Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009036.1 Hibiscus syriacus cultivar Beakdansim tig00112443_pilon, 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: 1934717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1249019 original size:16 final size:16
Alignment explanation
Indices: 1248998--1249030 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1248988 TAATAAATAA
1248998 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1249014 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1249030 A
1 A
1249031 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1249114 original size:16 final size:16
Alignment explanation
Indices: 1249093--1249149 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
1249083 TTCATTTAAT
*
1249093 AAATAAACGAACAAGA
1 AAATAAACGAACACGA
1249109 AAATAAACGAACACGA
1 AAATAAACGAACACGA
* *
1249125 ACATAAATGAACACGA
1 AAATAAACGAACACGA
*
1249141 ACATAAACG
1 AAATAAACG
1249150 TTGGAGACCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.61, C:0.18, G:0.12, T:0.09
Consensus pattern (16 bp):
AAATAAACGAACACGA
Found at i:1251639 original size:17 final size:17
Alignment explanation
Indices: 1251617--1251649 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1251607 ATTAAAATTT
*
1251617 AATAAATTAATCTAAAA
1 AATAAAATAATCTAAAA
1251634 AATAAAATAATCTAAA
1 AATAAAATAATCTAAA
1251650 TTAAGACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAAAATAATCTAAAA
Found at i:1251660 original size:28 final size:27
Alignment explanation
Indices: 1251619--1251698 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
1251609 TAAAATTTAA
*
1251619 TAAATTAA-TCTAAAAAATAAAATAATC
1 TAAATTAAGACTAAAAAATAAAA-AATC
* **
1251646 TAAATTAAGACTAAAATATCTAAAATC
1 TAAATTAAGACTAAAAAATAAAAAATC
*
1251673 TAAATATAAGGACTAAATAA-AAAAAA
1 TAAAT-TAA-GACTAAAAAATAAAAAA
1251699 CAAAATTTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 17 0.40
28 17 0.40
29 8 0.19
ACGTcount: A:0.62, C:0.07, G:0.04, T:0.26
Consensus pattern (27 bp):
TAAATTAAGACTAAAAAATAAAAAATC
Found at i:1251661 original size:27 final size:29
Alignment explanation
Indices: 1251628--1251698 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
1251618 ATAAATTAAT
*
1251628 CTAAAAAATAAAATAATCTAAAT-TAA-GA
1 CTAAAATATAAAA-AATCTAAATATAAGGA
**
1251656 CTAAAATATCTAAAATCTAAATATAAGGA
1 CTAAAATATAAAAAATCTAAATATAAGGA
*
1251685 CT-AAATAAAAAAAA
1 CTAAAATATAAAAAA
1251699 CAAAATTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 9 0.26
28 22 0.63
29 4 0.11
ACGTcount: A:0.63, C:0.08, G:0.04, T:0.24
Consensus pattern (29 bp):
CTAAAATATAAAAAATCTAAATATAAGGA
Found at i:1253902 original size:55 final size:55
Alignment explanation
Indices: 1253728--1254210 Score: 467
Period size: 55 Copynumber: 8.8 Consensus size: 55
1253718 GGATAAACCA
* * * * * *
1253728 GACTTGAAAAATCTTCGGAAAACATGTCTGCTCCCTATTCTTTCA-A-AGTATAG
1 GACTCGAACAATCTTCAGCAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATAG
* * * * * *
1253781 GACTCAAACAATCTTC-GACAAACGGGTTCACTCCCTATT-TTTCAGGGAGTATAT
1 GACTCGAACAATCTTCAG-CAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATAG
* *
1253835 GACTCGAACAATCTTCAGCAAACGTATCCGCTCCCTATTCTTTCAGATAGTATAG
1 GACTCGAACAATCTTCAGCAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATAG
* * ****
1253890 GACTCGAACAATCTTC-GACAAACATTTATATTCCCTATTCTTTCAG-GAAGTATAG
1 GACTCGAACAATCTTCAG-CAAACGTGTCCGCTCCCTATTCTTTCAGAG-AGTATAG
* * * *
1253945 GACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTCTTTCAGGGAGTACAT
1 GACTCGAACAATCTTCAGCAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATAG
* * * *
1254000 GACTCGAACAATCTTCAGTAAACGTGTTCACTCCCTATTCTTTCAGAGAGTATAA
1 GACTCGAACAATCTTCAGCAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATAG
* * ** * * *
1254055 AACTCAAACAATCTTCAAAAAACGTGTCCGCTCTCTATTTTTTCAGGGAGTATAG
1 GACTCGAACAATCTTCAGCAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATAG
** * *
1254110 GACTCGAACAATCTTCAATAAACGTGTCCGCTCTCTATTCTTTCA-AGGAGTATAT
1 GACTCGAACAATCTTCAGCAAACGTGTCCGCTCCCTATTCTTTCAGA-GAGTATAG
* * * * * **
1254165 AACTCAAACAATCTTCAACAAACATATATGCTCCCTATTCTTTCAG
1 GACTCGAACAATCTTCAGCAAACGTGTCCGCTCCCTATTCTTTCAG
1254211 GGAGATCAGA
Statistics
Matches: 355, Mismatches: 64, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
52 6 0.02
53 28 0.08
54 39 0.11
55 280 0.79
56 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (55 bp):
GACTCGAACAATCTTCAGCAAACGTGTCCGCTCCCTATTCTTTCAGAGAGTATAG
Found at i:1254017 original size:165 final size:165
Alignment explanation
Indices: 1253758--1254210 Score: 547
Period size: 165 Copynumber: 2.8 Consensus size: 165
1253748 AACATGTCTG
* * *
1253758 CTCCCTATTCTTTCA--AAGTATAGGACTCAAACAATCTTC-GACAAACGGGT-TCACTCCCTAT
1 CTCCCTATTCTTTCAGGAAGTATAGGACTCGAACAATCTTCAG-CAAACGTGTCT-GCTCCCTAT
* *
1253819 T-TTTCAGGGAGTATATGACTCGAACAATCTTCAGCAAACGTATCCGCTCCCTATTCTTTCAGAT
64 TCTTTCAGGGAGTATATGACTCGAACAATCTTCAGCAAACGTATACGCTCCCTATTCTTTCAGAG
** * * * * *
1253883 AGTATAGGACTCGAACAATCTTCGACAAACATTTATA
129 AGTATAAAACTCAAACAATCTTCAAAAAACATGTACA
*
1253920 TTCCCTATTCTTTCAGGAAGTATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTC
1 CTCCCTATTCTTTCAGGAAGTATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTC
* * * * *
1253985 TTTCAGGGAGTACATGACTCGAACAATCTTCAGTAAACGTGTTCACTCCCTATTCTTTCAGAGAG
66 TTTCAGGGAGTATATGACTCGAACAATCTTCAGCAAACGTATACGCTCCCTATTCTTTCAGAGAG
* * *
1254050 TATAAAACTCAAACAATCTTCAAAAAACGTGTCCG
131 TATAAAACTCAAACAATCTTCAAAAAACATGTACA
* * * ** * *
1254085 CTCTCTATTTTTTCAGGGAGTATAGGACTCGAACAATCTTCAATAAACGTGTCCGCTCTCTATTC
1 CTCCCTATTCTTTCAGGAAGTATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTC
* * * * * *
1254150 TTTCAAGGAGTATATAACTCAAACAATCTTCAACAAACATATATGCTCCCTATTCTTTCAG
66 TTTCAGGGAGTATATGACTCGAACAATCTTCAGCAAACGTATACGCTCCCTATTCTTTCAG
1254211 GGAGATCAGA
Statistics
Matches: 247, Mismatches: 39, Indels: 7
0.84 0.13 0.02
Matches are distributed among these distances:
162 14 0.06
164 40 0.16
165 193 0.78
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (165 bp):
CTCCCTATTCTTTCAGGAAGTATAGGACTCGAACAATCTTCAGCAAACGTGTCTGCTCCCTATTC
TTTCAGGGAGTATATGACTCGAACAATCTTCAGCAAACGTATACGCTCCCTATTCTTTCAGAGAG
TATAAAACTCAAACAATCTTCAAAAAACATGTACA
Found at i:1254211 original size:110 final size:109
Alignment explanation
Indices: 1253747--1254214 Score: 539
Period size: 110 Copynumber: 4.3 Consensus size: 109
1253737 AATCTTCGGA
* * * * *
1253747 AAACATGTCTGCTCCCTATTCTTTCA--AAGTATAGGACTCAAACAATCTTCGACAAACGGGTTC
1 AAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAACGTGTTC
* * *
1253810 ACTCCCTATT-TTTCAGGGAGTATATGACTCGAACAATCTTCAGC
66 ACTCCCTATTCTTTCA-GGAGTATATAACTCAAACAATCTTCAAC
* * ** * *
1253854 AAACGTATCCGCTCCCTATTCTTTCAGATAGTATAGGACTCGAACAATCTTCGACAAACAT-TTA
1 AAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAACGTGTT-
* * ** * *
1253918 TATTCCCTATTCTTTCAGGAAGTATAGGACTCGAACAATCTTCAGC
65 CACTCCCTATTCTTTCAGG-AGTATATAACTCAAACAATCTTCAAC
* * **
1253964 AAACGTGTCTGCTCCCTATTCTTTCAGGGAGTACATGACTCGAACAATCTTCAGTAAACGTGTTC
1 AAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAACGTGTTC
* *
1254029 ACTCCCTATTCTTTCAGAGAGTATAAAACTCAAACAATCTTCAAA
66 ACTCCCTATTCTTTCAG-GAGTATATAACTCAAACAATCTTCAAC
* * * * *
1254074 AAACGTGTCCGCTCTCTATTTTTTCAGGGAGTATAGGACTCGAACAATCTTCAATAAACGTGTCC
1 AAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAACGTGTTC
* *
1254139 GCTCTCTATTCTTTCAAGGAGTATATAACTCAAACAATCTTCAAC
66 ACTCCCTATTCTTTC-AGGAGTATATAACTCAAACAATCTTCAAC
* * *
1254184 AAACATATATGCTCCCTATTCTTTCAGGGAG
1 AAACGTGTCTGCTCCCTATTCTTTCAGGGAG
1254215 ATCAGACTCT
Statistics
Matches: 309, Mismatches: 44, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
107 23 0.07
108 2 0.01
109 40 0.13
110 239 0.77
111 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (109 bp):
AAACGTGTCTGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAACGTGTTC
ACTCCCTATTCTTTCAGGAGTATATAACTCAAACAATCTTCAAC
Found at i:1254416 original size:42 final size:40
Alignment explanation
Indices: 1254351--1254454 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 40
1254341 TTAAAAATGG
* * * *
1254351 CCCAAAGGACTT-ATCATCTTGCTCTAAAG-TCTGACAGATGA
1 CCCAAAGGATTTAATCATCATGCTCGAAAGCT-TG--AGATAA
* *
1254392 CCCGAAGGATTTAATCATCATGCTCGAAAGCTTGATATAA
1 CCCAAAGGATTTAATCATCATGCTCGAAAGCTTGAGATAA
*
1254432 CCTAAAGGATTTAATCATCATGC
1 CCCAAAGGATTTAATCATCATGC
1254455 CCGAGGGCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
40 25 0.47
41 10 0.19
42 17 0.32
43 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (40 bp):
CCCAAAGGATTTAATCATCATGCTCGAAAGCTTGAGATAA
Found at i:1254515 original size:37 final size:37
Alignment explanation
Indices: 1254474--1254702 Score: 359
Period size: 37 Copynumber: 6.2 Consensus size: 37
1254464 TACTGATGAC
* * * *
1254474 TTGCTTCACTGCTCTTCTGTTAAGGCTTAAGATTGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTGAT
