Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 13 of 199
Found at i:4120079 original size:13 final size:15
Alignment explanation
Indices: 4120049--4120080 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
4120039 TTTTGGGGCT
4120049 TTTTAGACTGTATGG
1 TTTTAGACTGTATGG
4120064 TTTTA-ACTGT-TGG
1 TTTTAGACTGTATGG
4120077 TTTT
1 TTTT
4120081 GGTTTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.16, C:0.06, G:0.22, T:0.56
Consensus pattern (15 bp):
TTTTAGACTGTATGG
Found at i:4120529 original size:54 final size:53
Alignment explanation
Indices: 4120455--4120852 Score: 252
Period size: 54 Copynumber: 7.4 Consensus size: 53
4120445 TAACCTCCCT
* * * * * *
4120455 TACTTAAAACATTTTTAGAATCTTATGGTTTGCTGATTTACGATGACGACCTCC
1 TACTTACAAGATTTTAAGAATCTTACGGTTCGCTGATTTACGATG-CGACCTTC
* * *
4120509 TACTTACAAGATTTTAAGAATTTTACGGTTCACTGATTTGCGATTGTC-ACCTTC
1 TACTTACAAGATTTTAAGAATCTTACGGTTCGCTGATTTACGA-TG-CGACCTTC
* * * * ** * * *
4120563 TACTTACAAGATTTTAAGAATATTGCGATTCACCCATTTATGATTGTGACCTTT
1 TACTTACAAGATTTTAAGAATCTTACGGTTCGCTGATTTACGA-TGCGACCTTC
* * * * * *
4120617 TACTTACAAGATTTCAAGAATCTTATGGTTTGCTAATTTACAATCGCAACCTTC
1 TACTTACAAGATTTTAAGAATCTTACGGTTCGCTGATTTACGAT-GCGACCTTC
* * * * * *
4120671 TACTTACAAGATTTCAAGGATTTTACGGTTGGTTGATTTACGAT-CGTTACCTTA
1 TACTTACAAGATTTTAAGAATCTTACGGTTCGCTGATTTACGATGCG--ACCTTC
* * * * *
4120725 TACTTACAAGATTTTAAGAATCTTATGATTC-ATCGATTTAC-AGTCGCAACCATC
1 TACTTACAAGATTTTAAGAATCTTACGGTTCGCT-GATTTACGA-T-GCGACCTTC
* * *** *
4120779 TACTTACAAAATTTTCAGAATCTTATAATTCG-TAGATTTATGATCGCGA-CTTCC
1 TACTTACAAGATTTTAAGAATCTTACGGTTCGCT-GATTTACGAT-GCGACCTT-C
*
4120833 TACTTACAAGATCTT-AGAAT
1 TACTTACAAGATTTTAAGAAT
4120853 TTCGCGGTTC
Statistics
Matches: 271, Mismatches: 61, Indels: 25
0.76 0.17 0.07
Matches are distributed among these distances:
52 1 0.00
53 10 0.04
54 255 0.94
55 4 0.01
56 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (53 bp):
TACTTACAAGATTTTAAGAATCTTACGGTTCGCTGATTTACGATGCGACCTTC
Found at i:4120785 original size:162 final size:162
Alignment explanation
Indices: 4120455--4120804 Score: 402
Period size: 162 Copynumber: 2.2 Consensus size: 162
4120445 TAACCTCCCT
* * * *
4120455 TACTTA-AAACATTTTTAGAATCTTATGGTTTGCTGATTTACGATGACGACCTCCTACTTACAAG
1 TACTTACAAA-ATTTTCAGAATCTTATGGTTTGCTAATTTACAATGACAACCTCCTACTTACAAG
* * * *
4120519 ATTTTAAGAATTTTACGGTTCACTGATTTGCGATTGTCACCTTCTACTTACAAGATTTTAAGAAT
65 ATTTCAAGAATTTTACGGTTCACTGATTTACGATCGTCACCTTATACTTACAAGATTTTAAGAAT
* * * ** * *
4120584 ATTGCGATTCACCCATTTATGATTGTGACCTTT
130 ATTACGATTCACCCATTTAAGATCGCAACCATC
* *
4120617 TACTTACAAGA-TTTCAAGAATCTTATGGTTTGCTAATTTACAATCG-CAACCTTCTACTTACAA
1 TACTTACAAAATTTTC-AGAATCTTATGGTTTGCTAATTTACAAT-GACAACCTCCTACTTACAA
* *** *
4120680 GATTTCAAGGATTTTACGGTTGGTTGATTTACGATCGTTACCTTATACTTACAAGATTTTAAGAA
64 GATTTCAAGAATTTTACGGTTCACTGATTTACGATCGTCACCTTATACTTACAAGATTTTAAGAA
* * * *
4120745 TCTTATGATTCATCGATTTACAG-TCGCAACCATC
129 TATTACGATTCACCCATTTA-AGATCGCAACCATC
4120779 TACTTACAAAATTTTCAGAATCTTAT
1 TACTTACAAAATTTTCAGAATCTTAT
4120805 AATTCGTAGA
Statistics
Matches: 156, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
161 3 0.02
162 145 0.93
163 8 0.05
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (162 bp):
TACTTACAAAATTTTCAGAATCTTATGGTTTGCTAATTTACAATGACAACCTCCTACTTACAAGA
TTTCAAGAATTTTACGGTTCACTGATTTACGATCGTCACCTTATACTTACAAGATTTTAAGAATA
TTACGATTCACCCATTTAAGATCGCAACCATC
Found at i:4120817 original size:108 final size:108
Alignment explanation
Indices: 4120489--4120908 Score: 295
Period size: 108 Copynumber: 3.9 Consensus size: 108
4120479 ATGGTTTGCT
** * * *
4120489 GATTTACGAT-GACGACCTCCTACTTACAAGATTTTAAGAATTTTACGGTTCA-CTGATTTGC-G
1 GATTTACGATCG-CGACCTTATACTTACAAGATTTTAAGAATCTTATGGTTCATC-GATTTACAG
* * * * * * ***
4120551 ATTGTC-ACCTTCTACTTACAAGATTTTAAGAATATTGCGATTCACC
64 -TCG-CAACCTTCTACTTACAAAATTTTCAGAATCTTACAATTCGTA
* * * * * * * *
4120597 CATTTATGATTGTGACCTTTTACTTACAAGATTTCAAGAATCTTATGGTT--TGCTAATTTACAA
1 GATTTACGATCGCGACCTTATACTTACAAGATTTTAAGAATCTTATGGTTCAT-C-GATTTACAG
* * * ** * *
4120660 TCGCAACCTTCTACTTACAAGA-TTTCAAGGATTTTACGGTTGGTT
64 TCGCAACCTTCTACTTACAAAATTTTC-AGAATCTTACAATTCGTA
** *
4120705 GATTTACGATCGTTACCTTATACTTACAAGATTTTAAGAATCTTATGATTCATCGATTTACAGTC
1 GATTTACGATCGCGACCTTATACTTACAAGATTTTAAGAATCTTATGGTTCATCGATTTACAGTC
* *
4120770 GCAACCATCTACTTACAAAATTTTCAGAATCTTATAATTCGTA
66 GCAACCTTCTACTTACAAAATTTTCAGAATCTTACAATTCGTA
* * * **
4120813 GATTTATGATCGCGA-CTTCCTACTTACAAGATCTT-AGAAT-TTCGCGGTTCATCGATTT-CAG
1 GATTTACGATCGCGACCTT-ATACTTACAAGATTTTAAGAATCTT-ATGGTTCATCGATTTACAG
* * *
4120874 ATCGCAACCTTTTACTTACAATATTTTCAAAATCT
64 -TCGCAACCTTCTACTTACAAAATTTTCAGAATCT
4120909 CGCAGTCCGT
Statistics
Matches: 249, Mismatches: 51, Indels: 25
0.77 0.16 0.08
Matches are distributed among these distances:
106 5 0.02
107 54 0.22
108 183 0.73
109 6 0.02
110 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (108 bp):
GATTTACGATCGCGACCTTATACTTACAAGATTTTAAGAATCTTATGGTTCATCGATTTACAGTC
GCAACCTTCTACTTACAAAATTTTCAGAATCTTACAATTCGTA
Found at i:4120838 original size:162 final size:162
Alignment explanation
Indices: 4120501--4120900 Score: 377
Period size: 162 Copynumber: 2.5 Consensus size: 162
4120491 TTTACGATGA
* * * * *
4120501 CGACCTCCTACTTACAAGATTTTAAGAATTTTACGGTTCACTGATTTGCGATTGTCACCTTCTAC
1 CGACTTCCTACTTACAAGATTTCAAGAATTTTACGGTTCACTGATTTACGATCGTCACCTTATAC
* * * ** * * *
4120566 TTACAAGATTTTAAGAATATTGCGATTCACCCATTTATGATTGTGACCTTTTACTTACAAGATTT
66 TTACAAGATTTTAAGAATATTACGATTCACCCATTTAAGATCGCAACCATCTACTTACAAAATTT
** *
4120631 CAAGAATCTTATGGTTTGCTAATTTACAATCG
131 CAAGAATCTTATAATTCGCTAATTTACAATCG
* * *** *
4120663 CAACCTT-CTACTTACAAGATTTCAAGGATTTTACGGTTGGTTGATTTACGATCGTTACCTTATA
1 CGA-CTTCCTACTTACAAGATTTCAAGAATTTTACGGTTCACTGATTTACGATCGTCACCTTATA
* * * *
4120727 CTTACAAGATTTTAAGAATCTTATGATTCATCGATTTACAG-TCGCAACCATCTACTTACAAAAT
65 CTTACAAGATTTTAAGAATATTACGATTCACCCATTTA-AGATCGCAACCATCTACTTACAAAA-
**
4120791 TTTC-AGAATCTTATAATTCG-TAGATTTATGATCG
128 TTTCAAGAATCTTATAATTCGCTA-ATTTACAATCG
**
4120825 CGACTTCCTACTTACAAGATCTT--AGAATTTCGCGGTTCA-TCGATTT-CAGATCG-CAACCTT
1 CGACTTCCTACTTACAAGAT-TTCAAGAATTTTACGGTTCACT-GATTTAC-GATCGTC-ACCTT
* *
4120885 TTACTTACAATATTTT
62 ATACTTACAAGATTTT
4120901 CAAAATCTCG
Statistics
Matches: 192, Mismatches: 37, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
160 2 0.01
161 45 0.23
162 136 0.71
163 9 0.05
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (162 bp):
CGACTTCCTACTTACAAGATTTCAAGAATTTTACGGTTCACTGATTTACGATCGTCACCTTATAC
TTACAAGATTTTAAGAATATTACGATTCACCCATTTAAGATCGCAACCATCTACTTACAAAATTT
CAAGAATCTTATAATTCGCTAATTTACAATCG
Found at i:4121513 original size:323 final size:324
Alignment explanation
Indices: 4121083--4121695 Score: 1032
Period size: 323 Copynumber: 1.9 Consensus size: 324
4121073 TAGTTCACCG
* * * * * *
4121083 ATTTCATATCACAACCTTTTAAATTACAATATTTTCATAATCTCACAGTTCTCTAATTTCAGATC
1 ATTTCATATCACAACCTTTTAAATTACAAGATCTTAAAAATCTCACAGTTCACCAATTTCAGATC
* * * *
4121148 GCGACATTTTAACTTACAATATTTTCAGAATCTCGTAATTCACCGATTTTAGATCATAAACTTTT
66 ACAACATTTTAAATTACAATATTTTCAGAATCTCGCAATTCACCGATTTTAGATCATAAACTTTT
* *
4121213 AACTTACGAAATTTTCATATTCTTGTGGTTCGTCGATTTCATAACGCAACTTTTAACTTACAAGA
131 AACTTACAAAATTTTCATAATCTTGTGGTTCGTCGATTTCATAACGCAACTTTTAACTTACAAGA
4121278 TTTTTAAAATTTT-GGGTTCGCTGATTTCAGATCTCTACTTTTTAATTTACAATATTTTCAGAGT
196 TTTTTAAAATTTTGGGGTTCGCTGATTTCAGATCTCTACTTTTTAATTTACAATATTTTCAGAGT
4121342 CTTGCAGTTTGTTGATTTTATATTGATTTTAACTTACAAGATTTTAGAGTCTTGCGGTTCGTCA
261 CTTGCAGTTTGTTGATTTTATATTGATTTTAACTTACAAGATTTTAGAGTCTTGCGGTTCGTCA
* * * *
4121406 ATTTCATATCACAA-CTTTTTAATTGACAAGATCTTAAAAATCTCATAGTTCACCGATTTCATAT
1 ATTTCATATCACAACCTTTTAAATT-ACAAGATCTTAAAAATCTCACAGTTCACCAATTTCAGAT
* *
4121470 CACAACCTTTTAAATTACAATATTTTCAGAATCTCGCAATTCACCGATTTTAGATCGTAAACTTT
65 CACAACATTTTAAATTACAATATTTTCAGAATCTCGCAATTCACCGATTTTAGATCATAAACTTT
*
4121535 TAACTTACAAAATTTTCATAATCTTGTGGTTCGTCGATTTCATATCGCAACTTTTAACTTACAAG
130 TAACTTACAAAATTTTCATAATCTTGTGGTTCGTCGATTTCATAACGCAACTTTTAACTTACAAG
4121600 ATTTTTAAAATTTTGGGGTTCGCTGATTTCAGATCTCTACTTTTTAATTTACAATATTTTCAGAG
195 ATTTTTAAAATTTTGGGGTTCGCTGATTTCAGATCTCTACTTTTTAATTTACAATATTTTCAGAG
4121665 TCTTGCAGTTTGTTGATTTTATATTGATTTT
260 TCTTGCAGTTTGTTGATTTTATATTGATTTT
4121696 GCTATCCGCC
Statistics
Matches: 269, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
322 9 0.03
323 179 0.67
324 81 0.30
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (324 bp):
ATTTCATATCACAACCTTTTAAATTACAAGATCTTAAAAATCTCACAGTTCACCAATTTCAGATC
ACAACATTTTAAATTACAATATTTTCAGAATCTCGCAATTCACCGATTTTAGATCATAAACTTTT
AACTTACAAAATTTTCATAATCTTGTGGTTCGTCGATTTCATAACGCAACTTTTAACTTACAAGA
TTTTTAAAATTTTGGGGTTCGCTGATTTCAGATCTCTACTTTTTAATTTACAATATTTTCAGAGT
CTTGCAGTTTGTTGATTTTATATTGATTTTAACTTACAAGATTTTAGAGTCTTGCGGTTCGTCA
Found at i:4121682 original size:55 final size:54
Alignment explanation
Indices: 4120780--4121688 Score: 397
Period size: 55 Copynumber: 16.8 Consensus size: 54
4120770 GCAACCATCT
* ** * * * * *
4120780 ACTTACAAAATTTTCAGAATCTTATAATTCGTAGATTT-ATGATCGCGACTTCCT-
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCAT-ATCTCAACTT-TTA
* * * * *
4120834 ACTTACAAGATCTT-AGAAT-TTCGCGGTTCATCGATTTCAGATCGCAACCTTTT-
1 ACTTACAAGATTTTCAGAATCTT-GCAGTTCGTCGATTTCATATCTCAA-CTTTTA
* * * * * * *
4120887 ACTTACAATATTTTCAAAATCTCGCAGTCCGTCGATTTGAAAT-TGCGACCTTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATCT-C-AACTTTTA
* * * *
4120942 ACTTACAATATTTTTCAGAGTC---CAATTTGAT-GATTTCATATCGT-AACATTTTA
1 ACTTACAAGA-TTTTCAGAATCTTGCAGTTCG-TCGATTTCATATC-TCAAC-TTTTA
* * * * *
4120995 ACTTACAAGA-TTTCAGAGTCTTACGGTTCGTCAATTTCATATCACAACTTTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATCTCAAC-TTTTA
* * * *** ** *
4121049 A-TTGACAAGATCTTAAAAATCTCATAGTTCACCGATTTCATATCACAACCTTTTA
1 ACTT-ACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATCTCAA-CTTTTA
* * * ** * * * *
4121104 AATTACAATATTTTCATAATCTCACAGTTC-TCTAATTTCAGATCGCGACATTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTC-GATTTCATATCTCAAC-TTTTA
