Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold42
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: 3911082
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 18191 characters in sequence are not A, C, G, or T
File 16 of 24
Found at i:2446859 original size:28 final size:28
Alignment explanation
Indices: 2446823--2446899 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
2446813 ATTTTTCACA
* * *
2446823 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2446851 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2446879 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2446900 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2446868 original size:212 final size:212
Alignment explanation
Indices: 2446501--2446906 Score: 620
Period size: 212 Copynumber: 1.9 Consensus size: 212
2446491 TTATCAATTC
* * *
2446501 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCAGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* * *
2446566 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAGTCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * *
2446631 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACTCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
2446696 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * *
2446713 TCCACAATCAGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCAGGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
*
2446777 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
2446840 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
2446905 AT
193 AT
2446907 TCCCAAAATA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 30 0.17
212 110 0.63
213 35 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCAGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:2446966 original size:107 final size:107
Alignment explanation
Indices: 2446561--2446973 Score: 279
Period size: 107 Copynumber: 3.9 Consensus size: 107
2446551 TTCTATAATC
* * * * * *
2446561 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAGTCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCC
* * * *
2446626 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGA
64 AACCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
* * * * * * *
2446670 GGGGATACTCCAACTCCG-GTTT-TATCGCTAAAACACTAATTTTTCCACAATC-AGGGATACTC
1 GGGGATACTCCAACCCCGACTTTATTTC-CAAAAATACCAATTTCT-CACAATCGA-GGATACTC
* * * ***** * * ** * *
2446732 CAATCCTGGT-TTTATTTTCAAAACGCCAATTTTCCTTTA-AT-C--
63 CAACCCCGTTATTTATCGGGGATACTCCAA--CCCCGTTACTTCCGA
* * *
2446774 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
2446839 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * *
2446882 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
2446946 CCCCGTTATTT-TCGAAGGGATACTCCAA
66 CCCCGTTATTTATCG--GGGATACTCCAA
2446974 TCCCAATTTT
Statistics
Matches: 232, Mismatches: 56, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
104 44 0.19
105 25 0.11
106 25 0.11
107 91 0.39
108 30 0.13
109 17 0.07
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:2448048 original size:14 final size:14
Alignment explanation
Indices: 2448029--2448163 Score: 88
Period size: 14 Copynumber: 9.9 Consensus size: 14
2448019 TTGCGACAGC
2448029 ATGCATGAAATGTA
1 ATGCATGAAATGTA
*
2448043 ATGCATGAAATGCAA
1 ATGCATGAAATG-TA
* * *
2448058 ATTACGTGAAATG-C
1 A-TGCATGAAATGTA
2448072 ATGCATGAAATGTA
1 ATGCATGAAATGTA
*
2448086 ATGCATGAAATGAAA
1 ATGCATGAAATG-TA
* *
2448101 ATTCTGTGAAATGCT-
1 ATGC-ATGAAATG-TA
2448116 -TGCATGAAATGTA
1 ATGCATGAAATGTA
* *
2448129 GTGC--G---TGAA
1 ATGCATGAAATGTA
2448138 ATGCATGAAATGTA
1 ATGCATGAAATGTA
2448152 ATGCATGAAATG
1 ATGCATGAAATG
2448164 CATGAAATTA
Statistics
Matches: 92, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
9 6 0.07
11 1 0.01
12 2 0.02
13 16 0.17
14 45 0.49
15 6 0.07
16 16 0.17
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (14 bp):
ATGCATGAAATGTA
Found at i:2448086 original size:43 final size:43
Alignment explanation
Indices: 2448027--2448142 Score: 180
Period size: 43 Copynumber: 2.7 Consensus size: 43
2448017 CGTTGCGACA
2448027 GCATGCATGAAATGTAATGCATGAAATGCAAATTAC-GTGAAAT
1 GCATGCATGAAATGTAATGCATGAAATGCAAATT-CTGTGAAAT
*
2448070 GCATGCATGAAATGTAATGCATGAAATGAAAATTCTGTGAAAT
1 GCATGCATGAAATGTAATGCATGAAATGCAAATTCTGTGAAAT
* * *
2448113 GCTTGCATGAAATGTAGTGCGTGAAATGCA
1 GCATGCATGAAATGTAATGCATGAAATGCA
2448143 TGAAATGTAA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
42 1 0.01
43 66 0.99
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (43 bp):
GCATGCATGAAATGTAATGCATGAAATGCAAATTCTGTGAAAT
Found at i:2448142 original size:23 final size:23
Alignment explanation
Indices: 2448116--2448179 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
2448106 GTGAAATGCT
* *
2448116 TGCATGAAATGTAGTGCGTGAAA
1 TGCATGAAATGTAATGCATGAAA
2448139 TGCATGAAATGTAATGCATGAAA
1 TGCATGAAATGTAATGCATGAAA
2448162 TGCATGAAAT-T-ATGCATG
1 TGCATGAAATGTAATGCATG
2448180 CAATATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.18
22 1 0.03
23 31 0.79
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (23 bp):
TGCATGAAATGTAATGCATGAAA
Found at i:2448253 original size:22 final size:21
Alignment explanation
Indices: 2448222--2448262 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2448212 TGTTTTTTTC
2448222 TTTTTTATTTATTTATTATTA
1 TTTTTTATTTATTTATTATTA
*
2448243 TTTTTTAATTTATTTTTTAT
1 TTTTTT-ATTTATTTATTAT
2448263 AAATGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTATTTATTTATTATTA
Found at i:2449436 original size:79 final size:79
Alignment explanation
Indices: 2449300--2449679 Score: 505
Period size: 79 Copynumber: 4.8 Consensus size: 79
2449290 AGATAACAAT
* * * **
2449300 GGGGCTGGAGTATCCCCGATTATGGAAAATTGGTGTTCGAGAAATAAAATCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATC
2449365 CCCTCGGAAATAAC
66 CCCTCGGAAATAAC
* * *
2449379 GGGGTTGGAGTATCCCTGACTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATC
2449444 CCCTCGGAAATAAC
66 CCCTCGGAAATAAC
* * * * * *
2449458 GGGGTTGGAGTATCCCCGATTAAGAAAAATTGATATTTTAGAAATAAAACCGAGGATGGGGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATC
* *
2449523 CTCTCGAAAATAAC
66 CCCTCGGAAATAAC
* * * *
2449537 GGGGTTAGAGTATCCCC-A--ATGAAAAATTGATGTTTTAGAAATAAAATCAGGGTTGAAGTGTC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATC
2449599 CCCTCGGAAATAAC
66 CCCTCGGAAATAAC
* * * * * *
2449613 GGGGTTGGAGTATCCCCGATTGTGAAAAGTCGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATC
2449678 CC
66 CC
2449680 TGATTATGGA
Statistics
Matches: 259, Mismatches: 39, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
76 63 0.24
77 1 0.00
78 1 0.00
79 194 0.75
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (79 bp):
GGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATC
CCCTCGGAAATAAC
Found at i:2449657 original size:155 final size:155
Alignment explanation
Indices: 2449300--2449679 Score: 478
Period size: 155 Copynumber: 2.4 Consensus size: 155
2449290 AGATAACAAT
* * * * *
2449300 GGGGCTGGAGTATCCCCGATTATGGAAAATTGGTG-TTCGAGAAATAAAATCGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTAT-GAAAATTGGTGTTTTG-GAAATAAAACCGAGGATGGAGTAT
* * *
2449364 CCCCTCGGAAATAACGGGGTTGGAGTATCCCTGACTATGAAAAATTGATGTTTTAGAAATAAAAC
64 CCCCTCGAAAATAACGGGGTTAGAGTATCCC--ACAATGAAAAATTGATGTTTTAGAAATAAAAC
* *
2449429 CGGGGTTGGAGTATCCCCTCGGAAATAAC
127 CAGGGTTGAAGTATCCCCTCGGAAATAAC
* * * * *
2449458 GGGGTTGGAGTATCCCCGATTAAGAAAAATTGATATTTTAGAAATAAAACCGAGGATGGGGTATC
1 GGGGTTGGAGTATCCCCGATTATG-AAAATTGGTGTTTTGGAAATAAAACCGAGGATGGAGTATC
* *
2449523 CTCTCGAAAATAACGGGGTTAGAGTATCCC-CAATGAAAAATTGATGTTTTAGAAATAAAATCAG
65 CCCTCGAAAATAACGGGGTTAGAGTATCCCACAATGAAAAATTGATGTTTTAGAAATAAAACCAG
*
2449587 GGTTGAAGTGTCCCCTCGGAAATAAC
130 GGTTGAAGTATCCCCTCGGAAATAAC
* * * *
2449613 GGGGTTGGAGTATCCCCGATTGTGAAAAGTCGGTGTTTTGGAAATAAAATCG-GAGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGATTATGAAAA-TTGGTGTTTTGGAAATAAAACCGAG-GATGGAGTAT
2449677 CCC
64 CCC
2449680 TGATTATGGA
Statistics
Matches: 190, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
154 5 0.03
155 105 0.55
157 1 0.01
158 77 0.41
159 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (155 bp):
GGGGTTGGAGTATCCCCGATTATGAAAATTGGTGTTTTGGAAATAAAACCGAGGATGGAGTATCC
CCTCGAAAATAACGGGGTTAGAGTATCCCACAATGAAAAATTGATGTTTTAGAAATAAAACCAGG
GTTGAAGTATCCCCTCGGAAATAAC
Found at i:2449791 original size:50 final size:51
Alignment explanation
Indices: 2449616--2449793 Score: 193
Period size: 51 Copynumber: 3.5 Consensus size: 51
2449606 AAATAACGGG
* *
2449616 GTTGGAGTATCCCCGATTG-TGAAAAGTCGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGA-TGATGAAAAATAGGTGTTTTGGAAATAAAATCGGA
* * * *
2449667 GTTGGAGTATCCCTGATTATGGAAAATAGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATGATGAAAAATAGGTGTTTTGGAAATAAAATCGGA
* * * * ** *