*
1254511 TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTGAT
* *
1254548 TTGCTTCATTACTTTTCCGTGAAGGCTTAATATTGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTGAT
* *
1254585 TTGCTTCACCACTCTTCCGTGAAGGCTTAATATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTGAT
1254622 TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTGAT
*
1254659 TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTTAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTGAT
*
1254696 TTTCTTC
1 TTGCTTC
1254703 GAAGGTCGAA
Statistics
Matches: 176, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 176 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.42
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAATATTGAT
Found at i:1257392 original size:99 final size:100
Alignment explanation
Indices: 1257229--1257423 Score: 311
Period size: 99 Copynumber: 1.9 Consensus size: 100
1257219 ATTATAATTT
*
1257229 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAATCGGGACGTTTAACCAATTGCTTTAAAGGGA
1 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAATCGGGACGTTTAACCAATTGCTCTAAAGGGA
**
1257294 CAGTTCAAGCTTTATTG-TACATATAATATAATCA
66 CAACTCAAGCTTTATTGATACATATAATATAATCA
* * * *
1257328 CCTTTATCAGGCTAGTTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGA
1 CCTTTATCAGGCTAGCTGAATCTTATCCATAAAATCGGGACGTTTAACCAATTGCTCTAAAGGGA
1257393 CAACTCAAGCTTTATTGTATACATATAATAT
66 CAACTCAAGCTTTATTG-ATACATATAATAT
1257424 TATAAACTGG
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
99 75 0.86
101 12 0.14
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (100 bp):
CCTTTATCAGGCTAGCTGAATCTTATCCATAAAATCGGGACGTTTAACCAATTGCTCTAAAGGGA
CAACTCAAGCTTTATTGATACATATAATATAATCA
Found at i:1262124 original size:26 final size:27
Alignment explanation
Indices: 1262095--1262159 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
1262085 ATCTAAAAAA
1262095 TAAAATAAAATAATCTAAAT-TAA-GAC
1 TAAAATAAAA-AATCTAAATATAAGGAC
**
1262121 TAAATATCTAAAATCTAAATATAAGGAC
1 TAAA-ATAAAAAATCTAAATATAAGGAC
1262149 T-AAATAAAAAA
1 TAAAATAAAAAA
1262160 CAACAACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 19 0.59
27 9 0.28
28 4 0.12
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (27 bp):
TAAAATAAAAAATCTAAATATAAGGAC
Found at i:1264492 original size:31 final size:30
Alignment explanation
Indices: 1264433--1264499 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
1264423 TAAACGAACA
*
1264433 AACATGAATATATTTGAAATATAATTAAATG
1 AACATGAATATATTTGAAATAT-ATTAAACG
1264464 AACATGAAATATGATATTGAAAT-T-TTAAACG
1 AACATG-AATAT-AT-TTGAAATATATTAAACG
1264495 AACAT
1 AACAT
1264500 TAATTGAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
31 17 0.53
32 5 0.16
33 3 0.09
34 7 0.22
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (30 bp):
AACATGAATATATTTGAAATATATTAAACG
Found at i:1265468 original size:23 final size:23
Alignment explanation
Indices: 1265428--1265472 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1265418 TGAGGCAATC
1265428 ATAATATTTAAAGTAATGCAACAA
1 ATAATATTTAAAGTAATG-AACAA
1265452 ATAA-ATTTAAA-TGAATGAACA
1 ATAATATTTAAAGT-AATGAACA
1265473 TATTTAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29
Consensus pattern (23 bp):
ATAATATTTAAAGTAATGAACAA
Found at i:1272717 original size:29 final size:27
Alignment explanation
Indices: 1272659--1272717 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
1272649 CTTGACTATT
* *
1272659 AATATTGTAATAGAATATATATGCATC
1 AATATTGTAACAGAACATATATGCATC
1272686 AATATTGTAACAGAAAACATATGATG-ATC
1 AATATTGTAACAG--AACATAT-ATGCATC
1272715 AAT
1 AAT
1272718 TTGAATGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.44
29 12 0.44
30 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.32
Consensus pattern (27 bp):
AATATTGTAACAGAACATATATGCATC
Found at i:1279059 original size:18 final size:18
Alignment explanation
Indices: 1279036--1279078 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1279026 AACTTGCCTA
* *
1279036 TTCATTTGTTTGTTTATG
1 TTCATTTGTTTATGTATG
* *
1279054 TTCATTCGTTTATGTCTG
1 TTCATTTGTTTATGTATG
1279072 TTCATTT
1 TTCATTT
1279079 ATATTCAACT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.63
Consensus pattern (18 bp):
TTCATTTGTTTATGTATG
Found at i:1279288 original size:14 final size:14
Alignment explanation
Indices: 1279266--1279299 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1279256 AGCTGATTAA
*
1279266 TTTTATGTTTGTTC
1 TTTTGTGTTTGTTC
1279280 TTTTGTGTTTGTTC
1 TTTTGTGTTTGTTC
*
1279294 ATTTGT
1 TTTTGT
1279300 ATTCGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.06, G:0.18, T:0.71
Consensus pattern (14 bp):
TTTTGTGTTTGTTC
Found at i:1279371 original size:37 final size:37
Alignment explanation
Indices: 1279321--1279401 Score: 162
Period size: 37 Copynumber: 2.2 Consensus size: 37
1279311 ATTTTAATGA
1279321 ACGAACATGAATGAGTTGCATTCTTTAATTAACGAAC
1 ACGAACATGAATGAGTTGCATTCTTTAATTAACGAAC
1279358 ACGAACATGAATGAGTTGCATTCTTTAATTAACGAAC
1 ACGAACATGAATGAGTTGCATTCTTTAATTAACGAAC
1279395 ACGAACA
1 ACGAACA
1279402 AAATTTCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (37 bp):
ACGAACATGAATGAGTTGCATTCTTTAATTAACGAAC
Found at i:1288829 original size:103 final size:103
Alignment explanation
Indices: 1288645--1288870 Score: 391
Period size: 103 Copynumber: 2.2 Consensus size: 103
1288635 GTAGAGGGTC
1288645 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1288710 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
1288748 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1288813 TTGATCCCTAGTATATGTATATGATTCTTAATGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1288851 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
1288871 TATTATATGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
103 116 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1288917 original size:23 final size:23
Alignment explanation
Indices: 1288887--1288930 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1288877 ATGGTACTAC
1288887 GGTGCAATTCTACGCGGCACTCT
1 GGTGCAATTCTACGCGGCACTCT
*
1288910 GGTGCAATTCTACGTGGCACT
1 GGTGCAATTCTACGCGGCACT
1288931 TCGGTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTCT
Found at i:1288936 original size:23 final size:22
Alignment explanation
Indices: 1288886--1288941 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
1288876 TATGGTACTA
1288886 CGGTGCAATTCTACGCGGCACT
1 CGGTGCAATTCTACGCGGCACT
*
1288908 CTGGTGCAATTCTACGTGGCACTT
1 C-GGTGCAATTCTACGCGGCAC-T
*
1288932 CGGTGTAATT
1 CGGTGCAATT
1288942 ATATGAGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 27 0.90
24 2 0.07
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (22 bp):
CGGTGCAATTCTACGCGGCACT
Found at i:1294577 original size:22 final size:22
Alignment explanation
Indices: 1294525--1294577 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1294515 TCAGGAGTTA
** *
1294525 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTACATGATATAATTC
*
1294547 CAAGG-GTTACATGATATAATTT
1 C-AGGAGTTACATGATATAATTC
1294569 CAGGAGTTA
1 CAGGAGTTA
1294578 TAACAGCTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 19 0.76
23 3 0.12
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (22 bp):
CAGGAGTTACATGATATAATTC
Found at i:1296598 original size:19 final size:20
Alignment explanation
Indices: 1296574--1296618 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1296564 TCCATTTCTT
1296574 AATATTAAAAAAAT-AAATA
1 AATATTAAAAAAATGAAATA
* *
1296593 AATATTAATAAAATGTAATA
1 AATATTAAAAAAATGAAATA
1296613 AATATT
1 AATATT
1296619 CCTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATATTAAAAAAATGAAATA
Found at i:1296647 original size:15 final size:14
Alignment explanation
Indices: 1296621--1296664 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
1296611 TAAATATTCC
1296621 TAAA-AAAATAATT
1 TAAATAAAATAATT
1296634 TAAATAAAACTAATT
1 TAAATAAAA-TAATT
*
1296649 TAAATATATATAATT
1 TAAATA-AAATAATT
1296664 T
1 T
1296665 TTATAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 4 0.15
14 4 0.15
15 17 0.63
16 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATAAAATAATT
Found at i:1298042 original size:3 final size:3
Alignment explanation
Indices: 1298036--1298078 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
1298026 ATTATTTTTT
* *
1298036 TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
1298079 AATGAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1300342 original size:21 final size:21
Alignment explanation
Indices: 1300316--1300371 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
1300306 ATTTACTGTG
**
1300316 ATTGCGGCCGTCGCGGGTGCT
1 ATTGCGGCCGTCGCGGACGCT
*
1300337 ATTGCGGCCGTCTCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
1300358 ATTGCGGCCGTCGC
1 ATTGCGGCCGTCGC
