713 AC
261 AC
*
121715 TAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATCTTCAAAACACCAATTTTCCTTTAA
1 TAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATCTTCAAAACACCAATTTTCCTTTAA
* *
121780 TCGGGGATACTTCAACTCCGATTTTATTTCCAAAAGCACCAATTTTTCACAATCGAGGATACTCC
66 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCC
* * *
121845 AATCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGC
131 AACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGAC
* *
121910 TTTATTTCCAAAATATTGATTTCTCATAATCGGGGATACTCTAACCCCGGTTTTATTTCTAAAAC
196 TTTATTTCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
121975 AC
261 AC
* *
121977 TAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATCTTCAAAACACCGATTTTCCTTTAA
1 TAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATCTTCAAAACACCAATTTTCCTTTAA
* * * * *
122042 TCGGGGATACTCCAACTCTGATTTTATTTTCAAAAACACCAATTTTTCACAACCGGGGATACTCT
66 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCC
* *
122107 AACCCCGTTATTTTCA-AGGGGATACTCCAACCCCGTTA
131 AACCTCGTTA-TTTCATCGGGGATACTCCAACCCCGTTA
122145 TTATCTCCAA
Statistics
Matches: 398, Mismatches: 31, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
262 393 0.99
263 5 0.01
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (262 bp):
TAATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATCTTCAAAACACCAATTTTCCTTTAA
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCC
AACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGAC
TTTATTTCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTTCTAAAAC
AC
Found at i:124216 original size:4 final size:4
Alignment explanation
Indices: 124207--124235 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
124197 TATTTTGAGG
124207 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
124236 GTTTTGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:129025 original size:19 final size:18
Alignment explanation
Indices: 129000--129064 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
128990 ATTTCAACGA
129000 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
129018 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
129034 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
129050 TATTGTATCGATACA
1 T-TTGTATCGATACA
129065 ATGCATCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:129038 original size:32 final size:32
Alignment explanation
Indices: 129002--129072 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
128992 TTCAACGATT
*
129002 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
129034 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
129066 TGCATCG
1 TGTATCG
129073 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:129039 original size:13 final size:13
Alignment explanation
Indices: 129021--129045 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
129011 ACATAAGTGT
129021 TGTATCGATACAA
1 TGTATCGATACAA
129034 TGTATCGATACA
1 TGTATCGATACA
129046 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:129135 original size:13 final size:13
Alignment explanation
Indices: 129117--129141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
129107 ATTACTCAAA
129117 TGTATCGATACAT
1 TGTATCGATACAT
129130 TGTATCGATACA
1 TGTATCGATACA
129142 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:129191 original size:52 final size:52
Alignment explanation
Indices: 129150--129278 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
129140 CACTGATCTT
129150 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
129202 TGTATCGATACATACAGGTAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
129254 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
129279 TCATATTTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:138117 original size:1 final size:1
Alignment explanation
Indices: 138113--138215 Score: 80
Period size: 1 Copynumber: 103.0 Consensus size: 1
138103 ATTCTTTTTT
* * * ** * * * *
138113 AAAAAAACAAAACAAAAAAAAACAACCAAAAAAAAACAAAAAAACAAAAAACAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
138178 AAAACAAAAAACAAAACAAAGAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
138216 GAGAGAAGAA
Statistics
Matches: 76, Mismatches: 26, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:138133 original size:15 final size:15
Alignment explanation
Indices: 138113--138204 Score: 99
Period size: 15 Copynumber: 6.5 Consensus size: 15
138103 ATTCTTTTTT
138113 AAAAAAACAAAACAA
1 AAAAAAACAAAACAA
*
138128 AAAAAAAC-AACCAA
1 AAAAAAACAAAACAA
138142 AAAAAAACAAAA-AA
1 AAAAAAACAAAACAA
138156 ACAAAAAACAAAA-AA
1 A-AAAAAACAAAACAA
*
138171 AACAAAA-AAAAC--
1 AAAAAAACAAAACAA
138183 -AAAAAACAAAACAA
1 AAAAAAACAAAACAA
138197 AGAAAAAA
1 A-AAAAAA
138205 AGAAAAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
11 5 0.08
12 5 0.08
13 4 0.06
14 21 0.32
15 24 0.37
16 6 0.09
ACGTcount: A:0.86, C:0.13, G:0.01, T:0.00
Consensus pattern (15 bp):
AAAAAAACAAAACAA
Found at i:138205 original size:25 final size:24
Alignment explanation
Indices: 138114--138212 Score: 109
Period size: 25 Copynumber: 4.2 Consensus size: 24
138104 TTCTTTTTTA
138114 AAAAAACAAAACAAAAAAAAACAAC
1 AAAAAACAAAACAAAAAAAAA-AAC
*
138139 CAAAAA-AAAAC----AAAAAAAC
1 AAAAAACAAAACAAAAAAAAAAAC
*
138158 AAAAAACAAAAAAAACAAAAAAAAC
1 AAAAAACAAAACAAA-AAAAAAAAC
* *
138183 AAAAAACAAAACAAAGAAAAAAAG
1 AAAAAACAAAACAAAAAAAAAAAC
138207 AAAAAA
1 AAAAAA
138213 AAAGAGAGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
19 8 0.13
20 9 0.15
24 18 0.29
25 27 0.44
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (24 bp):
AAAAAACAAAACAAAAAAAAAAAC
Found at i:138213 original size:25 final size:22
Alignment explanation
Indices: 138114--138215 Score: 107
Period size: 24 Copynumber: 4.5 Consensus size: 22
138104 TTCTTTTTTA
*
138114 AAAAAACAAAACAAAAAAAAACA
1 AAAAAAAAAAACAAAAAAAAA-A
*
138137 ACCAAAAAAAAACAAAAAAACAAA
1 A-AAAAAAAAAACAAAAAAA-AAA
*
138161 AAACAAAAAAAAC-AAAAAAAAC
1 AAA-AAAAAAAACAAAAAAAAAA
* *
138183 AAAAAACAAAACAAAGAAAAAA
1 AAAAAAAAAAACAAAAAAAAAA
*
138205 AGAAAAAAAAA
1 AAAAAAAAAAA
138216 GAGAGAAGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
21 8 0.12
22 21 0.32
23 8 0.12
24 27 0.41
25 2 0.03
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAACAAAAAAAAAA
Found at i:139395 original size:117 final size:115
Alignment explanation
Indices: 139210--139893 Score: 883
Period size: 110 Copynumber: 6.0 Consensus size: 115
139200 GATGCCTTTT
* *
139210 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCC--TTCCT
*
139275 TTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
64 TTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
*
139327 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCGCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTT--CCT
* *
139392 TTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCCCAAAGAGCAGGACG
64 TTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
139444 CCTTTCAAATCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGATGCC-T--TTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCCTTT
* ***
139505 -AAAGCCCACACGAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACG
66 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
*
139554 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGA---C-TCCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCCTTT
* * * *
139614 TAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGATG
66 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * * * * * *
139664 CCTTTCAATGCCCACACGAGTTGGTGGCA-TCTTCTAATCCTCAAATAGCAGGACACCTTTTCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCC--TTCCT
* *
139728 TTTAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
64 TTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
139780 CCTCTTC-AAGCCCACACAAGTTAGTGGCA-TTTTCCAATCCTCAAAGAGCAGGACGCCTTTCCT
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCC-TTCC-
* * *
139843 TTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGTAGGA
63 TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
139894 TGCACTTTAT
Statistics
Matches: 510, Mismatches: 42, Indels: 31
0.87 0.07 0.05
Matches are distributed among these distances:
107 2 0.00
109 6 0.01
110 182 0.36
111 3 0.01
113 1 0.00
115 7 0.01
116 159 0.31
117 150 0.29
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (115 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCCTTT
CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
Found at i:139471 original size:55 final size:55
Alignment explanation
Indices: 139210--139893 Score: 755
Period size: 55 Copynumber: 12.0 Consensus size: 55
139200 GATGCCTTTT
* * *
139210 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
*
139266 CCTTTTCCTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
1 ------CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
139327 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA------CG
* *
139389 CCTTTCAAAGCCCACACAAGTTAGTGGCATTTTCCAGTCCCCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
139444 CCTTTCAAATCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
* * ***
139499 CCTTTTAAAGCCCACACGAGTTGGTGGCACCCTCCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
139554 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACG
* * * *
139609 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGATG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * * * * * *
139664 CCTTTCAATGCCCACACGAGTTGGTGGCATCTTCTAATCCTCAAATAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
*
139719 CCTTTTCTTTTTAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
1 CC-TTTC-----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* *
139780 CCTCTTC-AAGCCCACACAAGTTAGTGGCATTTTCCAATCCTCAAAGAGCAGGACG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
* * *
139835 CCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGTAGGA
1 -----CC-TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
139894 TGCACTTTAT
Statistics
Matches: 538, Mismatches: 58, Indels: 53
0.83 0.09 0.08
Matches are distributed among these distances:
54 5 0.01
55 306 0.57
56 32 0.06
60 6 0.01
61 130 0.24
62 59 0.11
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACG
Found at i:139968 original size:42 final size:41
Alignment explanation
Indices: 139914--140051 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 41