2449718 GTTGGAGTAT-CCCAATGAAGAAAAATTGATGTTTTGGAAATGGAACCGG-
1 GTTGGAGTATCCCCGATGATGAAAAATAGGTGTTTTGGAAATAAAATCGGA
2449767 GATTGGAGTATCCCCGA-GATGAAAAAT
1 G-TTGGAGTATCCCCGATGATGAAAAAT
2449794 CTAGAAACTT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
49 1 0.01
50 47 0.45
51 57 0.54
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.28
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATGATGAAAAATAGGTGTTTTGGAAATAAAATCGGA
Found at i:2452374 original size:34 final size:35
Alignment explanation
Indices: 2452336--2452402 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2452326 CCTTACAACA
2452336 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2452370 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2452403 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2452879 original size:13 final size:13
Alignment explanation
Indices: 2452861--2452886 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2452851 CAATTTTTTG
2452861 TGTATCGATACAT
1 TGTATCGATACAT
2452874 TGTATCGATACAT
1 TGTATCGATACAT
2452887 ACTTGCTGTA
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:2452951 original size:21 final size:21
Alignment explanation
Indices: 2452925--2453000 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2452915 CTGCCAAGAA
*
2452925 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2452946 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2452966 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2452987 ATGTATCGATACAT
1 ATGTATCGATACAT
2453001 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2452971 original size:20 final size:20
Alignment explanation
Indices: 2452946--2453018 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2452936 CATCTTTTTT
2452946 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2452966 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2452987 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2453007 ATGTATCGATAC
1 ATGTATCGATAC
2453019 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2452982 original size:41 final size:41
Alignment explanation
Indices: 2452925--2453018 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2452915 CTGCCAAGAA
*
2452925 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2452966 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2453007 ATGTATCGATAC
1 ATGTATCGATAC
2453019 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2453637 original size:21 final size:21
Alignment explanation
Indices: 2453596--2453639 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2453586 CTCCCCTTTA
* *
2453596 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
2453617 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
2453638 TC
1 TC
2453640 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:2454435 original size:12 final size:12
Alignment explanation
Indices: 2454418--2454444 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2454408 TTTTTGAATG
2454418 AAACCAGCACAC
1 AAACCAGCACAC
2454430 AAACCAGCACAC
1 AAACCAGCACAC
2454442 AAA
1 AAA
2454445 TCAATCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.37, G:0.07, T:0.00
Consensus pattern (12 bp):
AAACCAGCACAC
Found at i:2454753 original size:13 final size:13
Alignment explanation
Indices: 2454735--2454759 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2454725 ACTGAAGCAA
2454735 TGTATCGATACAT
1 TGTATCGATACAT
2454748 TGTATCGATACA
1 TGTATCGATACA
2454760 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2457904 original size:34 final size:35
Alignment explanation
Indices: 2457866--2457932 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2457856 CCTTACAACA
2457866 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2457900 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2457933 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2458409 original size:13 final size:13
Alignment explanation
Indices: 2458391--2458416 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2458381 CAATTTTTTG
2458391 TGTATCGATACAT
1 TGTATCGATACAT
2458404 TGTATCGATACAT
1 TGTATCGATACAT
2458417 ACTTGCTGTA
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:2458481 original size:21 final size:21
Alignment explanation
Indices: 2458455--2458530 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2458445 CTGCCAAGAA
*
2458455 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
2458476 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2458496 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2458517 ATGTATCGATACAT
1 ATGTATCGATACAT
2458531 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2458501 original size:20 final size:20
Alignment explanation
Indices: 2458476--2458548 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2458466 CATCTTTTTT
2458476 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
2458496 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
2458517 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
2458537 ATGTATCGATAC
1 ATGTATCGATAC
2458549 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:2458512 original size:41 final size:41
Alignment explanation
Indices: 2458455--2458548 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2458445 CTGCCAAGAA
*
2458455 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2458496 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2458537 ATGTATCGATAC
1 ATGTATCGATAC
2458549 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2458881 original size:20 final size:20
Alignment explanation
Indices: 2458840--2458910 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
2458830 GATCCTAACA
* *
2458840 GATACATTGTAAAATATATC
1 GATACAATGTAAAATGTATC
* *
2458860 GATGCAATG-AGCAATGTATC
1 GATACAATGTA-AAATGTATC
2458880 GATACAATGTAAAATGTATC
1 GATACAATGTAAAATGTATC
2458900 GATACAATGTA
1 GATACAATGTA
2458911 TCGATACATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (20 bp):
GATACAATGTAAAATGTATC
Found at i:2458889 original size:13 final size:13
Alignment explanation
Indices: 2458871--2458918 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
2458861 ATGCAATGAG
2458871 CAATGTATCGATA
1 CAATGTATCGATA
2458884 CAATGTA---A-A
1 CAATGTATCGATA
2458893 --ATGTATCGATA
1 CAATGTATCGATA
2458904 CAATGTATCGATA
1 CAATGTATCGATA
2458917 CA
1 CA
2458919 TTGAATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 5 0.17
9 1 0.03
10 2 0.07
11 1 0.03
13 20 0.69
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2458913 original size:33 final size:33
Alignment explanation
Indices: 2458871--2458938 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
2458861 ATGCAATGAG
*
2458871 CAATGTATCGATACAATGTAA-AATGTATCGATA
1 CAATGTATCGATACAATG-AATAATGTATCAATA
*
2458904 CAATGTATCGATACATTGAATAATGTATCAATA
1 CAATGTATCGATACAATGAATAATGTATCAATA
2458937 CA
1 CA
2458939 TTTCCTTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (33 bp):
CAATGTATCGATACAATGAATAATGTATCAATA
Found at i:2459005 original size:32 final size:32
Alignment explanation
Indices: 2458964--2459032 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
2458954 CTTTGTAGCA
**
2458964 ATACACTGTATCGTTACAACACTTATGTATCG
1 ATACACTGTATCAATACAACACTTATGTATCG
*
2458996 ATACACTGTATCAATACAACACTTATGTATTG
1 ATACACTGTATCAATACAACACTTATGTATCG
2459028 ATACA
1 ATACA
2459033 TTTACTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.33
Consensus pattern (32 bp):
ATACACTGTATCAATACAACACTTATGTATCG
Found at i:2462455 original size:8 final size:8
Alignment explanation
Indices: 2462444--2462468 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2462434 TCTATTTTTA
2462444 AATTTCAT
1 AATTTCAT
2462452 AATTTCAT
1 AATTTCAT
2462460 AATTTCAT
1 AATTTCAT
2462468 A
1 A
2462469 TTCTTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTCAT
Found at i:2462905 original size:162 final size:162
Alignment explanation
Indices: 2462725--2463077 Score: 356
Period size: 162 Copynumber: 2.2 Consensus size: 162
2462715 CAAAATAAAA
* * * *
2462725 GAGTTTTCT-TCTCCATAAATTTTTTTGGGAAG-ATTTTCATCAGATTAGAATTTTTAAAATTCA
1 GAGTTTTCTAT-TCCATAAATATTTTGGGGAAGTATTTTC-TCAGATCAAAATTTTTAAAATTCA
* * * * * *
2462788 CCAAATATTATTATTATCTAATCACCATTTAATCAGTTTTGAAAAATTCATTTATTTTCATGAG-
64 CCAAATATCATCATT-T-AAATCA-CAGTAAATCAGTATTGAAAAATTCATTTATTTTCATGAGT
* * *
2462852 CTTTTTTTCC-TGAAATTTTTTTATTTT-TAAAAACT
126 CATTTTTTCCTTGAAATTTTCTTATTTTCGAAAAACT
** * * * * * *
2462887 GAGTTTTCTATTCCATAAATATTTTGGGGGGGTTTTTTCTCGGGTCAAAATTTTTAATATTTATC
1 GAGTTTTCTATTCCATAAATATTTTGGGGAAGTATTTTCTCAGATCAAAATTTTTAAAATTCACC
*
2462952 AAATATCATCATTTAAATCATAGTAAATCAGTATTGAAAAATTCATTTATTTTCATGAGTTTTTC
66 AAATATCATCATTTAAATCACAGTAAATCAGTATTGAAAAATTCATTTATTTTCATGAG----TC
* *
2463017 ATTTTTTCCTTTAAATTTTCTTGTTTTCGAAAAACT
127 ATTTTTTCCTTGAAATTTTCTTATTTTCGAAAAACT
* *
2463053 AAGTTTTCTATTCCATAAATGTTTT
1 GAGTTTTCTATTCCATAAATATTTT
2463078 CAGAGAGATG
Statistics
