Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold94
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: 2274668
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 33727 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:1308810 original size:13 final size:13
Alignment explanation
Indices: 1308792--1308817 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1308782 CATTTTTCTG
1308792 TGTATCGATACAT
1 TGTATCGATACAT
1308805 TGTATCGATACAT
1 TGTATCGATACAT
1308818 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1308814 original size:33 final size:33
Alignment explanation
Indices: 1308772--1308838 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1308762 GCCAAGGAAA
***
1308772 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1308805 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1308838 T
1 T
1308839 TGGGAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1311226 original size:51 final size:52
Alignment explanation
Indices: 1311168--1311616 Score: 238
Period size: 52 Copynumber: 8.6 Consensus size: 52
1311158 TTGAGTTTCT
* * * * *
1311168 CAATTTTCCGCAATCGAGGATA-TTCATTCTCCGATTTTATTTTC-AAAACAC
1 CAATTTTCCACAATCGGGGATACTCCA-ACTCCGATTTTATTTCCAAAAACAC
* * *
1311219 TAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACAC
* * * * *** * *
1311272 CAATTTTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTC
1 CAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACAC
* * ** ** * *
1311324 CAACCCCGTTATTTC-CGA--GGGGATACTCCAAC-CCCTTCTTTA-TTCTTAAAATAT
1 CAA-----TT-TTCCACAATCGGGGATACTCCAACTCCGAT-TTTATTTCCAAAAACAC
** * * * * *
1311378 TGATTTAT-CATAATCGGGGATACTCCAACTCCGGTTTTA-TTGCTAAAGCAC
1 CAATTT-TCCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
* * * **
1311429 TAATTTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT-TTAAAACAC
1 CAA-TTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
* ** * *
1311481 TAATTTTCCTTTAATCGGGGATACTCCAGCTCCGATTTTATTTTCAAAAACAC
1 CAATTTTCC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
***
1311534 CAATTTTTTCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAA--TTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
* * *
1311588 CAATTTTTCACAATTGAGGATACTCCAAC
1 CAATTTTCCACAATCGGGGATACTCCAAC
1311617 CTCGTTATTT
Statistics
Matches: 308, Mismatches: 64, Indels: 51
0.73 0.15 0.12
Matches are distributed among these distances:
48 2 0.01
49 4 0.01
51 70 0.23
52 105 0.34
53 46 0.15
54 49 0.16
55 21 0.07
57 7 0.02
58 4 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (52 bp):
CAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
Found at i:1311314 original size:27 final size:28
Alignment explanation
Indices: 1311284--1311358 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
1311274 ATTTTTCACA
1311284 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
1311311 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
1311339 CGAGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
1311359 TTCTTTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:1311560 original size:54 final size:53
Alignment explanation
Indices: 1311388--1311596 Score: 260
Period size: 52 Copynumber: 4.0 Consensus size: 53
1311378 TGATTTATCA
* * * * * **
1311388 TAATCGGGGATACTCCAACTCCGGTTTTA-TTGCTAAAGCACTAATTTTTCCA
1 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTTCTT
* * * * * *
1311440 CAATCGGGGATACTCCAACCCCGGTTTTATTTT-TAAAACACTAATTTTCCTT
1 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTTCTT
*
1311492 TAATCGGGGATACTCCAGCTCCGATTTTATTTTCAAAAACACCAATTTTTTCTT
1 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAA-TTTTTCTT
*
1311546 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC
1 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTTC
1311597 ACAATTGAGG
Statistics
Matches: 138, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
52 71 0.51
53 17 0.12
54 50 0.36
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (53 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTTCTT
Found at i:1311574 original size:106 final size:104
Alignment explanation
Indices: 1311388--1311577 Score: 263
Period size: 106 Copynumber: 1.8 Consensus size: 104
1311378 TGATTTATCA
* * * *
1311388 TAATCGGGGATACTCCAACTCCGGTTTTATTGCTAAAGCACTAATTTTTCCACAATCGGGGATAC
1 TAATCGGGGATACTCCAACTCCGATTTTATTGCAAAAACACCAATTTTTCCACAATCGGGGATAC
*
1311453 TCCAACCCCGGTTTTATTTTTAAAACACTAATTTTCCTT
66 TCCAACCCCGATTTTATTTTTAAAACACTAATTTTCCTT
* * ***
1311492 TAATCGGGGATACTCCAGCTCCGATTTTATTTTCAAAAACACCAATTTTTTCTTTAATCGGGGAT
1 TAATCGGGGATACTCCAACTCCGATTTTA-TTGCAAAAACACCAA-TTTTTCCACAATCGGGGAT
*
1311557 ACTCCAACTCCGATTTTATTT
64 ACTCCAACCCCGATTTTATTT
1311578 CCAAAAACAC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
104 27 0.37
105 11 0.15
106 35 0.48
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (104 bp):
TAATCGGGGATACTCCAACTCCGATTTTATTGCAAAAACACCAATTTTTCCACAATCGGGGATAC
TCCAACCCCGATTTTATTTTTAAAACACTAATTTTCCTT
Found at i:1311669 original size:27 final size:27
Alignment explanation
Indices: 1311605--1311674 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
1311595 TCACAATTGA
* **
1311605 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACCTCA-CGG
1311633 GGATACTCCAACCCCGTTACCTC-CGGG
1 GGATACTCCAACCCCGTTACCTCAC-GG
1311660 GGATACTCCAACCCC
1 GGATACTCCAACCCC
1311675 AGTTTTATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 17 0.45
28 20 0.53
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (27 bp):
GGATACTCCAACCCCGTTACCTCACGG
Found at i:1311670 original size:107 final size:106
Alignment explanation
Indices: 1311551--1311751 Score: 262
Period size: 106 Copynumber: 1.9 Consensus size: 106
1311541 TTCTTTAATC
* *
1311551 GGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGATACTCCA
1 GGGGATACTCCAACCCCAG-TTTTA-TTCCAAAAACACCAATTTATCACAATTGAGGATACTCCA
*
1311615 ACCTCGTTATTTCAT-CGGGGATACTCCAACCCCGTTACCTCCG
64 ACCTCGTTATTTC-TGAGGGGATACTCCAACCCCGTTACCTCCG
* * *** * * *
1311658 GGGGATACTCCAACCCCAGTTTTATTCCCAAAATATTGATTTATCATAATTGGGGATACTCTAAC
1 GGGGATACTCCAACCCCAGTTTTATTCCAAAAACACCAATTTATCACAATTGAGGATACTCCAAC
1311723 CTCGTTATTTCTGAGGGGATACTCCAACC
66 CTCGTTATTTCTGAGGGGATACTCCAACC
1311752 TCGACTTTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
105 1 0.01
106 58 0.72
107 21 0.26
108 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (106 bp):
GGGGATACTCCAACCCCAGTTTTATTCCAAAAACACCAATTTATCACAATTGAGGATACTCCAAC
CTCGTTATTTCTGAGGGGATACTCCAACCCCGTTACCTCCG
Found at i:1311713 original size:158 final size:156
Alignment explanation
Indices: 1311228--1311718 Score: 490
Period size: 158 Copynumber: 3.1 Consensus size: 156
1311218 CTAATTTTCT
1311228 ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGGGGAT
1 ATAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTTTTCACAATCGGGGAT
* *
1311293 ACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACC
65 ACTCCAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTA-ATCCG-GGGGATACTCCAACC
* **
1311357 CCTTCTTTATTCTTAAAATATTGATTTATC
128 CCGT-TTTATTCCAAAAATATTGATTTATC
* * * * *
1311387 ATAATCGGGGATACTCCAACTCCGGTTTTA-TTGCTAAAGCACTAATTTTTCCACAATCGGGGAT
1 ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT-CACAATCGGGGAT
* ***** * * * ** * * *
1311451 ACTCCAACCCCGGT-TTT-ATTTTTAAAACACTAATTTTCCTTTAAT-C-GGGGATACTCCAGCT
65 ACTCCAACCCCGTTATTTCATCGGGGATACTCCAA--CCCCGTTAATCCGGGGGATACTCCAACC
* * *** *
1311512 CCGATTTTATTTTCAAAAACACCAATTTTTTC
128 CCG-TTTTA-TTCCAAAAATATTGA-TTTATC
* * *
1311544 TTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTGAGGAT
1 -ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGAT
* *
1311609 ACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGGGGGATACTCCAACCC
65 ACTCCAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTA-ATCCGGGGGATACTCCAACCC
*
1311674 CAGTTTTATTCCCAAAATATTGATTTATC
129 C-GTTTTATTCCAAAAATATTGATTTATC
*
1311703 ATAATTGGGGATACTC
1 ATAATCGGGGATACTC
1311719 TAACCTCGTT
Statistics
Matches: 254, Mismatches: 63, Indels: 31
0.73 0.18 0.09
Matches are distributed among these distances:
155 19 0.07
156 9 0.04
157 27 0.11
158 101 0.40
159 59 0.23
160 18 0.07
161 20 0.08
162 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (156 bp):
ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATA
CTCCAACCCCGTTATTTCATCGGGGATACTCCAACCCCGTTAATCCGGGGGATACTCCAACCCCG
TTTTATTCCAAAAATATTGATTTATC
Found at i:1311889 original size:78 final size:78
Alignment explanation
Indices: 1311628--1311909 Score: 309
Period size: 79 Copynumber: 3.6 Consensus size: 78
1311618 TCGTTATTTC
** * *
1311628 ATCGGGGATACTCCAACCCCGTTACCTCCG-GGGGATACTCCAACCCCAGTTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCGACTTTT-TTCCCAAAAT
*
1311692 ATTGATTTATCATA
65 ATTGATTTCTCATA
* * * * *
1311706 ATTGGGGATACTCTAACCTCGTTATTTCTGAGGGGATACTCCAACCTCGACTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACC-CGACTTTTTTCCCAAAAT
1311771 ATTGATTTCTCATA
65 ATTGATTTCTCATA
* * ** *
1311785 ATTGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATCCCGA-TTTTTTTTC-TAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCGACTTTTTTCCCAAAAT
* *
1311848 CATCGATTTCTCACA
65 -ATTGATTTCTCATA
* * * * *
1311863 ACCGGGGATACTCCAGCCCCGTTATTTTCAAGGGGACACTCCAACCC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCC
1311910 CGTTATTATC
Statistics
Matches: 175, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
77 6 0.03
78 79 0.45
79 83 0.47
80 7 0.04
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCGACTTTTTTCCCAAAATA
TTGATTTCTCATA
Found at i:1319641 original size:51 final size:51
Alignment explanation
Indices: 1319574--1319689 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
1319564 AAATAACGAG
* * * * * * *
1319574 GTTGGAGTATCTCCGATTGTGAGAAATTGGTGTTTTGGAACTAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAACCGGA
* *
1319625 GTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAGCCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAACCGGA
*
1319676 GTTGGAGCATCCCC
1 GTTGGAGTATCCCC
1319690 TCAAAAATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAACCGGA
Found at i:1319720 original size:79 final size:79
Alignment explanation
Indices: 1319625--1319828 Score: 291
Period size: 79 Copynumber: 2.6 Consensus size: 79
1319615 TAAAATCGGA
* * *
1319625 GTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAGCCGGGGTTGGAGCATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGCATCCCC
1319690 TCAAAAATAACGAG
66 TCAAAAATAACGAG
* * * *
1319704 GTTGGAGCATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGCATCCCC
** * *
1319769 TCGGAAATAATGGG
66 TCAAAAATAACGAG
* *
1319783 GTTGGAGTATCCCCGATTGTGAAAAACTAGTGTTTTGGAAATAAAA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAA
1319829 TCGGAGTTGG
Statistics
Matches: 109, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 109 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (79 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGCATCCCC
TCAAAAATAACGAG
Found at i:1319720 original size:130 final size:131
Alignment explanation
Indices: 1319449--1319768 Score: 364
Period size: 130 Copynumber: 2.4 Consensus size: 131
