Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, whole genome shotgun sequence
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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 12 of 20
Found at i:4386421 original size:35 final size:35
Alignment explanation
Indices: 4386370--4386438 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
4386360 TCTCTCTAGT
*
4386370 TTTCAAAATAGCAAAGAATTAGGAAACAAAAGAGA
1 TTTCAAAATAGCAAAGAATTAAGAAACAAAAGAGA
* *
4386405 TTTCAAAATAGTAAAGAATTAAGAAACAGAAGAG
1 TTTCAAAATAGCAAAGAATTAAGAAACAAAAGAG
4386439 GGCATCTTGG
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:0.57, C:0.07, G:0.17, T:0.19
Consensus pattern (35 bp):
TTTCAAAATAGCAAAGAATTAAGAAACAAAAGAGA
Found at i:4396181 original size:29 final size:29
Alignment explanation
Indices: 4396148--4396204 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
4396138 TATTCGATCT
*
4396148 AAAATAAAAGTAA-AAAAATTTGATTGAAC
1 AAAATAAAAG-AATAAAAAGTTGATTGAAC
* *
4396177 AAAATAGAAGAATAAAAAGTTGTTTGAA
1 AAAATAAAAGAATAAAAAGTTGATTGAA
4396205 TTTTCTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.60, C:0.02, G:0.14, T:0.25
Consensus pattern (29 bp):
AAAATAAAAGAATAAAAAGTTGATTGAAC
Found at i:4401407 original size:13 final size:13
Alignment explanation
Indices: 4401389--4401413 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4401379 AAACATTTGC
4401389 TCCTGTTCTCTTA
1 TCCTGTTCTCTTA
4401402 TCCTGTTCTCTT
1 TCCTGTTCTCTT
4401414 CTGATGAGAG
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:0.04, C:0.32, G:0.08, T:0.56
Consensus pattern (13 bp):
TCCTGTTCTCTTA
Found at i:4405120 original size:31 final size:31
Alignment explanation
Indices: 4405072--4405138 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
4405062 AACATATTAA
* *
4405072 GTTATTGAGTTAAATTATTGAGATATAATAT
1 GTTATTGAGTTAAATTATTAAAATATAATAT
* *
4405103 GTTATTGGGTTAGATTATTAAAATATAATAT
1 GTTATTGAGTTAAATTATTAAAATATAATAT
4405134 GTTAT
1 GTTAT
4405139 AATAGGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.46
Consensus pattern (31 bp):
GTTATTGAGTTAAATTATTAAAATATAATAT
Found at i:4405934 original size:21 final size:23
Alignment explanation
Indices: 4405895--4405940 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
4405885 ATTTATAAAA
4405895 AAATAAAAATTTTATAAATTATG
1 AAATAAAAATTTTATAAATTATG
* *
4405918 AAAT-AAATTTTTA-AAATTTTG
1 AAATAAAAATTTTATAAATTATG
4405939 AA
1 AA
4405941 GAACCATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 8 0.38
23 4 0.19
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
AAATAAAAATTTTATAAATTATG
Found at i:4419895 original size:21 final size:21
Alignment explanation
Indices: 4419863--4419905 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4419853 GAAAGATTAT
4419863 AATTAGTTTTTAACTTTTCAA
1 AATTAGTTTTTAACTTTTCAA
**
4419884 AATTA-TTATTTATTTTTTCAA
1 AATTAGTT-TTTAACTTTTCAA
4419905 A
1 A
4419906 TCTAAACGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTAGTTTTTAACTTTTCAA
Found at i:4421387 original size:13 final size:16
Alignment explanation
Indices: 4421369--4421409 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 16
4421359 TTTTTAAAAG
4421369 AAATAACAA-AAT-A-
1 AAATAACAATAATGAC
4421382 AAATAACAATAATGAC
1 AAATAACAATAATGAC
4421398 AAATAACTAATA
1 AAATAAC-AATA
4421410 GTAATCTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.38
14 3 0.12
15 1 0.04
16 7 0.29
17 4 0.17
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.20
Consensus pattern (16 bp):
AAATAACAATAATGAC
Found at i:4426110 original size:43 final size:43
Alignment explanation
Indices: 4426063--4426145 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
4426053 TTAACCATTG
*
4426063 TGGCA-TAGGTTATAATCATAACAAAAATCACAATTAACCTCAA
1 TGGCATTA-GTTATAATCATAACAAAAACCACAATTAACCTCAA
* ** *
4426106 TGGCATTAGTTATAATTATATTAAAAACCTCAATTAACCT
1 TGGCATTAGTTATAATCATAACAAAAACCACAATTAACCT
4426146 TAGTAGCATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 32 0.94
44 2 0.06
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.31
Consensus pattern (43 bp):
TGGCATTAGTTATAATCATAACAAAAACCACAATTAACCTCAA
Found at i:4441202 original size:29 final size:30
Alignment explanation
Indices: 4441144--4441203 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4441134 ATAAAAAATA
*
4441144 ATTTTAAAAAATTTTATATGGTGTTTAATT
1 ATTTTAAAAAATTTTATATGGTATTTAATT
*
4441174 ATTTTATAAAATTTT-TAT-GTAATTTAATT
1 ATTTTAAAAAATTTTATATGGT-ATTTAATT
4441203 A
1 A
4441204 AATTTGATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 11 0.41
30 14 0.52
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (30 bp):
ATTTTAAAAAATTTTATATGGTATTTAATT
Found at i:4441465 original size:95 final size:89
Alignment explanation
Indices: 4441327--4441623 Score: 254
Period size: 95 Copynumber: 3.2 Consensus size: 89
4441317 TAGGCATAGT
*
4441327 TTTTTATCTCTCAAAGTGATGGTA-CTAAGGTCTAAT-GGCTTCCATTGCCCTACTCAAAATCCC
1 TTTTTATCTCTCAAAGTGATGGTATTTAA-GTCTAATAGG-TTCCATTGCCCTACT--AAATCCC
4441390 TCTTATAACCCATTTGATTGAATTGGGCATAC
62 TC--A-AACCCATTTGATTGAATT-GGCATAC
* * * *
4441422 TTTTTATCTCTCCAAGTGATGGTATTTAAGTCTAATAGGTTCCACTGCCCCACT--GT-CC-C-A
1 TTTTTATCTCTCAAAGTGATGGTATTTAAGTCTAATAGGTTCCATTGCCCTACTAAATCCCTCAA
** *
4441482 ACCCA-TTGAATTGAATTCACATCC
66 ACCCATTTG-ATTGAATTGGCATAC
* *
4441506 TTTTTATCTCTCAAAGTGATGGTATTTAAGTCTAATAATAGCTTTCATTGCCCCTACTTTAAATC
1 TTTTTATCTCTCAAAGTGATGGTATTTAAGTC---TAATAGGTTCCATTG-CCCTAC--TAAATC
*
4441571 AATCC-CAAA-CCATTTGATTAAATTGGCATAC
60 ---CCTCAAACCCATTTGATTGAATTGGCATAC
*
4441602 TTTTTATCTCTCAAGGTGATGG
1 TTTTTATCTCTCAAAGTGATGG
4441624 CAAATGGGAC
Statistics
Matches: 166, Mismatches: 19, Indels: 33
0.76 0.09 0.15
Matches are distributed among these distances:
84 38 0.23
85 14 0.08
87 12 0.07
88 5 0.03
89 1 0.01
90 3 0.02
91 1 0.01
92 1 0.01
95 43 0.26
96 43 0.26
97 5 0.03
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (89 bp):
TTTTTATCTCTCAAAGTGATGGTATTTAAGTCTAATAGGTTCCATTGCCCTACTAAATCCCTCAA
ACCCATTTGATTGAATTGGCATAC
Found at i:4461163 original size:62 final size:63
Alignment explanation
Indices: 4461043--4461165 Score: 149
Period size: 62 Copynumber: 2.0 Consensus size: 63
4461033 ATTCTCAGAT
* * * *
4461043 ATTTTTATTATCAATCAAATAATCAATTCATTTTTTAAGGTGGACAAGAAAATTAACAACAAAC
1 ATTTTCATTACCAATCAAATAATCAATT-ATTTTTTAAGGTAGACAAGAAAATCAACAACAAAC
* * * * *
4461107 ATTTTCATTACCAATCATATGATCAATT-TTTTTTAGGGTAGATATGAAAATCAACAACA
1 ATTTTCATTACCAATCAAATAATCAATTATTTTTTAAGGTAGACAAGAAAATCAACAACA
4461166 CATCAACTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 26 0.52
64 24 0.48
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (63 bp):
ATTTTCATTACCAATCAAATAATCAATTATTTTTTAAGGTAGACAAGAAAATCAACAACAAAC
Found at i:4461347 original size:17 final size:14
Alignment explanation
Indices: 4461312--4461346 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
4461302 TTTTTAATTT
4461312 TTTTTATTTTTATC
1 TTTTTATTTTTATC
4461326 TTTTTATTATTTATC
1 TTTTTATT-TTTATC
4461341 TATTTT
1 T-TTTT
4461347 TGGTGGGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 7 0.37
16 4 0.21
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTATTTTTATC
Found at i:4461375 original size:28 final size:28
Alignment explanation
Indices: 4461344--4461404 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
4461334 ATTTATCTAT
*
4461344 TTTTGGTGGGTTA-AAAGTATTCAATCAC
1 TTTTGGTGAGTTACAAA-TATTCAATCAC
* *
4461372 TTTTGGTGAGTTACAAATATTCATTTAC
1 TTTTGGTGAGTTACAAATATTCAATCAC
4461400 TTTTG
1 TTTTG
4461405 ATGGATTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (28 bp):
TTTTGGTGAGTTACAAATATTCAATCAC
Found at i:4461478 original size:26 final size:26
Alignment explanation
Indices: 4461446--4461524 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
4461436 TTAAGGTATC
4461446 CATCCACTTCTGGTGACAAAATTATT
1 CATCCACTTCTGGTGACAAAATTATT
* * *
4461472 CGTCCACTTCTGATGACAAAATTATC
1 CATCCACTTCTGGTGACAAAATTATT
* **
4461498 CATCCACTTCTCGTGGTAAAATTATT
1 CATCCACTTCTGGTGACAAAATTATT
4461524 C
1 C
4461525 TTAAAATTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (26 bp):
CATCCACTTCTGGTGACAAAATTATT
Found at i:4462520 original size:12 final size:12
Alignment explanation
Indices: 4462503--4462533 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4462493 GACACTTTTT
*
4462503 ATTAAATATATG
1 ATTAAATATATA
4462515 ATTAAATATATA
1 ATTAAATATATA
4462527 ATTAAAT
1 ATTAAAT
4462534 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
ATTAAATATATA
Found at i:4496209 original size:61 final size:61
Alignment explanation
Indices: 4496109--4496377 Score: 371
Period size: 61 Copynumber: 4.4 Consensus size: 61
4496099 TTTTTTACTA
*
4496109 CTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTACCATCCCTTATAGTTCACACACCTTT
1 CTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCTTT
* * * ****
4496170 CTTTCTACTTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTCTCTACTT-A-TTTTCTGCTT
1 CTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCT-TATAGTTCACACACCT--TT
* * * *
4496232 CTTTCTACTTGAGTTTTTTTTTTCTATTGTTATTGCCATCCCTTATAGTTCACACACATTT
1 CTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCTTT
4496293 CTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCTTT
1 CTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCTTT
*
