Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold28
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: 2815568
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.30
Warning! 166732 characters in sequence are not A, C, G, or T
File 10 of 16
Found at i:1573351 original size:24 final size:23
Alignment explanation
Indices: 1573283--1573348 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
1573273 CAAAATTAAC
*
1573283 TTTTAAATAAAATAATTTTATTA
1 TTTTAAATATAATAATTTTATTA
*
1573306 TTTTCACATAATAA-AATTTTATTA
1 TTTT-AAAT-ATAATAATTTTATTA
*
1573330 TTTTAAATATAATTATTTT
1 TTTTAAATATAATAATTTT
1573349 TATATTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 4 0.11
23 12 0.33
24 17 0.47
25 3 0.08
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTAAATATAATAATTTTATTA
Found at i:1573696 original size:4 final size:4
Alignment explanation
Indices: 1573687--1573711 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1573677 AAGTAGGGGG
1573687 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1573712 GAAACTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1573878 original size:22 final size:22
Alignment explanation
Indices: 1573852--1573911 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
1573842 CTAATTATTT
1573852 TTTATAAAAATAATTTTCATA-A
1 TTTATAAAAATAATTTT-ATACA
*
1573874 TTTATAAATA-AATTTTATACA
1 TTTATAAAAATAATTTTATACA
*
1573895 TATTAATAATAATAATT
1 T-TT-ATAAAAATAATT
1573912 AATGTATTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.10
21 8 0.26
22 11 0.35
23 5 0.16
24 4 0.13
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTATAAAAATAATTTTATACA
Found at i:1575944 original size:8 final size:8
Alignment explanation
Indices: 1575933--1575976 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
1575923 TTAATCATAA
1575933 TATTAAAT
1 TATTAAAT
1575941 TATTAAAT
1 TATTAAAT
*
1575949 TATTAAAA
1 TATTAAAT
1575957 TA-TAAA-
1 TATTAAAT
1575963 TATT-AA-
1 TATTAAAT
1575969 TATTAAAT
1 TATTAAAT
1575977 ACTTAAAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 8 0.25
7 7 0.22
8 17 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TATTAAAT
Found at i:1576037 original size:21 final size:21
Alignment explanation
Indices: 1575960--1576042 Score: 60
Period size: 23 Copynumber: 3.7 Consensus size: 21
1575950 ATTAAAATAT
*
1575960 AAATATTAATATTAAATACTTAA
1 AAATATT-ATATT-AATATTTAA
* * *
1575983 AGTGATATTAT-TTATTATTAAA
1 A--AATATTATATTAATATTTAA
1576005 AAATTAATTATATTAATATTTAA
1 AAA-T-ATTATATTAATATTTAA
*
1576028 AAATATTATAATAAT
1 AAATATTATATTAAT
1576043 TGTCAAATAT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
20 1 0.02
21 11 0.23
22 13 0.28
23 15 0.32
24 2 0.04
25 5 0.11
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (21 bp):
AAATATTATATTAATATTTAA
Found at i:1576197 original size:22 final size:22
Alignment explanation
Indices: 1576172--1576222 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
1576162 GTAAACTATT
1576172 TAATTATATTAAATACTT-AAAA
1 TAATTATATTAAATA-TTAAAAA
* *
1576194 TAA-TACTATTTATTATTAAAAA
1 TAATTA-TATTAAATATTAAAAA
1576216 TAATTAT
1 TAATTAT
1576223 GAATAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 4 0.17