* * * * ** * * *
4121159 ACTTACAATATTTTCAGAATCTCGTAATTCACCGATTTTAGATCATAAACTTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATC-TCAACTTTTA
* * ** * *
4121214 ACTTACGAA-ATTTTCATATTCTTGTGGTTCGTCGATTTCATAACGCAACTTTTA
1 ACTTAC-AAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATCTCAACTTTTA
* * * * * *
4121268 ACTTACAAGATTTTTAAAATTTTG-GGTTCG-CTGATTTCAGATCTCTACTTTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTC-GATTTCATATCTCAAC-TTTTA
* * * * * * *
4121322 ATTTACAATATTTTCAGAGTCTTGCAGTTTGTTGATTTTATAT-T-GA-TTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATCTCAACTTTTA
* * * *
4121373 ACTTACAAGATTTT-AGAGTCTTGCGGTTCGTCAATTTCATATCACAACTTTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATCTCAAC-TTTTA
* * * *** ** *
4121427 A-TTGACAAGATCTTAAAAATCTCATAGTTCACCGATTTCATATCACAACCTTTTA
1 ACTT-ACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATCTCAA-CTTTTA
* * * * ** * * *
4121482 AATTACAATATTTTCAGAATCTCGCAATTCACCGATTTTAGATCGTAAACTTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATC-TCAACTTTTA
* * ** *
4121537 ACTTACAAAATTTTCATAATCTTGTGGTTCGTCGATTTCATATCGCAACTTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATCTCAACTTTTA
* * * ** * *
4121591 ACTTACAAGATTTTTAAAATTTTGGGGTTCG-CTGATTTCAGATCTCTACTTTTTA
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTC-GATTTCATATCTCAAC-TTTTA
* * * * * *
4121646 ATTTACAATATTTTCAGAGTCTTGCAGTTTGTTGATTTTATAT
1 ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATAT
4121689 TGATTTTGCT
Statistics
Matches: 648, Mismatches: 163, Indels: 87
0.72 0.18 0.10
Matches are distributed among these distances:
50 23 0.04
51 27 0.04
52 6 0.01
53 86 0.13
54 184 0.28
55 300 0.46
56 22 0.03
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (54 bp):
ACTTACAAGATTTTCAGAATCTTGCAGTTCGTCGATTTCATATCTCAACTTTTA
Found at i:4128038 original size:54 final size:56
Alignment explanation
Indices: 4127956--4128094 Score: 183
Period size: 54 Copynumber: 2.5 Consensus size: 56
4127946 ATAAATTAGG
** * * * *
4127956 TGCACCTACCTTATTGGCAAACTATGTTGATGGCTAGGTAAACG-A-ATATATATA
1 TGCACCTACCTTGCTGGCGAACTGTGTTGACGGCTAAGTAAACGAATATATATATA
* *
4128010 TGCACCTACCTTGCTAGCGAACTGTGTTGGCGGCTAAGTAAACGAATATATATATA
1 TGCACCTACCTTGCTGGCGAACTGTGTTGACGGCTAAGTAAACGAATATATATATA
*
4128066 TGCACCTACCTTGCTGGAGAACTGTGTTG
1 TGCACCTACCTTGCTGGCGAACTGTGTTG
4128095 GCAAATAGGT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 36 0.49
55 1 0.01
56 36 0.49
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (56 bp):
TGCACCTACCTTGCTGGCGAACTGTGTTGACGGCTAAGTAAACGAATATATATATA
Found at i:4128088 original size:56 final size:54
Alignment explanation
Indices: 4127956--4128096 Score: 176
Period size: 56 Copynumber: 2.6 Consensus size: 54
4127946 ATAAATTAGG
** * ** *
4127956 TGCACCTACCTTATTGGCA-AACTATGTTGATGGCTAGGTAAACGAATATATATA
1 TGCACCTACCTTGCTGG-AGAACTGTGTTGGCGGCTAAGTAAACGAATATATATA
* *
4128010 TGCACCTACCTTGCTAGCGAACTGTGTTGGCGGCTAAGTAAACGAATATATATATA
1 TGCACCTACCTTGCTGGAGAACTGTGTTGGCGGCTAAGTAAACG-A-ATATATATA
4128066 TGCACCTACCTTGCTGGAGAACTGTGTTGGC
1 TGCACCTACCTTGCTGGAGAACTGTGTTGGC
4128097 AAATAGGTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
54 35 0.47
55 1 0.01
56 38 0.51
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (54 bp):
TGCACCTACCTTGCTGGAGAACTGTGTTGGCGGCTAAGTAAACGAATATATATA
Found at i:4137333 original size:30 final size:30
Alignment explanation
Indices: 4137297--4137353 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
4137287 TTCAACGAGC
4137297 TAGTGGAGAGATCAATTTGACATACGTAAT
1 TAGTGGAGAGATCAATTTGACATACGTAAT
* *
4137327 TAGTGGAGAGATCAATTTTACTTACGT
1 TAGTGGAGAGATCAATTTGACATACGT
4137354 CAAAGTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (30 bp):
TAGTGGAGAGATCAATTTGACATACGTAAT
Found at i:4152075 original size:29 final size:30
Alignment explanation
Indices: 4152026--4152086 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
4152016 TTTTATAATG
* * *
4152026 TTTTAAATATTTTAATTATATAT-TTTTAT
1 TTTTAAAGATTTTAATAATATATATTTCAT
4152055 TTTTATAAGATTTT-ATAATATATATTTCAT
1 TTTTA-AAGATTTTAATAATATATATTTCAT
4152085 TT
1 TT
4152087 AATATTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTTAAAGATTTTAATAATATATATTTCAT
Found at i:4153623 original size:15 final size:16
Alignment explanation
Indices: 4153589--4153623 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
4153579 ATTACTTGTT
4153589 TTTTATTATTATTTAA
1 TTTTATTATTATTTAA
4153605 -TTTATTATT-TTTAA
1 TTTTATTATTATTTAA
4153619 TTTTA
1 TTTTA
4153624 CGAAGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTATTATTTAA
Found at i:4166637 original size:22 final size:20
Alignment explanation
Indices: 4166614--4166653 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4166604 ATACAATTAT
4166614 TTTAAAAATAAAAACAAAAAA
1 TTTAAAAATAAAAA-AAAAAA
* *
4166635 TTTCAAATTAAAAAAAAAA
1 TTTAAAAATAAAAAAAAAA
4166654 CATATTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (20 bp):
TTTAAAAATAAAAAAAAAAA
Found at i:4166709 original size:9 final size:9
Alignment explanation
Indices: 4166689--4166771 Score: 53
Period size: 10 Copynumber: 8.9 Consensus size: 9
4166679 CTACGTAAAC
4166689 TTTTATATAT
1 TTTTATA-AT
4166699 TTTTATAATT
1 TTTTATAA-T
4166709 TTTTATAA-
1 TTTTATAAT
*
4166717 ATTT-TAAT
1 TTTTATAAT
* *
4166725 CTTTATAAA
1 TTTTATAAT
*
4166734 TTTAATTAAT
1 TTTTA-TAAT
*
4166744 TTTTTTACAT
1 TTTTATA-AT
*
4166754 TTTTATGATT
1 TTTTAT-AAT
4166764 TTTTATAA
1 TTTTATAA
4166772 ATTTAAATGA
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
7 3 0.05
8 6 0.11
9 10 0.18
10 36 0.64
11 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:4166781 original size:20 final size:20
Alignment explanation
Indices: 4166726--4166781 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
4166716 AATTTTAATC
* *
4166726 TTTATAAATTTAATTAATTT
1 TTTATAAATTTAAATGATTT
* **
4166746 TTT-TACATTTTTATGATTT
1 TTTATAAATTTAAATGATTT
4166765 TTTATAAATTTAAATGA
1 TTTATAAATTTAAATGA
4166782 ACCAAGACAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (20 bp):
TTTATAAATTTAAATGATTT
Found at i:4169568 original size:50 final size:50
Alignment explanation
Indices: 4169453--4169595 Score: 205
Period size: 50 Copynumber: 2.8 Consensus size: 50
4169443 GATAATAACA
**
4169453 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * *
4169504 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTTGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
4169554 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
4169596 TTACCCAACT
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 48 0.59
51 33 0.41
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:4184754 original size:17 final size:16
Alignment explanation
Indices: 4184728--4184761 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4184718 TACACACATA
*
4184728 TTTTTATTTTGTATTT
1 TTTTTATTTTATATTT
4184744 TTTTATATTTTATATTT
1 TTTT-TATTTTATATTT
4184761 T
1 T
4184762 AAAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTATATTT
Found at i:4184792 original size:28 final size:28
Alignment explanation
Indices: 4184739--4184792 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
4184729 TTTTATTTTG
* * *
4184739 TATTTTTTTATATTTTATATTTTAAAAT
1 TATTTTTATAAATTTTATATTATAAAAT
4184767 TATTTTTATAAATTTT-TATCTATAAA
1 TATTTTTATAAATTTTATAT-TATAAA
4184793 TGAAATTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TATTTTTATAAATTTTATATTATAAAAT
Found at i:4198511 original size:109 final size:107
Alignment explanation
Indices: 4198277--4198516 Score: 333
Period size: 109 Copynumber: 2.2 Consensus size: 107
4198267 AATAAAATTA
* * * *
4198277 GGGATAAGGTCACTTTTGACCCCTGAACTTTTTTTTAGCCACTTTGACCTTTGAACTTGAAAACC
1 GGGATAATGTAACTTTTGACCCCTAAACTTTTTTTTA-CCACTTTGACCCTTGAACTTGAAAACC
4198342 GTTATTCATTTAAGCTCATTTTGCAATGACTGTGAAAAAAATG
65 GTTATTCATTTAAGCTCATTTTGCAATGACTGTGAAAAAAATG
4198385 GGGATAATGTAACTTTTGACCTACCCTAAACTTTTTTTGT-CCACTTTGACCCTT-AAGCTTGAA
1 GGGATAATGTAACTTTTGA-C--CCCTAAACTTTTTTT-TACCACTTTGACCCTTGAA-CTTGAA
* * *
4198448 AATCTTTATTCATTTAAGCTCA-TTTGTAATGACTGTGAAAAAAATG
61 AACCGTTATTCATTTAAGCTCATTTTGCAATGACTGTGAAAAAAATG
*
4198494 GGGATAATGTAACTTTTGGCCCC
1 GGGATAATGTAACTTTTGACCCC
4198517 AAAATTTGGC
Statistics
Matches: 119, Mismatches: 8, Indels: 12
0.86 0.06 0.09
Matches are distributed among these distances:
106 3 0.03
108 18 0.15
109 44 0.37
110 39 0.33
111 14 0.12
112 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (107 bp):
GGGATAATGTAACTTTTGACCCCTAAACTTTTTTTTACCACTTTGACCCTTGAACTTGAAAACCG
TTATTCATTTAAGCTCATTTTGCAATGACTGTGAAAAAAATG
Found at i:4201025 original size:106 final size:106
Alignment explanation
Indices: 4200840--4201034 Score: 266
Period size: 106 Copynumber: 1.8 Consensus size: 106
4200830 AAGTTTTAAG
* * * * * **
4200840 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTCTCTCGA
1 AGGATATTCGACTATTTAGTCAAAAGAGAAATCGAAACACAGCACATTAGAACACGTTCTCTCGA
4200905 ATGTCCAAACGCAAAATATCGCCTCGTTTTGAAAATTCGAA
66 ATGTCCAAACGCAAAATATCGCCTCGTTTTGAAAATTCGAA
* *
4200946 AGGATATTCGACTATTTGGTCAAAAGAGAAATCGAAACACAGCACGTTAGAACACGCTT-TCTCG
1 AGGATATTCGACTATTTAGTCAAAAGAGAAATCGAAACACAGCACATTAGAACACG-TTCTCTCG
* * *
4201010 ATTTTCCAAACGCAAAATATTGCCT
65 AATGTCCAAACGCAAAATATCGCCT
4201035 TAAAAAAATT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
106 74 0.97
107 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (106 bp):
AGGATATTCGACTATTTAGTCAAAAGAGAAATCGAAACACAGCACATTAGAACACGTTCTCTCGA
ATGTCCAAACGCAAAATATCGCCTCGTTTTGAAAATTCGAA
Found at i:4203587 original size:14 final size:14
Alignment explanation
Indices: 4203568--4203595 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4203558 ATTTAGAATC
4203568 TGTTTATATAACAA
1 TGTTTATATAACAA
4203582 TGTTTATATAACAA
1 TGTTTATATAACAA
4203596 ATCTAGATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TGTTTATATAACAA
Found at i:4208310 original size:4 final size:4
Alignment explanation