1300372 AGGTAACTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.07, C:0.32, G:0.38, T:0.23
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:1301991 original size:14 final size:14
Alignment explanation
Indices: 1301952--1301983 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1301942 TTGCTGCTAA
1301952 GAGAGATATAAATT
1 GAGAGATATAAATT
1301966 GAGAGATATAAATT
1 GAGAGATATAAATT
1301980 GAGA
1 GAGA
1301984 TATCTAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (14 bp):
GAGAGATATAAATT
Found at i:1303513 original size:17 final size:17
Alignment explanation
Indices: 1303491--1303524 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1303481 TATTAATTTG
1303491 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
1303508 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
1303525 GTCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:1306571 original size:14 final size:14
Alignment explanation
Indices: 1306535--1306573 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1306525 TTCATATATG
1306535 CATTTT-CATTTTC
1 CATTTTGCATTTTC
*
1306548 CATCTTTGCATTTTT
1 CAT-TTTGCATTTTC
1306563 CATTTTGCATT
1 CATTTTGCATT
1306574 CATACTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.15, C:0.21, G:0.05, T:0.59
Consensus pattern (14 bp):
CATTTTGCATTTTC
Found at i:1309498 original size:16 final size:16
Alignment explanation
Indices: 1309479--1309531 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
1309469 AAAAAAAGAT
1309479 GAAAAAGGAAAAATGA
1 GAAAAAGGAAAAATGA
*
1309495 GAAAAAAGAAAAA-GAA
1 GAAAAAGGAAAAATG-A
*
1309511 AAAAAAGGAAAAATGGA
1 GAAAAAGGAAAAAT-GA
1309528 GAAA
1 GAAA
1309532 TTGAATCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.03
16 24 0.80
17 4 0.13
18 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.04
Consensus pattern (16 bp):
GAAAAAGGAAAAATGA
Found at i:1309516 original size:32 final size:32
Alignment explanation
Indices: 1309462--1309531 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
1309452 CAGCAAAGGA
**
1309462 AGAAGAAAAAAAAAGATGAAAAAGGAAAAAT-G
1 AGAA-AAAAAAAAAGAAAAAAAAGGAAAAATGG
1309494 AGAAAAAAGAAAAAGAAAAAAAAGGAAAAATGG
1 AGAAAAAA-AAAAAGAAAAAAAAGGAAAAATGG
1309527 AGAAA
1 AGAAA
1309532 TTGAATCAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 4 0.12
32 24 0.71
33 6 0.18
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (32 bp):
AGAAAAAAAAAAAGAAAAAAAAGGAAAAATGG
Found at i:1311848 original size:114 final size:114
Alignment explanation
Indices: 1311648--1311981 Score: 546
Period size: 114 Copynumber: 2.9 Consensus size: 114
1311638 CATGTTCTCG
*
1311648 TAGTAGAAATAAGGAG-CCCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 TAGTAGAAATAAGGAGACCC-AATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTT
*
1311712 TGGTATGAACCTCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
65 TGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
** * *
1311762 TAGTAGAAATAATAAGACCCAATAGCATCTTATGGAATTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTT
*
1311827 GGTATGAACCCCAAAACCAATCATCGGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
*
1311876 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTT
* *
1311941 GGTA-GAAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTATG-AACCCCAAAACCAATCATTGGATTTGAAAGATGAA
1311982 CTGCATGATC
Statistics
Matches: 204, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
113 1 0.00
114 200 0.98
115 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTT
GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
Found at i:1314002 original size:50 final size:53
Alignment explanation
Indices: 1313870--1314025 Score: 203
Period size: 54 Copynumber: 3.0 Consensus size: 53
1313860 TAATTGAGAA
*
1313870 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTAC-AAC
* *
1313924 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAAC
* ***
1313977 -TC-GA-CAGAAACCACAGGAAAA-GATGAATGCACTGTCAAATGTTTTACAA
1 ATCTGAGCAGAAGCCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTACAA
1314026 ACCTGCTATT
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
50 33 0.36
51 7 0.08
52 2 0.02
53 2 0.02
54 48 0.52
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (53 bp):
ATCTGAGCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAAC
Found at i:1314364 original size:22 final size:21
Alignment explanation
Indices: 1314327--1314379 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
1314317 ATTTCAAGAG
1314327 TCAAAGATG-AGATTCTCTTT
1 TCAAAGATGAAGATTCTCTTT
*
1314347 TTAAAGATGATAGATTCTCTTT
1 TCAAAGATGA-AGATTCTCTTT
1314369 TCAAAGATGAA
1 TCAAAGATGAA
1314380 AGCTTTATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.28
21 1 0.03
22 20 0.69
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (21 bp):
TCAAAGATGAAGATTCTCTTT
Found at i:1315252 original size:186 final size:185
Alignment explanation
Indices: 1314928--1315296 Score: 659
Period size: 186 Copynumber: 2.0 Consensus size: 185
1314918 CCAATCAACA
1314928 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
1 TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
1314993 AAATTGCTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
66 AAATTGCTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
*
1315058 TGTAAGTCCTGCAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATAT
131 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATAT
**
1315113 TGTTATTTTGAAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTTTATCTTTTTCT-AAAA
1 TGTTATTTTG-AAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATC-TTTTCTAAAAA
* * *
1315177 TGAAATTGTTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTATTAAACTATTTCCTACA
64 TGAAATTGCTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACA
1315242 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
129 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
1315297 GTTTTCAAAG
Statistics
Matches: 176, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
185 10 0.06
186 160 0.91
187 6 0.03
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (185 bp):
TGTTATTTTGAAAAATAATGAGAAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATG
AAATTGCTGAAAAGTAAGAAAACGATTTCCTTAGTTTTTTTACTTAGTAAACTATTTCCCACATC
TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATAT
Found at i:1315505 original size:3 final size:3
Alignment explanation
Indices: 1315497--1315544 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
1315487 TTTTTCTTAA
**
1315497 ATT ATT ATT AAA ATT ATT ATTT ATT ATT ATT ATT ATTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT A-TT ATT ATT ATT
1315544 A
1 A
1315545 CAAGCCCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1315522 original size:19 final size:17
Alignment explanation
Indices: 1315498--1315541 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 17
1315488 TTTTCTTAAA
1315498 TTATTATTAAAATTATTAT
1 TTATTATT--AATTATTAT
1315517 TTATTATT-ATTATTAT
1 TTATTATTAATTATTAT
1315533 TTATTATTA
1 TTATTATTA
1315542 TTACAAGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 16 0.67
19 8 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATTAATTATTAT
Found at i:1315527 original size:13 final size:14
Alignment explanation
Indices: 1315497--1315544 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 14
1315487 TTTTTCTTAA
*
1315497 ATTATTATTA-A-A
1 ATTATTATTATATT
1315509 ATTATTATT-TATT
1 ATTATTATTATATT
1315522 ATTATTATTAT-TT
1 ATTATTATTATATT
1315535 ATTATTATTA
1 ATTATTATTA
1315545 CAAGCCCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
12 10 0.31
13 21 0.66
14 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:1315539 original size:16 final size:16
Alignment explanation
Indices: 1315509--1315544 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1315499 TATTATTAAA
1315509 ATTATTATTTATTATT
1 ATTATTATTTATTATT
1315525 ATTATTATTTATTATT
1 ATTATTATTTATTATT
1315541 ATTA
1 ATTA
1315545 CAAGCCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTATTATTTATTATT
Found at i:1315542 original size:19 final size:18
Alignment explanation
Indices: 1315497--1315544 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1315487 TTTTTCTTAA
1315497 ATTATTATTAAAATTATT
1 ATTATTATTAAAATTATT
**
1315515 ATTTATTATTATTATTATTT
1 A-TTATTATTAAAATTA-TT
1315535 ATTATTATTA
1 ATTATTATTA
1315545 CAAGCCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 22 0.85
20 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATTATTAAAATTATT
Found at i:1316815 original size:17 final size:17
Alignment explanation
Indices: 1316793--1316826 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1316783 TATTAATTTG
1316793 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
1316810 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
1316827 GTCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:1317228 original size:29 final size:29
