Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 20 of 47
Found at i:2966648 original size:10 final size:10
Alignment explanation
Indices: 2966621--2966686 Score: 71
Period size: 10 Copynumber: 6.6 Consensus size: 10
2966611 AGTCTTAGAG
2966621 TTTTTATTTA
1 TTTTTATTTA
*
2966631 GATTTTATTTA
1 -TTTTTATTTA
2966642 TTTTTATTTA
1 TTTTTATTTA
** *
2966652 TTTAAAATTA
1 TTTTTATTTA
*
2966662 GTTTTATTTA
1 TTTTTATTTA
2966672 -TTTTATTTA
1 TTTTTATTTA
2966681 TTTTTA
1 TTTTTA
2966687 AATTATATAG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
9 9 0.20
10 27 0.60
11 9 0.20
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:2976588 original size:66 final size:66
Alignment explanation
Indices: 2976482--2976612 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 66
2976472 CCTATAACTT
*
2976482 GAAATATGGCATATATGGTGGTTGCATGTCACGGTCCATATTTTTTGCAAAAAGGGTTTTAGGGT
1 GAAATATGGCATATATGGTGGTTGCACGTCACGGTCCATATTTTTTGCAAAAAGGGTTTTAGGGT
2976547 C
66 C
* * *
2976548 GAAATATGGCATATTTGGTGGTTGTACGTCACGGTCCATATTTTTTGCAGAAAGGGTTTTAGGGT
1 GAAATATGGCATATATGGTGGTTGCACGTCACGGTCCATATTTTTTGCAAAAAGGGTTTTAGGGT
2976613 GAAGGTGTGA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.36
Consensus pattern (66 bp):
GAAATATGGCATATATGGTGGTTGCACGTCACGGTCCATATTTTTTGCAAAAAGGGTTTTAGGGT
C
Found at i:2983013 original size:21 final size:21
Alignment explanation
Indices: 2982973--2983013 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2982963 TTAAGTATAA
*
2982973 ATATTTTTCAAGCTATAAATT
1 ATATTTTTCAAGCTAAAAATT
2982994 ATATGTTTTCAAG-TAAAAAT
1 ATAT-TTTTCAAGCTAAAAAT
2983014 AATCCAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (21 bp):
ATATTTTTCAAGCTAAAAATT
Found at i:2983320 original size:20 final size:20
Alignment explanation
Indices: 2983295--2983347 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
2983285 TTCAAATGCA
*
2983295 TGTATCGATACATTATGAAT
1 TGTATCGATACATTAAGAAT
2983315 TGTATCGATACATTAAGAAT
1 TGTATCGATACATTAAGAAT
2983335 TGTATCGATACAT
1 TGTATCGATACAT
2983348 AGGAGCGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTAAGAAT
Found at i:2983573 original size:34 final size:35
Alignment explanation
Indices: 2983534--2983606 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
2983524 ATTTTCTACA
*
2983534 TTTCAAAGAGCTTTTATATT-CTTTGTTG-TTATTC
1 TTTCAAAGAGCATTTATATTCCTTTG-TGCTTATTC
** *
2983568 TTTCAAAGCTCATTTGTATTCCTTTGTGCTTATTC
1 TTTCAAAGAGCATTTATATTCCTTTGTGCTTATTC
2983603 TTTC
1 TTTC
2983607 CACAAACACA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 18 0.55
35 15 0.45
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (35 bp):
TTTCAAAGAGCATTTATATTCCTTTGTGCTTATTC
Found at i:2985284 original size:33 final size:33
Alignment explanation
Indices: 2985242--2985306 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2985232 TTAGAAGTAA
*
2985242 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATAT-ACCATGTATCGATACAT
2985275 TGTATCGATACAATATACCATGTATCGATACA
1 TGTATCGATACAATATACCATGTATCGATACA
2985307 AATAGTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATATACCATGTATCGATACAT
Found at i:2985305 original size:13 final size:13
Alignment explanation
Indices: 2985262--2985286 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2985252 CAATTCATCA
2985262 TGTATCGATACAT
1 TGTATCGATACAT
2985275 TGTATCGATACA
1 TGTATCGATACA
2985287 ATATACCATG
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:2986186 original size:17 final size:18
Alignment explanation
Indices: 2986164--2986201 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2986154 TTATAAAAAC
* *
2986164 AAAGTCA-AATTACAATG
1 AAAGTCACAATAAAAATG
2986181 AAAGTCACAATAAAAATG
1 AAAGTCACAATAAAAATG
2986199 AAA
1 AAA
2986202 AACAAGTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.18
Consensus pattern (18 bp):
AAAGTCACAATAAAAATG
Found at i:2991372 original size:13 final size:13
Alignment explanation
Indices: 2991354--2991379 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2991344 TACACAAAGT
2991354 ATGTATCGATACA
1 ATGTATCGATACA
2991367 ATGTATCGATACA
1 ATGTATCGATACA
2991380 CAAAAAAATT
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:2991398 original size:34 final size:32
Alignment explanation
Indices: 2991336--2991400 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2991326 TAGCCAAACT
**
2991336 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
2991368 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
2991401 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:2995467 original size:15 final size:15
Alignment explanation
Indices: 2995447--2995477 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2995437 TAAAAATGTC
*
2995447 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2995462 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2995477 C
1 C
2995478 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:2997568 original size:13 final size:13
Alignment explanation
Indices: 2997550--2997574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2997540 CATTTTTCTT
2997550 TGTATCGATACAA
1 TGTATCGATACAA
2997563 TGTATCGATACA
1 TGTATCGATACA
2997575 GGGGGATTAT
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:3000151 original size:13 final size:13
Alignment explanation
Indices: 3000133--3000158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3000123 TACACAAAGT
3000133 ATGTATCGATACA
1 ATGTATCGATACA
3000146 ATGTATCGATACA
1 ATGTATCGATACA
3000159 TAAAAAAATT
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:3004961 original size:79 final size:79
Alignment explanation
Indices: 3004830--3005026 Score: 224
Period size: 79 Copynumber: 2.5 Consensus size: 79
3004820 ACAACGGGGC
3004830 TGGAGTATCCCCGATTATAAAAAATCGATGTTCTAGAAATAAAACTGGGGTTGGAGTATCCCCTC
1 TGGAGTATCCCCGATTATAAAAAATCGATGTTCTAGAAATAAAACTGGGGTTGGAGTATCCCCTC
**
3004895 GGAAATAACAGGGT
66 AAAAATAACAGGGT
* * *
3004909 TGGAGTATCCCTGATTATAGAAAATCAGTAT-TT-T-GAAAATGAAA-TCGGGGTTGGAGTATCC
1 TGGAGTATCCCCGATTATAAAAAATC-G-ATGTTCTAG-AAATAAAACT-GGGGTTGGAGTATCC
3004970 CCTCAAAAATAACAGGGT
62 CCTCAAAAATAACAGGGT
* * * * *
3004988 TAGAGCATCCCCAATTGTGAAAAATCGATGATT-TAGAAA
1 TGGAGTATCCCCGATTATAAAAAATCGATG-TTCTAGAAA
3005027 CAAGGGCGGG
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
77 2 0.02
78 3 0.03
79 88 0.89
80 4 0.04
81 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26
Consensus pattern (79 bp):
TGGAGTATCCCCGATTATAAAAAATCGATGTTCTAGAAATAAAACTGGGGTTGGAGTATCCCCTC
AAAAATAACAGGGT
Found at i:3005107 original size:51 final size:51
Alignment explanation
Indices: 3005038--3005150 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 51
3005028 AAGGGCGGGA
* * *
3005038 TTGAAGTAT-CCTCGATTATG-AGAATTCGATATTTTGGAAATAAAATCGGAG
1 TTGAAGTATCCCT-AATTATGAAAAATT-GATATTTTAGAAATAAAATCGGAG
* * *
3005089 TTGGAGTATCCCTAATTATGAAAAATTGGTATTTTAGAAATAAAATCGGGG
1 TTGAAGTATCCCTAATTATGAAAAATTGATATTTTAGAAATAAAATCGGAG
3005140 TTGAAGTATCC
1 TTGAAGTATCC
3005151 TCTCAAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
51 45 0.85
52 8 0.15
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (51 bp):
TTGAAGTATCCCTAATTATGAAAAATTGATATTTTAGAAATAAAATCGGAG
Found at i:3005253 original size:109 final size:108
Alignment explanation
Indices: 3005086--3005368 Score: 313
Period size: 109 Copynumber: 2.6 Consensus size: 108
3005076 AATAAAATCG
* ** * *
3005086 GAGTTGGAGTATCCCTAATTATG-AAAAATTGGTATTTTAGAAATAAAATCGGGGTTGAAGTATC
1 GAGTTGGAGTATCCCCAATTATGAAAAAATTAATATTTTAGAAATAAAACCAGGGTTGAAGTATC
*
3005150 CTCTCAAAAATAACGAGATTGGAGTATCC-CTGATGAAATAACA
66 CCCTCAAAAATAACGAGATTGGAGTATCCTC-GATGAAATAACA
* * * * *
3005193 GGGTTGGAGTACCCCCGATTATGAAAAAATTAATATTTTTAGATATAAAGCCAGGGTTGAAGTAT
1 GAGTTGGAGTATCCCCAATTATGAAAAAATTAATA-TTTTAGAAATAAAACCAGGGTTGAAGTAT
* * * *
3005258 CCCCTTAGAAATAACGGGGTTGGAGTATCCTCGATGAAATAACA
65 CCCCTCAAAAATAACGAGATTGGAGTATCCTCGATGAAATAACA
* ** * * * *
3005302 GAGTTGGAGTATCCCCAATTGTG-AAAAATTGGTGTTTTGGAAATAAAATC-GGAGTTGGAGTAT
1 GAGTTGGAGTATCCCCAATTATGAAAAAATTAATATTTTAGAAATAAAACCAGG-GTTGAAGTAT
3005365 CCCC
65 CCCC
3005369 AATTGTGGTA
Statistics
Matches: 145, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
106 2 0.01
107 44 0.30
108 17 0.12
109 81 0.56
110 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (108 bp):
GAGTTGGAGTATCCCCAATTATGAAAAAATTAATATTTTAGAAATAAAACCAGGGTTGAAGTATC
CCCTCAAAAATAACGAGATTGGAGTATCCTCGATGAAATAACA
Found at i:3005361 original size:51 final size:51
Alignment explanation
Indices: 3005302--3005447 Score: 193
Period size: 51 Copynumber: 2.9 Consensus size: 51
3005292 TGAAATAACA
*
3005302 GAGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATCG
1 GAGTTGGAGTATCCCCAATTGTGAAAAATTGATGTTTTGGAAATAAAATCG
** * * *
3005353 GAGTTGGAGTATCCCCAATTGTGGTAAATCGATGCTTTAGAAATAAAATCG
1 GAGTTGGAGTATCCCCAATTGTGAAAAATTGATGTTTTGGAAATAAAATCG
* * ** *
3005404 GAGTTAGAGTATCCCCGATTAAGAAAGATTGATGTTTTGGAAAT
1 GAGTTGGAGTATCCCCAATTGTGAAAAATTGATGTTTTGGAAAT
3005448 GGAACCGGGA
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 79 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GAGTTGGAGTATCCCCAATTGTGAAAAATTGATGTTTTGGAAATAAAATCG
Found at i:3007832 original size:20 final size:20
Alignment explanation
Indices: 3007807--3007860 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