Indices: 4208288--4208326 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
4208278 TTATTCTTTT
* *
4208288 ATTC TTTC ATTC AAATC ATTC ATTC ATTC ATTC ATTC AT
1 ATTC ATTC ATTC -ATTC ATTC ATTC ATTC ATTC ATTC AT
4208327 AATCATACTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 27 0.90
5 3 0.10
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (4 bp):
ATTC
Found at i:4209152 original size:13 final size:13
Alignment explanation
Indices: 4209117--4209156 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
4209107 AAAAATAGGA
4209117 GAAAAAGAAAGAAG
1 GAAAAAGAAA-AAG
4209131 G-AAAA-AAAAAG
1 GAAAAAGAAAAAG
4209142 GAAAAAGAAAAAG
1 GAAAAAGAAAAAG
4209155 GA
1 GA
4209157 GAGGTCAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.17
12 7 0.29
13 12 0.50
14 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
GAAAAAGAAAAAG
Found at i:4212102 original size:88 final size:88
Alignment explanation
Indices: 4211215--4212094 Score: 1361
Period size: 88 Copynumber: 10.0 Consensus size: 88
4211205 TAAATGAAAA
* * * * *
4211215 ACAACAGATCTTGTCTCCCTGCCTTGACAGCGAAGCAGATCGAAGATACAAACCTTGCATTTCTC
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
**
4211280 AATTGTAGTGGAGCTGGTTGAAG
66 GGTTGTAGTGGAGCTGGTTGAAG
* *
4211303 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAAATCGAAGACACAAACCTTGTCTCTCTC
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
4211368 GGTTGTAGTGGAGCTGGTTGAAG
66 GGTTGTAGTGGAGCTGGTTGAAG
*
4211391 ACAACAAATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAA-CTTGCCTCTCTC
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
4211455 GGTTGTAGTGGAGCTGGTTGAAG
66 GGTTGTAGTGGAGCTGGTTGAAG
* *
4211478 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGTAGATCGAAGACACAAACCTTGACTCTCTC
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
*
4211543 GGTTGTAATGGAGCTGGTTGAAG
66 GGTTGTAGTGGAGCTGGTTGAAG
* * * * *
4211566 ACAATATATCTTGCCTTCTTACCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTTTCTC
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
*
4211631 GGTTGTAGTGGAGCTGGGTGAAG
66 GGTTGTAGTGGAGCTGGTTGAAG
* * *
4211654 ACAACAGATCTTGCCTTTCTACTTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
*
4211719 GGTTGTAGTGGAGTTGGTTGAAG
66 GGTTGTAGTGGAGCTGGTTGAAG
* * * * *
4211742 ACAACAGATCTTACATTCCTGACTTGACAGCAAAGTAGATCGAAGACACAAACCTTGCCTCTCTC
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
4211807 GGTTGTAGTGGAGCTGGTTGAAG
66 GGTTGTAGTGGAGCTGGTTGAAG
*
4211830 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAAACTTGCCTCTCTC
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
* *
4211895 AGTTGTAGTAGAGCTGGTTGAAG
66 GGTTGTAGTGGAGCTGGTTGAAG
4211918 ACAACAGATCTTGCCTTCCTGCCTTGACAGC-ACAGCAGATCGAAGACACAAACCTTGCCTCTCT
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGA-AGCAGATCGAAGACACAAACCTTGCCTCTCT
*
4211982 CGGTTGCAGTGGAGCTGGTTGAAG
65 CGGTTGTAGTGGAGCTGGTTGAAG
* * * ** * *
4212006 ATAACAGATCTTGCCTTCCTGCATCGACAGTAAAGCAGATCGAAGACACAAGCCTTGTCT-TCCT
1 ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCT-CT
*
4212070 CGGTTGTAGTGGAGCAGGTTGAAG
65 CGGTTGTAGTGGAGCTGGTTGAAG
4212094 A
1 A
4212095 TTTCAGATTG
Statistics
Matches: 726, Mismatches: 62, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
87 86 0.12
88 639 0.88
89 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (88 bp):
ACAACAGATCTTGCCTTCCTGCCTTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTC
GGTTGTAGTGGAGCTGGTTGAAG
Found at i:4212616 original size:95 final size:95
Alignment explanation
Indices: 4212232--4212622 Score: 586
Period size: 95 Copynumber: 4.1 Consensus size: 95
4212222 AAAGTGGGGC
* * * * *
4212232 AGATCGAAAATGGCAGATTTTACCTCCCTATGACTACAGTGGAGTATATTGAAGCCGATAATTCT
1 AGATTGAAGATGGCAGATTTTACCTCCTTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCT
* * *
4212297 ATCTCCCTAGTTGGCAATAGAATAGATTGA
66 ATCTCCCTGGTTGGCAGTGGAATAGATTGA
* * * *
4212327 AGATCGAAGATGACAGATTTTACCT-CTCTGTGACTACAGTGGAGTACATTGAAACCGATAATTA
1 AGATTGAAGATGGCAGATTTTACCTCCT-TGTGACTACAGTGGAGTACATTGAAGCCGATAATTC
*
4212391 TATCTCCCTGGTTGGCAGTGGAATAGATTGC
65 TATCTCCCTGGTTGGCAGTGGAATAGATTGA
4212422 AGATTGAAGATGGCAGATTTTACCTCCTTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCT
1 AGATTGAAGATGGCAGATTTTACCTCCTTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCT
*
4212487 ATCTCCTTGGTTGGCAGTGGAATAGATTGA
66 ATCTCCCTGGTTGGCAGTGGAATAGATTGA
* *
4212517 AGATTGAATATGGCAGATTTTACCTCCTTGTGACTACAGTGGAGTACATTGAAGCCAATAATTCT
1 AGATTGAAGATGGCAGATTTTACCTCCTTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCT
***
4212582 ATCTCCCTGGACAGCAGTGGAATAGATTGA
66 ATCTCCCTGGTTGGCAGTGGAATAGATTGA
*
4212612 AGATTGCAGAT
1 AGATTGAAGAT
4212623 TCTGTCCCCC
Statistics
Matches: 269, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
94 1 0.00
95 266 0.99
96 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (95 bp):
AGATTGAAGATGGCAGATTTTACCTCCTTGTGACTACAGTGGAGTACATTGAAGCCGATAATTCT
ATCTCCCTGGTTGGCAGTGGAATAGATTGA
Found at i:4214099 original size:13 final size:14
Alignment explanation
Indices: 4214083--4214142 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 14
4214073 TATATCTCAG
4214083 TATTA-TATTATTA
1 TATTATTATTATTA
* * *
4214096 TATTATGTTAATCTTG
1 TATTA--TTATTATTA
4214112 TATTATTATTATTGA
1 TATTATTATTATT-A
4214127 TTATTATTATTATTA
1 -TATTATTATTATTA
4214142 T
1 T
4214143 TTACTCATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
13 5 0.14
14 7 0.19
15 1 0.03
16 23 0.64
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:4214120 original size:3 final size:3
Alignment explanation
Indices: 4214112--4214143 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
4214102 GTTAATCTTG
4214112 TAT TAT TAT TAT TGAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT T
4214144 TACTCATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4214249 original size:2 final size:2
Alignment explanation
Indices: 4214242--4214327 Score: 52
Period size: 2 Copynumber: 44.0 Consensus size: 2
4214232 TTTCATAATT
* * * *
4214242 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA AA CA TA CA TA CT-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * * *
4214284 TA TA TA TA TT TT TA TA T- TC TA TA -A TC TA TA TA CA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4214324 TA TA
1 TA TA
4214328 CTTTTTTTAA
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
1 3 0.05
2 60 0.94
3 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4214367 original size:41 final size:38
Alignment explanation
Indices: 4214275--4214374 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 38
4214265 ATATATAAAC
* * * *
4214275 ATACATACTTATATATATTTTTATATTCTATAATCTAT
1 ATACATATTTATATATATTTTTAAATTCTATAATATAA
* * *
4214313 ATACATATCTATATACTTTTTTTAAATTTTCATGAATATAA
1 ATACATATTTATATA-TATTTTTAAATTCT-AT-AATATAA
4214354 ATACATATTTATATATATTTT
1 ATACATATTTATATATATTTT
4214375 ATATATATAT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
38 13 0.26
39 11 0.22
40 7 0.14
41 19 0.38
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (38 bp):
ATACATATTTATATATATTTTTAAATTCTATAATATAA
Found at i:4220133 original size:27 final size:27
Alignment explanation
Indices: 4220047--4220133 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
4220037 GACTTTTATG
* *
4220047 TCTTCATCCTGATCTGTTGAAGTTTTT
1 TCTTCATCATGATCTGCTGAAGTTTTT
*
4220074 TCTTCATCAGATTGAT-TACT-AA--TTTT
1 TCTTCATC--A-TGATCTGCTGAAGTTTTT
*
4220100 T-AT-ATCATGATCTGCTGAAGTTTTT
1 TCTTCATCATGATCTGCTGAAGTTTTT
4220125 TCTTCATCA
1 TCTTCATCA
4220134 GATTGATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
21 4 0.09
22 4 0.09
23 2 0.04
24 3 0.07
25 6 0.13
26 6 0.13
27 12 0.27
28 2 0.04
29 2 0.04
30 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.49
Consensus pattern (27 bp):
TCTTCATCATGATCTGCTGAAGTTTTT
Found at i:4220394 original size:10 final size:9
Alignment explanation
Indices: 4220372--4220406 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4220362 GTTTATCATC
*
4220372 TTTTTTACG
1 TTTTTTATG
4220381 TTTTTTATG
1 TTTTTTATG
4220390 TTTTTTATG
1 TTTTTTATG
4220399 ATTTTTTA
1 -TTTTTTA
4220407 ACATAGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.71
10 7 0.29
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTTTATG
Found at i:4223026 original size:2 final size:2
Alignment explanation
Indices: 4223021--4223074 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
4223011 TTTTTTTCCT
4223021 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4223063 TA TA TA TA TA TA
1 TA TA TA TA TA TA
4223075 ANNNNNNNNN
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4223220 original size:2 final size:2
Alignment explanation
Indices: 4223213--4223264 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
4223203 GTTTTATTAT
4223213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4223255 TA TA CA TA TA
1 TA TA TA TA TA
4223265 ACTCGTACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4223814 original size:107 final size:106
Alignment explanation
Indices: 4223628--4223955 Score: 410
Period size: 106 Copynumber: 3.1 Consensus size: 106
4223618 CATCAAAAAG
* *
4223628 AAACTTTAAAAATAAGGCAATATTTCGCATTTGGAAACTCGAGAAAACGTGCCCTAACGTGCTGG
1 AAACTTTCAAAATAAGGCAATATTTCGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* * * *
4223693 GTTTCGGTTTCTCGTTCGACCGAATAGCCAAATATCATTTTT
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATC-CTTTC
* *
4223735 AAACTTTCAAAATAAGGCAATATTTCG-AGTTTGAAAATTCGAGAAAACGTGCCCTAACGTGTTG
1 AAACTTTCAAAATAAGGCAATATTTCGCA-TTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
* * ***
4223799 GGTTTCGATTACTCGTTTGACCAAATAGTTGAATATCCTTTC
65 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
* ** * * * *
4223841 AAAATTTCAAAACGAGGCAATGTTTTGCATTTGGAAATTCGAGAGAACGGGCCCTAACGTGCTGG
1 AAACTTTCAAAATAAGGCAATATTTCGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
* *
4223906 GTTTCGATTTCTTGTTCGACTAAATAGCCAAATATCCTCTT-
66 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCT-TTC