Alignment explanation
Indices: 1317196--1317252 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1317186 CTGATATTTC
1317196 TAAATAAATAAATATT-TTATAAATATATT
1 TAAATAAATAAATATTCTTA-AAATATATT
* * *
1317225 TAAATTAATATATTTTCTTAAAATATAT
1 TAAATAAATAAATATTCTTAAAATATAT
1317253 AGTAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAATAAATAAATATTCTTAAAATATATT
Found at i:1330470 original size:18 final size:17
Alignment explanation
Indices: 1330444--1330488 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
1330434 AAAACACACA
1330444 AAAATAATTAAAAAGAT
1 AAAATAATTAAAAAGAT
*
1330461 AAAATAAATTAAAAATAT
1 AAAAT-AATTAAAAAGAT
1330479 AAAAATAATT
1 -AAAATAATT
1330489 GAATTACTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATAATTAAAAAGAT
Found at i:1330654 original size:31 final size:32
Alignment explanation
Indices: 1330604--1330664 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1330594 ACGGGTAAAT
*
1330604 TATGTATTTAGTACTTAAATTATCAGTTTTAG
1 TATGTATTTAGTACCTAAATTATCAGTTTTAG
* * *
1330636 TATGT-TTTTGTACCTAAATTTTCATTTTT
1 TATGTATTTAGTACCTAAATTATCAGTTTT
1330665 GTCAAACTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (32 bp):
TATGTATTTAGTACCTAAATTATCAGTTTTAG
Found at i:1332313 original size:21 final size:21
Alignment explanation
Indices: 1332283--1332323 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1332273 ATATAAATTG
1332283 TGTATCGATGCACTACTACAA
1 TGTATCGATGCACTACTACAA
* *
1332304 TGTATTGATGCACTGCTACA
1 TGTATCGATGCACTACTACA
1332324 GTAACTTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (21 bp):
TGTATCGATGCACTACTACAA
Found at i:1332964 original size:24 final size:24
Alignment explanation
Indices: 1332937--1333007 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
1332927 CACCACAGCT
* *
1332937 CGTATAAATTGCATCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
* *
1332961 CGTAGAATTTGCACCGAAGTGCCG
1 CGTAGAAATTGCACCGAAGTGCCA
* *
1332985 CATAGAAA-TGCACCGTAGTGCCA
1 CGTAGAAATTGCACCGAAGTGCCA
1333008 TATAAGATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 13 0.33
24 26 0.67
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTGCCA
Found at i:1340855 original size:60 final size:60
Alignment explanation
Indices: 1340701--1340861 Score: 175
Period size: 60 Copynumber: 2.7 Consensus size: 60
1340691 TCATTATAAA
* *
1340701 TTGATCCCTAAACTTTTAAAT-ATTCTAATTTCATCCTCAAACTATGATCTTCATTCAAAAT
1 TTGA-CCCTAAACTTTTAAATCTTTC-AATTTCATCCTCAAACAATGATCTTCATTCAAAAT
** * * * *
1340762 TTGTTCTTAAACTTTTGAA-CATTTCAATCTCATCCTCAAACAATTACTCTT-ATTCAAAAT
1 TTGACCCTAAACTTTTAAATC-TTTCAATTTCATCCTCAAACAATGA-TCTTCATTCAAAAT
* *
1340822 TTGACCCTAAACTTTTAAATCTTTCGATTTCATCATCAAA
1 TTGACCCTAAACTTTTAAATCTTTCAATTTCATCCTCAAA
1340862 TTCATTCAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
60 70 0.86
61 11 0.14
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.41
Consensus pattern (60 bp):
TTGACCCTAAACTTTTAAATCTTTCAATTTCATCCTCAAACAATGATCTTCATTCAAAAT
Found at i:1350838 original size:31 final size:30
Alignment explanation
Indices: 1350799--1350864 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
1350789 TGTAATATAA
*
1350799 TCCCCAACATTTTGTCTGTTTACAATATGG
1 TCCCCAACATTTAGTCTGTTTACAATATGG
*
1350829 TCCCTCAACATTTAGTCTGTTTGCAATATGG
1 TCCC-CAACATTTAGTCTGTTTACAATATGG
1350860 TCCCC
1 TCCCC
1350865 GACGTAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (30 bp):
TCCCCAACATTTAGTCTGTTTACAATATGG
Found at i:1352233 original size:23 final size:23
Alignment explanation
Indices: 1352207--1352281 Score: 96
Period size: 23 Copynumber: 3.2 Consensus size: 23
1352197 AGCTCATATA
1352207 ATAATTGCACCGAAGTGCCACAT
1 ATAATTGCACCGAAGTGCCACAT
* *
1352230 ATAATTGCACCGGAGTGCCGCAT
1 ATAATTGCACCGAAGTGCCACAT
* * *
1352253 AGAATTGCACCGTAGTGCCATAT
1 ATAATTGCACCGAAGTGCCACAT
1352276 AATAAT
1 -ATAAT
1352282 GTCCATAAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 40 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (23 bp):
ATAATTGCACCGAAGTGCCACAT
Found at i:1352459 original size:103 final size:103
Alignment explanation
Indices: 1352288--1352505 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
1352278 TAATGTCCAT
* *
1352288 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1352353 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAAAACATATATGTCCCG
*
1352391 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1352456 GACTTCACACATGTTCCAAAGAAAACATATATGTCCCG
66 GACTTCACACATATTCCAAAGAAAACATATATGTCCCG
*
1352494 AATGACCACATA
1 AAGGACCACATA
1352506 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATATTCCAAAGAAAACATATATGTCCCG
Found at i:1353232 original size:22 final size:21
Alignment explanation
Indices: 1353207--1353248 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1353197 TTTTCCTTTA
1353207 GGGGGAATCGGTTCCCTCCTGT
1 GGGGGAATCGGTT-CCTCCTGT
*
1353229 GGGGGTATCGGTTCCTCCTG
1 GGGGGAATCGGTTCCTCCTG
1353249 GACATTCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.07, C:0.26, G:0.38, T:0.29
Consensus pattern (21 bp):
GGGGGAATCGGTTCCTCCTGT
Found at i:1356985 original size:39 final size:39
Alignment explanation
Indices: 1356881--1356987 Score: 106
Period size: 39 Copynumber: 2.7 Consensus size: 39
1356871 TACCGAGCCA
* * * * *
1356881 AAGAGTCCAAGCTTACTTGGTGTCTTCAAGCCAACCACG
1 AAGACTCCAAGCTTACTTGGCGTCTTCAGGCAAAACACG
* * * * * *
1356920 AAGTCTCCATGCTTACCTGACGTCTTCAGGCAAAATAGG
1 AAGACTCCAAGCTTACTTGGCGTCTTCAGGCAAAACACG
*
1356959 AAGACTCCAAGCTTACTTGGCATCTTCAG
1 AAGACTCCAAGCTTACTTGGCGTCTTCAG
1356988 TTCATGTAGA
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (39 bp):
AAGACTCCAAGCTTACTTGGCGTCTTCAGGCAAAACACG
Found at i:1357654 original size:103 final size:101
Alignment explanation
Indices: 1357340--1357722 Score: 307
Period size: 103 Copynumber: 3.7 Consensus size: 101
1357330 ATTGTTTCAT
* *
1357340 TTTTAATTTTTATTTGA-AATATAAATTAATTAGATTATTTATTTTGATTTTACACATTAAATTG
1 TTTTAATTTTTA-TTGATAATATAAATT-ATTAGACTATTTATTTTGATTTTACAAATTAAATTG
* * *
1357404 TATTCGAGTGATTTGGTAAGTTTAATTTAAATTT-TAG
64 TATTTGAGTGATTTGGTAAGTTTAGTTTAAATTTATTG
* * * *
1357441 -TGTAATTTTGT-TT-TTAAT-TATAATTATTAGACTATTTATTTTGATTTTACATATTAAGTTG
1 TTTTAATTTT-TATTGATAATATA-AATTATTAGACTATTTATTTTGATTTTACAAATTAAATTG
* * * *
1357502 TATTTGAGTAAAACTTGATAAGTGTAGTTTAAA-TTATTAG
64 TATTTGAGT--GATTTGGTAAGTTTAGTTTAAATTTATT-G
* * * * *
1357542 -ATTAATTTTTATTGAGTAATATAAATTATTAGAGTAATTATTTTTATTTTACAAATTAAATCGT
1 TTTTAATTTTTATTGA-TAATATAAATTATTAGACTATTTATTTTGATTTTACAAATTAAATTGT
* *
1357606 ATTTAAGTGGTTTGGTAAGTTTAGTTTAAACTTTATTG
65 ATTTGAGTGATTTGGTAAGTTTAGTTTAAA-TTTATTG
* * * * *
1357644 TTTTATTTTTTGTTTTTATTG-TAAATATATATTAATTAGATTATTTATTATGATTTTACAGATT
1 TTTTA------ATTTTTATTGAT-AATATAAATT-ATTAGACTATTTATTTTGATTTTACAAATT
* *
1357708 AAATTTTATTCGAGT
58 AAATTGTATTTGAGT
1357723 TGGTAAGTTA
Statistics
Matches: 221, Mismatches: 39, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
98 43 0.19
99 11 0.05
100 27 0.12
101 28 0.13
102 1 0.00
103 54 0.24
104 2 0.01
107 1 0.00
108 9 0.04
109 45 0.20
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (101 bp):
TTTTAATTTTTATTGATAATATAAATTATTAGACTATTTATTTTGATTTTACAAATTAAATTGTA
TTTGAGTGATTTGGTAAGTTTAGTTTAAATTTATTG
Found at i:1357900 original size:310 final size:304
Alignment explanation
Indices: 1357322--1357901 Score: 694
Period size: 310 Copynumber: 1.9 Consensus size: 304
1357312 AAATTTAATG
* *
1357322 TAAATTTTATTGTTTCATTTTTAATTTTTATTTGAAATATAAATTAATTAGATTATTTATTTTGA
1 TAAACTTTATTGTTTCATTTTTAATTTTTATTTGAAATATAAATTAATTAGATTATTTATTATGA
** * *
1357387 TTTTACACATTAAATTGTATTCGAGTGATTTGGTAAGTTTAATTTAAATTTTAGTGTAATTTTGT
66 TTTTACACATTAAATTGTATTCGAGTGATAAGGTAAATTTAATTTAAATTTTAGTATAATTTTGT
* *
1357452 TTTTAATTATAATTATTAGACTATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAAAACT
131 TTTTAATTATAATTATTAGAATATTTATTTTGATTTTACATATTAAGTCGTATTTGAGT-AAACT
*
1357517 TGATAAGTGTAGTTTAAATTATTAGATTAATTTTTATTGAGTAATATAAATTATTAGAGTAATTA
195 TGATAAGTGTAGTTTAAA-TATTA-ATT-ATTTTTATTGAGTAATATAAATTATTAGAG-AACTA
1357582 TTTTTATTTTACAAATTAAATCGTATTTAAGTGGTTTGGTAAGTTTAGTT
256 -TTTTATTTTACAAATTAAATCGTATTTAAGTGGTTTGGTAAGTTTAGTT
* ** *
1357632 TAAACTTTATTGTTTTATTTTTTGTTTTTA-TTGTAAATATATATTAATTAGATTATTTATTATG
1 TAAACTTTATTGTTTCATTTTTAATTTTTATTTG-AAATATAAATTAATTAGATTATTTATTATG
* * * * *
1357696 ATTTTACAGATTAAATTTTATTCGAGTTGGTAAGTTAAATTTAATTTTTCGTGTAATTTTTAGTA
65 ATTTTACACATTAAATTGTATTCGAG-TGATAAGGTAAATTTAA----T--T-TAAATTTTAGTA
*
1357761 TAATTTATGTTTTTAATTTAAATTAGAATTATTATAATATTTATTTTGATTTTACATATTAAGTC
122 TAATTT-TGTTTTTAA-TT--A-T--AATTATTAGAATATTTATTTTGATTTTACATATTAAGTC
** *
1357826 GTATTTGAGT-ATTTTGATAAGTTTAGTTT-AA-ATT-ATT-TTTTTATTGAGTAATATAAATTA
180 GTATTTGAGTAAACTTGATAAGTGTAGTTTAAATATTAATTATTTTTATTGAGTAATATAAATTA
1357886 TT-G-G-ACTA-TTTATTTT
245 TTAGAGAACTATTTTATTTT
1357902 GATTTAACAT
Statistics