Matches: 156, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
159 35 0.22
160 5 0.03
161 1 0.01
162 56 0.36
163 6 0.04
164 9 0.06
165 14 0.09
166 30 0.19
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (162 bp):
GAGTTTTCTATTCCATAAATATTTTGGGGAAGTATTTTCTCAGATCAAAATTTTTAAAATTCACC
AAATATCATCATTTAAATCACAGTAAATCAGTATTGAAAAATTCATTTATTTTCATGAGTCATTT
TTTCCTTGAAATTTTCTTATTTTCGAAAAACT
Found at i:2463094 original size:166 final size:159
Alignment explanation
Indices: 2462773--2463123 Score: 378
Period size: 166 Copynumber: 2.1 Consensus size: 159
2462763 ATCAGATTAG
* * * * * * * *
2462773 AATTTTTAAAATTCACCAAATATTATTATTATCTAATCACCATTTAATCAGTTTTGAAAAATTCA
1 AATTTTTAAAATTCATCAAATATCATCATT-T-AAATCA-TAGTAAATCAGTATTGAAAAATTCA
* * * *
2462838 TTTATTTTCATGAGCTTTTTTTCCTGAAATTTTTTTATTTTTAAAAACTGAGTTTTCTATTCCAT
63 TTTATTTTCATGAGCATTTTTTCCTGAAATTTTCTTATTTTGAAAAACTAAGTTTTCTATTCCAT
** * * * *
2462903 AAATATTTTGGGGGGGTTTTTTCTCGGGTCAA
128 AAATATTTTCAGAGAGATGTTTCTCGGGTCAA
* *
2462935 AATTTTTAATATTTATCAAATATCATCATTTAAATCATAGTAAATCAGTATTGAAAAATTCATTT
1 AATTTTTAAAATTCATCAAATATCATCATTTAAATCATAGTAAATCAGTATTGAAAAATTCATTT
* *
2463000 ATTTTCATGAGTTTTTCATTTTTTCCTTTAAATTTTCTTGTTTTCGAAAAACTAAGTTTTCTATT
66 ATTTTCATGAG-----CATTTTTTCC-TGAAATTTTCTTATTTT-GAAAAACTAAGTTTTCTATT
* * *
2463065 CCATAAATGTTTTCAGAGAGATGTTTCTCGGTTTAA
124 CCATAAATATTTTCAGAGAGATGTTTCTCGGGTCAA
*
2463101 AATTTTTAAAATTCATCTAATAT
1 AATTTTTAAAATTCATCAAATAT
2463124 TGTCATTGAA
Statistics
Matches: 154, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
159 35 0.23
160 5 0.03
161 1 0.01
162 25 0.16
164 9 0.06
165 14 0.09
166 65 0.42
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.48
Consensus pattern (159 bp):
AATTTTTAAAATTCATCAAATATCATCATTTAAATCATAGTAAATCAGTATTGAAAAATTCATTT
ATTTTCATGAGCATTTTTTCCTGAAATTTTCTTATTTTGAAAAACTAAGTTTTCTATTCCATAAA
TATTTTCAGAGAGATGTTTCTCGGGTCAA
Found at i:2463541 original size:16 final size:16
Alignment explanation
Indices: 2463516--2463557 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2463506 AAGGGCATGG
2463516 AAAAAAAT-AAAATGA
1 AAAAAAATAAAAATGA
*
2463531 AAAAAAGATAAAAAT-T
1 AAAAAA-ATAAAAATGA
2463547 AAAAAAATAAA
1 AAAAAAATAAA
2463558 GAAAAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 11 0.46
16 8 0.33
17 5 0.21
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (16 bp):
AAAAAAATAAAAATGA
Found at i:2463650 original size:11 final size:11
Alignment explanation
Indices: 2463643--2463673 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2463633 AAAAAAAGAG
2463643 AGAAA-AAAAA
1 AGAAAGAAAAA
2463653 AGAAAGAAAAA
1 AGAAAGAAAAA
2463664 AGAAAGAAAA
1 AGAAAGAAAA
2463674 CAATTAAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:2463651 original size:14 final size:14
Alignment explanation
Indices: 2463632--2463672 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
2463622 TAGCAGGTAG
*
2463632 AAAAAAAAGAGAGA
1 AAAAAAAAGAAAGA
2463646 AAAAAAAAGAAAGA
1 AAAAAAAAGAAAGA
2463660 AAAAAGAAAGAAA
1 AAAAA-AAAGAAA
2463673 ACAATTAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAGA
Found at i:2468562 original size:139 final size:138
Alignment explanation
Indices: 2468074--2468605 Score: 650
Period size: 139 Copynumber: 3.8 Consensus size: 138
2468064 TCACTGAATA
* **
2468074 AAAATTATTATCTTAATTTTTCAAGATTTCTAGTATTCCTATAATTTTTCGTAGGGGTATAGAAA
1 AAAATTA-T-TCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTTCGTAGGGGTATAGAAA
* * *** * * * * *
2468139 TCTTCAACACTTTTTATATCTTTTCAATTTTTCATTAAAGTACGAAATAAATTTTTTAAAAATTA
64 TCTTCAAAACTTTTCATATCTTTTTGGTTCTCCATTAAGGTACGAAATGAATTTTTTGAAAATTA
2468204 AAAATTAAAT
129 AAAATTAAAT
* * * *
2468214 AAAAATTATTCTTACTTTTTTCAAAATTTTTAATATTCCCTATGG-TTTTCTATAGGGGTATAGA
1 -AAAATTATTCTTA-ATTTTTCAAGATTTCTAATATT-CCTATGGTTTTTC-GTAGGGGTATAGA
* * * *
2468278 AATCTTCAAAACTTTTCATATTTTTTTGGGTCTTCATTAAGGTACAAAATGAATTTTTTGAAAAT
62 AATCTTCAAAACTTTTCATATCTTTTTGGTTCTCCATTAAGGTACGAAATGAATTTTTTGAAAAT
2468343 T--AAA-T--A-
127 TAAAAATTAAAT
* * *
2468349 AAAATTATTCTTAATTTTTTCAAGATTTTTAATATCCCTATGGTCTTTCGT-GGGGTTATAGAAA
1 AAAATTATTCTTAA-TTTTTCAAGATTTCTAATATTCCTATGGTTTTTCGTAGGGG-TATAGAAA
* *
2468413 TCTTCTAAACTTTTCGTATCTTTTTGGTTCTCCATTAAGGTACGAAATGAATTTTTTGAAAATTA
64 TCTTCAAAACTTTTCATATCTTTTTGGTTCTCCATTAAGGTACGAAATGAATTTTTTGAAAATTA
2468478 AAAATTAAAT
129 AAAATTAAAT
*
2468488 GAAAATTATTCTCAATTTTTCAAGATTTCTAATATTCCTATGGTTTTTCGTAGGGGTATAGAAAT
1 -AAAATTATTCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTTCGTAGGGGTATAGAAAT
* *
2468553 CTTCAAAACTTTTCGTATCTTTTTGGTTCTCCATTAAGATA-GAAATGAGATTT
65 CTTCAAAACTTTTCATATCTTTTTGGTTCTCCATTAAGGTACGAAATGA-ATTT
2468606 CAAAATTTAT
Statistics
Matches: 340, Mismatches: 36, Indels: 32
0.83 0.09 0.08
Matches are distributed among these distances:
132 4 0.01
133 74 0.22
134 36 0.11
135 3 0.01
136 2 0.01
138 9 0.03
139 93 0.27
140 41 0.12
141 78 0.23
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (138 bp):
AAAATTATTCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTTCGTAGGGGTATAGAAATC
TTCAAAACTTTTCATATCTTTTTGGTTCTCCATTAAGGTACGAAATGAATTTTTTGAAAATTAAA
AATTAAAT
Found at i:2473867 original size:52 final size:51
Alignment explanation
Indices: 2473782--2473905 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
2473772 ATATGAAAAG
* *
2473782 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
2473833 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
2473885 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
2473906 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:2473918 original size:51 final size:51
Alignment explanation
Indices: 2473782--2473925 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
2473772 ATATGAAAAG
*
2473782 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
2473834 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
2473885 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2473926 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:2473932 original size:13 final size:13
Alignment explanation
Indices: 2473914--2473938 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2473904 CAAAGATCAG
2473914 TGTATCGATACAA
1 TGTATCGATACAA
2473927 TGTATCGATACA
1 TGTATCGATACA
2473939 TTTGCGTAAT
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:2474016 original size:33 final size:33
Alignment explanation
Indices: 2473979--2474045 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2473969 AGTAGCTTAA
2473979 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2474012 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2474045 A
1 A
2474046 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2474019 original size:13 final size:13
Alignment explanation
Indices: 2474001--2474025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2473991 CAAAAAAATA
2474001 TGTATCGATACAT
1 TGTATCGATACAT
2474014 TGTATCGATACA
1 TGTATCGATACA
2474026 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2475010 original size:22 final size:22
Alignment explanation
Indices: 2474985--2475053 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
2474975 ATGCTGATTC
2474985 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * *
2475007 AAGG--TGCCA-ATGTGCTGA-TTC
1 AAGGCCAGCTATAT-TG--GACTTA
2475028 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
2475050 AAGG
1 AAGG
2475054 TGAAGGTGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 12 0.35
23 5 0.15
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:2475079 original size:49 final size:49
Alignment explanation
Indices: 2474861--2475147 Score: 327
Period size: 49 Copynumber: 5.8 Consensus size: 49
2474851 GTGATAAAGA
* * * *
2474861 TGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATAAGAAAAAGG
1 TGCCAATATGCT-GATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG
* * *
2474915 ATGTCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGG
2474968 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
2475011 TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
*
2475060 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
* *
2475109 TGCCAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
2475148 GAAGGGTTGC
Statistics
Matches: 207, Mismatches: 18, Indels: 20
0.84 0.07 0.08
Matches are distributed among these distances:
43 41 0.20
48 1 0.00
49 87 0.42
52 35 0.17
53 6 0.03
54 1 0.00
55 35 0.17
56 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGG
Found at i:2475278 original size:30 final size:29
Alignment explanation
Indices: 2475149--2475388 Score: 213
Period size: 28 Copynumber: 8.2 Consensus size: 29
2475139 TTGGGCTTAG
* *
2475149 AAGGGTTGCCACCGACTTGTGTGGGCTTTGGAA
1 AAGGG-TGCCACTGAC-T-TGTGGGCTTTTG-A
*
2475182 AAGGGTGCCACTGATTTGTGGGC-TTTG-
1 AAGGGTGCCACTGACTTGTGGGCTTTTGA
**
2475209 AAGATTGCCACTGACTTGTGGGCTTTT-A
1 AAGGGTGCCACTGACTTGTGGGCTTTTGA
*