22 18 0.75
23 2 0.08
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATTATATTAAATATTAAAAA
Found at i:1576458 original size:33 final size:32
Alignment explanation
Indices: 1576421--1576522 Score: 79
Period size: 32 Copynumber: 3.1 Consensus size: 32
1576411 AAATTTAAAC
1576421 ATATTGTTAATGTTACAATTTATTATTAAAATA
1 ATATTGTTAATGTTA-AATTTATTATTAAAATA
*
1576454 ATATTTGTTTAA--ATAATATTT-TTATTAAAATA
1 ATA-TTG-TTAATGTTAA-ATTTATTATTAAAATA
**
1576486 ATA-AATT-ATGTTAATAATTTATTATTAAAAATA
1 ATATTGTTAATGTT-A-AATTTATTATT-AAAATA
1576519 ATAT
1 ATAT
1576523 ATATTTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
28 1 0.02
29 2 0.04
30 1 0.02
31 5 0.09
32 21 0.38
33 18 0.33
34 3 0.05
35 4 0.07
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (32 bp):
ATATTGTTAATGTTAAATTTATTATTAAAATA
Found at i:1576469 original size:15 final size:17
Alignment explanation
Indices: 1576444--1576488 Score: 67
Period size: 15 Copynumber: 2.8 Consensus size: 17
1576434 TACAATTTAT
1576444 TATTAAAATAATATTTG
1 TATTAAAATAATATTTG
*
1576461 T-TT-AAATAATATTTT
1 TATTAAAATAATATTTG
1576476 TATTAAAATAATA
1 TATTAAAATAATA
1576489 AATTATGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 12 0.48
16 4 0.16
17 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TATTAAAATAATATTTG
Found at i:1576479 original size:32 final size:31
Alignment explanation
Indices: 1576438--1576536 Score: 96
Period size: 32 Copynumber: 3.1 Consensus size: 31
1576428 TAATGTTACA
1576438 ATTTATTATTAAAATAATATT-TGTTTAAATAAT
1 ATTT-TTATTAAAATAATATTATG-TT-AATAAT
1576471 ATTTTTATTAAAATAATAAATTATGTTAATAAT
1 ATTTTTATTAAAATAAT--ATTATGTTAATAAT
* *
1576504 -TTATTATTAAAAATAATATATATTTTAA-AAT
1 ATTTTTATT-AAAATAATAT-TATGTTAATAAT
1576535 AT
1 AT
1576537 ATACATGTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
31 5 0.09
32 28 0.48
33 18 0.31
34 5 0.09
35 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
ATTTTTATTAAAATAATATTATGTTAATAAT
Found at i:1576494 original size:16 final size:16
Alignment explanation
Indices: 1576442--1576535 Score: 50
Period size: 17 Copynumber: 5.8 Consensus size: 16
1576432 GTTACAATTT
1576442 ATTATTAAAATAAT-A
1 ATTATTAAAATAATAA
* * * *
1576457 TTTGTTTAAATAATATT
1 ATTATTAAAATAATA-A
*
1576474 TTTATTAAAATAATAA
1 ATTATTAAAATAATAA
* **
1576490 ATTATGT-TAATAATTT
1 ATTAT-TAAAATAATAA
1576506 ATTATTAAAAATAATATA
1 ATTATT-AAAATAATA-A
1576524 TATT-TTAAAATA
1 -ATTATTAAAATA
1576536 TATACATGTA
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
15 12 0.21
16 15 0.26
17 26 0.45
18 2 0.03
19 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATTATTAAAATAATAA
Found at i:1577030 original size:27 final size:26
Alignment explanation
Indices: 1576983--1577035 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
1576973 TTTTAAGTTT
* * * *
1576983 TTCATAAAAATTATTATAAATTATAA
1 TTCATAAAAATGATAAAAAATAATAA
1577009 TTCATTAAAAATGATAAAAAATAATAA
1 TTCA-TAAAAATGATAAAAAATAATAA
1577036 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (26 bp):
TTCATAAAAATGATAAAAAATAATAA
Found at i:1577301 original size:2 final size:2
Alignment explanation