Matches: 232, Mismatches: 22, Indels: 32
0.81 0.08 0.11
Matches are distributed among these distances:
309 3 0.01
310 86 0.37
311 12 0.05
312 3 0.01
314 1 0.00
315 2 0.01
316 25 0.11
317 1 0.00
318 19 0.08
319 9 0.04
320 5 0.02
322 3 0.01
323 17 0.07
325 46 0.20
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (304 bp):
TAAACTTTATTGTTTCATTTTTAATTTTTATTTGAAATATAAATTAATTAGATTATTTATTATGA
TTTTACACATTAAATTGTATTCGAGTGATAAGGTAAATTTAATTTAAATTTTAGTATAATTTTGT
TTTTAATTATAATTATTAGAATATTTATTTTGATTTTACATATTAAGTCGTATTTGAGTAAACTT
GATAAGTGTAGTTTAAATATTAATTATTTTTATTGAGTAATATAAATTATTAGAGAACTATTTTA
TTTTACAAATTAAATCGTATTTAAGTGGTTTGGTAAGTTTAGTT
Found at i:1364201 original size:31 final size:31
Alignment explanation
Indices: 1364131--1364189 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1364121 TTACGTCAAT
* *
1364131 GACCATATTTCAAACAAACTAAATTTTGAGG
1 GACCATATTGCAAACAAACTAAATGTTGAGG
*
1364162 GACCATATTGCAAACAGACTAAATGTTG
1 GACCATATTGCAAACAAACTAAATGTTG
1364190 GGGTATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (31 bp):
GACCATATTGCAAACAAACTAAATGTTGAGG
Found at i:1366185 original size:18 final size:20
Alignment explanation
Indices: 1366147--1366185 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
1366137 TAAGTGTTAA
*
1366147 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
1366167 TGAATTTT-A-ATTATATAT
1 TGAATTTTAAGATTATATAT
1366185 T
1 T
1366186 TGATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:1366470 original size:21 final size:20
Alignment explanation
Indices: 1366446--1366484 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1366436 ATTACTTGGA
1366446 GGGTACCGATTCCCTCCCAGG
1 GGGTACCGATTCCC-CCCAGG
*
1366467 GGGTATCGATTCCCCCCA
1 GGGTACCGATTCCCCCCA
1366485 TCTCATAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (20 bp):
GGGTACCGATTCCCCCCAGG
Found at i:1370996 original size:45 final size:46
Alignment explanation
Indices: 1370908--1370998 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
1370898 TTGAAATAGC
* * *
1370908 CTAAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCA
1 CTAAGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCA
1370954 CTAAGTGCATCAATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTAAGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCA
1370999 TTCGATGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (46 bp):
CTAAGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCA
Found at i:1373748 original size:23 final size:22
Alignment explanation
Indices: 1373718--1373797 Score: 99
Period size: 22 Copynumber: 3.6 Consensus size: 22
1373708 GCATGGCCTT
1373718 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
1373740 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
1373762 GTGTATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
1373784 ATGCATCGATGCAC
1 GTGCATCGATGCAC
1373798 TGTTAGGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.32
22 16 0.34
23 16 0.34
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1373772 original size:44 final size:42
Alignment explanation
Indices: 1373696--1373816 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 42
1373686 AAAACCCAAT
* ** *
1373696 GGATGCATCGATGCA-TGGCCTTGTGCATCGATGCACATTCAA
1 GGATGCATCGATGCACT-GTCAGGTGTATCGATGCACATTCAA
* *
1373738 GGCGTGCATCGGTGCACCT-TCATGGTGTATCGATGCACATTCAA
1 GG-ATGCATCGATGCA-CTGTCA-GGTGTATCGATGCACATTCAA
*
1373782 GGATGCATCGATGCACTGTTAGGTGTATCGATGCA
1 GGATGCATCGATGCACTGTCAGGTGTATCGATGCA
1373817 TGAAGCACAA
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
42 18 0.28
43 25 0.38
44 21 0.32
45 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (42 bp):
GGATGCATCGATGCACTGTCAGGTGTATCGATGCACATTCAA
Found at i:1373813 original size:20 final size:21
Alignment explanation
Indices: 1373722--1373816 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
1373712 GGCCTTGTGC
*
1373722 ATCGATGCACATTCAAGGCGTGC
1 ATCGATGCACATTCAA-G-GTGT
* * *
1373745 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
*
1373766 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACATTCAAGG-TGT
*
1373788 ATCGATGCAC-TGT-TAGGTGT
1 ATCGATGCACAT-TCAAGGTGT
1373808 ATCGATGCA
1 ATCGATGCA
1373817 TGAAGCACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 22 0.37
22 14 0.23
23 13 0.22
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:1377544 original size:21 final size:21
Alignment explanation
Indices: 1377510--1377549 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1377500 TAAGTTATGC
*
1377510 AAATCAGTATTTTTCTTTTCA
1 AAATCAGTAATTTTCTTTTCA
* *
1377531 AAATCATTAATTTTGTTTT
1 AAATCAGTAATTTTCTTTT
1377550 GCAATTCTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (21 bp):
AAATCAGTAATTTTCTTTTCA
Found at i:1377648 original size:22 final size:21
Alignment explanation
Indices: 1377606--1377645 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1377596 AAGACTATTT
1377606 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
1377627 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
1377646 ATAGAGTCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1379298 original size:46 final size:46
Alignment explanation
Indices: 1379247--1379343 Score: 194
Period size: 46 Copynumber: 2.1 Consensus size: 46
1379237 GTACAAGTAG
1379247 TGCTCTTGAAAGAAAAATGAATATTGAATGAAAAATAGGCTTGAAA
1 TGCTCTTGAAAGAAAAATGAATATTGAATGAAAAATAGGCTTGAAA
1379293 TGCTCTTGAAAGAAAAATGAATATTGAATGAAAAATAGGCTTGAAA
1 TGCTCTTGAAAGAAAAATGAATATTGAATGAAAAATAGGCTTGAAA
1379339 TGCTC
1 TGCTC
1379344 AAACTTGAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (46 bp):
TGCTCTTGAAAGAAAAATGAATATTGAATGAAAAATAGGCTTGAAA
Found at i:1382663 original size:18 final size:20
Alignment explanation
Indices: 1382625--1382663 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
1382615 TAAGTGTTAA
*
1382625 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
1382645 TGAATTTT-A-ATTATATAT
1 TGAATTTTAAGATTATATAT
1382663 T
1 T
1382664 CGATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:1384535 original size:23 final size:23
Alignment explanation
Indices: 1384494--1384557 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1384484 TAGTGCAGGA
* *
1384494 GGAATCGA-TACCCCATTGAAAG
1 GGAATCGATTCCCCCTTTGAAAG
*
1384516 GGAA-CTGATTCCCCCTTTGAATG
1 GGAATC-GATTCCCCCTTTGAAAG
1384539 GGAATCGATTCCCCTCTTT
1 GGAATCGATTCCCC-CTTT
1384558 AGGGAATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 1 0.03
22 6 0.17
23 23 0.66
24 5 0.14
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (23 bp):
GGAATCGATTCCCCCTTTGAAAG
Found at i:1386828 original size:18 final size:20
Alignment explanation
Indices: 1386790--1386828 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
1386780 TAAGTGTTAA
*
1386790 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
1386810 TGAATTTT-A-ATTATATAT
1 TGAATTTTAAGATTATATAT
1386828 T
1 T
1386829 CGATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:1389024 original size:27 final size:27
Alignment explanation
Indices: 1388984--1389042 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1388974 ATTTATTTTT
*
1388984 AATATTGATATTAATCACATTAATTCA
1 AATATTGATATTAATCACATTAATTAA
* *
1389011 AATATTGATTTTAATCACATTCATTAA
1 AATATTGATATTAATCACATTAATTAA
1389038 AATAT
1 AATAT
1389043 AGCGTCAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.42
Consensus pattern (27 bp):
AATATTGATATTAATCACATTAATTAA
Found at i:1391927 original size:11 final size:11
Alignment explanation
Indices: 1391913--1391955 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1391903 AAATAAATTA
1391913 ATTATTAAAAT
1 ATTATTAAAAT
**
1391924 ATTATTAATTT
1 ATTATTAAAAT
*
1391935 ATTATAATAAAT
1 ATTATTA-AAAT
1391947 ATTATTAAA
1 ATTATTAAA
1391956 GTTTCAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTATTAAAAT
Found at i:1392112 original size:46 final size:45
Alignment explanation
Indices: 1392021--1392113 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 45
1392011 AACGATATTT
*
1392021 TTTTAACATTTTTACTATAATACTAAATCAATTGATGATCTAATTA
1 TTTTAACATTTTTACTATAATACTAAATCAATTGAT-ATCAAATTA
* *
1392067 TTTTAACATTTTTACTTTAAATACTAAATCAATCTTAT-TCAAATTA
1 TTTTAACATTTTTACTAT-AATACTAAATCAAT-TGATATCAAATTA
1392113 T
1 T
1392114 ACTAATGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
46 25 0.60
47 14 0.33
48 3 0.07
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (45 bp):
TTTTAACATTTTTACTATAATACTAAATCAATTGATATCAAATTA
Found at i:1392827 original size:16 final size:17
Alignment explanation
Indices: 1392797--1392829 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1392787 GAACCATCCC
1392797 ATTTCTTCTTCTTCCTT
1 ATTTCTTCTTCTTCCTT
1392814 ATTTCTTC-TCTTCCTT
1 ATTTCTTCTTCTTCCTT
1392830 CTCTCAACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTCTTCTTCTTCCTT
Found at i:1393434 original size:66 final size:65