2475237 AAGGTTGCCACTGACTTGTGGGCTTTTGA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGA
*
2475266 ACAGGGTGCCACTAACTTGTGGGCTTTT-A
1 A-AGGGTGCCACTGACTTGTGGGCTTTTGA
* *
2475295 AAGGTTGCCACTGACTTGTGGGCTTTCGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTG-A
*** *
2475325 AAAAATGCCACCGACTTGTGGGC-TTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTG-A
*** * *
2475354 AAAAATGTCACTGACTTGTGGACTTTTG-
1 AAGGGTGCCACTGACTTGTGGGCTTTTGA
2475382 AAGGGTG
1 AAGGGTG
2475389 ATGAATGTCT
Statistics
Matches: 177, Mismatches: 23, Indels: 19
0.81 0.11 0.09
Matches are distributed among these distances:
27 20 0.11
28 56 0.32
29 32 0.18
30 55 0.31
31 1 0.01
32 8 0.05
33 5 0.03
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (29 bp):
AAGGGTGCCACTGACTTGTGGGCTTTTGA
Found at i:2475286 original size:85 final size:88
Alignment explanation
Indices: 2475152--2475320 Score: 254
Period size: 85 Copynumber: 2.0 Consensus size: 88
2475142 GGCTTAGAAG
* * *
2475152 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTGAAGATTG
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGATTG
2475216 CCACTGACTTGTGGGCTTTTAAA
66 CCACTGACTTGTGGGCTTTTAAA
* * * *
2475239 GGTTGCCACTGAC-T-TGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTTAAAGGTTG
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGATTG
2475302 CCACTGACTTGTGGGCTTT
66 CCACTGACTTGTGGGCTTT
2475321 CGAAAAAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
85 33 0.45
86 29 0.39
87 12 0.16
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.33
Consensus pattern (88 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTAACTTGTGGGCTTTTAAAGATTG
CCACTGACTTGTGGGCTTTTAAA
Found at i:2475295 original size:58 final size:57
Alignment explanation
Indices: 2475181--2475383 Score: 230
Period size: 58 Copynumber: 3.5 Consensus size: 57
2475171 GGGCTTTGGA
* * *
2475181 AAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGATTGCCACTGACTTGTGGGCTTTT
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAGAATGCCACTGACTTGTGGGCTTTT
** *
2475236 AAAGGTTGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAA-AGAATGCCACTGACTTGTGGGCTTTT
* * * *
2475294 AAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCACCGACTTGTGGGCTTTGA
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAGAATGCCACTGACTTGTGGGCTTT-T
*** * *
2475353 AAAAAATGTCACTGACTTGTGGACTTTTGAA
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAA
2475384 GGGTGATGAA
Statistics
Matches: 125, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
55 22 0.18
56 4 0.03
57 1 0.01
58 73 0.58
59 25 0.20
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (57 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAGAATGCCACTGACTTGTGGGCTTTT
Found at i:2476828 original size:1 final size:1
Alignment explanation
Indices: 2476824--2476933 Score: 58
Period size: 1 Copynumber: 110.0 Consensus size: 1
2476814 CCGGACCCCC
* * * * * * * * * * *
2476824 TTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTCTTTTGTTTTTTTGTTTTTTATC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * ** *
2476889 ATCATTTTTTTTTGTTTTTTTCATTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2476934 GGAGGACGCC
Statistics
Matches: 76, Mismatches: 33, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.05, C:0.04, G:0.08, T:0.84
Consensus pattern (1 bp):
T
Found at i:2476852 original size:21 final size:22
Alignment explanation
Indices: 2476827--2476931 Score: 103
Period size: 22 Copynumber: 4.9 Consensus size: 22
2476817 GACCCCCTTT
2476827 TTGTTTTTGTTTGTTTTTTT-A
1 TTGTTTTTGTTTGTTTTTTTCA
2476848 TTGTTTTTG-TT-TTTTTTTC-
1 TTGTTTTTGTTTGTTTTTTTCA
*
2476867 TT-TTGTTTTTTTGTTTTTTATCA
1 TTGTT-TTTGTTTGTTTTTT-TCA
** *
2476890 TCATTTTTTTTTGTTTTTTTCA
1 TTGTTTTTGTTTGTTTTTTTCA
* *
2476912 TTTTTTTTGTTTTTTTTTTT
1 TTGTTTTTGTTTGTTTTTTT
2476932 TTGGAGGACG
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.03
19 12 0.17
20 4 0.06
21 15 0.21
22 21 0.30
23 15 0.21
24 2 0.03
ACGTcount: A:0.05, C:0.04, G:0.09, T:0.83
Consensus pattern (22 bp):
TTGTTTTTGTTTGTTTTTTTCA
Found at i:2486641 original size:10 final size:10
Alignment explanation
Indices: 2486626--2486652 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2486616 ATGTATCAAG
2486626 CAAAAACAAA
1 CAAAAACAAA
2486636 CAAAAACAAA
1 CAAAAACAAA
2486646 CAAAAAC
1 CAAAAAC
2486653 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:2490343 original size:52 final size:51
Alignment explanation
Indices: 2490258--2490381 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
2490248 ATATGAAAAG
* *
2490258 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
2490309 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
2490361 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
2490382 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:2490394 original size:51 final size:51
Alignment explanation
Indices: 2490258--2490401 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
2490248 ATATGAAAAG
*
2490258 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
2490310 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
2490361 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2490402 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:2490408 original size:13 final size:13
Alignment explanation
Indices: 2490390--2490414 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2490380 CAAAGATCAG
2490390 TGTATCGATACAA
1 TGTATCGATACAA
2490403 TGTATCGATACA
1 TGTATCGATACA
2490415 TTTGCGTAAT
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:2490482 original size:20 final size:19
Alignment explanation
Indices: 2490453--2490490 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
2490443 GCAGTAGCTT
2490453 AAATTGTATCGATACAAAA
1 AAATTGTATCGATACAAAA
2490472 AAATATGTATCGATACAAA
1 AAAT-TGTATCGATACAAA
2490491 TCGTTGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (19 bp):
AAATTGTATCGATACAAAA
Found at i:2491335 original size:50 final size:49
Alignment explanation
Indices: 2491231--2491381 Score: 153
Period size: 50 Copynumber: 3.1 Consensus size: 49
2491221 CTATCCAAAA
* * * ** * *
2491231 AAAGTCTACATGAGTTGGCACCTAATAGAAGGTAAAGTCTTATAAAGTC
1 AAAGTCCACATAAGATGGCACCTAATAGGGGGTAAAGTCCTATAAAGAC
*
2491280 AAAGTCCACATAAGATGGCACCTAATAGGTGGGTAAAGTCCTATAGAGAC
1 AAAGTCCACATAAGATGGCACCTAATAGG-GGGTAAAGTCCTATAAAGAC
* * * * *
2491330 CAAGTCCATACAA-ATTGGCACC-AATAGGGGGTAAAATCCTATAAAGTC
1 AAAGTCCACATAAGA-TGGCACCTAATAGGGGGTAAAGTCCTATAAAGAC
2491378 AAAG
1 AAAG
2491382 GGTAAAGTCC
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
48 20 0.24
49 32 0.38
50 33 0.39
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (49 bp):
AAAGTCCACATAAGATGGCACCTAATAGGGGGTAAAGTCCTATAAAGAC
Found at i:2491384 original size:23 final size:23
Alignment explanation
Indices: 2491358--2491404 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2491348 CACCAATAGG
2491358 GGGTAAAATCCTATAAAGTCAAA
1 GGGTAAAATCCTATAAAGTCAAA
* *
2491381 GGGTAAAGTCCTTTAAAGTCAAA
1 GGGTAAAATCCTATAAAGTCAAA
2491404 G
1 G
2491405 TTCACATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (23 bp):
GGGTAAAATCCTATAAAGTCAAA
Found at i:2491442 original size:50 final size:48
Alignment explanation
Indices: 2491382--2491673 Score: 169
Period size: 50 Copynumber: 5.9 Consensus size: 48
2491372 AAAGTCAAAG
2491382 GGTAAAGTCCTT-TAAAGTCAAAGTTCACATAAGTTGGCACCTAAAATGAA
1 GGTAAAGT-CTTATAAAGTCAAAG-TCACATAAGTTGGCACCTAAAA-GAA
* * * * * * * *
2491432 GCTAAAGTCCTATAGAGTCTAAGTC-CATGCTAGCTAGCACCTAATAGAA
1 GGTAAAGTCTTATAAAGTCAAAGTCACAT--AAGTTGGCACCTAAAAGAA
* * * *
2491481 GGTAAAGTCTTATAGAGTCAAAGTTTACACAAGTTGGCACCTAATAAGAT
1 GGTAAAGTCTTATAAAGTCAAAG-TCACATAAGTTGGCACCTAA-AAGAA
* * * *
2491531 GGTAAAGTCTTATAAAGTCTAAGTCTACACT-AGTTGGCACCTAGTAGGAG
1 GGTAAAGTCTTATAAAGTCAAAGTC-ACA-TAAGTTGGCACCTA-AAAGAA
* * * * ** * *
2491581 GGTAAAGTAC-TATAAAGTTAAAGTCTAGACAAATTAACACCTAATAGGAG
1 GGTAAAGT-CTTATAAAGTCAAAGTC-ACATAAGTTGGCACCTAA-AAGAA
* * * * *
2491631 GGTAAAGTCTTATAGAGCCCAAGTTCATATAAGGTGGCACCTA
1 GGTAAAGTCTTATAAAGTCAAAG-TCACATAAGTTGGCACCTA
2491674 GTATAAAAGT
Statistics
Matches: 185, Mismatches: 43, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
48 3 0.02
49 40 0.22
50 137 0.74
51 5 0.03
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.26
Consensus pattern (48 bp):
GGTAAAGTCTTATAAAGTCAAAGTCACATAAGTTGGCACCTAAAAGAA
Found at i:2491571 original size:99 final size:101
Alignment explanation
Indices: 2491382--2491644 Score: 275
Period size: 99 Copynumber: 2.6 Consensus size: 101
2491372 AAAGTCAAAG
* * * * *
2491382 GGTAAAGTCCTT-TAAAGTCAAAGTTCACATAAGTTGGCACCTAA-AATGAAGCTAAAGTCCTAT
1 GGTAAAGTACTTATAAAGTCAAAGTTTACACAAGTTGGCACCTAATAA-GAAGGTAAAGTCTTAT
* **
2491445 AGAGTCTAAGTCCATGCTAGCTAGCACCTAATA-GAA
65 AAAGTCTAAGTCCACACTAGCTAGCACCTAATAGGAA
* *
2491481 GGTAAAGT-CTTATAGAGTCAAAGTTTACACAAGTTGGCACCTAATAAGATGGTAAAGTCTTATA