Indices: 1577294--1577320 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1577284 TTTGAGCCAC
1577294 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1577321 CACCTTCAAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1577882 original size:4 final size:4
Alignment explanation
Indices: 1577873--1577900 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1577863 CACTGTCATC
1577873 TTCT TTCT TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT
1577901 CTAAACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTCT
Found at i:1586877 original size:18 final size:18
Alignment explanation
Indices: 1586854--1586893 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1586844 GTGCGGTAAT
*
1586854 TATTTTTATTTTAT-TTTA
1 TATTTTT-TTATATATTTA
1586872 TATTTTTTTATATATTTA
1 TATTTTTTTATATATTTA
1586890 TATT
1 TATT
1586894 ATATTCGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TATTTTTTTATATATTTA
Found at i:1586895 original size:23 final size:21
Alignment explanation
Indices: 1586856--1586898 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
1586846 GCGGTAATTA
*
1586856 TTTTTATTTTATTTTATATTT
1 TTTTTATTTTATATTATATTT
1586877 TTTTATATATTTATATTATATT
1 TTTT-TAT-TTTATATTATATT
1586899 CGTATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 3 0.16
23 12 0.63
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTATTTTATATTATATTT
Found at i:1587174 original size:19 final size:19
Alignment explanation
Indices: 1587139--1587175 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1587129 TATGATATAT
**
1587139 TTTTTTATGTTCGTATTAC
1 TTTTTTATGTTAATATTAC
1587158 TTTTTTATGTTAATATTA
1 TTTTTTATGTTAATATTA
1587176 TATATTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.05, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTTTTATGTTAATATTAC
Found at i:1602540 original size:14 final size:14
Alignment explanation
Indices: 1602521--1602562 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
1602511 ATTAGACTTC
1602521 ACATCATGCATTCA
1 ACATCATGCATTCA
*
1602535 ACATCATGCATTCC
1 ACATCATGCATTCA
1602549 ACATCATGCATTCA
1 ACATCATGCATTCA
1602563 CATTACCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.07, T:0.29
Consensus pattern (14 bp):
ACATCATGCATTCA
Found at i:1603091 original size:32 final size:28
Alignment explanation
Indices: 1603049--1603127 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 28
1603039 TATAGCATCT
1603049 CTTTTTAAAGCCCACGCAAGTTAGTGGCA
1 CTTTTTAAAGCCCAC-CAAGTTAGTGGCA
1603078 TCATTTTTCAAAGCCCA-CAAGTTAGTGGCA
1 -C-TTTTT-AAAGCCCACCAAGTTAGTGGCA
1603108 CTCTTTTAAAGCCCA-CAAGT
1 CT-TTTTAAAGCCCACCAAGT
1603128 CGATGGCAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
28 14 0.30
29 5 0.11
30 14 0.30
31 5 0.11
32 8 0.17
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CTTTTTAAAGCCCACCAAGTTAGTGGCA
Found at i:1603101 original size:30 final size:30
Alignment explanation
Indices: 1603003--1603127 Score: 125
Period size: 30 Copynumber: 4.2 Consensus size: 30
1602993 TTAAGCTCAT
* * *
1603003 ACAAGTTGGTGGCAACT-TTTTCAAAGTCC
1 ACAAGTTAGTGGCATCTCTTTTCAAAGCCC
* * *
1603032 ACAACTCTA-TAGCATCTCTTTTTAAAGCCC
1 ACAAGT-TAGTGGCATCTCTTTTCAAAGCCC