4223947 AAA-TTTCAA
1 AAACTTTCAA
4223956 TCCATGTCAT
Statistics
Matches: 189, Mismatches: 29, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
105 6 0.03
106 92 0.49
107 91 0.48
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (106 bp):
AAACTTTCAAAATAAGGCAATATTTCGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGG
GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTC
Found at i:4224919 original size:17 final size:16
Alignment explanation
Indices: 4224899--4224963 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 16
4224889 TTTCTCATAA
4224899 AAATAATAAAAAATTAT
1 AAAT-ATAAAAAATTAT
*
4224916 AAATATCAGAAAA-TAT
1 AAATAT-AAAAAATTAT
* *
4224932 CAAAAATATAAAAATGATT
1 -AAATATA-AAAAATTA-T
4224951 AAATATAAAAAAT
1 AAATATAAAAAAT
4224964 ATGAAAATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 6 0.16
17 24 0.63
18 7 0.18
19 1 0.03
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATATAAAAAATTAT
Found at i:4224954 original size:25 final size:27
Alignment explanation
Indices: 4224926--4224980 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
4224916 AAATATCAGA
*
4224926 AAATATCAAAAATAT-AAAAATGAT-T
1 AAATATAAAAAATATGAAAAATGATAT
*
4224951 AAATATAAAAAATATGAAAATTGATAT
1 AAATATAAAAAATATGAAAAATGATAT
4224978 AAA
1 AAA
4224981 CTTATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 14 0.54
26 8 0.31
27 4 0.15
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.27
Consensus pattern (27 bp):
AAATATAAAAAATATGAAAAATGATAT
Found at i:4225011 original size:23 final size:24
Alignment explanation
Indices: 4224976--4225025 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
4224966 GAAAATTGAT
*
4224976 ATAAACTTAT-AAATATTATAAAA
1 ATAAACTTATAAAAAATTATAAAA
* * *
4224999 ATAAATTTCTAAAAAATTCTAAAA
1 ATAAACTTATAAAAAATTATAAAA
4225023 ATA
1 ATA
4225026 TATAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (24 bp):
ATAAACTTATAAAAAATTATAAAA
Found at i:4226257 original size:10 final size:10
Alignment explanation
Indices: 4226215--4226267 Score: 60
Period size: 9 Copynumber: 5.7 Consensus size: 10
4226205 ATTAAATTTC
*
4226215 TATAAAATCA
1 TATAAAATTA
*
4226225 TA-AAAAGTA
1 TATAAAATTA
4226234 T-TAAAATTA
1 TATAAAATTA
4226243 T-TAAAATTA
1 TATAAAATTA
4226252 TATAAAATTA
1 TATAAAATTA
4226262 TA-AAAA
1 TATAAAA
4226268 AATCATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
9 26 0.68
10 12 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (10 bp):
TATAAAATTA
Found at i:4226267 original size:19 final size:19
Alignment explanation
Indices: 4226215--4226267 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
4226205 ATTAAATTTC
*
4226215 TATAAAATCATAAAAAGTA
1 TATAAAATTATAAAAAGTA
* *
4226234 T-TAAAATTATTAAAATTA
1 TATAAAATTATAAAAAGTA
4226252 TATAAAATTATAAAAA
1 TATAAAATTATAAAAA
4226268 AATCATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
TATAAAATTATAAAAAGTA
Found at i:4226275 original size:19 final size:19
Alignment explanation
Indices: 4226235--4226277 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4226225 TAAAAAGTAT
**
4226235 TAAAATTATTAAAATTATA
1 TAAAATTATTAAAAAAATA
4226254 TAAAATTA-TAAAAAAATCA
1 TAAAATTATTAAAAAAAT-A
4226273 TAAAA
1 TAAAA
4226278 ATTTGAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATTATTAAAAAAATA
Found at i:4226776 original size:17 final size:15
Alignment explanation
Indices: 4226739--4226781 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 15
4226729 ATTTTTTAAG
4226739 TTTTACTAATTTTATTT
1 TTTTA-TAA-TTTATTT
4226756 TTTTATAATTTATTAT
1 TTTTATAATTTATT-T
4226772 ATTTTATAAT
1 -TTTTATAAT
4226782 ATTTACAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.25
16 4 0.17
17 14 0.58
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTATAATTTATTT
Found at i:4230290 original size:102 final size:102
Alignment explanation
Indices: 4230163--4230365 Score: 300
Period size: 102 Copynumber: 2.0 Consensus size: 102
4230153 TAGGGATAAG
* *
4230163 GTAACTTTTGACCCCTGCACTTTTTTTTAGCCACTTTAACCTTTGAA-CTTAAAAACCGTTATTC
1 GTAACTTTTGACCCCTGAACTTTTTTTTAGCCACTTTAACCCTT-AAGCTTAAAAACCGTTATTC
* *
4230227 ATTTAAGCTCATTTGCAATGACTGTGAAAAAAATGGGA
65 ATTTAAGCTCATTTACAATGACTCTGAAAAAAATGGGA
* * * * *
4230265 GTAACTTTTGACCCCTGAACTTTTTTTTATCCACTTTGACCCTTAAGCTTGAAAAGCTTTATTCA
1 GTAACTTTTGACCCCTGAACTTTTTTTTAGCCACTTTAACCCTTAAGCTTAAAAACCGTTATTCA
*
4230330 TTTAAGCTCATTTATAATGACTCTGAAAAAAATGGG
66 TTTAAGCTCATTTACAATGACTCTGAAAAAAATGGG
4230366 GATAATGTAA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 2 0.02
102 88 0.98
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37
Consensus pattern (102 bp):
GTAACTTTTGACCCCTGAACTTTTTTTTAGCCACTTTAACCCTTAAGCTTAAAAACCGTTATTCA
TTTAAGCTCATTTACAATGACTCTGAAAAAAATGGGA
Found at i:4233935 original size:25 final size:25
Alignment explanation
Indices: 4233896--4233959 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
4233886 CCATAAAAAT
*
4233896 AATA-AAAAAATATAAATATCAGAA
1 AATATAAAAAATATAAAAATCAGAA
* * **
4233920 AATATCAAAAATATAAAAATGATTA
1 AATATAAAAAATATAAAAATCAGAA
4233945 AATATAAAAAATATA
1 AATATAAAAAATATA
4233960 TGAAAATTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 4 0.12
25 29 0.88
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (25 bp):
AATATAAAAAATATAAAAATCAGAA
Found at i:4233960 original size:27 final size:26
Alignment explanation
Indices: 4233892--4233975 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 26
4233882 TTTCCCATAA
* * **
4233892 AAATAATAAAAAAATATAAATATCAGA
1 AAAT-ATAAAAAAATATAAAAATGATT
*
4233919 AAATAT-CAAAAATATAAAAATGATT
1 AAATATAAAAAAATATAAAAATGATT
*
4233944 AAATATAAAAAATATATGAAAATTGATAT
1 AAATATAAAAAA-ATAT-AAAAATGAT-T
4233973 AAA
1 AAA
4233976 CTTATAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 20 0.43
26 6 0.13
27 8 0.17
28 8 0.17
29 4 0.09
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (26 bp):
AAATATAAAAAAATATAAAAATGATT
Found at i:4234069 original size:22 final size:21
Alignment explanation
Indices: 4234013--4234081 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
4234003 TAAAAAATTC
*
4234013 TAAAAAAATATATAAAA-TTAA
1 TAAAAAAATAT-TAAAATTTTA
*
4234034 T-AAAATATATTTAAAATTTTA
1 TAAAAAAATA-TTAAAATTTTA
4234055 TAAAAAACATATT-AAATTTCTA
1 TAAAAAA-ATATTAAAATTT-TA
4234077 TAAAA
1 TAAAA
4234082 TCATAAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 12 0.30
21 12 0.30
22 13 0.32
23 3 0.08
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAAAATATTAAAATTTTA
Found at i:4234086 original size:21 final size:22
Alignment explanation
Indices: 4234020--4234086 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 22
4234010 TTCTAAAAAA
* *
4234020 ATATATAAAA-TTAATAAAAT-
1 ATATTTAAAATTTTATAAAATC
*
4234040 ATATTTAAAATTTTATAAAAAAC
1 ATATTTAAAATTTTAT-AAAATC
4234063 ATA-TT-AAATTTCTATAAAATC
1 ATATTTAAAATTT-TATAAAATC
4234084 ATA
1 ATA
4234087 AAAAGTATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 9 0.23
21 18 0.46
22 9 0.23
23 3 0.08
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTTAAAATTTTATAAAATC
Found at i:4234116 original size:37 final size:37
Alignment explanation
Indices: 4234064--4234136 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
4234054 ATAAAAAACA
* * *
4234064 TATTAAATTTCTATAAAATCATAAAAAGTATTAAAAT
1 TATTAAAATTATATAAAATCATAAAAAGTATAAAAAT
* *
4234101 TATTAAAATTATATAAAATTATAAAAATTATAAAAA
1 TATTAAAATTATATAAAATCATAAAAAGTATAAAAA
4234137 AAATCATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (37 bp):
TATTAAAATTATATAAAATCATAAAAAGTATAAAAAT
Found at i:4234137 original size:10 final size:10
Alignment explanation
Indices: 4233996--4234137 Score: 62
Period size: 10 Copynumber: 14.4 Consensus size: 10
4233986 TTATAAAAAT
*
4233996 AAAATTCTAA
1 AAAATTATAA
*
4234006 AAAATTCTAA
1 AAAATTATAA
* *
4234016 AAAAATATAT
1 AAAATTATAA
4234026 AAAATTAATAA
1 AAAATT-ATAA
4234037 AATATATT-TAA
1 AA-A-ATTATAA
**
4234048 AATTTTATAA
1 AAAATTATAA
* *
4234058 AAAA-CATATT
1 AAAATTATA-A
* * *
4234068 AAATTTCTAT
1 AAAATTATAA
*
4234078 AAAATCAT-A
1 AAAATTATAA
* *
4234087 AAAAGTAT-T
1 AAAATTATAA
*
4234096 AAAATTAT-T
1 AAAATTATAA
*
4234105 AAAATTATAT
1 AAAATTATAA
4234115 AAAATTAT-A
1 AAAATTATAA
4234124 AAAATTATAA
1 AAAATTATAA
4234134 AAAA
1 AAAA
4234138 AATCATAAAA
Statistics
Matches: 101, Mismatches: 23, Indels: 16
0.72 0.16 0.11
Matches are distributed among these distances:
9 35 0.35
10 50 0.50
11 12 0.12
12 1 0.01
13 3 0.03
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (10 bp):
AAAATTATAA
Found at i:4234148 original size:9 final size:9
Alignment explanation
Indices: 4233888--4234136 Score: 77
Period size: 9 Copynumber: 26.8 Consensus size: 9
4233878 ATATTTTCCC
*
4233888 ATAAAAATA
1 ATAAAAATT
*
4233897 ATAAAAA-A
1 ATAAAAATT
*
4233905 ATATAAA-T
1 ATAAAAATT
4233913 ATCAGAAAA-T
1 AT-A-AAAATT
4233923 ATCAAAAA-T
1 AT-AAAAATT
*
4233932 ATAAAAATG
1 ATAAAAATT
*
4233941 AT-TAAA-T
1 ATAAAAATT
4233948 ATAAAAAATAT
1 AT-AAAAAT-T
*
4233959 ATGAAAATT
1 ATAAAAATT
*
4233968 GATATAAACTT
1 -ATA-AAAATT
*
4233979 ATAAATATT
1 ATAAAAATT
4233988 AT-AAAA--
1 ATAAAAATT
4233994 AT-AAAATT
1 ATAAAAATT
*
4234002 CTAAAAAATT
1 AT-AAAAATT
* *
4234012 CTAAAAAAAT
1 AT-AAAAATT
4234022 ATATAAAATT
1 ATA-AAAATT
4234032 AATAAAATATAT
1 -ATAAAA-AT-T
* *
4234044 TTAAAATTTT
1 ATAAAA-ATT
*
4234054 ATAAAAAACAT
1 AT-AAAAA-TT
* *
4234065 ATTAAATTT
1 ATAAAAATT
* *
4234074 CTATAAAATC
1 ATA-AAAATT
*
4234084 ATAAAAAGT
1 ATAAAAATT
*
4234093 ATTAAAATT
1 ATAAAAATT
*
4234102 ATTAAAATT
1 ATAAAAATT
4234111 ATATAAAATT
1 ATA-AAAATT
4234121 ATAAAAATT
1 ATAAAAATT
4234130 ATAAAAA
1 ATAAAAA
4234137 AAATCATAAA
Statistics
Matches: 184, Mismatches: 35, Indels: 42
0.70 0.13 0.16
Matches are distributed among these distances:
6 6 0.03
7 2 0.01
8 21 0.11
9 65 0.35
10 62 0.34
11 27 0.15
12 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:4234699 original size:9 final size:9
Alignment explanation
Indices: 4234623--4234742 Score: 58
Period size: 9 Copynumber: 13.6 Consensus size: 9
4234613 CTTCTAATAC
4234623 ATTTTT-TA