Alignment explanation
Indices: 1393297--1393430 Score: 216
Period size: 66 Copynumber: 2.1 Consensus size: 65
1393287 ACCCATTCAA
* *
1393297 GGGGAACCGATACCCTCAACGAATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCAGG
* *
1393362 GGGGAACCGATACCCCTCAACGGATATGAAATTCCAGAATGCTAGAGGGGAACCGATA-CCCCAG
1 GGGGAACCGATA-CCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCAG
1393426 G
65 G
1393427 GGGG
1 GGGG
1393431 GAACGATTCC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 23 0.36
66 41 0.64
ACGTcount: A:0.32, C:0.25, G:0.28, T:0.15
Consensus pattern (65 bp):
GGGGAACCGATACCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCCAGG
Found at i:1394072 original size:23 final size:23
Alignment explanation
Indices: 1394039--1394098 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1394029 ATCATTATAT
*
1394039 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
1394062 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
1394085 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1394099 TTATACGAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:1400121 original size:21 final size:21
Alignment explanation
Indices: 1400079--1400121 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1400069 TTTATGGGTT
* * *
1400079 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1400100 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1400121 A
1 A
1400122 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1400188 original size:67 final size:67
Alignment explanation
Indices: 1400101--1400252 Score: 225
Period size: 67 Copynumber: 2.3 Consensus size: 67
1400091 ACCCATTCAA
* *
1400101 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATA-CCCCA
1400166 -GG
65 GGG
* * *
1400168 GGGGAACCGATACCCCCTCAACGGATATGAAATTCTAGAATGCTAGAGGGGAACCGATACCCCAG
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCA-
1400233 GGG
65 GGG
*
1400236 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
1400253 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
66 5 0.06
67 54 0.70
68 18 0.23
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATACTAGAGGGGAACCGATACCCCAG
GG
Found at i:1400909 original size:23 final size:23
Alignment explanation
Indices: 1400842--1400901 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1400832 ATCATTATAT
*
1400842 GGCACTACGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
1400865 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
1400888 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1400902 TTTATACGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:1408156 original size:2 final size:2
Alignment explanation
Indices: 1408149--1408177 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1408139 AATATTTATT
1408149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1408178 TAGTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1408207 original size:73 final size:71
Alignment explanation
Indices: 1408092--1408229 Score: 183
Period size: 73 Copynumber: 1.9 Consensus size: 71
1408082 CTATTTTTAT
* *
1408092 TATATATATATATGTATTTATTTCTTTTGTTTATTTAATTT-AACGTTAATATTTATTTATATAT
1 TATATATATATATGTATTTATTTCTTTTGATTATTTAATTTAAACATT--T-TTTATTTATATAT
1408156 ATATATATA
63 ATATATATA
*
1408165 TATATATATATAT-TAGTTTATTTCTTTTGATTA-TTATTTTTAAACATTTTTTATTTATATATA
1 TATATATATATATGTA-TTTATTTCTTTTGATTATTTA-ATTTAAACATTTTTTATTTATATATA
1408228 TA
64 TA
1408230 ACCTTTTCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
71 16 0.27
72 6 0.10
73 32 0.54
74 5 0.08
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (71 bp):
TATATATATATATGTATTTATTTCTTTTGATTATTTAATTTAAACATTTTTTATTTATATATATA
TATATA
Found at i:1408283 original size:24 final size:24
Alignment explanation
Indices: 1408256--1408321 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
1408246 ATTTTTTTAT
1408256 TTTTTCACTTTTTCTTTATTCAA-C
1 TTTTTCACTTTTTCTTTATT-AACC
*
1408280 -TTTTCAACTTTTTCATT-TTAACC
1 TTTTTC-ACTTTTTCTTTATTAACC
*
1408303 TTTTTGACTTTTT-TTTATT
1 TTTTTCACTTTTTCTTTATT
1408322 TTTTGAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
22 4 0.11
23 17 0.49
24 14 0.40
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTTCACTTTTTCTTTATTAACC
Found at i:1419731 original size:21 final size:21
Alignment explanation
Indices: 1419675--1419731 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1419665 ATTACGGTAC
*
1419675 TGACGTGGTAGTTCACAATGT
1 TGACGTGGTAGTTCACAATAT
* * *
1419696 TGATGTGG-CGATTCACGATAT
1 TGACGTGGTAG-TTCACAATAT
1419717 TGACGTGGTAGTTCA
1 TGACGTGGTAGTTCA
1419732 TCTGTCATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (21 bp):
TGACGTGGTAGTTCACAATAT
Found at i:1421164 original size:28 final size:29
Alignment explanation
Indices: 1421132--1421192 Score: 106
Period size: 28 Copynumber: 2.1 Consensus size: 29
1421122 ATTAGGTTAC
1421132 AATTTCCAAGTGTTTTGTT-CTCACAAAA
1 AATTTCCAAGTGTTTTGTTGCTCACAAAA
*
1421160 AATTTCCAAGTGTTTTGTTGCTCATAAAA
1 AATTTCCAAGTGTTTTGTTGCTCACAAAA
1421189 AATT
1 AATT
1421193 GCCACGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 19 0.61
29 12 0.39
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
AATTTCCAAGTGTTTTGTTGCTCACAAAA
Found at i:1430907 original size:43 final size:44
Alignment explanation
Indices: 1430858--1430963 Score: 142
Period size: 43 Copynumber: 2.4 Consensus size: 44
1430848 GAAGGACCAT
* * *
1430858 TACGTCCCTAAGGACCACTGGATATGTCACG-AGGACCACTGGA
1 TACGTCCCGAAGGACCACTGGATATGTCACGAAAGACCACTAGA
* *
1430901 TACGTCCCGAATGACCACTGGATATGTCCCGAAAGACCACTAGA
1 TACGTCCCGAAGGACCACTGGATATGTCACGAAAGACCACTAGA
* *
1430945 TATGTCCCGAAGGGCCACT
1 TACGTCCCGAAGGACCACT
1430964 ATAAACCCTC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
43 28 0.52
44 26 0.48
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (44 bp):
TACGTCCCGAAGGACCACTGGATATGTCACGAAAGACCACTAGA
Found at i:1430964 original size:22 final size:22
Alignment explanation
Indices: 1430861--1430963 Score: 136
Period size: 22 Copynumber: 4.7 Consensus size: 22
1430851 GGACCATTAC
*
1430861 GTCCCTAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* *
1430883 GTCACG-AGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAT
*
1430904 GTCCCGAATGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* *
1430926 GTCCCGAAAGACCACTAGATAT
1 GTCCCGAAGGACCACTGGATAT
*
1430948 GTCCCGAAGGGCCACT
1 GTCCCGAAGGACCACT
1430964 ATAAACCCTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
21 19 0.27
22 51 0.73
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.18
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAT
Found at i:1431599 original size:44 final size:45
Alignment explanation
Indices: 1431551--1431635 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
1431541 TACACAAATC
*
1431551 TCATTCGATGTTTGAATATT-AAGGGGTGCATCGATACACTGATG
1 TCATTCGATGTTTGAATATTAAAGGAGTGCATCGATACACTGATG
* ** *
1431595 TCATTTGATGTTTTTATTTTAAAGGAGTGCATCGATACACT
1 TCATTCGATGTTTGAATATTAAAGGAGTGCATCGATACACT
1431636 TCATGTGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 16 0.46
45 19 0.54
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (45 bp):
TCATTCGATGTTTGAATATTAAAGGAGTGCATCGATACACTGATG
Found at i:1434389 original size:16 final size:16
Alignment explanation
Indices: 1434368--1434400 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1434358 CCCATTTATC
1434368 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
1434384 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
1434400 A
1 A
1434401 AAACACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:1436696 original size:23 final size:21
Alignment explanation
Indices: 1436670--1436727 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
1436660 TTCCCTTGTG
1436670 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
1436693 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
1436713 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
1436728 TCTGCAGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 2 0.06
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:1449222 original size:42 final size:45
Alignment explanation
Indices: 1449162--1449245 Score: 120
Period size: 42 Copynumber: 1.9 Consensus size: 45
1449152 TTGAAACATA
* *
1449162 TAAATTAAATAAATATATAATA-ATAATATA-TTATTAAATATAC
1 TAAATTAAATAAATATATAATATAAAATATAGTAATTAAATATAC
*
1449205 TAAA-TAATTAAATATATAATATAAAATATAGTAATTAAATA
1 TAAATTAAATAAATATATAATATAAAATATAGTAATTAAATA
1449246 GATATTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 16 0.44
43 11 0.31
44 9 0.25
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (45 bp):
TAAATTAAATAAATATATAATATAAAATATAGTAATTAAATATAC
Found at i:1449228 original size:17 final size:16
Alignment explanation
Indices: 1449159--1449228 Score: 67
Period size: 17 Copynumber: 4.5 Consensus size: 16
1449149 AATTTGAAAC
*
1449159 ATATA-AATTAAATAA