1319439 GGGCTAGAGT
* * * * * *
1319449 ATCCCCGATTATGGAAAATCGATGTTCTAAAAAATAAAATCGG-GATTAGAGTATCCCCGATTAT
1 ATCCCCGATTATGAAAAATTGGTGTT-TTAGAAATAAAATCGGAG-TTGGAGTATCCCCGATTAT
* * * * *
1319513 GAAAAAATTGATGCTTTAGAAATAAGGTCCGGGGTTGGGGTATCCTCGTGAAAATAACGAGGTTG
64 GAAAAAATTGAT-CTTTAGAAATAAAGTCCGGGGTTGGAGCATCCTCCTAAAAATAACGAGGTTG
*
1319578 GAGT
128 GAGC
* * * * * *
1319582 ATCTCCGATTGTGAGAAATTGGTGTTTTGGAACTAAAATCGGAGTTGGAGTATCCCCGATTGTG-
1 ATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTATGA
1319646 AAAAATTAGTAT-TTTAGAAATAAAG-CCGGGGTTGGAGCATCC-CCTCAAAAATAACGAGGTTG
66 AAAAATT-G-ATCTTTAGAAATAAAGTCCGGGGTTGGAGCATCCTCCT-AAAAATAACGAGGTTG
1319708 GAGC
128 GAGC
*
1319712 ATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAA-CCGAGGTTGGAGTATCCCC
1 ATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATCGGA-GTTGGAGTATCCCC
1319769 TCGGAAATAA
Statistics
Matches: 158, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
129 5 0.03
130 80 0.51
131 19 0.12
132 31 0.20
133 23 0.15
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (131 bp):
ATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTATGA
AAAAATTGATCTTTAGAAATAAAGTCCGGGGTTGGAGCATCCTCCTAAAAATAACGAGGTTGGAG
C
Found at i:1319845 original size:51 final size:51
Alignment explanation
Indices: 1319783--1320224 Score: 337
Period size: 51 Copynumber: 8.5 Consensus size: 51
1319773 AAATAATGGG
* *
1319783 GTTGGAGTATCCCCGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGA
* * * * * *
1319834 GTTGGAATATCCCCGATTGAAGGAAAATTGGTGTTTT-GAAATAAGACCGGG
1 GTTGGAGTATCCCCGATTG-TGAAAAATTAGTGTTTTGGAAATAAAACCGGA
* * * *
1319885 GTTGAAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGA
* * * * * *
1319936 GTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGCCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGA
* * ***
1319987 GTTGGAGTATCCCC--TTG-GAGGTAACGAGGTTGGAGTATCCCCGATGAAATAATAA---G-
1 GTTGGAGTATCCCCGATTGTGA---AA--A-ATT--AGTGT-TTTG--GAAATAA-AACCGGA
* * *
1320043 GTTGGAGTATCCTCGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGA
* * * * * *
1320094 GTTGGAATATCCCCGATTGAAGGAAAATTGGTGTTTTGAAAATAAGACCGG-
1 GTTGGAGTATCCCCGATTG-TGAAAAATTAGTGTTTTGGAAATAAAACCGGA
* * * *
1320145 GATTGGAGTATCCCCAATTATGGAAAATTAGTGTTTTAGAAATAAAACC-GA
1 G-TTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGA
*
1320196 GGTTGGAGTATCCCCGATTATGAAAAATT
1 -GTTGGAGTATCCCCGATTGTGAAAAATT
1320225 GAGAAACTTA
Statistics
Matches: 311, Mismatches: 55, Indels: 50
0.75 0.13 0.12
Matches are distributed among these distances:
47 2 0.01
48 9 0.03
49 2 0.01
50 18 0.06
51 189 0.61
52 53 0.17
53 2 0.01
54 2 0.01
56 19 0.06
57 2 0.01
58 3 0.01
59 9 0.03
60 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGA
Found at i:1319923 original size:260 final size:254
Alignment explanation
Indices: 1319597--1320210 Score: 712
Period size: 260 Copynumber: 2.4 Consensus size: 254
1319587 CGATTGTGAG
* * * * * *
1319597 AAATTGGTGTTTTGGAACTAAAATCGGAGTTGGAGTATCCCCGATTGTGAAAAATTAGTATTTTA
1 AAATTGGTGTTTT-GAAATAAGACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTA
* * * *
1319662 GAAATAAAGCCGGGGTTGGAGCATCCCC-TCAAAAAT-AACGAGGTTGGAGCAT-CCCCGATTAT
65 GAAATAAAACCGGGGTTGGAGTATCCCCATCAAAAATCAA-GAGGTTGGA-AATACCCCGAGT-T
**** ** **
1319724 GAAAAATTGGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGA
127 GAAAAA-T--CCCCTTAGAAAT--AA-CGAGGTTGGAGTATCCCCGAGGAAATAATAAGGTTGGA
1319789 GTATCCCCGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCCGATTGA
186 GTATCCCCGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCCGATTGA
1319854 AGGA
251 AGGA
*
1319858 AAATTGGTGTTTTGAAATAAGACCGGGGTTGAAGTATCCCCGATTGTGGAAAATTAGTGTTTTAG
1 AAATTGGTGTTTTGAAATAAGACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAG
* * ** * * *
1319923 AAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGG
66 AAATAAAACCGGGGTTGGAGTATCCCC----ATCAAAAATCAAGAGGTTGGAAAT--ACCCCGAG
* ** * ** *
1319988 TTGGAGTATCCCCTTGGAGGTAACGAGGTTGGAGTATCCCCGATGAAATAATAAGGTTGGAGTAT
125 TTGAAAAATCCCCTTAGAAATAACGAGGTTGGAGTATCCCCGAGGAAATAATAAGGTTGGAGTAT
*
1320053 CCTCGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCCGATTGAAGGA
190 CCCCGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCCGATTGAAGGA
* * *
1320118 AAATTGGTGTTTTGAAAATAAGACCGGGATTGGAGTATCCCCAATTATGGAAAATTAGTGTTTTA
1 AAATTGGTGTTTTG-AAATAAGACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTA
*
1320183 GAAATAAAACCGAGGTTGGAGTATCCCC
65 GAAATAAAACCGGGGTTGGAGTATCCCC
1320211 GATTATGAAA
Statistics
Matches: 304, Mismatches: 39, Indels: 20
0.84 0.11 0.06
Matches are distributed among these distances:
260 185 0.61
261 88 0.29
263 5 0.02
264 2 0.01
265 14 0.05
266 6 0.02
267 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (254 bp):
AAATTGGTGTTTTGAAATAAGACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAG
AAATAAAACCGGGGTTGGAGTATCCCCATCAAAAATCAAGAGGTTGGAAATACCCCGAGTTGAAA
AATCCCCTTAGAAATAACGAGGTTGGAGTATCCCCGAGGAAATAATAAGGTTGGAGTATCCCCGA
TTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGAGTTGGAATATCCCCGATTGAAGGA
Found at i:1325164 original size:13 final size:13
Alignment explanation
Indices: 1325146--1325170 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1325136 CATTTTATGG
1325146 TGTATCGATACAA
1 TGTATCGATACAA
1325159 TGTATCGATACA
1 TGTATCGATACA
1325171 TACTGTGTGT
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:1325186 original size:32 final size:33
Alignment explanation
Indices: 1325123--1325190 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1325113 CGTTACAGGC
**
1325123 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
1325156 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1325188 CAA
1 CAA
1325191 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1333341 original size:13 final size:13
Alignment explanation
Indices: 1333323--1333347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1333313 CATTTTATGG
1333323 TGTATCGATACAA
1 TGTATCGATACAA
1333336 TGTATCGATACA
1 TGTATCGATACA
1333348 TACTGTGTGT
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:1333363 original size:32 final size:33
Alignment explanation
Indices: 1333300--1333367 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1333290 CGTTACAAGC
**
1333300 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
1333333 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1333365 CAA
1 CAA
1333368 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1333463 original size:33 final size:33
Alignment explanation
Indices: 1333421--1333484 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1333411 TCTTTTTGAA
1333421 GTATCGATACAATGCAACAGGTATCGATACATT
1 GTATCGATACAATGCAACAGGTATCGATACATT
** *
1333454 GTATCGATACTGTGCAACATGTATCGATACA
1 GTATCGATACAATGCAACAGGTATCGATACA
1333485 ATTAAAAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (33 bp):
GTATCGATACAATGCAACAGGTATCGATACATT
Found at i:1341802 original size:80 final size:79
Alignment explanation
Indices: 1341568--1341814 Score: 223
Period size: 80 Copynumber: 3.1 Consensus size: 79
1341558 TCTAAGCCCA
* * * * * *
1341568 TTTTTACTACCAAAACATCGAATTTTTCATC-TCTAGGGATGCTCCAATTCCACCATCTCCG-AG
1 TTTTTACTTCCAAAACATCGAATTTTTTATCTTC-GGGGATACTCCAA-CCCACCATCTCAGAAG
* *
1341631 GGATACTT-CAACCCCA
64 GGATA-TTCCAACTCCG
* * * *
1341647 TTTTTACTTCCAAAACATCAAATTTTTTTATCTTCGAGGATACTCTAAACCCACCATCTCCAAAA
1 TTTTTACTTCCAAAACATCGAA-TTTTTTATCTTCGGGGATACTC-CAACCCACCATCT-CAGAA
* *
1341712 AGG-TACTCCAACTCCG
63 GGGATATTCCAACTCCG
* ** * *
1341728 TTTTTATTTTTAAAACACCGAATTTTTTATCTTCGGGGATACTCCAACGCCACCATCTCTGAAGG
1 TTTTTACTTCCAAAACATCGAATTTTTTATCTTCGGGGATACTCCAAC-CCACCATCTCAGAAGG
*
1341793 GATATTCCAACTTCG
65 GATATTCCAACTCCG
1341808 TTTTTAC
1 TTTTTAC
1341815 CTTAAAATTT
Statistics
Matches: 133, Mismatches: 27, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
79 28 0.21
80 72 0.54
81 30 0.23
82 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (79 bp):
TTTTTACTTCCAAAACATCGAATTTTTTATCTTCGGGGATACTCCAACCCACCATCTCAGAAGGG
ATATTCCAACTCCG
Found at i:1343881 original size:67 final size:65
Alignment explanation
Indices: 1343741--1343881 Score: 183
Period size: 67 Copynumber: 2.1 Consensus size: 65
1343731 GTAATTAATG
* * *
1343741 TGTAGATTGTTGATGGGAATCAAATTCCTTCTAATATGAAAGAAATTGATAAGAATAATGCATGA
1 TGTAAATTCTTGATAGGAATCAAATTCCTTCTAATATGAAAGAAATTGATAAGAATAATGCATGA
* * * *
1343806 TGCATAAATTCTTGATAGGAATCAGATTCTTTCTAATATGAGAGAAGTTGATAAGAATAATGCAT
1 TG--TAAATTCTTGATAGGAATCAAATTCCTTCTAATATGAAAGAAATTGATAAGAATAATGCAT
1343871 GGA
64 -GA
1343874 TTGTAAAT
1 -TGTAAAT
1343882 ATCAGACTGC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
65 2 0.03
67 59 0.91
68 2 0.03
69 2 0.03
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (65 bp):
TGTAAATTCTTGATAGGAATCAAATTCCTTCTAATATGAAAGAAATTGATAAGAATAATGCATGA
Found at i:1344013 original size:91 final size:92
Alignment explanation
Indices: 1343872--1344065 Score: 216
Period size: 91 Copynumber: 2.1 Consensus size: 92
1343862 ATAATGCATG
** * ** * *
1343872 GATTGTAAATATCAGACTGCAAGGATTAGAATAATGCATGAATTGTATTTAAGAA-TCGAATTCT
1 GATTGTAAATGCCAGACTGCAAGGATTAGAATAATGCATAAATAATATTTAAAAATTAGAATTCT
**
1343936 TTTGGTACAACA-AAAGAAAAGTTGATT
66 TTTGACACAACAGAAA-AAAAGTTGATT
*
1343963 GATTGTAAATGCCAGAC-GACAAGGATTA-AAGTAATGCATAAATAATATTTAAAAATTAGATTT
1 GATTGTAAATGCCAGACTG-CAAGGATTAGAA-TAATGCATAAATAATATTTAAAAATTAGAATT
* * *
1344026 CTTTTGACAGAATAGTAAAAAAGTTGATT
64 CTTTTGACACAACAGAAAAAAAGTTGATT
1344055 GATTGTAAATG
1 GATTGTAAATG
1344066 TTACAATTTA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
90 3 0.03
91 44 0.51
92 37 0.43
93 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (92 bp):
GATTGTAAATGCCAGACTGCAAGGATTAGAATAATGCATAAATAATATTTAAAAATTAGAATTCT
TTTGACACAACAGAAAAAAAGTTGATT
Found at i:1348854 original size:20 final size:20
Alignment explanation
Indices: 1348829--1348896 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
1348819 TATATCCTAA
1348829 AAATAAATTTAAACTTTTAT
1 AAATAAATTTAAACTTTTAT
** *
1348849 AAATAAAAATAAA-TATATTTT
1 AAATAAATTTAAACT-T-TTAT
* *
1348870 AAAAAAATTTAAACTTGTAT
1 AAATAAATTTAAACTTTTAT
*
1348890 AATTAAA
1 AAATAAA
1348897 CTAAAAAGTA
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
19 1 0.03
20 19 0.54
21 14 0.40
22 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (20 bp):
AAATAAATTTAAACTTTTAT
Found at i:1348875 original size:74 final size:71
Alignment explanation
Indices: 1348757--1350758 Score: 1759
Period size: 73 Copynumber: 27.5 Consensus size: 71
1348747 TTATTAGAAT
* * * *
1348757 ATAAATTTAAACTTCTACAAATAGAAATAAATTATAGCTTAAAAAATTTAAACTCATATAATTAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAA-TATATCCT-AAAAATTTAAACTCATATAATCAT
*
1348822 ATCCTAAAA
64 A-CCAAAAA
* * ** ** * *
1348831 ATAAATTTAAACTTTTATAAATAAAAATAAATATATTTTAAAAAAATTTAAACTTGTATAATTAA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATATCCT--AAAAATTTAAACTCATATAATCAT
*
1348896 ACTAAAAA
64 ACCAAAAA
* * * ** * * * *
1348904 GTAAATTTAAAGTTCTATAAATAAAAATAAATCATATATTAAAATTTTAAATTCGTATAATTATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAAT-ATATCCTAAAAATTTAAACTCATATAATCATA