139904 TTTCCTCTTT
*
139914 CTTTCGTCCTCAAAGAGCATGACATATTTCGTTTCCCTTTTTC
1 CTTT-GTCCTCAAAGAGCAAGACATATTTC-TTTCCCTTTTTC
* * * *
139957 CTTTGTACTC-AAGAAGCAGGACA-CTTTCTTTTCCTTCTCTTC
1 CTTTGTCCTCAAAG-AGCAAGACATATTTCTTTCCCTT-T-TTC
* * * * *
139999 CTTCGTCCTCAAGGAGCAAGACCTATTTCATTCTC-TTTTC
1 CTTTGTCCTCAAAGAGCAAGACATATTTCTTTCCCTTTTTC
140039 CTTTGTCCTCAAA
1 CTTTGTCCTCAAA
140052 AAGTGGGGCA
Statistics
Matches: 75, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
40 21 0.28
41 9 0.12
42 32 0.43
43 13 0.17
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.40
Consensus pattern (41 bp):
CTTTGTCCTCAAAGAGCAAGACATATTTCTTTCCCTTTTTC
Found at i:139989 original size:82 final size:82
Alignment explanation
Indices: 139896--140050 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 82
139886 GAGTAGGATG
* * *
139896 CACTTTATTTTCC-TCT-TTCTTTCGTCCTCAAAGAGCATGACATATTTCGTTTCCCTTTTTCCT
1 CACTTTATTTTCCTTCTCTTCCTTCGTCCTCAAAGAGCAAGACATATTTC-ATTCCC-TTTTCCT
139959 TTGTACTCAAGAAGCAGGA
64 TTGTACTCAAGAAGCAGGA
* * * *
139978 CACTTTCTTTTCCTTCTCTTCCTTCGTCCTCAAGGAGCAAGACCTATTTCATTCTCTTTTCCTTT
1 CACTTTATTTTCCTTCTCTTCCTTCGTCCTCAAAGAGCAAGACATATTTCATTCCCTTTTCCTTT
*
140043 GTCCTCAA
66 GTACTCAA
140051 AAAGTGGGGC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 28 0.44
83 7 0.11
84 28 0.44
ACGTcount: A:0.18, C:0.29, G:0.10, T:0.43
Consensus pattern (82 bp):
CACTTTATTTTCCTTCTCTTCCTTCGTCCTCAAAGAGCAAGACATATTTCATTCCCTTTTCCTTT
GTACTCAAGAAGCAGGA
Found at i:140662 original size:28 final size:28
Alignment explanation
Indices: 140622--140694 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
140612 TTCTCACAAT
140622 CGGGGATACTCCAACCCCGTTATTTTCG
1 CGGGGATACTCCAACCCCGTTATTTTCG
*
140650 CGGGGATACTCCAACCCCGTTATTTTTG
1 CGGGGATACTCCAACCCCGTTATTTTCG
*
140678 AGGGGATACTCCAACCC
1 CGGGGATACTCCAACCC
140695 TAATTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.26
Consensus pattern (28 bp):
CGGGGATACTCCAACCCCGTTATTTTCG
Found at i:140735 original size:79 final size:79
Alignment explanation
Indices: 140652--140826 Score: 206
Period size: 79 Copynumber: 2.2 Consensus size: 79
140642 TATTTTCGCG
*** * * * *
140652 GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCTAATTTTATTTTCAAAACACCA
1 GGGATACTCCAACCCCGTTATTTCCAAGAGAATACTCCAACCCCAATTTTATTTCCAAAACACCA
* *
140717 ATTTTCTATAATTA
66 ATTTTCCATAATCA
* * * * *
140731 GGGATACTCTAACCCTGTTATTTCCAAGAGAATACTCCAACCCCGATTTTATTTCCAGAACACCG
1 GGGATACTCCAACCCCGTTATTTCCAAGAGAATACTCCAACCCCAATTTTATTTCCAAAACACCA
140796 ATTTTCCATAATCA
66 ATTTTCCATAATCA
* *
140810 GGGGTACTCCAGCCCCG
1 GGGATACTCCAACCCCG
140827 CCGTTATCTC
Statistics
Matches: 78, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTCCAAGAGAATACTCCAACCCCAATTTTATTTCCAAAACACCA
ATTTTCCATAATCA
Found at i:146737 original size:104 final size:104
Alignment explanation
Indices: 146557--146765 Score: 328
Period size: 104 Copynumber: 2.0 Consensus size: 104
146547 TATGATCATA
146557 TCACGGGTCGAGATTCAAACCCTAAGTTTGAACAAACATCTTTGTTAAGCTTGGTAGATAGATTT
1 TCACGGGTCGAGATTCAAACCCTAAGTTTGAACAAACATCTTTGTTAAGCTTGGTAGATAGATTT
* * *
146622 AAGTATGAATCTATGCACAGAATATGATATACAAAATTT
66 AAGCATGAATCTATGCACAAAATATGACATACAAAATTT
* * *
146661 TCACGGGTTGAGATTCAAACTCTAAGTTTGAACAAACATCTTTGTTAAGCTTGGTTGATAGATTT
1 TCACGGGTCGAGATTCAAACCCTAAGTTTGAACAAACATCTTTGTTAAGCTTGGTAGATAGATTT
** * *
146726 TGGCATGAATCTGTGCACAAAATATGACATACAAATTTT
66 AAGCATGAATCTATGCACAAAATATGACATACAAAATTT
146765 T
1 T
146766 TTTTTATTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (104 bp):
TCACGGGTCGAGATTCAAACCCTAAGTTTGAACAAACATCTTTGTTAAGCTTGGTAGATAGATTT
AAGCATGAATCTATGCACAAAATATGACATACAAAATTT
Found at i:146800 original size:24 final size:26
Alignment explanation
Indices: 146763--146817 Score: 87
Period size: 24 Copynumber: 2.2 Consensus size: 26
146753 CATACAAATT
*
146763 TTTTTTTTATTTTTTTTAATTTTA-A
1 TTTTTTTTAGTTTTTTTAATTTTATA
146788 TTTTTTTT-GTTTTTTTAATTTTATA
1 TTTTTTTTAGTTTTTTTAATTTTATA
146813 TTTTT
1 TTTTT
146818 AATTTAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (26 bp):
TTTTTTTTAGTTTTTTTAATTTTATA
Found at i:146809 original size:14 final size:14
Alignment explanation
Indices: 146775--146822 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
146765 TTTTTTATTT
146775 TTTTTAATTTTA-A
1 TTTTTAATTTTATA
146788 TTTTT--TTTGT-T-
1 TTTTTAATTT-TATA
146799 TTTTTAATTTTATA
1 TTTTTAATTTTATA
146813 TTTTTAATTT
1 TTTTTAATTT
146823 AATTGATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
13 9 0.31
14 10 0.34
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTAATTTTATA
Found at i:147154 original size:29 final size:30
Alignment explanation
Indices: 147122--147179 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
147112 TGTATTTTTA
*
147122 AAATAATATTAATAAAAATTTAA-TAAAAT
1 AAATAATATTAATAAAAATTAAATTAAAAT
** *
147151 AAATTTTATTATTAAAAATTAAATTAAAA
1 AAATAATATTAATAAAAATTAAATTAAAA
147180 ATATATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (30 bp):
AAATAATATTAATAAAAATTAAATTAAAAT
Found at i:148542 original size:17 final size:17
Alignment explanation
Indices: 148507--148547 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
148497 CCCAAATTCA
*
148507 ATAATTATAATTATTAT
1 ATAATTATAATTATAAT
148524 ATAATTAT-ATTAATAAT
1 ATAATTATAATT-ATAAT
148541 AT-ATTAT
1 ATAATTAT
148548 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATAATTATAATTATAAT
Found at i:149550 original size:21 final size:21
Alignment explanation
Indices: 149510--149562 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
149500 TATGATATTA
*
149510 TATAAATATTTACTAGAATTG
1 TATAAATATTTACTACAATTG
* *
149531 TATAAGTATTTATTACAA-T-
1 TATAAATATTTACTACAATTG
*
149550 TATACATATTTAC
1 TATAAATATTTAC
149563 ATAACTATTG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.38
20 1 0.04
21 15 0.58
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
TATAAATATTTACTACAATTG
Found at i:149658 original size:23 final size:23
Alignment explanation
Indices: 149590--149673 Score: 59
Period size: 27 Copynumber: 3.7 Consensus size: 23
149580 TATTTTTTTA
* *
149590 TATTATAA-TATATA-AATACAT
1 TATTATAATTATATATAGTATAT
*
149611 T-TAATAATTATATATACGATCTATAT
1 TATTATAATTATATATA-G---TATAT
149637 TATTATAATTATATATAGTATAT
1 TATTATAATTATATATAGTATAT
* *
149660 AATTA-AAATATATA
1 TATTATAATTATATA
149674 ATATCATGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
20 5 0.10
21 7 0.14
22 9 0.18
23 9 0.18
26 6 0.12
27 14 0.28
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATTATATATAGTATAT
Found at i:150532 original size:17 final size:15
Alignment explanation
Indices: 150386--150551 Score: 91
Period size: 17 Copynumber: 10.0 Consensus size: 15
150376 TCTGAATTCA
150386 AAAATAATTTAAATAT
1 AAAATAATTTAAAT-T
* * *
150402 AAAAAAAAGTTATATAT
1 -AAAATAATTTAAAT-T
150419 AAAATAATTTAAATT
1 AAAATAATTTAAATT
150434 AATTCAA-AATTATCTAAACTT
1 AA---AATAA-T-T-TAAA-TT
* *
150455 AAAAAAATCTAAATTT
1 AAAATAATTTAAA-TT
* *
150471 AAAAGAAAATTAAACTT
1 AAAA-TAATTTAAA-TT
* *
150488 AAAAATATTTTAACTT
1 -AAAATAATTTAAATT
150504 AAAATAATTTAAATT
1 AAAATAATTTAAATT
150519 CAAAATATATTTAAATTT
1 -AAAATA-ATTTAAA-TT
150537 AAAATAATTTAAATT
1 AAAATAATTTAAATT
150552 TTAAAAAATA
Statistics
Matches: 119, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
15 18 0.15
16 36 0.30
17 42 0.35
18 12 0.10
19 3 0.03
20 4 0.03
21 4 0.03
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (15 bp):
AAAATAATTTAAATT
Found at i:150533 original size:49 final size:48
Alignment explanation
Indices: 150450--150548 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 48
150440 AAATTATCTA
* *
150450 AACTTAAAAAAATCTAAATTTAAAAGAAAATTAAACTTAAAAATATTTT
1 AACTTAAAAAAATCTAAATTCAAAAGAAAATTAAA-TTAAAAATAATTT
* * * * * *
150499 AACTTAAAATAATTTAAATTCAAAATATATTTAAATTTAAAATAATTT
1 AACTTAAAAAAATCTAAATTCAAAAGAAAATTAAATTAAAAATAATTT
150547 AA
1 AA
150549 ATTTTAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
48 13 0.31
49 29 0.69
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (48 bp):
AACTTAAAAAAATCTAAATTCAAAAGAAAATTAAATTAAAAATAATTT
Found at i:150539 original size:33 final size:31
Alignment explanation
Indices: 150434--150551 Score: 110
Period size: 33 Copynumber: 3.6 Consensus size: 31
150424 AATTTAAATT
* * * * *
150434 AATTCAAAATTATCTAAACTTAAAAAAATCTA
1 AATTTAAAATAATTTAAA-TTAAAAATATTTA
* * *
150466 AATTTAAAAGAAAATTAAACTTAAAAATATTTT
1 AATTTAAAA-TAATTTAAA-TTAAAAATATTTA
*
150499 AACTTAAAATAATTTAAATTCAAAATATATTTA
1 AATTTAAAATAATTTAAATT-AAAA-ATATTTA
150532 AATTTAAAATAATTTAAATT
1 AATTTAAAATAATTTAAATT
150552 TTAAAAAATA
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
31 2 0.03
32 19 0.27
33 49 0.70
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (31 bp):
AATTTAAAATAATTTAAATTAAAAATATTTA
Found at i:150554 original size:17 final size:16
Alignment explanation
Indices: 150386--150557 Score: 112
Period size: 16 Copynumber: 10.2 Consensus size: 16
150376 TCTGAATTCA
*
150386 AAAATAATTTAAATATA
1 AAAATAATTTAAAT-TT
* * * *
150403 AAAAAAAGTTATATAT
1 AAAATAATTTAAATTT
150419 AAAATAATTTAAATTAATT
1 AAAATAATTTAAA-T--TT
* * *
150438 CAAAATTATCTAAACTT
1 -AAAATAATTTAAATTT
* *
150455 AAAAAAATCTAAATTT
1 AAAATAATTTAAATTT
* * *
150471 AAAAGAAAATTAAACTT
1 AAAA-TAATTTAAATTT
* *
150488 AAAA-ATATTTTAACTT
1 AAAATA-ATTTAAATTT
*
150504 AAAATAATTTAAATTC
1 AAAATAATTTAAATTT
150520 AAAATATATTTAAATTT
1 AAAATA-ATTTAAATTT
150537 AAAATAATTTAAATTTT
1 AAAATAATTTAAA-TTT
150554 AAAA
1 AAAA
150558 AATAAAATCT
Statistics
Matches: 122, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
15 1 0.01
16 59 0.48
17 50 0.41
19 1 0.01
20 11 0.09
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:150725 original size:2 final size:2
Alignment explanation
Indices: 150713--150757 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
150703 AAACTACCCT
*
150713 TA TA AA 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
150755 TA T
1 TA T
150758 GTAATTTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:152452 original size:15 final size:15
Alignment explanation
Indices: 152428--152481 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
152418 CTAAAAAGAA
152428 AATA-TATTAATTTT
1 AATATTATTAATTTT
* *
152442 AATATTATTAAATTC
1 AATATTATTAATTTT
152457 AATATT-TTAATCTTT
1 AATATTATTAAT-TTT
*
152472 -ATATTTTTAA
1 AATATTATTAA