1 ATTTTTATA
*
4234631 AGTTTTACTA
1 ATTTTTA-TA
4234641 A-TTTTAT-
1 ATTTTTATA
4234648 -TTTTTATA
1 ATTTTTATA
4234656 ATTTATTAT-
1 ATTT-TTATA
4234665 ATTTTTATA
1 ATTTTTATA
* *
4234674 ATATTTACA
1 ATTTTTATA
4234683 AGTTTTTTTATA
1 A---TTTTTATA
*
4234695 ATTTTAATA
1 ATTTTTATA
*
4234704 A-ATTTAT-
1 ATTTTTATA
*
4234711 ATTCTTTTTA
1 ATT-TTTATA
*
4234721 A-ATTTATA
1 ATTTTTATA
*
4234729 TTTTTTATA
1 ATTTTTATA
4234738 ATTTT
1 ATTTT
4234743 AATGAGTTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
7 7 0.08
8 19 0.23
9 42 0.51
10 8 0.10
12 7 0.08
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.64
Consensus pattern (9 bp):
ATTTTTATA
Found at i:4234711 original size:17 final size:17
Alignment explanation
Indices: 4234689--4234743 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
4234679 TACAAGTTTT
*
4234689 TTTATAATTTTAATAAA
1 TTTATAATTTTTATAAA
*
4234706 TTTAT-ATTCTTTTTAAA
1 TTTATAATT-TTTATAAA
* *
4234723 TTTATATTTTTTATAAT
1 TTTATAATTTTTATAAA
4234740 TTTA
1 TTTA
4234744 ATGAGTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 3 0.10
17 26 0.84
18 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATAATTTTTATAAA
Found at i:4235873 original size:25 final size:26
Alignment explanation
Indices: 4235845--4235896 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
4235835 AAAGCTAAAG
4235845 ATAATA-ATTT-AAATAATTAAT-TTTT
1 ATAATATATTTCAAA-AA-TAATATTTT
4235870 ATAATATATTTCAAAAATAATATTTT
1 ATAATATATTTCAAAAATAATATTTT
4235896 A
1 A
4235897 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 10 0.42
26 11 0.46
27 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
ATAATATATTTCAAAAATAATATTTT
Found at i:4235902 original size:15 final size:16
Alignment explanation
Indices: 4235870--4235904 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4235860 ATTAATTTTT
*
4235870 ATAATATATTTCAAAA
1 ATAATATATTTAAAAA
4235886 ATAATAT-TTTAAAAA
1 ATAATATATTTAAAAA
4235901 ATAA
1 ATAA
4235905 AATTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATATATTTAAAAA
Found at i:4245286 original size:3 final size:3
Alignment explanation
Indices: 4245278--4245324 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
4245268 TATCAAAATG
4245278 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4245325 AAAATTAGCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4252548 original size:11 final size:12
Alignment explanation
Indices: 4252534--4252571 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4252524 ACAAAGCGAA
4252534 GAAAAAGAAA-T
1 GAAAAAGAAATT
*
4252545 GAAAAAAAAATT
1 GAAAAAGAAATT
*
4252557 GAAAAAGAACTT
1 GAAAAAGAAATT
4252569 GAA
1 GAA
4252572 TAGAAGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.68, C:0.03, G:0.16, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:4255626 original size:24 final size:24
Alignment explanation
Indices: 4255608--4255677 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
4255598 GATGAAATCG
4255608 AGGGTGGAGATGAAAATGAAGACA
1 AGGGTGGAGATGAAAATGAAGACA
*
4255632 ATGGTGGAGATGAAAATG-AGTACA
1 AGGGTGGAGATGAAAATGAAG-ACA
* *
4255656 AGGGTGGAGGTGAAGATGAAGA
1 AGGGTGGAGATGAAAATGAAGA
4255678 AGATGATCCG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.05
24 36 0.90
25 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.40, T:0.16
Consensus pattern (24 bp):
AGGGTGGAGATGAAAATGAAGACA
Found at i:4256832 original size:33 final size:31
Alignment explanation
Indices: 4256775--4256845 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 31
4256765 AAACCCTAAA
*
4256775 AACCC-AACCCTAACAAAAATAAAAAACCCT
1 AACCCTAACCCTAACAAAAATAAAAAACCAT
*
4256805 AACTCTAACCCTAACAAAAATAAAAAAAACCAT
1 AACCCTAACCCTAACAAAAAT--AAAAAACCAT
4256838 AACCCTAA
1 AACCCTAA
4256846 GAGAGAGTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 15 0.43
33 16 0.46
ACGTcount: A:0.58, C:0.30, G:0.00, T:0.13
Consensus pattern (31 bp):
AACCCTAACCCTAACAAAAATAAAAAACCAT
Found at i:4267852 original size:53 final size:53
Alignment explanation
Indices: 4267789--4267894 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
4267779 TTACCGATTC
* *
4267789 TCTCTCTCGGTCTCTTTTTTCATTTTTTCCTTGTCATTTGTTGTGGTTTTTGA
1 TCTCTCTCGGTCTATTTTTTCATTTTTTCCCTGTCATTTGTTGTGGTTTTTGA
*
4267842 TCTCTTTCGGTCTATTTTTTCATTTTTTCCCTGTCATTTGTTGTGGTTTTTGA
1 TCTCTCTCGGTCTATTTTTTCATTTTTTCCCTGTCATTTGTTGTGGTTTTTGA
4267895 AATCCACTGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.07, C:0.18, G:0.15, T:0.60
Consensus pattern (53 bp):
TCTCTCTCGGTCTATTTTTTCATTTTTTCCCTGTCATTTGTTGTGGTTTTTGA
Found at i:4272415 original size:47 final size:47
Alignment explanation
Indices: 4272362--4272505 Score: 165
Period size: 47 Copynumber: 3.1 Consensus size: 47
4272352 TCATATAAGA
4272362 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
* ** *
4272409 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATT-AT-TAA-ATT
* *
4272453 AAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
4272500 ATATTT
1 ATATTT
4272506 TATAATAATT
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.31
45 8 0.10
46 8 0.10
47 31 0.40
48 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
Found at i:4272461 original size:91 final size:91
Alignment explanation
Indices: 4272347--4272562 Score: 351
Period size: 91 Copynumber: 2.4 Consensus size: 91
4272337 ATGATTGTAG
*
4272347 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* *
4272412 TTTAATATTAATTATTTTAAATTATA
66 TTTAATAATAATTATATTAAATTATA
*
4272438 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
4272503 TTTTATAATAATTATATTAAATTATA
66 TTTAATAATAATTATATTAAATTATA
* * * *
4272529 CAAATTCATATAAGAAAAATTATTACTAATAATT
1 TAAATTCATATAAGAAAATTTATTATTAAGAATT
4272563 ATTTTAAATT
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 115 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATAATAATTATATTAAATTATA
Found at i:4272493 original size:101 final size:99
Alignment explanation
Indices: 4272377--4272630 Score: 242
Period size: 91 Copynumber: 2.6 Consensus size: 99
4272367 TATTATTAAG
* * *
4272377 AATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAA
1 AATTATATTAAATTATATAT-ATTATTAAA-TATATTTAATAATAATTATTTTAAATTATATAAA
*
4272442 TTCATATAAGAAAATTTATTA-TCAAGAATT-TTATGA
64 TTCATATAAGAAAAATTATTACT-AAGAATTATT-TGA
* * *
4272478 AATTATA-TATCATTAT-TA-A--ATT--ATAT-TTT-ATAATAATTATATTAAATTATACAAAT
1 AATTATATTA-AATTATATATATTATTAAATATATTTAATAATAATTATTTTAAATTATATAAAT
* *
4272534 TCATATAAGAAAAATTATTACTAATAATTATTTTA
65 TCATATAAGAAAAATTATTACTAAGAATTATTTGA
* * * * *
4272569 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCACATTATAT
1 AATTATATTAAATTATATATATT-ATT-AAATATATTTAATAATAATTATTTTAAATTATAT
4272631 TTTATACTAT
Statistics
Matches: 122, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
91 61 0.50
92 10 0.08
93 3 0.02
94 1 0.01
96 6 0.05
98 1 0.01
99 4 0.03
100 6 0.05
101 30 0.25
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (99 bp):
AATTATATTAAATTATATATATTATTAAATATATTTAATAATAATTATTTTAAATTATATAAATT
CATATAAGAAAAATTATTACTAAGAATTATTTGA
Found at i:4272570 original size:47 final size:46
Alignment explanation
Indices: 4272420--4272587 Score: 159
Period size: 47 Copynumber: 3.7 Consensus size: 46
4272410 TATTTAATAT
*
4272420 TAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAA
1 TAATTATTTTAAATTATATAAATTCATATAAGAAAAATTATTAT-AA
* * * * *
4272467 GAATT-TTATGAAATTATATATCATT-AT-TAA-ATTATATT-TTATAA
1 TAATTATT-TTAAATTATATA-AATTCATATAAGA-AAAATTATTATAA
* *
4272511 TAATTATATTAAATTATACAAATTCATATAAGAAAAATTATTACTAA
1 TAATTATTTTAAATTATATAAATTCATATAAGAAAAATTATTA-TAA
*
4272558 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAATTATA-TAAATTCATATA
4272588 TTTTAATTAA
Statistics
Matches: 95, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
43 3 0.03
44 18 0.19
45 13 0.14
46 12 0.13
47 43 0.45
48 6 0.06
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (46 bp):
TAATTATTTTAAATTATATAAATTCATATAAGAAAAATTATTATAA
Found at i:4272693 original size:120 final size:120
Alignment explanation
Indices: 4272569--4272864 Score: 486
Period size: 120 Copynumber: 2.5 Consensus size: 120
4272559 AATTATTTTA
* *
4272569 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCACATTATATTT
1 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATCTT-AAATTATATTT
* *
4272633 TATACTATCACATATTATGGTTTTAGTAAATTCATATAAGAATATTGATTATTAAG
65 TATACTATCACATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
4272689 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTTTATTTT
1 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTATATTTT
* * *
4272754 ATAGTATCATATATTATGATTTGAGTAAATTTATATAAGAATATTGATTATTAAG
66 ATACTATCACATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
4272809 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAA
4272865 ATATGATTAA
Statistics
Matches: 165, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
120 163 0.99
121 2 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATCTTAAATTATATTTT
ATACTATCACATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:4272743 original size:15 final size:16
Alignment explanation
Indices: 4272699--4272735 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
4272689 AATTTTATTA
4272699 AATAATATATTTTAATT
1 AATAATATA-TTTAATT
4272716 AA-AATATATTTAA-T
1 AATAATATATTTAATT
4272730 AATAAT
1 AATAAT
4272736 TATCTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 8 0.42
16 6 0.32
17 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAATATATTTAATT
Found at i:4272838 original size:18 final size:17
Alignment explanation
Indices: 4272810--4272844 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4272800 ATTATTAAGA
*
4272810 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
4272827 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
4272845 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:4273094 original size:45 final size:44
Alignment explanation
Indices: 4273003--4273099 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 44
4272993 CTATTACACC
*