1348969 CTCAAAAA
65 C-CAAAAA
* * *
1348977 ATCAAATTTAAACTT-TCACAAATTAAATTAAATTATATCCTAAAAATTTAAACTCGTATAATCA
1 AT-AAATTTAAACTTCT-ACAAATAAAAATAAA-TATATCCTAAAAATTTAAACTCATATAATCA
1349041 TACCCAAAAA
63 TA-CCAAAAA
* * * *
1349051 ATAAATTTAAACGTCTACAAATAAAGATAAATAGTATCTTAAAAATTTAAACTCATAAAATCATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATA-TATCCTAAAAATTTAAACTCATATAATCATA
1349116 CACAAAAA
65 C-CAAAAA
* * ** * * * * *
1349124 ATCAAATTAAAACTACTATTAATAAAGATAAATAATACCCTAAAAATTTACACTCGTATAATTA-
1 AT-AAATTTAAACTTCTACAAATAAAAATAAAT-ATATCCTAAAAATTTAAACTCATATAATCAT
*
1349188 ACCGACAAA
64 ACC-AAAAA
* *
1349197 ATAAATTTAAACTTCTACAAATAAAAATAAAT-TATACCATAAAAAATTGAAACTCATATAGTCA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATAT-CC-T-AAAAATTTAAACTCATATAATCA
1349261 TACCCAAAAA
63 TA-CCAAAAA
* * * * * * **
1349271 ACATATTTAAATTTTTATAAATAAAAATAAAT-TATACTTTAAAAATTTAAACTTGTATAATCAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATAT-C-CTAAAAATTTAAACTCATATAATCAT
1349335 ACCTAAAAA
64 ACC-AAAAA
* * * *
1349344 ATAAATTTAAACTTCTATAAATAAAAATAAATA-ATTACCTAGAAATTTAAA-TTATATAATTA-
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATA-T-CCTAAAAATTTAAACTCATATAATCAT
1349406 ACCCAAAAA
64 A-CCAAAAA
* *
1349415 ATAAATTTAAACTTCTACAAATAAAAATAAAT-TATACCTTCAAAAATTTAAACTCGTATAATTA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATAT-CC-T-AAAAATTTAAACTCATATAATCA
*
1349479 TACCCAAAA
63 TACCAAAAA
* * * * * * *
1349488 ACATATTTAAACTTCTACAAATCAAAATAAACTATACCCT-AAAATTTAAACTCACAAAATCAAA
1 ATAAATTTAAACTTCTACAAATAAAAATAAA-TATATCCTAAAAATTTAAACTCATATAATCATA
*
1349552 CAAAAAA
65 CCAAAAA
* * ** *
1349559 ACAAATTTAAACTTCTATAAATAAAAATAAATTATATAATAAAAAATATAAACTCATATAATCAT
1 ATAAATTTAAACTTCTACAAATAAAAATAAA-TATATCCT-AAAAATTTAAACTCATATAATCAT
1349624 ACTCAAAAA
64 AC-CAAAAA
* * * * * * * *
1349633 ACACAGTTGAACTTTTACAAATAAAAATAAATTATATCCTAAAAATTTAAACTCGTATAATTAAA
1 ATAAATTTAAACTTCTACAAATAAAAATAAA-TATATCCTAAAAATTTAAACTCATATAATCATA
* *
1349698 CTAGAAA
65 CCAAAAA
** * * ** * * *
1349705 GCAAATTTAAAGTTCTATAAATAAAAATAAATCATATATTAAAAATTTAAATTCGTATAATTATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAAT-ATATCCTAAAAATTTAAACTCATATAATCATA
*
1349770 TTC-AAAA
65 -CCAAAAA
* * ** *
1349777 ACAAATTTAAACTTCTACAAATAAAATTAAACTATATCCTAAAAATTTAAACTTGTATAATTATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAA-TATATCCTAAAAATTTAAACTCATATAATCATA
1349842 CCCAAAAA
65 -CCAAAAA
* * *
1349850 ATAAATTTAAACATCTACAAA-AAAAGATAAATAGTATCTTAAAAATTTAAACTCATAAAATCAT
1 ATAAATTTAAACTTCTACAAATAAAA-ATAAATA-TATCCTAAAAATTTAAACTCATATAATCAT
1349914 ACACAAAAA
64 AC-CAAAAA
* ** * * * *
1349923 ATTAAATTTAAACTACTATTAATAAAGATAAATAATATCCTAAATATTTAAACTCGTATAATTA-
1 A-TAAATTTAAACTTCTACAAATAAAAATAAAT-ATATCCTAAAAATTTAAACTCATATAATCAT
*
1349987 ACCCACAAA
64 A-CCAAAAA
* * *
1349996 ACAAATTTAAACTTCTACAAATAAAAATAAAT-TTTACCATAAAAAAATTGAAACTCATATAATC
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATAT-CC-T--AAAAATTTAAACTCATATAATC
1350060 ATACTCAAAAA
62 ATAC-CAAAAA
* * * * *
1350071 A-ACACTTTTAAACTTTTATAGATAAAAATAAATTATACCCTAAAAATTTAAACT-AGTATAATC
1 ATA-A-ATTTAAACTTCTACAAATAAAAATAAA-TATATCCTAAAAATTTAAACTCA-TATAATC
1350134 ATACCCAAAAA
62 ATA-CCAAAAA
*
1350145 ATAAATTTAAACTTCTACAAATAAAAATAAATA-ATTACCTAGAAATTTAAACTCATATAATCA-
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATA-T-CCTAAAAATTTAAACTCATATAATCAT
1350208 ACCCAAAAA
64 A-CCAAAAA
* *
1350217 ATAAATTTAAATTTCTACAAATAAAAATAAATA-ATTACCTAGAAATTTAAACTCATATAATCA-
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATA-T-CCTAAAAATTTAAACTCATATAATCAT
*
1350280 ACCCAAAA
64 ACCAAAAA
* * * *
1350288 A-AAATTTAAACTTCTACAAATAAAAATAAAT-TATACTTTCAAAATTTTAAACCCATATAATTA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATAT-C-CT-AAAAATTTAAACTCATATAATCA
1350351 TACCTAAAAA
63 TACC-AAAAA
* * * * * * *
1350361 ACACATTTAAACTTCTACAAATCAAAATAAATTATACCCT-AAAATTTAAACTTACATAATCAAA
1 ATAAATTTAAACTTCTACAAATAAAAATAAA-TATATCCTAAAAATTTAAACTCATATAATCATA
*
1350425 CAAAAAA
65 CCAAAAA
* * *
1350432 ATGAATTTAAACTTCTACAAATAAAAATAAAT-TATACCATAAAAAATTTAAACCCATACAATCA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATAT-CC-T-AAAAATTTAAACTCATATAATCA
1350496 TACCCAAAAA
63 TA-CCAAAAA
* * * *
1350506 A-ACACATTTGAACTTTTATAAATAAAAATAAATTATATCCTAAAAATTTAAACTCGTATAATCA
1 ATA-A-ATTTAAACTTCTACAAATAAAAATAAA-TATATCCTAAAAATTTAAACTCATATAATCA
*
1350570 TACCTGAAAA
63 TACC-AAAAA
* * * * * * *
1350580 ACAAATTCAAACGTCTACAAATAAAGATAAATAATATCCTAAAAATTCAAACTCGTATAATCAAA
1 ATAAATTTAAACTTCTACAAATAAAAATAAAT-ATATCCTAAAAATTTAAACTCATATAATCATA
* *
1350645 GCAACAA
65 CCAAAAA
* * * *
1350652 ACAAATTTAAATTTCTACAAATAAAAATAAAT-TATACCTTCAAAAATTTAAACTCGTATAATTA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATATAT-CC-T-AAAAATTTAAACTCATATAATCA
* *
1350716 TACCCTACAA
63 TA-CCAAAAA
1350726 ATAAATTTAAACTTCTACAAATAAAAATAAATA
1 ATAAATTTAAACTTCTACAAATAAAAATAAATA
1350759 ATACCTTTAA
Statistics
Matches: 1596, Mismatches: 247, Indels: 169
0.79 0.12 0.08
Matches are distributed among these distances:
69 5 0.00
70 45 0.03
71 163 0.10
72 353 0.22
73 500 0.31
74 445 0.28
75 49 0.03
76 29 0.02
77 6 0.00
78 1 0.00
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (71 bp):
ATAAATTTAAACTTCTACAAATAAAAATAAATATATCCTAAAAATTTAAACTCATATAATCATAC
CAAAAA
Found at i:1349600 original size:22 final size:22
Alignment explanation
Indices: 1349575--1349620 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1349565 TTAAACTTCT
*
1349575 ATAAATAAAAATAAA-TTATATA
1 ATAAA-AAAAATAAACTCATATA
*
1349597 ATAAAAAATATAAACTCATATA
1 ATAAAAAAAATAAACTCATATA
1349619 AT
1 AT
1349621 CATACTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAAAAAAATAAACTCATATA
Found at i:1351183 original size:66 final size:63
Alignment explanation
Indices: 1351112--1351247 Score: 191
Period size: 66 Copynumber: 2.1 Consensus size: 63
1351102 AAGTTATTTG
* * *
1351112 TTTTATTAAAAAATTAATAATTAATATTTTAATTTTTCAATATAAATTATTTCAAATTTAGTTAA
1 TTTTATTAAAAAATTAATAATTAATATATTAA--TTTCAACATAAATT-TTTCAAATTTAATTAA
1351177 A
63 A
* * *
1351178 TTTTATTAAAAAATTAATAATTAATATATTGATTTCAACATGAATTTTTTAAATTTAATTAAA
1 TTTTATTAAAAAATTAATAATTAATATATTAATTTCAACATAAATTTTTCAAATTTAATTAAA
1351241 TTTTATT
1 TTTTATT
1351248 TTTTTTAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 22 0.34
64 12 0.19
66 30 0.47
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (63 bp):
TTTTATTAAAAAATTAATAATTAATATATTAATTTCAACATAAATTTTTCAAATTTAATTAAA
Found at i:1352235 original size:5 final size:5
Alignment explanation
Indices: 1352227--1352264 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
1352217 GCATATATTA
1352227 TATAT TATAT TATAT TATA- T-TAT TACTAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATA
1352265 AAGATATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 2 0.07
4 2 0.07
5 21 0.70
6 5 0.17
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:1352241 original size:19 final size:20
Alignment explanation
Indices: 1352219--1352264 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1352209 TGAAATTGGC
1352219 ATATATTATA-TATTA-TAT
1 ATATATTATATTATTACTAT
1352237 -TATATTATATTATTACTAT
1 ATATATTATATTATTACTAT
1352256 -TATATTATA
1 ATATATTATA
1352265 AAGATATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.35
18 5 0.19
19 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTATATTATTACTAT
Found at i:1352256 original size:24 final size:22
Alignment explanation
Indices: 1352220--1352264 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
1352210 GAAATTGGCA
1352220 TATATTATATATTATATTATAT
1 TATATTATATATTATATTATAT
1352242 TATATTATTACTATTATATTATA
1 TATATTA-TA-TATTATATTATA
1352265 AAGATATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.33
23 2 0.10
24 12 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATTATATATTATATTATAT
Found at i:1353901 original size:60 final size:60
Alignment explanation
Indices: 1353808--1353925 Score: 209
Period size: 60 Copynumber: 2.0 Consensus size: 60
1353798 CACTATGACC
*
1353808 ACCTATTTTCTGGCCGAAAATTGTTTGAACACATCCTGATAGAATTAATACTCTTCCCCG
1 ACCTATTTTCTGGCCGAAAATTGTTTGAACACATCCTAATAGAATTAATACTCTTCCCCG
* *
1353868 ACCTATTTTCTGGCTGGAAATTGTTTGAACACATCCTAATAGAATTAATACTCTTCCC
1 ACCTATTTTCTGGCCGAAAATTGTTTGAACACATCCTAATAGAATTAATACTCTTCCC
1353926 TGACGTTTAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (60 bp):
ACCTATTTTCTGGCCGAAAATTGTTTGAACACATCCTAATAGAATTAATACTCTTCCCCG
Found at i:1357004 original size:3 final size:3
Alignment explanation
Indices: 1356996--1357029 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1356986 TAATTGCAGG
1356996 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1357030 AAAAGGCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1358500 original size:18 final size:18
Alignment explanation
Indices: 1358477--1358513 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1358467 ATTAAATATT
*
1358477 TAATAAATTGATTTTATA
1 TAATAAATTAATTTTATA
1358495 TAATAAATTAATTTTATA
1 TAATAAATTAATTTTATA
1358513 T
1 T
1358514 CTTTTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TAATAAATTAATTTTATA
Found at i:1358696 original size:16 final size:17
Alignment explanation
Indices: 1358653--1358696 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1358643 CTAATATAGA
1358653 TCAAATCCAAAAAAATC
1 TCAAATCCAAAAAAATC
* *
1358670 TCAAA-CTAAAATAATC
1 TCAAATCCAAAAAAATC
1358686 -CAAATCCAAAA
1 TCAAATCCAAAA
1358697 CAATTTGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 14 0.61
17 5 0.22
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.18
Consensus pattern (17 bp):
TCAAATCCAAAAAAATC
Found at i:1362897 original size:2 final size:2
Alignment explanation
Indices: 1362890--1362928 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1362880 ATTGGTGTTG
1362890 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1362929 GTGTGTGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1363844 original size:34 final size:33
Alignment explanation
Indices: 1363796--1364016 Score: 266
Period size: 34 Copynumber: 6.5 Consensus size: 33
1363786 TGGTAAAAAC
*
1363796 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1363829 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1363863 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1363897 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1363931 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
1363965 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1363999 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1364017 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.14
34 133 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1363912 original size:68 final size:67
Alignment explanation
Indices: 1363798--1364016 Score: 296
Period size: 68 Copynumber: 3.2 Consensus size: 67
1363788 GTAAAAACCA
* * *
1363798 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
1363863 CAC
65 CAC
* * * *
1363866 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
1363931 CTC
65 CAC
* * * *
1363934 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1363999 CA-
65 CAC