3007797 GTATCGGTAT
*
3007807 AATGTATCGATACAATG-AGC
1 AATGTATCGATACAATGCA-A
3007827 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATGCAA
3007847 AATGTATCGATACA
1 AATGTATCGATACA
3007861 TCTGGGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACAATGCAA
Found at i:3007894 original size:13 final size:13
Alignment explanation
Indices: 3007876--3007905 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3007866 GTAAACCTAG
3007876 AATGTATCGATAC
1 AATGTATCGATAC
*
3007889 AATGTATGGATAC
1 AATGTATCGATAC
3007902 AATG
1 AATG
3007906 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:3007912 original size:20 final size:20
Alignment explanation
Indices: 3007887--3007943 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
3007877 ATGTATCGAT
*
3007887 ACAATGTATGGATACAATGA
1 ACAATGTATCGATACAATGA
* *
3007907 ACAATGTATCAATATAATGA
1 ACAATGTATCGATACAATGA
*
3007927 ATAATGTATCGATACAA
1 ACAATGTATCGATACAA
3007944 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:3008819 original size:42 final size:43
Alignment explanation
Indices: 3008684--3008830 Score: 176
Period size: 42 Copynumber: 3.4 Consensus size: 43
3008674 AAATGCATCT
* *
3008684 TGCTCTTTGAGGAC-AAAAGAAAGAGGAAAATAAAGTGCGTCC
1 TGCTCTTTGAGGACTAAAGGAAAGAGGAAAATAAAGTGTGTCC
* * * *
3008726 TGCTGC-CTAAGGACAAAAGAGAAAAGAAGG-GAATAAAGTGTGTCC
1 TGCT-CTTTGAGGACTAAAG-G-AAAG-AGGAAAATAAAGTGTGTCC
3008771 TGCTCTTTGAGGA-TAAAGGAAAGAGGAAAATAAAGTGTGTCC
1 TGCTCTTTGAGGACTAAAGGAAAGAGGAAAATAAAGTGTGTCC
3008813 TGCTCTTTGAGGACTAAA
1 TGCTCTTTGAGGACTAAA
3008831 AAGTGCCACC
Statistics
Matches: 88, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
41 3 0.03
42 41 0.47
43 9 0.10
44 6 0.07
45 26 0.30
46 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.21
Consensus pattern (43 bp):
TGCTCTTTGAGGACTAAAGGAAAGAGGAAAATAAAGTGTGTCC
Found at i:3008907 original size:28 final size:29
Alignment explanation
Indices: 3008876--3008930 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
3008866 AGGCTTCCTA
* * *
3008876 CTCTTTGCGGACT-GGAAGGTGCCACCTG
1 CTCTTTGAGGACTAGAAAAGTGCCACCTG
3008904 CTCTTTGAGGACTAGAAAAGTGCCACC
1 CTCTTTGAGGACTAGAAAAGTGCCACC
3008931 AACTTGTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (29 bp):
CTCTTTGAGGACTAGAAAAGTGCCACCTG
Found at i:3009026 original size:94 final size:94
Alignment explanation
Indices: 3008904--3009140 Score: 307
Period size: 94 Copynumber: 2.5 Consensus size: 94
3008894 GTGCCACCTG
* *
3008904 CTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTATTCTTTGAG
1 CTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTAAG
** * *
3008969 GACTAAAAGGCGAA-A-GAAGAGAGAATCCTA
65 GACTAAAA-AAGAAGAGGAAAAG-GAATCATA
* *
3008999 CTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTAAGG
1 CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTAAGG
** *
3009064 ACTAAAAAAGAAGAGGAAAAGGCGTCATG
66 ACTAAAAAAGAAGAGGAAAAGGAATCATA
* *
3009093 CTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAG
1 CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAG
3009141 AAAAGGCATC
Statistics
Matches: 125, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
93 3 0.02
94 99 0.79
95 23 0.18
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (94 bp):
CTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTACTCTTTAAGG
ACTAAAAAAGAAGAGGAAAAGGAATCATA
Found at i:3009156 original size:61 final size:61
Alignment explanation
Indices: 3009079--3009235 Score: 217
Period size: 61 Copynumber: 2.6 Consensus size: 61
3009069 AAAAGAAGAG
* *
3009079 GAAAAGGCGTCATGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA
1 GAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA
* ** * *
3009140 GAAAAGGCATCCTGCTCTTTGAGGACTAGACGGTGCCACCAACTTGTGTGGGCTTTGTAAA
1 GAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA
* *
3009201 GAGAAA-GCATCCTGCTCTTTGAGAACTGAAAAGTG
1 GA-AAAGGCATCCTGCTCTTTGAGGACTAAAAAGTG
3009236 AAAGGAGAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
61 80 0.96
62 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (61 bp):
GAAAAGGCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAA
Found at i:3010263 original size:24 final size:24
Alignment explanation
Indices: 3010209--3010265 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3010199 CTTTTCTCTC
* *
3010209 TTTTTTCTTTGTTTTTTTTTGTTG
1 TTTTTTGTTTGTTTTTTTTTATTG
*
3010233 TTTTTTGTTTTTTATTTTTTTATT-
1 TTTTTTGTTTGTT-TTTTTTTATTG
3010257 TTTTTTGTT
1 TTTTTTGTT
3010266 AGTGGGATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.04, C:0.02, G:0.09, T:0.86
Consensus pattern (24 bp):
TTTTTTGTTTGTTTTTTTTTATTG
Found at i:3022820 original size:79 final size:78
Alignment explanation
Indices: 3022605--3022833 Score: 221
Period size: 79 Copynumber: 2.9 Consensus size: 78
3022595 TGGAGATAAC
* * * *
3022605 AACGGGGCTAGAGTATCCCCGATTATGGAAAATCGATG-TTCCAGAAATAAAACAGGGGTTGGAG
1 AACGGGGTTAGAGTATCCCCGATTATGAAAAATCGATGATT-TAGAAAT-AAACCGGGGTTGGAG
* *
3022669 TATCCCCTCGGAAGT
64 TATCCCCTCGAAAAT
* * * * * *
3022684 AACAGGGTTAGAGTATCTCTGATTAT-AGAAAATCGGT-ATTTTGAAAATGAAATCGGGGTTGGA
1 AACGGGGTTAGAGTATCCCCGATTATGA-AAAATCGATGATTTAG-AAAT-AAACCGGGGTTGGA
* *
3022747 GTATCTCCTCTAAAAT
63 GTATCCCCTCGAAAAT
* * * *
3022763 AACGGGGTTAGAGCATCCCCGATTGTGAAAAATCGATGATTTAGAAATAAGGCCGGGGTTGAAGT
1 AACGGGGTTAGAGTATCCCCGATTATGAAAAATCGATGATTTAGAAATAA-ACCGGGGTTGGAGT
3022828 ATCCCC
65 ATCCCC
3022834 GATTATGAGA
Statistics
Matches: 118, Mismatches: 26, Indels: 12
0.76 0.17 0.08
Matches are distributed among these distances:
78 3 0.03
79 109 0.92
80 6 0.05
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (78 bp):
AACGGGGTTAGAGTATCCCCGATTATGAAAAATCGATGATTTAGAAATAAACCGGGGTTGGAGTA
TCCCCTCGAAAAT
Found at i:3022905 original size:51 final size:51
Alignment explanation
Indices: 3022777--3022935 Score: 153
Period size: 51 Copynumber: 3.1 Consensus size: 51
3022767 GGGTTAGAGC
* * * *** * *
3022777 ATCCCCGATTGTGAAAAATCGATGA-TTTAGAAATAAGGCCGGGGTTGAAGT
1 ATCCCCGATTATGAGAAATCAAT-ATTTTAGAAATAAAATCGGAGTTGGAGT
3022828 ATCCCCGATTATGAGAAATCAATATTTT-GAAAATAAAATCGGAGTTGGAGT
1 ATCCCCGATTATGAGAAATCAATATTTTAG-AAATAAAATCGGAGTTGGAGT
*** * *
3022879 ATCCCCGATTATG-GAAAATTGGTATTTTAGAACTAAAATCGGGGTTGGAGT
1 ATCCCCGATTATGAG-AAATCAATATTTTAGAAATAAAATCGGAGTTGGAGT
3022930 ATCCCC
1 ATCCCC
3022936 TCGGAAATAA
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
50 3 0.03
51 87 0.96
52 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (51 bp):
ATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAATCGGAGTTGGAGT
Found at i:3022954 original size:28 final size:28
Alignment explanation
Indices: 3022923--3022991 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
3022913 AAAATCGGGG
** *
3022923 TTGGAGTATCCCCTCGGAAATAACAGGA
1 TTGGAGTATCCCCGAGAAAATAACAGGA
* *
3022951 TTGGAGTATCCCCGATAAAATAACAGGG
1 TTGGAGTATCCCCGAGAAAATAACAGGA
3022979 TTGGAGTACTCCC
1 TTGGAGTA-TCCC
3022992 GATTATGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 31 0.89
29 4 0.11
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (28 bp):
TTGGAGTATCCCCGAGAAAATAACAGGA
Found at i:3023067 original size:28 final size:28
Alignment explanation
Indices: 3023027--3023098 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
3023017 GATATAAAGC
3023027 CGGGGTTGGAGTATCCCCTCA-AAAATAA
1 CGGGGTTGGAGTATCCCC-CATAAAATAA
* *
3023055 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCCATAAAATAA
**
3023083 CATGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
3023099 TTAATTGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 38 0.97
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCCATAAAATAA
Found at i:3023230 original size:51 final size:51
Alignment explanation
Indices: 3023107--3023230 Score: 160
Period size: 51 Copynumber: 2.4 Consensus size: 51
3023097 CCTTAATTGT
* *
3023107 GAAAAATTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAC
1 GAAAAATTGATGTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAA
** * * *
3023158 GGTAAATCGATGCTTTAGAAATAAAATC-GAAGTTGGAGTATCCCCGATTAA
1 GAAAAATTGATGTTTTGGAAATAAAATCAG-AGTTGGAGTATCCCCGATTAA
*
3023209 GAAAAATTAATGTTTTGGAAAT
1 GAAAAATTGATGTTTTGGAAAT
3023231 GGAACCGGGA
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
50 1 0.02
51 58 0.98
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (51 bp):
GAAAAATTGATGTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAA
Found at i:3023781 original size:51 final size:51
Alignment explanation
Indices: 3023658--3023781 Score: 158
Period size: 51 Copynumber: 2.4 Consensus size: 51
3023648 CCTTAATTGT
* *
3023658 GAAAAATTGGTGTTTTGGAAATAAAATCAGAGTTGGAATATCCCCGATTAC
1 GAAAAATTGATGTTTTGGAAATAAAATCAGAGTTGGAATATCCCCGATTAA
** * * * * *
3023709 GGTAAATCGATGCTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
1 GAAAAATTGATGTTTTGGAAATAAAATCAGAGTTGGAATATCCCCGATTAA
*
3023760 GAAAAATTAATGTTTTGGAAAT
1 GAAAAATTGATGTTTTGGAAAT
3023782 GGAACCGGGA
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (51 bp):
GAAAAATTGATGTTTTGGAAATAAAATCAGAGTTGGAATATCCCCGATTAA
Found at i:3026121 original size:20 final size:19
Alignment explanation
Indices: 3026096--3026170 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
3026086 AAAATGCCTG
3026096 AATGTATCGATACATTGTAA
1 AATGTATCGATACATTG-AA