4496354 CTTTCCTAGCTGAGTTCTTTTTTT
1 CTTT-CTACCTGAGTTCTTTTTTT
4496378 TTCTGTTGTT
Statistics
Matches: 180, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
60 2 0.01
61 110 0.61
62 67 0.37
63 1 0.01
ACGTcount: A:0.15, C:0.25, G:0.08, T:0.51
Consensus pattern (61 bp):
CTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCTTT
Found at i:4496254 original size:123 final size:123
Alignment explanation
Indices: 4496087--4496335 Score: 417
Period size: 123 Copynumber: 2.0 Consensus size: 123
4496077 CACAATACAA
*
4496087 CCTCTCTACTTATTTTTTACTACTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTACCATCCCT
1 CCTCTCTACTTATTTTCTACTACTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTACCATCCCT
* *
4496152 TATAGTTCACACACCTTTCTTTCTACTTGAGTTCTTTTTTTCTATTGTTACTGCCATC
66 TATAGTTCACACACATTTCTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATC
* * * * * *
4496210 CCTCTCTACTTATTTTCTGCTTCTTTCTACTTGAGTTTTTTTTTTCTATTGTTATTGCCATCCCT
1 CCTCTCTACTTATTTTCTACTACTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTACCATCCCT
4496275 TATAGTTCACACACATTTCTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATC
66 TATAGTTCACACACATTTCTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATC
4496333 CCT
1 CCT
4496336 TATAGTTCAC
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
123 117 1.00
ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52
Consensus pattern (123 bp):
CCTCTCTACTTATTTTCTACTACTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTACCATCCCT
TATAGTTCACACACATTTCTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATC
Found at i:4496368 original size:123 final size:121
Alignment explanation
Indices: 4496109--4496407 Score: 368
Period size: 123 Copynumber: 2.4 Consensus size: 121
4496099 TTTTTTACTA
* * * *
4496109 CTTTCTACCTGAGTTCTTTTTTTCTATTGTTACTACCATCCCTTATAGTTCACACACCTTTCTTT
1 CTTTCTA-CTGAGTTTTTTTTTTCTATTGTTATTGCCATCCCTTATAGTTCACACACATTTCTTT
* * ****
4496174 CTACTTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTCTCTACTTATTTTCTGCTT
65 CTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTCTATACTTAACACCT-CTT
4496232 CTTTCTACTTGAGTTTTTTTTTTCTATTGTTATTGCCATCCCTTATAGTTCACACACATTTCTTT
1 CTTTCTAC-TGAGTTTTTTTTTTCTATTGTTATTGCCATCCCTTATAGTTCACACACATTTCTTT
*
4496297 CTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCT-TATAGTTCACACACCT-TT
65 CTACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTCTATACTT-A-ACACCTCTT
* * *
4496354 CTTTCCTAGCTGAGTTCTTTTTTTTTCTGTTGTTATTGTCATCCTTTACTAGTT
1 CTTT-CTA-CTGAG-T-TTTTTTTTTCTATTGTTATTGCCATCCCTTA-TAGTT
4496408 TGTCTTCCTT
Statistics
Matches: 154, Mismatches: 14, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
122 12 0.08
123 105 0.68
124 4 0.03
125 28 0.18
126 5 0.03
ACGTcount: A:0.15, C:0.24, G:0.09, T:0.52
Consensus pattern (121 bp):
CTTTCTACTGAGTTTTTTTTTTCTATTGTTATTGCCATCCCTTATAGTTCACACACATTTCTTTC
TACCTGAGTTCTTTTTTTCTATTGTTACTGCCATCCCTCTATACTTAACACCTCTT
Found at i:4496531 original size:106 final size:107
Alignment explanation
Indices: 4496406--4496621 Score: 398
Period size: 106 Copynumber: 2.0 Consensus size: 107
4496396 CCTTTACTAG
4496406 TTTGTCTTCCTTCACTCACAACACAACCTCTCTACTTATTTTCTACTTCTTTCTACCTGAGTTCT
1 TTTGTCTTCCTTCACTCACAACACAACCTCTCTACTTATTTTCTACTTCTTTCTACCTGAGTTCT
4496471 TTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCT
66 TTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCT
* * *
4496513 TTTG-CTTCTTTCACTCACAACACAACCTTTCTACTTATTTTCTACTTCTTTCTACTTGAGTTCT
1 TTTGTCTTCCTTCACTCACAACACAACCTCTCTACTTATTTTCTACTTCTTTCTACCTGAGTTCT
4496577 TTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCT
66 TTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCT
4496619 TTT
1 TTT
4496622 CTTTCTTAGC
Statistics
Matches: 106, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
106 102 0.96
107 4 0.04
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.47
Consensus pattern (107 bp):
TTTGTCTTCCTTCACTCACAACACAACCTCTCTACTTATTTTCTACTTCTTTCTACCTGAGTTCT
TTTTTTCTATTGTTACTGCCATCCCTTATAGTTCACACACCT
Found at i:4496700 original size:55 final size:55
Alignment explanation
Indices: 4496589--4496699 Score: 188
Period size: 55 Copynumber: 2.0 Consensus size: 55
4496579 TTTTCTATTG
* *
4496589 TTACTGCCATCCCTTATAGTTCACACACCTTTTCTTTCTTAGCTGAGTTCTTTTT
1 TTACTGCCATCCCTTATAATTCACACACCTTTTCTTTCCTAGCTGAGTTCTTTTT
*
4496644 TTACTGCCATCCTTTATAATTCACACACC-TTTCTTTCCTAGCTGAGTTCTTTTT
1 TTACTGCCATCCCTTATAATTCACACACCTTTTCTTTCCTAGCTGAGTTCTTTTT
4496698 TT
1 TT
4496700 TTCTGTTGTT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 26 0.49
55 27 0.51
ACGTcount: A:0.17, C:0.27, G:0.08, T:0.48
Consensus pattern (55 bp):
TTACTGCCATCCCTTATAATTCACACACCTTTTCTTTCCTAGCTGAGTTCTTTTT
Found at i:4496763 original size:47 final size:47
Alignment explanation
Indices: 4496705--4496795 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
4496695 TTTTTTTCTG
* * *
4496705 TTGTTATTGTCATCCTTTACTAGTTTGTGCAAACTATAAGGAAATGT
1 TTGTTACTGTCACCCCTTACTAGTTTGTGCAAACTATAAGGAAATGT
4496752 TTGTTACTGTCACCCCTTACTAGTTTGTGCAAACTATAAGGAAA
1 TTGTTACTGTCACCCCTTACTAGTTTGTGCAAACTATAAGGAAA
4496796 GATCTATTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (47 bp):
TTGTTACTGTCACCCCTTACTAGTTTGTGCAAACTATAAGGAAATGT
Found at i:4497198 original size:27 final size:27
Alignment explanation
Indices: 4497147--4497201 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
4497137 AGCTGAGTTC
*
4497147 TTTTTTTCTGTTGTTATTGCTATCCCT
1 TTTTTTTCTGTTGTTACTGCTATCCCT
4497174 TTTTTTTCTGTTGTTACTG-TCATCCCT
1 TTTTTTTCTGTTGTTACTGCT-ATCCCT
4497201 T
1 T
4497202 ATAGTTCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.07, C:0.20, G:0.11, T:0.62
Consensus pattern (27 bp):
TTTTTTTCTGTTGTTACTGCTATCCCT
Found at i:4497442 original size:27 final size:28
Alignment explanation
Indices: 4497405--4497458 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
4497395 TGTCTCCAAA
4497405 TTTTTCTCAATTAGAAGAATATGCTTAT
1 TTTTTCTCAATTAGAAGAATATGCTTAT
4497433 TTTTTC-CAATTAGAAGAATATGCTTA
1 TTTTTCTCAATTAGAAGAATATGCTTA
4497459 AAAGGCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (28 bp):
TTTTTCTCAATTAGAAGAATATGCTTAT
Found at i:4498407 original size:210 final size:199
Alignment explanation
Indices: 4498188--4498572 Score: 420
Period size: 199 Copynumber: 1.9 Consensus size: 199
4498178 CTTTAAAATC
* * *
4498188 AAAAAAAAATTCC-AATCATGT-GTGAGGAGTGACTAAGAGA-ACTAGATAACAGTGATATGTTG
1 AAAAAAAAAATCCAAATCATGTAG-GAGGAGTAACTAAGAAATAC-AGATAA-AGTGATATGTTG
* *
4498250 TTAAAAAGCATAATAGAAAAAATACCAAACTATCAAAAA-GCAAACAAACACATGTTTTTCATTT
63 TTAAAAAG--T-ATA-AAAAAAT----AA-T-CCAAAAACG-AAACAAACACACGTTTTTCATTT
* * ** * *
4498314 AATAGCTAGCAAAATACCAAAAAGA-ACCTGTTAAATGATATAAAATGATTATAATACCCTCTGA
117 AATAGATAACAAAATACCAAAAA-ACACCTACTAAAAGATATAAAATGAATATAATACCCTCTGA
4498378 ATCATTATAGTTTAGATTG
181 ATCATTATAGTTTAGATTG
* * ** *
4498397 AAAAAAAAAATCCAAATGATGTAGGAGGAGTAATTGTGAAATACAGATAATGTGATATGTTGTTA
1 AAAAAAAAAATCCAAATCATGTAGGAGGAGTAACTAAGAAATACAGATAAAGTGATATGTTGTTA
* * *
4498462 AAAAGTATAAAAAAATAATCCAAGAACGAGATAAACACACGTTTTTCATTTAATAGATAACAAAA
66 AAAAGTATAAAAAAATAATCCAAAAACGAAACAAACACACGTTTTTCATTTAATAGATAACAAAA
*
4498527 TATCAAAAAACACCTACTAAAAGATATAAAATGAATATAATACCCT
131 TACCAAAAAACACCTACTAAAAGATATAAAATGAATATAATACCCT
4498573 TTGTAGGTGA
Statistics
Matches: 151, Mismatches: 20, Indels: 20
0.79 0.10 0.10
Matches are distributed among these distances:
198 1 0.01
199 76 0.50
200 2 0.01
201 2 0.01
205 7 0.05
206 3 0.02
207 1 0.01
209 31 0.21
210 25 0.17
211 3 0.02
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (199 bp):
AAAAAAAAAATCCAAATCATGTAGGAGGAGTAACTAAGAAATACAGATAAAGTGATATGTTGTTA
AAAAGTATAAAAAAATAATCCAAAAACGAAACAAACACACGTTTTTCATTTAATAGATAACAAAA
TACCAAAAAACACCTACTAAAAGATATAAAATGAATATAATACCCTCTGAATCATTATAGTTTAG
ATTG
Found at i:4511830 original size:25 final size:25
Alignment explanation
Indices: 4511802--4511865 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
4511792 AGGAAAATAA
4511802 AATCCCTATAATTATGATGATTTCC
1 AATCCCTATAATTATGATGATTTCC
* *
4511827 AATCCCTATAATTATGGTGATTTCT
1 AATCCCTATAATTATGATGATTTCC
* *
4511852 AGTTCCTATAATTA
1 AATCCCTATAATTA
4511866 CGTTACTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.42
Consensus pattern (25 bp):
AATCCCTATAATTATGATGATTTCC
Found at i:4514036 original size:25 final size:24
Alignment explanation
Indices: 4513977--4514036 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
4513967 AAATAAAATC
*
4513977 CCTATAATCATGATGATTCCCAAT
1 CCTATAATTATGATGATTCCCAAT
* * *
4514001 CCTTATCATTATGATGATTTCTAATT
1 CC-TATAATTATGATGATTCCCAA-T
4514027 CCTATAATTA
1 CCTATAATTA
4514037 CGTTAATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 2 0.07
25 24 0.83
26 3 0.10
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.42
Consensus pattern (24 bp):
CCTATAATTATGATGATTCCCAAT
Found at i:4538155 original size:24 final size:24
Alignment explanation
Indices: 4538128--4538173 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4538118 ACTTCACCTT
4538128 ATCTCATT-TCAGTCTTGTCTTTTA
1 ATCTC-TTCTCAGTCTTGTCTTTTA
*
4538152 ATCTCTTCTCAGTCTTTTCTTT
1 ATCTCTTCTCAGTCTTGTCTTT
4538174 CTACAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.13, C:0.24, G:0.07, T:0.57
Consensus pattern (24 bp):
ATCTCTTCTCAGTCTTGTCTTTTA