1364001 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1364017 TCTCCCACTT
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 17 0.13
68 114 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:1363940 original size:102 final size:101
Alignment explanation
Indices: 1363796--1364016 Score: 352
Period size: 102 Copynumber: 2.2 Consensus size: 101
1363786 TGGTAAAAAC
* *
1363796 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
1363861 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
1363897 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
1363962 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1363999 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1364017 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1368468 original size:34 final size:33
Alignment explanation
Indices: 1368420--1368638 Score: 244
Period size: 34 Copynumber: 6.5 Consensus size: 33
1368410 TGGTAAAAAC
*
1368420 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1368453 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1368487 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1368521 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1368555 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
1368589 CACTCATTTAATCAACAATGGTAAACTATCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
*
1368623 CAACATTTAATCAACA
1 CACCATTTAATCAACA
1368639 CTCTTTACCA
Statistics
Matches: 158, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 21 0.13
34 131 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1368507 original size:68 final size:69
Alignment explanation
Indices: 1368422--1368638 Score: 291
Period size: 68 Copynumber: 3.2 Consensus size: 69
1368412 GTAAAAACCA
* *
1368422 CCATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGTAAGCCACCAAA
1 CCATTTAATCAACAATGGCAACCTACCAAATCTACTCATTTAATCAACAATGGTAAGCTACCAAA
1368486 TCAC
66 TCAC
* * * *
1368490 CCATTTAATCAATAATGGTAAGCTACCAAAT-TTCTCATTTAATCAACAATGGTAAGCTACCAAA
1 CCATTTAATCAACAATGGCAACCTACCAAATCTACTCATTTAATCAACAATGGTAAGCTACCAAA
*
1368554 TCTC
66 TCAC
* * *
1368558 CCATTTAGTCAACAATGGCAAACC-ACCAAATC-ACTCATTTAATCAACAATGGTAAACTATCAA
1 CCATTTAATCAACAATGGC-AACCTACCAAATCTACTCATTTAATCAACAATGGTAAGCTACCAA
1368621 ATCA-
65 ATCAC
*
1368625 ACATTTAATCAACA
1 CCATTTAATCAACA
1368639 CTCTTTACCA
Statistics
Matches: 129, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
67 14 0.11
68 112 0.87
69 3 0.02
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (69 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTACTCATTTAATCAACAATGGTAAGCTACCAAA
TCAC
Found at i:1368564 original size:102 final size:101
Alignment explanation
Indices: 1368423--1368638 Score: 317
Period size: 102 Copynumber: 2.1 Consensus size: 101
1368413 TAAAAACCAC
* *
1368423 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATC
* * *
1368488 ACCCATTTAATCAATAATGGTAAGCTACCAAATTTC-T
66 ACCCATTTAATCAACAATGGTAAACTACCAAA--TCAA
* * *
1368525 CATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATC
* *
1368590 ACTCATTTAATCAACAATGGTAAACTATCAAATCAA
66 ACCCATTTAATCAACAATGGTAAACTACCAAATCAA
1368626 CATTTAATCAACA
1 CATTTAATCAACA
1368639 CTCTTTACCA
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
100 2 0.02
101 13 0.13
102 88 0.85
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (101 bp):
CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATC
ACCCATTTAATCAACAATGGTAAACTACCAAATCAA
Found at i:1378040 original size:18 final size:19
Alignment explanation
Indices: 1377996--1378033 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1377986 ATCAATTACT
1377996 TTAAAT-AAAATTTTAATA
1 TTAAATAAAAATTTTAATA
1378014 TTAAAATAAAAATATTTAAT
1 TT-AAATAAAAAT-TTTAAT
1378034 TAAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 4 0.24
20 5 0.29
21 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAATAAAAATTTTAATA
Found at i:1379756 original size:32 final size:34
Alignment explanation
Indices: 1379720--1379808 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 34
1379710 TATAGATTCG
1379720 TATTTTTATTATTTTTTATAT-TTAA-AATATTA-
1 TATTTTTATTATTTTTTATATATTAATAAT-TTAT
1379752 TATTTTTA-TATTTTTTATATATTAATAATTTAT
1 TATTTTTATTATTTTTTATATATTAATAATTTAT
*
1379785 TTTATTTTATATATTTTTT-TATAT
1 TAT-TTTTAT-TATTTTTTATATAT
1379809 GTGCGTCTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
31 12 0.24
32 15 0.30
33 5 0.10
34 5 0.10
35 5 0.10
36 8 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (34 bp):
TATTTTTATTATTTTTTATATATTAATAATTTAT
Found at i:1379758 original size:24 final size:25
Alignment explanation
Indices: 1379731--1379793 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 25
1379721 ATTTTTATTA
1379731 TTTTTTATATTTAAAATATT-AT-AT
1 TTTTTTAT-TTTAAAATATTAATAAT
* * *
1379755 TTTTATATTTTTTATATATTAATAAT
1 TTTTTTA-TTTTAAAATATTAATAAT
1379781 TTATTTTATTTTA
1 TT-TTTTATTTTA
1379794 TATATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
24 15 0.50
25 3 0.10
26 8 0.27
27 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTTTATTTTAAAATATTAATAAT
Found at i:1379802 original size:35 final size:31
Alignment explanation
Indices: 1379723--1379808 Score: 86
Period size: 35 Copynumber: 2.6 Consensus size: 31
1379713 AGATTCGTAT
1379723 TTTTAT-TATTTTTTATATTTAAAATATTATA
1 TTTTATATATTTTTTATA-TTAAAATATTATA
*
1379754 TTTT-TATATTTTTTATATATTAATAATTTATTTTA
1 TTTTATATA-TTTTT-TATATTAA-AA--TATTATA
1379789 TTTTATATATTTTTTTATAT
1 TTTTATATA-TTTTTTATAT
1379809 GTGCGTCTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
30 1 0.02
31 6 0.13
32 9 0.19
33 6 0.13
35 15 0.32
36 10 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (31 bp):
TTTTATATATTTTTTATATTAAAATATTATA
Found at i:1380162 original size:8 final size:8
Alignment explanation
Indices: 1380134--1380189 Score: 60
Period size: 8 Copynumber: 6.8 Consensus size: 8
1380124 CAAAGCTGAA
1380134 AAAAAAAG
1 AAAAAAAG
1380142 AAAGAAAGGAG
1 AAA-AAA--AG
1380153 AAAAAAAG
1 AAAAAAAG
*
1380161 -AAAAATG
1 AAAAAAAG
*
1380168 AAAGAAAG
1 AAAAAAAG
1380176 AAAAAAAG
1 AAAAAAAG
1380184 AAAAAA
1 AAAAAA
1380190 GTTTATGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 6 0.15
8 23 0.57
9 3 0.08
10 3 0.08
11 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1380177 original size:23 final size:21
Alignment explanation
Indices: 1380131--1380188 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
1380121 GGGCAAAGCT
*
1380131 GAAAAAAA-AAGAAAGAAAGGA
1 GAAAAAAAGAA-AAAGAAAGAA
1380152 GAAAAAAAGAAAAATGAAAGAAA
1 GAAAAAAAGAAAAA-GAAAG-AA
1380175 GAAAAAAAGAAAAA
1 GAAAAAAAGAAAAA
1380189 AGTTTATGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 11 0.33
22 7 0.21
23 15 0.45
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (21 bp):
GAAAAAAAGAAAAAGAAAGAA
Found at i:1380843 original size:21 final size:21
Alignment explanation
Indices: 1380810--1380850 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1380800 CTAAGTAAAA
1380810 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1380831 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1380851 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1381014 original size:53 final size:53
Alignment explanation
Indices: 1380933--1381067 Score: 216
Period size: 53 Copynumber: 2.5 Consensus size: 53
1380923 ATTGCATAGT
*
1380933 ATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTGC
1 ATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAAATTGC
* *
1380987 ATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAAATTGT
1 ATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATTGC
* *
1381040 ATCGATATACAAAATATGTATCGATACA
1 ATCGATACACACAATATGTATCGATACA
1381068 TTGGTAGTAG
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 64 0.84
54 12 0.16
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (53 bp):
ATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAAATTGC
Found at i:1381110 original size:10 final size:10
Alignment explanation
Indices: 1381091--1381121 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1381081 AATCTCATTT
1381091 TCACTGTTCA
1 TCACTGTTCA
*
1381101 TCACTATTCA
1 TCACTGTTCA
1381111 TCACTGTTCA
1 TCACTGTTCA
1381121 T
1 T
1381122 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:1381143 original size:21 final size:22
Alignment explanation
Indices: 1381109--1381162 Score: 101
Period size: 21 Copynumber: 2.5 Consensus size: 22
1381099 CATCACTATT
1381109 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
1381131 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
1381152 CATCACTGTTC
1 CATCACTGTTC
1381163 GTAGGTCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:1382643 original size:27 final size:29
Alignment explanation
Indices: 1382613--1382672 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
1382603 AATTTAATTT
*
1382613 TAAATTTATTTATTA-AATATT-TTTAAA
1 TAAATTTATTAATTATAATATTATTTAAA
* *
1382640 TAAATTTATTAATTATAATTTTATTTAAT
1 TAAATTTATTAATTATAATATTATTTAAA
1382669 TAAA
1 TAAA
1382673 AATTTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 14 0.50
28 5 0.18
29 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
TAAATTTATTAATTATAATATTATTTAAA
Found at i:1382895 original size:8 final size:9
Alignment explanation
Indices: 1382882--1382942 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
1382872 ATATAAAATA
1382882 TTATAT-TT
1 TTATATATT
1382890 TTATATATT
1 TTATATATT
* *
1382899 TTTTATATA
1 TTATATATT
*
1382908 TTA-ATAAT
1 TTATATATT
*
1382916 TTATTTATT
1 TTATATATT
1382925 TTATATATAT
1 TTATATAT-T
*
1382935 TTTTATAT
1 TTATATAT
1382943 GTACGTATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 12 0.29
9 21 0.51
10 8 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATATATT
Found at i:1382903 original size:11 final size:11
Alignment explanation
Indices: 1382883--1382942 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
1382873 TATAAAATAT
1382883 TATA-TTTTTA
1 TATATTTTTTA
1382893 TATATTTTTTA
1 TATATTTTTTA
1382904 TATATTAATAATTTA
1 TATATT--T--TTTA
* *
1382919 TTTATTTTATA
1 TATATTTTTTA
1382930 TATA-TTTTTA
1 TATATTTTTTA
1382940 TAT
1 TAT
1382943 GTACGTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 12 0.29
11 18 0.44
13 2 0.05
15 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTTTTA
Found at i:1383099 original size:24 final size:23
Alignment explanation
Indices: 1383065--1383110 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1383055 TTTTTACACG
*
1383065 TTAATTATTTATTTATCTATATT
1 TTAATTATTTATGTATCTATATT
*
1383088 TTAATATATTTATGTATTTATAT
1 TTAAT-TATTTATGTATCTATAT
1383111 CGTATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
TTAATTATTTATGTATCTATATT
Found at i:1389555 original size:16 final size:17
Alignment explanation
Indices: 1389524--1389565 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
1389514 GATTATAAAA
1389524 TAATTATTTATTATTATT
1 TAATT-TTTATTATTATT
1389542 TAATTTTT-TTATTATT
1 TAATTTTTATTATTATT
1389558 T-ATTTTTA
1 TAATTTTTA
1389566 ATTTAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.26
16 9 0.39
17 3 0.13
18 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TAATTTTTATTATTATT