* *
3026116 AATGTATCGATACAATGAGC
1 AATGTATCGATACATTGA-A
3026136 AATGTATCGATAC-TATGCAA
1 AATGTATCGATACAT-TG-AA
*
3026156 AATATATCGATACAT
1 AATGTATCGATACAT
3026171 CTGGGTAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.02
20 43 0.93
21 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:3026232 original size:13 final size:13
Alignment explanation
Indices: 3026185--3026214 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3026175 GTAAACCCAA
3026185 AATGTATCGATAC
1 AATGTATCGATAC
3026198 AATGTATCGATAC
1 AATGTATCGATAC
3026211 AATG
1 AATG
3026215 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:3027620 original size:20 final size:19
Alignment explanation
Indices: 3027584--3027622 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3027574 AGGTCAAAAC
*
3027584 CCTTAAATGTATCGATACA
1 CCTTAAATCTATCGATACA
*
3027603 CCTTCAAATCTATTGATACA
1 CCTT-AAATCTATCGATACA
3027623 GAATGCACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (19 bp):
CCTTAAATCTATCGATACA
Found at i:3027671 original size:20 final size:21
Alignment explanation
Indices: 3027646--3027696 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3027636 CGATACATTA
*
3027646 TATCGATACATG-ACCA-AATG
1 TATCGATACATGCA-AAGAATG
*
3027666 TATCGATACTTGCAAAGAATG
1 TATCGATACATGCAAAGAATG
3027687 TATCGATACA
1 TATCGATACA
3027697 GGTGATTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (21 bp):
TATCGATACATGCAAAGAATG
Found at i:3027774 original size:13 final size:13
Alignment explanation
Indices: 3027756--3027781 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3027746 TACACACAAG
3027756 ATGTATCGATACA
1 ATGTATCGATACA
3027769 ATGTATCGATACA
1 ATGTATCGATACA
3027782 TACCAAATTG
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:3027779 original size:32 final size:33
Alignment explanation
Indices: 3027738--3027801 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3027728 CTTAACTGTT
3027738 TGTATCGATACACA-CAAGA-TGTATCGATACAA
1 TGTATCGATACACACCAA-ATTGTATCGATACAA
*
3027770 TGTATCGATACATACCAAATTGTATCGATACA
1 TGTATCGATACACACCAAATTGTATCGATACA
3027802 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACACCAAATTGTATCGATACAA
Found at i:3030596 original size:13 final size:13
Alignment explanation
Indices: 3030578--3030603 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3030568 TATACAAAGT
3030578 ATGTATCGATACA
1 ATGTATCGATACA
3030591 ATGTATCGATACA
1 ATGTATCGATACA
3030604 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:3030601 original size:32 final size:33
Alignment explanation
Indices: 3030560--3030623 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3030550 TAGCCAAACT
* **
3030560 TGTATCGATATACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3030592 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3030624 TTGGCTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3034915 original size:8 final size:8
Alignment explanation
Indices: 3034902--3034932 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
3034892 ATTTGATTAA
3034902 ATTTTGTG
1 ATTTTGTG
3034910 ATTTTGTG
1 ATTTTGTG
3034918 ATTTTGTG
1 ATTTTGTG
3034926 ATGTTTG
1 AT-TTTG
3034933 ATGTTGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.26, T:0.61
Consensus pattern (8 bp):
ATTTTGTG
Found at i:3035153 original size:13 final size:13
Alignment explanation
Indices: 3035131--3035168 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3035121 CAACATTCTC
*
3035131 TGTATGGATACAT
1 TGTATTGATACAT
*
3035144 TGTATTGATATAT
1 TGTATTGATACAT
3035157 TGTATTGATACA
1 TGTATTGATACA
3035169 AAGGGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (13 bp):
TGTATTGATACAT
Found at i:3037386 original size:21 final size:21
Alignment explanation
Indices: 3037362--3037402 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3037352 TATAACAAAG
3037362 AATTGAATAAAA-CCAAAAATT
1 AATTGAA-AAAATCCAAAAATT
*
3037383 AATTTAAAAAATCCAAAAAT
1 AATTGAAAAAATCCAAAAAT
3037403 GTGTTTTATT
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:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (21 bp):
AATTGAAAAAATCCAAAAATT
Found at i:3037770 original size:13 final size:13
Alignment explanation
Indices: 3037752--3037777 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3037742 TACACACAAG
3037752 ATGTATCGATACA
1 ATGTATCGATACA
3037765 ATGTATCGATACA
1 ATGTATCGATACA
3037778 TCCCAAATTG
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:3037775 original size:32 final size:33
Alignment explanation
Indices: 3037734--3037795 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
3037724 CTTAACTGTT
3037734 TGTATCGATACA-CACAAGA-TGTATCGATACAA
1 TGTATCGATACATCACAA-ATTGTATCGATACAA
*
3037766 TGTATCGATACATCCCAAATTGTATCGATA
1 TGTATCGATACATCACAAATTGTATCGATA
3037796 GATTGGCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (33 bp):
TGTATCGATACATCACAAATTGTATCGATACAA
Found at i:3044954 original size:20 final size:20
Alignment explanation
Indices: 3044904--3044957 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 20
3044894 GCTTGTCTTG
* *
3044904 ATATTTTCTACATAAATGCA
1 ATATATTCTACATGAATGCA
3044924 ATATA---TACATGAATGCA
1 ATATATTCTACATGAATGCA
3044941 ATATATTCTACATGAAT
1 ATATATTCTACATGAAT
3044958 CCTTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (20 bp):
ATATATTCTACATGAATGCA
Found at i:3048187 original size:156 final size:159
Alignment explanation
Indices: 3047759--3048236 Score: 424
Period size: 160 Copynumber: 3.0 Consensus size: 159
3047749 TAAGATCAAG
* * * * * * * * *
3047759 AAAAATT-ACGAAAATACTCATAAGGGATAGCTTCGACAT-AGAAGTA-CCCGATACCCCTAAAA
1 AAAAATTCACGAAAATACCCTTAAGGAACACCTTAGACATGA-AAGTATCCCGGTAACCCTAAAG
* * * *
3047821 AACTTTAAAAAGGACTATA-AA-AT-GGATTAACCTATCCTAAATACCCA-CTTTCGGCATAAAA
65 GAC-TTAAAAA-GAATATAGAAGATGGGATAAACCTATCCTAAATACCCACCTTT-GACATAAAA
* * ** * * *
3047882 ACGAACCTGGTGATAACCTAGGACTTGATTTTG
127 GCGAACCCGGTGGCAACCTAGGACTTGGTTCTA
* *
3047915 AAAAA-TCACGAAAATACCCTTAAGGAACACTTTAGACATGAAAGTATCCCGGTACCCCTAAAGG
1 AAAAATTCACGAAAATACCCTTAAGGAACACCTTAGACATGAAAGTATCCCGGTAACCCTAAAGG
* * * *
3047979 ACTTAAAAAGAATATTGCTAAGATGGGATGAACCTATCCTAAATACCTACCTTTGACATAGAAGC
66 ACTTAAAAAGAATATAG--AAGATGGGATAAACCTATCCTAAATACCCACCTTTGACATAAAAGC
* *
3048044 AAACCCGGTGGCAACCTAGGACTCGGTTCTA
129 GAACCCGGTGGCAACCTAGGACTTGGTTCTA
* * * * * * * *
3048075 AAAAATTC-TGAAAATGCCTTTATGGTACACCTTCGACGTGAAAGTATCCCCGGTAATCCTAAAG
1 AAAAATTCACGAAAATACCCTTAAGGAACACCTTAGACATGAAAGTAT-CCCGGTAACCCTAAAG
* * *
3048139 GACTT-AAAAGGAT-TAG-AGATGGGATAAACCTATCCTAAATACCCACCTTCGACATAAAAGTG
65 GACTTAAAAAGAATATAGAAGATGGGATAAACCTATCCTAAATACCCACCTTTGACATAAAAGCG
* * *
3048201 GACCCGGT-GCGACCTAGGAATTGGTTCTA
130 AACCCGGTGGCAACCTAGGACTTGGTTCTA
3048230 AAAAATT
1 AAAAATT
3048237 ACAAAAGATG
Statistics
Matches: 264, Mismatches: 47, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
155 31 0.12
156 89 0.34
157 17 0.06
158 2 0.01
159 4 0.02
160 96 0.36
161 25 0.09
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (159 bp):
AAAAATTCACGAAAATACCCTTAAGGAACACCTTAGACATGAAAGTATCCCGGTAACCCTAAAGG
ACTTAAAAAGAATATAGAAGATGGGATAAACCTATCCTAAATACCCACCTTTGACATAAAAGCGA
ACCCGGTGGCAACCTAGGACTTGGTTCTA
Found at i:3049492 original size:164 final size:162
Alignment explanation
Indices: 3049260--3049740 Score: 469
Period size: 165 Copynumber: 2.9 Consensus size: 162
3049250 AAATATTATC
* * * * *
3049260 ATTAAATCAGTTTCAAAAATTTCCTTCTATTTT-ACGAGTTATTGATTTTTCTTTGAAACTCTTC
1 ATTAAATCAGTTTTAAAAA-TTCTTTC-ATTTTCATGAGTT-TTGATTTTTCTTTCAAAATC-TC
* * *
3049324 CTATTTTTGAAATATGAAGTTTTCTACTCCGTAAATATTTTTGAGGA-GATTTTTCTTAGTTTTA
62 CTATTTTAGAAATATGAA-TTTTCTACTCCATAAATATTTTTCAGGAGGATTTTTCTTAGTTTTA
3049388 A-TTTTAAAATTCATCAAATATTAATAGTTAATTCAT
126 ATTTTTAAAATTCATCAAATATTAATAGTTAATTCAT
* *
3049424 ATTAAATCAGTTTGTAAAAATTCTTTCATTTTCATGAGTTGTGGATTTTTTCTTTCAAATTCTCC
1 ATTAAATCAGTTT-TAAAAATTCTTTCATTTTCATGAGTT-TTGA-TTTTTCTTTCAAAATCTCC
* * * * * * * *
3049489 TATTTTCGAAATACGAAATGTTCTTCTCCAT-AA-ATTTTTCAAGAGGA-TTTTCATCGATTTAA
63 TATTTTAGAAATATG-AATTTTCTACTCCATAAATATTTTTCAGGAGGATTTTTCTTAG-TTTTA
* *
3049551 ATTTTTTAAAATTCATCAAATATTATTATTTAATTCAT
126 A-TTTTTAAAATTCATCAAATATTAATAGTTAATTCAT
* * * *
3049589 ATTAAATTATTTTTGAAAAATTAATTT-ATTTTCATGGGTTTTGAATTTTT-TTTCAAAATCTCC
1 ATTAAATCAGTTTT-AAAAATT-CTTTCATTTTCATGAGTTTTG-ATTTTTCTTTCAAAATCT-C
* * *
3049652 CTATTTTCAAAAAAACTGAATTTTCTA-TCCTATAAATA-ATTTCAGGAGGATTTTTCTTAGTTT
62 CTATTTT-AGAAATA-TGAATTTTCTACTCC-ATAAATATTTTTCAGGAGGATTTTTCTTAGTTT
*
3049715 TAAATTTTTAAAATTCATCTAATATT
124 T-AATTTTTAAAATTCATCAAATATT
3049741 GTTACAAAAA
Statistics
Matches: 261, Mismatches: 37, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
162 16 0.06
163 24 0.09
164 73 0.28
165 98 0.38
166 40 0.15
167 10 0.04
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.48
Consensus pattern (162 bp):
ATTAAATCAGTTTTAAAAATTCTTTCATTTTCATGAGTTTTGATTTTTCTTTCAAAATCTCCTAT
TTTAGAAATATGAATTTTCTACTCCATAAATATTTTTCAGGAGGATTTTTCTTAGTTTTAATTTT
TAAAATTCATCAAATATTAATAGTTAATTCAT
Found at i:3050233 original size:20 final size:20
Alignment explanation
Indices: 3050201--3050276 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
3050191 ATTTTACCAA
*
3050201 AATGTATCAATACATGATTC
1 AATGTATCGATACATGATTC
*
3050221 AATATATCGATACATGATTC