Found at i:4541058 original size:12 final size:12
Alignment explanation
Indices: 4541041--4541068 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
4541031 TTTTTTTACT
4541041 TTCTCGTAAAGG
1 TTCTCGTAAAGG
4541053 TTCTCGTAAAGG
1 TTCTCGTAAAGG
4541065 TTCT
1 TTCT
4541069 TGAGGTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (12 bp):
TTCTCGTAAAGG
Found at i:4541943 original size:13 final size:13
Alignment explanation
Indices: 4541927--4541969 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
4541917 ACGCTTTTGT
4541927 TTATTTATTTTTC
1 TTATTTATTTTTC
4541940 TTATTTA--TTTC
1 TTATTTATTTTTC
*
4541951 TTATTTTATTTTTT
1 TTA-TTTATTTTTC
4541965 TTATT
1 TTATT
4541970 CAAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 7 0.27
12 4 0.15
13 9 0.35
14 6 0.23
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTTATTTTTC
Found at i:4546658 original size:27 final size:26
Alignment explanation
Indices: 4546628--4546682 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
4546618 TGCTTCAACA
* * *
4546628 CTTGAAATGCCCATGGGTGCTTTCTCG
1 CTTGAAACGCCC-TGGGGGCTTTCGCG
*
4546655 CTTGGAACGCCCTGGGGGCTTTCGCG
1 CTTGAAACGCCCTGGGGGCTTTCGCG
4546681 CT
1 CT
4546683 CGTAACACCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.11, C:0.29, G:0.31, T:0.29
Consensus pattern (26 bp):
CTTGAAACGCCCTGGGGGCTTTCGCG
Found at i:4554907 original size:2 final size:2
Alignment explanation
Indices: 4554900--4554926 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4554890 CTGGTTGATT
4554900 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4554927 GCAGATATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4565918 original size:2 final size:2
Alignment explanation
Indices: 4565911--4565937 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4565901 AAACAGACAC
4565911 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 A
4565938 CCTGAGCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4571000 original size:3 final size:3
Alignment explanation
Indices: 4570994--4571027 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4570984 CTCCTCACCG
*
4570994 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCG TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
4571028 GACTTTCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:4587125 original size:33 final size:33
Alignment explanation
Indices: 4587064--4587127 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
4587054 ATTTAACCAA
* * *
4587064 TTAGTGAGATGATAAGCTCACTATTATAACTCG
1 TTAGTGAGATCATAAGCTAACTACTATAACTCG
4587097 TTAGTGAGATCATACA-CTAACTACTATAACT
1 TTAGTGAGATCATA-AGCTAACTACTATAACT
4587128 TGTCTAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (33 bp):
TTAGTGAGATCATAAGCTAACTACTATAACTCG
Found at i:4609793 original size:1 final size:1
Alignment explanation
Indices: 4609787--4609815 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
4609777 TCGATGCTTA
4609787 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4609816 TGCATAGGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4610535 original size:49 final size:49
Alignment explanation
Indices: 4610463--4610561 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
4610453 CTTCGCCTCC
4610463 ATCTCTGTTTGTTTCCTCTGTGACTGCAAATTAAGGTGCCGTAAAATGT
1 ATCTCTGTTTGTTTCCTCTGTGACTGCAAATTAAGGTGCCGTAAAATGT
4610512 ATCTCTGTTTGTTTCCTCTGTGACTGCAAATTAAGGTGCCGTAAAATGT
1 ATCTCTGTTTGTTTCCTCTGTGACTGCAAATTAAGGTGCCGTAAAATGT
4610561 A
1 A
4610562 AATTGTAGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38
Consensus pattern (49 bp):
ATCTCTGTTTGTTTCCTCTGTGACTGCAAATTAAGGTGCCGTAAAATGT
Found at i:4615562 original size:51 final size:52
Alignment explanation
Indices: 4615488--4615596 Score: 157
Period size: 51 Copynumber: 2.1 Consensus size: 52
4615478 TATTCAATAA
* * * *
4615488 ATTTTTAATTTTTTATTACCTCAACTGCGTACAAAAATTATTTAATAGCTGC
1 ATTTTTAATTTTATATTACCTCAACTACATACAAAAATGATTTAATAGCTGC
* *
4615540 ATTTTTAA-TTTATATTACCTCAATTACATACAAAAATGATTTAATATCTGC
1 ATTTTTAATTTTATATTACCTCAACTACATACAAAAATGATTTAATAGCTGC
4615591 ATTTTT
1 ATTTTT
4615597 CTGTTAGGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 43 0.84
52 8 0.16
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.46
Consensus pattern (52 bp):
ATTTTTAATTTTATATTACCTCAACTACATACAAAAATGATTTAATAGCTGC
Found at i:4619271 original size:25 final size:25
Alignment explanation
Indices: 4619222--4619279 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
4619212 AGAGGCCGGC
*
4619222 GAAGAAAGAAGAAAGAAAGAGAAAG
1 GAAGAAAGAAGAAAGAAAGAAAAAG
*
4619247 GAAGGAAGAAGAAAGAGAA-AAAAA-
1 GAAGAAAGAAGAAAGA-AAGAAAAAG
4619271 GAA-AAAGAA
1 GAAGAAAGAA
4619280 TTGATATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.17
24 3 0.10
25 19 0.66
26 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (25 bp):
GAAGAAAGAAGAAAGAAAGAAAAAG
Found at i:4624560 original size:14 final size:15
Alignment explanation
Indices: 4624541--4624572 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
4624531 TTGTTTATTA
4624541 TATTTTAAAT-TTTT
1 TATTTTAAATATTTT
4624555 TATTTTAAATATTTT
1 TATTTTAAATATTTT
4624570 TAT
1 TAT
4624573 CATTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTAAATATTTT
Found at i:4624647 original size:16 final size:16
Alignment explanation
Indices: 4624628--4624658 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4624618 ATCGAATAAC
4624628 TTTTATTAAAAATATT
1 TTTTATTAAAAATATT
*
4624644 TTTTATTATAAATAT
1 TTTTATTAAAAATAT
4624659 AATAATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTATTAAAAATATT
Found at i:4633059 original size:75 final size:75
Alignment explanation
Indices: 4632901--4633042 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 75
4632891 TACCCACCTT
* * * * *
4632901 GATCTTTCATCTAACAACTTGAGTGGAGTCATCAAGCCAGATCTGCTTTCAAAGCTCGAGAATCT
1 GATCTTTCATCAAACAACTTGAGTGGACTCATCAAGCCAGAACTGATTTCAAAGCTCAAGAATCT
4632966 TCAAATGCTC
66 TCAAATGCTC
* * * * * *
4632976 GACCTTTCATCAAATAATTTTAGTGGCCTCATCGAGCCAGAACTGATTTCAAAGCTCAAGAATCT
1 GATCTTTCATCAAACAACTTGAGTGGACTCATCAAGCCAGAACTGATTTCAAAGCTCAAGAATCT
4633041 TC
66 TC
4633043 GGAGACTTCA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 56 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (75 bp):
GATCTTTCATCAAACAACTTGAGTGGACTCATCAAGCCAGAACTGATTTCAAAGCTCAAGAATCT
TCAAATGCTC
Found at i:4637050 original size:25 final size:25
Alignment explanation
Indices: 4637008--4637056 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
4636998 AATAAAAAAT
*
4637008 AAATCTAAATCAACTAAAATTAGAAA
1 AAATCTAAATCAAATAAAA-TAGAAA
*
4637034 AAAT-TAAATTAAATAAAATAGAA
1 AAATCTAAATCAAATAAAATAGAA
4637057 TCTTGGATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.24
Consensus pattern (25 bp):
AAATCTAAATCAAATAAAATAGAAA
Found at i:4648325 original size:25 final size:27
Alignment explanation
Indices: 4648297--4648353 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
4648287 TTTTGAAATT
4648297 TAAAATTA-ATTTTAAAATATTAAT-A
1 TAAAATTATATTTTAAAATATTAATAA
** *
4648322 TAAAA-TATATTTTATTATTTTAATAA
1 TAAAATTATATTTTAAAATATTAATAA
4648348 TAAAAT
1 TAAAAT
4648354 AACTAACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 2 0.08
25 18 0.69
26 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAAATTATATTTTAAAATATTAATAA
Found at i:4653232 original size:83 final size:81
Alignment explanation
Indices: 4653095--4653246 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 81
4653085 NNNNNNNNNC
* * *
4653095 ACAAAATGCCCTATTGAAAACGATGGACAAGACTGCGAAGGAAACTTATAATTTGGGTTGGATGG
1 ACAAAATGCCCTATTGAAAACAATGGACAAGACTGCGAAGGAAACTTACAATTTGGGTTGAATGG
4653160 TAGATCATTTCTAACG
66 TAGATCATTTCTAACG
* * * * * *
4653176 ACAAAATGTCCTATTGAGAAAACAATGGACCAGATTGCGACGTAAACTTGCAATTTGGGTTGAAT
1 ACAAAATGCCCTATT--GAAAACAATGGACAAGACTGCGAAGGAAACTTACAATTTGGGTTGAAT
4653241 GGTAGA
64 GGTAGA
4653247 ATTTGTTTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
81 14 0.23
83 46 0.77
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (81 bp):
ACAAAATGCCCTATTGAAAACAATGGACAAGACTGCGAAGGAAACTTACAATTTGGGTTGAATGG
TAGATCATTTCTAACG
Found at i:4661504 original size:2 final size:2
Alignment explanation
Indices: 4661492--4661521 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4661482 ATATAGTCAA
*
4661492 AT AT AT TT 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
4661522 CACATAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4662790 original size:16 final size:15
Alignment explanation
Indices: 4662764--4662802 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
4662754 TTTAATTTGT
*
4662764 TAATAAAATAAAAAA
1 TAATTAAATAAAAAA
*
4662779 TAAATTAAATAAATAA
1 T-AATTAAATAAAAAA
4662795 TAATTAAA
1 TAATTAAA
4662803 AAGCACAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATTAAATAAAAAA
Found at i:4665839 original size:26 final size:26
Alignment explanation
Indices: 4665810--4665863 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
4665800 TCTTTTTGAG
4665810 ATATAAACATAGAGTTATTTAATACT
1 ATATAAACATAGAGTTATTTAATACT
4665836 ATATAAACATAGAGTTATTTAATACT
1 ATATAAACATAGAGTTATTTAATACT
4665862 AT
1 AT
4665864 TTTTTGAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (26 bp):
ATATAAACATAGAGTTATTTAATACT
Found at i:4668079 original size:30 final size:30
Alignment explanation