Found at i:1389677 original size:21 final size:21
Alignment explanation
Indices: 1389653--1389692 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1389643 TAATATAAAT
1389653 TAAAAAATATATAAAAATACA
1 TAAAAAATATATAAAAATACA
* * *
1389674 TAAAATATTTTTAAAAATA
1 TAAAAAATATATAAAAATA
1389693 AAATAATAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATATATAAAAATACA
Found at i:1389700 original size:20 final size:21
Alignment explanation
Indices: 1389664--1389707 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1389654 AAAAAATATA
*
1389664 TAAAAATACATAAAATATTTT
1 TAAAAATACATAAAATAATTT
1389685 TAAAAATA-A-AATAATAATTT
1 TAAAAATACATAA-AATAATTT
1389705 TAA
1 TAA
1389708 TAGGTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 11 0.52
21 8 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAATACATAAAATAATTT
Found at i:1390125 original size:2 final size:2
Alignment explanation
Indices: 1390118--1390160 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
1390108 GCTAATGAGT
1390118 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA 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
1390161 ACAACTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1392089 original size:313 final size:315
Alignment explanation
Indices: 1391518--1392258 Score: 822
Period size: 313 Copynumber: 2.3 Consensus size: 315
1391508 CTAGCCAAAC
* * * ** * *
1391518 TGCAAAAGATGTTCCTTCACTCGCTTCCAGCACGTTAA-CTAAAAACAATGGAA-CAGAAGAATT
1 TGCAAAAGGTGTTACTTCACTCCCTTCCAGCAC-ACAATCT-AAAACAAT-AAAGAAGAAGAATT
* * * ** ** *
1391581 AAATAA-ATTCCAAAATTCTACTATATCATCTAAACA-CTTAACTTGGTCCGGATTCTCAAATAA
63 AAATAATA-TCCAAAATCCTACTACATCATCTAAACATC-TAATTTTATCTAGACTCTCAAATAA
* * * * *
1391644 TTAAATTTTTTTTTTAATTTTTTGATCACCAAAGGATATCTCGTTGCTCTAATTTTCGTAACGGA
126 TTAAATTTTTTTATT-ATTTTTTGATCACCAAAAGATATCTCGTTGATCTAATTCTCATAACGGA
*
1391709 TATTTTGAAAGGATGACGAAAGAATAAAATTGAAGAAACTTAATTAATGATGGGATGAAATTGAA
190 TATTTTGAAAGGATGACGAAAGAATAAAATTGAAGAAACTTAATTAATGATGGGATGAAACTGAA
* *
1391774 AATTGGTTGTAGGAAAATTAGTGAAATGACTAAATT-AAAAAAAAATGG-AAGTATGAGAA
255 AATTGATTGTAGGAAAATTAGTGAAATGACTAAATTAAAAAAAAAATGGAAAGTAAGAGAA
* * * *
1391833 TGCAAAAGGTGTT-CATTCACTTCCTTCCGGGACACAATCTAAAACAATAAAGAATAAGAATTAA
1 TGCAAAAGGTGTTAC-TTCACTCCCTTCCAGCACACAATCTAAAACAATAAAGAAGAAGAATTAA
* * *
1391897 ATAGATGTCCAAAATCCTACTACATCATTTAAATATCTAATTTTATCTAGACTCTCAAATAATT-
65 ATA-ATATCCAAAATCCTACTACATCATCTAAACATCTAATTTTATCTAGACTCTCAAATAATTA
* * * * **
1391961 AATTTTCTTTATT-TTTTTTG-TCACGAAAAGATATTTCTTTTATCTAATTCTCATATTGGATAT
129 AATTTT-TTTATTATTTTTTGATCACCAAAAGATATCTCGTTGATCTAATTCTCATAACGGATA-
* ** *
1392024 TTTTGGAAGGATGGTGAAAGGATAAAATTGAAGAAA-TTAAATTAAT-AGTGGGATGAAACTGAA
192 TTTTGAAAGGATGACGAAAGAATAAAATTGAAGAAACTT-AATTAATGA-TGGGATGAAACTGAA
* *
1392087 AATTGATTGTAGGAGAATTAGTGGAATGACTAAATTAAAAAAAAAAAATGGAAAGTAAGAGAA
255 AATTGATTGTAGGAAAATTAGTGAAATGACTAAATT--AAAAAAAAAATGGAAAGTAAGAGAA
* * * * *
1392150 TGCAAAAGGTGTTACTTCACTCCCTTCTAGCACATAATCTAAATCAATAAAGCAGAAGTATTAAA
1 TGCAAAAGGTGTTACTTCACTCCCTTCCAGCACACAATCTAAAACAATAAAGAAGAAGAATTAAA
* * *
1392215 TAATATCCAAAATCTTACTACATCATCTAGACGTCTAATTTTAT
66 TAATATCCAAAATCCTACTACATCATCTAAACATCTAATTTTAT
1392259 GGAAATAATT
Statistics
Matches: 355, Mismatches: 56, Indels: 29
0.81 0.13 0.07
Matches are distributed among these distances:
312 35 0.10
313 95 0.27
314 30 0.08
315 79 0.22
316 49 0.14
317 66 0.19
318 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (315 bp):
TGCAAAAGGTGTTACTTCACTCCCTTCCAGCACACAATCTAAAACAATAAAGAAGAAGAATTAAA
TAATATCCAAAATCCTACTACATCATCTAAACATCTAATTTTATCTAGACTCTCAAATAATTAAA
TTTTTTTATTATTTTTTGATCACCAAAAGATATCTCGTTGATCTAATTCTCATAACGGATATTTT
GAAAGGATGACGAAAGAATAAAATTGAAGAAACTTAATTAATGATGGGATGAAACTGAAAATTGA
TTGTAGGAAAATTAGTGAAATGACTAAATTAAAAAAAAAATGGAAAGTAAGAGAA
Found at i:1392371 original size:294 final size:303
Alignment explanation
Indices: 1391727--1392414 Score: 740
Period size: 294 Copynumber: 2.3 Consensus size: 303
1391717 AAGGATGACG
* * *
1391727 AAAGAATAAAATTGAAGAAACTT-AATTAATGATGGGATGAAATTGAAAATTGGTTGTAGGAAAA
1 AAAG-ATAAAATTGAAGAAA-TTAAATTAATGGTGGGATGAAATTGAAAATTGATTGTAGGAGAA
* *
1391791 TTAGTGAAATGACTAAATTAAAAAAAAATGGAAGTATGAGAATGCAAAAGGTGTTCATTCACTTC
64 TTAGTGAAATGACTAAATTAAAAAAAAATGGAAGTAAGAGAATGCAAAAGGTGTTCATTCACTCC
* * * *
1391856 CTTCCGGGACACAATCTAAAACAATAAAGAATAAGAATTAAATAGATGTCCAAAATCCTACTACA
129 CTTCCAGCACACAATCTAAAACAATAAAGAAGAAGAATTAAATAGATATCCAAAATCCTACTACA
* * * *
1391921 TCATTTAAATATCTAATTTTATCTAGACTCTCAAATAATTAATTTTCTTTATTTTTTTTGTCACG
194 TCATCTAAACATCTAATTTTA-CTAG---C-CAAATAATTAATTTTCTTTATATTTGTTGTCACG
* * * * ***
1391986 AAAAGATATTTCTTTTATCTAATTCTCATATTGGATATTTTTGGAAGGATGGTGA
254 AAAAGATATATC---T-TCTAATTCTCAGATTAGATATTTTTGGAA-GAAGACAA
* * *
1392041 AAGGATAAAATTGAAGAAATTAAATTAATAGTGGGATGAAACTGAAAATTGATTGTAGGAGAATT
1 AAAGATAAAATTGAAGAAATTAAATTAATGGTGGGATGAAATTGAAAATTGATTGTAGGAGAATT
*
1392106 AGTGGAATGACTAAATTAAAAAAAAAAAATGGAAAGTAAGAGAATGCAAAAGGTGTT-ACTTCAC
66 AGTGAAATGACTAAATT---AAAAAAAAATGG-AAGTAAGAGAATGCAAAAGGTGTTCA-TTCAC
* * * * * *
1392170 TCCCTTCTAGCACATAATCTAAATCAATAAAGCAGAAGTATTAAATA-ATATCCAAAATCTTACT
126 TCCCTTCCAGCACACAATCTAAAACAATAAAGAAGAAGAATTAAATAGATATCCAAAATCCTACT
* * * **
1392234 ACATCATCTAGACGTCTAATTTTA-T-G-GAAATAATTAA-TTT-TTTA-ATTTGTT-TCA-TTA
191 ACATCATCTAAACATCTAATTTTACTAGCCAAATAATTAATTTTCTTTATATTTGTTGTCACGAA
* *
1392291 AA-ATATATC-TCTAATTCTCGGATTAGATATTTTT-TAA-AAGACAA
256 AAGATATATCTTCTAATTCTCAGATTAGATATTTTTGGAAGAAGACAA
* ** *
1392335 AAAGATAAAATTAAAGAAATTAAATTAATGGTGGGATGAAATTGAAAATCAATTATAGGAGAATT
1 AAAGATAAAATTGAAGAAATTAAATTAATGGTGGGATGAAATTGAAAATTGATTGTAGGAGAATT
*
1392400 AGTGCAATGACTAAA
66 AGTGAAATGACTAAA
1392415 CATGAGGCAC
Statistics
Matches: 323, Mismatches: 45, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
294 75 0.23
296 2 0.01
297 22 0.07
302 6 0.02
303 3 0.01
304 3 0.01
305 5 0.02
306 4 0.01
307 3 0.01
308 10 0.03
312 2 0.01
313 70 0.22
314 4 0.01
316 48 0.15
317 66 0.20
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (303 bp):
AAAGATAAAATTGAAGAAATTAAATTAATGGTGGGATGAAATTGAAAATTGATTGTAGGAGAATT
AGTGAAATGACTAAATTAAAAAAAAATGGAAGTAAGAGAATGCAAAAGGTGTTCATTCACTCCCT
TCCAGCACACAATCTAAAACAATAAAGAAGAAGAATTAAATAGATATCCAAAATCCTACTACATC
ATCTAAACATCTAATTTTACTAGCCAAATAATTAATTTTCTTTATATTTGTTGTCACGAAAAGAT
ATATCTTCTAATTCTCAGATTAGATATTTTTGGAAGAAGACAA
Found at i:1392569 original size:2 final size:2
Alignment explanation
Indices: 1392562--1392592 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1392552 ATTTTCTTTC
1392562 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1392593 TAGGATCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1394580 original size:38 final size:38
Alignment explanation
Indices: 1394529--1394607 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
1394519 CCAAAGAGAA
1394529 AAAGTCGACAAATATCACCAAAAATGAGTTTACTATTC
1 AAAGTCGACAAATATCACCAAAAATGAGTTTACTATTC
*
1394567 AAAGTTGACAAATATCACCAAAAATGAGTTTACTATTC
1 AAAGTCGACAAATATCACCAAAAATGAGTTTACTATTC
1394605 AAA
1 AAA
1394608 CAATAGATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (38 bp):
AAAGTCGACAAATATCACCAAAAATGAGTTTACTATTC
Found at i:1395727 original size:32 final size:32
Alignment explanation
Indices: 1395688--1395775 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
1395678 AATGATATTG
*
1395688 CTCATAAATTTGATGAATATTAAACATAATTA
1 CTCATAAATTTGATAAATATTAAACATAATTA
* * *
1395720 TTTATAAATTTGATAAATATTAAGCATAATTA
1 CTCATAAATTTGATAAATATTAAACATAATTA
* *
1395752 CTCATAAATTTGACAATTATTAAA
1 CTCATAAATTTGATAAATATTAAA
1395776 AATTTTAGCT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (32 bp):
CTCATAAATTTGATAAATATTAAACATAATTA
Found at i:1395904 original size:17 final size:19
Alignment explanation
Indices: 1395882--1395922 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1395872 TAATTTAATT
1395882 TATTT-TATAT-TTAAAAA
1 TATTTATATATATTAAAAA
1395899 TATTTTATATATATTAAAAA
1 TA-TTTATATATATTAAAAA
1395919 TATT
1 TATT
1395923 CAAATTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 2 0.10
18 3 0.14
19 7 0.33
20 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTATATATATTAAAAA
Found at i:1397534 original size:170 final size:172
Alignment explanation
Indices: 1397211--1397554 Score: 541
Period size: 170 Copynumber: 2.0 Consensus size: 172
1397201 AACCTCAAAA
1397211 TATATATAAATTTATATATTAACAATAAATTATAGTATACCATCTATTAAAATATATTTATTTAT
1 TATATATAAATTTATATATTAACAATAAATTATAGTATACCATCTATTAAAATATATTTATTTAT
1397276 TTATTAATAAAATATCATAATATAATTATAAACATATATATTGACATTACATCAAATATAAACTA
66 TTATTAATAAAATATCATAATATAATTATAAACA-ATATATTGACATTACATCAAATATAAACTA
* *
1397341 TAATTTAATTATTGTTAAACCTAGCTAGTAGGTGATACTAATT
130 TAATTTAATTATTGTCAAACCTAGCTAGTAGGTGACACTAATT
* * * *
1397384 TATATATAAATTTATATATTGATAATAAATTATATTATATCATCTATT-AAATAT-TTCTATTTA
1 TATATATAAATTTATATATTAACAATAAATTATAGTATACCATCTATTAAAATATATT-TATTTA
* * **
1397447 TTTATTAATAAAATATTATAATATAATTATAAAC-ATATATTGATATTACATTTAATATAAACTA
65 TTTATTAATAAAATATCATAATATAATTATAAACAATATATTGACATTACATCAAATATAAACTA
* *
1397511 TAATTTAATTGTTGTCAAACCTAGCTAGTAGGTGGCACTAATT
130 TAATTTAATTATTGTCAAACCTAGCTAGTAGGTGACACTAATT
1397554 T
1 T
1397555 CTTGGGAAGC
Statistics
Matches: 158, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
170 67 0.42
171 2 0.01
172 45 0.28
173 44 0.28
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (172 bp):
TATATATAAATTTATATATTAACAATAAATTATAGTATACCATCTATTAAAATATATTTATTTAT
TTATTAATAAAATATCATAATATAATTATAAACAATATATTGACATTACATCAAATATAAACTAT
AATTTAATTATTGTCAAACCTAGCTAGTAGGTGACACTAATT
Found at i:1397614 original size:2 final size:2
Alignment explanation
Indices: 1397607--1397643 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1397597 ATTTTCATTT
1397607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1397644 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1398456 original size:16 final size:16
Alignment explanation
Indices: 1398435--1398466 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1398425 AGTGCCTTAT
1398435 TATGTAATTAAATGAC
1 TATGTAATTAAATGAC
*
1398451 TATGTAATTCAATGAC
1 TATGTAATTAAATGAC
1398467 AACCCAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (16 bp):
TATGTAATTAAATGAC
Found at i:1398565 original size:21 final size:20
Alignment explanation
Indices: 1398526--1398583 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
1398516 CAAAATTTAT
**
1398526 TTTTTTATTTATATTTAAATAA
1 TTTTTTATTT-TAAATAAA-AA
1398548 TTTTTTATTTTAAATAAAAA
1 TTTTTTATTTTAAATAAAAA
* *
1398568 TTAATTTATATTAAAT
1 TT-TTTTATTTTAAAT
1398584 TAATTTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 4 0.13
21 17 0.55
22 10 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTATTTTAAATAAAAA
Found at i:1400217 original size:2 final size:2
Alignment explanation
Indices: 1400212--1400241 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1400202 TATCAAAATT
1400212 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
1400242 ATGTTCTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1400425 original size:18 final size:19
Alignment explanation