1 AATGTATCGATACATGATTC
* *
3050241 AATGTATTGATACATTATTC
1 AATGTATCGATACATGATTC
3050261 AATGTATCGATACATG
1 AATGTATCGATACATG
3050277 TAGGCAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATGATTC
Found at i:3054235 original size:20 final size:20
Alignment explanation
Indices: 3054187--3054239 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3054177 GTATTGATAC
*
3054187 AATGTATCGATACAATATCT
1 AATGTATCGATACAATAGCT
* *
3054207 CATGCATCGATACAA-AGCAT
1 AATGTATCGATACAATAGC-T
3054227 AATGTATCGATAC
1 AATGTATCGATAC
3054240 TTCTAGATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
AATGTATCGATACAATAGCT
Found at i:3054251 original size:20 final size:21
Alignment explanation
Indices: 3054228--3054266 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3054218 ACAAAGCATA
3054228 ATGTATCGATAC-TTCTAGAT
1 ATGTATCGATACTTTCTAGAT
3054248 ATGTATCGATACTTTCTAG
1 ATGTATCGATACTTTCTAG
3054267 GGTTTTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACTTTCTAGAT
Found at i:3054559 original size:14 final size:15
Alignment explanation
Indices: 3054540--3054569 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3054530 AATTTTTATC
3054540 TTAATTTTTA-AATT
1 TTAATTTTTACAATT
3054554 TTAATTTTTACAATT
1 TTAATTTTTACAATT
3054569 T
1 T
3054570 AATCTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TTAATTTTTACAATT
Found at i:3054887 original size:12 final size:12
Alignment explanation
Indices: 3054870--3054914 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
3054860 AAGAAACTTG
3054870 GAGAAAAAAAGA
1 GAGAAAAAAAGA
*
3054882 GAGAAAAAAAAA
1 GAGAAAAAAAGA
*
3054894 GAAAAAGAAAAGA
1 GAGAAA-AAAAGA
3054907 GAAGAAAA
1 G-AGAAAA
3054915 GAAAAATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 16 0.59
13 7 0.26
14 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
GAGAAAAAAAGA
Found at i:3054902 original size:16 final size:15
Alignment explanation
Indices: 3054873--3054920 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
3054863 AAACTTGGAG
*
3054873 AAAAAAAG-AGAGAA
1 AAAAAAAGAAAAGAA
3054887 AAAAAAAGAAAAAGAA
1 AAAAAAAG-AAAAGAA
* *
3054903 AAGAGAAGAAAAGAA
1 AAAAAAAGAAAAGAA
3054918 AAA
1 AAA
3054921 TTGTAGGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 8 0.29
15 9 0.32
16 11 0.39
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAGAA
Found at i:3057189 original size:158 final size:156
Alignment explanation
Indices: 3056918--3057282 Score: 403
Period size: 158 Copynumber: 2.3 Consensus size: 156
3056908 CCATTAGGGT
* * * ** *
3056918 TATCGGGTTACTTTTACGTCAAAGGTATCCCCTAAAGGTATTTTCATAATTTTTTCGAATGAACT
1 TATCGGGTTACTTTTACATCAAAGGTATCCCCTAAAGGTATTTTCATAATTTATTAGAACCAAAT
** ** *
3056983 CCTAGGTCATCGTCGGGTCCGCTTTTATGTCGAAGGTAGATATTTAGGATATAGGTTCATCCCTT
66 CCTAGGTCATCCCCAAGTCCACTTTTATGTCGAAGGTAGATATTTAGG--ATAGGTTCATCCCTT
3057048 TTAAAATCCTCTTTAAATCTTTTCGAGG
129 TTAAAATCCTCTTTAAATCTTTTCGAGG
** **
3057076 TATCGGG-TACTTTTTACATCAAAGGTATCCCCTAGGGGTATTTTTGTAATTTATTAGAACCAAA
1 TATCGGGTTAC-TTTTACATCAAAGGTATCCCCTAAAGGTATTTTCATAATTTATTAGAACCAAA
* *
3057140 TCCTAGGTCGTCCCCAAGTCTACTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCATCCCTTT
65 TCCTAGGTCATCCCCAAGTCCACTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCATCCCTTT
* * * * * * *
3057205 TATGAAT-TTTTTTAAGTCCTTTAGGGG
130 TA-AAATCCTCTTTAAATCTTTTCGAGG
* * * * **
3057232 TATAGAG-TACTTTTATATCGAAGGTATCCCCTAAAGACATTTTCATAATTT
1 TATCGGGTTACTTTTACATCAAAGGTATCCCCTAAAGGTATTTTCATAATTT
3057283 TTTAAAATCG
Statistics
Matches: 171, Mismatches: 34, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
155 33 0.19
156 40 0.23
157 6 0.04
158 92 0.54
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (156 bp):
TATCGGGTTACTTTTACATCAAAGGTATCCCCTAAAGGTATTTTCATAATTTATTAGAACCAAAT
CCTAGGTCATCCCCAAGTCCACTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCATCCCTTTT
AAAATCCTCTTTAAATCTTTTCGAGG
Found at i:3057650 original size:153 final size:153
Alignment explanation
Indices: 3057181--3057753 Score: 486
Period size: 156 Copynumber: 3.7 Consensus size: 153
3057171 CGAAGGTAGA
* * * *
3057181 TATTTAGGATAGGTTCATCCCTTTTATGAATT--TTTTTAAGTCCTTTAGGGGTATAGAGTACTT
1 TATTTAGGATAGGTTCACCCCATTTAT--ATTCATTTTTAAGTCTTTTA-GGGTATGGA-TACTT
* * * * ** *
3057244 TTATATCGAAGGTAT-CCC-CTAAAGACATTTTCATAATTTTTTAAAATCGAGTTTTAGGTTGTC
62 TTACATCGAAGGTATACCCAC-AAAGGCATTTTCATAATTTTTTAGAATCAAGTCCTAAGTTGTC
* * * *
3057307 A-TTGGGTTCACTTTCATGCAAAAGGCAGG
126 ACCT-AGTTCACTTTCATGCCAAAGG-TGG
* * * *
3057336 TATTTAGGATAAGTTCACCCCATTTATA-TCTTTTTTATGTCTTTTAGGGTTTTCGGGATACTTT
1 TATTTAGGATAGGTTCACCCCATTTATATTCATTTTTAAGTCTTTTAGGG-TAT--GGATACTTT
* * * * * * **
3057400 AACGTTGAAGATATACCCACAAAGGCATTTTCATAATTTTTTAGAACCAACTCCT-AGATCATCA
63 TACATCGAAGGTATACCCACAAAGGCATTTTCATAATTTTTTAGAATCAAGTCCTAAG-TTGTCA
* * * *
3057464 CCGAATTCGCTTTTATGCCAAAGGTCGG
127 CCTAGTTCACTTTCATGCCAAAGGT-GG
* * * * * *
3057492 CATTTAGGATAGGTTCAACCCATTTCTATTC-TTTTTAAATCTTTTAGGGTAGTGGACACTTTCA
1 TATTTAGGATAGGTTCACCCCATTTATATTCATTTTTAAGTCTTTTAGGGTA-TGGATACTTTTA
* *
3057556 CATCGAAGGTATTCCC-C-AGGGACATTTTCATAATTTTTTAGAATCAAGTCCTAAGTTGTCACC
65 CATCGAAGGTATACCCACAAAGG-CATTTTCATAATTTTTTAGAATCAAGTCCTAAGTTGTCACC
* *
3057619 TCGTCCACTTTCATGCCAAAGGTGG
129 TAGTTCACTTTCATGCCAAAGGTGG
*
3057644 ATATTTAGGATAGGTTCACCCCATCTATA-TCATTTTTAAGTCTTTTAGGGTTACTGGATACTTT
1 -TATTTAGGATAGGTTCACCCCATTTATATTCATTTTTAAGTCTTTTAGGG-TA-TGGATACTTT
* * * *
3057708 TACGTC-ATAGGTATACCCATAAGGGTATTTTCATAATTTTTTAGAA
63 TACATCGA-AGGTATACCCACAAAGGCATTTTCATAATTTTTTAGAA
3057754 CTAACTCCTA
Statistics
Matches: 332, Mismatches: 66, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
152 8 0.02
153 98 0.30
154 62 0.19
155 61 0.18
156 100 0.30
157 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (153 bp):
TATTTAGGATAGGTTCACCCCATTTATATTCATTTTTAAGTCTTTTAGGGTATGGATACTTTTAC
ATCGAAGGTATACCCACAAAGGCATTTTCATAATTTTTTAGAATCAAGTCCTAAGTTGTCACCTA
GTTCACTTTCATGCCAAAGGTGG
Found at i:3057864 original size:309 final size:308
Alignment explanation
Indices: 3057079--3057864 Score: 843
Period size: 309 Copynumber: 2.5 Consensus size: 308
3057069 TTCGAGGTAT
* * * ** * *
3057079 CGGG-TACTTTTTACATCAAAGGTAT-CCCCTAGGGGTATTTTTGTAATTTATTAGAACCAAATC
1 CGGGATAC-TTTTACGTC-AAGGTATACCCATAAGGGTATTTTCATAATTTTTTAGAACCAACTC
* * ** * *
3057142 CTAGGTCGTCCCCAAGTCTACTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCATCCCTTTTA
64 CTAGGTCATCACCAAGTCTACTTTTATGTCGAAGGTAGGCATTTAGGATAGGTTCATCCCATTTC
* * * * * *
3057207 TGAATTTTTTTAAGTCCTTTAGGGGTATAGAGTACTTTTATATCGAAGGTATCCCCTAAAGACAT
129 T-AATCTTTTTAAGTCTTTTAAGGGTATGGA-TACTTTCACATCGAAGGTATCCCCTAAAGACAT
* ** * * * *
3057272 TTTCATAATTTTTTAAAATCGAGTTTTAGGTTGTCATTGGGTTCACTTTCATGCAAAAGGCAGGT
192 TTTCATAATTTTTTAAAATCAAGTCCTAAGTTGTCACTGCGTCCACTTTCATGCAAAAGGCAGGT
* * * *
3057337 ATTTAGGATAAGTTCACCCCATTTATATCTTTTTTATGTCTTTTAGGGTTTT
257 ATTTAGGATAAGTTCACCCCATCTATATCATTTTTAAGTCTTTTAGGGTTTA
* * * * * *
3057389 CGGGATACTTTAACGTTGAAGATATACCCACAAAGGCATTTTCATAATTTTTTAGAACCAACTCC
1 CGGGATACTTTTACG-TCAAGGTATACCCATAAGGGTATTTTCATAATTTTTTAGAACCAACTCC
* * * * * * *
3057454 TAGATCATCACCGAATTC-GCTTTTATGCCAAAGGTCGGCATTTAGGATAGGTTCAACCCATTTC
65 TAGGTCATCACC-AAGTCTACTTTTATGTCGAAGGTAGGCATTTAGGATAGGTTCATCCCATTTC
* * * **
3057518 TATTCTTTTTAAATCTTTT-AGGGTAGTGGACACTTTCACATCGAAGGTATTCCCC-AGGGACAT
129 TAATCTTTTTAAGTCTTTTAAGGGTA-TGGATACTTTCACATCGAAGGTA-TCCCCTAAAGACAT
* * *
3057581 TTTCATAATTTTTTAGAATCAAGTCCTAAGTTGTCACCT-CGTCCACTTTCATGCCAAAGG-TGG
192 TTTCATAATTTTTTAAAATCAAGTCCTAAGTTGTCA-CTGCGTCCACTTTCATGCAAAAGGCAGG
*
3057644 ATATTTAGGATAGGTTCACCCCATCTATATCATTTTTAAGTCTTTTAGGG-TTA
256 -TATTTAGGATAAGTTCACCCCATCTATATCATTTTTAAGTCTTTTAGGGTTTA
* *
3057697 CTGGATACTTTTACGTCATAGGTATACCCATAAGGGTATTTTCATAATTTTTTAGAACTAACTCC
1 CGGGATACTTTTACGTCA-AGGTATACCCATAAGGGTATTTTCATAATTTTTTAGAACCAACTCC
* * * * * *
3057762 TAGGTCATCACTAGGTCTATTTTTATGTCGAAGGT-GGCATTTAGAATAAGTTCATCCGATTTCT
65 TAGGTCATCACCAAGTCTACTTTTATGTCGAAGGTAGGCATTTAGGATAGGTTCATCCCATTTCT
*
3057826 AATCTTTTTAAGTCTTTTAAGAGTACTGGGATACTTTCA
130 AATCTTTTTAAGTCTTTTAAGGGTA-T-GGATACTTTCA
3057865 TGTCAAATGT
Statistics
Matches: 387, Mismatches: 77, Indels: 25
0.79 0.16 0.05
Matches are distributed among these distances:
307 46 0.12
308 87 0.22
309 131 0.34
310 38 0.10
311 81 0.21
312 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (308 bp):
CGGGATACTTTTACGTCAAGGTATACCCATAAGGGTATTTTCATAATTTTTTAGAACCAACTCCT
AGGTCATCACCAAGTCTACTTTTATGTCGAAGGTAGGCATTTAGGATAGGTTCATCCCATTTCTA
ATCTTTTTAAGTCTTTTAAGGGTATGGATACTTTCACATCGAAGGTATCCCCTAAAGACATTTTC
ATAATTTTTTAAAATCAAGTCCTAAGTTGTCACTGCGTCCACTTTCATGCAAAAGGCAGGTATTT
AGGATAAGTTCACCCCATCTATATCATTTTTAAGTCTTTTAGGGTTTA
Found at i:3057888 original size:309 final size:309
Alignment explanation
Indices: 3057267--3057960 Score: 742
Period size: 309 Copynumber: 2.2 Consensus size: 309
3057257 ATCCCCTAAA
* ** * * * *
3057267 GACATTTTCATAATTTTTTAAAATCGAGTTTTAGGTTGTCA-TTGGGTTCACTTTCATGCAAAAG
1 GACATTTTCATAATTTTTTAGAATCGAGTCCTAAGTTGTCACCT-AGTCCACTTTCATGCAAAAG
* * * * *
3057331 GCAGG-TATTTAGGATAAGTTCACCCCATTTATATCTTTTTTATGTCTTTTAGGGTTTTCGGGAT
65 G-TGGATATTTAGGATAAGTTCACCCCATCTATATCATTTTTAAGTCTTTTAGGGTTTACGGGAT
*
3057395 ACTTTAACGTTGAAGATATACCCACAAAGGCATTTTCATAATTTTTTAGAACCAACTCCTAGATC