152482 AATTATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (15 bp):
AATATTATTAATTTT
Found at i:152742 original size:15 final size:15
Alignment explanation
Indices: 152724--152773 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
152714 TGTTACAATT
152724 TTAAAAATATATAAA
1 TTAAAAATATATAAA
152739 TT-AAAATAT-TAAA
1 TTAAAAATATATAAA
* *
152752 TTTAATAATATAAAAA
1 -TTAAAAATATATAAA
152768 TTAAAA
1 TTAAAA
152774 TACTTTGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 4 0.14
14 9 0.31
15 13 0.45
16 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAAATATATAAA
Found at i:152758 original size:12 final size:14
Alignment explanation
Indices: 152727--152775 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
152717 TACAATTTTA
152727 AAAATATATAAATT
1 AAAATATATAAATT
152741 AAAATAT-TAAATTT
1 AAAATATATAAA-TT
*
152755 AATAATATAAAAATT
1 AA-AATATATAAATT
152770 AAAATA
1 AAAATA
152776 CTTTGTTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 9 0.29
16 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATATATAAATT
Found at i:155923 original size:26 final size:27
Alignment explanation
Indices: 155894--155944 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
155884 AAATAAAAAT
*
155894 ATTAATATA-AAAAT-AATATTTTGATA
1 ATTAATAAACAAAATCAA-ATTTTGATA
155920 ATTAATAAACAAAATCAAATTTTGA
1 ATTAATAAACAAAATCAAATTTTGA
155945 AATGAGTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 12 0.55
28 2 0.09
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (27 bp):
ATTAATAAACAAAATCAAATTTTGATA
Found at i:156531 original size:14 final size:14
Alignment explanation
Indices: 156514--156563 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 14
156504 ATATAAATAA
156514 ATATGTCAAAATTT
1 ATATGTCAAAATTT
*
156528 ATATAGTATAAAATATT
1 ATAT-GT-CAAAAT-TT
156545 AATATGTCAAAATTT
1 -ATATGTCAAAATTT
156560 ATAT
1 ATAT
156564 CAATAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 8 0.27
15 4 0.13
16 10 0.33
17 4 0.13
18 4 0.13
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (14 bp):
ATATGTCAAAATTT
Found at i:156531 original size:32 final size:32
Alignment explanation
Indices: 156495--156563 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
156485 TATATTTTAA
156495 TATATTAGAATATAAATA-AATATGTCAAAATT
1 TATATTAGAATA-AAATATAATATGTCAAAATT
*
156527 TATA-TAGTATAAAATATTAATATGTCAAAATT
1 TATATTAGAATAAAATA-TAATATGTCAAAATT
156559 TATAT
1 TATAT
156564 CAATAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 5 0.15
31 6 0.18
32 22 0.67
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.41
Consensus pattern (32 bp):
TATATTAGAATAAAATATAATATGTCAAAATT
Found at i:156736 original size:17 final size:18
Alignment explanation
Indices: 156706--156739 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
156696 GAAAAAAATA
156706 ATTAAAATATAATATAAT
1 ATTAAAATATAATATAAT
*
156724 ATTAAATTA-AATATAA
1 ATTAAAATATAATATAA
156740 CACAAATATA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAAAATATAATATAAT
Found at i:156830 original size:27 final size:27
Alignment explanation
Indices: 156772--156830 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
156762 ATTATATAAA
* *
156772 ATAAATTATTAATATTTTAAAATTTAT
1 ATAAATTATTAATATCTTAAAATATAT
156799 ATAAA-TATATAATATCTT-AAATATAT
1 ATAAATTAT-TAATATCTTAAAATATAT
156825 ACTAAA
1 A-TAAA
156831 AAAGATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (27 bp):
ATAAATTATTAATATCTTAAAATATAT
Found at i:157175 original size:24 final size:25
Alignment explanation
Indices: 157135--157182 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
157125 TATTGATAAA
157135 TAATGATCCTACATATAA-AAAATG
1 TAATGATCCTACATATAATAAAATG
*
157159 TAATGATCTTA-ATTATAATAAAAT
1 TAATGATCCTACA-TATAATAAAAT
157183 TATTATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 15 0.71
25 5 0.24
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (25 bp):
TAATGATCCTACATATAATAAAATG
Found at i:163930 original size:13 final size:13
Alignment explanation
Indices: 163912--163936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
163902 ATACAAGGAT
163912 CAATGTATCGATG
1 CAATGTATCGATG
163925 CAATGTATCGAT
1 CAATGTATCGAT
163937 ACATTGAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATG
Found at i:164805 original size:49 final size:49
Alignment explanation
Indices: 164591--165249 Score: 460
Period size: 49 Copynumber: 13.8 Consensus size: 49
164581 GATAAAGGGA
* * * *
164591 CCAATACGCTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAGAATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGA-AAG--TG
* * * * * * * *
164643 ACAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAGAAG-AA-TG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
* * * *
164690 CCAATGTGCTAGA--CAAGGCCAGCGACATTGGGCTTAGGAATG-TTAAAGATG
1 CCAATATGCT-GATTCAAGGCCAGCGATATTGGTCTTA--AA-GATGAAAG-TG
* * * * *
164741 CTAATATGCTGATTCAAGGCCAACGATATCGGACTTAGAGATGAAAGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
* * *
164790 CCAATATGCTTATTCAAGGCCAGCGACATTGGTCTTAAAGAT-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
** * * *
164838 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAGGGA-CAAGGTA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
* * *
164886 CCAATATGCTAATTCAAGGCCAGTGATATTGGGC-T-----T----GTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
* * * *
164925 CCATTGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGAT-AAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAA-GTG
* * * * *
164974 CTAATATACTGATTCAAGGCCAGCGATATCGGACTTACAGATG-AAGATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAG-TG
* * * * *
165023 CCAATGTGCTGATTCAAGGCCGGCGACATTGGTCTTAAAGGTGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
* * * *
165072 CCAATATGCTGATTCAAGGCCGGCGACATTGGTCTTAAAGGTGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
* * *
165121 CCAATATGCTGATTCAAGGCCAGCGATATCGGAC-T-----T----GCG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
* * * * * *
165160 CCAATATGCTGATTCAAGGCCAGCAACATTGGTTTTAGAGA-CAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
* *
165208 CCAATATGCTGATTCAAGGCCAACGATATTGGACTTAGAAGA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTA-AAGA
165250 AGATGCCACC
Statistics
Matches: 484, Mismatches: 87, Indels: 75
0.75 0.13 0.12
Matches are distributed among these distances:
39 60 0.12
40 2 0.00
43 1 0.00
45 1 0.00
46 20 0.04
47 12 0.02
48 117 0.24
49 198 0.41
50 12 0.02
51 10 0.02
52 51 0.11
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (49 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAAGTG
Found at i:165139 original size:27 final size:27
Alignment explanation
Indices: 165060--165139 Score: 62
Period size: 27 Copynumber: 3.1 Consensus size: 27
165050 ATTGGTCTTA
165060 AAGGTGAAGGTGCCAATATGCTGATTC
1 AAGGTGAAGGTGCCAATATGCTGATTC
** * * * * *
165087 AA-G-GCCGGCGAC-AT-TGGT-CTTA
1 AAGGTGAAGGTGCCAATATGCTGATTC
165109 AAGGTGAAGGTGCCAATATGCTGATTC
1 AAGGTGAAGGTGCCAATATGCTGATTC
165136 AAGG
1 AAGG
165140 CCAGCGATAT
Statistics
Matches: 34, Mismatches: 14, Indels: 10
0.59 0.24 0.17
Matches are distributed among these distances:
22 4 0.12
23 4 0.12
24 7 0.21
25 7 0.21
26 4 0.12
27 8 0.24
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (27 bp):
AAGGTGAAGGTGCCAATATGCTGATTC
Found at i:165235 original size:87 final size:88
Alignment explanation
Indices: 165071--165243 Score: 267
Period size: 87 Copynumber: 2.0 Consensus size: 88
165061 AGGTGAAGGT
* * **
165071 GCCAATATGCTGATTCAAGGCCGGCGACATTGGTCTTAAAGGTGAAGGTGCCAATATGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGGACAAGGTGCCAATATGCTGATTC
*
165136 AAGGCCAGCGATATCGGACTTGC
66 AAGGCCAACGATATCGGACTTGC
* *
165159 GCCAATATGCTGATTCAAGGCCAGCAACATTGGTTTTAGA-GACAAGGTGCCAATATGCTGATTC
1 GCCAATATGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGGACAAGGTGCCAATATGCTGATTC
*
165223 AAGGCCAACGATATTGGACTT
66 AAGGCCAACGATATCGGACTT
165244 AGAAGAAGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 41 0.53
88 36 0.47
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (88 bp):
GCCAATATGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGGACAAGGTGCCAATATGCTGATTC
AAGGCCAACGATATCGGACTTGC
Found at i:165351 original size:61 final size:62
Alignment explanation
Indices: 165278--165801 Score: 202
Period size: 67 Copynumber: 8.1 Consensus size: 62
165268 TGGGCTTTTG
* * * *
165278 AAAAGGGTGCCATTGACTTATGGGCTTAAAAGGAGAA-ATATGCCACGGAATTGTGGAC-TTA
1 AAAAGGGTGCCATGGACTTATAGACTTAAAAGGA-AACAGATGCCACGGAATTGTGGACTTTA
* * * * *
165339 AAAAGGGTGCCATGGAGTTGTAGACTTAAAAGGAAACAGATGCCATGGAGTTGTGGGCTTTA
1 AAAAGGGTGCCATGGACTTATAGACTTAAAAGGAAACAGATGCCACGGAATTGTGGACTTTA
* * * * *
165401 AAAAGAAAAAGGTGCCATAGAGTTATGGACTTAAAAGGAAACAGAGTGCCACGGAGTTATAGG-C
1 AAAAG-----GGTGCCATGGACTTATAGACTTAAAAGGAAACAGA-TGCCACGGAATTGT-GGAC
*
165465 TTAAAA
59 TT--TA
*** * * * * *
165471 GGGAAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGAAACAGATGCCACGGAGTTGTGGGCTTTA
1 ---AAAAGGGTGCCATGGACTTATAGACTTAAAAGGAAACAGATGCCACGGAATTGTGGACTTTA
** * * * * * * *
165536 AAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAATAGATGCCACAGAGTTGTGGGCTT
1 AAAAG-----GGTGCCATGGACTTATAGACTTAAAAGGAAACAGATGCCACGGAATTGTGGACTT
165601 TA
61 TA
* * * * * * * *
165603 AAAAGAAAAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAATAGTGCCACGGAGTTGTGGA-T
1 AAAAG-----GGTGCCATGGACTTATAGACTTAAAAGGAAACAGA-TGCCACGGAATTGTGGACT
165667 TT-
60 TTA
** * * * * * * *
165669 AAAAGGAACAATGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGC
1 AAAAGG------GTGCCATGGACTTATAGACTTAAAAGGAAACAGA-TGCCACGGAATTGTGGAC
165734 -TT-
59 TTTA
* * * * * *
165736 AAAAGGGTGCCACGGAGTTATGGATTTAAAAGG-AACAAGGTGCCACGGAGTTGTGGAC-TTA
1 AAAAGGGTGCCATGGACTTATAGACTTAAAAGGAAAC-AGATGCCACGGAATTGTGGACTTTA
165797 AAAAG
1 AAAAG
165802 AAAAAAAGTG
Statistics
Matches: 392, Mismatches: 41, Indels: 60
0.80 0.08 0.12
Matches are distributed among these distances:
60 22 0.06
61 77 0.20
62 13 0.03
65 1 0.00
66 7 0.02
67 202 0.52
68 62 0.16
69 2 0.01
70 1 0.00
73 5 0.01
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (62 bp):
AAAAGGGTGCCATGGACTTATAGACTTAAAAGGAAACAGATGCCACGGAATTGTGGACTTTA
Found at i:165417 original size:34 final size:33
Alignment explanation
Indices: 165298--165835 Score: 468
Period size: 34 Copynumber: 16.4 Consensus size: 33
165288 CATTGACTTA