Indices: 1400399--1400456 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
1400389 AATTTAAAAT
*
1400399 ATTTTATATTTATATA-AA
1 ATTTGATATTTATATATAA
1400417 ATTTGATATTTTTATTATATAA
1 ATTTGATA--TTTA-TATATAA
*
1400439 ATTTTGATATTTTTATAT
1 A-TTTGATATTTATATAT
1400457 GTTTGTGCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 7 0.21
20 9 0.27
21 7 0.21
22 3 0.09
23 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
ATTTGATATTTATATATAA
Found at i:1400451 original size:22 final size:23
Alignment explanation
Indices: 1400397--1400454 Score: 89
Period size: 23 Copynumber: 2.4 Consensus size: 23
1400387 TAAATTTAAA
1400397 ATATTTTATATTTATATAAAATTTG
1 ATATTTT-TA-TTATATAAAATTTG
*
1400422 ATATTTTTATTATATAAATTTTG
1 ATATTTTTATTATATAAAATTTG
1400445 ATATTTTTAT
1 ATATTTTTAT
1400455 ATGTTTGTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 23 0.72
24 2 0.06
25 7 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (23 bp):
ATATTTTTATTATATAAAATTTG
Found at i:1400952 original size:23 final size:26
Alignment explanation
Indices: 1400910--1400963 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 26
1400900 ATATTTATAT
1400910 ATTTTTATAATTAAAAAATAA-TAAA
1 ATTTTTATAATTAAAAAATAATTAAA
* *
1400935 ATTTTT-T-ATTAAATAATAATTTAA
1 ATTTTTATAATTAAAAAATAATTAAA
1400959 ATTTT
1 ATTTT
1400964 ACTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
24 9 0.35
25 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTTTATAATTAAAAAATAATTAAA
Found at i:1401174 original size:16 final size:16
Alignment explanation
Indices: 1401155--1401269 Score: 53
Period size: 16 Copynumber: 6.8 Consensus size: 16
1401145 TAATTTAATT
1401155 TTAAATTTATTTTTAA
1 TTAAATTTATTTTTAA
*
1401171 TTAAATTAATATTTT-A
1 TTAAATTTAT-TTTTAA
*
1401187 TT-AATTTATAATATTAA
1 TTAAATTTAT--TTTTAA
*
1401204 TTTAA-TTATATTTTAA
1 TTAAATTTAT-TTTTAA
1401220 -TAATATTAATAATTTTTAAA
1 TTAA-ATT--T-ATTTTT-AA
1401240 TTAAAATTTTATTATTTAA
1 TT-AAA-TTTATT-TTTAA
1401259 --AAATTTATTTT
1 TTAAATTTATTTT
1401270 ATTTTAATTA
Statistics
Matches: 80, Mismatches: 5, Indels: 30
0.70 0.04 0.26
Matches are distributed among these distances:
14 2 0.03
15 14 0.17
16 26 0.32
17 12 0.15
18 2 0.03
19 10 0.12
20 8 0.10
21 2 0.03
22 4 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAATTTATTTTTAA
Found at i:1401236 original size:19 final size:19
Alignment explanation
Indices: 1401201--1401238 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1401191 TTTATAATAT
*
1401201 TAATTTAATTATATTTTAA
1 TAATTTAATAATATTTTAA
1401220 TAATATTAATAAT-TTTTAA
1 TAAT-TTAATAATATTTTAA
1401239 ATTAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATTTAATAATATTTTAA
Found at i:1401533 original size:2 final size:2
Alignment explanation
Indices: 1401526--1401557 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1401516 CACAAATTAA
1401526 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1401558 GTGGTTCCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1418177 original size:6 final size:6
Alignment explanation
Indices: 1418087--1418173 Score: 120
Period size: 6 Copynumber: 14.5 Consensus size: 6
1418077 AGCTATATAC
* * * * *
1418087 ATACAT ACACAT ACACAT ACACAT ACACAT ACACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
*
1418135 ATACAT ATACAT ATACAT ATACAT ATACAT ATATAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATA
1418174 TATAGAGAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 78 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.29
Consensus pattern (6 bp):
ATACAT
Found at i:1418182 original size:2 final size:2
Alignment explanation
Indices: 1418177--1418217 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1418167 ATATATATAT
1418177 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1418218 AGATCTCCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1419593 original size:2 final size:2
Alignment explanation
Indices: 1419586--1419614 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1419576 CTAGTTTTTC
1419586 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1419615 CCCCCCCCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1420396 original size:10 final size:10
Alignment explanation
Indices: 1420378--1420408 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1420368 AATAAATCTA
1420378 CAGAATAAAT
1 CAGAATAAAT
*
1420388 CATAATAAAT
1 CAGAATAAAT
1420398 CAGAATAAAT
1 CAGAATAAAT
1420408 C
1 C
1420409 TACAGCTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (10 bp):
CAGAATAAAT
Found at i:1421362 original size:59 final size:59
Alignment explanation
Indices: 1421291--1421406 Score: 214
Period size: 59 Copynumber: 2.0 Consensus size: 59
1421281 ACCAAGCTAA
*
1421291 GTCTAGAACATACTTCCGTTGGGAAACAAAAATACCTTTCTTGGATTCTGCAGGTTCTT
1 GTCTAGAACATACTTCCGTTGGGAAACAAAAATACCTTTCTTGGATTCTGCAAGTTCTT
*
1421350 GTCTAGAACATACTTCTGTTGGGAAACAAAAATACCTTTCTTGGATTCTGCAAGTTC
1 GTCTAGAACATACTTCCGTTGGGAAACAAAAATACCTTTCTTGGATTCTGCAAGTTC
1421407 CATTCCAAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (59 bp):
GTCTAGAACATACTTCCGTTGGGAAACAAAAATACCTTTCTTGGATTCTGCAAGTTCTT
Found at i:1427363 original size:29 final size:29
Alignment explanation
Indices: 1427230--1427376 Score: 111
Period size: 31 Copynumber: 4.9 Consensus size: 29
1427220 AGTGAAGTTT
* * * *
1427230 TATTT-TCATTCATCACCTTTAAAATTTA
1 TATTTATCATCCATAACTTTTAAAAATTA
* * *
1427258 TATTTATCATCCACAATCTTTATTAATATT-
1 TATTTATCATCCATAA-CTTT-TAAAAATTA
* *
1427288 TCATTT-TCATCCCTATAAATTTTAAAAGTTA
1 T-ATTTATCAT-CC-ATAACTTTTAAAAATTA
*
1427319 CATTTTATTCATCCATAACTTTTAAAAATTA
1 TA-TTTA-TCATCCATAACTTTTAAAAATTA
1427350 TATTTATCATCCATAACTTTTCAAAAA
1 TATTTATCATCCATAACTTTT-AAAAA
1427377 ATTTTATCAT
Statistics
Matches: 92, Mismatches: 16, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
28 5 0.05
29 22 0.24
30 23 0.25
31 33 0.36
32 5 0.05
33 4 0.04
ACGTcount: A:0.36, C:0.17, G:0.01, T:0.46
Consensus pattern (29 bp):
TATTTATCATCCATAACTTTTAAAAATTA
Found at i:1427391 original size:31 final size:28
Alignment explanation
Indices: 1427324--1427394 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 28
1427314 AGTTACATTT
1427324 TATTCATCCATAACTTTTAAAAATTATA
1 TATTCATCCATAACTTTTAAAAATTATA
* *
1427352 TTTATCATCCATAACTTTTCAAAAAATTTTA
1 TAT-TCATCCATAACTTTT--AAAAATTATA
1427383 TCATTCATCCAT
1 T-ATTCATCCAT
1427395 TTTTTAGTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 2 0.06
29 15 0.42
31 18 0.50
32 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (28 bp):
TATTCATCCATAACTTTTAAAAATTATA
Found at i:1430560 original size:3 final size:3
Alignment explanation
Indices: 1430552--1430581 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1430542 TTCTCTTAAT
1430552 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1430582 CTTTTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1431158 original size:19 final size:18
Alignment explanation
Indices: 1431113--1431163 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 18
1431103 AAAAATTTTA
1431113 AATAAAAT-TAT-AATAT
1 AATAAAATATATAAATAT
1431129 AATAAAATATATAAATAT
1 AATAAAATATATAAATAT
*
1431147 AATACGAATATATAAAT
1 AATA-AAATATATAAAT
1431164 TATCAAATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 8 0.26
17 3 0.10
18 9 0.29
19 11 0.35
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AATAAAATATATAAATAT
Found at i:1431791 original size:13 final size:13
Alignment explanation
Indices: 1431779--1431817 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
1431769 AAAGTGAAAG
1431779 GAAAA-AAAAAAA
1 GAAAAGAAAAAAA
1431791 GAAAAGAAAAAAA
1 GAAAAGAAAAAAA
1431804 GAAAAGAAAGAAAA
1 GAAAAGAAA-AAAA
1431818 TTAATTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 5 0.20
13 16 0.64
14 4 0.16
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAAAAA
Found at i:1431794 original size:17 final size:17
Alignment explanation
Indices: 1431774--1431817 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
1431764 GAAGAAAAGT
1431774 GAAAGGAAAAAAA-AAAA
1 GAAA-GAAAAAAAGAAAA
1431791 GAAAAGAAAAAAAGAAAA
1 G-AAAGAAAAAAAGAAAA
1431809 GAAAGAAAA
1 GAAAGAAAA
1431818 TTAATTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAAAAGAAAA
Found at i:1435201 original size:13 final size:13
Alignment explanation
Indices: 1435183--1435239 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1435173 TGTTAGGTGT
1435183 TGTATCGATACAA
1 TGTATCGATACAA
1435196 TGTATCGATACATAA
1 TGTATCGATAC--AA
1435211 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1435228 TGTATCGATACA
1 TGTATCGATACA
1435240 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1435205 original size:36 final size:33
Alignment explanation
Indices: 1435158--1435260 Score: 147
Period size: 32 Copynumber: 3.1 Consensus size: 33
1435148 TTTTTGTCCA
*
1435158 AATGTATCGATACATTGTTAGGTGTTGTATCGATAC
1 AATGTATCGATACA---TTAAGTGTTGTATCGATAC
1435194 AATGTATCGATACA-TAAGTGTTGTATCGATAC
1 AATGTATCGATACATTAAGTGTTGTATCGATAC
*
1435226 AATGTATCGATACA-TAAGTTTTGTATCGATAC
1 AATGTATCGATACATTAAGTGTTGTATCGATAC
1435258 AAT
1 AAT
1435261 TTAAGCTACT
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
32 51 0.78
36 14 0.22
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (33 bp):
AATGTATCGATACATTAAGTGTTGTATCGATAC
Found at i:1435220 original size:19 final size:18
Alignment explanation
Indices: 1435196--1435258 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1435186 ATCGATACAA
1435196 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1435215 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1435228 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1435247 TGTATCGATACA
1 TGTATCGATACA
1435259 ATTTAAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1435220 original size:32 final size:32
Alignment explanation
Indices: 1435179--1435260 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
1435169 ACATTGTTAG
1435179 GTGTTGTATCGATACAATGTATCGATACATAA
1 GTGTTGTATCGATACAATGTATCGATACATAA
1435211 GTGTTGTATCGATACAATGTATCGATACATAA
1 GTGTTGTATCGATACAATGTATCGATACATAA
*
1435243 GTTTTGTATCGATACAAT
1 GTGTTGTATCGATACAAT
1435261 TTAAGCTACT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
GTGTTGTATCGATACAATGTATCGATACATAA
Found at i:1435319 original size:13 final size:13
Alignment explanation
Indices: 1435301--1435326 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1435291 ATTACTAAAA
1435301 TGTATCGATACAT
1 TGTATCGATACAT
1435314 TGTATCGATACAT
1 TGTATCGATACAT
1435327 GCAGGCAAAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1435442 original size:52 final size:52
Alignment explanation
Indices: 1435314--1435435 Score: 226
Period size: 52 Copynumber: 2.3 Consensus size: 52
1435304 ATCGATACAT
1435314 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1435366 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1435418 TGTATCGATACATGCAGG
1 TGTATCGATACATGCAGG
1435436 TGAATTTTCA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1435462 original size:18 final size:18
Alignment explanation
Indices: 1435439--1435502 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 18
1435429 ATGCAGGTGA
1435439 ATTTTCATATTTCGGGAC
1 ATTTTCATATTTCGGGAC
* *