129 ACTTTAACGTTCAAGATATACCCACAAAGGCATTTTCATAATTTTTTAGAACCAACTCCTAGATC
* * * * *
3057460 ATCACCGAATTCGCTTTTATGCCAAAGGTCGGCATTTAGGATAGGTTCAACCCATTTCTATTCTT
194 ATCACCGAAGTCACTTTTATGCCAAAGGTCGGCATTTAGAATAAGTTCAACCCATTTCTAATCTT
* * *
3057525 TTTAAATCTTTTAGGGTAGTGGACACTTTCACATCGAAGGTATTCCCCAGG
259 TTTAAATCTTTTAGAGTACTGGACACTTTCACATCAAAGGTATTCCCCAGG
* * *
3057576 GACATTTTCATAATTTTTTAGAATCAAGTCCTAAGTTGTCACCTCGTCCACTTTCATGCCAAAGG
1 GACATTTTCATAATTTTTTAGAATCGAGTCCTAAGTTGTCACCTAGTCCACTTTCATGCAAAAGG
* *
3057641 TGGATATTTAGGATAGGTTCACCCCATCTATATCATTTTTAAGTCTTTTAGGG-TTACTGGATAC
66 TGGATATTTAGGATAAGTTCACCCCATCTATATCATTTTTAAGTCTTTTAGGGTTTACGGGATAC
* * * * * * *
3057705 TTTTACG-TCATAGGTATACCCATAAGGGTATTTTCATAATTTTTTAGAACTAACTCCTAGGTCA
131 TTTAACGTTCA-AGATATACCCACAAAGGCATTTTCATAATTTTTTAGAACCAACTCCTAGATCA
* * * * * * *
3057769 TCA-CTAGGTCTATTTTTATGTCGAAGGT-GGCATTTAGAATAAGTTCATCCGATTTCTAATCTT
195 TCACCGAAGTC-ACTTTTATGCCAAAGGTCGGCATTTAGAATAAGTTCAACCCATTTCTAATCTT
* * ** * ***
3057832 TTTAAGTCTTTTAAGAGTACTGGGATACTTTCATGTCAAATGTA-TCTTTTAGG
259 TTTAAATCTTTT-AGAGTACT-GGACACTTTCACATCAAAGGTATTC-CCCAGG
* * * * *
3057885 GACAGTTTCATAATTTTCTAGAA-CTGAGTCCT-AGATTGTCACCGAGTCCACTTTTATGCTGAA
1 GACATTTTCATAATTTTTTAGAATC-GAGTCCTAAG-TTGTCACCTAGTCCACTTTCATGC-AAA
*
3057948 A-GTAGATATTTAG
63 AGGTGGATATTTAG
3057961 AGTTACTGGG
Statistics
Matches: 320, Mismatches: 55, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
307 47 0.15
308 91 0.28
309 178 0.56
310 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (309 bp):
GACATTTTCATAATTTTTTAGAATCGAGTCCTAAGTTGTCACCTAGTCCACTTTCATGCAAAAGG
TGGATATTTAGGATAAGTTCACCCCATCTATATCATTTTTAAGTCTTTTAGGGTTTACGGGATAC
TTTAACGTTCAAGATATACCCACAAAGGCATTTTCATAATTTTTTAGAACCAACTCCTAGATCAT
CACCGAAGTCACTTTTATGCCAAAGGTCGGCATTTAGAATAAGTTCAACCCATTTCTAATCTTTT
TAAATCTTTTAGAGTACTGGACACTTTCACATCAAAGGTATTCCCCAGG
Found at i:3057940 original size:154 final size:152
Alignment explanation
Indices: 3057337--3057943 Score: 458
Period size: 154 Copynumber: 3.9 Consensus size: 152
3057327 AAAGGCAGGT
* * * * * * *
3057337 ATTTAGGATAAGTTCACCCCATTTAT-ATCTTTTTTATGTCTTTTAGGGTTTTCGGGATACTTTA
1 ATTTAGGATAGGTTCAACCCATTTCTAATC-TTTTTAAGTCTTTTAGGG--TACTGGATACTTTC
** * * * * *
3057401 ACGTTGAAGATATACCCACAAAGG-CATTTTCATAATTTTTTAGAACCAACTCCTAGATCATCAC
63 ACGTCAAAGGTAT--CTATAAGGGACATTTTCATAATTTTTTAGAACTAACTCCTAGATCATCAC
* * *
3057465 CGAATTCGCTTTTATGCCAAAGGTCGGC
126 CGAGTCCACTTTTATGCCAAAGGT-GGC
* * * * *
3057493 ATTTAGGATAGGTTCAACCCATTTCTATTCTTTTTAAATCTTTTAGGGTAGTGGACACTTTCACA
1 ATTTAGGATAGGTTCAACCCATTTCTAATCTTTTTAAGTCTTTTAGGGTACTGGATACTTTCACG
* *** * ** *
3057558 TCGAAGGTAT-TCCCCAGGGACATTTTCATAATTTTTTAGAA-TCAAGTCCTA-AGTTGTCACCT
66 TCAAAGGTATCT-ATAAGGGACATTTTCATAATTTTTTAGAACT-AACTCCTAGA-TCATCACCG
* * *
3057620 CGTCCACTTTCATGCCAAAGGTGGAT
128 AGTCCACTTTTATGCCAAAGGTGG-C
* *
3057646 ATTTAGGATAGGTTCACCCCA--TCTATATCATTTTTAAGTCTTTTAGGGTTACTGGATACTTTT
1 ATTTAGGATAGGTTCAACCCATTTCTA-ATC-TTTTTAAGTCTTTTAGGG-TACTGGATACTTTC
* * * *
3057709 ACGTCATAGGTATACCCATAAGGG-TATTTTCATAATTTTTTAGAACTAACTCCTAGGTCATCA-
63 ACGTCAAAGGTAT--CTATAAGGGACATTTTCATAATTTTTTAGAACTAACTCCTAGATCATCAC
* * * * *
3057772 CTAGGTCTATTTTTATGTCGAAGGTGGC
126 CGA-GTCCACTTTTATGCCAAAGGTGGC
* * * * *
3057800 ATTTAGAATAAGTTCATCCGATTTCTAATCTTTTTAAGTCTTTTAAGAGTACTGGGATACTTTCA
1 ATTTAGGATAGGTTCAACCCATTTCTAATCTTTTTAAGTCTTTT-AGGGTACT-GGATACTTTCA
* * * * * * * * **
3057865 TGTCAAATGTATCTTTTAGGGACAGTTTCATAATTTTCTAGAACTGAGTCCTAGATTGTCACCGA
64 CGTCAAAGGTATCTATAAGGGACATTTTCATAATTTTTTAGAACTAACTCCTAGATCATCACCGA
3057930 GTCCACTTTTATGC
129 GTCCACTTTTATGC
3057944 TGAAAGTAGA
Statistics
Matches: 352, Mismatches: 78, Indels: 44
0.74 0.16 0.09
Matches are distributed among these distances:
151 4 0.01
152 9 0.03
153 94 0.27
154 119 0.34
155 76 0.22
156 48 0.14
157 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (152 bp):
ATTTAGGATAGGTTCAACCCATTTCTAATCTTTTTAAGTCTTTTAGGGTACTGGATACTTTCACG
TCAAAGGTATCTATAAGGGACATTTTCATAATTTTTTAGAACTAACTCCTAGATCATCACCGAGT
CCACTTTTATGCCAAAGGTGGC
Found at i:3058282 original size:34 final size:34
Alignment explanation
Indices: 3058215--3058336 Score: 138
Period size: 34 Copynumber: 3.5 Consensus size: 34
3058205 GTTACCTTTG
* * * *
3058215 AGGCTAAGGTATAACCTTACAACCCTATTTTTTCAC
1 AGGCTAAGATAGAACCTT-CTA-CCTATCTTTTCAC
3058251 AGGCTAAGATAGAACCTTCTACCTATCTTTTCAC
1 AGGCTAAGATAGAACCTTCTACCTATCTTTTCAC
* * *
3058285 AGGCTAATATAGAACC-TCTTCCCTATCTTTTACAA
1 AGGCTAAGATAGAACCTTC-TACCTATCTTTT-CAC
3058320 AGGCTAAGATAGAACCT
1 AGGCTAAGATAGAACCT
3058337 CTCAATCACT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
33 2 0.03
34 38 0.51
35 19 0.25
36 16 0.21
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (34 bp):
AGGCTAAGATAGAACCTTCTACCTATCTTTTCAC
Found at i:3058332 original size:35 final size:35
Alignment explanation
Indices: 3058237--3058339 Score: 147
Period size: 34 Copynumber: 3.0 Consensus size: 35
3058227 AACCTTACAA
*
3058237 CCCTATTTTTTCACAGGCTAAGATAGAACCT-TCT
1 CCCTATCTTTTCACAGGCTAAGATAGAACCTCTCT
* *
3058271 ACCTATCTTTTCACAGGCTAATATAGAACCTCT-T
1 CCCTATCTTTTCACAGGCTAAGATAGAACCTCTCT
*
3058305 CCCTATCTTTTACAAAGGCTAAGATAGAACCTCTC
1 CCCTATCTTTT-CACAGGCTAAGATAGAACCTCTC
3058340 AATCACTCTG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
34 39 0.65
35 21 0.35
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (35 bp):
CCCTATCTTTTCACAGGCTAAGATAGAACCTCTCT
Found at i:3058879 original size:20 final size:20
Alignment explanation
Indices: 3058856--3058907 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3058846 TAATTCATGA
3058856 TGTATCGATACAAAGCAATT
1 TGTATCGATACAAAGCAATT
**
3058876 TGTATCGATACTTAGCAATT
1 TGTATCGATACAAAGCAATT
*
3058896 TGTATTGATACA
1 TGTATCGATACA
3058908 TTTGGATGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAAGCAATT
Found at i:3063527 original size:34 final size:36
Alignment explanation
Indices: 3063470--3063562 Score: 95
Period size: 34 Copynumber: 2.7 Consensus size: 36
3063460 CAACCTTATA
* * *
3063470 TTTTCACA-AGCTAAGATAAAACCTTC-TCCTTGT-C
1 TTTTCACAGA-CTAAGATAGAACCTTCTTCCCTATCC
*
3063504 TTTTCACAGACTAATATAGAACC-TCTTCCCTATCC
1 TTTTCACAGACTAAGATAGAACCTTCTTCCCTATCC
* *
3063539 TTTTCAAAGGCTAAGATAGAACCT
1 TTTTCACAGACTAAGATAGAACCT
3063563 CTCAATCACT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
33 2 0.04
34 24 0.50
35 22 0.46
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (36 bp):
TTTTCACAGACTAAGATAGAACCTTCTTCCCTATCC
Found at i:3063558 original size:35 final size:35
Alignment explanation
Indices: 3063470--3063565 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 35
3063460 CAACCTTATA
* * *
3063470 TTTTCACAA-GCTAAGATAAAACCT-TCTCCTTGTC
1 TTTTCA-AAGGCTAAGATAGAACCTCTCTCCCTATC
* * *
3063504 TTTTCACAGACTAATATAGAACCTCT-TCCCTATCC
1 TTTTCAAAGGCTAAGATAGAACCTCTCTCCCTAT-C
3063539 TTTTCAAAGGCTAAGATAGAACCTCTC
1 TTTTCAAAGGCTAAGATAGAACCTCTC
3063566 AATCACTCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
33 1 0.02
34 23 0.47
35 25 0.51
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.33
Consensus pattern (35 bp):
TTTTCAAAGGCTAAGATAGAACCTCTCTCCCTATC
Found at i:3066867 original size:8 final size:8
Alignment explanation
Indices: 3066854--3066911 Score: 57
Period size: 8 Copynumber: 7.1 Consensus size: 8
3066844 TTTTCTTTAG
3066854 TTTTTCTT
1 TTTTTCTT
3066862 TTTTTCTCT
1 TTTTTCT-T
3066871 TTTTTCTT
1 TTTTTCTT
3066879 TCTTTT-TT
1 T-TTTTCTT
*
3066887 TCTCTT-TT
1 T-TTTTCTT
*
3066895 TTTTTCTA
1 TTTTTCTT
3066903 TTTTTCTT
1 TTTTTCTT
3066911 T
1 T
3066912 CACTCTCCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
7 3 0.07
8 28 0.65
9 12 0.28
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:3066871 original size:10 final size:10
Alignment explanation
Indices: 3066854--3066909 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
3066844 TTTTCTTTAG
3066854 TTTT-TCTTT
1 TTTTCTCTTT
3066863 TTTTCTCTTT
1 TTTTCTCTTT
*
3066873 TTTCTTTCTTT
1 TTT-TCTCTTT
3066884 TTTTCTCTTT
1 TTTTCTCTTT
* *
3066894 TTTTTTCTAT
1 TTTTCTCTTT
3066904 TTTTCT
1 TTTTCT
3066910 TTCACTCTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
9 4 0.10
10 27 0.68
11 9 0.22
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:3066885 original size:12 final size:12
Alignment explanation
Indices: 3066856--3066912 Score: 56
Period size: 9 Copynumber: 5.3 Consensus size: 12
3066846 TTCTTTAGTT
3066856 TTTCTTTTTTTC
1 TTTCTTTTTTTC
3066868 --TC-TTTTTTC
1 TTTCTTTTTTTC
3066877 TTTCTTTTTTTC
1 TTTCTTTTTTTC
3066889 --TC-TTTTTT-
1 TTTCTTTTTTTC
*
3066897 TTTCTATTTTTC
1 TTTCTTTTTTTC
3066909 TTTC
1 TTTC
3066913 ACTCTCCCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
9 13 0.35
10 6 0.16
11 7 0.19
12 11 0.30
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:3066886 original size:20 final size:20
Alignment explanation
Indices: 3066854--3066909 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 20
3066844 TTTTCTTTAG
3066854 TTTTTCTTTTTTTCTCTTTT
1 TTTTTCTTTTTTTCTCTTTT
3066874 TTCTTTCTTTTTTTCTCTTTT
1 TT-TTTCTTTTTTTCTCTTTT
*
3066895 TTTTTCTATTTTTCT
1 TTTTTCTTTTTTTCT
3066910 TTCACTCTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTTTTCTCTTTT
Found at i:3067769 original size:165 final size:166
Alignment explanation
Indices: 3067550--3067852 Score: 445