* ** *
165298 TGGGCTTAAAAGGAGAAATATGCCACGGAATTG
1 TGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTG
* * *
165331 TGGACTT---A--AAAAGGGTGCCATGGAGTTG
1 TGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTG
* * * * *
165359 TAGACTTAAAAGGAAACAGATGCCATGGAGTTG
1 TGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTG
* ** *
165392 TGGGCTTTAAAAAGAAAAAGGTGCCATAGAGTTA
1 TGGGC-TTAAAAGGAAAAAGGTGCCACGGAGTTG
* * *
165426 TGGACTTAAAAGGAAACAGAGTGCCACGGAGTTA
1 TGGGCTTAAAAGGAAAAAG-GTGCCACGGAGTTG
* * **
165460 TAGGCTTAAAAGGGAAAAGGGTGCCACAAAGTTG
1 TGGGCTTAAAA-GGAAAAAGGTGCCACGGAGTTG
* * *
165494 TGGACTTAAAAGGAAACAGATGCCACGGAGTTG
1 TGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTG
* *
165527 TGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTG
1 TGGGC-TTAAAAGGAAAAAGGTGCCACGGAGTTG
* * * *
165561 TGGACTTAAAAGGAAATAGATGCCACAGAGTTG
1 TGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTG
* *
165594 TGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTG
1 TGGGC-TTAAAAGGAAAAAGGTGCCACGGAGTTG
* *
165628 TGGACTTAAAAGGAAAAATAGTGCCACGGAGTTG
1 TGGGCTTAAAAGGAAAAA-GGTGCCACGGAGTTG
** * * *
165662 TGGATTTAAAAGGAACAATGTGCCACAGAGTTG
1 TGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTG
* *
165695 TGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTG
1 TGGGCTTAAAAGGAAAAAG-GTGCCACGGAGTTG
*
165729 TGGGCTTAAAA-G-----GGTGCCACGGAGTTA
1 TGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTG
** *
165756 TGGATTTAAAAGGAACAAGGTGCCACGGAGTTG
1 TGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTG
* * * *
165789 TGGACTTAAAAAGAAAAAAAGTGCCACAGAGTTG
1 TGGGCTT-AAAAGGAAAAAGGTGCCACGGAGTTG
165823 TGGGCTTAAAAGG
1 TGGGCTTAAAAGG
165836 TTGCCACTGA
Statistics
Matches: 412, Mismatches: 74, Indels: 38
0.79 0.14 0.07
Matches are distributed among these distances:
27 21 0.05
28 22 0.05
30 1 0.00
31 1 0.00
33 155 0.38
34 206 0.50
35 6 0.01
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (33 bp):
TGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTG
Found at i:165424 original size:67 final size:67
Alignment explanation
Indices: 165338--165835 Score: 586
Period size: 67 Copynumber: 7.5 Consensus size: 67
165328 TTGTGGACTT
** * *
165338 AAAAAGGGTGCCATGGAGTTGTAGACTTAAAAGGAAACAGATGCCATGGAGTTGTGGGCTTTAAA
1 AAAAA-GGTGCCACAGAGTTGTGGACTTAAAAGGAAACAGATGCCACGGAGTTGTGGGCTTTAAA
165403 AAG
65 AAG
* * * *
165406 AAAAAGGTGCCATAGAGTTATGGACTTAAAAGGAAACAGAGTGCCACGGAGTTATAGGC-TTAAA
1 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAACAGA-TGCCACGGAGTTGTGGGCTTTAAA
*
165470 AGGG
65 A-AG
* *
165474 AAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGAAACAGATGCCACGGAGTTGTGGGCTTTAAAA
1 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAACAGATGCCACGGAGTTGTGGGCTTTAAAA
165539 AG
66 AG
* *
165541 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAATAGATGCCACAGAGTTGTGGGCTTTAAAA
1 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAACAGATGCCACGGAGTTGTGGGCTTTAAAA
165606 AG
66 AG
* * * * *
165608 AAAAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAATAGTGCCACGGAGTTGT-GGATTTAAA
1 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAACAGA-TGCCACGGAGTTGTGGGCTTTAAA
*
165672 AGG
65 AAG
* * * *
165675 AACAATGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TT-AA
1 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAACAGA-TGCCACGGAGTTGTGGGCTTTAAA
165738 AAG
65 AAG
* * * * *
165741 -----GGTGCCACGGAGTTATGGATTTAAAAGG-AACAAGGTGCCACGGAGTTGTGGAC-TTAAA
1 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAC-AGATGCCACGGAGTTGTGGGCTTTAAA
165799 AAG
65 AAG
* *
165802 AAAAAAAGTGCCACAGAGTTGTGGGCTTAAAAGG
1 -AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGG
165836 TTGCCACTGA
Statistics
Matches: 372, Mismatches: 45, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
60 20 0.05
61 31 0.08
66 4 0.01
67 239 0.64
68 78 0.21
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (67 bp):
AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAACAGATGCCACGGAGTTGTGGGCTTTAAAA
AG
Found at i:165503 original size:101 final size:99
Alignment explanation
Indices: 165338--165835 Score: 521
Period size: 101 Copynumber: 5.0 Consensus size: 99
165328 TTGTGGACTT
* * * * ** *
165338 AAAAAGGGTGCCATGGAGTTGTAGACTTAAAAGGAA-ACAGATGCCATGGAGTTGTGGGCTTTAA
1 AAAAA-GGTGCCACGGAGTTATGGACTTAAAAGGAACA-AGGTGCCACAGAGTTGTGGAC-TTAA
* * *
165402 AAAGAAAAAGGTGCCATAGAGTTATGGACTTAAAAGG
63 AAAGAAAAAGGTGCCACAGAGTTGTGGGCTTAAAAGG
* *
165439 AAACAGAGTGCCACGGAGTTATAGG-CTTAAAAGGGAA-AAGGGTGCCACAAAGTTGTGGACTTA
1 AAAAAG-GTGCCACGGAGTTAT-GGACTTAAAA-GGAACAA-GGTGCCACAGAGTTGTGGACTTA
* * * * *
165502 AAAGGAAACAGATGCCACGGAGTTGTGGGCTTTAAAAAG
62 AAAAGAAAAAGGTGCCACAGAGTTGTGGGC-TTAAAAGG
* * * *
165541 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA-ATAGATGCCACAGAGTTGTGGGCTTTAAA
1 AAAAAGGTGCCACGGAGTTATGGACTTAAAAGGAACA-AGGTGCCACAGAGTTGTGGAC-TTAAA
* * *
165605 AAGAAAAAAGTGCCACGGAGTTGTGGACTTAAAAGG
64 AAGAAAAAGGTGCCACAGAGTTGTGGGCTTAAAAGG
* * * *
165641 AAAAATAGTGCCACGGAGTTGTGGATTTAAAAGGAACAATGTGCCACAGAGTTGTGGACTTAAAA
1 AAAAA-GGTGCCACGGAGTTATGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTAAAA
*
165706 GGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAA-G
65 AGAAAAAG-GTGCCACAGAGTTGTGGGCTTAAAAGG
* *
165741 -----GGTGCCACGGAGTTATGGATTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTAAAAA
1 AAAAAGGTGCCACGGAGTTATGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTAAAAA
*
165801 GAAAAAAAGTGCCACAGAGTTGTGGGCTTAAAAGG
66 G-AAAAAGGTGCCACAGAGTTGTGGGCTTAAAAGG
165836 TTGCCACTGA
Statistics
Matches: 339, Mismatches: 45, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
94 81 0.24
95 6 0.02
100 50 0.15
101 168 0.50
102 34 0.10
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (99 bp):
AAAAAGGTGCCACGGAGTTATGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTAAAAA
GAAAAAGGTGCCACAGAGTTGTGGGCTTAAAAGG
Found at i:165747 original size:27 final size:27
Alignment explanation
Indices: 165709--165890 Score: 85
Period size: 27 Copynumber: 6.2 Consensus size: 27
165699 CTTAAAAGGA
*
165709 AAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACAGAGTTGTGGGCTT
* * **
165736 AAAAGGGTGCCACGGAGTTATGGATTT
1 AAAAGGGTGCCACAGAGTTGTGGGCTT
* *
165763 AAAAGGAACAAGGTGCCACGGAGTTGTGGACTT
1 AAAA-G-----GGTGCCACAGAGTTGTGGGCTT
*
165796 AAAAAGAAAAAAAGTGCCACAGAGTTGTGGGCTT
1 -AAAAG------GGTGCCACAGAGTTGTGGGCTT
* * *
165830 AAAAGGTTGCCACTGACTTGTGGGCTT
1 AAAAGGGTGCCACAGAGTTGTGGGCTT
*** * *
165857 TTGAGGGTTGCCACTGACTTGTGGGCTT
1 AAAAGGG-TGCCACAGAGTTGTGGGCTT
*
165885 TAAAGG
1 AAAAGG
165891 TGAGGAATGT
Statistics
Matches: 125, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
27 47 0.38
28 25 0.20
33 26 0.21
34 27 0.22
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAGTTGTGGGCTT
Found at i:165787 original size:94 final size:93
Alignment explanation
Indices: 165541--165852 Score: 392
Period size: 94 Copynumber: 3.2 Consensus size: 93
165531 CTTTAAAAAG
* * * * *
165541 AAAAAGGTGCCACAGAGTTGTGGACTTAAAAGGAA-ATAGATGCCACAGAGTTGTGGGCTTTAAA
1 AAAAGGGTGCCACGGAGTTGTGGATTTAAAAGGAACA-AGGTGCCACAGAGTTGTGGAC-TTAAA
* *
165605 AAGAAAAAAGTGCCACGGAGTTGTGGACTT
64 AAGAAAAAAGTGCCACAGAGTTGTGGGCTT
*
165635 AAAAGGAAAAATAGTGCCACGGAGTTGTGGATTTAAAAGGAACAATGTGCCACAGAGTTGTGGAC
1 AAAAGG-------GTGCCACGGAGTTGTGGATTTAAAAGGAACAAGGTGCCACAGAGTTGTGGAC
*
165700 TTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
59 TTAAAAAGAAAAA-AGTGCCACAGAGTTGTGGGCTT
* *
165736 AAAAGGGTGCCACGGAGTTATGGATTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTAAAAA
1 AAAAGGGTGCCACGGAGTTGTGGATTTAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTAAAAA
165801 GAAAAAAAGTGCCACAGAGTTGTGGGCTT
66 G-AAAAAAGTGCCACAGAGTTGTGGGCTT
* * *
165830 AAAAGGTTGCCACTGACTTGTGG
1 AAAAGGGTGCCACGGAGTTGTGG
165853 GCTTTTGAGG
Statistics
Matches: 191, Mismatches: 17, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
94 102 0.53
95 5 0.03
100 12 0.06
101 71 0.37
102 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (93 bp):
AAAAGGGTGCCACGGAGTTGTGGATTTAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTAAAAA
GAAAAAAGTGCCACAGAGTTGTGGGCTT
Found at i:166291 original size:37 final size:35
Alignment explanation
Indices: 166243--166315 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 35
166233 CAAAGAAAAG
166243 ATGAAGTACAAATAAATCATGCAAAATGAAATGTT
1 ATGAAGTACAAATAAATCATGCAAAATGAAATGTT
**
166278 ATGAATGTCACAAATGCATCATGCAAAATGAAATGTT
1 ATGAA-GT-ACAAATAAATCATGCAAAATGAAATGTT
166315 A
1 A
166316 CAAATGCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 5 0.15
36 2 0.06
37 27 0.79
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (35 bp):
ATGAAGTACAAATAAATCATGCAAAATGAAATGTT
Found at i:167362 original size:1 final size:1
Alignment explanation
Indices: 167358--167439 Score: 56
Period size: 1 Copynumber: 82.0 Consensus size: 1
167348 CTTTTTGTTG
* * * * * * * * * *
167358 TTTTTGTTTTTTTTGTTTTTTGTTTTTTTATTTTTTTTGTTTGTTTTTTTTGTCTCTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
167423 GTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTT
167440 GTGGAGGACG
Statistics
Matches: 57, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.01, C:0.04, G:0.10, T:0.85
Consensus pattern (1 bp):
T
Found at i:167428 original size:9 final size:9
Alignment explanation
Indices: 167349--167437 Score: 85
Period size: 9 Copynumber: 9.6 Consensus size: 9
167339 ATCCGGACCC
*
167349 TTTTTGTTG
1 TTTTTGTTT
167358 TTTTTGTTT
1 TTTTTGTTT
167367 TTTTTGTTT
1 TTTTTGTTT
167376 TTTGTT-TTT
1 TTT-TTGTTT
167385 TTATTT-TTT
1 TT-TTTGTTT
167394 TTGTTTGTTT
1 TT-TTTGTTT
167404 TTTTTGTCTCT
1 TTTTTGT-T-T
*
167415 CTTTTT-TTG
1 -TTTTTGTTT
167424 TTTTTGTTT
1 TTTTTGTTT
167433 TTTTT
1 TTTTT
167438 TTGTGGAGGA
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
8 5 0.07
9 47 0.68
10 10 0.14
11 2 0.03
12 5 0.07
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.84
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:167438 original size:33 final size:32
Alignment explanation
Indices: 167348--167439 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 32
167338 CATCCGGACC
* *
167348 CTTTTTGTTGTTTTTGTTTTTTTTGTTTTTTGT
1 CTTTTTATTGTTTTTGTTTTTTTT-TTTTTTCT
* * *
167381 TTTTTTATTTTTTTTGTTTGTTTTTTTTGTCTCT
1 CTTTTTATTGTTTTTGTTT-TTTTTTTT-TTTCT
167415 CTTTTT-TTGTTTTTGTTTTTTTTTT