1603062 ACGCAAGTTAGTGGCATCAT-TTTTCAAAGCCC
1 A--CAAGTTAGTGGCATC-TCTTTTCAAAGCCC
1603094 ACAAGTTAGTGGCA-CTCTTTT-AAAGCCC
1 ACAAGTTAGTGGCATCTCTTTTCAAAGCCC
1603122 ACAAGT
1 ACAAGT
1603128 CGATGGCAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
28 14 0.17
29 16 0.20
30 25 0.31
31 2 0.03
32 22 0.28
33 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (30 bp):
ACAAGTTAGTGGCATCTCTTTTCAAAGCCC
Found at i:1603268 original size:52 final size:52
Alignment explanation
Indices: 1603191--1603629 Score: 335
Period size: 52 Copynumber: 8.4 Consensus size: 52
1603181 CCAATTCTCA
** *
1603191 CTGGCCTTGAATTTGCATATTGGCACTTCTATCATTTTTAAGTCCAATGTCT
1 CTGGCCTTGAATCAGCACATTGGCACTTCTATCATTTTTAAGTCCAATGTCT
* * * *
1603243 TTGGCCTTGAAACAGCACATAGGCACCTT-TATCATCTTTAAGTTCCACA--TCAT
1 CTGGCCTTGAATCAGCACATTGGCA-CTTCTATCATTTTTAAG-TCCA-ATGTC-T
* * * *
1603296 -TGGCCTTGAATCAGCATATTGGCACTTCTATTATTTTTAAGTCTAATGTCG
1 CTGGCCTTGAATCAGCACATTGGCACTTCTATCATTTTTAAGTCCAATGTCT
* * * ** *
1603347 CTGGCCTTGAATCAGCACATTGGCACCAT-TGTCATCTTTAAGTCTGATAT-T
1 CTGGCCTTGAATCAGCACATTGGCA-CTTCTATCATTTTTAAGTCCAATGTCT
* * * * *
1603398 GCTGGCCTTGAATTAGCATATTGGCACTTATATCATTGTTAAGCCCAATGT-T
1 -CTGGCCTTGAATCAGCACATTGGCACTTCTATCATTTTTAAGTCCAATGTCT
* ** * * * *
1603450 GCTGGACTTGAATCAATACATTGGCAC-CCTTATCATTTTTAAGCCCAATATCA
1 -CTGGCCTTGAATCAGCACATTGGCACTTC-TATCATTTTTAAGTCCAATGTCT
* *
1603503 CTAGCCTTGAATCAGTACATTGGCA-TTCTTATCATTTTTAAGTCCAATGT-T
1 CTGGCCTTGAATCAGCACATTGGCACTTC-TATCATTTTTAAGTCCAATGTCT
* * * * * *
1603554 GCTAGCCTTGAATTAGCATATTGGCA-TTCTTCTCATCTTCAAGTCCAATGT-T
1 -CTGGCCTTGAATCAGCACATTGGCACTTC-TATCATTTTTAAGTCCAATGTCT
* *
1603606 GCTGGCCTTGAATTAGCTCATTGG
1 -CTGGCCTTGAATCAGCACATTGG
1603630 TACTCTTTTC
Statistics
Matches: 314, Mismatches: 58, Indels: 30
0.78 0.14 0.07
Matches are distributed among these distances:
50 1 0.00
51 8 0.03
52 294 0.94
53 10 0.03
54 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (52 bp):
CTGGCCTTGAATCAGCACATTGGCACTTCTATCATTTTTAAGTCCAATGTCT
Found at i:1603628 original size:156 final size:156
Alignment explanation
Indices: 1603296--1603629 Score: 374
Period size: 156 Copynumber: 2.1 Consensus size: 156
1603286 TCCACATCAT
* * * * * * *
1603296 TGGCCTTGAATCAGCAT-ATTGGCACTTCTATTATTTTTAAGTCTAATGTCGCTGGCCTTGAATC
1 TGGCCTTGAATCAGC-TCATTGGCACCTCTATCATTTTTAAGCCCAATATCACTAGCCTTGAATC
* ** *
1603360 AGCACATTGGCACCATTGTCATCTTTAAGTCTGATATTGCTGGCCTTGAATTAGCATATTGGCAC
65 AGCACATTGGCACCATTATCATCTTTAAGTCCAATATTGCTAGCCTTGAATTAGCATATTGGCAC
*
1603425 TTATATCATTGTTAAGCCCAATGTTGC
130 TTATATCATTGTCAAGCCCAATGTTGC
* *
1603452 TGGACTTGAATCA-ATACATTGGCACC-CTTATCATTTTTAAGCCCAATATCACTAGCCTTGAAT
1 TGGCCTTGAATCAGCT-CATTGGCACCTC-TATCATTTTTAAGCCCAATATCACTAGCCTTGAAT
* * * *
1603515 CAGTACATTGGCATTC-TTATCATTTTTAAGTCCAATGTTGCTAGCCTTGAATTAGCATATTGGC
64 CAGCACATTGGCA-CCATTATCATCTTTAAGTCCAATATTGCTAGCCTTGAATTAGCATATTGGC
* * *
1603579 A-TTCTTCTCATCT-TCAAGTCCAATGTTGC
128 ACTT-ATATCAT-TGTCAAGCCCAATGTTGC
*
1603608 TGGCCTTGAATTAGCTCATTGG
1 TGGCCTTGAATCAGCTCATTGG
1603630 TACTCTTTTC
Statistics
Matches: 147, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
154 1 0.01
155 3 0.02
156 140 0.95