1 GGTAAAGTACTTATAAAGTCAAAGTTTACACAAGTTGGCACCTAATAAGAAGGTAAAGTCTTATA
* * * * *
2491545 AAGTCTAAGTCTACACTAGTTGGCACCTAGTAGGAG
66 AAGTCTAAGTCCACACTAGCTAGCACCTAATAGGAA
* * * * ** * *
2491581 GGTAAAGTAC-TATAAAGTTAAAGTCTAGACAAATTAACACCTAATAGGAGGGTAAAGTCTTATA
1 GGTAAAGTACTTATAAAGTCAAAGTTTACACAAGTTGGCACCTAATAAGAAGGTAAAGTCTTATA
2491645 GAGCCCAAGT
Statistics
Matches: 137, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
98 3 0.02
99 76 0.55
100 57 0.42
101 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (101 bp):
GGTAAAGTACTTATAAAGTCAAAGTTTACACAAGTTGGCACCTAATAAGAAGGTAAAGTCTTATA
AAGTCTAAGTCCACACTAGCTAGCACCTAATAGGAA
Found at i:2492959 original size:20 final size:20
Alignment explanation
Indices: 2492934--2493011 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
2492924 TTTTTACCCA
*
2492934 AATGTATCGAAACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
2492954 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
* *
2492974 AATGTATTGATACATTCTTC
1 AATGTATCGATACATTTTTC
2492994 AATGTATCGATACATTTT
1 AATGTATCGATACATTTT
2493012 GTCTTTTTAC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:2493019 original size:91 final size:91
Alignment explanation
Indices: 2492864--2493034 Score: 288
Period size: 91 Copynumber: 1.9 Consensus size: 91
2492854 TTTTACCTAG
* * *
2492864 ATGTATCAATACATGTATGAATGTTTTAATACATTTTTCAATGTGTCGATACATTTTGTCTTTTT
1 ATGTATCAATACATGTATGAATGTATTAATACATTCTTCAATGTATCGATACATTTTGTCTTTTT
2492929 ACCCAAATGTATCGAAACATTTTTCA
66 ACCCAAATGTATCGAAACATTTTTCA
* *
2492955 ATGTATCGATACATGTATGAATGTATTGATACATTCTTCAATGTATCGATACATTTTGTCTTTTT
1 ATGTATCAATACATGTATGAATGTATTAATACATTCTTCAATGTATCGATACATTTTGTCTTTTT
*
2493020 ACCCAGATGTATCGA
66 ACCCAAATGTATCGA
2493035 TATACTGAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (91 bp):
ATGTATCAATACATGTATGAATGTATTAATACATTCTTCAATGTATCGATACATTTTGTCTTTTT
ACCCAAATGTATCGAAACATTTTTCA
Found at i:2493049 original size:91 final size:91
Alignment explanation
Indices: 2492864--2493059 Score: 279
Period size: 91 Copynumber: 2.2 Consensus size: 91
2492854 TTTTACCTAG
* * * *
2492864 ATGTATCAATACATGTATGAATGTTTTAATACATTTTTCAATGTGTCGATACATTTTGTCTTTTT
1 ATGTATCGATACATGTATGAATGTATTAATACATTCTTCAATGTATCGATACATTTTGTCTTTTT
***
2492929 ACCCAAATGTATCGAAACATTTTTCA
66 ACCCAAATGTATCGAAACATGAATCA
*
2492955 ATGTATCGATACATGTATGAATGTATTGATACATTCTTCAATGTATCGATACATTTTGTCTTTTT
1 ATGTATCGATACATGTATGAATGTATTAATACATTCTTCAATGTATCGATACATTTTGTCTTTTT
*
2493020 ACCCAGATGTATCGATATAC-TGAAT-A
66 ACCCAAATGTATCGA-A-ACATGAATCA
2493046 ATGTATCGATACAT
1 ATGTATCGATACAT
2493060 CTAGTTAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
91 89 0.95
92 3 0.03
93 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (91 bp):
ATGTATCGATACATGTATGAATGTATTAATACATTCTTCAATGTATCGATACATTTTGTCTTTTT
ACCCAAATGTATCGAAACATGAATCA
Found at i:2494696 original size:10 final size:11
Alignment explanation
Indices: 2494681--2494709 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
2494671 CCACTAGATG
2494681 ATTTTTCAAA-
1 ATTTTTCAAAC
2494691 ATTTTTCAAAC
1 ATTTTTCAAAC
2494702 ATTTTTCA
1 ATTTTTCA
2494710 TAAAAACGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTTCAAAC
Found at i:2507011 original size:9 final size:9
Alignment explanation
Indices: 2506997--2507071 Score: 64
Period size: 9 Copynumber: 7.9 Consensus size: 9
2506987 CATCTTTCGT
2506997 ACAAAAAAA
1 ACAAAAAAA
2507006 ACAAAAAAA
1 ACAAAAAAA
2507015 A-ACAAAAAA
1 ACA-AAAAAA
2507024 ACAGAAAAAA
1 ACA-AAAAAA
*
2507034 CCAAAAGCAAAAA
1 --ACAA--AAAAA
2507047 ACAAAAAAA
1 ACAAAAAAA
*
2507056 AC-AAACAA
1 ACAAAAAAA
2507064 ACAAAAAA
1 ACAAAAAA
2507072 GAGGTCCAGA
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
8 8 0.15
9 28 0.52
10 7 0.13
11 4 0.07
12 2 0.04
13 5 0.09
ACGTcount: A:0.83, C:0.15, G:0.03, T:0.00
Consensus pattern (9 bp):
ACAAAAAAA
Found at i:2507013 original size:8 final size:8
Alignment explanation
Indices: 2507000--2507071 Score: 67
Period size: 8 Copynumber: 8.8 Consensus size: 8
2506990 CTTTCGTACA
2507000 AAAAAAAC
1 AAAAAAAC
2507008 AAAAAAAAAC
1 --AAAAAAAC
2507018 AAAAAAAC
1 AAAAAAAC
2507026 AGAAAAAAC
1 A-AAAAAAC
* *
2507035 -CAAAAGC
1 AAAAAAAC
2507042 -AAAAAAC
1 AAAAAAAC
2507049 AAAAAAAAC
1 -AAAAAAAC
*
2507058 AAACAAAC
1 AAAAAAAC
2507066 AAAAAA
1 AAAAAA
2507072 GAGGTCCAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
7 10 0.19
8 21 0.40
9 14 0.26
10 8 0.15
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:2507045 original size:23 final size:24
Alignment explanation
Indices: 2506997--2507071 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 24
2506987 CATCTTTCGT
*
2506997 ACAAAAAAAACAAAAAAAAACAAAAAA
1 ACAAAAAAAAC--AAACAAAC-AAAAA
* * *
2507024 ACAGAAAAAACCAA-AAGCAAAAA
1 ACAAAAAAAACAAACAAACAAAAA
2507047 ACAAAAAAAACAAACAAACAAAAA
1 ACAAAAAAAACAAACAAACAAAAA
2507071 A
1 A
2507072 GAGGTCCAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
23 17 0.41
24 12 0.29
25 2 0.05
27 10 0.24
ACGTcount: A:0.83, C:0.15, G:0.03, T:0.00
Consensus pattern (24 bp):
ACAAAAAAAACAAACAAACAAAAA
Found at i:2508485 original size:32 final size:28
Alignment explanation
Indices: 2508319--2508519 Score: 213
Period size: 28 Copynumber: 6.9 Consensus size: 28
2508309 CGCTCATCTC
* * *
2508319 TTCAAAGCCCACAGGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
2508347 TTGAAATCCCACAAGTCAGTAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
2508375 TTCAAAGCCCAGAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
2508403 TTTAAAGCCCACAAGTCAGTAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
2508431 TTCAAAGCTCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGC--ACCCT
* *
2508461 TTCAAAGCCCACACAAGTCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CCT
*
2508493 TTCAAAGCCCGCACAAGTTAGTGGCAC
1 TTCAAAG-CC-CACAAGTCAGTGGCAC
2508520 TTTTTTTTAA
Statistics
Matches: 145, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
28 91 0.63
30 12 0.08
31 5 0.03
32 37 0.26
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.21
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:2509461 original size:20 final size:20
Alignment explanation
Indices: 2509436--2509613 Score: 131
Period size: 20 Copynumber: 8.3 Consensus size: 20
2509426 TTTTTACCCA
2509436 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
2509456 AATGTATCAATACATGTGTG
1 AATGTATCGATACATTTTTC
* *
2509476 AATGTATCGATATATTCTTC
1 AATGTATCGATACATTTTTC
*
2509496 AATGTGTCGATACATTTTATCTTTTTACTC
1 AATGTATCGATAC-----A---TTTT--TC
*
2509526 AGATGTATCGATACTTTTTTC
1 A-ATGTATCGATACATTTTTC
2509547 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * * *
2509567 AATGTATCAATACATGTATG
1 AATGTATCGATACATTTTTC
*
2509587 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTTTTC
*
2509607 ATTGTAT
1 AATGTAT
2509614 TAATACATTC
Statistics
Matches: 121, Mismatches: 26, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
20 96 0.79
21 3 0.02
23 4 0.03
25 1 0.01
28 3 0.02
30 3 0.02
31 11 0.09
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:2509591 original size:91 final size:91
Alignment explanation
Indices: 2509426--2509602 Score: 230
Period size: 91 Copynumber: 1.9 Consensus size: 91
2509416 AAACATCACA
* * *
2509426 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCAATACATGTGTGAATGTATCGATATAT
1 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCAATACATGTGTCAATGTATCAATACAT
* *
2509491 TCTTCAATGTGTCGATACATTTTATC
66 TCATCAATGTATCGATACATTTTATC
* * * * * *
2509517 TTTTTACTCAGATGTATCGATACTTTTTTCAATGTATCGATACATTTTTCAATGTATCAATACAT
1 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCAATACATGTGTCAATGTATCAATACAT
*
2509582 GT-ATGAATGTATCGATACATT
66 -TCATCAATGTATCGATACATT
2509603 CTTCATTGTA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
91 72 0.99
92 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.44
Consensus pattern (91 bp):
TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCAATACATGTGTCAATGTATCAATACAT
TCATCAATGTATCGATACATTTTATC
Found at i:2509630 original size:111 final size:111
Alignment explanation
Indices: 2509436--2509650 Score: 340
Period size: 111 Copynumber: 1.9 Consensus size: 111
2509426 TTTTTACCCA
* *
2509436 AATGTATCGATACATTTTTCAATGTATCAATACATGTGTGAATGTATCGATATATTCTTCAATGT
1 AATGTATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACATTCTTCAATGT
* * * *
2509501 GTCGATACATTTTATCTTTTTACTCAGATGTATCGATACTTTTTTC
66 ATCAATACATTCTATCTTTTTACCCAGATGTATCGATACTTTTTTC
*
2509547 AATGTATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACATTCTTCATTGT
1 AATGTATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACATTCTTCAATGT
* * *
2509612 ATTAATACATTCTGTCTTTTTACCCAGATGTCTCGATAC
66 ATCAATACATTCTATCTTTTTACCCAGATGTATCGATAC
2509651 AATGAATAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 94 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (111 bp):
AATGTATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACATTCTTCAATGT
ATCAATACATTCTATCTTTTTACCCAGATGTATCGATACTTTTTTC
Found at i:2509667 original size:20 final size:21
Alignment explanation
Indices: 2509639--2509691 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
2509629 TTTTACCCAG
*
2509639 ATGTCTCGATACAAT-GAATA
1 ATGTATCGATACAATCGAATA
2509659 ATGTATCGATA-AATCGAATA
1 ATGTATCGATACAATCGAATA
2509679 ATGTATCGATACA
1 ATGTATCGATACA
2509692 TCTAGTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACAATCGAATA
Found at i:2509682 original size:111 final size:111
Alignment explanation
Indices: 2509436--2509692 Score: 275
Period size: 111 Copynumber: 2.3 Consensus size: 111
2509426 TTTTTACCCA
* *** * *
2509436 AATGTATCGATACATTTTTCAATGTATCAATACATGTGTGAATGTATCGATATATTCTTCAATGT
1 AATGTATCGATAAATGAATCAATGTATCAATACATGTATGAATGTATCGATACATTCTTCAATGT
* * * * * ***
2509501 GTCGATACATTTTATCTTTTTACTCAGATGTATCGATACTTTTTTC
66 ATCAATACATTCTATCTTTTTACCCAGATGTATCGATACATGAATC
* *** *
2509547 AATGTATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACATTCTTCATTGT
1 AATGTATCGATAAATGAATCAATGTATCAATACATGTATGAATGTATCGATACATTCTTCAATGT
* * *
2509612 ATTAATACATTCTGTCTTTTTACCCAGATGTCTCGATACAATGAAT-
66 ATCAATACATTCTATCTTTTTACCCAGATGTATCGATAC-ATGAATC
*
2509658 AATGTATCGATAAATCGAAT-AATGTATCGATACAT
1 AATGTATCGATAAAT-GAATCAATGTATCAATACAT
2509693 CTAGTTAAAA
Statistics
Matches: 125, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
111 122 0.98
112 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (111 bp):
AATGTATCGATAAATGAATCAATGTATCAATACATGTATGAATGTATCGATACATTCTTCAATGT
ATCAATACATTCTATCTTTTTACCCAGATGTATCGATACATGAATC
Found at i:2515782 original size:20 final size:20
Alignment explanation
Indices: 2515759--2515831 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2515749 ACAATTCAAA
2515759 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2515779 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
2515800 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2515820 GTATCGATACAT
1 GTATCGATACAT
2515832 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2515802 original size:21 final size:21
Alignment explanation
Indices: 2515776--2515852 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
2515766 TACATGTTGC
2515776 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
2515797 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
2515817 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
2515837 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
2515853 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:2515810 original size:41 final size:41
Alignment explanation
Indices: 2515759--2515852 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
2515749 ACAATTCAAA
2515759 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
2515800 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2515841 GTATCGATACAT
1 GTATCGATACAT
2515853 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2515909 original size:13 final size:13
Alignment explanation
Indices: 2515891--2515916 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2515881 TACAGCAAGT
2515891 ATGTATCGATACA
1 ATGTATCGATACA
2515904 ATGTATCGATACA
1 ATGTATCGATACA
2515917 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2519998 original size:15 final size:15
Alignment explanation
Indices: 2519978--2520008 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2519968 TAAAAATGTC
*
2519978 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2519993 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2520008 C
1 C
2520009 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2522105 original size:13 final size:13
Alignment explanation
Indices: 2522087--2522125 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2522077 ACATTTTTCC
2522087 TTGTATCGATACA
1 TTGTATCGATACA
2522100 TTGTATCGATACA
1 TTGTATCGATACA
*
2522113 CTGTATCGATACA
1 TTGTATCGATACA
2522126 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2523281 original size:34 final size:35
Alignment explanation
Indices: 2523243--2523309 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2523233 CCTTACAACA
2523243 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2523277 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2523310 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2523785 original size:13 final size:13
Alignment explanation
Indices: 2523767--2523792 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2523757 CAATTTTTTG
2523767 TGTATCGATACAT
1 TGTATCGATACAT
2523780 TGTATCGATACAT
1 TGTATCGATACAT
2523793 ACTTGCTGTA
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:2523857 original size:21 final size:21
Alignment explanation
Indices: 2523831--2523906 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2523821 CTGCCAAGAA
2523831 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
2523852 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2523872 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2523893 ATGTATCGATACAT
1 ATGTATCGATACAT
2523907 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2523876 original size:20 final size:20
Alignment explanation
Indices: 2523851--2523924 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
2523841 ACATCTTTTT
2523851 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
2523871 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
2523892 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
2523912 CATGTATCGATAC
1 CATGTATCGATAC
2523925 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:2523888 original size:41 final size:41
Alignment explanation
Indices: 2523831--2523924 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
2523821 CTGCCAAGAA
2523831 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2523872 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2523913 ATGTATCGATAC
1 ATGTATCGATAC
2523925 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2525718 original size:13 final size:13
Alignment explanation
Indices: 2525700--2525724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2525690 ACTGAAGCAA
2525700 TGTATCGATACAT
1 TGTATCGATACAT
2525713 TGTATCGATACA
1 TGTATCGATACA
2525725 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2528885 original size:34 final size:35
Alignment explanation
Indices: 2528847--2528913 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2528837 CCTTACAACA
2528847 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
2528881 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
2528914 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:2529389 original size:13 final size:13
Alignment explanation
Indices: 2529371--2529396 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2529361 CAATTTTTTG
2529371 TGTATCGATACAT
1 TGTATCGATACAT
2529384 TGTATCGATACAT
1 TGTATCGATACAT
2529397 ACTTGCTGTA
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:2529461 original size:21 final size:21
Alignment explanation
Indices: 2529435--2529510 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2529425 CTGCCAAGAA
2529435 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
2529456 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2529476 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2529497 ATGTATCGATACAT
1 ATGTATCGATACAT
2529511 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2529480 original size:20 final size:20
Alignment explanation
Indices: 2529455--2529528 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
2529445 ACATCTTTTT
2529455 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
2529475 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
2529496 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
2529516 CATGTATCGATAC
1 CATGTATCGATAC
2529529 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:2529492 original size:41 final size:41
Alignment explanation
Indices: 2529435--2529528 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
2529425 CTGCCAAGAA
2529435 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2529476 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2529517 ATGTATCGATAC
1 ATGTATCGATAC
2529529 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2531406 original size:20 final size:20
Alignment explanation
Indices: 2531383--2531455 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2531373 ACAATTCAAA
2531383 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2531403 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
2531424 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2531444 GTATCGATACAT
1 GTATCGATACAT
2531456 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2531426 original size:21 final size:21
Alignment explanation
Indices: 2531400--2531476 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