Period size: 165 Copynumber: 1.8 Consensus size: 166
3067540 TGAAAAATGA
*
3067550 ATGAAAATGAATGAATTTTTTGAAAAATGATTTAATATAAAATAATTAATAATATTTGATGAATT
1 ATGAAAATGAATGAATTTTTTGAAAAATGATTTAATATAAAATAAATAATAATATTTGATGAATT
*
3067615 CTAAAAATTAAAAA-CTAAGAAAAATCTTCC-CAAAAAAAATTTA-AAGTAGAAAACTCCATATT
66 CTAAAAATTAAAAATC-AAGAAAAAT-TCCCTCAAAAAAAATTTAGAA-TAGAAAACTCCATATT
3067677 TCAAAAATAAGAAAATTTTAAGAAAAAATTCAAAAACTC
128 TCAAAAATAAGAAAATTTTAAGAAAAAATTCAAAAACTC
* *
3067716 ATGAAGATGAATGAA-TTTTT-AAAAACTGATTTAATATGAAATAAATAATAATATTTGATGAAT
1 ATGAAAATGAATGAATTTTTTGAAAAA-TGATTTAATATAAAATAAATAATAATATTTGATGAAT
* * **
3067779 TTTAAAAATTAAAAATCAAGAAAAATTCCCTCGAAAAAAATTTACGGAATAGAAAACTCTGTATT
65 TCTAAAAATTAAAAATCAAGAAAAATTCCCTCAAAAAAAATTTA--GAATAGAAAACTCCATATT
3067844 TCAAAAATA
128 TCAAAAATA
3067853 GGAGAATTCC
Statistics
Matches: 123, Mismatches: 8, Indels: 11
0.87 0.06 0.08
Matches are distributed among these distances:
164 8 0.07
165 75 0.61
166 15 0.12
167 23 0.19
168 2 0.02
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.31
Consensus pattern (166 bp):
ATGAAAATGAATGAATTTTTTGAAAAATGATTTAATATAAAATAAATAATAATATTTGATGAATT
CTAAAAATTAAAAATCAAGAAAAATTCCCTCAAAAAAAATTTAGAATAGAAAACTCCATATTTCA
AAAATAAGAAAATTTTAAGAAAAAATTCAAAAACTC
Found at i:3067947 original size:166 final size:165
Alignment explanation
Indices: 3067531--3067947 Score: 379
Period size: 165 Copynumber: 2.5 Consensus size: 165
3067521 GGAGATTTCA
* * * * * **
3067531 AAGAAAAAA-TGAAAAA-TGAATGAAAATGAATGAATTTTTTGAAAAA-TGATTTAATATAAAAT
1 AAGAAAAAATTCAAAAACT-AATGAAGATAAAGGAA-TTTTT-AAAAACTGACTTAATAGGAAAT
* *
3067593 -AATTAATAATATTTGATGAATTCTAAAAATTAAAAACTAAGAAAAATCTTCCCAAAAAAAATTT
63 AAATT-ATAATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCTCCCCAAAAAAAATTT
**
3067657 AAAGTAGAAAACTCCATATTTCAAAAATAAGAAAATTTT
127 AAAGTAGAAAACTCCATATTTCAAAAATAAGAAAATTCC
* * * * *
3067696 AAGAAAAAATTCAAAAACTCATGAAGATGAATGAATTTTTAAAAACTGATTTAATATGAAATAAA
1 AAGAAAAAATTCAAAAACTAATGAAGATAAAGGAATTTTTAAAAACTGACTTAATAGGAAATAAA
* *
3067761 TAATAATATTTGATGAATTTTAAAAATTAAAAA-TCAAGAAAAAT-TCCCTCGAAAAAAATTTAC
66 TTATAATATTTGATGAATTTTAAAAATTAAAAACT-AAGAAAAATCTCCC-CAAAAAAAATTTA-
** * *
3067824 GGAA-TAGAAAACTCTGTATTTCAAAAATAGGAGAATTCC
128 --AAGTAGAAAACTCCATATTTCAAAAATAAGAAAATTCC
** * * * **
3067863 AA-AAGAAAA-TCAATAATTTAAT-AA-ATAAAAGGAATTTTTCAAAACTGACTTAGTGGGAGTT
1 AAGAA-AAAATTCAA-AAACTAATGAAGAT-AAAGGAATTTTTAAAAACTGACTTAATAGGAAAT
*
3067924 AAATTATAATATTTGAAGAATTTT
63 AAATTATAATATTTGATGAATTTT
3067948 GATGTATGAA
Statistics
Matches: 212, Mismatches: 28, Indels: 23
0.81 0.11 0.09
Matches are distributed among these distances:
164 9 0.04
165 82 0.39
166 78 0.37
167 41 0.19
168 2 0.01
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (165 bp):
AAGAAAAAATTCAAAAACTAATGAAGATAAAGGAATTTTTAAAAACTGACTTAATAGGAAATAAA
TTATAATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATCTCCCCAAAAAAAATTTAAAG
TAGAAAACTCCATATTTCAAAAATAAGAAAATTCC
Found at i:3067957 original size:17 final size:17
Alignment explanation
Indices: 3067937--3067975 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
3067927 TTATAATATT
3067937 TGAAGAATTTTGATGTA
1 TGAAGAATTTTGATGTA
3067954 TGAAGAATTTTGATGTA
1 TGAAGAATTTTGATGTA
3067971 TGAAG
1 TGAAG
3067976 CTCGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (17 bp):
TGAAGAATTTTGATGTA
Found at i:3070724 original size:34 final size:37
Alignment explanation
Indices: 3070684--3070768 Score: 108
Period size: 36 Copynumber: 2.4 Consensus size: 37
3070674 TTTCATAGCT
3070684 TAAGATAGAACCTCTT-T-ACTATC-TTTTCACAAG-C
1 TAAGATAGAACCTCTTCTCACTATCTTTTTCA-AAGAC
* *
3070718 TGAGATAGAACCT-TTCTCCCTATCTTTTTCAAAGAC
1 TAAGATAGAACCTCTTCTCACTATCTTTTTCAAAGAC
3070754 TAAGATAGAACCTCT
1 TAAGATAGAACCTCT
3070769 CAATCATTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 2 0.05
34 13 0.30
35 8 0.19
36 19 0.44
37 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (37 bp):
TAAGATAGAACCTCTTCTCACTATCTTTTTCAAAGAC
Found at i:3070760 original size:36 final size:34
Alignment explanation
Indices: 3070671--3070768 Score: 103
Period size: 34 Copynumber: 2.8 Consensus size: 34
3070661 GAACCTCCAT
*
3070671 TCTTTTCA-TAGCTTAAGATAGAACCTCTTTACTA
1 TCTTTTCACAAGC-TAAGATAGAACCTCTTTACTA
* *
3070705 TCTTTTCACAAGCTGAGATAGAACCT-TTCTCCCTA
1 TCTTTTCACAAGCTAAGATAGAACCTCTT-T-ACTA
3070740 TCTTTTTCA-AAGACTAAGATAGAACCTCT
1 TC-TTTTCACAAG-CTAAGATAGAACCTCT
3070769 CAATCATTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
33 2 0.04
34 21 0.39
35 11 0.20
36 19 0.35
37 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (34 bp):
TCTTTTCACAAGCTAAGATAGAACCTCTTTACTA
Found at i:3071229 original size:20 final size:20
Alignment explanation
Indices: 3071204--3071241 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3071194 CCGTAGGGCT
*
3071204 TAATGTATCGATATAATTCA
1 TAATGTATCGATACAATTCA
3071224 TAATGTATCGATACAATT
1 TAATGTATCGATACAATT
3071242 ATAGTCGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (20 bp):
TAATGTATCGATACAATTCA
Found at i:3071403 original size:33 final size:32
Alignment explanation
Indices: 3071341--3071404 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
3071331 CATTTTATGG
*
3071341 TGTATCGATACAAAGAACATGTATTGATACAA
1 TGTATCGATACAAAGAACATGTATCGATACAA
* * *
3071373 TGTATGGATACCAAGCAATATGTATCGATACA
1 TGTATCGATACAAAG-AACATGTATCGATACA
3071405 TCTGGGTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAA
Found at i:3072300 original size:32 final size:32
Alignment explanation
Indices: 3072264--3072331 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
3072254 TTCAACGATT
*
3072264 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGCATCGATACAA
* *
3072296 TGTATCGATACATAAGTTTTGCATCGATATAA
1 TGTATCGATACATAAGTGTTGCATCGATACAA
3072328 TGTA
1 TGTA
3072332 CAGTTACGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGCATCGATACAA
Found at i:3072301 original size:13 final size:13
Alignment explanation
Indices: 3072283--3072307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3072273 ACATAAGTGT
3072283 TGTATCGATACAA
1 TGTATCGATACAA
3072296 TGTATCGATACA
1 TGTATCGATACA
3072308 TAAGTTTTGC
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:3072397 original size:13 final size:12
Alignment explanation
Indices: 3072357--3072437 Score: 70
Period size: 13 Copynumber: 7.1 Consensus size: 12
3072347 TGCCAAGAAA
3072357 ATGTATCGATAC
1 ATGTATCGATAC
3072369 AT-TACTC-A-A-
1 ATGTA-TCGATAC
3072378 ATGTATCGATAC
1 ATGTATCGATAC
3072390 ATTGTATCGATAC
1 A-TGTATCGATAC
3072403 AT-TACTC-A-A-
1 ATGTA-TCGATAC
3072412 ATGTATCGATAC
1 ATGTATCGATAC
3072424 ATTGTATCGATAC
1 A-TGTATCGATAC
3072437 A
1 A
3072438 CTGATCTTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 23
0.71 0.00 0.29
Matches are distributed among these distances:
9 8 0.14
10 8 0.14
11 8 0.14
12 9 0.16
13 24 0.42
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:3072401 original size:34 final size:34
Alignment explanation
Indices: 3072358--3072437 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
3072348 GCCAAGAAAA
3072358 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
3072392 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
3072426 TGTATCGATACA
1 TGTATCGATACA
3072438 CTGATCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (34 bp):
TGTATCGATACATTACTCAAATGTATCGATACAT
Found at i:3073327 original size:20 final size:21
Alignment explanation
Indices: 3073302--3073340 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3073292 TCCCGTGTAA
3073302 ATGTATCGATACA-ATTTTTG
1 ATGTATCGATACATATTTTTG
3073322 ATGTATCGATACATATTTT
1 ATGTATCGATACATATTTT
3073341 AAAATATAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (21 bp):
ATGTATCGATACATATTTTTG
Found at i:3073412 original size:13 final size:13
Alignment explanation
Indices: 3073394--3073419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3073384 CAATTTTTTG
3073394 TGTATCGATACAT
1 TGTATCGATACAT
3073407 TGTATCGATACAT
1 TGTATCGATACAT
3073420 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:3074168 original size:21 final size:21
Alignment explanation
Indices: 3074127--3074170 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3074117 CTCCCCTTTA
* *
3074127 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
3074148 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
3074169 TC
1 TC
3074171 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:3075982 original size:13 final size:13
Alignment explanation
Indices: 3075964--3076002 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
3075954 ATAATCACCC
3075964 TGTATCGATACAA
1 TGTATCGATACAA
3075977 TGTATCGATACAA
1 TGTATCGATACAA
3075990 TGTATCGATACAA
1 TGTATCGATACAA
3076003 GGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3078093 original size:15 final size:15
Alignment explanation
Indices: 3078073--3078102 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3078063 GTTCATCAAT
3078073 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
3078088 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
3078103 CCCAATTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:3079962 original size:21 final size:21
Alignment explanation
Indices: 3079915--3079959 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3079905 AAGTTTTCAT