1435457 ATTTTCTTCTTTTGCCAGGTGA-
1 ATTTTCAT-ATTT--C-GG-GAC
1435479 ATTTTCATATTTCGGGAC
1 ATTTTCATATTTCGGGAC
1435497 ATTTTC
1 ATTTTC
1435503 TTCTTTTGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 2 0.06
18 15 0.42
19 4 0.11
21 4 0.11
22 9 0.25
23 2 0.06
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (18 bp):
ATTTTCATATTTCGGGAC
Found at i:1435487 original size:40 final size:40
Alignment explanation
Indices: 1435432--1435513 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1435422 TCGATACATG
1435432 CAGGTGAATTTTCATATTTCGGGACATTTTCTTCTTTTGC
1 CAGGTGAATTTTCATATTTCGGGACATTTTCTTCTTTTGC
1435472 CAGGTGAATTTTCATATTTCGGGACATTTTCTTCTTTTGC
1 CAGGTGAATTTTCATATTTCGGGACATTTTCTTCTTTTGC
1435512 CA
1 CA
1435514 AAACACATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (40 bp):
CAGGTGAATTTTCATATTTCGGGACATTTTCTTCTTTTGC
Found at i:1444011 original size:21 final size:19
Alignment explanation
Indices: 1443980--1444054 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 19
1443970 TTCAAAATGA
*
1443980 CAAAAAAAAAAGTCAAAAG
1 CAAAATAAAAAGTCAAAAG
* *
1443999 CAAAAGTACAAAATATGAAAAG
1 CAAAA-TA-AAAA-GTCAAAAG
*
1444021 AAAAATAAAAAAAGTGCAAAAG
1 CAAAAT--AAAAAGT-CAAAAG
1444043 CAAAATAAAAAG
1 CAAAATAAAAAG
1444055 GGAACAACAA
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
19 5 0.12
20 7 0.16
21 6 0.14
22 24 0.56
23 1 0.02
ACGTcount: A:0.71, C:0.08, G:0.12, T:0.09
Consensus pattern (19 bp):
CAAAATAAAAAGTCAAAAG
Found at i:1444019 original size:22 final size:23
Alignment explanation
Indices: 1443995--1444053 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
1443985 AAAAAAGTCA
* *
1443995 AAAGCAAAAGTACAAAATA-TG-A
1 AAAGCAAAAATA-AAAAAAGTGCA
1444017 AAAG-AAAAATAAAAAAAGTGCA
1 AAAGCAAAAATAAAAAAAGTGCA
1444039 AAAGC-AAAATAAAAA
1 AAAGCAAAAATAAAAA
1444054 GGGAACAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 5 0.16
21 8 0.25
22 19 0.59
ACGTcount: A:0.71, C:0.07, G:0.12, T:0.10
Consensus pattern (23 bp):
AAAGCAAAAATAAAAAAAGTGCA
Found at i:1444075 original size:44 final size:43
Alignment explanation
Indices: 1443984--1444077 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 43
1443974 AAATGACAAA
* *
1443984 AAAAAAAGTCAAAAGCAAAAGTACAAAATATGAAAAGAAAAAT
1 AAAAAAAGTCAAAAGCAAAAGTACAAAATAGGAAAACAAAAAT
*
1444027 AAAAAAAGTGCAAAAGCAAAA-TA-AAAA-GGGAACAACAAAAAT
1 AAAAAAAGT-CAAAAGCAAAAGTACAAAATAGGAA-AACAAAAAT
1444069 CCAAAAAAA
1 --AAAAAAA
1444078 AAGACATGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
41 3 0.07
42 12 0.27
43 11 0.25
44 18 0.41
ACGTcount: A:0.70, C:0.10, G:0.12, T:0.09
Consensus pattern (43 bp):
AAAAAAAGTCAAAAGCAAAAGTACAAAATAGGAAAACAAAAAT
Found at i:1445406 original size:28 final size:28
Alignment explanation
Indices: 1445319--1445464 Score: 179
Period size: 28 Copynumber: 5.2 Consensus size: 28
1445309 CCACGATTTA
*
1445319 GTGGCATTTCTTTTCAAAGTCCACAACTCC
1 GTGGCA-TCCTTTT-AAAGTCCACAACTCC
* *
1445349 ATGGCATCCTTTT-AAGTCCACAACTTC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
*
1445376 GTGGCATCCTTTTAAAGTTCACAACTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
*
1445404 GTGGCA-CTCTTTTAAAGTCCACAACTCT
1 GTGGCATC-CTTTTAAAGTCCACAACTCC
* **
1445432 GTGGCACCCTTTTAAAGTCCACCGCTCC
1 GTGGCATCCTTTTAAAGTCCACAACTCC
1445460 GTGGC
1 GTGGC
1445465 TCCACAACTC
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
27 26 0.25
28 64 0.63
29 7 0.07
30 5 0.05
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.31
Consensus pattern (28 bp):
GTGGCATCCTTTTAAAGTCCACAACTCC
Found at i:1445445 original size:83 final size:82
Alignment explanation
Indices: 1445327--1445708 Score: 380
Period size: 83 Copynumber: 4.7 Consensus size: 82
1445317 TAGTGGCATT
*
1445327 TCTTTTCAAAGTCCACAACTCCATGGCATCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAA
1 TCTTTT-AAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTTCGTGGCATCCTTTT-AA
1445392 GTTCACAACTCCGTGGCAC
64 GTTCACAACTCCGTGGCAC
** ** *
1445411 TCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACCGCTCCGTGGC-T-C-------
1 TCTTTTAAAGTCCACAACTCCATGGCACCCTTTT-AAGTCCACAACTTCGTGGCATCCTTTTAAG
**
1445467 --CACAACTCTATGGCA-
65 TTCACAACTCCGTGGCAC
* *
1445482 TCCTTTT-AAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAAC-TCTGTGGCAT-CTGTTTC
1 T-CTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTTC-GTGGCATCCT-TTT-
**
1445544 AAGTTCACAACTCCGTGGCGT
62 AAGTTCACAACTCCGTGGCAC
*
1445565 TCTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGT
1 TCTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGT
* * *
1445630 CCACAACTTCGTGGCAT
66 TCACAACTCCGTGGCAC
* * * * ** *
1445647 TCTTTTTAAGCCCACAAGTCAATGGCACCCTTCCAAAGTCCATAACTTCGTGGCATCCTTTT
1 TCTTTTAAAGTCCACAACTCCATGGCACCCTT-TTAAGTCCACAACTTCGTGGCATCCTTTT
1445709 TAAGCCAATA
Statistics
Matches: 248, Mismatches: 30, Indels: 41
0.78 0.09 0.13
Matches are distributed among these distances:
69 1 0.00
70 14 0.06
71 28 0.11
72 18 0.07
82 64 0.26
83 98 0.40
84 25 0.10
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (82 bp):
TCTTTTAAAGTCCACAACTCCATGGCACCCTTTTAAGTCCACAACTTCGTGGCATCCTTTTAAGT
TCACAACTCCGTGGCAC
Found at i:1445507 original size:27 final size:27
Alignment explanation
Indices: 1445477--1445708 Score: 227
Period size: 27 Copynumber: 8.4 Consensus size: 27
1445467 CACAACTCTA
1445477 TGGCATCCTTTTAAGTCCACAACTTCG
1 TGGCATCCTTTTAAGTCCACAACTTCG
*
1445504 TGGCACCCTTTTAAGTCCACAAC-TCTG
1 TGGCATCCTTTTAAGTCCACAACTTC-G
* *
1445531 TGGCAT-CTGTTTCAAGTTCACAACTCCG
1 TGGCATCCT-TTT-AAGTCCACAACTTCG
* * * *
1445559 TGGCGTTCTTTTAAAGTCCACAACTCCA
1 TGGCATCCTTTT-AAGTCCACAACTTCG
* *
1445587 TGGCACCCTTTTAAGTCCACAACTCCG
1 TGGCATCCTTTTAAGTCCACAACTTCG
1445614 TGGCATCCTTTTAAGTCCACAACTTCG
1 TGGCATCCTTTTAAGTCCACAACTTCG
* * * *
1445641 TGGCATTCTTTTTAAGCCCACAA-GTCAA
1 TGGCA-TCCTTTTAAGTCCACAACTTC-G
* ** *
1445669 TGGCACCCTTCCAAAGTCCATAACTTCG
1 TGGCATCCTT-TTAAGTCCACAACTTCG
1445697 TGGCATCCTTTT
1 TGGCATCCTTTT
1445709 TAAGCCAATA
Statistics
Matches: 167, Mismatches: 29, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.02
27 80 0.48
28 78 0.47
29 5 0.03
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (27 bp):
TGGCATCCTTTTAAGTCCACAACTTCG
Found at i:1445507 original size:43 final size:44
Alignment explanation
Indices: 1445421--1445507 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
1445411 TCTTTTAAAG
* **
1445421 TCCACAACTCTGTGGCACCCTTTTAAAGTCCACCGCTCCGTGGC
1 TCCACAACTCTATGGCACCCTTTTAAAGTCCACAACTCCGTGGC
* *
1445465 TCCACAACTCTATGGCATCCTTTT-AAGTCCACAACTTCGTGGC
1 TCCACAACTCTATGGCACCCTTTTAAAGTCCACAACTCCGTGGC
1445508 ACCCTTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
43 16 0.42
44 22 0.58
ACGTcount: A:0.21, C:0.36, G:0.16, T:0.28
Consensus pattern (44 bp):
TCCACAACTCTATGGCACCCTTTTAAAGTCCACAACTCCGTGGC
Found at i:1445663 original size:110 final size:110
Alignment explanation
Indices: 1445465--1445663 Score: 303
Period size: 110 Copynumber: 1.8 Consensus size: 110
1445455 GCTCCGTGGC
* * *
1445465 TCCACAACTCTATGGCATCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCT
1 TCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCT
**
1445530 GTGGCATCTGTTTCAAGTTCACAACTCCGTGGCGTTCTTTTAAAG
66 GTGGCATCTGTTTCAAGCCCACAACTCCGTGGCGTTCTTTTAAAG
*
1445575 TCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACT-T
1 TCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCT
*
1445639 CGTGGCATTCT-TTTTAAGCCCACAA
66 -GTGGCA-TCTGTTTCAAGCCCACAA
1445664 GTCAATGGCA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
109 1 0.01
110 76 0.95
111 3 0.04
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (110 bp):
TCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCT
GTGGCATCTGTTTCAAGCCCACAACTCCGTGGCGTTCTTTTAAAG
Found at i:1445685 original size:110 final size:110
Alignment explanation
Indices: 1445465--1445708 Score: 294
Period size: 110 Copynumber: 2.2 Consensus size: 110
1445455 GCTCCGTGGC
* *
1445465 TCCACAACTCTATGGCATCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCT
1 TCCACAACTCCATGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCT
** ** *** **
1445530 GTGGCATCTGTTTCAAGTTCACAACTCCGTGGCGTTCTTTTAAAG
66 GTGGCATCTGTTTCAAGCCCACAACTCAATGGCACCCTTCCAAAG
* *
1445575 TCCACAACTCCATGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACT-T
1 TCCACAACTCCATGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCT
* *
1445639 CGTGGCATTCT-TTTTAAGCCCACAAGTCAATGGCACCCTTCCAAAG
66 -GTGGCA-TCTGTTTCAAGCCCACAACTCAATGGCACCCTTCCAAAG
* * *
1445685 TCCATAACTTCGTGGCATCCTTTT
1 TCCACAACTCCATGGCATCCTTTT
1445709 TAAGCCAATA
Statistics
Matches: 113, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
109 1 0.01
110 109 0.96
111 3 0.03
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (110 bp):
TCCACAACTCCATGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCT
GTGGCATCTGTTTCAAGCCCACAACTCAATGGCACCCTTCCAAAG
Found at i:1445719 original size:28 final size:28
Alignment explanation
Indices: 1445477--1445712 Score: 216
Period size: 28 Copynumber: 8.6 Consensus size: 28
1445467 CACAACTCTA
1445477 TGGCATCC-TTTTAAGTCCACAACTTCG
1 TGGCATCCTTTTTAAGTCCACAACTTCG
*
1445504 TGGCA-CCCTTTTAAGTCCACAAC-TCTG
1 TGGCATCCTTTTTAAGTCCACAACTTC-G
* * *
1445531 TGGCAT-CTGTTTCAAGTTCACAACTCCG
1 TGGCATCCT-TTTTAAGTCCACAACTTCG
* * * * *
1445559 TGGCGTTCTTTTAAAGTCCACAACTCCA
1 TGGCATCCTTTTTAAGTCCACAACTTCG
* *
1445587 TGGCA-CCCTTTTAAGTCCACAACTCCG
1 TGGCATCCTTTTTAAGTCCACAACTTCG
1445614 TGGCATCC-TTTTAAGTCCACAACTTCG
1 TGGCATCCTTTTTAAGTCCACAACTTCG
* * * *
1445641 TGGCATTCTTTTTAAGCCCACAA-GTCAA
1 TGGCATCCTTTTTAAGTCCACAACTTC-G
* *** *
1445669 TGGCACCCTTCCAAAGTCCATAACTTCG
1 TGGCATCCTTTTTAAGTCCACAACTTCG
1445697 TGGCATCCTTTTTAAG
1 TGGCATCCTTTTTAAG
1445713 CCAATAAGTT
Statistics
Matches: 168, Mismatches: 31, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
26 4 0.02
27 77 0.46
28 82 0.49
29 5 0.03
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.31
Consensus pattern (28 bp):
TGGCATCCTTTTTAAGTCCACAACTTCG
Found at i:1445727 original size:28 final size:28
Alignment explanation
Indices: 1445465--1445729 Score: 179
Period size: 28 Copynumber: 9.6 Consensus size: 28
1445455 GCTCCGTGGC
1445465 TCCACAACTCTA-TGGCATCC-TTTTAAG
1 TCCACAACT-TAGTGGCATCCTTTTTAAG
* *
1445492 TCCACAACTTCGTGGCA-CCCTTTTAAG
1 TCCACAACTTAGTGGCATCCTTTTTAAG
*
1445519 TCCACAACTCT-GTGGCAT-CTGTTTCAAG
1 TCCACAACT-TAGTGGCATCCT-TTTTAAG
* ** * * *
1445547 TTCACAACTCCGTGGCGTTCTTTTAAAG
1 TCCACAACTTAGTGGCATCCTTTTTAAG
* *
1445575 TCCACAACTCCA-TGGCA-CCCTTTTAAG
1 TCCACAACT-TAGTGGCATCCTTTTTAAG
**
1445602 TCCACAACTCCGTGGCATCC-TTTTAAG
1 TCCACAACTTAGTGGCATCCTTTTTAAG
* *
1445629 TCCACAACTTCGTGGCATTCTTTTTAAG
1 TCCACAACTTAGTGGCATCCTTTTTAAG
* * * * * ***
1445657 CCCACAAGTCAATGGCACCCTTCCAAAG
1 TCCACAACTTAGTGGCATCCTTTTTAAG
* *
1445685 TCCATAACTTCGTGGCATCCTTTTTAAG
1 TCCACAACTTAGTGGCATCCTTTTTAAG
* *
1445713 -CCAATAAGTTAGTGGCA
1 TCC-ACAACTTAGTGGCA
1445730 CTCTTCCAAA
Statistics
Matches: 188, Mismatches: 38, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
26 4 0.02
27 85 0.45
28 96 0.51
29 3 0.02
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.31
Consensus pattern (28 bp):