2531390 TACATGTTGC
2531400 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
2531421 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
2531441 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
2531461 AGATGTATCGATACAT
1 A-ATGTATCGATACAT
2531477 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:2531434 original size:41 final size:41
Alignment explanation
Indices: 2531383--2531476 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
2531373 ACAATTCAAA
2531383 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAAGAT
2531424 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2531465 GTATCGATACAT
1 GTATCGATACAT
2531477 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 6 0.12
41 46 0.88
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2531533 original size:13 final size:13
Alignment explanation
Indices: 2531515--2531540 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2531505 TACAGCAAGT
2531515 ATGTATCGATACA
1 ATGTATCGATACA
2531528 ATGTATCGATACA
1 ATGTATCGATACA
2531541 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2534816 original size:24 final size:24
Alignment explanation
Indices: 2534789--2534860 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
2534779 ACTGTTCATT
* * *
2534789 ACTGTTTATCCCTATTCATGTATC
1 ACTGTTCATCACTGTTCATGTATC
*
2534813 ACTGTTCATCATTGTTCATGTATC
1 ACTGTTCATCACTGTTCATGTATC
*
2534837 ACTATTCATCACTGTTCATGTATC
1 ACTGTTCATCACTGTTCATGTATC
2534861 GATACAATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (24 bp):
ACTGTTCATCACTGTTCATGTATC
Found at i:2534872 original size:13 final size:13
Alignment explanation
Indices: 2534854--2534884 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2534844 ATCACTGTTC
2534854 ATGTATCGATACA
1 ATGTATCGATACA
2534867 ATGTATCGATACA
1 ATGTATCGATACA
*
2534880 GTGTA
1 ATGTA
2534885 AATAGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2543496 original size:20 final size:21
Alignment explanation
Indices: 2543471--2543519 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
2543461 TGCAAGCATG
*
2543471 TCGATACATTCACTTG-TGTA
1 TCGATACATTAACTTGTTGTA
*
2543491 TCGATAAATTAACTTGTTGTA
1 TCGATACATTAACTTGTTGTA
2543512 TCGATACA
1 TCGATACA
2543520 AATTGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (21 bp):
TCGATACATTAACTTGTTGTA
Found at i:2544610 original size:29 final size:28
Alignment explanation
Indices: 2544574--2544632 Score: 109
Period size: 29 Copynumber: 2.1 Consensus size: 28
2544564 AAATTTTGAC
2544574 AATTTTTATTCTTGTCTTAAAATCGATA
1 AATTTTTATTCTTGTCTTAAAATCGATA
2544602 AATTATTTATTCTTGTCTTAAAATCGATA
1 AATT-TTTATTCTTGTCTTAAAATCGATA
2544631 AA
1 AA
2544633 GTATCGTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (28 bp):
AATTTTTATTCTTGTCTTAAAATCGATA
Found at i:2545442 original size:22 final size:23
Alignment explanation
Indices: 2545416--2545466 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
2545406 ATTTTTTATA
*
2545416 ATAATATAA-ATGTAAAGATAAAT
1 ATAAT-TAACATGTAAAAATAAAT
2545439 -TAATTAACATGTAAAAATAAAT
1 ATAATTAACATGTAAAAATAAAT
2545461 ATAATT
1 ATAATT
2545467 TATTACAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 17 0.68
23 5 0.20
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (23 bp):
ATAATTAACATGTAAAAATAAAT
Found at i:2547498 original size:24 final size:24
Alignment explanation
Indices: 2547471--2547542 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
2547461 CTAACTTTAA
2547471 ATTATACTAGTTCTCAGGAAACAG
1 ATTATACTAGTTCTCAGGAAACAG
* ****
2547495 ATTAT-CT--TTCTAACTTTA-A-
1 ATTATACTAGTTCTCAGGAAACAG
2547514 ATTATACTAGTTCTCAGGAAACAG
1 ATTATACTAGTTCTCAGGAAACAG
2547538 ATTAT
1 ATTAT
2547543 CCTACATGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 6 0.18
22 6 0.18
23 3 0.09
24 10 0.30
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (24 bp):
ATTATACTAGTTCTCAGGAAACAG
Found at i:2547515 original size:43 final size:43
Alignment explanation
Indices: 2547454--2547543 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
2547444 GAATGGTAGG
2547454 TATCTTTCTAACTTTAAATTATACTAGTTCTCAGGAAACAGAT
1 TATCTTTCTAACTTTAAATTATACTAGTTCTCAGGAAACAGAT
2547497 TATCTTTCTAACTTTAAATTATACTAGTTCTCAGGAAACAGAT
1 TATCTTTCTAACTTTAAATTATACTAGTTCTCAGGAAACAGAT
2547540 TATC
1 TATC
2547544 CTACATGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (43 bp):
TATCTTTCTAACTTTAAATTATACTAGTTCTCAGGAAACAGAT
Found at i:2550365 original size:129 final size:128
Alignment explanation
Indices: 2550215--2550477 Score: 429
Period size: 129 Copynumber: 2.0 Consensus size: 128
2550205 AAATTGCATT
* *
2550215 TAAAAAATACAAACTCGTTTTCTTCTTTCTGTTTGATTATAGCACATTCATTATTTGAGCATTTA
1 TAAAAAATACAAACTCATTTTCTTCTTTCTGTTTGATTATAGCACATTCATTATGTGAGCATTTA
* * * *
2550280 AAAAAATATGAATAAAAATTTATTT-TTTAAAAAATTTTAATTAGTGAATAATTTTTATTTTTTA
66 AAAAAATATGAATAAAAA--AATTTAATAAAAAAATTTTAATTAGTAAATAATTTTTATTTTTTA
*
2550344 TAAAAAATACAAACTCATTTTCTTCTTTCTGTTTGGTTATAGCACATTCATTATGTGAGCATTTA
1 TAAAAAATACAAACTCATTTTCTTCTTTCTGTTTGATTATAGCACATTCATTATGTGAGCATTTA
*
2550409 AAAAACTATGAATAAAAAAATTTAATAAAAAAATTTTAATTAGTAAATAATTTTTATTTTTTA
66 AAAAAATATGAATAAAAAAATTTAATAAAAAAATTTTAATTAGTAAATAATTTTTATTTTTTA
2550472 TAAAAA
1 TAAAAA
2550478 GTATAAATTT
Statistics
Matches: 125, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
127 4 0.03
128 42 0.34
129 79 0.63
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (128 bp):
TAAAAAATACAAACTCATTTTCTTCTTTCTGTTTGATTATAGCACATTCATTATGTGAGCATTTA
AAAAAATATGAATAAAAAAATTTAATAAAAAAATTTTAATTAGTAAATAATTTTTATTTTTTA
Found at i:2550448 original size:14 final size:13
Alignment explanation
Indices: 2550419--2550444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2550409 AAAAACTATG
2550419 AATAAAAAAATTT
1 AATAAAAAAATTT
2550432 AATAAAAAAATTT
1 AATAAAAAAATTT
2550445 TAATTAGTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAAAAAAATTT
Found at i:2550574 original size:30 final size:30
Alignment explanation
Indices: 2550535--2550596 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2550525 TTAAAATGTG
*
2550535 ATATCAAATT-TAATTATTTTTATTATATATA
1 ATATCAAATTAT-ATTATATTTATTATAT-TA
2550566 ATAT-AAATTATATTATATTTATTATATTA
1 ATATCAAATTATATTATATTTATTATATTA
2550595 AT
1 AT
2550597 TTTATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 4 0.14
30 20 0.69
31 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
ATATCAAATTATATTATATTTATTATATTA
Found at i:2550600 original size:14 final size:15
Alignment explanation
Indices: 2550553--2550601 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
2550543 TTTAATTATT
2550553 TTTATTATATATAATA
1 TTTATTATAT-TAATA
**
2550569 TAAATTATATT-ATA
1 TTTATTATATTAATA
2550583 TTTATTATATTAAT-
1 TTTATTATATTAATA
2550597 TTTAT
1 TTTAT
2550602 ATTTATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 17 0.61
15 3 0.11
16 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTATTATATTAATA
Found at i:2551558 original size:23 final size:23
Alignment explanation
Indices: 2551513--2551559 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2551503 ATTAAATTTT
* *
2551513 AAATATTTTTAATTTATATATAA
1 AAATATTTTTAATATATAAATAA
2551536 AAATATTTTTAA-ATATAAAATAA
1 AAATATTTTTAATATAT-AAATAA
2551559 A
1 A
2551560 TAAATCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATTTTTAATATATAAATAA
Found at i:2551715 original size:32 final size:31
Alignment explanation
Indices: 2551679--2551774 Score: 140
Period size: 31 Copynumber: 3.1 Consensus size: 31
2551669 TTTAATAATG
2551679 TTAAATTTATAAATAATTATATATAATATTTA
1 TTAAATTTATAAATAATTATATATAATA-TTA
* * *
2551711 TTAAATTTATAATTAATTTTATTTAATATTA
1 TTAAATTTATAAATAATTATATATAATATTA
*
2551742 ATAAATTTATAAATAATTATATATAAT-TTA
1 TTAAATTTATAAATAATTATATATAATATTA
2551772 TTA
1 TTA
2551775 TCTTTACAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 5 0.09
31 26 0.46
32 25 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
TTAAATTTATAAATAATTATATATAATATTA
Found at i:2552889 original size:16 final size:16
Alignment explanation
Indices: 2552868--2552978 Score: 91
Period size: 16 Copynumber: 6.9 Consensus size: 16
2552858 GATTATTTTT
2552868 GAGTTCGGATCATTTC
1 GAGTTCGGATCATTTC
*
2552884 GAGTTC-GAGTTATTTC
1 GAGTTCGGA-TCATTTC
* *
2552900 AAGTTCGAATCATTTC
1 GAGTTCGGATCATTTC
* *
2552916 GGGTTC-GAGTTATTTC
1 GAGTTCGGA-TCATTTC
*
2552932 AAGTTCGGATCATTTC
1 GAGTTCGGATCATTTC
* * *
2552948 GGGTTCAGATTATTTC
1 GAGTTCGGATCATTTC
* *
2552964 GAATTCAGATCATTT
1 GAGTTCGGATCATTT
2552979 TAGATTCGGG
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
15 3 0.04
16 67 0.92
17 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.41
Consensus pattern (16 bp):
GAGTTCGGATCATTTC
Found at i:2552906 original size:32 final size:32
Alignment explanation
Indices: 2552869--2552978 Score: 161
Period size: 32 Copynumber: 3.4 Consensus size: 32
2552859 ATTATTTTTG