Indices: 4668042--4668112 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
4668032 TAGTCACAAG
* *
4668042 GGCTTATTTGATTCAGAATATAAGTATAAA
1 GGCTTATTTGATTCAAAATAAAAGTATAAA
* * *
4668072 GGTTTATTTGGTTCAAAATAAAAGTGTAAA
1 GGCTTATTTGATTCAAAATAAAAGTATAAA
*
4668102 GGCTTAATTGA
1 GGCTTATTTGA
4668113 ATAACATAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.37
Consensus pattern (30 bp):
GGCTTATTTGATTCAAAATAAAAGTATAAA
Found at i:4674943 original size:31 final size:31
Alignment explanation
Indices: 4674908--4674979 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
4674898 TTATGAAGTG
* *
4674908 AAGATATCAAACGGCA-ACAAAGTTCGTGATC
1 AAGATATCAAACGGCAGA-AAAGTTCATGACC
** *
4674939 AAGATATCAAGGGGCAGAGAAGTTCATGACC
1 AAGATATCAAACGGCAGAAAAGTTCATGACC
4674970 AAGATATCAA
1 AAGATATCAA
4674980 GTTTAGTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (31 bp):
AAGATATCAAACGGCAGAAAAGTTCATGACC
Found at i:4675588 original size:17 final size:17
Alignment explanation
Indices: 4675566--4675600 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4675556 TTCATTCAGA
*
4675566 AGCATTTGAAGATTGAG
1 AGCATTCGAAGATTGAG
*
4675583 AGCATTCGGAGATTGAG
1 AGCATTCGAAGATTGAG
4675600 A
1 A
4675601 AGGGTAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (17 bp):
AGCATTCGAAGATTGAG
Found at i:4679252 original size:55 final size:54
Alignment explanation
Indices: 4679175--4679291 Score: 148
Period size: 54 Copynumber: 2.1 Consensus size: 54
4679165 TGTGTAAATA
* **
4679175 ATTTTTTTTATATAGCGTTGTAACATGTTTTTATACATAGGCG-TGTAACAACAAT
1 ATTTTTTTTACATAGCGTTGTAACAT-TTTTTATA-ATACACGATGTAACAACAAT
* *
4679230 ATTTTTTTTACATA-CGTGTGTAACATTTTTTATAATACATGATGTAACATCAAT
1 ATTTTTTTTACATAGCGT-TGTAACATTTTTTATAATACACGATGTAACAACAAT
4679284 ATTTTTTT
1 ATTTTTTT
4679292 CAACATGGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
53 4 0.07
54 30 0.55
55 21 0.38
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.48
Consensus pattern (54 bp):
ATTTTTTTTACATAGCGTTGTAACATTTTTTATAATACACGATGTAACAACAAT
Found at i:4679259 original size:24 final size:24
Alignment explanation
Indices: 4679230--4679350 Score: 77
Period size: 24 Copynumber: 4.8 Consensus size: 24
4679220 TAACAACAAT
4679230 ATTTTTTTTACATACGTGTGTAAC
1 ATTTTTTTTACATACGTGTGTAAC
* *
4679254 ATTTTTTATA-ATACATGATGTAAC
1 ATTTTTTTTACATACGTG-TGTAAC
* *
4679278 ATCAATATTTTTTTCA-ACATGGCTGTAAC
1 AT---T-TTTTTTACATACGT-G-TGTAAC
*
4679307 AATTTTTTTTAACATA-GCGTGTAAC
1 -ATTTTTTTT-ACATACGTGTGTAAC
* *
4679332 ATTTTTTGTACAAACGTGT
1 ATTTTTTTTACATACGTGT
4679351 AACATGTTTA
Statistics
Matches: 75, Mismatches: 11, Indels: 22
0.69 0.10 0.20
Matches are distributed among these distances:
23 10 0.13
24 28 0.37
25 6 0.08
26 7 0.09
27 4 0.05
28 10 0.13
29 8 0.11
30 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (24 bp):
ATTTTTTTTACATACGTGTGTAAC
Found at i:4679330 original size:54 final size:54
Alignment explanation
Indices: 4679175--4679333 Score: 141
Period size: 54 Copynumber: 2.9 Consensus size: 54
4679165 TGTGTAAATA
* * * * *
4679175 ATTTTTTTTATATAGCGTTGTAACA-TGTTTTTATACATAGGCGTGTAACAACAAT
1 ATTTTTTTAACATAGTG-TGTAACATTTTTTTTATACATA-GCGTGTAACATCAAT
* * *
4679230 ATTTTTTTTACATACGTGTGTAACATTTTTTATAATACAT-G-ATGTAACATCAAT
1 ATTTTTTTAACATA-GTGTGTAACATTTTTT-TTATACATAGCGTGTAACATCAAT
4679284 ATTTTTTTCAACAT-G-GCTGTAACAATTTTTTTTA-ACATAGCGTGTAACAT
1 ATTTTTTT-AACATAGTG-TGTAAC-ATTTTTTTTATACATAGCGTGTAACAT
4679334 TTTTTGTACA
Statistics
Matches: 87, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
52 5 0.06
53 10 0.11
54 34 0.39
55 25 0.29
56 6 0.07
57 7 0.08
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (54 bp):
ATTTTTTTAACATAGTGTGTAACATTTTTTTTATACATAGCGTGTAACATCAAT
Found at i:4679349 original size:22 final size:22
Alignment explanation
Indices: 4679301--4679368 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 22
4679291 TCAACATGGC
* *
4679301 TGTAACAATTTTTTTTAACATAGCG
1 TGTAAC-ATTTTTTGT-ACA-AACG
4679326 TGTAACATTTTTTGTACAAACG
1 TGTAACATTTTTTGTACAAACG
4679348 TGTAACATGTTTATTGTACAA
1 TGTAACAT-TTT-TTGTACAA
4679369 GTTACAATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.28
23 6 0.15
24 16 0.41
25 6 0.15
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (22 bp):
TGTAACATTTTTTGTACAAACG
Found at i:4681658 original size:51 final size:51
Alignment explanation
Indices: 4681596--4681702 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 51
4681586 ACTTTGCTCG
* *
4681596 ATCTTCACTTCAATGATCTTAACGACTTAATCTTGATCATAAACAATTGAT
1 ATCTTCACTTCAAGGATCTTAACGACTTAATCTTGATCACAAACAATTGAT
* * * * * * *
4681647 ATCTTCACTTCAAGGGTCTTGATGACTTGATTTTGATCACGAACACTTGAT
1 ATCTTCACTTCAAGGATCTTAACGACTTAATCTTGATCACAAACAATTGAT
4681698 ATCTT
1 ATCTT
4681703 GATCACAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (51 bp):
ATCTTCACTTCAAGGATCTTAACGACTTAATCTTGATCACAAACAATTGAT
Found at i:4681753 original size:17 final size:17
Alignment explanation
Indices: 4681700--4681754 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
4681690 CACTTGATAT
*
4681700 CTTGATCACAAACTTCG
1 CTTGATCACGAACTTCG
*
4681717 CTTGAT---G-ACTTAG
1 CTTGATCACGAACTTCG
4681730 TCTTGATCACGAACTTCG
1 -CTTGATCACGAACTTCG
4681748 CTTGATC
1 CTTGATC
4681755 TTCACTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
13 5 0.17
14 6 0.20
17 14 0.47
18 5 0.17
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (17 bp):
CTTGATCACGAACTTCG
Found at i:4682006 original size:30 final size:29
Alignment explanation
Indices: 4681944--4682063 Score: 99
Period size: 30 Copynumber: 4.2 Consensus size: 29
4681934 GGCATTAAAA
*
4681944 TGTAACAACAATATTTTTTCAACATAGTG
1 TGTAACAACAATATTTTTTCAACATAGCG
* * * *
4681973 TGTAATAATAATATTTTTTTTAATATAGCG
1 TGTAACAACAATA-TTTTTTCAACATAGCG
*
4682003 TGT---AAC-AT-GTTTTT-ATACATAGCG
1 TGTAACAACAATATTTTTTCA-ACATAGCG
* *
4682027 TGTAACAACAATATTTTTTTTATCATAGCG
1 TGTAACAACAATA-TTTTTTCAACATAGCG
4682057 TGTAACA
1 TGTAACA
4682064 TGTTTTTATA
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
23 1 0.01
24 15 0.21
26 2 0.03
27 5 0.07
28 2 0.03
29 11 0.15
30 35 0.49
31 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (29 bp):
TGTAACAACAATATTTTTTCAACATAGCG
Found at i:4682023 original size:54 final size:53
Alignment explanation
Indices: 4681965--4682117 Score: 184
Period size: 54 Copynumber: 2.8 Consensus size: 53
4681955 TATTTTTTCA
4681965 ACATAGTGTGTAATAATAATATTTTTTTTAATATAGCGTGTAACATGTTTTTAT
1 ACATAGTGTGTAA-AATAATATTTTTTTTAATATAGCGTGTAACATGTTTTTAT
* *
4682019 ACATAGCGTGTAACAACAATATTTTTTTT-ATCATAGCGTGTAACATGTTTTTAT
1 ACATAGTGTGTAA-AATAATATTTTTTTTAAT-ATAGCGTGTAACATGTTTTTAT
* * * * *
4682073 ACAT-GATGTGCAACATCAATATTTTTTTCAACATGGCGTGTAACA
1 ACATAG-TGTGTAAAAT-AATATTTTTTTTAATATAGCGTGTAACA
4682118 ACTTTTTTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 4 0.05
54 80 0.94
55 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (53 bp):
ACATAGTGTGTAAAATAATATTTTTTTTAATATAGCGTGTAACATGTTTTTAT
Found at i:4682036 original size:27 final size:24
Alignment explanation
Indices: 4681989--4682076 Score: 88
Period size: 24 Copynumber: 3.5 Consensus size: 24
4681979 AATAATATTT
*
4681989 TTTTTA-ATATAGCGTGTAACATG
1 TTTTTATACATAGCGTGTAACATG
*
4682012 TTTTTATACATAGCGTGTAACAACAATAT
1 TTTTTATACATAGCGTGT---AAC-AT-G
*
4682041 TTTTTTTATCATAGCGTGTAACATG
1 TTTTTATA-CATAGCGTGTAACATG
4682066 TTTTTATACAT
1 TTTTTATACAT
4682077 GATGTGCAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
23 6 0.11
24 13 0.25
25 7 0.13
26 2 0.04
27 6 0.11
28 2 0.04
29 7 0.13
30 10 0.19
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (24 bp):
TTTTTATACATAGCGTGTAACATG
Found at i:4682124 original size:54 final size:54
Alignment explanation
Indices: 4681982--4682117 Score: 193
Period size: 54 Copynumber: 2.5 Consensus size: 54
4681972 GTGTAATAAT
* *
4681982 AATATTTTTTTTAATATAGCGTGTAACATGTTTTTATACATAGCGTGTAACAAC
1 AATATTTTTTTTAACATAGCGTGTAACATGTTTTTATACATAGCGTGCAACAAC
* * *
4682036 AATATTTTTTTTATCATAGCGTGTAACATGTTTTTATACAT-GATGTGCAACATC
1 AATATTTTTTTTAACATAGCGTGTAACATGTTTTTATACATAG-CGTGCAACAAC
* *
4682090 AATATTTTTTTCAACATGGCGTGTAACA
1 AATATTTTTTTTAACATAGCGTGTAACA
4682118 ACTTTTTTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.01
54 72 0.99
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (54 bp):
AATATTTTTTTTAACATAGCGTGTAACATGTTTTTATACATAGCGTGCAACAAC
Found at i:4683052 original size:31 final size:31
Alignment explanation
Indices: 4683011--4683078 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
4683001 CTCTAAGGGT
*
4683011 CTTGACGACTT-GATCTTAATCACGAACTTCG
1 CTTGATGACTTAG-TCTTAATCACGAACTTCG
* * *
4683042 CTTGATGACTTAGTCTTGATCATGAACTTCT
1 CTTGATGACTTAGTCTTAATCACGAACTTCG
4683073 CTTGAT
1 CTTGAT
4683079 TTTCACTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
CTTGATGACTTAGTCTTAATCACGAACTTCG
Found at i:4683094 original size:83 final size:83
Alignment explanation
Indices: 4682948--4683120 Score: 197
Period size: 83 Copynumber: 2.1 Consensus size: 83
4682938 TTGTAACAAC
*
4682948 CACGAACTTCACTTGGTGACTTGATCTTGATCACAAACATCGCTTAATCTTCACTCTAAGGGTCT
1 CACGAACTTCACTTGATGACTTGATCTTGATCACAAACATCGCTTAATCTTCACTCTAAGGGTCT
* * *
4683013 TGACGACTTGATCTTAAT
66 TAACAACTTAATCTTAAT
* ** * * * * *
4683031 CACGAACTTCGCTTGATGACTT-AGTCTTGATCATGAACTTCTCTTGATTTTCACT-TCACGGGT