3079915 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
3079935 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
3079957 TTT
1 TTT
3079960 CATCTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:3082102 original size:20 final size:21
Alignment explanation
Indices: 3082077--3082115 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3082067 TCCCGTGTAA
3082077 ATGTATCGATACA-ATTTTTG
1 ATGTATCGATACATATTTTTG
3082097 ATGTATCGATACATATTTT
1 ATGTATCGATACATATTTT
3082116 AAAATATAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (21 bp):
ATGTATCGATACATATTTTTG
Found at i:3082187 original size:13 final size:13
Alignment explanation
Indices: 3082169--3082194 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3082159 CAATTTTTTG
3082169 TGTATCGATACAT
1 TGTATCGATACAT
3082182 TGTATCGATACAT
1 TGTATCGATACAT
3082195 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:3087886 original size:22 final size:21
Alignment explanation
Indices: 3087861--3087905 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
3087851 ATAAAATTTG
*
3087861 ATTAATGTTTATATTTTATAAA
1 ATTAATGTTTATAATTT-TAAA
* *
3087883 ATTATTGTTTTTAATTTTAAA
1 ATTAATGTTTATAATTTTAAA
3087904 AT
1 AT
3087906 AAAATTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTAATGTTTATAATTTTAAA
Found at i:3088381 original size:2 final size:2
Alignment explanation
Indices: 3088374--3088426 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3088364 GTTTATTGTG
3088374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3088416 AT AT AT AT AT A
1 AT AT AT AT AT A
3088427 AGGGAAAATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3089006 original size:19 final size:19
Alignment explanation
Indices: 3088978--3089047 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
3088968 TTTCTCTCTC
3088978 TTTTTT-TTTTTTTTTTCT
1 TTTTTTCTTTTTTTTTTCT
*
3088996 TTTTTTCTTTTGTTTTGTC-
1 TTTTTTCTTTT-TTTTTTCT
* * * *
3089015 TTGTTTCTATTGTTTTTGT
1 TTTTTTCTTTTTTTTTTCT
* *
3089034 TTTGTCCTTTTTTT
1 TTTTTTCTTTTTTT
3089048 ACTATTTTAT
Statistics
Matches: 38, Mismatches: 11, Indels: 5
0.70 0.20 0.09
Matches are distributed among these distances:
18 10 0.26
19 22 0.58
20 6 0.16
ACGTcount: A:0.01, C:0.09, G:0.09, T:0.81
Consensus pattern (19 bp):
TTTTTTCTTTTTTTTTTCT
Found at i:3089006 original size:20 final size:19
Alignment explanation
Indices: 3088976--3089030 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3088966 AGTTTCTCTC
3088976 TCTTTTTTTTTTT-TTTT-
1 TCTTTTTTTTTTTGTTTTG
3088993 TCTTTTTTTCTTTTGTTTTG
1 TCTTTTTTT-TTTTGTTTTG
* * *
3089013 TCTTGTTTCTATTGTTTT
1 TCTTTTTTTTTTTGTTTT
3089031 TGTTTTGTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 9 0.28
18 4 0.12
19 12 0.38
20 7 0.22
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.82
Consensus pattern (19 bp):
TCTTTTTTTTTTTGTTTTG
Found at i:3089055 original size:25 final size:25
Alignment explanation
Indices: 3089003--3089055 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
3088993 TCTTTTTTTC
* *
3089003 TTTTGTTTTGTCTTGTTTCTATTGT
1 TTTTGTTTTGTCTTGTTTCTACTAT
*
3089028 TTTTGTTTTGTCCTT-TTTTTACTAT
1 TTTTGTTTTGT-CTTGTTTCTACTAT
3089053 TTT
1 TTT
3089056 ATACTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.06, C:0.09, G:0.11, T:0.74
Consensus pattern (25 bp):
TTTTGTTTTGTCTTGTTTCTACTAT
Found at i:3091405 original size:2 final size:2
Alignment explanation
Indices: 3091361--3091397 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3091351 CCAAGGGGGA
3091361 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 A
3091398 TGGAGAGATT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3092029 original size:2 final size:2
Alignment explanation
Indices: 3092022--3092057 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3092012 AAAGGACCAC
*
3092022 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3092058 GAGGGAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3098213 original size:18 final size:19
Alignment explanation
Indices: 3098184--3098221 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3098174 TTTTATATTT
3098184 TGTGTAGTAGTATGTGTTA
1 TGTGTAGTAGTATGTGTTA
*
3098203 TGTGT-GTAGTATTTGTTA
1 TGTGTAGTAGTATGTGTTA
3098221 T
1 T
3098222 AAAAATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (19 bp):
TGTGTAGTAGTATGTGTTA
Found at i:3098547 original size:21 final size:20
Alignment explanation
Indices: 3098523--3098561 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3098513 TTCTACCCAC
3098523 TAATTCAATATATT-TTTATTG
1 TAATT-AAT-TATTGTTTATTG
3098544 TAATTAATTATTGTTTAT
1 TAATTAATTATTGTTTAT
3098562 ATCATAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (20 bp):
TAATTAATTATTGTTTATTG
Found at i:3099703 original size:23 final size:23
Alignment explanation
Indices: 3099659--3099704 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3099649 TCAGATTTTG
* *
3099659 AATATTTTTAATTTATATATAAA
1 AATATTTTTAATATATAAATAAA
3099682 AATATTTTTAA-ATATAAAATAAA
1 AATATTTTTAATATAT-AAATAAA
3099705 TAAGGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AATATTTTTAATATATAAATAAA
Found at i:3099858 original size:32 final size:32
Alignment explanation
Indices: 3099811--3099878 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
3099801 CGAAGCTTTT
* ** *
3099811 TAATAATTATTAAATTTATGAATAATTATATC
1 TAATAATTATCAAATTTACCAACAATTATATC
* *
3099843 TAATATTTATCAAATTTACCAACAATTATATT
1 TAATAATTATCAAATTTACCAACAATTATATC
3099875 TAAT
1 TAAT
3099879 TCATCAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (32 bp):
TAATAATTATCAAATTTACCAACAATTATATC
Found at i:3100306 original size:20 final size:20
Alignment explanation
Indices: 3100267--3100304 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3100257 TTCAAAGCTT
*
3100267 TAAAAAAGAGAAAAGAAAAG
1 TAAAAAAGAAAAAAGAAAAG
3100287 TAAAAAA-AAAAAAGAAAA
1 TAAAAAAGAAAAAAGAAAA
3100305 AGGAAGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (20 bp):
TAAAAAAGAAAAAAGAAAAG
Found at i:3101789 original size:22 final size:22
Alignment explanation
Indices: 3101764--3101806 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3101754 GACAAGTCTA
3101764 AATATTTTTC-AAGTAATAAATC
1 AATATTTTTCAAAGTAA-AAATC
3101786 AATATTTTTCAAAGTAAAAAT
1 AATATTTTTCAAAGTAAAAAT
3101807 ACTTACTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (22 bp):
AATATTTTTCAAAGTAAAAATC
Found at i:3102917 original size:79 final size:78
Alignment explanation
Indices: 3102807--3103282 Score: 404
Period size: 79 Copynumber: 6.1 Consensus size: 78
3102797 TATTTTGGAG
* * * * ***
3102807 ATAAAAACGGGGTTAGAGTATCCC-CAAAAATAATAGGGTTGGGGTATCTTTGATTGTGGAAAAT
1 ATAAAATCGGAGTTAGAGTATCCCTCGAAAATAATAGGGTTGGAGTATCCCCGATTGTGGAAAAT
3102871 CGGTGTTTTAGAA
66 CGGTGTTTTAGAA
* * * * ** * *
3102884 AAAAAATCGAAGTTAGAGCATCCTCTCGAAAATAA-CGGGATTAAAGTATCTCCGATTATGGAAA
1 ATAAAATCGGAGTTAGAGTATCC-CTCGAAAATAATAGGG-TTGGAGTATCCCCGATTGTGGAAA
*
3102948 ATTGGTGTTTTAGAA
64 ATCGGTGTTTTAGAA
* * * * ** **
3102963 ATAAAATTGGAGTTAGAGTATATCCTCAAAAATAATAAGGTTGGAGTATCCTTGATTGTAAAAAA
1 ATAAAATCGGAGTTAGAGTAT-CCCTCGAAAATAATAGGGTTGGAGTATCCCCGATTGTGGAAAA
*
3103028 TCAGTGTTTTAGAA
65 TCGGTGTTTTAGAA
* * * * ** *
3103042 ATAAAACCGGGGTT-GTAGTGTCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAA
1 ATAAAATCGGAGTTAG-AGTAT-CCCTCGAAAATAATAGGGTTGGAGTATCCCCGATTGTGGAAA
**
3103106 ATTAGTGTTTTAGAA
64 ATCGGTGTTTTAGAA
* * * * * **
3103121 ATAAAACCGGGGTTAGAGTATCCCATTGAAAATAATGGGGTTGGAGTATCCCCGATGGTAAAAAA
1 ATAAAATCGGAGTTAGAGTATCCC-TCGAAAATAATAGGGTTGGAGTATCCCCGATTGTGGAAAA
* *
3103186 TTGAT-TTTTAGAA
65 TCGGTGTTTTAGAA
* * ** * *
3103199 ATAAAATCAGAGTTGGAGTATCCCTTCGAAAATAGCAGAGTTGGAGTAT-CCCGATAGTGGAAAA
1 ATAAAATCGGAGTTAGAGTATCCC-TCGAAAATAATAGGGTTGGAGTATCCCCGATTGTGGAAAA
3103263 TCGGTGTTTTAGAA
65 TCGGTGTTTTAGAA
*
3103277 ACAAAA
1 ATAAAA
3103283 ATATCAATGA
Statistics
Matches: 319, Mismatches: 71, Indels: 17
0.78 0.17 0.04
Matches are distributed among these distances:
77 33 0.10
78 68 0.21
79 214 0.67
80 4 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (78 bp):
ATAAAATCGGAGTTAGAGTATCCCTCGAAAATAATAGGGTTGGAGTATCCCCGATTGTGGAAAAT
CGGTGTTTTAGAA
Found at i:3103153 original size:158 final size:156
Alignment explanation
Indices: 3102807--3103283 Score: 484
Period size: 158 Copynumber: 3.0 Consensus size: 156
3102797 TATTTTGGAG
* * * **
3102807 ATAAAAACGGGGTTAGAGTATCCCCA-AAAATAATAGGGTTGGGGTATCTTTGATTGTGGAAAAT
1 ATAAAAACGGGGTTAGAGTATACCCATAAAATAATAGGGTTGGAGTATCCTTGATTGTAAAAAAT
* * * * * * * ** *
3102871 CGGTGTTTTAGAAAAAAAATCGAAGTTAGAGCATCCTCTCGAAAATAACGGGATTAAAGTATCTC
66 CAGTGTTTTAGAAATAAAATCGGAGTT-GAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCC
3102936 CGATTA-TGGAAAATTGGTGTTTTAGAA
130 CGA-TAGTGGAAAATTGGTGTTTTAGAA
** * *
3102963 ATAAAATTGGAGTTAGAGTATATCCTCA-AAAATAATAAGGTTGGAGTATCCTTGATTGTAAAAA
1 ATAAAAACGGGGTTAGAGTATA-CC-CATAAAATAATAGGGTTGGAGTATCCTTGATTGTAAAAA
* * *
3103027 ATCAGTGTTTTAGAAATAAAACCGGGGTTGTAGTGTCCCCTTGAAAATAACGGGGTTGGAGTATC
64 ATCAGTGTTTTAGAAATAAAATCGGAGTTG-AGTATCCCCTTGAAAATAACGGGGTTGGAGTATC
* *
3103092 CCCGATGGTGGAAAATTAGTGTTTTAGAA
128 CCCGATAGTGGAAAATTGGTGTTTTAGAA
* * ** *
3103121 ATAAAACCGGGGTTAGAGTAT-CCCATTGAAAATAATGGGGTTGGAGTATCCCCGATGGTAAAAA
1 ATAAAAACGGGGTTAGAGTATACCCA-T-AAAATAATAGGGTTGGAGTATCCTTGATTGTAAAAA