4273003 TCCATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACACAAGAATACTATTACGCCTCTAT
**
4273047 TCCATTACATTCAACCAAACA-ATTAATTTACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACACAAGAA--TACTATTACGCCTCTAT
4273092 TCCATTAC
1 TCCATTAC
4273100 GCTTTTATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 3 0.06
44 20 0.42
45 25 0.52
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (44 bp):
TCCATTACATTCAACCAAACACAAGAATACTATTACGCCTCTAT
Found at i:4280198 original size:22 final size:24
Alignment explanation
Indices: 4280173--4280218 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4280163 GAATACAACC
4280173 TTTA-AAAATTTT-TATATTTATT
1 TTTACAAAATTTTATATATTTATT
**
4280195 TTTACATGATTTTATATATTTATT
1 TTTACAAAATTTTATATATTTATT
4280219 ATGTACCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTACAAAATTTTATATATTTATT
Found at i:4281880 original size:3 final size:3
Alignment explanation
Indices: 4281872--4281897 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4281862 TTCTCCATTT
4281872 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
4281898 TTTAATCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:4282437 original size:16 final size:17
Alignment explanation
Indices: 4282404--4282441 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4282394 TATTTTGGTA
* *
4282404 TATTGTTTTTAATTTAT
1 TATTATTTTTAATATAT
4282421 TATTATTTTTAA-ATAT
1 TATTATTTTTAATATAT
4282437 TATTA
1 TATTA
4282442 AATTTTGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
TATTATTTTTAATATAT
Found at i:4300471 original size:21 final size:21
Alignment explanation
Indices: 4300439--4300480 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4300429 TTCAGTTGAG
4300439 ATAATATCCAAG-TTTCTCCCT
1 ATAATATCCAAGCTTT-TCCCT
4300460 ATAA-ATCACAAGCTTTTCCCT
1 ATAATATC-CAAGCTTTTCCCT
4300481 TGTTATTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.16
21 13 0.68
22 3 0.16
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (21 bp):
ATAATATCCAAGCTTTTCCCT
Found at i:4303509 original size:6 final size:6
Alignment explanation
Indices: 4303498--4303522 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4303488 AAAAGTGTTA
4303498 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
4303523 TCTCAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:4304495 original size:14 final size:15
Alignment explanation
Indices: 4304473--4304549 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
4304463 CAATCAAACG
4304473 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
4304487 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
4304502 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
4304522 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
4304536 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
4304550 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:4304514 original size:20 final size:20
Alignment explanation
Indices: 4304489--4304528 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4304479 AATATTTTCC
*
4304489 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
4304509 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
4304529 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:4304534 original size:34 final size:35
Alignment explanation
Indices: 4304477--4304543 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
4304467 CAAACGCCAG
*
4304477 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
4304512 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
4304544 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:4317264 original size:76 final size:76
Alignment explanation
Indices: 4317184--4317334 Score: 302
Period size: 76 Copynumber: 2.0 Consensus size: 76
4317174 AAGATTACTT
4317184 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
1 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
4317249 ACAAACAATTA
66 ACAAACAATTA
4317260 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
1 ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
4317325 ACAAACAATT
66 ACAAACAATT
4317335 CTGGAAAACC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (76 bp):
ATTTGAATTTAATTACAAACAATCAAATCTTAAAAATAAAAAATGATTATAATATACAAGTAATT
ACAAACAATTA
Found at i:4318635 original size:8 final size:8
Alignment explanation
Indices: 4318624--4318657 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
4318614 AGTGAAGCAC
4318624 CGTGGAGT
1 CGTGGAGT
4318632 CGTGGAGT
1 CGTGGAGT
4318640 CGTGGA--
1 CGTGGAGT
4318646 CGTGGAGT
1 CGTGGAGT
4318654 CGTG
1 CGTG
4318658 AATCAGTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
8 18 0.75
ACGTcount: A:0.12, C:0.15, G:0.50, T:0.24
Consensus pattern (8 bp):
CGTGGAGT
Found at i:4318652 original size:22 final size:22
Alignment explanation
Indices: 4318624--4318675 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
4318614 AGTGAAGCAC
*
4318624 CGTGGAGTCGTGGAGTC-GTGGA
1 CGTGGAGTCGT-GAATCAGTGGA
4318646 CGTGGAGTCGTGAATCAGTGGA
1 CGTGGAGTCGTGAATCAGTGGA
*
4318668 GGTGGAGT
1 CGTGGAGT
4318676 TAGATCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.17, C:0.12, G:0.48, T:0.23
Consensus pattern (22 bp):
CGTGGAGTCGTGAATCAGTGGA
Found at i:4321086 original size:30 final size:29
Alignment explanation
Indices: 4321024--4321086 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
4321014 TCTAATATGT
* *
4321024 AATTTTATACATAAACTTTGATTTTGTAC
1 AATTTTATACATAAAATTTGATTTTATAC
*
4321053 AATTTTATACATGAAAATTTGATTTTATCC
1 AATTTTATACAT-AAAATTTGATTTTATAC
4321083 AATT
1 AATT
4321087 CTCACAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (29 bp):
AATTTTATACATAAAATTTGATTTTATAC
Found at i:4321273 original size:29 final size:31
Alignment explanation
Indices: 4321220--4321298 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
4321210 GGTTTAACCA
*
4321220 AAATTAAAGTTTCATGT-GCATAATTG-CACT
1 AAATTAAAG-TTCATGTATCATAATTGACACT
*
4321250 AAATTAAAGTTCATGTATCA-AATTGTACATT
1 AAATTAAAGTTCATGTATCATAATTG-ACACT
* *
4321281 TAATAAAAGTTCATGTAT
1 AAATTAAAGTTCATGTAT
4321299 AATTTTGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 12 0.29
30 11 0.26
31 19 0.45
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (31 bp):
AAATTAAAGTTCATGTATCATAATTGACACT
Found at i:4322698 original size:124 final size:124
Alignment explanation
Indices: 4322486--4322853 Score: 592
Period size: 124 Copynumber: 3.0 Consensus size: 124
4322476 TTAGGTCTTG
** * *
4322486 GAAGAAATAATTTTGAGTTAACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGCAGGATGCTA
1 GAAGAAATAATTTT-TTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTA
* * *
4322551 TTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTACTACAGTAGGTCATA
65 TTTGAGAAGAATTTGTAAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAGGTAATA
* *
4322611 GAAGAAATAATTTTTTTTGATGTTTCTGAGCAAATAGTATAAAATTGCTTCTAGCAGGATGCTAT
1 GAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTAT
* *
4322676 TTGAGAAGAATTTGTAAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTCGGTAATG
66 TTGAGAAGAATTTGTAAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAGGTAATA
*
4322735 GAAGAAATACTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTAT
1 GAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTAT
* *
4322800 TTGAGAAGAATTTGTGCAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 TTGAGAAGAATTTGT-AAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAG
4322854 CATGTTTAGG
Statistics
Matches: 225, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
124 176 0.78
125 49 0.22
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (124 bp):
GAAGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTAT
TTGAGAAGAATTTGTAAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAGGTAATA
Found at i:4324509 original size:11 final size:11
Alignment explanation
Indices: 4324493--4324534 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
4324483 AAAAAGGGAG
4324493 TTAAGAGAAAC
1 TTAAGAGAAAC
*
4324504 TTAAGAGGAAC
1 TTAAGAGAAAC
*
4324515 TTAAGAGGAAC
1 TTAAGAGAAAC
*
4324526 TTGAGAGAA
1 TTAAGAGAA
4324535 TTTTTGAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.48, C:0.07, G:0.26, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:4324562 original size:22 final size:22
Alignment explanation
Indices: 4324520--4324563 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4324510 GGAACTTAAG
* *
4324520 AGGAACTTGAGAGAATTTTTGA
1 AGGAAATTGAGAGAATATTTGA
4324542 AGGAAATTGAGAGGAA-ATTTGA
1 AGGAAATTGAGA-GAATATTTGA
4324564 GAGAGGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.41, C:0.02, G:0.30, T:0.27
Consensus pattern (22 bp):
AGGAAATTGAGAGAATATTTGA
Found at i:4329462 original size:20 final size:19
Alignment explanation
Indices: 4329437--4329477 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
4329427 TTAGTATTAG
*
4329437 AATTTATTTATATATTTATT
1 AATTTATTTATA-ATATATT
4329457 AATTTATTTATAATATATT
1 AATTTATTTATAATATATT
4329476 AA
1 AA
4329478 AATATTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTATTTATAATATATT
Found at i:4329483 original size:19 final size:20
Alignment explanation
Indices: 4329441--4329483 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
4329431 TATTAGAATT
* **
4329441 TATTTATATATTTATTAATT
1 TATTTATATATATATTAAAA
4329461 TATTTATA-ATATATTAAAA
1 TATTTATATATATATTAAAA
4329480 TATT
1 TATT
4329484 ATGTTAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTATATATATATTAAAA
Found at i:4331511 original size:18 final size:17
Alignment explanation
Indices: 4331478--4331516 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
4331468 ATTTATAAAT
4331478 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
4331496 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
4331513 TGTG
1 TGTG
4331517 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:4332835 original size:46 final size:46
Alignment explanation
Indices: 4332732--4332984 Score: 415
Period size: 46 Copynumber: 5.6 Consensus size: 46
4332722 TACGTATGAT
* *