1 CACGAACTTCACTTGATGACTTGA-TCTTGATCACAAACATCGCTTAATCTTCACTCT-AAGGGT
*
4683094 CTTAACAACTTAATCTTGAT
64 CTTAACAACTTAATCTTAAT
4683114 CACGAAC
1 CACGAAC
4683121 ACTTAATATC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
82 2 0.03
83 73 0.97
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (83 bp):
CACGAACTTCACTTGATGACTTGATCTTGATCACAAACATCGCTTAATCTTCACTCTAAGGGTCT
TAACAACTTAATCTTAAT
Found at i:4683157 original size:105 final size:105
Alignment explanation
Indices: 4683023--4683237 Score: 265
Period size: 105 Copynumber: 2.0 Consensus size: 105
4683013 TGACGACTTG
* * * *
4683023 ATCTTAATCACGAACTTCGCTTGATGACTT-AGTCTTGATCATGAACTTC-TCTTGAT-TTTCAC
1 ATCTTAATCACGAACTTCACTTAATGACTTGA-TCTTGATCACGAACTTCGT-TTAATCTTT-AC
* * *
4683085 TTCACGGGTCTTAACAACTTAATCTTGATCACGAACACTTAAT
63 TTCAAGGGTCTTAACAACTTAATCTTAATCACAAACACTTAAT
* *
4683128 ATCTTGATCATGAACTTCACTTAATGACTTGATCTTGATCACGAACTTCGTTTAATCTTTACTTC
1 ATCTTAATCACGAACTTCACTTAATGACTTGATCTTGATCACGAACTTCGTTTAATCTTTACTTC
** *
4683193 AAGGGTCTTAATGACTTAATTTTAATCACAAACACTTAAT
66 AAGGGTCTTAACAACTTAATCTTAATCACAAACACTTAAT
*
4683233 CTCTT
1 ATCTT
4683238 CGCTTGAAGG
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
105 89 0.95
106 5 0.05
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (105 bp):
ATCTTAATCACGAACTTCACTTAATGACTTGATCTTGATCACGAACTTCGTTTAATCTTTACTTC
AAGGGTCTTAACAACTTAATCTTAATCACAAACACTTAAT
Found at i:4683285 original size:134 final size:134
Alignment explanation
Indices: 4683128--4683405 Score: 360
Period size: 134 Copynumber: 2.1 Consensus size: 134
4683118 AACACTTAAT
* * ** *
4683128 ATCTTGATCATGAACTTCACTTAATGACTT-GATCTTGATCACGAACTTCGTTTAATCTTTACTT
1 ATCTTGATCACGAACTTCACTTAATGACTTAG-TCTTAATCACGAACTTCACTTAATCTTCACTT
* * * * * *
4683192 CAAGGGTCTTAATGACTTAATTTTAATCACAAACACTTAATCTCTTCGCTTGAAGGGTCTTGATA
65 CAAGGGTCTTAACGACTTAATCTTAATCACAAACACTTAATATCTTCACTTCAAGGGTCTTGAAA
4683257 ACTTG
130 ACTTG
* ** * *
4683262 ATCTTGATTACGAACTTTGCTTAATGACTTAGTCTTAATCACGAATTTCACTTGATCTTCACTTC
1 ATCTTGATCACGAACTTCACTTAATGACTTAGTCTTAATCACGAACTTCACTTAATCTTCACTTC
* * * *
4683327 AAGTGTCTTAACGACTTAATCTTGATCACGAACACTTGATATCTTCACTTCAAGGGTCTTGAAAA
66 AAGGGTCTTAACGACTTAATCTTAATCACAAACACTTAATATCTTCACTTCAAGGGTCTTGAAAA
4683392 CTTG
131 CTTG
4683396 ATCTTGATCA
1 ATCTTGATCA
4683406 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
134 121 0.99
135 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (134 bp):
ATCTTGATCACGAACTTCACTTAATGACTTAGTCTTAATCACGAACTTCACTTAATCTTCACTTC
AAGGGTCTTAACGACTTAATCTTAATCACAAACACTTAATATCTTCACTTCAAGGGTCTTGAAAA
CTTG
Found at i:4683343 original size:52 final size:50
Alignment explanation
Indices: 4683281--4683386 Score: 133
Period size: 52 Copynumber: 2.1 Consensus size: 50
4683271 ACGAACTTTG
* * *
4683281 CTTAATGACTTAGTCTTAATCACGAATTTCACTTG-ATCTTCACTTCAAGTGT
1 CTTAACGACTTAATCTTAATCACGAA---CACTTGAATCTTCACTTCAAGGGT
*
4683333 CTTAACGACTTAATCTTGATCACGAACACTTGATATCTTCACTTCAAGGGT
1 CTTAACGACTTAATCTTAATCACGAACACTTGA-ATCTTCACTTCAAGGGT
4683384 CTT
1 CTT
4683387 GAAAACTTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
49 6 0.12
51 19 0.40
52 23 0.48
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (50 bp):
CTTAACGACTTAATCTTAATCACGAACACTTGAATCTTCACTTCAAGGGT
Found at i:4683386 original size:51 final size:49
Alignment explanation
Indices: 4683281--4683405 Score: 135
Period size: 51 Copynumber: 2.4 Consensus size: 49
4683271 ACGAACTTTG
* * *
4683281 CTTAATGACTTAGTCTTAATCACGAATTTCACTTGATCTTCACTTCAAGTGT
1 CTTAA-GACTTAATCTTGATCACGAA--TCACTTGATCTTCACTTCAAGGGT
4683333 CTTAACGACTTAATCTTGATCACGAA-CACTTGATATCTTCACTTCAAGGGT
1 CTTAA-GACTTAATCTTGATCACGAATCACTTG--ATCTTCACTTCAAGGGT
* *
4683384 CTTGAAAACTTGATCTTGATCA
1 CTT-AAGACTTAATCTTGATCA
4683406 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
49 6 0.09
51 33 0.52
52 25 0.39
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (49 bp):
CTTAAGACTTAATCTTGATCACGAATCACTTGATCTTCACTTCAAGGGT
Found at i:4683991 original size:18 final size:18
Alignment explanation
Indices: 4683970--4684008 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4683960 AAATGCTCTC
*
4683970 AATCTTCGAATGCCTCCA
1 AATCTTAGAATGCCTCCA
*
4683988 AATCTTAGAATGCTTCCA
1 AATCTTAGAATGCCTCCA
4684006 AAT
1 AAT
4684009 GAATCAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (18 bp):
AATCTTAGAATGCCTCCA
Found at i:4684519 original size:92 final size:92
Alignment explanation
Indices: 4684357--4684530 Score: 303
Period size: 92 Copynumber: 1.9 Consensus size: 92
4684347 AATTGGATGA
* *
4684357 TCAATAGTTAAATTTTGATTGGTCAAAACTATGAATATTATCCCTAAACTACCTTGATTTATTTA
1 TCAATAATTAAATTTTGATTGGTCAAAAATATGAATATTATCCCTAAACTACCTTGATTTATTTA
* *
4684422 GAGATAAATTGGATGATCAAAATTTAT
66 AAGATAAATTAGATGATCAAAATTTAT
*
4684449 TCAATAATTAAATTTTGATTGGTCAAAAATATGAATATTATCCCTAAATTACCTTGATTTATTTA
1 TCAATAATTAAATTTTGATTGGTCAAAAATATGAATATTATCCCTAAACTACCTTGATTTATTTA
4684514 AAGATAAATTAGATGAT
66 AAGATAAATTAGATGAT
4684531 TAATAATTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 77 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (92 bp):
TCAATAATTAAATTTTGATTGGTCAAAAATATGAATATTATCCCTAAACTACCTTGATTTATTTA
AAGATAAATTAGATGATCAAAATTTAT
Found at i:4690409 original size:17 final size:18
Alignment explanation
Indices: 4690384--4690417 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4690374 ATGGATAACT
4690384 TTTAGTTTAT-TTATAAA
1 TTTAGTTTATATTATAAA
*
4690401 TTTATTTTATATTATAA
1 TTTAGTTTATATTATAA
4690418 TATATATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTAGTTTATATTATAAA
Found at i:4697582 original size:17 final size:18
Alignment explanation
Indices: 4697551--4697584 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4697541 TAGGCAAAAC
4697551 ATTGATTCTTATATTCTA
1 ATTGATTCTTATATTCTA
*
4697569 ATTG-TTCTTGTATTCT
1 ATTGATTCTTATATTCT
4697585 TTTTTAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (18 bp):
ATTGATTCTTATATTCTA
Found at i:4700102 original size:20 final size:20
Alignment explanation
Indices: 4700059--4700158 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
4700049 AGGTTTGATG
*
4700059 AATATTAATATTTAACCTT-G
1 AATATTAATATTTAA-CTTAA
*
4700079 AATATTAATATTTAATTTAA
1 AATATTAATATTTAACTTAA
*
4700099 AATATT--T-TTTAA--AAA
1 AATATTAATATTTAACTTAA
*
4700114 AATATTACTATTTAACTT-A
1 AATATTAATATTTAACTTAA
4700133 AA-A-T--T-TTTAACTTAA
1 AATATTAATATTTAACTTAA
4700148 AATATTAATAT
1 AATATTAATAT
4700159 GTAAATTGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
14 8 0.12
15 12 0.19
16 1 0.02
17 8 0.12
18 7 0.11
19 6 0.09
20 22 0.34
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (20 bp):
AATATTAATATTTAACTTAA
Found at i:4700143 original size:14 final size:14
Alignment explanation
Indices: 4700124--4700150 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4700114 AATATTACTA
4700124 TTTAACTTAAAATT
1 TTTAACTTAAAATT
4700138 TTTAACTTAAAAT
1 TTTAACTTAAAAT
4700151 ATTAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTAACTTAAAATT
Found at i:4703820 original size:2 final size:2
Alignment explanation
Indices: 4703813--4703846 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4703803 ACTACAAGCT
4703813 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
4703847 ATTTCAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4718208 original size:15 final size:15
Alignment explanation
Indices: 4718180--4718220 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
4718170 TTTACAATGC
*
4718180 AATGTGATTACAAGT
1 AATGTGATTGCAAGT
*
4718195 AATGTAATTGCAAGT
1 AATGTGATTGCAAGT
4718210 AATGTGATTGC
1 AATGTGATTGC
4718221 CAGCAATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:4727203 original size:40 final size:40
Alignment explanation
Indices: 4727128--4727206 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
4727118 ATGACCATTT
* *
4727128 TTCACCTTATTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
* * * *
4727168 TTCATCTTAGTGGGGTTTTTAACCTCGTCATGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTG
4727207 CTTTTCACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:4737860 original size:22 final size:25
Alignment explanation
Indices: 4737835--4737888 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
4737825 AATACATGTT
*
4737835 ATAATATTGAT-T-TATAA-AAATA
1 ATAATATTCATATCTATAATAAATA
*
4737857 ATAAAATTCATATCTATAATAAATA
1 ATAATATTCATATCTATAATAAATA
*
4737882 GTAATAT
1 ATAATAT
4737889 ATTATAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 9 0.36
23 1 0.04
24 5 0.20
25 10 0.40
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (25 bp):
ATAATATTCATATCTATAATAAATA
Found at i:4738967 original size:22 final size:22
Alignment explanation
Indices: 4738941--4738984 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4738931 TTTTAAAATT
4738941 TGGGTTTACTCTATCAAGAAAA
1 TGGGTTTACTCTATCAAGAAAA
*
4738963 TGGGTTTCCTCTATCAAGAAAA
1 TGGGTTTACTCTATCAAGAAAA
4738985 AAAATAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (22 bp):
TGGGTTTACTCTATCAAGAAAA
Found at i:4743692 original size:40 final size:40
Alignment explanation
Indices: 4743613--4743693 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
4743603 TTTGTTCAAT
**
4743613 TTAGCACCATTAATTAAGTAATTATTCGAGATTGGTAATG
1 TTAGCACCATTAATTAAGTAATTATTCGAGATTCATAATG
* *
4743653 TTAGTACCATTAATTAAGTAATTATTTGAGATTCATAATG