1 CTTTTTATTGTTTTTGTTTTTTTTTT
167440 GTGGAGGACG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 7 0.14
33 30 0.60
34 13 0.26
ACGTcount: A:0.01, C:0.04, G:0.11, T:0.84
Consensus pattern (32 bp):
CTTTTTATTGTTTTTGTTTTTTTTTTTTTTCT
Found at i:180417 original size:20 final size:21
Alignment explanation
Indices: 180394--180435 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
180384 AAAGGTGTTG
180394 AACATACTGT-AAATGCATGA
1 AACATACTGTGAAATGCATGA
*
180414 AACATAGTGTGAAATGCATGA
1 AACATACTGTGAAATGCATGA
180435 A
1 A
180436 TCATGGGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (21 bp):
AACATACTGTGAAATGCATGA
Found at i:181378 original size:13 final size:13
Alignment explanation
Indices: 181360--181387 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
181350 ATACAAGGAT
181360 CAATGTATCGATA
1 CAATGTATCGATA
181373 CAATGTATCGATA
1 CAATGTATCGATA
181386 CA
1 CA
181388 TTGAATGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:184520 original size:34 final size:32
Alignment explanation
Indices: 184469--184544 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
184459 TTGTGAAATA
*
184469 TAAAAATATATAATATTTTTAAATTAATTATAAT
1 TAAAAATATATAATA-TTTTAAATT-ATAATAAT
* *
184503 TAAAAATAGTAT-GTATTTTATATTATAATAAT
1 TAAAAATA-TATAATATTTTAAATTATAATAAT
*
184535 AAAAAATATA
1 TAAAAATATA
184545 AAAATGGATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 2 0.05
32 14 0.38
33 8 0.22
34 10 0.27
35 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (32 bp):
TAAAAATATATAATATTTTAAATTATAATAAT
Found at i:187369 original size:15 final size:15
Alignment explanation
Indices: 187337--187378 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
187327 AAAGTTTATA
* *
187337 AAAAAATATTAAACAT
1 AAAAAATA-AAAAAAT
187353 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
187368 -AAAAATAAAAA
1 AAAAAATAAAAA
187379 TTTTATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 5 0.21
16 8 0.33
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:187379 original size:12 final size:12
Alignment explanation
Indices: 187353--187401 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
187343 TATTAAACAT
187353 AAAA-AATAA-A
1 AAAATAATAATA
*
187363 AAAATAAAAATA
1 AAAATAATAATA
* *
187375 AAAAT-TTTATA
1 AAAATAATAATA
187386 AAAATAATAATA
1 AAAATAATAATA
187398 AAAA
1 AAAA
187402 AAATGAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
10 4 0.13
11 12 0.40
12 14 0.47
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:187502 original size:14 final size:14
Alignment explanation
Indices: 187469--187614 Score: 79
Period size: 14 Copynumber: 11.2 Consensus size: 14
187459 TTTCACGTAA
*
187469 CATTTCA-TGCATG
1 CATTTCATTTCATG
187482 CATTTTCATTTCATG
1 CA-TTTCATTTCATG
187497 CATTTCA---CAT-
1 CATTTCATTTCATG
*
187507 AATTTTCATTTCATG
1 CA-TTTCATTTCATG
187522 CATTTCATTTCAT-
1 CATTTCATTTCATG
** *
187535 -A-AACATTTCAAG
1 CATTTCATTTCATG
* *
187547 C--TCCA-TGCATG
1 CATTTCATTTCATG
187558 CATTTTCATTTCATG
1 CA-TTTCATTTCATG
187573 CATTTCA---CAT-
1 CATTTCATTTCATG
*
187583 AATTTTCATTTCATG
1 CA-TTTCATTTCATG
187598 CATTTCATTTCATG
1 CATTTCATTTCATG
187612 CAT
1 CAT
187615 GCATTTTCAT
Statistics
Matches: 101, Mismatches: 14, Indels: 35
0.67 0.09 0.23
Matches are distributed among these distances:
10 2 0.02
11 28 0.28
12 3 0.03
13 2 0.02
14 50 0.50
15 16 0.16
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (14 bp):
CATTTCATTTCATG
Found at i:187621 original size:134 final size:133
Alignment explanation
Indices: 187469--187713 Score: 454
Period size: 133 Copynumber: 1.8 Consensus size: 133
187459 TTTCACGTAA
*
187469 CATTTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATTTCATTTCA
1 CATTTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCA-TGCATTTCA
187534 TAAACATTTCAAGCTCCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGC
65 TAAACATTTCAAGCTCCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGC
187599 ATTT
130 ATTT
*
187603 CATTTCATGCATGCATTTTCATTTCATGCGTTTCACATAATTTTCATTTCATGCATGCATTTCAT
1 CATTTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATGCATTTCAT
*
187668 AAACATTTCAAGCTTCATGCATGCATTTTCATTTCATGCATTTCAC
66 AAACATTTCAAGCTCCATGCATGCATTTTCATTTCATGCATTTCAC
187714 GTAACAATTC
Statistics
Matches: 108, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
133 54 0.50
134 54 0.50
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Consensus pattern (133 bp):
CATTTCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATGCATTTCAT
AAACATTTCAAGCTCCATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCA
TTT
Found at i:187627 original size:58 final size:57
Alignment explanation
Indices: 187550--187667 Score: 209
Period size: 58 Copynumber: 2.1 Consensus size: 57
187540 TTTCAAGCTC
*
187550 CATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATTTCATTT
1 CATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCA-TGCATTT
*
187608 CATGCATGCATTTTCATTTCATGCGTTTCACATAATTTTCATTTCATGCATGCATTT
1 CATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATGCATTT
187665 CAT
1 CAT
187668 AAACATTTCA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 9 0.16
58 49 0.84
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (57 bp):
CATGCATGCATTTTCATTTCATGCATTTCACATAATTTTCATTTCATGCATGCATTT
Found at i:187636 original size:14 final size:14
Alignment explanation
Indices: 187586--187637 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
187576 TTCACATAAT
*
187586 TTTCATTTCATGCA
1 TTTCATTTCATGCG
187600 TTTCATTTCATGCATG
1 TTTCATTTCATGC--G
187616 CATTTTCATTTCATGCG
1 ---TTTCATTTCATGCG
187633 TTTCA
1 TTTCA
187638 CATAATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 18 0.56
17 1 0.03
19 13 0.41
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (14 bp):
TTTCATTTCATGCG
Found at i:187656 original size:25 final size:25
Alignment explanation
Indices: 187483--187604 Score: 122
Period size: 25 Copynumber: 4.8 Consensus size: 25
187473 TCATGCATGC
187483 ATTTTCATTTCATGCATTTCACATA
1 ATTTTCATTTCATGCATTTCACATA
** *
187508 ATTTTCATTTCATGCATTTCATTTC
1 ATTTTCATTTCATGCATTTCACATA
*** * * *
187533 ATAAACATTTCAAGC--TCCATGCATGC
1 ATTTTCATTTCATGCATTTCA--CAT-A
187559 ATTTTCATTTCATGCATTTCACATA
1 ATTTTCATTTCATGCATTTCACATA
187584 ATTTTCATTTCATGCATTTCA
1 ATTTTCATTTCATGCATTTCA
187605 TTTCATGCAT
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
23 3 0.04
25 55 0.72
26 15 0.20
28 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (25 bp):
ATTTTCATTTCATGCATTTCACATA
Found at i:187688 original size:31 final size:31
Alignment explanation
Indices: 187650--187792 Score: 112
Period size: 31 Copynumber: 4.4 Consensus size: 31
187640 TAATTTTCAT
187650 TTCATGCATGCATTTCATAAACATTTCAAGC
1 TTCATGCATGCATTTCATAAACATTTCAAGC
** *
187681 TTCATGCATGCATTTTCATTTCATGCATTTCACGTAAC
1 TTCATGCATGCA-TTTCA--T-AAACATTTCA---AGC
* * *
187719 AATTCATGCATGCATTTCACATAA-TTTTC-A-T
1 --TTCATGCATGCATTTCATA-AACATTTCAAGC
*
187750 TTCATGCATGCATTTCATAAACATTTCATGC
1 TTCATGCATGCATTTCATAAACATTTCAAGC
187781 TTCATGCATGCA
1 TTCATGCATGCA
187793 AATTTTCATT
Statistics
Matches: 87, Mismatches: 12, Indels: 26
0.70 0.10 0.21
Matches are distributed among these distances:
28 2 0.02
29 22 0.25
31 24 0.28
32 6 0.07
34 1 0.01
35 8 0.09
36 5 0.06
38 2 0.02
39 5 0.06
40 12 0.14
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (31 bp):
TTCATGCATGCATTTCATAAACATTTCAAGC
Found at i:187703 original size:50 final size:50
Alignment explanation
Indices: 187594--187810 Score: 185
Period size: 44 Copynumber: 4.4 Consensus size: 50
187584 ATTTTCATTT
187594 CATGCA-TTTCATTTCATGCATGCATTT--T---CATTTCATGCGTTTCA--
1 CATGCATTTTCATTTCATGCATGCATTTCATAAACATTTCATGC--TTCATG
* *
187638 CAT-AATTTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATG
1 CATGCATTTTCATTTCATGCATGCATTTCATAAACATTTCATGCTTCATG
* * *
187687 CATGCATTTTCA-TT--T-CATGCATTTCACGT-AACAATTCATGCATGCATTTCA
1 CATGCATTTTCATTTCATGCATGCATTTCA--TAAACATTTCATGC-TTCA--T-G
*
187738 CAT-AATTTTCATTTCATGCATGCATTTCATAAACATTTCATGCTTCATG
1 CATGCATTTTCATTTCATGCATGCATTTCATAAACATTTCATGCTTCATG
187787 CATGCAAATTTTCATTTCATGCAT
1 CATGC--ATTTTCATTTCATGCAT
187811 ATATGCATTT
Statistics
Matches: 138, Mismatches: 12, Indels: 38
0.73 0.06 0.20
Matches are distributed among these distances:
43 1 0.01
44 24 0.17
46 12 0.09
47 15 0.11
48 4 0.03
49 17 0.12
50 16 0.12
51 5 0.04
52 21 0.15
53 12 0.09
54 11 0.08
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (50 bp):
CATGCATTTTCATTTCATGCATGCATTTCATAAACATTTCATGCTTCATG
Found at i:187731 original size:25 final size:26
Alignment explanation
Indices: 187702--187766 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 26
187692 ATTTTCATTT
*
187702 CATGCATTTCACGTAA-CAATTCATG
1 CATGCATTTCACATAATCAATTCATG
*
187727 CATGCATTTCACATAATTTTCATTTCATG
1 CATGCATTTCACATAA---TCAATTCATG
187756 CATGCATTTCA
1 CATGCATTTCA
187767 TAAACATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 15 0.44
29 19 0.56
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.38
Consensus pattern (26 bp):
CATGCATTTCACATAATCAATTCATG
Found at i:187747 original size:100 final size:101
Alignment explanation
Indices: 187627--187810 Score: 334
Period size: 100 Copynumber: 1.8 Consensus size: 101
187617 ATTTTCATTT
*
187627 CATGCGTTTCACATAATTTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATGCATGC
1 CATGCATTTCACATAATTTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATGCATGC
187692 -ATTTTCATTTCATGCATTTCACGTAACAATTCATG
66 AATTTTCATTTCATGCATTTCACGTAACAATTCATG
*
187727 CATGCATTTCACATAATTTTCATTTCATGCATGCATTTCATAAACATTTCATGCTTCATGCATGC
1 CATGCATTTCACATAATTTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATGCATGC
187792 AAATTTTCATTTCATGCAT
66 -AATTTTCATTTCATGCAT
187811 ATATGCATTT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
100 63 0.79
102 17 0.21
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (101 bp):
CATGCATTTCACATAATTTTCATTTCATGCATGCATTTCATAAACATTTCAAGCTTCATGCATGC
AATTTTCATTTCATGCATTTCACGTAACAATTCATG
Found at i:187763 original size:29 final size:30
Alignment explanation
Indices: 187721--187792 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
187711 CACGTAACAA
*
187721 TTCATGCATGCATTTCACATAA-TTTTCAT-
1 TTCATGCATGCATTTCACA-AACATTTCATC
*
187750 TTCATGCATGCATTTCATAAACATTTCATGC
1 TTCATGCATGCATTTCACAAACATTTCAT-C