1 ATATATAATTAAATAT
1449174 ATATATAA-T-AATA-
1 ATATATAATTAAATAT
*
1449187 ATATATTATTAAATAT
1 ATATATAATTAAATAT
*
1449203 ACTAAATAATTAAATAT
1 A-TATATAATTAAATAT
1449220 ATAATATAA
1 AT-ATATAA
1449229 AATATAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 7 0.16
14 5 0.11
15 10 0.22
16 4 0.09
17 19 0.42
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATATAATTAAATAT
Found at i:1449233 original size:12 final size:12
Alignment explanation
Indices: 1449171--1449245 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 12
1449161 ATAAATTAAA
1449171 TAAATATATAAT
1 TAAATATATAAT
* *
1449183 AATAATATATTAT
1 TA-AATATATAAT
1449196 TAAATATACTAAATAAT
1 T-AA-ATA-T--ATAAT
1449213 TAAATATATAAT
1 TAAATATATAAT
1449225 ATAAAATATAGTAAT
1 -T-AAATATA-TAAT
1449240 TAAATA
1 TAAATA
1449246 GATATTTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
12 6 0.12
13 16 0.32
14 13 0.26
15 8 0.16
16 2 0.04
17 5 0.10
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (12 bp):
TAAATATATAAT
Found at i:1452744 original size:19 final size:20
Alignment explanation
Indices: 1452709--1452748 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1452699 GATTATAAAA
1452709 AAAATAAATTTTAAAATTTT
1 AAAATAAATTTTAAAATTTT
1452729 AAAAT-AATTATT-AAATTTT
1 AAAATAAATT-TTAAAATTTT
1452748 A
1 A
1452749 TTAAAACATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
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 (20 bp):
AAAATAAATTTTAAAATTTT
Found at i:1452944 original size:20 final size:21
Alignment explanation
Indices: 1452919--1452963 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1452909 TGATTATAAA
1452919 AAAATAAATT-TTAAAATT-TT
1 AAAAT-AATTATTAAAATTATT
*
1452939 AAAATAATTATTAAATTTATT
1 AAAATAATTATTAAAATTATT
1452960 AAAA
1 AAAA
1452964 CATCACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 12 0.55
21 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATAATTATTAAAATTATT
Found at i:1452994 original size:211 final size:212
Alignment explanation
Indices: 1452630--1453053 Score: 784
Period size: 211 Copynumber: 2.0 Consensus size: 212
1452620 TTGCTGATGC
*
1452630 TGTAATTATATACACAATCCCGACAAACCTTTGTAAAAAAAATTAAAAATAGGTAAATTACCTCC
1 TGTAATTATATACACAATCACGACAAACCTTTGTAAAAAAAATTAAAAATAGGTAAATTACCTCC
1452695 AAATGATTATAAAAAAAATAAATTTTAAAATTTTAAAATAATTATTAAATTTTATTAAAACATCA
66 AAATGATTATAAAAAAAATAAATTTTAAAATTTTAAAATAATTATTAAATTTTATTAAAACATCA
1452760 CTATTATTTGTAATTTTATTATAATTCAATAAATTTGAGATTCTT-AAACCTCATAATGATGATA
131 CTATTATTTGTAATTTTATTATAATTCAATAAATTTGAGATTCTTAAAACCTCATAATGATGATA
1452824 ATTTATTGTAGTTCAAT
196 ATTTATTGTAGTTCAAT
1452841 TGTAATTATATACACAATCACGACAAACCTTTGTAAAAAAAATTAAAAATAGGTAAATTACCTCC
1 TGTAATTATATACACAATCACGACAAACCTTTGTAAAAAAAATTAAAAATAGGTAAATTACCTCC
1452906 AAATGATTAT-AAAAAAATAAATTTTAAAATTTTAAAATAATTATTAAA-TTTATTAAAACATCA
66 AAATGATTATAAAAAAAATAAATTTTAAAATTTTAAAATAATTATTAAATTTTATTAAAACATCA
1452969 CTATTA-TTGTAATATTTTTATTATAATTCAATAAATTTGAGATTCTTAAAACCTCATAATGATG
131 CTATTATTTGT-A-A-TTTTATTATAATTCAATAAATTTGAGATTCTTAAAACCTCATAATGATG
1453033 ATAATTTATTGTAGTTCAAT
193 ATAATTTATTGTAGTTCAAT
1453053 T
1 T
1453054 TGAGAATAAT
Statistics
Matches: 208, Mismatches: 1, Indels: 7
0.96 0.00 0.03
Matches are distributed among these distances:
208 4 0.02
209 22 0.11
210 39 0.19
211 106 0.51
212 37 0.18
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (212 bp):
TGTAATTATATACACAATCACGACAAACCTTTGTAAAAAAAATTAAAAATAGGTAAATTACCTCC
AAATGATTATAAAAAAAATAAATTTTAAAATTTTAAAATAATTATTAAATTTTATTAAAACATCA
CTATTATTTGTAATTTTATTATAATTCAATAAATTTGAGATTCTTAAAACCTCATAATGATGATA
ATTTATTGTAGTTCAAT
Found at i:1461051 original size:32 final size:31
Alignment explanation
Indices: 1461015--1461079 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 31
1461005 TAAAGAATTT
***
1461015 AACTAAAGACGCCGGGTAATCCTATGGAGCAA
1 AACTAAAGACGCCGAACAAT-CTATGGAGCAA
*
1461047 AACTAAAGACGTCGAACAATCTATGGAGCAA
1 AACTAAAGACGCCGAACAATCTATGGAGCAA
1461078 AA
1 AA
1461080 TTTTAGTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (31 bp):
AACTAAAGACGCCGAACAATCTATGGAGCAA
Found at i:1462494 original size:15 final size:15
Alignment explanation
Indices: 1462476--1462506 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1462466 AAATTCTAAA
1462476 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1462491 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1462506 T
1 T
1462507 CTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1462589 original size:21 final size:22
Alignment explanation
Indices: 1462565--1462608 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1462555 ATTTTAATTT
1462565 TAATTAATATT-AAATTTTACA
1 TAATTAATATTAAAATTTTACA
*
1462586 TAATTTATATTAAAATTTTACA
1 TAATTAATATTAAAATTTTACA
1462608 T
1 T
1462609 CAACATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTAATATTAAAATTTTACA
Found at i:1472594 original size:22 final size:21
Alignment explanation
Indices: 1472563--1472626 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1472553 ATATGAAATT
* * *
1472563 TTATCACGAATGACCTGTGAA
1 TTATCCCGAAGGACCTATGAA
* *
1472584 TATGTCCCGAAGGACCTATGAG
1 T-TATCCCGAAGGACCTATGAA
1472606 TTATCCCGAAGGACCTATGAA
1 TTATCCCGAAGGACCTATGAA
1472627 ACCCTCGACT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (21 bp):
TTATCCCGAAGGACCTATGAA
Found at i:1492455 original size:13 final size:13
Alignment explanation
Indices: 1492434--1492464 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1492424 CACCATGCCT
*
1492434 GCCTTGGTGATCA
1 GCCTCGGTGATCA
1492447 GCCTCGGTGATCA
1 GCCTCGGTGATCA
1492460 GCCTC
1 GCCTC
1492465 TCTCGAGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.32, G:0.29, T:0.26
Consensus pattern (13 bp):
GCCTCGGTGATCA
Found at i:1494042 original size:19 final size:19
Alignment explanation
Indices: 1494018--1494066 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1494008 TACCTAGTGT
*
1494018 ATCGGTACACTTCAGGTGC
1 ATCGGTACACTCCAGGTGC
1494037 ATCGGTACACTCCAGGTGC
1 ATCGGTACACTCCAGGTGC
1494056 ATCGGTACACT
1 ATCGGTACACT
1494067 AATTGCATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (19 bp):
ATCGGTACACTCCAGGTGC
Found at i:1504583 original size:22 final size:22
Alignment explanation
Indices: 1504556--1504607 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1504546 AGAGTTACAA
* *
1504556 GAGTTATTTGATTTAATTCCAG
1 GAGTTATATGATATAATTCCAG
* * *
1504578 GGGTTACATGATATAATTTCAG
1 GAGTTATATGATATAATTCCAG
1504600 GAGTTATA
1 GAGTTATA
1504608 ACAGCTGAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (22 bp):
GAGTTATATGATATAATTCCAG
Found at i:1506634 original size:16 final size:16
Alignment explanation
Indices: 1506613--1506670 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
1506603 GGTATTACCC
1506613 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
1506629 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1506645 GGCCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1506661 GACATGTTTT
1 GACCTGTTTT
1506671 TAACTTGATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.17, C:0.28, G:0.16, T:0.40
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:1506940 original size:14 final size:14
Alignment explanation
Indices: 1506918--1506964 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1506908 TGCAAAGGAA
*
1506918 AATTAATATAGTTT
1 AATTTATATAGTTT
1506932 AATTTATATA----
1 AATTTATATAGTTT
1506942 AA-TTATATAGTTT
1 AATTTATATAGTTT
1506955 AATTTATATA
1 AATTTATATA
1506965 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:1506951 original size:23 final size:24
Alignment explanation
Indices: 1506917--1506966 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1506907 ATGCAAAGGA
1506917 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1506941 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1506964 AAA
1 AAA
1506967 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:1507142 original size:7 final size:7
Alignment explanation
Indices: 1507130--1507200 Score: 63
Period size: 7 Copynumber: 10.3 Consensus size: 7
1507120 TCTATTTATA
1507130 TTAGGGT
1 TTAGGGT
1507137 TTAGGGT
1 TTAGGGT
1507144 TTAGGGT
1 TTAGGGT
*
1507151 TTATGGT
1 TTAGGGT
***
1507158 TTAAAAT
1 TTAGGGT
1507165 TTAGGGT
1 TTAGGGT
*
1507172 TTAAGGT
1 TTAGGGT
* *
1507179 TTA-TGA
1 TTAGGGT
*
1507185 TTAAGGT
1 TTAGGGT
1507192 TTAGGGT
1 TTAGGGT
1507199 TT
1 TT
1507201 CTATAATTTA
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
6 4 0.08
7 46 0.92
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (7 bp):
TTAGGGT
Found at i:1507147 original size:14 final size:14
Alignment explanation
Indices: 1507134--1507200 Score: 73
Period size: 14 Copynumber: 4.9 Consensus size: 14
1507124 TTTATATTAG
*
1507134 GGTTTAGGGTTTAG
1 GGTTTAGGGTTTAA
*
1507148 GGTTTATGGTTTAA
1 GGTTTAGGGTTTAA
**
1507162 AATTTAGGGTTTAA
1 GGTTTAGGGTTTAA