1 TTAGCACCATTAATTAAGTAATTATTCGAGATTCATAATG
4743693 T
1 T
4743694 GGCTATATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.41
Consensus pattern (40 bp):
TTAGCACCATTAATTAAGTAATTATTCGAGATTCATAATG
Found at i:4745332 original size:38 final size:38
Alignment explanation
Indices: 4745276--4745350 Score: 87
Period size: 38 Copynumber: 2.0 Consensus size: 38
4745266 CCATTTGTCC
*
4745276 AAAAATAATTAATACATCATAAACATTTAAATAATCAA
1 AAAAATAATTAATACATCAAAAACATTTAAATAATCAA
* * * * * *
4745314 AAAAATAGTTAGTCCATCAAAAAGATTTCAGTAATCA
1 AAAAATAATTAATACATCAAAAACATTTAAATAATCA
4745351 CTTTGTCATC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (38 bp):
AAAAATAATTAATACATCAAAAACATTTAAATAATCAA
Found at i:4746847 original size:21 final size:21
Alignment explanation
Indices: 4746823--4746862 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4746813 CATCGGTAAA
*
4746823 ACTTGTTATTCAAGCGATCTT
1 ACTTGTTATACAAGCGATCTT
*
4746844 ACTTGTTGTACAAGCGATC
1 ACTTGTTATACAAGCGATC
4746863 ACTTCTCAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (21 bp):
ACTTGTTATACAAGCGATCTT
Found at i:4753001 original size:3 final size:3
Alignment explanation
Indices: 4752993--4753017 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4752983 AATTTTTAAT
4752993 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
4753018 ATGTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4753058 original size:11 final size:11
Alignment explanation
Indices: 4753033--4753068 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
4753023 TAAAATTTGA
4753033 TATAATTATTTT
1 TATAATTA-TTT
4753045 TATAATTATTT
1 TATAATTATTT
4753056 TATAATTATTT
1 TATAATTATTT
4753067 TA
1 TA
4753069 ATATAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATAATTATTT
Found at i:4753096 original size:24 final size:24
Alignment explanation
Indices: 4753021--4753099 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 24
4753011 TTATTATATG
4753021 TATAAAATTTGATATAATTATTTT--
1 TATAAAATTT--TATAATTATTTTAA
*
4753045 TATAATTATTTTATAATTATTTTAA
1 TATAA-AATTTTATAATTATTTTAA
4753070 TATAAAATTTTA-AATTCATTATTATA
1 TATAAAATTTTATAATT-ATT-TTA-A
4753096 TATA
1 TATA
4753100 TATTTAAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
23 16 0.34
24 14 0.30
25 12 0.26
26 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
TATAAAATTTTATAATTATTTTAA
Found at i:4753393 original size:14 final size:14
Alignment explanation
Indices: 4753351--4753394 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
4753341 TTGACTCAAT
* *
4753351 TTTAAATTTTTTTA
1 TTTATATTTATTTA
4753365 TTTATA-TTA-TTA
1 TTTATATTTATTTA
4753377 TTTATATTTATTTA
1 TTTATATTTATTTA
4753391 TTTA
1 TTTA
4753395 CATGTTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.35
13 5 0.19
14 12 0.46
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATATTTATTTA
Found at i:4772509 original size:23 final size:23
Alignment explanation
Indices: 4772440--4772510 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 23
4772430 AAATTCTATG
*
4772440 TAATTAATTATATTA-ATAAAATT
1 TAATT-ATTATATTATTTAAAATT
* * **
4772463 ATTATT-TTTTAATTATTTTTAATT
1 -TAATTATTAT-ATTATTTAAAATT
4772487 TAATTATTATATTATTTAAAATT
1 TAATTATTATATTATTTAAAATT
4772510 T
1 T
4772511 TTTTTAAATT
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
22 3 0.09
23 20 0.57
24 12 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATTATTATATTATTTAAAATT
Found at i:4772520 original size:29 final size:29
Alignment explanation
Indices: 4772458--4772520 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
4772448 TATATTAATA
*
4772458 AAATTATTATTTTTTAATTATTTTTAATTT
1 AAATTATTATTTTTTAATAATTTTT-ATTT
4772488 -AATTATTATATTATTTAA-AATTTTT-TTT
1 AAATTATTAT-TT-TTTAATAATTTTTATTT
4772516 AAATT
1 AAATT
4772521 CGTCCTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
28 3 0.10
29 13 0.45
30 8 0.28
31 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
AAATTATTATTTTTTAATAATTTTTATTT
Found at i:4775491 original size:2 final size:2
Alignment explanation
Indices: 4775484--4775515 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4775474 TATTCTCTTC
4775484 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
4775516 TAAAAACGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4776253 original size:2 final size:2
Alignment explanation
Indices: 4776246--4776288 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
4776236 GTTCTCATAA
* *
4776246 CT CT CT CT CT CT CT CT CT CT CT CT CG CT CT CT CT -T TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4776287 CT
1 CT
4776289 TTTTCTGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
CT
Found at i:4776714 original size:3 final size:3
Alignment explanation
Indices: 4776706--4776746 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4776696 CAATGGCGAG
4776706 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4776747 GCAAGGTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4786676 original size:10 final size:10
Alignment explanation
Indices: 4786642--4786675 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
4786632 TTAGAGTGTC
4786642 GTTTCGGTCG
1 GTTTCGGTCG
4786652 GTTTCGGTCG
1 GTTTCGGTCG
*
4786662 GTTTTGGTCG
1 GTTTCGGTCG
4786672 GTTT
1 GTTT
4786676 TTTATGATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.15, G:0.38, T:0.47
Consensus pattern (10 bp):
GTTTCGGTCG
Found at i:4786789 original size:30 final size:31
Alignment explanation
Indices: 4786740--4786812 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
4786730 GCCACAGGCC
*
4786740 GGCA-GGGG-ATC-GGAGCTCGTGGGAGGGG
1 GGCAGGGGGAATCGGGAGCTCGTGGGAAGGG
4786768 GGCAGGGGGAATCGGGA-CTCGTGGGAAGGG
1 GGCAGGGGGAATCGGGAGCTCGTGGGAAGGG
* *
4786798 GCCGGGGGGAATCGG
1 GGCAGGGGGAATCGG
4786813 TAGATGGGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 4 0.10
29 4 0.10
30 28 0.72
31 3 0.08
ACGTcount: A:0.16, C:0.15, G:0.59, T:0.10
Consensus pattern (31 bp):
GGCAGGGGGAATCGGGAGCTCGTGGGAAGGG
Found at i:4804165 original size:30 final size:27
Alignment explanation
Indices: 4804100--4804162 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
4804090 AACAGCCCTC
4804100 AGAAGAAGACCCAAATGAAGGATCAGA
1 AGAAGAAGACCCAAATGAAGGATCAGA
4804127 AGAAGAAGACCCAAATGAAGGATCAGA
1 AGAAGAAGACCCAAATGAAGGATCAGA
*
4804154 GGAAGAAGA
1 AGAAGAAGA
4804163 AGAAGAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.52, C:0.13, G:0.29, T:0.06
Consensus pattern (27 bp):
AGAAGAAGACCCAAATGAAGGATCAGA
Found at i:4804173 original size:27 final size:27
Alignment explanation
Indices: 4804100--4804175 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
4804090 AACAGCCCTC
* *
4804100 AGAAGAAGACCCAAATGAAGGATCAGA
1 AGAAGAAGACACAAAAGAAGGATCAGA
* *
4804127 AGAAGAAGACCCAAATGAAGGATCAGA
1 AGAAGAAGACACAAAAGAAGGATCAGA
* *
4804154 GGAAGAAGA-AGAAGAAGAAGGA
1 AGAAGAAGACACAA-AAGAAGGA
4804176 GAGTGTGGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 2 0.05
27 42 0.95
ACGTcount: A:0.54, C:0.11, G:0.30, T:0.05
Consensus pattern (27 bp):
AGAAGAAGACACAAAAGAAGGATCAGA
Found at i:4822670 original size:20 final size:20
Alignment explanation
Indices: 4822645--4822682 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4822635 AATATTTTAT
* *
4822645 AATATTATAATTAAAATAAA
1 AATATTAAAATAAAAATAAA
4822665 AATATTAAAATAAAAATA
1 AATATTAAAATAAAAATA
4822683 TTAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATTAAAATAAAAATAAA
Found at i:4822688 original size:13 final size:14
Alignment explanation
Indices: 4822654--4822697 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
4822644 TAATATTATA
4822654 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
4822668 ATTAAAATAAAAAT
1 ATTAAAATAAAAAT
4822682 ATT-AAATAAAATAT
1 ATTAAAATAAAA-AT
4822696 AT
1 AT
4822698 AATATAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.28
14 21 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATTAAAATAAAAAT
Found at i:4822797 original size:29 final size:28
Alignment explanation
Indices: 4822762--4822955 Score: 82
Period size: 29 Copynumber: 6.8 Consensus size: 28
4822752 AGGTAAAACA
4822762 ATTT-AAATAAAATATATAATATAAAAAAT
1 ATTTAAAATAAAATA-A-AATATAAAAAAT
*
4822791 ATTTAAAAATAAAATAAAATATATAAAAT
1 ATTT-AAAATAAAATAAAATATAAAAAAT
* *
4822820 -TATAATAAT-AAATAAAATA-AAATATAT
1 ATTTAA-AATAAAATAAAATATAAA-AAAT
** * * *
4822847 GATATTAAAATATATTTAAAATATGATATAT
1 -AT-TTAAAATA-AAATAAAATATAAAAAAT
* *
4822878 ATATAAAATTAATAATATAAATAT-AAATAT
1 ATTTAAAA-TAA-AATA-AAATATAAAAAAT
* * *
4822908 A-TTAAAAAATAAATATAAATAT-TATAAT
1 ATTTAAAATA-AAATA-AAATATAAAAAAT
*
4822936 A-AT-AAATAAAATAAAATATA
1 ATTTAAAATAAAATAAAATATA
4822956 TGACATTATA
Statistics
Matches: 130, Mismatches: 20, Indels: 33
0.71 0.11 0.18
Matches are distributed among these distances:
25 6 0.05
26 7 0.05
27 19 0.15
28 22 0.17
29 31 0.24
30 16 0.12
31 28 0.22
32 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (28 bp):
ATTTAAAATAAAATAAAATATAAAAAAT
Found at i:4822804 original size:31 final size:32
Alignment explanation
Indices: 4822765--4822846 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 32
4822755 TAAAACAATT
*
4822765 TAAATAAAATATATAATATA-AAAAATAT-TTAA
1 TAAATAAAATA-A-AATATATAAAAATATAATAA
*
4822797 -AAATAAAATAAAATATATAAAATTATAATAA
1 TAAATAAAATAAAATATATAAAAATATAATAA
4822828 TAAATAAAATAAAATATAT