187781 TTCATGCATGCA
1 TTCATGCATGCA
187793 AATTTTCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.63
31 12 0.32
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.40
Consensus pattern (30 bp):
TTCATGCATGCATTTCACAAACATTTCATC
Found at i:188083 original size:21 final size:20
Alignment explanation
Indices: 188053--188091 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
188043 CACATTTTTC
*
188053 TCTAAATGTATCGATACATT
1 TCTAAATGTATCAATACATT
188073 TCTAGAATGTATCAATACA
1 TCTA-AATGTATCAATACA
188092 AGGTCCCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATCAATACATT
Found at i:188187 original size:13 final size:13
Alignment explanation
Indices: 188169--188194 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
188159 ACATAAGTGT
188169 TGTATCGATACAA
1 TGTATCGATACAA
188182 TGTATCGATACAA
1 TGTATCGATACAA
188195 AAGCTACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:188245 original size:20 final size:20
Alignment explanation
Indices: 188220--188257 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
188210 TTGCTAAGGA
188220 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
188240 AATGTATCGATACATTAT
1 AATGTATCGATACATTAT
188258 ATCGGTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:198787 original size:12 final size:12
Alignment explanation
Indices: 198772--198807 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
198762 TAGTGAAGTT
*
198772 GATTCTGAAGAA
1 GATTCCGAAGAA
*
198784 GATTCCAAAGAA
1 GATTCCGAAGAA
198796 GATTCCGAAGAA
1 GATTCCGAAGAA
198808 AACTTTGTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.19
Consensus pattern (12 bp):
GATTCCGAAGAA
Found at i:203704 original size:28 final size:28
Alignment explanation
Indices: 203664--203860 Score: 227
Period size: 28 Copynumber: 7.0 Consensus size: 28
203654 CATTCCTCAC
*
203664 CCTTCAAAAGCCCACAAGTTAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* * *
203692 CCTTCAAAAGCCCACAGGTCAATGGCAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
203720 CTTTTTC-AAAGCCCACAAGTTAGTGGCAA
1 C--CTTCAAAAGCCCACAAGTCAGTGGCAA
*
203749 CCTTCAAAAGCCCATAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* * * *
203777 CCTTTAAAAGCCCATAGGTCAGTGGCAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
203805 CTTTTTC-AAAGCCCACAAGTCAGTGGCAA
1 C--CTTCAAAAGCCCACAAGTCAGTGGCAA
*
203834 CCTTCAAAAGCCCACAAGTCCGTGGCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCA
203861 TCTTTTTCCT
Statistics
Matches: 141, Mismatches: 22, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
27 6 0.04
28 91 0.65
29 39 0.28
30 5 0.04
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:203774 original size:85 final size:85
Alignment explanation
Indices: 203664--203860 Score: 331
Period size: 85 Copynumber: 2.3 Consensus size: 85
203654 CATTCCTCAC
*
203664 CCTTCAAAAGCCCACAAGTTAGTGGCAACCTTCAAAAGCCCACAGGTCAATGGCATCTTTTTCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAGGTCAATGGCATCTTTTTCAA
*
203729 AGCCCACAAGTTAGTGGCAA
66 AGCCCACAAGTCAGTGGCAA
* * * *
203749 CCTTCAAAAGCCCATAAGTCAGTGGCAACCTTTAAAAGCCCATAGGTCAGTGGCATCTTTTTCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAGGTCAATGGCATCTTTTTCAA
203814 AGCCCACAAGTCAGTGGCAA
66 AGCCCACAAGTCAGTGGCAA
*
203834 CCTTCAAAAGCCCACAAGTCCGTGGCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCA
203861 TCTTTTTCCT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 104 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (85 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAGGTCAATGGCATCTTTTTCAA
AGCCCACAAGTCAGTGGCAA
Found at i:203868 original size:57 final size:56
Alignment explanation
Indices: 203664--203860 Score: 227
Period size: 57 Copynumber: 3.5 Consensus size: 56
203654 CATTCCTCAC
* * * *
203664 CCTTCAAAAGCCCACAAGTTAGTGGCAACCTTCAAAAGCCCACAGGTCAATGGCAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAA
* * *
203720 CTTTTTC-AAAGCCCACAAGTTAGTGGCAACCTTCAAAAGCCCATAAGTCAGTGGCAA
1 C--CTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAA
* * * * *
203777 CCTTTAAAAGCCCATAGGTCAGTGGCATCTTTTTC-AAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAAC--CTTCAAAAGCCCACAAGTCAGTGGCAA
*
203834 CCTTCAAAAGCCCACAAGTCCGTGGCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCA
203861 TCTTTTTCCT
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
55 2 0.02
56 20 0.17
57 91 0.76
58 6 0.05
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (56 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:203957 original size:34 final size:34
Alignment explanation
Indices: 203845--204186 Score: 326
Period size: 34 Copynumber: 10.5 Consensus size: 34
203835 CTTCAAAAGC
*
203845 CCACAAGTCCGTGGCA-TCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
* *
203878 CCACAACTCCGTGGCAC-CTTTTTTCTTTTCAAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTTT--AAGT
203913 CCACAACTCCGTGGCACTCTTTTTCCTTTTAA-T
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
*
203946 CCCACAGCTCCGTGGCACTCTTTTTCCTTTTAAGT
1 -CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
* *
203981 CAACAACTTCGTGGCA--C-----CCTTTTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
204008 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
*
204042 CCACAACTCCATGGCA--C-----CCTTTTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
**
204069 CCACAACTCCGTGGCAC-CTTTTTTTTTTTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
** * * * *
204102 CCATGACTCTGTGGCACCCTTTTCCCTTTTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
* * * *
204136 CCACACCTCCGTGGCATCTTTTTTTCC-TGTAAGC
1 CCACAACTCCGTGGCA-CTCTTTTTCCTTTTAAGT
* *
204170 CCACAAGTCGGTGGCAC
1 CCACAACTCCGTGGCAC
204187 CCCTTTCAAA
Statistics
Matches: 255, Mismatches: 33, Indels: 42
0.77 0.10 0.13
Matches are distributed among these distances:
27 49 0.19
28 1 0.00
29 1 0.00
32 2 0.01
33 49 0.19
34 114 0.45
35 28 0.11
36 11 0.04
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.35
Consensus pattern (34 bp):
CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
Found at i:204012 original size:61 final size:61
Alignment explanation
Indices: 203937--204124 Score: 265
Period size: 61 Copynumber: 3.1 Consensus size: 61
203927 CACTCTTTTT
* *
203937 CCTTTTAA-TCCCACAGCTCCGTGGCACTCTTTTTCCTTTTAAGTCAACAACTTCGTGGCAC
1 CCTTTTAAGT-CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCAC
* *
203998 CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCATGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCAC
** **
204059 CCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTTTTTTTTAAGTCCATGAC-TCTGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTC-GTGGCAC
204119 CCTTTT
1 CCTTTT
204125 CCCTTTTAAG
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
59 1 0.01
60 31 0.27
61 82 0.71
62 1 0.01
ACGTcount: A:0.19, C:0.32, G:0.13, T:0.36
Consensus pattern (61 bp):
CCTTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTTCGTGGCAC
Found at i:204013 original size:27 final size:27
Alignment explanation
Indices: 203971--204091 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 27
203961 CACTCTTTTT
* *
203971 CCTTTTAAGTCAACAACTTCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
203998 CCTTTTAAGTCCACAACTCCGTGGCACTC
1 CCTTTTAAGTCCACAACTCCGTGGCA--C
*
204027 TTTTTCCTTTTAAGTCCACAACTCCATGGCAC
1 -----CCTTTTAAGTCCACAACTCCGTGGCAC
204059 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
*
204086 CTTTTT
1 CCTTTT
204092 TTTTTTAAGT
Statistics
Matches: 82, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
27 55 0.67
29 1 0.01
32 1 0.01
34 25 0.30
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.33
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:204022 original size:95 final size:98
Alignment explanation
Indices: 203844--204204 Score: 302
Period size: 95 Copynumber: 3.7 Consensus size: 98
203834 CCTTCAAAAG
*
203844 CCCACAAG-TCCGTGGCA-TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTTCTTTT
1 CCCAC-AGCTCCGTGGCACTCTTTTTCCTTTTAAGTCAACAACTCCGTGGCACC-----TCTTTT
203907 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAA-T
60 -AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
* *
203946 CCCACAGCTCCGTGGCACTCTTTTTCCTTTTAAGTCAACAACTTCGTGGCACC-CTTTT-AAGTC
1 CCCACAGCTCCGTGGCACTCTTTTTCCTTTTAAGTCAACAACTCCGTGGCACCTCTTTTAAAGCC
204009 CACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
66 CACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
* * * * *
204042 -CCACAACTCCATGGCA--C-----CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTTTTTTTA
1 CCCACAGCTCCGTGGCACTCTTTTTCCTTTTAAGTCAACAACTCCGTGGCACC----TCTTTTAA
* ** * * *
204099 AGTCCATGACTCTGTGGCACCCTTTTCCCTTTTAAG-
62 AGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
* * * * * * * * *
204135 CCCACACCTCCGTGGCATCTTTTTTTCC-TGTAAGCCCACAAGTCGGTGGCACCCCTTTCAAAGC
1 CCCACAGCTCCGTGGCA-CTCTTTTTCCTTTTAAGTCAACAACTCCGTGGCACCTCTTTTAAAGC
204199 CCACAA
65 CCACAA
204205 GTTGGTGCAA
Statistics
Matches: 214, Mismatches: 27, Indels: 41
0.76 0.10 0.15
Matches are distributed among these distances:
88 26 0.12
93 5 0.02
94 46 0.21
95 49 0.23
96 1 0.00
97 15 0.07
101 23 0.11
102 16 0.07
103 33 0.15
ACGTcount: A:0.19, C:0.34, G:0.13, T:0.34
Consensus pattern (98 bp):
CCCACAGCTCCGTGGCACTCTTTTTCCTTTTAAGTCAACAACTCCGTGGCACCTCTTTTAAAGCC
CACAACTCCGTGGCACTCTTTTTCCTTTTAAGT
Found at i:204211 original size:29 final size:27
Alignment explanation
Indices: 204166--204269 Score: 111
Period size: 29 Copynumber: 3.6 Consensus size: 27
204156 TTTTTCCTGT
*
204166 AAGCCCACAAGTCGGTGGCACCCCTTTCA
1 AAGCCCACAAGTTGGT-GCA-CCCTTTCA
*
204195 AAGCCCACAAGTTGGTGCAACC-TTCAA
1 AAGCCCACAAGTTGGTGCACCCTTTC-A
*
204222 AAGCACACAAGTTGGTGCAACCCTTTCA
1 AAGCCCACAAGTTGGTGC-ACCCTTTCA
204250 GAAGCCCACACAAGTTGGTG
1 -AAG-CC-CACAAGTTGGTG
204270 GCAGTCTTCT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.05
27 20 0.31
28 7 0.11
29 21 0.33
30 1 0.02
31 12 0.19
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (27 bp):
AAGCCCACAAGTTGGTGCACCCTTTCA
Found at i:204230 original size:27 final size:29
Alignment explanation
Indices: 204166--204269 Score: 115
Period size: 27 Copynumber: 3.6 Consensus size: 29
204156 TTTTTCCTGT
* * *
204166 AAGCCCACAAGTCGGTGGCACCCCTTTC-A
1 AAGCACACAAGTTGGT-GCAACCCTTTCAA
*
204195 AAGCCCACAAGTTGGTGCAA-CC-TTCAA
1 AAGCACACAAGTTGGTGCAACCCTTTCAA
*