* *
1507176 GGTTTA-TGATTAA
1 GGTTTAGGGTTTAA
1507189 GGTTTAGGGTTT
1 GGTTTAGGGTTT
1507201 CTATAATTTA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 11 0.27
14 30 0.73
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:1507289 original size:2 final size:2
Alignment explanation
Indices: 1507284--1507340 Score: 62
Period size: 2 Copynumber: 28.0 Consensus size: 2
1507274 TTATATAGTT
**
1507284 TA TA TA TA TA TA TA TA TA TA TA GG T- 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
*
1507325 GTT TA TA TA TA CTA TA
1 -TA TA TA TA TA -TA TA
1507341 CATGATTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
1 1 0.02
2 43 0.91
3 3 0.06
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1507299 original size:19 final size:19
Alignment explanation
Indices: 1507290--1507340 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
1507280 AGTTTATATA
1507290 TATATATATATATATAGGT
1 TATATATATATATATAGGT
*
1507309 TATATATATATATATAGTT
1 TATATATATATATATAGGT
1507328 TATATATACTATA
1 TATATATA-TATA
1507341 CATGATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (19 bp):
TATATATATATATATAGGT
Found at i:1507303 original size:25 final size:25
Alignment explanation
Indices: 1507275--1507324 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1507265 TAATTTATTT
*
1507275 TATATAGTTTATATATATATATATA
1 TATATAGGTTATATATATATATATA
1507300 TATATAGGTTATATATATATATATA
1 TATATAGGTTATATATATATATATA
1507325 GTTTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (25 bp):
TATATAGGTTATATATATATATATA
Found at i:1507364 original size:14 final size:16
Alignment explanation
Indices: 1507332--1507365 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
1507322 ATAGTTTATA
1507332 TATACTATACATGATT
1 TATACTATACATGATT
1507348 TATAC-ATACAT-ATT
1 TATACTATACATGATT
1507362 TATA
1 TATA
1507366 TAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 6 0.33
16 5 0.28
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (16 bp):
TATACTATACATGATT
Found at i:1507761 original size:28 final size:28
Alignment explanation
Indices: 1507693--1507770 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
1507683 TTATATTAGG
** * *
1507693 GTTTATGGTTTAGGGTTTAGTGTTTAGT
1 GTTTATGGTTTAAAGTTTAGGGTATAGT
* * *
1507721 GTGTATGATTTAAAGTTTAGGGTATATT
1 GTTTATGGTTTAAAGTTTAGGGTATAGT
1507749 GTTTATGGTTT-AAGATTTAGGG
1 GTTTATGGTTTAAAG-TTTAGGG
1507771 GTTTTTAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 3 0.08
28 37 0.93
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (28 bp):
GTTTATGGTTTAAAGTTTAGGGTATAGT
Found at i:1507766 original size:35 final size:35
Alignment explanation
Indices: 1507700--1507767 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
1507690 AGGGTTTATG
* *
1507700 GTTTAGGGTTTAGTGTTTAGTGTGTATGATTTAAA
1 GTTTAGGGTATAGTGTTTAGTGTGTAAGATTTAAA
* *
1507735 GTTTAGGGTATATTGTTTA-TGGTTTAAGATTTA
1 GTTTAGGGTATAGTGTTTAGT-GTGTAAGATTTA
1507768 GGGGTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.04
35 27 0.96
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (35 bp):
GTTTAGGGTATAGTGTTTAGTGTGTAAGATTTAAA
Found at i:1507967 original size:16 final size:16
Alignment explanation
Indices: 1507946--1507983 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1507936 ATATATAGTT
*
1507946 TATATACATGCATACA
1 TATATACATACATACA
*
1507962 TATATACATACATATA
1 TATATACATACATACA
1507978 TATATA
1 TATATA
1507984 TATATGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (16 bp):
TATATACATACATACA
Found at i:1508227 original size:19 final size:19
Alignment explanation
Indices: 1508203--1508276 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 19
1508193 TTCTATTCTC
1508203 TCTAAATTCTCAATTTCCT
1 TCTAAATTCTCAATTTCCT
1508222 TCTAAATTCTCAATTTCTCTATAT
1 TCTAAATTCTCAATTTC-C----T
1508246 TCTCAAAATTTCTCAATTTCCT
1 TCT--AAA-TTCTCAATTTCCT
1508268 TCTAAATTC
1 TCTAAATTC
1508277 CCAAATAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
19 20 0.43
20 4 0.09
22 4 0.09
24 4 0.09
26 4 0.09
27 11 0.23
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTAAATTCTCAATTTCCT
Found at i:1508264 original size:46 final size:44
Alignment explanation
Indices: 1508189--1508276 Score: 133
Period size: 46 Copynumber: 2.0 Consensus size: 44
1508179 AACTTCCCAA
*
1508189 AATTTTCTATTCTCTCTAAATTCTCAATTTCCTTCTAAATTCTC
1 AATTTTCTATTCTCTCAAAATTCTCAATTTCCTTCTAAATTCTC
1508233 AATTTCTCTATAT-TCTCAAAATTTCTCAATTTCCTTCTAAATTC
1 AATTT-TCTAT-TCTCTCAAAA-TTCTCAATTTCCTTCTAAATTC
1508277 CCAAATAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 5 0.12
45 12 0.30
46 23 0.57
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.49
Consensus pattern (44 bp):
AATTTTCTATTCTCTCAAAATTCTCAATTTCCTTCTAAATTCTC
Found at i:1508430 original size:30 final size:32
Alignment explanation
Indices: 1508352--1508456 Score: 85
Period size: 34 Copynumber: 3.3 Consensus size: 32
1508342 ACTCTGAATA
**
1508352 ATATATATATATAT-TA-TATTA-ATATAAATT
1 ATATATATATATATATACT-TTATATATAGTTT
* *
1508382 ATAGTTTATAAACTATATACTTT-T-TATAGTTT
1 ATA-TATATATA-TATATACTTTATATATAGTTT
*
1508414 ATATATATATATATATAGTTTGCATATATAGTTT
1 ATATATATATATATATACTTT--ATATATAGTTT
1508448 ATATATATA
1 ATATATATA
1508457 GTTCATATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
30 12 0.20
31 12 0.20
32 12 0.20
33 5 0.08
34 18 0.31
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (32 bp):
ATATATATATATATATACTTTATATATAGTTT
Found at i:1508464 original size:13 final size:13
Alignment explanation
Indices: 1508421--1508544 Score: 87
Period size: 13 Copynumber: 9.6 Consensus size: 13
1508411 TTTATATATA
1508421 TATATATATAGTT
1 TATATATATAGTT
**
1508434 TGCATATATAGTT
1 TATATATATAGTT
1508447 TATATATATAGTT
1 TATATATATAGTT
* * *
1508460 CATATAAACATAATT
1 --TATATATATAGTT
*
1508475 TATATATATAGCT
1 TATATATATAGTT
1508488 TATA-ATA-A--T
1 TATATATATAGTT
* *
1508497 TATATAGTTTA-TAA
1 TATATA-TATAGT-T
*
1508511 TATAAATATAGTT
1 TATATATATAGTT
*
1508524 TATATATATAATT
1 TATATATATAGTT
1508537 TATATATA
1 TATATATA
1508545 AACTTATATT
Statistics
Matches: 85, Mismatches: 18, Indels: 16
0.71 0.15 0.13
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 2 0.02
12 4 0.05
13 57 0.67
14 6 0.07
15 10 0.12
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (13 bp):
TATATATATAGTT
Found at i:1508519 original size:18 final size:18
Alignment explanation
Indices: 1508475--1508534 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
1508465 AAACATAATT
* *
1508475 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
1508493 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
1508511 TATAAATATAGTTTATATA
1 TATAAATATAGTTTATA-A
1508530 TATAA
1 TATAA
1508535 TTTATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 29 0.78
19 7 0.19
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:1521257 original size:18 final size:19
Alignment explanation
Indices: 1521234--1521270 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1521224 AGTATCTTAC
*
1521234 AGTGAAG-AACAAGGACAA
1 AGTGAAGAAACAAAGACAA
1521252 AGTGAAGAAACAAAGACAA
1 AGTGAAGAAACAAAGACAA
1521271 GAAGACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.59, C:0.11, G:0.24, T:0.05
Consensus pattern (19 bp):
AGTGAAGAAACAAAGACAA
Found at i:1526558 original size:55 final size:55
Alignment explanation
Indices: 1526466--1526572 Score: 187
Period size: 55 Copynumber: 1.9 Consensus size: 55
1526456 ACATGGGTGA
*
1526466 CCTGCACAAGGGGTATCATGGCACTCTAATAATATGTCGACATCCCTTTTTTCAC
1 CCTGCACAAGGGGTATCATGGCACTCTAATAAAATGTCGACATCCCTTTTTTCAC
* *
1526521 CCTGCACAAGGGGTATCATGGCACTCTCATAAAATGTCGTCATCCCTTTTTT
1 CCTGCACAAGGGGTATCATGGCACTCTAATAAAATGTCGACATCCCTTTTTT
1526573 TTACAAGATA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (55 bp):
CCTGCACAAGGGGTATCATGGCACTCTAATAAAATGTCGACATCCCTTTTTTCAC
Found at i:1527318 original size:20 final size:21
Alignment explanation
Indices: 1527274--1527318 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1527264 AAGATTCCTC
* * *
1527274 CTAATTAACATAAATGAAGAT
1 CTAATTAAAACAAATGAAAAT
1527295 CTAATTAAAACAAA-GAAAAT
1 CTAATTAAAACAAATGAAAAT
1527315 CTAA
1 CTAA
1527319 AGGTGTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.24
Consensus pattern (21 bp):
CTAATTAAAACAAATGAAAAT
Found at i:1527517 original size:35 final size:35
Alignment explanation
Indices: 1527463--1527546 Score: 150
Period size: 35 Copynumber: 2.4 Consensus size: 35
1527453 AAAAACTAAT
*
1527463 AAAAACTAAAAGGACATTAAATTAAAATTTGACTAC
1 AAAAA-TAAAAGGAAATTAAATTAAAATTTGACTAC
1527499 AAAAATAAAAGGAAATTAAATTAAAATTTGACTAC
1 AAAAATAAAAGGAAATTAAATTAAAATTTGACTAC
1527534 AAAAATAAAAGGA
1 AAAAATAAAAGGA
1527547 TTGAAGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 42 0.89
36 5 0.11
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.23
Consensus pattern (35 bp):
AAAAATAAAAGGAAATTAAATTAAAATTTGACTAC
Done.