*
2552869 AGTTCGGATCATTTCGAGTTCGAGTTATTTCA
1 AGTTCGGATCATTTCGGGTTCGAGTTATTTCA
*
2552901 AGTTCGAATCATTTCGGGTTCGAGTTATTTCA
1 AGTTCGGATCATTTCGGGTTCGAGTTATTTCA
2552933 AGTTCGGATCATTTCGGGTTC-AGATTATTTCGA
1 AGTTCGGATCATTTCGGGTTCGAG-TTATTTC-A
*
2552966 A-TTCAGATCATTT
1 AGTTCGGATCATTT
2552979 TAGATTCGGG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
31 2 0.03
32 68 0.94
33 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (32 bp):
AGTTCGGATCATTTCGGGTTCGAGTTATTTCA
Found at i:2553102 original size:22 final size:21
Alignment explanation
Indices: 2553064--2553104 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2553054 AACATTCGAG
*
2553064 TTAAATTGGGTTCAAGTCATT
1 TTAAATTAGGTTCAAGTCATT
*
2553085 TTAAATTTAGGTTTAAGTCA
1 TTAAA-TTAGGTTCAAGTCA
2553105 ATCAGGATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (21 bp):
TTAAATTAGGTTCAAGTCATT
Found at i:2553831 original size:16 final size:16
Alignment explanation
Indices: 2553812--2553904 Score: 100
Period size: 16 Copynumber: 5.8 Consensus size: 16
2553802 ATTGTTCGAG
*
2553812 TCATTTTGGGTTCGGA
1 TCATTTTGAGTTCGGA
* *
2553828 TCATTTCGGGTTC-GA
1 TCATTTTGAGTTCGGA
*
2553843 GTCATTTTGAGTTCCGA
1 -TCATTTTGAGTTCGGA
*
2553860 TCATTTTGGGTT-GCGA
1 TCATTTTGAGTTCG-GA
*
2553876 TCATTTTGAATTCGGA
1 TCATTTTGAGTTCGGA
2553892 TCATTTTGAGTTC
1 TCATTTTGAGTTC
2553905 AAGTCATTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
15 2 0.03
16 60 0.92
17 3 0.05
ACGTcount: A:0.16, C:0.15, G:0.25, T:0.44
Consensus pattern (16 bp):
TCATTTTGAGTTCGGA
Found at i:2553841 original size:32 final size:32
Alignment explanation
Indices: 2553805--2553929 Score: 153
Period size: 32 Copynumber: 3.9 Consensus size: 32
2553795 CGGGTTAATT
* *
2553805 GTTCGAGTCATTTTGGGTTCGGATCATTTCGG
1 GTTCGAGTCATTTTGAGTTCGGATCATTTTGG
*
2553837 GTTCGAGTCATTTTGAGTTCCGATCATTTTGG
1 GTTCGAGTCATTTTGAGTTCGGATCATTTTGG
* *
2553869 GTTGCGA-TCATTTTGAATTCGGATCATTTTGA
1 GTT-CGAGTCATTTTGAGTTCGGATCATTTTGG
* * * *
2553901 GTTCAAGTCATTTCGAGTTTGGATTATTT
1 GTTCGAGTCATTTTGAGTTCGGATCATTT
2553930 CAGGTTTCGG
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
31 2 0.03
32 75 0.94
33 3 0.04
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.44
Consensus pattern (32 bp):
GTTCGAGTCATTTTGAGTTCGGATCATTTTGG
Found at i:2553896 original size:48 final size:48
Alignment explanation
Indices: 2553812--2553904 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 48
2553802 ATTGTTCGAG
**
2553812 TCATTTTGGGTTCGGATCATTTCGGGTTCGAGTCATTTTGAGTTCCGA
1 TCATTTTGGGTTCGGATCATTTCGAATTCGAGTCATTTTGAGTTCCGA
*
2553860 TCATTTTGGGTT-GCGATCATTTTGAATTCG-GATCATTTTGAGTTC
1 TCATTTTGGGTTCG-GATCATTTCGAATTCGAG-TCATTTTGAGTTC
2553905 AAGTCATTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
47 2 0.05
48 38 0.95
ACGTcount: A:0.16, C:0.15, G:0.25, T:0.44
Consensus pattern (48 bp):
TCATTTTGGGTTCGGATCATTTCGAATTCGAGTCATTTTGAGTTCCGA
Found at i:2553911 original size:16 final size:15
Alignment explanation
Indices: 2553805--2553919 Score: 70
Period size: 16 Copynumber: 7.2 Consensus size: 15
2553795 CGGGTTAATT
*
2553805 GTTCGAGTCATTTTGG
1 GTTC-AGTCATTTTGA
* * *
2553821 GTTCGGATCATTTCGG
1 GTTCAG-TCATTTTGA
2553837 GTTCGAGTCATTTTGA
1 GTTC-AGTCATTTTGA
* *
2553853 GTTCCGATCATTTTGG
1 GTTCAG-TCATTTTGA
2553869 GTTGC-GATCATTTTGA
1 GTT-CAG-TCATTTTGA
* *
2553885 ATTCGGATCATTTTGA
1 GTTCAG-TCATTTTGA
*
2553901 GTTCAAGTCATTTCGA
1 GTTC-AGTCATTTTGA
2553917 GTT
1 GTT
2553920 TGGATTATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
15 3 0.04
16 75 0.93
17 3 0.04
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43
Consensus pattern (15 bp):
GTTCAGTCATTTTGA
Found at i:2553912 original size:48 final size:47
Alignment explanation
Indices: 2553805--2553913 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 47
2553795 CGGGTTAATT
**
2553805 GTTCGAGTCATTTTGGGTTCGGATCATTTCGGGTTCGAGTCATTTTGA
1 GTTC-AGTCATTTTGGGTTCGGATCATTTCGAATTCGAGTCATTTTGA
* *
2553853 GTTCCGATCATTTTGGGTT-GCGATCATTTTGAATTCG-GATCATTTTGA
1 GTTCAG-TCATTTTGGGTTCG-GATCATTTCGAATTCGAG-TCATTTTGA
2553901 GTTCAAGTCATTT
1 GTTC-AGTCATTT
2553914 CGAGTTTGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
47 3 0.06
48 48 0.92
49 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43
Consensus pattern (47 bp):
GTTCAGTCATTTTGGGTTCGGATCATTTCGAATTCGAGTCATTTTGA
Found at i:2557801 original size:19 final size:21
Alignment explanation
Indices: 2557760--2557809 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
2557750 CAATAATTTT
*
2557760 TATCGATACATTCAGTAAATG
1 TATCGATACATTAAGTAAATG
2557781 TATCGATACA-TAAGT-AATG
1 TATCGATACATTAAGTAAATG
2557800 TATCGATACA
1 TATCGATACA
2557810 GTGTATCGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 14 0.50
20 4 0.14
21 10 0.36
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (21 bp):
TATCGATACATTAAGTAAATG
Found at i:2560458 original size:28 final size:27
Alignment explanation
Indices: 2560384--2560458 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
2560374 TTTTTATAAT
* *
2560384 CGGGGGTACTCCAACCCTGTTATTTCA
1 CGGGGATACTCCAACCCCGTTATTTCA
*
2560411 TCGGGGATACTCCAATCCCGTTATTTTCGA
1 -CGGGGATACTCCAACCCCGTTA-TTTC-A
2560441 -GGGGATACTCCAACCCCG
1 CGGGGATACTCCAACCCCG
2560459 ATTTTATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.27
Consensus pattern (27 bp):
CGGGGATACTCCAACCCCGTTATTTCA
Found at i:2560568 original size:51 final size:50
Alignment explanation
Indices: 2560441--2560627 Score: 225
Period size: 51 Copynumber: 3.7 Consensus size: 50
2560431 TTATTTTCGA
*
2560441 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAA-T
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAA-TTTTCACAATT
* * * *
2560491 CGGGATTCTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATT
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTT-TCACAATT
* * * *
2560542 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTCTATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTC-ACAATT
* *
2560593 GGGGATACTCCAGCCCCG-TTGTTATCTCCAAAATA
1 GGGGATACTCCAACCCCGATT-TTATTTCCAAAATA
2560628 TTAAATTTTT
Statistics
Matches: 117, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
49 3 0.03
50 44 0.38
51 70 0.60
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTCACAATT
Found at i:2570442 original size:13 final size:13
Alignment explanation
Indices: 2570424--2570449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2570414 CAATTTTTTG
2570424 TGTATCGATACAT
1 TGTATCGATACAT
2570437 TGTATCGATACAT
1 TGTATCGATACAT
2570450 ACTTGCTGTA
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:2571146 original size:21 final size:21
Alignment explanation
Indices: 2571105--2571148 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2571095 CTCCCCTTTA
* *
2571105 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
2571126 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
2571147 TC
1 TC
2571149 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:2572974 original size:13 final size:13
Alignment explanation
Indices: 2572956--2572992 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
2572946 AATCACCCTA
2572956 TATCGATACAATG
1 TATCGATACAATG
2572969 TATCGATACAATG
1 TATCGATACAATG
2572982 TATCGATACAA
1 TATCGATACAA
2572993 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:2575083 original size:15 final size:15
Alignment explanation
Indices: 2575063--2575093 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2575053 ATTTCGTTTG
*
2575063 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2575078 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2575093 G
1 G
2575094 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2576926 original size:21 final size:21
Alignment explanation
Indices: 2576897--2576941 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2576887 AAGTTTTCAT
*
2576897 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2576917 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2576939 TTT
1 TTT
2576942 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2579179 original size:13 final size:13
Alignment explanation
Indices: 2579161--2579186 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2579151 CAATTTTTTG
2579161 TGTATCGATACAT
1 TGTATCGATACAT
2579174 TGTATCGATACAT
1 TGTATCGATACAT
2579187 ACTTGCTGTA
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:2579693 original size:16 final size:17
Alignment explanation
Indices: 2579652--2579693 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2579642 AGATGATTTG
*
2579652 TTTAATTAAACTTAGGA
1 TTTAATTGAACTTAGGA
*
2579669 TTTAA-TGAAGTTA-GA
1 TTTAATTGAACTTAGGA
2579684 TTTAATTGAA
1 TTTAATTGAA
2579694 TAAAAGGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 7 0.32
16 10 0.45
17 5 0.23
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.43
Consensus pattern (17 bp):
TTTAATTGAACTTAGGA
Done.