4332732 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
4332775 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
4332821 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
4332867 CACTTATCACTTTGTCACTTGATCAGATAAGCGTAGCTAAACCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
4332913 CACTTATCACTTTGTCCCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
4332959 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
4332985 AGTACTCAAA
Statistics
Matches: 196, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
43 10 0.05
44 5 0.03
45 28 0.14
46 153 0.78
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:4347848 original size:66 final size:66
Alignment explanation
Indices: 4347739--4347900 Score: 182
Period size: 66 Copynumber: 2.5 Consensus size: 66
4347729 TAAGAACTTG
** * * * * * * *
4347739 AGAAGACCCAATATCTTGTTTAGGAGCTTGGGAAGACTTAATA-TGCCGTTCAGGATCTTGGGAT
1 AGAAGACCTGATATCTCGTTCAGGAGCTTGAGAAGACTCAATATTGCAGTTC-GGAGCTTAGGAT
4347803 TA
65 TA
* *
4347805 AGAAGACTTGATATCTCGTTCAGGAGCTTGAGAAGACTCAATATTGCATTTCGGAGCTTAGGATT
1 AGAAGACCTGATATCTCGTTCAGGAGCTTGAGAAGACTCAATATTGCAGTTCGGAGCTTAGGATT
4347870 A
66 A
* * *
4347871 AGAAGGCCTGATATCTCATTCAGAAGCTTG
1 AGAAGACCTGATATCTCGTTCAGGAGCTTG
4347901 GAAAGATCTA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
66 74 0.93
67 6 0.08
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (66 bp):
AGAAGACCTGATATCTCGTTCAGGAGCTTGAGAAGACTCAATATTGCAGTTCGGAGCTTAGGATT
A
Found at i:4350582 original size:19 final size:19
Alignment explanation
Indices: 4350545--4350583 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4350535 TTTTGCTACA
*
4350545 TAGACTAAATCGTAAAAAC
1 TAGACTAAATCGAAAAAAC
4350564 TAGACTAAATC-AAATAAAC
1 TAGACTAAATCGAAA-AAAC
4350583 T
1 T
4350584 TCAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (19 bp):
TAGACTAAATCGAAAAAAC
Found at i:4351968 original size:14 final size:14
Alignment explanation
Indices: 4351949--4351977 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4351939 CCTCATTGCC
4351949 TTAGCAAAACTGAG
1 TTAGCAAAACTGAG
4351963 TTAGCAAAACTGAG
1 TTAGCAAAACTGAG
4351977 T
1 T
4351978 ATAATTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (14 bp):
TTAGCAAAACTGAG
Found at i:4355321 original size:6 final size:6
Alignment explanation
Indices: 4355304--4355340 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
4355294 GCCTTACGTC
*
4355304 TTTCTT TCTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
4355341 CTTTCTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:4360469 original size:20 final size:22
Alignment explanation
Indices: 4360421--4360470 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
4360411 AAATAAAATT
*
4360421 ACGTAACAAATATATTTATAAA
1 ACGTAAAAAATATATTTATAAA
**
4360443 AATTAAAAAATA-ATTT-TAAA
1 ACGTAAAAAATATATTTATAAA
4360463 ACGTAAAA
1 ACGTAAAA
4360471 GATTAGACTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 10 0.43
21 4 0.17
22 9 0.39
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (22 bp):
ACGTAAAAAATATATTTATAAA
Found at i:4362264 original size:16 final size:16
Alignment explanation
Indices: 4362243--4362294 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
4362233 CGGCCAAATT
4362243 TTTATTTAAAGGTAAA
1 TTTATTTAAAGGTAAA
***
4362259 TTTATTT-TTTGT-AA
1 TTTATTTAAAGGTAAA
4362273 -TTATTTAAAGGTAAA
1 TTTATTTAAAGGTAAA
4362288 TTTATTT
1 TTTATTT
4362295 TTAGTTTTGG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 4 0.15
16 13 0.48
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.56
Consensus pattern (16 bp):
TTTATTTAAAGGTAAA
Found at i:4363632 original size:22 final size:24
Alignment explanation
Indices: 4363601--4363645 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
4363591 TTATAGTAAA
4363601 TTAATGTTTT-A-AAACTTTTGAC
1 TTAATGTTTTAACAAACTTTTGAC
*
4363623 TTAATTTTTTAACAAACTTTTGA
1 TTAATGTTTTAACAAACTTTTGA
4363646 TTTTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (24 bp):
TTAATGTTTTAACAAACTTTTGAC
Found at i:4367433 original size:24 final size:23
Alignment explanation
Indices: 4367406--4367481 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
4367396 AGATATTTAT
*
4367406 ATTATTTATTTATATAATATATAA
1 ATTAATTATTTATATAATAT-TAA
** *
4367430 ATTAATTATAAAGTATATTATTAA
1 ATTAATTATTTA-TATAATATTAA
*
4367454 ATTAATTATATTATA-AATATTAT
1 ATTAATTAT-TTATATAATATTAA
4367477 ATTAA
1 ATTAA
4367482 GAAATAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.26
24 23 0.55
25 8 0.19
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTAATTATTTATATAATATTAA
Found at i:4367449 original size:12 final size:11
Alignment explanation
Indices: 4367420--4367463 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
4367410 TTTATTTATA
4367420 TAATATATAAAT
1 TAAT-TATAAAT
*
4367432 TAATTATAAAG
1 TAATTATAAAT
4367443 TATATTATTAAAT
1 TA-ATTA-TAAAT
4367456 TAATTATA
1 TAATTATA
4367464 TTATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:4367475 original size:14 final size:17
Alignment explanation
Indices: 4367443--4367480 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
4367433 AATTATAAAG
4367443 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
4367460 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
4367474 TATATTA
1 TATATTA
4367481 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:4367717 original size:15 final size:17
Alignment explanation
Indices: 4367699--4367730 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4367689 CAGAATAGAA
4367699 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
4367714 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
4367731 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:4369470 original size:28 final size:25
Alignment explanation
Indices: 4369424--4369476 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 25
4369414 ACATTATCTC
* *
4369424 AATTTAAAAAAATTTTGTATCTTTA
1 AATTTAAAAAAATTATGTAACTTTA
4369449 AATTTAAGTAAAAATTGATGTAACTTTA
1 AATTTAA--AAAAATT-ATGTAACTTTA
4369477 TTTTATACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 7 0.30
27 7 0.30
28 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (25 bp):
AATTTAAAAAAATTATGTAACTTTA
Found at i:4386125 original size:6 final size:6
Alignment explanation
Indices: 4386114--4386139 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4386104 AGAATATGCG
4386114 TATACA TATACA TATACA TATACA TA
1 TATACA TATACA TATACA TATACA TA
4386140 CCGTATCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
TATACA
Found at i:4386324 original size:15 final size:15
Alignment explanation
Indices: 4386306--4386458 Score: 62
Period size: 15 Copynumber: 10.3 Consensus size: 15
4386296 AAGCCAAAGG
4386306 AGCTGGTGGTGGGGT
1 AGCTGGTGGTGGGGT
* * *
4386321 AGCTGGAGGAGGAGT
1 AGCTGGTGGTGGGGT
* * *
4386336 AGCAGGAGG-GGGAGA
1 AGCTGGTGGTGGG-GT
*
4386351 AGCAGGTGGTGGGGT
1 AGCTGGTGGTGGGGT
* * *
4386366 AGCCT-GAGGTGGAGA
1 AG-CTGGTGGTGGGGT
*
4386381 AGCCGGTGG-GGGAGT
1 AGCTGGTGGTGGG-GT
* * *
4386396 TGCGGGAGGTGGGGT
1 AGCTGGTGGTGGGGT
* * *
4386411 AGCTGGGGGAGGAGT
1 AGCTGGTGGTGGGGT
* * * *
4386426 AGCCGGTGGAGGAGA
1 AGCTGGTGGTGGGGT
4386441 AGCTGGTGGTGGGG-
1 AGCTGGTGGTGGGGT
4386455 AGCT
1 AGCT
4386459 AACGGGCGGG
Statistics
Matches: 102, Mismatches: 30, Indels: 13
0.70 0.21 0.09
Matches are distributed among these distances:
14 9 0.09
15 86 0.84
16 7 0.07
ACGTcount: A:0.18, C:0.09, G:0.58, T:0.15
Consensus pattern (15 bp):
AGCTGGTGGTGGGGT
Found at i:4386392 original size:45 final size:45
Alignment explanation
Indices: 4386310--4386458 Score: 176
Period size: 45 Copynumber: 3.3 Consensus size: 45
4386300 CAAAGGAGCT
* *
4386310 GGTGGTGGGGTAGCTGGAGGAGGAGTAGCAGGAGGGGGAGAAGCA
1 GGTGGTGGGGTAGCTGGAGGAGGAGTAGCCGGTGGGGGAGAAGCA
* * ** *
4386355 GGTGGTGGGGTAGCCT-GAGGTGGAGAAGCCGGTGGGGGAGTTGCG
1 GGTGGTGGGGTAG-CTGGAGGAGGAGTAGCCGGTGGGGGAGAAGCA
* * * *
4386400 GGAGGTGGGGTAGCTGGGGGAGGAGTAGCCGGTGGAGGAGAAGCT
1 GGTGGTGGGGTAGCTGGAGGAGGAGTAGCCGGTGGGGGAGAAGCA
4386445 GGTGGTGGGG-AGCT
1 GGTGGTGGGGTAGCT
4386459 AACGGGCGGG
Statistics
Matches: 86, Mismatches: 16, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
44 6 0.07
45 78 0.91
46 2 0.02
ACGTcount: A:0.18, C:0.09, G:0.58, T:0.15
Consensus pattern (45 bp):
GGTGGTGGGGTAGCTGGAGGAGGAGTAGCCGGTGGGGGAGAAGCA
Found at i:4386405 original size:30 final size:31
Alignment explanation
Indices: 4386331--4386453 Score: 92
Period size: 30 Copynumber: 4.1 Consensus size: 31
4386321 AGCTGGAGGA
*
4386331 GGAGTAGCAGGAGGGGGAGAAGCAGGTGGTG
1 GGAGTAGCAGGAGGTGGAGAAGCAGGTGGTG
** *
4386362 GG-GTAGCCTGAGGTGGAGAAGCCGGTGG-G
1 GGAGTAGCAGGAGGTGGAGAAGCAGGTGGTG
* * * * *
4386391 GGAGTTGCGGGAGGTGGGGTAGCTGG-GG-G
1 GGAGTAGCAGGAGGTGGAGAAGCAGGTGGTG
* * * *
4386420 AGGAGTAGCCGGTGGAGGAGAAGCTGGTGGTG
1 -GGAGTAGCAGGAGGTGGAGAAGCAGGTGGTG
4386452 GG
1 GG
4386454 GAGCTAACGG
Statistics
Matches: 72, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
29 6 0.08
30 59 0.82
31 6 0.08
32 1 0.01
ACGTcount: A:0.19, C:0.09, G:0.59, T:0.14
Consensus pattern (31 bp):
GGAGTAGCAGGAGGTGGAGAAGCAGGTGGTG
Found at i:4394321 original size:19 final size:20
Alignment explanation
Indices: 4394292--4394341 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4394282 AAAATATAAT
*
4394292 TTTTGGAATTTTTATAAA-TA
1 TTTT-GAATTTTTAAAAATTA
4394312 TTTTGAA-TTTTAAAAATTA
1 TTTTGAATTTTTAAAAATTA
4394331 TTTTG-ATTTTT
1 TTTTGAATTTTT
4394342 TTTTGTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.33
19 14 0.52
20 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
TTTTGAATTTTTAAAAATTA
Found at i:4399793 original size:22 final size:22
Alignment explanation
Indices: 4399768--4399817 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
4399758 GTAAAAAGAT
*
4399768 ATATATATGTATGTATATTA-AA
1 ATATATATATATGTAT-TTACAA
*
4399790 ATATATGTATATGTATTTACAA
1 ATATATATATATGTATTTACAA
4399812 A-ATATA
1 ATATATA
4399818 AAAAATGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (22 bp):
ATATATATATATGTATTTACAA