1 TAAATAAAATAAAATATAT
4822847 GATATTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 6 0.13
30 8 0.18
31 13 0.29
32 18 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (32 bp):
TAAATAAAATAAAATATATAAAAATATAATAA
Found at i:4822824 original size:22 final size:22
Alignment explanation
Indices: 4822768--4822970 Score: 73
Period size: 22 Copynumber: 8.7 Consensus size: 22
4822758 AACAATTTAA
*
4822768 ATAAAATATATAATATAAAAAATAT
1 ATAAAAT-TATAA-A-ATAAAATAT
*
4822793 TTAAAA--ATAAAATAAAATAT
1 ATAAAATTATAAAATAAAATAT
*
4822813 ATAAAATTATAATAAT-AAATAAA
1 ATAAAATTATAA-AATAAAAT-AT
* *
4822836 ATAAAATATATGATATTAAAATAT
1 ATAAAAT-TAT-AAAATAAAATAT
4822860 ATTTAAAATATGATATATATATAAAAT-T
1 A--TAAAAT-T-ATA-A-A-ATAAAATAT
*
4822888 A-ATAA-TAT-AAATATAAATAT
1 ATAAAATTATAAAATA-AAATAT
*
4822908 ATTAAAA-AAT-AAATATAAATATT
1 A-TAAAATTATAAAATA-AAATA-T
*
4822931 ATAATAATAAATAAAATAAAATAT
1 ATAA-AAT-TATAAAATAAAATAT
* *
4822955 ATGACATTATAAAATA
1 ATAAAATTATAAAATA
4822971 TATTTAAGAA
Statistics
Matches: 141, Mismatches: 15, Indels: 47
0.69 0.07 0.23
Matches are distributed among these distances:
18 3 0.02
19 5 0.04
20 16 0.11
21 1 0.01
22 41 0.29
23 18 0.13
24 11 0.08
25 21 0.15
26 14 0.10
27 2 0.01
28 3 0.02
29 6 0.04
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (22 bp):
ATAAAATTATAAAATAAAATAT
Found at i:4822835 original size:63 final size:63
Alignment explanation
Indices: 4822765--4822909 Score: 161
Period size: 67 Copynumber: 2.2 Consensus size: 63
4822755 TAAAACAATT
4822765 TAAATAAAATATATA-ATA-TAAAAAATATTTAAAAATAAAATAAAATATATAAAATT-ATAATA
1 TAAATAAAATATATAGATATTAAAAAATATTT-AAAATAAAAT-AAATATATAAAATTAATAAT-
4822827 A
63 A
* ** *
4822828 TAAATAAAATAAAATATATGATATTAAAATATATTTAAAATATGATATATATATAAAATTAATAA
1 TAAATAAAAT---ATATA-GATATTAAAAAATATTTAAAATAAAATAAATATATAAAATTAATAA
4822893 TA
62 TA
4822895 TAAATATAAATATAT
1 TAAATA-AAATATAT
4822910 TAAAAAATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
63 10 0.14
65 4 0.06
66 5 0.07
67 20 0.29
68 20 0.29
69 11 0.16
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (63 bp):
TAAATAAAATATATAGATATTAAAAAATATTTAAAATAAAATAAATATATAAAATTAATAATA
Found at i:4822838 original size:9 final size:9
Alignment explanation
Indices: 4822765--4822840 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 9
4822755 TAAAACAATT
4822765 TAAATAAAA
1 TAAATAAAA
* *
4822774 TATATAATA
1 TAAATAAAA
4822783 T-AA-AAAA
1 TAAATAAAA
**
4822790 TATTTAAAAA
1 TAAAT-AAAA
4822800 TAAAATAAAA
1 T-AAATAAAA
*
4822810 TATATAAAA
1 TAAATAAAA
*
4822819 T-TATAATAA
1 TAAATAA-AA
4822828 TAAATAAAA
1 TAAATAAAA
4822837 TAAA
1 TAAA
4822841 ATATATGATA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
7 4 0.08
8 6 0.12
9 25 0.49
10 14 0.27
11 2 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
TAAATAAAA
Found at i:4822861 original size:10 final size:10
Alignment explanation
Indices: 4822767--4823064 Score: 94
Period size: 10 Copynumber: 30.1 Consensus size: 10
4822757 AAACAATTTA
4822767 AATAAAATAT
1 AATAAAATAT
4822777 -AT--AATAT
1 AATAAAATAT
4822784 AA-AAAATAT
1 AATAAAATAT
* *
4822793 -TTAAAAATAA
1 AAT-AAAATAT
4822803 AATAAAATAT
1 AATAAAATAT
4822813 -ATAAAAT-T
1 AATAAAATAT
4822821 -ATAATAATA-
1 AATAA-AATAT
*
4822830 AATAAAATAA
1 AATAAAATAT
*
4822840 AAT-ATATGAT
1 AATAAAAT-AT
*
4822850 ATTAAAATAT
1 AATAAAATAT
*
4822860 ATTTAAAATAT
1 A-ATAAAATAT
* *
4822871 GAT-ATATAT
1 AATAAAATAT
4822880 -ATAAAAT-T
1 AATAAAATAT
*
4822888 AATAATATA-
1 AATAAAATAT
4822897 AATATAAATAT
1 AATA-AAATAT
* *
4822908 ATTAAAAAAT
1 AATAAAATAT
4822918 AAATATAAATAT
1 -AATA-AAATAT
*
4822930 TATAATAATA-
1 AATAA-AATAT
*
4822940 AATAAAATAA
1 AATAAAATAT
* *
4822950 AATATATGACAT
1 AATA-A-AATAT
*
4822962 TATAAAATAT
1 AATAAAATAT
*
4822972 ATTTAAGAA-AT
1 A-ATAA-AATAT
* **
4822983 GATATTATAT
1 AATAAAATAT
*
4822993 AA-AAATTAAT
1 AATAAAAT-AT
4823003 AATAAAATAT
1 AATAAAATAT
* * *
4823013 AAATATATTAA
1 -AATAAAATAT
4823024 AATAAAATAT
1 AATAAAATAT
*
4823034 -ATAAATTAT
1 AATAAAATAT
4823043 AATATAAAT-T
1 AATA-AAATAT
4823053 AAATAAAATAT
1 -AATAAAATAT
4823064 A
1 A
4823065 TGATATTAAA
Statistics
Matches: 209, Mismatches: 45, Indels: 68
0.65 0.14 0.21
Matches are distributed among these distances:
7 5 0.02
8 9 0.04
9 57 0.27
10 74 0.35
11 52 0.25
12 12 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
AATAAAATAT
Found at i:4822868 original size:68 final size:68
Alignment explanation
Indices: 4822765--4823125 Score: 193
Period size: 68 Copynumber: 5.1 Consensus size: 68
4822755 TAAAACAATT
4822765 TAAATAAAATATATAATATAAAAAATATTTAAAAATAAAATAAAATATATAAAATT-ATAATAAT
1 TAAATAAAATATATAATATAAAAAATATTTAAAAATAAAAT-AAATATATAAAATTAATAAT-AT
4822829 AAATA
64 AAATA
* * ** *
4822834 -AAATAAAATATATGATATTAAAATATATTT-AAAATATGATATATATATAAAATTAATAATATA
1 TAAATAAAATATATAATA-TAAAAAATATTTAAAAATAAAATAAATATATAAAATTAATAATATA
4822897 AATA
65 AATA
* * * * * * *
4822901 TAAATATATTAAAAAATAAATATAAATATTATAATAATAAATAAAATAAAATATATGACATT-AT
1 TAAATA-A--AATATAT-AATATAAAAAATAT-TTAA-AAATAAAAT-AAATATATAAAATTAAT
* *
4822965 AAAATATAT-
59 AATATAAATA
* * * * * * * *
4822974 TTAA-GAAATGATATTATATAAAAATTAATAATAAAATATAAATATATTAAAATAAAA-TATATA
1 TAAATAAAAT-ATATAATATAAAAAATATTTA-AAAATA-AAATA-AAT-ATATAAAATTA-AT-
4823037 AATTATAATATAAA
59 AA-TATAA-AT--A
* ** *
4823051 TTAAATAAAATATATGATATTAAAAATATATTT-AAAATATGAT-ATTATATAAAAATTAAT-AT
1 -TAAATAAAATATATAATA-TAAAAA-ATATTTAAAAATAAAATAAATATAT-AAAATTAATAAT
4823113 ATAAATA
62 ATAAATA
4823120 TAAATA
1 TAAATA
4823126 TATTAAAAAT
Statistics
Matches: 219, Mismatches: 43, Indels: 61
0.68 0.13 0.19
Matches are distributed among these distances:
67 20 0.09
68 47 0.21
69 34 0.16
70 8 0.04
71 17 0.08
72 11 0.05
73 8 0.04
74 21 0.10
75 20 0.09
76 2 0.01
77 2 0.01
78 16 0.07
79 10 0.05
80 3 0.01
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (68 bp):
TAAATAAAATATATAATATAAAAAATATTTAAAAATAAAATAAATATATAAAATTAATAATATAA
ATA
Found at i:4822889 original size:24 final size:24
Alignment explanation
Indices: 4822814--4822928 Score: 78
Period size: 24 Copynumber: 4.8 Consensus size: 24
4822804 ATAAAATATA
*
4822814 TAAAATTATAATA-ATAAATAAAAT
1 TAAAA-TATGATATATAAATAAAAT
* * *
4822838 AAAATATATGATAT-TAAAATATATT
1 TAAA-ATATGATATAT-AAATAAAAT
*
4822863 TAAAATATGATATATATATAAAAT
1 TAAAATATGATATATAAATAAAAT
* *
4822887 TAATAATAT-AAATATAAAT-ATAT
1 TAA-AATATGATATATAAATAAAAT
* *
4822910 TAAAAAAT-AAATATAAATA
1 TAAAATATGATATATAAATA
4822929 TTATAATAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
22 14 0.19
23 6 0.08
24 36 0.49
25 17 0.23
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAAATATGATATATAAATAAAAT
Found at i:4823026 original size:79 final size:76
Alignment explanation
Indices: 4822896--4823243 Score: 241
Period size: 78 Copynumber: 4.6 Consensus size: 76
4822886 TTAATAATAT
* * *
4822896 AAATATAAATATATTAAAAAATA-AATATAAATATTATAATAATAAATAAAATAAAATATATGAC
1 AAATAT-ATTATA-TAAAAATTATAATA-AAATA-TATAAT-AT-ATTAAAATAAAATATAT-A-
4822960 ATTATAAAATATATTTAAG
58 ATTATAAAATATATTTAAG
4822979 AAATGATATTATATAAAAATTAATAATAAAATATA-AATATATTAAAATAAAATATATAAATTAT
1 AAAT-ATATTATATAAAAATT-ATAATAAAATATATAATATATTAAAATAAAATATAT-AATTAT
* * * *
4823043 AATATAAATTAAATA
63 AAAATATATTTAA-G
* * * * * *
4823058 AAATATATGATATTAAAAA-TATATTTAAAATATGATATTATATAAAAAT-TAATATATAAATAT
1 AAATATATTATA-TAAAAATTATA-ATAAAATAT-ATAATATATTAAAATAAAATATATAATTAT
4823121 -AAATATA-TTAA-
63 AAAATATATTTAAG
* *
4823132 AAATA-A-AATAT-AAAA-TAT--TATAATA-ATAA-ATA--AAAATAAAATATATGATATTA-A
1 AAATATATTATATAAAAATTATAATAAAATATATAATATATTAAAATAAAATATAT-A-ATTATA
4823186 AAATATATTT-AG
64 AAATATATTTAAG
*
4823198 AAATGATATTATAT-AAAATTAATAATAAAAAATATAATATATTAAA
1 AAAT-ATATTATATAAAAATT-ATAATAAAATATATAATATATTAAA
4823244 CTTATATTTT
Statistics
Matches: 215, Mismatches: 25, Indels: 56
0.73 0.08 0.19
Matches are distributed among these distances:
62 5 0.02
63 7 0.03
64 4 0.02
65 14 0.07
66 6 0.03
67 7 0.03
68 1 0.00
69 8 0.04
70 8 0.04
71 3 0.01
72 3 0.01
73 6 0.03
74 9 0.04
75 3 0.01
76 3 0.01
77 11 0.05
78 36 0.17
79 35 0.16
80 13 0.06
81 3 0.01
82 9 0.04
83 15 0.07
84 6 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (76 bp):
AAATATATTATATAAAAATTATAATAAAATATATAATATATTAAAATAAAATATATAATTATAAA
ATATATTTAAG
Found at i:4823032 original size:110 final size:111
Alignment explanation
Indices: 4822800--4823243 Score: 685
Period size: 110 Copynumber: 4.0 Consensus size: 111
4822790 TATTTAAAAA
*
4822800 TAAAATAAAATATATAAAATTATAATAATAAATAAAATAAAATATATGATATT-AAAATATATTT
1 TAAAATAAAATATATAATATTATAATAATAAATAAAATAAAATATATGATATTAAAAATATATTT
4822864 AAAATATGATA-TATATATAAAATTAATAATATAAATATAAATATAT
66 AAAATATGATATTATATA-AAAATTAATAATATAAATATAAATATAT
* *
4822910 TAAAAAATAAATATA-AATATTATAATAATAAATAAAATAAAATATATGACATTATAAAATATAT
1 TAAAATA-AAATATATAATATTATAATAATAAATAAAATAAAATATATGATATTA-AAAATATAT
4822974 TTAAGAA-ATGATATTATATAAAAATTAATAATA-AAATATAAATATAT
64 TTAA-AATATGATATTATATAAAAATTAATAATATAAATATAAATATAT
*
4823021 TAAAATAAAATATATAA-ATTATAAT-ATAAATTAAATAAAATATATGATATTAAAAATATATTT
1 TAAAATAAAATATATAATATTATAATAATAAATAAAATAAAATATATGATATTAAAAATATATTT
4823084 AAAATATGATATTATATAAAAATTAAT-ATATAAATATAAATATAT
66 AAAATATGATATTATATAAAAATTAATAATATAAATATAAATATAT
*
4823129 TAAAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATAT
1 T-AAAATAAAATATATAATATTATAATAATAAAT-AAAATAAAATATATGATATTAAAAATATAT
* *
4823194 TTAGAA-ATGATATTATAT-AAAATTAATAATA-AAAAATATAATATAT
64 TTAAAATATGATATTATATAAAAATTAATAATATAAATATA-AATATAT
4823240 TAAA
1 TAAA
4823244 CTTATATTTT
Statistics
Matches: 310, Mismatches: 10, Indels: 28
0.89 0.03 0.08
Matches are distributed among these distances:
107 5 0.02
108 50 0.16
109 40 0.13
110 83 0.27
111 58 0.19
112 66 0.21
113 8 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (111 bp):
TAAAATAAAATATATAATATTATAATAATAAATAAAATAAAATATATGATATTAAAAATATATTT
AAAATATGATATTATATAAAAATTAATAATATAAATATAAATATAT
Found at i:4823086 original size:62 final size:58
Alignment explanation
Indices: 4823013--4823239 Score: 173
Period size: 54 Copynumber: 3.9 Consensus size: 58
4823003 AATAAAATAT
4823013 AAATATATTAAAATAAAATATATAAATTATAATATAAATTAAATAAAATATATGATATTAA
1 AAATATATTAAAATAAAATAT-TAAATTATAATATAAA--AAATAAAATATATGATATTAA
** * * * * * *
4823074 AAATATATTTAAAATATGATATTATATAAAAAT-TAATATATAAATATAAAT-ATATTAA
1 AAATATA-TTAAAATAAAATATTAAATTATAATATAAAAAATAAA-ATATATGATATTAA
* *
4823132 AAATA-A--AATATAAAATATTATAATAATAA-AT-AAAAATAAAATATATGATATTAA
1 AAATATATTAAAATAAAATATTA-AATTATAATATAAAAAATAAAATATATGATATTAA
* * * *
4823186 AAATATATTTAGAAATGATATTATATAAAAT-TAATAATAAAAAATATAATATAT
1 AAATATA-TTA-AAAT-AAAATAT-TAAATTATAAT-ATAAAAAATAAAATATAT
4823240 TAAACTTATA
Statistics
Matches: 129, Mismatches: 22, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
53 5 0.04
54 30 0.23
55 8 0.06
57 1 0.01
58 19 0.15
59 11 0.09
60 10 0.08
61 19 0.15
62 26 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (58 bp):
AAATATATTAAAATAAAATATTAAATTATAATATAAAAAATAAAATATATGATATTAA
Found at i:4823129 original size:219 final size:221
Alignment explanation
Indices: 4822800--4823243 Score: 751
Period size: 219 Copynumber: 2.0 Consensus size: 221
4822790 TATTTAAAAA
4822800 TAAAATAAAATATATAAAATTATAATAATAAATAAAATAAAATATATGATATTAAAATATATTTA
1 TAAAATAAAATATATAAAATTATAATAATAAATAAAATAAAATATATGATATTAAAATATATTTA
4822865 AAATATGATATATATATAAAATTAATAATATAAATATAAATATATTAAAAA-ATAAATAT-AAAT
66 AAATATGATATATATATAAAATTAATAATATAAATATAAATATATTAAAAATA-AAATATAAAAT
4822928 ATTATAATAATAAAT-AAAATAAAATATATGACATTATAAAATATATTTAAGAAATGATATTATA
130 ATTATAATAATAAATAAAAATAAAATATATGACATTA-AAAATATATTT-AGAAATGATATTATA
*
4822992 TAAAAATTAATAATAAAATATA-AATATAT
193 T-AAAATTAATAATAAAAAATATAATATAT
*
4823021 TAAAATAAAATATAT-AAATTATAAT-ATAAATTAAATAAAATATATGATATTAAAAATATATTT
1 TAAAATAAAATATATAAAATTATAATAATAAATAAAATAAAATATATGATATT-AAAATATATTT
4823084 AAAATATGATAT-TATATAAAAATTAAT-ATATAAATATAAATATATTAAAAATAAAATATAAAA
65 AAAATATGATATATATAT-AAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAA
*
4823147 TATTATAATAATAAATAAAAATAAAATATATGATATTAAAAATATATTTAGAAATGATATTATAT
129 TATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAGAAATGATATTATAT
4823212 AAAATTAATAATAAAAAATATAATATAT
194 AAAATTAATAATAAAAAATATAATATAT
4823240 TAAA
1 TAAA
4823244 CTTATATTTT
Statistics
Matches: 214, Mismatches: 3, Indels: 14
0.93 0.01 0.06
Matches are distributed among these distances:
218 19 0.09
219 87 0.41
220 73 0.34
221 35 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (221 bp):
TAAAATAAAATATATAAAATTATAATAATAAATAAAATAAAATATATGATATTAAAATATATTTA
AAATATGATATATATATAAAATTAATAATATAAATATAAATATATTAAAAATAAAATATAAAATA
TTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAGAAATGATATTATATAA
AATTAATAATAAAAAATATAATATAT
Found at i:4823231 original size:57 final size:56
Alignment explanation
Indices: 4823057--4823252 Score: 195
Period size: 57 Copynumber: 3.5 Consensus size: 56
4823047 TAAATTAAAT
4823057 AAAATATATGATATTAAAAATATATTTAAAATATGATATTATATAAAAATTAAT-ATATA
1 AAAATATAT-ATATTAAAAATATATTTAAAA-ATGATATTATAT-AAAATTAATAATA-A
* * ** * * * *
4823116 AATATAAATATATTAAAAATA-AAATATAAA--ATATTATA-ATAATAAATAAAAA
1 AAAATATATATATTAAAAATATATTTAAAAATGATATTATATAAAATTAATAATAA
*
4823168 TAAAATATATGATATTAAAAATATATTTAGAAATGATATTATATAAAATTAATAATAA
1 -AAAATATAT-ATATTAAAAATATATTTAAAAATGATATTATATAAAATTAATAATAA
**
4823226 AAAATATAATATATTAAACTTATATTT
1 AAAATAT-ATATATTAAAAATATATTT
4823253 TAATAATTAG
Statistics
Matches: 111, Mismatches: 18, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
52 8 0.07
53 9 0.08
54 20 0.18
55 6 0.05
56 1 0.01
57 35 0.32
58 25 0.23
59 7 0.06
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.37
Consensus pattern (56 bp):
AAAATATATATATTAAAAATATATTTAAAAATGATATTATATAAAATTAATAATAA
Found at i:4823412 original size:15 final size:15
Alignment explanation
Indices: 4823387--4823432 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
4823377 TGTTATTTTC
*
4823387 CCTGTAATCACATTG
1 CCTGCAATCACATTG
* *
4823402 CTTGCAATCACATTA
1 CCTGCAATCACATTG
*
4823417 CCTGTAATCACATTG
1 CCTGCAATCACATTG
4823432 C
1 C
4823433 ATTGTAATGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.33
Consensus pattern (15 bp):
CCTGCAATCACATTG
Found at i:4834852 original size:2 final size:2
Alignment explanation
Indices: 4834845--4834872 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4834835 TTTTATTAAG
4834845 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
4834873 AAATTGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4836192 original size:37 final size:37
Alignment explanation
Indices: 4836142--4836215 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
4836132 AATTTTCATG
*
4836142 GTTCATTGTTTTAACCATTTATTTTCTTAGCTTCAAA
1 GTTCATTGTTTTAACCATCTATTTTCTTAGCTTCAAA
4836179 GTTCATTGTTTTAACCATCTATTTTCTTAGCTTCAAA
1 GTTCATTGTTTTAACCATCTATTTTCTTAGCTTCAAA
4836216 TCCCTTCCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (37 bp):
GTTCATTGTTTTAACCATCTATTTTCTTAGCTTCAAA
Found at i:4839296 original size:22 final size:22
Alignment explanation
Indices: 4839256--4839298 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4839246 TAATTAACTA
*
4839256 TTAATTTTATTCTTATATTTTC
1 TTAATTTTATTCATATATTTTC
4839278 TTAATTGTTATTCAT-TATTTT
1 TTAATT-TTATTCATATATTTT
4839299 ATTTTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (22 bp):
TTAATTTTATTCATATATTTTC
Found at i:4840935 original size:19 final size:19
Alignment explanation
Indices: 4840899--4840937 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4840889 TATTAGTTTC
*
4840899 ATTATTTTATTTTATAAAA
1 ATTATTTTATTTAATAAAA
4840918 ATTATTTT-TTTAATTAAAA
1 ATTATTTTATTTAA-TAAAA
4840937 A
1 A
4840938 AATATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATTTTATTTAATAAAA
Found at i:4843797 original size:21 final size:22
Alignment explanation
Indices: 4843773--4843816 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4843763 ATTATAAAAA
4843773 TAAA-AATATTATGTTATT-TTT
1 TAAATAATATTAT-TTATTATTT
*
4843794 TAAATATTATTATTTATTATTT
1 TAAATAATATTATTTATTATTT
4843816 T
1 T
4843817 TATTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TAAATAATATTATTTATTATTT
Found at i:4843846 original size:21 final size:21
Alignment explanation
Indices: 4843822--4843865 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4843812 ATTTTTATTA
4843822 TTTAAAGTTAAAAAAT-TAAAT
1 TTTAAA-TTAAAAAATATAAAT
* *
4843843 TTTATATTAAAAATTATAAAT
1 TTTAAATTAAAAAATATAAAT
4843864 TT
1 TT
4843866 ATTTAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTAAATTAAAAAATATAAAT
Found at i:4843856 original size:19 final size:19
Alignment explanation
Indices: 4843832--4843871 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
4843822 TTTAAAGTTA
*
4843832 AAAAATTA-AATTTTATATT
1 AAAAATTATAAATTTAT-TT
4843851 AAAAATTATAAATTTATTT
1 AAAAATTATAAATTTATTT
4843870 AA
1 AA
4843872 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATTATAAATTTATTT
Found at i:4844143 original size:16 final size:16
Alignment explanation
Indices: 4844122--4844162 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4844112 TCAATTAAAA
4844122 AATAATAATATAAATT
1 AATAATAATATAAATT
4844138 AATAATTAAT-TAAATT
1 AATAA-TAATATAAATT
*
4844154 TATAA-AATA
1 AATAATAATA
4844163 ATATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 3 0.14
16 15 0.68
17 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAATATAAATT
Found at i:4844164 original size:17 final size:17
Alignment explanation
Indices: 4844125--4844167 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
4844115 ATTAAAAAAT
4844125 AATAATATAAATTAATA
1 AATAATATAAATTAATA
* *
4844142 ATTAAT-TAAATTTATAA
1 AATAATATAAATTAAT-A
4844159 AATAATATA
1 AATAATATA
4844168 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 8 0.38
17 11 0.52
18 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATATAAATTAATA
Found at i:4845208 original size:2 final size:2
Alignment explanation
Indices: 4845201--4845228 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4845191 TGATGATTAC
4845201 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
4845229 GCAGGCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4850667 original size:21 final size:21
Alignment explanation
Indices: 4850641--4850683 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4850631 ATCGGAGGAA
4850641 AGGAAAGAGGA-GAGGGCGAAG
1 AGGAAAGA-GACGAGGGCGAAG
*
4850662 AGGAAAGAGACGATGGCGAAG
1 AGGAAAGAGACGAGGGCGAAG
4850683 A
1 A
4850684 CGAGGAGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.44, C:0.07, G:0.47, T:0.02
Consensus pattern (21 bp):
AGGAAAGAGACGAGGGCGAAG
Done.