204222 AAGCACACAAGTTGGTGCAACCCTTTCAG
1 AAGCACACAAGTTGGTGCAACCCTTTCAA
204251 AAGCCCACACAAGTTGGTG
1 AAG--CACACAAGTTGGTG
204270 GCAGTCTTCT
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
26 3 0.05
27 22 0.33
28 5 0.08
29 22 0.33
31 14 0.21
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (29 bp):
AAGCACACAAGTTGGTGCAACCCTTTCAA
Found at i:204428 original size:87 final size:87
Alignment explanation
Indices: 204282--204455 Score: 278
Period size: 87 Copynumber: 2.0 Consensus size: 87
204272 AGTCTTCTTC
* * *
204282 TAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
1 TAAGCCCAATATCGCTAGCCTTGAATCAACATATAGGCACCTTGTCTATAAGACCAATGTCGCTG
204347 GCCTTAAATCAGCACT-TTGGCA
66 GCCTTAAATCAGCA-TATTGGCA
* *
204369 TAAGCCCAATATCGCTAGCCTTGAATTAGCATATAGGCACCTTGTCTATAAGACCAATGTCGCTG
1 TAAGCCCAATATCGCTAGCCTTGAATCAACATATAGGCACCTTGTCTATAAGACCAATGTCGCTG
*
204434 GCCTTGAATCAGCATATTGGCA
66 GCCTTAAATCAGCATATTGGCA
204456 CCTTGTCTCT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
86 1 0.01
87 79 0.99
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (87 bp):
TAAGCCCAATATCGCTAGCCTTGAATCAACATATAGGCACCTTGTCTATAAGACCAATGTCGCTG
GCCTTAAATCAGCATATTGGCA
Found at i:204507 original size:87 final size:87
Alignment explanation
Indices: 204416--205026 Score: 835
Period size: 87 Copynumber: 6.9 Consensus size: 87
204406 CACCTTGTCT
* *
204416 ATAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCT
1 ATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCT
* * *
204481 GGCCTTAAATCAGCACTTTAGC
66 GGCCTTGAATCAGCACATTGGC
* * * *
204503 ATAAGCCCAATATCGCTAGCCTTGAATTAGCATATAGGCACCTTGTCTATAAGACCAATGTCGCT
1 ATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCT
*
204568 GGCCTTGAATCAGCACTTTGGC
66 GGCCTTGAATCAGCACATTGGC
* * *
204590 ATAAACCCAATATCGCTGGCCTTGAATCAGTATATTGACACCTTGTCTCTAAGACCAATGTCGCT
1 ATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCT
*
204655 GGCCTTGAATCAGCACATTGAC
66 GGCCTTGAATCAGCACATTGGC
*
204677 ATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCT
1 ATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCT
204742 GGCCTTGAATCAGCACATTGGC
66 GGCCTTGAATCAGCACATTGGC
*
204764 ATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCT
1 ATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCT
204829 GGCCTTGAATCAGCACATTGGC
66 GGCCTTGAATCAGCACATTGGC
* * * * *
204851 ACAAGCCCAATATTGTTGGCCTTGAATCAGCATATTGGTACCTTTGTCATCTCTAAGTCCAATGT
1 ATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTCTAAGACCAATGT
* *
204916 CGCTTGCCTTGAATCAGCATATTGGC
62 CGCTGGCCTTGAATCAGCACATTGGC
* * * * ** * * *
204942 ACCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCCTCATCTTTAAGTCCAATA
1 A----TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTTGTCTCTAAGACCAATG
* *
205007 TCACTGGCCTTGAATTAGCA
61 TCGCTGGCCTTGAATCAGCA
205027 TATTTGCGCT
Statistics
Matches: 472, Mismatches: 43, Indels: 13
0.89 0.08 0.02
Matches are distributed among these distances:
87 364 0.77
88 3 0.01
91 39 0.08
92 30 0.06
95 34 0.07
96 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (87 bp):
ATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCT
GGCCTTGAATCAGCACATTGGC
Found at i:204529 original size:135 final size:135
Alignment explanation
Indices: 204282--204852 Score: 671
Period size: 135 Copynumber: 4.3 Consensus size: 135
204272 AGTCTTCTTC
* * *
204282 TAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
*
204347 GCCTTAAATCAGCACTTTGGCATAAGCCCAATATCGCTAGCCTTGAATTAGCATATAGGCACCTT
66 GCCTTAAATCAGCACTTTAGCATAAGCCCAATATCGCTAGCCTTGAATTAGCATATAGGCACCTT
204412 GTCTA
131 GTCTA
204417 TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
204482 GCCTTAAATCAGCACTTTAGCATAAGCCCAATATCGCTAGCCTTGAATTAGCATATAGGCACCTT
66 GCCTTAAATCAGCACTTTAGCATAAGCCCAATATCGCTAGCCTTGAATTAGCATATAGGCACCTT
204547 GTCTA
131 GTCTA
*
204552 TAAGACCAATGTCGCTGGCCTTGAATCAGCACT-TTGGCA---------TAA-ACCCAATATCGC
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCA-TATTGGCACCTTGTCTCTAAGA-CCAATGTCGC
* * * * * *
204606 TGGCCTTGAATCAGTA-TATTGACACCTTGTCTCTAAGACCAATGTCGCTGGCCTTGAA-T--C-
64 TGGCCTTAAATCAGCACT-TT---A----G-C-ATAAGCCCAATATCGCTAGCCTTGAATTAGCA
* *
204666 ---A-GCACATTGAC-A
119 TATAGGCACCTTGTCTA
* * *
204678 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTG
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
* * * * * *
204743 GCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
66 GCCTTAAATCAGCACTTTAGCATAAGCCCAATATCGCTAGCCTTGAATTAGCATATAGGCACCTT
*
204808 GTCTT
131 GTCTA
*
204813 TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCAC
204853 AAGCCCAATA
Statistics
Matches: 373, Mismatches: 30, Indels: 66
0.80 0.06 0.14
Matches are distributed among these distances:
125 3 0.01
126 87 0.23
127 9 0.02
128 2 0.01
129 2 0.01
132 1 0.00
133 1 0.00
134 10 0.03
135 256 0.69
136 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (135 bp):
TAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTCTAAGACCAATGTCGCTG
GCCTTAAATCAGCACTTTAGCATAAGCCCAATATCGCTAGCCTTGAATTAGCATATAGGCACCTT
GTCTA
Found at i:204935 original size:52 final size:49
Alignment explanation
Indices: 204867--205082 Score: 203
Period size: 52 Copynumber: 4.4 Consensus size: 49
204857 CCAATATTGT
* *
204867 TGGCCTTGAATCAGCATATTGGTACCTTTGTCATCTCTAAGTCCAATGTCGC
1 TGGCCTTGAATCAGCATATTGGCACC---GTCATCTTTAAGTCCAATGTCGC
* *
204919 TTGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATGTTGC
1 TGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCGC
* * * *
204962 TGGCCTTGAATCAGCACATTGGCACCCTCATCTTTAAGTCCAATATCAC
1 TGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCGC
* ** **
205011 TGGCCTTGAATTAGCATATTTGCGCTTTCGTCATCTTTAAAACCAATGTCGC
1 TGGCCTTGAATCAGCATA-TTG-GC-ACCGTCATCTTTAAGTCCAATGTCGC
*
205063 TGGCCATGAATCAGCA-ATTG
1 TGGCCTTGAATCAGCATATTG
205083 TCATTTTTCA
Statistics
Matches: 135, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
43 38 0.28
45 1 0.01
47 1 0.01
49 31 0.23
50 6 0.04
51 3 0.02
52 55 0.41
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
TGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCGC
Found at i:204968 original size:43 final size:43
Alignment explanation
Indices: 204904--204987 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
204894 TTGTCATCTC
* *
204904 TAAGTCCAATGTCGCTTGCCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
*
204947 TAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACC
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
204988 CTCATCTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (43 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
Found at i:205489 original size:20 final size:20
Alignment explanation
Indices: 205464--205518 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
205454 TTACCCGAGA
*
205464 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
205484 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
205504 TGTATCGATACATTG
1 TGTATCGATACATTG
205519 TATCGATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:205523 original size:33 final size:33
Alignment explanation
Indices: 205481--205550 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
205471 ATACATTTTG
*
205481 CATTGTATCGATACATTGCT-CATTGTATCGATA
1 CATTGTATCGATACATT-CTACAATGTATCGATA
*
205514 CATTGTATCGATACATTTTACAATGTATCGATA
1 CATTGTATCGATACATTCTACAATGTATCGATA
205547 CATT
1 CATT
205551 CAGGCATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (33 bp):
CATTGTATCGATACATTCTACAATGTATCGATA
Found at i:205535 original size:20 final size:20
Alignment explanation
Indices: 205464--205550 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
205454 TTACCCGAGA
*
205464 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTTACAT
*
205484 TGTATCGATACATTGCT-CAT
1 TGTATCGATACATT-TTACAT
205504 TGTATCG----A---TACAT
1 TGTATCGATACATTTTACAT
*
205517 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTTACAT
205537 TGTATCGATACATT
1 TGTATCGATACATT
205551 CAGGCATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
12 1 0.02
13 10 0.18
16 1 0.02
17 1 0.02
20 42 0.75
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTTTACAT
Found at i:205548 original size:13 final size:13
Alignment explanation
Indices: 205501--205530 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
205491 ATACATTGCT
205501 CATTGTATCGATA
1 CATTGTATCGATA
205514 CATTGTATCGATA
1 CATTGTATCGATA
205527 CATT
1 CATT
205531 TTACAATGTA
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:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:207193 original size:13 final size:13
Alignment explanation
Indices: 207175--207202 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
207165 TACATAAAAT
207175 ATTGTATCGATAC
1 ATTGTATCGATAC
207188 ATTGTATCGATAC
1 ATTGTATCGATAC
207201 AT
1 AT
207203 AAGTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:207193 original size:33 final size:32
Alignment explanation
Indices: 207156--207220 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
207146 TTTCAACGAT
207156 TTGTATCGATACATAAAATATTGTATCGATACA
1 TTGTATCGATACAT-AAATATTGTATCGATACA
* *
207189 TTGTATCGATACATAAGTTTTGTATCGATACA
1 TTGTATCGATACATAAATATTGTATCGATACA
207221 ATTTAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.38
Consensus pattern (32 bp):
TTGTATCGATACATAAATATTGTATCGATACA
Found at i:207281 original size:13 final size:13
Alignment explanation
Indices: 207263--207287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
207253 ATTACTCAAA
207263 TGTATCGATACAT
1 TGTATCGATACAT
207276 TGTATCGATACA
1 TGTATCGATACA
207288 CTATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:207302 original size:33 final size:34
Alignment explanation
Indices: 207242--207308 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
207232 TGCCAAAAAA
* *
207242 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACACTACTAAAATGTATCGATACAT
207276 TGTATCGATACACTA-TAAAATGTATCGATACAT
1 TGTATCGATACACTACTAAAATGTATCGATACAT
207309 ACAGGCAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (34 bp):
TGTATCGATACACTACTAAAATGTATCGATACAT
Found at i:211442 original size:51 final size:51
Alignment explanation
Indices: 211337--211515 Score: 200
Period size: 51 Copynumber: 3.5 Consensus size: 51
211327 AAATTTCTAG
* * * * * *
211337 ATTTTTCAT-CTCGGGGATACTCTAA-TCCCGGTTTCATTTCCAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCC
* * ** *
211387 ATTTTTCTTAATCGGGGATACTCCAACTTCGATTTTATTTTTAGAACACCC
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCC
* *
211438 ATTTTCCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCG
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCC
* *
211489 ACTTTTCACAATCGGGGATACTCCAAC
1 ATTTTTCATAATCGGGGATACTCCAAC
211516 CCCGTTATTT
Statistics
Matches: 106, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
50 8 0.08
51 97 0.92
52 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCC
Found at i:211542 original size:79 final size:78
Alignment explanation
Indices: 211451--211857 Score: 457
Period size: 79 Copynumber: 5.2 Consensus size: 78
211441 TTCCATAATC
* * *
211451 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCGACTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAAC-CCGATTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCAAC
211516 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * *
211530 GGGGACACTCCAACCCTAGTTTTATTTCTAAAACATC-AATTTT-TC-ATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCGA-TTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCAAC
211592 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* ** ** * * *
211606 GGGGATACCCCAACCCCGGCTTTATTTCTAAAATGT-TAATTTCTCATAATCGGGGATGCTCCAA
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAACATCGAATTT-TCACAATCGGGGATACTCCAA
*
211670 CCCCGTTATTTCCGA
64 CCCCGTTATTTTCGA
* * * * *
211685 GGGGATACTCTAACCCTGGTTTTATTTCTAAAACATC-AATTTTTCATAGTCGGAGATACTCCAA
1 GGGGATACTCCAACCC-GATTTTATTTCTAAAACATCGAA-TTTTCACAATCGGGGATACTCCAA
*
211749 CCCCCTTATTTTCGA
64 CCCCGTTATTTTCGA
* ** * * *
211764 GGGGATATTCCAATCCTAATTTTATTTCTAAATCATCGATTTTTCACAATCAGGGATACTCCAAC
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCAAC
211829 CCCGTTACTTTT-GA
65 CCCGTTA-TTTTCGA
211843 GGGGATACTCCAACC
1 GGGGATACTCCAACC
211858 TCGTTATTAT
Statistics
Matches: 276, Mismatches: 40, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
76 61 0.22
77 5 0.02
78 13 0.05
79 187 0.68
80 10 0.04
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCGATTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:214165 original size:21 final size:22
Alignment explanation
Indices: 214132--214172 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
214122 CCATGTTAAC
214132 AGCTCATGATTCATGCATTTTG
1 AGCTCATGATTCATGCATTTTG
*
214154 AGCT-ATGTTTCATGCATTT
1 AGCTCATGATTCATGCATTT
214173 ACAGCATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (22 bp):
AGCTCATGATTCATGCATTTTG
Found at i:217002 original size:22 final size:22
Alignment explanation
Indices: 216977--217031 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
216967 TCTAGCAACT
216977 TCCAGCAGCTCCCACAACAGCC
1 TCCAGCAGCTCCCACAACAGCC
***
216999 TCCAGCAGCTCCCACGGTAGCC
1 TCCAGCAGCTCCCACAACAGCC
*
217021 TCCAACAGCTC
1 TCCAGCAGCTC
217032 AGCAACCACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.24, C:0.47, G:0.16, T:0.13
Consensus pattern (22 bp):
TCCAGCAGCTCCCACAACAGCC
Found at i:217058 original size:72 final size:72
Alignment explanation
Indices: 216982--217157 Score: 208
Period size: 72 Copynumber: 2.4 Consensus size: 72
216972 CAACTTCCAG
* * * * *
216982 CAGCTCCCACAACAGCCTCCAGCAGCTCCCACGGTAGCCTCCAACAGCTCAGCAACCACGAGCAG
1 CAGCTCCCACAACAACCTCCAACAGCTCCCACGGCAGCCTCCAACAGCTCAACAACCACAAGCAG
*
217047 CCCCTCA
66 CCCCCCA
* ** * * *
217054 CAGCTCCTACAGTAACTTCCAATAGCTCCTACGGCAGCCTCCAACAGCTCAACAACCACAAGCAG
1 CAGCTCCCACAACAACCTCCAACAGCTCCCACGGCAGCCTCCAACAGCTCAACAACCACAAGCAG
217119 CCCCCCA
66 CCCCCCA
* ** *
217126 CAGCTCCTACAGTAACTTCCAACAGCTCCCAC
1 CAGCTCCCACAACAACCTCCAACAGCTCCCAC
217158 AGCAACTTCC
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 90 1.00
ACGTcount: A:0.28, C:0.45, G:0.14, T:0.13
Consensus pattern (72 bp):
CAGCTCCCACAACAACCTCCAACAGCTCCCACGGCAGCCTCCAACAGCTCAACAACCACAAGCAG
CCCCCCA
Found at i:217153 original size:22 final size:22
Alignment explanation
Indices: 217125--217168 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
217115 GCAGCCCCCC
* *
217125 ACAGCTCCTACAGTAACTTCCA
1 ACAGCTCCCACAGCAACTTCCA
217147 ACAGCTCCCACAGCAACTTCCA
1 ACAGCTCCCACAGCAACTTCCA
217169 GCAATGACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.41, G:0.09, T:0.18
Consensus pattern (22 bp):
ACAGCTCCCACAGCAACTTCCA
Found at i:220433 original size:5 final size:5
Alignment explanation
Indices: 220417--220465 Score: 53
Period size: 5 Copynumber: 9.2 Consensus size: 5
220407 TTTTTTCTAC
* *
220417 TTTTA TTTTT TTATTT TTTTA CTTTTA TTTTA CTTTTA TTTTA TTTTA
1 TTTTA TTTTA TT-TTA TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA
220465 T
1 T
220466 ATCAAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 24 0.62
6 15 0.38
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:220436 original size:11 final size:11
Alignment explanation
Indices: 220414--220465 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
220404 TGTTTTTTTC
220414 TACTTTTATTT
1 TACTTTTATTT
* *
220425 T-TTTATTTTTT
1 TACTT-TTATTT
220436 TACTTTTATTT
1 TACTTTTATTT
220447 TACTTTTATTT
1 TACTTTTATTT
220458 TA-TTTTAT
1 TACTTTTAT
220466 ATCAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 8 0.23
11 25 0.71
12 2 0.06
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (11 bp):
TACTTTTATTT
Found at i:220458 original size:22 final size:20
Alignment explanation
Indices: 220406--220465 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 20
220396 TTTTTTGGTG
*
220406 TTTTTTTCTACTTTTATTTTTT
1 TTTTTTT-TACTTTTA-TTTTC
220428 TATTTTTTTACTTTTATTTTAC
1 T-TTTTTTTACTTTTATTTT-C
220450 TTTTATTTTA-TTTTAT
1 TTTT-TTTTACTTTTAT
220466 ATCAAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 13 0.38
22 15 0.44
23 6 0.18
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTTTACTTTTATTTTC
Found at i:221016 original size:43 final size:43
Alignment explanation
Indices: 220952--222142 Score: 1284
Period size: 43 Copynumber: 28.0 Consensus size: 43
220942 CCGACTTTAG
* * *
220952 GGTCAAGGCCGACAGGTAGACTAAGGGATAGGAAAGTCTCCAC
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
** * * * * *
220995 GGTCAAAGTTGACAGGCAGACTAAGGAATAAGAAAGACTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * * * * *
221038 GGTCAAAGCCGACAAGCAAATTAAGGGATAGGAAAGTTTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * * *
221081 GGTCAAAGCCGACACGTAGACTAAGGGATAGGAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* *
221124 GGTCAAAGTCGACAGGTAGACTAAGGGATAGGAAAGTCTCC-A
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * *
221166 GAGTCAAAGCCGATAAGCAGATTAAGGGATAGGAAAGTCTCCAA
1 G-GTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * *
221210 GGTCAAAGACGACAGGCAGACTAAGGGATAAGAAAGTCTTCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * * *
221253 GGTCAAAACCAATAGGCAGACTAAGGGATAGGAAAGTCTCAAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * * *
221296 GGTCAAAGCCGACAGGCAGACCAAGGGA-AAGAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
*
221338 GGTCAAAGCCGACAGGTAGACTAAGGGATAGGAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * *
221381 GGTCAAAACCGACAGGCAGA-TAAGGGA-AGGAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
** * * *
221422 GGTCAAAGTTGATAAGCAGACTGAA-GGATAGAAAAGTCTCC-A
1 GGTCAAAGCCGACAGGCAGACT-AAGGGATAGGAAAGTCTCCAA
* *
221464 GG-GAAA-TCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * *
221505 GGTCAAAACCGACAGGCAGACTGAA-GGATAGAAAAGTCTCTAA
1 GGTCAAAGCCGACAGGCAGACT-AAGGGATAGGAAAGTCTCCAA
* *
221548 GGTCAAAGCCGACAAGCAAACTAAGGGATAGGAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
*
221591 GGTCAAAGCCGACAGGCAGACTAAGGGCA-AGGAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGG-ATAGGAAAGTCTCCAA
* * *
221634 GGTCAAAGCCGACAAGCAGACTAAGGGATAGAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * *
221677 GGTCAAAACCGACTGGCAGACTAAGGGATAGGAAAATCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * * * *
221720 GGTCAAAGCCGACAGGCAAATTAA-AGAAAGGAAAGTCTCAAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * * * * *
221762 AGTCAAAGTCGATAGGCAGACTAAGGGATAAGAAAATCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * * * *
221805 GGTCAAAGCCGACAGGTAGACTAAAGGA-AAGAAAATCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * *
221847 GGTCAAAGTCGACAGGCAAACTAAGGGATAGGAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * * * *
221890 GGTCAAAGCCGATAGGCAAACTAAGGGA-A-AAAAGTTTTCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * *
221931 GGTCAAAGTCGACAGGCTA-ACTGAGGGATAGAAAAGTCTCCAA
1 GGTCAAAGCCGACAGGC-AGACTAAGGGATAGGAAAGTCTCCAA
* * * ** * *
221974 GGTCAAAGCCAACAGACATACTGGGGGATAGAAAAGTCTCCAG
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * *
222017 GGTCAAAGCTGATAGGTAGACTAAGGGATAGGAAAGTCTCCAA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
* * *
222060 GGTCAAAGCTGACAGGCAGACTAAGGGCA-AGGAAAGTCTCTAG
1 GGTCAAAGCCGACAGGCAGACTAAGGG-ATAGGAAAGTCTCCAA
* * *
222103 GGTCAAAGCCAACAAGCAGACTAAGGGA-A-AAAAGTCTCCA
1 GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCA
222143 TAAGTTTAAT
Statistics
Matches: 968, Mismatches: 159, Indels: 44
0.83 0.14 0.04
Matches are distributed among these distances:
39 2 0.00
40 26 0.03
41 73 0.08
42 134 0.14
43 727 0.75
44 6 0.01
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (43 bp):
GGTCAAAGCCGACAGGCAGACTAAGGGATAGGAAAGTCTCCAA
Found at i:234502 original size:5 final size:5
Alignment explanation
Indices: 234486--234549 Score: 58
Period size: 5 Copynumber: 12.2 Consensus size: 5
234476 TTTTTTCTAC
* * *
234486 TTTTA TTTTT TTATTT TTTTA CTTTTA TTTTA TTTT- TTATTT TTTTA
1 TTTTA TTTTA TT-TTA TTTTA -TTTTA TTTTA TTTTA TT-TTA TTTTA
234533 CTTTTA TTTTA TTTTA T
1 -TTTTA TTTTA TTTTA T
234550 ATCGAATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
4 2 0.04
5 32 0.63
6 17 0.33
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:234503 original size:14 final size:14
Alignment explanation
Indices: 234494--234542 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
234484 ACTTTTATTT
234494 TTTTATTTTTTTAC
1 TTTTATTTTTTTAC
*
234508 TTTTATTTTATT--
1 TTTTATTTTTTTAC
234520 TTTTATTTTTTTAC
1 TTTTATTTTTTTAC
234534 TTTTATTTT
1 TTTTATTTT
234543 ATTTTATATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 11 0.35
14 20 0.65
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTATTTTTTTAC
Done.