Found at i:4400031 original size:2 final size:2
Alignment explanation
Indices: 4400024--4400077 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
4400014 TATGCATGCT
4400024 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
4400066 TA TA TG TA TA TA
1 TA TA TA TA TA TA
4400078 ACAAGATTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4400155 original size:14 final size:15
Alignment explanation
Indices: 4400116--4400168 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 15
4400106 GGTGTAACCG
4400116 AATAAATAATAA--T
1 AATAAATAATAATGT
4400129 AATAAATAATAATGT
1 AATAAATAATAATGT
*
4400144 AAT-AATATTAATAGT
1 AATAAATAATAAT-GT
*
4400159 ATTAAATAAT
1 AATAAATAAT
4400169 TACTTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 12 0.36
14 8 0.24
15 8 0.24
16 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (15 bp):
AATAAATAATAATGT
Found at i:4400891 original size:32 final size:32
Alignment explanation
Indices: 4400850--4400913 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
4400840 CACTATCAAA
4400850 ATATGGATCTTGTTCCAAAATCAAACAATCAC
1 ATATGGATCTTGTTCCAAAATCAAACAATCAC
4400882 ATATGGATCTTGTTCCAAAATCAAACAATCAC
1 ATATGGATCTTGTTCCAAAATCAAACAATCAC
4400914 CTTGAGATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (32 bp):
ATATGGATCTTGTTCCAAAATCAAACAATCAC
Found at i:4401230 original size:23 final size:24
Alignment explanation
Indices: 4401204--4401248 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
4401194 GGTCAGTGGG
4401204 TTTTGGGTTGT-AA-TGGGCTAGTA
1 TTTTGGGTT-TCAATTGGGCTAGTA
4401227 TTTTGGGTTTCAATTGGGCTAG
1 TTTTGGGTTTCAATTGGGCTAG
4401249 GGTGTTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 11 0.55
24 8 0.40
ACGTcount: A:0.16, C:0.07, G:0.33, T:0.44
Consensus pattern (24 bp):
TTTTGGGTTTCAATTGGGCTAGTA
Found at i:4403552 original size:39 final size:40
Alignment explanation
Indices: 4403503--4403593 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 40
4403493 GAATTCTAAC
* *
4403503 AAAA-GCCGCAATATG-T-AAGCAATAGCGGCGCTTTTACT
1 AAAACGCCGCAA-ATGATCAAGCAATAGCGGCGCTTATACA
* * *
4403541 AAAACGCCGCAAATGATCAAGCATTAGGGGCGCTTATAGA
1 AAAACGCCGCAAATGATCAAGCAATAGCGGCGCTTATACA
4403581 AAAACGCCGCAAA
1 AAAACGCCGCAAA
4403594 AAACTTGGGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 7 0.16
39 8 0.18
40 30 0.67
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (40 bp):
AAAACGCCGCAAATGATCAAGCAATAGCGGCGCTTATACA
Found at i:4403999 original size:7 final size:7
Alignment explanation
Indices: 4403987--4404065 Score: 63
Period size: 7 Copynumber: 11.4 Consensus size: 7
4403977 TACACTTTTT
4403987 GGTTTAG
1 GGTTTAG
4403994 GGTTTATG
1 GGTTTA-G
* *
4404002 GTTTTAA
1 GGTTTAG
*
4404009 GGTTTAA
1 GGTTTAG
*
4404016 AGTTTA-
1 GGTTTAG
4404022 GGTTTAG
1 GGTTTAG
4404029 GG-TTAG
1 GGTTTAG
** *
4404035 TATTTAA
1 GGTTTAG
4404042 GGTTTAG
1 GGTTTAG
*
4404049 GGTTTAA
1 GGTTTAG
4404056 GGTTTAG
1 GGTTTAG
4404063 GGT
1 GGT
4404066 ATAATGTTTA
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
6 9 0.16
7 41 0.73
8 6 0.11
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:4404003 original size:14 final size:14
Alignment explanation
Indices: 4403987--4404075 Score: 83
Period size: 14 Copynumber: 6.4 Consensus size: 14
4403977 TACACTTTTT
*
4403987 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAA
*
4404001 GGTTTTAAGGTTTAA
1 GG-TTTAGGGTTTAA
*
4404016 AGTTTA-GGTTT-A
1 GGTTTAGGGTTTAA
* **
4404028 GGGTTAGTATTTAA
1 GGTTTAGGGTTTAA
4404042 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
*
4404056 GGTTTAGGGTATAA
1 GGTTTAGGGTTTAA
*
4404070 TGTTTA
1 GGTTTA
4404076 TTATTTTCGG
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
12 5 0.08
13 8 0.13
14 36 0.60
15 11 0.18
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:4404032 original size:20 final size:20
Alignment explanation
Indices: 4404004--4404063 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
4403994 GGTTTATGGT
*
4404004 TTTAAGGTTTAAAGTTTAGG
1 TTTAGGGTTTAAAGTTTAGG
*
4404024 TTTAGGG-TTAGTA-TTTAAGG
1 TTTAGGGTTTA-AAGTTT-AGG
*
4404044 TTTAGGGTTTAAGGTTTAGG
1 TTTAGGGTTTAAAGTTTAGG
4404064 GTATAATGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 6 0.19
20 20 0.62
21 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (20 bp):
TTTAGGGTTTAAAGTTTAGG
Found at i:4404119 original size:28 final size:28
Alignment explanation
Indices: 4404087--4404146 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
4404077 TATTTTCGGA
* * *
4404087 TTAGAATTT-TGAGTTTTGCGTTTATGGT
1 TTAGAATTTGTGA-TTTGGAGTTTAAGGT
*
4404115 TTAGAGTTTGTGATTTGGAGTTTAAGGT
1 TTAGAATTTGTGATTTGGAGTTTAAGGT
4404143 TTAG
1 TTAG
4404147 GGTTTAGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (28 bp):
TTAGAATTTGTGATTTGGAGTTTAAGGT
Found at i:4404918 original size:43 final size:43
Alignment explanation
Indices: 4404861--4405176 Score: 402
Period size: 43 Copynumber: 7.3 Consensus size: 43
4404851 GTTTTTAGAA
* * *
4404861 ACAAAAGCCACTAAAGAACAAGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * *
4404904 ACAAACGCCGCTAAAGACCAAAACCATTAGCGGCGCTTCTT-TC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-TTCCC
* * *
4404947 ACAAACGCCGTTAAAGACCATGACCTTTAGCGGCGCTTTTACC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* ** *
4404990 ACAAACGCCGCTAAAGACCAAGACCATTAGCGGCAATTTTACC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* *
4405033 ACAAACGCCGCTAAAGACAAAGACCTTTAGCGGCGCTTTTCCT
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* * *
4405076 ACAAACGCCACTAAAGACCATGATCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
* **
4405119 ACAAACGCCGCTAAAGACCATA-ACCTTTAGCGGCGCTTCTCGA
1 ACAAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTTCCC
*
4405162 AAAAACGCCGCTAAA
1 ACAAACGCCGCTAAA
4405177 AACATAACCT
Statistics
Matches: 236, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
42 2 0.01
43 232 0.98
44 2 0.01
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCC
Found at i:4405540 original size:43 final size:43
Alignment explanation
Indices: 4405474--4405564 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
4405464 ACATATGCAA
* * *
4405474 GGTAATAAAACATACAATGCATTT-TCTTAATCAAGTAAGTCTT
1 GGTAATAAAACATACAATACATTTAT-TTAATCAAGGAAATCTT
* *
4405517 GGTAATAAAATATATAATACATTTATTTAATCAAGGAAATCTT
1 GGTAATAAAACATACAATACATTTATTTAATCAAGGAAATCTT
4405560 -GTAAT
1 GGTAAT
4405565 GAACTCAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 5 0.12
43 36 0.86
44 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (43 bp):
GGTAATAAAACATACAATACATTTATTTAATCAAGGAAATCTT
Found at i:4406964 original size:41 final size:41
Alignment explanation
Indices: 4406907--4407197 Score: 469
Period size: 41 Copynumber: 7.1 Consensus size: 41
4406897 TAAGCTTAGT
* * *
4406907 GCTAAAGGCCCGAGCATTAGCGGTGCTTATTCAAAAACGCC
1 GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCC
*
4406948 GCTAAAGGCCAGAGCATTA--GTCGCTTCTTCAAAAACGCC
1 GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCC
*
4406987 GCTAAAGGCCGGAGCATTAGCGGCGCTTCTTCAAAAACGCC
1 GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCC
* *
4407028 GCTAAAGGCCCGAGCATTAGCGGCGCTTCGTCAAAAACGCC
1 GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCC
*
4407069 GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAATGCC
1 GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCC
* *
4407110 GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTTAAAAATGCC
1 GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCC
*
4407151 GCTAAAGGCCAGAGCAGTAGCGGCGCTTCTTCAAAAACGCC
1 GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCC
4407192 GCTAAA
1 GCTAAA
4407198 TGCCCCAAAA
Statistics
Matches: 233, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.15
41 198 0.85
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (41 bp):
GCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACGCC
Found at i:4407331 original size:40 final size:39
Alignment explanation
Indices: 4407245--4407333 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 39
4407235 GGCTTTTTGC
4407245 GGCGCTTTTTAGAAAACGCCGCTAATGCTTATTTTTAGAA
1 GGCG-TTTTTAGAAAACGCCGCTAATGCTTATTTTTAGAA
** * * *
4407285 AACGTTTTTATAAAAGCGCCGTTAATGCTTGATTTTTAG-T
1 GGCGTTTTTAGAAAA-CGCCGCTAATGCTT-ATTTTTAGAA
4407325 GGCGTTTTT
1 GGCGTTTTT
4407334 TGCCCAAACG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
39 10 0.25
40 22 0.55
41 8 0.20
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (39 bp):
GGCGTTTTTAGAAAACGCCGCTAATGCTTATTTTTAGAA
Found at i:4407740 original size:20 final size:20
Alignment explanation
Indices: 4407717--4407757 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4407707 TGCACCCGGC
4407717 CCCTAATTCCCCTTCCAAAT
1 CCCTAATTCCCCTTCCAAAT
*
4407737 CCCTAATTCCCCTTCGAAAT
1 CCCTAATTCCCCTTCCAAAT
4407757 C
1 C
4407758 TCTTCCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.44, G:0.02, T:0.29
Consensus pattern (20 bp):
CCCTAATTCCCCTTCCAAAT
Found at i:4408605 original size:13 final size:13
Alignment explanation
Indices: 4408583--4408614 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
4408573 TTTGCTGCAA
4408583 GTTG-TGGTTAAT
1 GTTGCTGGTTAAT
4408595 GTTGCTGGTTAAT
1 GTTGCTGGTTAAT
4408608 GTTGCTG
1 GTTGCTG
4408615 CAAGTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.12, C:0.06, G:0.34, T:0.47
Consensus pattern (13 bp):
GTTGCTGGTTAAT
Found at i:4408658 original size:52 final size:52
Alignment explanation
Indices: 4408548--4408650 Score: 136
Period size: 52 Copynumber: 2.0 Consensus size: 52
4408538 TTTAGGAATT
* * **
4408548 TGGTTAATGTTGCTGCAAGTTCTTTTTTGCTGCAAGTTGTGGTTAATGTTGC
1 TGGTTAATGTTGCTGCAAGTTCTTTTTTGCTCCAAGTTCTGACTAATGTTGC
**
4408600 TGGTTAATGTTGCTGCAAGTTCTTTTTTGCTCCATTTTCT-ACTAAGTGTTG
1 TGGTTAATGTTGCTGCAAGTTCTTTTTTGCTCCAAGTTCTGACTAA-TGTTG
4408651 TATGTTAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
51 3 0.07
52 41 0.93
ACGTcount: A:0.16, C:0.14, G:0.23, T:0.48
Consensus pattern (52 bp):
TGGTTAATGTTGCTGCAAGTTCTTTTTTGCTCCAAGTTCTGACTAATGTTGC
Done.