TCCACAACTTAGTGGCATCCTTTTTAAG
Found at i:1445871 original size:28 final size:28
Alignment explanation
Indices: 1445603--1446185 Score: 490
Period size: 28 Copynumber: 20.2 Consensus size: 28
1445593 CCTTTTAAGT
* * * *
1445603 CCACAACTCCGTGGCATCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * **
1445630 CCACAACTTC-GTGGCATTCTTTTTAAGC
1 CCACAA-GTCAGTGGCATCCTTTCAAAGC
* * * *
1445658 CCACAAGTCAATGGCACCCTTCCAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * **
1445686 CCATAACTTC-GTGGCATCCTTTTTAAGC
1 CCACAA-GTCAGTGGCATCCTTTCAAAGC
* * * *
1445714 CAATAAGTTAGTGGCA-CTCTTCCAAAGCC
1 CCACAAGTCAGTGGCATC-CTTTCAAAG-C
* *
1445743 CACACAAATCAGTGGCATCTTTTCAAAGC
1 C-CACAAGTCAGTGGCATCCTTTCAAAGC
* * *
1445772 CCATACAAGTCTGTGGTAACCTATTTCAAAGCC
1 CC--ACAAGTCAGTGGCATCC--TTTCAAAG-C
* *
1445805 CACACAAGTCAGTGGCAACCCACTTCAAAGC
1 C-CACAAGTCAGTGGC-ATCC-TTTCAAAGC
* *
1445836 CCATAAGTCAGTGGCATCCTTTCAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
1445864 CCACAAGTCAGTGGCATCCTTCTCAAAGC
1 CCACAAGTCAGTGGCATCCTT-TCAAAGC
*
1445893 CTACAAGTCAGTGGCATCCTTCTCAAAGCC
1 CCACAAGTCAGTGGCATCCTT-TCAAAG-C
* * *
1445923 CACACAAATCAATGGCATCTTTTCAAAGC
1 C-CACAAGTCAGTGGCATCCTTTCAAAGC
1445952 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
1445980 CCATAAGTCAGTGGCATTCTTCTCAAAGT
1 CCACAAGTCAGTGGCATCCTT-TCAAAGC
* * *
1446009 TCACAAGTTAGTGACATCCTTCTCAAAGC
1 CCACAAGTCAGTGGCATCCTT-TCAAAGC
* *
1446038 CCACAAGTTAGTGGCATCATTCTCAAAGCC
1 CCACAAGTCAGTGGCATCCTT-TCAAAG-C
* * *
1446068 CGCAAAAATCAGTGGCATCTTTTCAAAGC
1 C-CACAAGTCAGTGGCATCCTTTCAAAGC
* *
1446097 CCACAAGTTAATGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
1446125 CCACAAGTCAATGACATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
1446153 GCACAAGTCAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
1446181 CCACA
1 CCACA
1446186 CAAGTTGATA
Statistics
Matches: 452, Mismatches: 82, Indels: 43
0.78 0.14 0.07
Matches are distributed among these distances:
27 21 0.05
28 204 0.45
29 100 0.22
30 59 0.13
31 35 0.08
32 27 0.06
33 5 0.01
34 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGC
Found at i:1445965 original size:116 final size:115
Alignment explanation
Indices: 1445718--1446185 Score: 491
Period size: 116 Copynumber: 4.0 Consensus size: 115
1445708 TTAAGCCAAT
* * * *
1445718 AAGTTAGTGGCA-CTCTTCCAAAGCCCACACAAATCAGTGGCAT-CTTTTCAAAGCCCATACAAG
1 AAGTCAGTGGCATC-CTTTCAAAG-CC-CACAAGTCAGTGGCATCCTTCTCAAAG-CC-TACAAG
* ** * * * * *
1445781 TCTGTGGTAACCTATTTCAAAGCCCACACAAGTCAGTGGCAACCCACTTCAAAGCCCAT
61 TCAGTGACATCCT-TCTCAAAG-CCACACAAGTCAGTGGC-A-TCATTTCAAAGCCCAC
*
1445840 AAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCATCCTTCTCAAAGCCTACAAGTCAGT
1 AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCTACAAGTCAGT
* * * *
1445905 GGCATCCTTCTCAAAGCCCACACAAATCAATGGCATCTTTTCAAAGCCCAC
66 GACATCCTTCTCAAAG-CCACACAAGTCAGTGGCATCATTTCAAAGCCCAC
* * * *
1445956 AAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCATTCTTCTCAAAG-TTCACAAGTTAG
1 AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCT-ACAAGTCAG
* *
1446020 TGACATCCTTCTCAAAGCC-CACAAGTTAGTGGCATCATTCTCAAAGCCCGCAA
65 TGACATCCTTCTCAAAGCCACACAAGTCAGTGGCATCATT-TCAAAG-CC-CAC
* * * * * *
1446073 AAATCAGTGGCATCTTTTCAAAGCCCACAAGTTAATGGCATCCTT-TCAAAGCCCACAAGTCAAT
1 AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCTACAAGTCAGT
*
1446137 GACATCCTT-TCAAAG-CGCACAAGTCAGTGGCATCATTTCAAAGCCCAC
66 GACATCCTTCTCAAAGCCACACAAGTCAGTGGCATCATTTCAAAGCCCAC
1446185 A
1 A
1446186 CAAGTTGATA
Statistics
Matches: 300, Mismatches: 38, Indels: 26
0.82 0.10 0.07
Matches are distributed among these distances:
112 3 0.01
113 2 0.01
114 23 0.08
115 34 0.11
116 110 0.37
117 42 0.14
118 23 0.08
119 16 0.05
120 17 0.06
121 10 0.03
122 19 0.06
123 1 0.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (115 bp):
AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCTACAAGTCAGT
GACATCCTTCTCAAAGCCACACAAGTCAGTGGCATCATTTCAAAGCCCAC
Found at i:1446033 original size:145 final size:144
Alignment explanation
Indices: 1445640--1446185 Score: 595
Period size: 145 Copynumber: 3.8 Consensus size: 144
1445630 CCACAACTTC
* * * * * *
1445640 GTGGCATTCTTTT-TAAGCCCACAAGTCAATGGCACCCTTCCAAAGTCCATAACTTC-GTGGCAT
1 GTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAA-GTCAGTGGCAT
** * * *
1445703 CCTTTTTAAG-CCAATAAGTTAGTGGCA-CTCTTC-CAAAGCCCACACAAATCAGTGGCAT-CTT
64 CCTTTCAAAGTCC-ACAAGTCAGTGGCATC-CTTCTCAAAG-CC-CACAAGTCAGTGGCATCCTT
* * * *
1445764 TTCAAAGCCCATACAAGTCT
125 CTCAAAGCCCACACAAATCA
* * * *
1445784 GTGGTAACCTATTTCAAAGCCCACACAAGTCAGTGGCAACCCACTTCAAAGCCCATAAGTCAGTG
1 GTGG-CATCT-TTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-TTTCAAAGCCCATAAGTCAGTG
*
1445849 GCATCCTTTCAAAGTCCACAAGTCAGTGGCATCCTTCTCAAAGCCTACAAGTCAGTGGCATCCTT
60 GCATCCTTTCAAAGTCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATCCTT
1445914 CTCAAAGCCCACACAAATCA
125 CTCAAAGCCCACACAAATCA
* *
1445934 ATGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCATTC
1 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCATCC
* * * * *
1445999 TTCTCAAAGTTCACAAGTTAGTGACATCCTTCTCAAAGCCCACAAGTTAGTGGCATCATTCTCAA
66 TT-TCAAAGTCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAA
* *
1446064 AGCCCGCAAAAATCA
130 AGCCCACACAAATCA
* * * * *
1446079 GTGGCATCTTTTCAAAGCCCACAAGTTAATGGCATCCTTTCAAAGCCCACAAGTCAATGACATCC
1 GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCATCC
*
1446144 TTTCAAAG-CGCACAAGTCAGTGGCATCATT-TCAAAGCCCACA
66 TTTCAAAGTC-CACAAGTCAGTGGCATCCTTCTCAAAGCCCACA
1446186 CAAGTTGATA
Statistics
Matches: 345, Mismatches: 43, Indels: 29
0.83 0.10 0.07
Matches are distributed among these distances:
143 12 0.03
144 57 0.17
145 136 0.39
146 17 0.05
147 4 0.01
148 21 0.06
149 23 0.07
150 67 0.19
151 8 0.02
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.25
Consensus pattern (144 bp):
GTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCAGTGGCATCC
TTTCAAAGTCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAA
GCCCACACAAATCA
Found at i:1446385 original size:48 final size:48
Alignment explanation
Indices: 1446329--1446450 Score: 199
Period size: 48 Copynumber: 2.5 Consensus size: 48
1446319 GGCACCTTTA
* * *
1446329 TTAGCTCAATGTCACTGGCCTTGAATCAACACATTGTCCACTTTTCTC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAACACATTATCCACTTTTCCC
*
1446377 TTAGCTCAATTTCGCTGGCCTTGAATCAACACATTATCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAACACATTATCCACTTTTCCC
*
1446425 TTAGCTCGATGTCGCTGGCCTTGAAT
1 TTAGCTCAATGTCGCTGGCCTTGAAT
1446451 TGGCATTTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 68 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAACACATTATCCACTTTTCCC
Found at i:1450670 original size:25 final size:25
Alignment explanation
Indices: 1450629--1450677 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1450619 AATTAGAAAA
* *
1450629 GTATGGAAGAATCAGGAAATGCTAG
1 GTATGGAAAAATCAGGAAAGGCTAG
*
1450654 GTATGGAAAAATTAGGAAAGGCTA
1 GTATGGAAAAATCAGGAAAGGCTA
1450678 ACATTAGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.06, G:0.31, T:0.20
Consensus pattern (25 bp):
GTATGGAAAAATCAGGAAAGGCTAG
Found at i:1453446 original size:10 final size:9
Alignment explanation
Indices: 1453427--1453487 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 9
1453417 CAAACAAGAG
1453427 AAAGAAAAA
1 AAAGAAAAA
1453436 AAAGTAAAAAAA
1 AAAG---AAAAA
1453448 AAAGAAAACA
1 AAAGAAAA-A
*
1453458 AGAAGAGCAAA
1 A-AAGA-AAAA
1453469 AAAGAAAAA
1 AAAGAAAAA
1453478 AAAGAGAAAA
1 AAAGA-AAAA
1453488 TCACGTAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
9 16 0.37
10 10 0.23
11 6 0.14
12 11 0.26
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:1453453 original size:21 final size:19
Alignment explanation
Indices: 1453427--1453487 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 19
1453417 CAAACAAGAG
1453427 AAAGAAAAAAAAGTAAAAAAA
1 AAAGAAAAAAAAG--AAAAAA
**
1453448 AAAGAAAACAAGAAGAGCAAA
1 AAAGAAAA-AA-AAGAAAAAA
1453469 AAAGAAAAAAAAGAGAAAA
1 AAAGAAAAAAAAGA-AAAA
1453488 TCACGTAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 20 0.61
22 2 0.06
23 3 0.09
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAAAAGAAAAAA
Found at i:1453455 original size:11 final size:11
Alignment explanation
Indices: 1453431--1453487 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
1453421 CAAGAGAAAG
1453431 AAAAAAAAGTAA
1 AAAAAAAAG-AA
1453443 AAAAAAAAGAA
1 AAAAAAAAGAA
* *
1453454 AACAAGAAG-A
1 AAAAAAAAGAA
**
1453464 GCAAAAAAGAA
1 AAAAAAAAGAA
*
1453475 AAAAAAGAGAA
1 AAAAAAAAGAA
1453486 AA
1 AA
1453488 TCACGTAACT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
10 6 0.17
11 20 0.57
12 9 0.26
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:1457815 original size:2 final size:2
Alignment explanation
Indices: 1457810--1457837 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1457800 TATATATAGA
1457810 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1457838 AAGAAACGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1467522 original size:32 final size:32
Alignment explanation
Indices: 1467481--1467545 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1467471 GGGTGCTAGC
1467481 CACGTAGGAGTTGTGTAGACACCAAATTTTGT
1 CACGTAGGAGTTGTGTAGACACCAAATTTTGT
1467513 CACGTAGGAGTTGTGTAGACACCAAATTTTGT
1 CACGTAGGAGTTGTGTAGACACCAAATTTTGT
1467545 C
1 C
1467546 CGGTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (32 bp):
CACGTAGGAGTTGTGTAGACACCAAATTTTGT
Found at i:1468436 original size:17 final size:15
Alignment explanation
Indices: 1468416--1468464 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
1468406 TTAAGTAAAA
1468416 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
1468433 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
1468447 AA-AAAGAAA-AAA-
1 AAGAAAGAAAGAAAG
1468459 AAGAAA
1 AAGAAA
1468465 AAATATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.07
13 6 0.20
14 9 0.30
15 1 0.03
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:1468830 original size:2 final size:2
Alignment explanation
Indices: 1468817--1468851 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1468807 TTATTTTATT
* *
1468817 TA TA TG TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1468852 TTTAAAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1468838 original size:16 final size:16
Alignment explanation
Indices: 1468817--1468851 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1468807 TTATTTTATT
1468817 TATATGTATATATATA
1 TATATGTATATATATA
1468833 TATATGTATATATATA
1 TATATGTATATATATA
1468849 TAT
1 TAT
1468852 TTTAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
TATATGTATATATATA
Found at i:1474882 original size:22 final size:22
Alignment explanation
Indices: 1474854--1474896 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1474844 CAAAATGACA
* *
1474854 ACAAAAAGTCAAAAGCAAAAGC
1 ACAAAAAATCAAAAGAAAAAGC
*
1474876 ACAAAAAATGAAAAGAAAAAG
1 ACAAAAAATCAAAAGAAAAAG
1474897 TGCAAAAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.70, C:0.12, G:0.14, T:0.05
Consensus pattern (22 bp):
ACAAAAAATCAAAAGAAAAAGC
Done.