* * * * *
3103185 AT-TGAT-TTTTAGAAATAAAATCAGAGTTGGAGTAT-CCCTTCGAAAATAGCAGAGTTGGAGTA
64 ATCAG-TGTTTTAGAAATAAAATCGGAGTT-GAGTATCCCCTT-GAAAATAACGGGGTTGGAGTA
*
3103247 T-CCCGATAGTGGAAAATCGGTGTTTTAGAA
126 TCCCCGATAGTGGAAAATTGGTGTTTTAGAA
*
3103277 ACAAAAA
1 ATAAAAA
3103284 TATCAATGAA
Statistics
Matches: 266, Mismatches: 45, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
155 2 0.01
156 56 0.21
157 47 0.18
158 161 0.61
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (156 bp):
ATAAAAACGGGGTTAGAGTATACCCATAAAATAATAGGGTTGGAGTATCCTTGATTGTAAAAAAT
CAGTGTTTTAGAAATAAAATCGGAGTTGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCC
GATAGTGGAAAATTGGTGTTTTAGAA
Found at i:3110838 original size:13 final size:13
Alignment explanation
Indices: 3110820--3110845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3110810 TACAGCAAGT
3110820 ATGTATCGATACA
1 ATGTATCGATACA
3110833 ATGTATCGATACA
1 ATGTATCGATACA
3110846 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:3113094 original size:21 final size:21
Alignment explanation
Indices: 3113061--3113105 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3113051 TTGCAAGTTG
*
3113061 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3113083 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3113103 AAA
1 AAA
3113106 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3117033 original size:13 final size:13
Alignment explanation
Indices: 3117015--3117040 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3117005 ACATTTTTCT
3117015 TTGTATCGATACA
1 TTGTATCGATACA
3117028 TTGTATCGATACA
1 TTGTATCGATACA
3117041 GGGTGATTAT
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):
TTGTATCGATACA
Found at i:3117204 original size:20 final size:20
Alignment explanation
Indices: 3117161--3117206 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3117151 AAATCTTTTG
3117161 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3117182 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3117202 CAAAA
1 CAAAA
3117207 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3119602 original size:13 final size:13
Alignment explanation
Indices: 3119584--3119609 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3119574 TACAGCAAGT
3119584 ATGTATCGATACA
1 ATGTATCGATACA
3119597 ATGTATCGATACA
1 ATGTATCGATACA
3119610 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:3121923 original size:21 final size:21
Alignment explanation
Indices: 3121894--3121936 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3121884 ATTTTTTGAA
*
3121894 TGATCTTGTGTTGTTAATTGT
1 TGATCTTGTGTGGTTAATTGT
*
3121915 TGATGTTGTGTGGTTAATTGT
1 TGATCTTGTGTGGTTAATTGT
3121936 T
1 T
3121937 CGTGAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.02, G:0.28, T:0.56
Consensus pattern (21 bp):
TGATCTTGTGTGGTTAATTGT
Found at i:3122811 original size:13 final size:13
Alignment explanation
Indices: 3122793--3122818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3122783 TACATAAGTG
3122793 TTGTATCGATACA
1 TTGTATCGATACA
3122806 TTGTATCGATACA
1 TTGTATCGATACA
3122819 CTGATCTTTG
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):
TTGTATCGATACA
Found at i:3122896 original size:51 final size:51
Alignment explanation
Indices: 3122807--3122954 Score: 215
Period size: 51 Copynumber: 2.9 Consensus size: 51
3122797 ATCGATACAT
***
3122807 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAAAGTATCGATACATGCAGGCAAATTTGCCCAGA
*
3122859 TGTATCGATACACTATCAAAGTATCGATACATACAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATCAAAGTATCGATACATGCAGGCAAATTTGCCCAGA
* * *
3122910 TGTATTGATACACTATGAAATGTATCGATACATGCAGGCCAATTT
1 TGTATCGATACACTATCAAA-GTATCGATACATGCAGGCAAATTT
3122955 TCATATTTCG
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 51 0.59
52 36 0.41
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAAAGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:3127545 original size:13 final size:13
Alignment explanation
Indices: 3127527--3127552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3127517 TACACCAAGT
3127527 ATGTATCGATACA
1 ATGTATCGATACA
3127540 ATGTATCGATACA
1 ATGTATCGATACA
3127553 CCAAAAATTG
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:3127550 original size:32 final size:33
Alignment explanation
Indices: 3127509--3127572 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3127499 TAGCCAAACT
**
3127509 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
3127541 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
3127573 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:3129802 original size:21 final size:21
Alignment explanation
Indices: 3129769--3129813 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3129759 TTGCAAGTTG
*
3129769 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3129791 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3129811 AAA
1 AAA
3129814 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3131637 original size:15 final size:15
Alignment explanation
Indices: 3131617--3131647 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3131607 TAAAAATGTC
*
3131617 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3131632 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3131647 C
1 C
3131648 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:3136309 original size:13 final size:13
Alignment explanation
Indices: 3136291--3136316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3136281 TACACCAAGT
3136291 ATGTATCGATACA
1 ATGTATCGATACA
3136304 ATGTATCGATACA
1 ATGTATCGATACA
3136317 CCAAAAATTG
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:3136314 original size:32 final size:33
Alignment explanation
Indices: 3136273--3136336 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
3136263 TAGCCAAACT
**
3136273 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
3136305 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
3136337 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:3137467 original size:13 final size:13
Alignment explanation
Indices: 3137449--3137474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3137439 AAAAACTGTT
3137449 GTTTATAAATTTG
1 GTTTATAAATTTG
3137462 GTTTATAAATTTG
1 GTTTATAAATTTG
3137475 AAGGAGAACA
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:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
GTTTATAAATTTG
Found at i:3138086 original size:22 final size:22
Alignment explanation
Indices: 3138061--3138103 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3138051 GACAAGTCTA
3138061 AATGTTTTTC-AAGTAATAAATT
1 AATGTTTTTCAAAGTAA-AAATT
3138083 AATGTTTTTCAAAGTAAAAAT
1 AATGTTTTTCAAAGTAAAAAT
3138104 ACTTGCTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (22 bp):
AATGTTTTTCAAAGTAAAAATT
Found at i:3140522 original size:35 final size:35
Alignment explanation
Indices: 3140481--3140549 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
3140471 CAAGCAAGCA
* *
3140481 AGCAAAAGAAGCATATACAAGCAGCAAGGGATAGT
1 AGCAAAAAAAACATATACAAGCAGCAAGGGATAGT
*
3140516 AGCAAAAAAAACATATACGAGCAGCAAGGGATAG
1 AGCAAAAAAAACATATACAAGCAGCAAGGGATAG
3140550 CAATAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.51, C:0.14, G:0.25, T:0.10
Consensus pattern (35 bp):
AGCAAAAAAAACATATACAAGCAGCAAGGGATAGT
Found at i:3142230 original size:97 final size:96
Alignment explanation
Indices: 3142055--3142235 Score: 238
Period size: 97 Copynumber: 1.9 Consensus size: 96
3142045 CGGGGATACA
* *
3142055 CCAACCCCATTCCGCCGAGGGGATACTCCAACCTCACTTTTAAACTTATCAAAATTTAAATCTTA
1 CCAACCCCATTCCGCCGAAGGGATACTCCAACCTCACTTTTAAACTAATCAAAATTTAAATCTTA
* *
3142120 TTTTCGGTTAAATTTTCATCATCGGAGACACT
66 TTTTC-GTCAAATTATCATCATCGGAGACACT
* *** **
3142152 CCAACCCCATTCCTCCGAAGGGATACTCCAACCATGTTTTTTAAACTAATTGAAATTTAAATCTT
1 CCAACCCCATTCCGCCGAAGGGATACTCCAACC-TCACTTTTAAACTAATCAAAATTTAAATCTT
3142217 ATTTT-GTCCAAATTATCAT
65 ATTTTCGT-CAAATTATCAT
3142236 AGTTGAAAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
96 2 0.03
97 40 0.56
98 30 0.42
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (96 bp):
CCAACCCCATTCCGCCGAAGGGATACTCCAACCTCACTTTTAAACTAATCAAAATTTAAATCTTA
TTTTCGTCAAATTATCATCATCGGAGACACT
Found at i:3142250 original size:97 final size:96
Alignment explanation
Indices: 3142050--3142256 Score: 229
Period size: 97 Copynumber: 2.1 Consensus size: 96
3142040 TTTATCGGGG
* * *
3142050 ATACACCAACCCCATTCCGCCGAGGGGATACTCCAACCTCACTTTTAAACTTATCAAAATTTAAA
1 ATACTCCAACCCCATTCCGCCGAAGGGATACTCCAACCTCACTTTTAAACTAATCAAAATTTAAA
* * * *
3142115 TCTTATTTTCGGTTAAATTTTCATCATCGGAG
66 TCTTATTTTC-GTCAAATTATCATCATCGAAA
* * *** **
3142147 ACACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCATGTTTTTTAAACTAATTGAAATTTAA
1 ATACTCCAACCCCATTCCGCCGAAGGGATACTCCAACC-TCACTTTTAAACTAATCAAAATTTAA
*
3142212 ATCTTATTTT-GTCCAAATTATCAT-AGTTGAAA
65 ATCTTATTTTCGT-CAAATTATCATCA-TCGAAA
3142244 ATACTCCAACCCC
1 ATACTCCAACCCC
3142257 GTTTTTAAAC
Statistics
Matches: 91, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
96 3 0.03
97 58 0.64
98 30 0.33
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (96 bp):
ATACTCCAACCCCATTCCGCCGAAGGGATACTCCAACCTCACTTTTAAACTAATCAAAATTTAAA
TCTTATTTTCGTCAAATTATCATCATCGAAA
Done.