157 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (156 bp):
TGGCCTTGAATCAGCTCATTGGCACCTCTATCATTTTTAAGCCCAATATCACTAGCCTTGAATCA
GCACATTGGCACCATTATCATCTTTAAGTCCAATATTGCTAGCCTTGAATTAGCATATTGGCACT
TATATCATTGTCAAGCCCAATGTTGC
Found at i:1603629 original size:104 final size:104
Alignment explanation
Indices: 1603191--1603622 Score: 462
Period size: 104 Copynumber: 4.2 Consensus size: 104
1603181 CCAATTCTCA
* * *
1603191 CTGGCCTTGAATTTGCATATTGGCACTTCTATCATTTTTAAGTCCAATGTCT-TTGGCCTTGAAA
1 CTGGCCTTGAATTAGCATATTGGCACTTCTATCATTTTTAAGTCCAATGT-TGCTGGCCTTGAAT
* *
1603255 CAGCACATAGGCACCTTTATCATCTTTAAGTTCCACATCA-T-
65 CAGCACATTGGCACCATTATCATCTTTAAG-TCCA-AT-ATTG
* * * *
1603296 -TGGCCTTGAATCAGCATATTGGCACTTCTATTATTTTTAAGTCTAATGTCGCTGGCCTTGAATC
1 CTGGCCTTGAATTAGCATATTGGCACTTCTATCATTTTTAAGTCCAATGTTGCTGGCCTTGAATC
* **
1603360 AGCACATTGGCACCATTGTCATCTTTAAGTCTGATATTG
66 AGCACATTGGCACCATTATCATCTTTAAGTCCAATATTG
* * * *
1603399 CTGGCCTTGAATTAGCATATTGGCACTTATATCATTGTTAAGCCCAATGTTGCTGGACTTGAATC
1 CTGGCCTTGAATTAGCATATTGGCACTTCTATCATTTTTAAGTCCAATGTTGCTGGCCTTGAATC
** * * * **
1603464 AATACATTGGCACCCTTATCATTTTTAAGCCCAATATCA
66 AGCACATTGGCACCATTATCATCTTTAAGTCCAATATTG
* * * * *
1603503 CTAGCCTTGAATCAGTACATTGGCA-TTCTTATCATTTTTAAGTCCAATGTTGCTAGCCTTGAAT
1 CTGGCCTTGAATTAGCATATTGGCACTTC-TATCATTTTTAAGTCCAATGTTGCTGGCCTTGAAT
* * * * * *
1603567 TAGCATATTGGCATTC-TTCTCATCTTCAAGTCCAATGTTG
65 CAGCACATTGGCA-CCATTATCATCTTTAAGTCCAATATTG
1603607 CTGGCCTTGAATTAGC
1 CTGGCCTTGAATTAGC
1603623 TCATTGGTAC
Statistics
Matches: 267, Mismatches: 54, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
101 1 0.00
102 3 0.01
103 4 0.01
104 258 0.97
105 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (104 bp):
CTGGCCTTGAATTAGCATATTGGCACTTCTATCATTTTTAAGTCCAATGTTGCTGGCCTTGAATC
AGCACATTGGCACCATTATCATCTTTAAGTCCAATATTG
Found at i:1607898 original size:37 final size:33
Alignment explanation
Indices: 1607840--1607930 Score: 96
Period size: 32 Copynumber: 2.7 Consensus size: 33
1607830 AATTGTTGAC
* * *
1607840 CTTT-AAGGCTAAGGTATAACCTTATAACCCTAT
1 CTTTCAAGGCTAAGATAGAACCTTAT-ACACTAT
*
1607873 CTTTTACAAAGGCTAAGATAGAACC-TCTACACTAT
1 C-TTT-C-AAGGCTAAGATAGAACCTTATACACTAT
1607908 CTTTCAAGGCTAAGATAGAACCT
1 CTTTCAAGGCTAAGATAGAACCT
1607931 CTCAATCACT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
32 17 0.35
33 2 0.04
34 6 0.12
35 7 0.14
36 2 0.04
37 15 0.31
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (33 bp):
CTTTCAAGGCTAAGATAGAACCTTATACACTAT
Found at i:1611650 original size:21 final size:21
Alignment explanation
Indices: 1611626--1611669 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1611616 TTTTTTCTCC
* *
1611626 TCTAATTAATTTATTTTCTTT
1 TCTAATTAACTTAATTTCTTT
* *
1611647 TCTATTTCACTTAATTTCTTT
1 TCTAATTAACTTAATTTCTTT
1611668 TC
1 TC
1611670 AAGAATATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (21 bp):
TCTAATTAACTTAATTTCTTT
Found at i:1614544 original size:14 final size:14
Alignment explanation
Indices: 1614525--1614570 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1614515 TCACATCGAG
1614525 TTATATAATTATAT
1 TTATATAATTATAT
*
1614539 TTATATTA-TA-AT
1 TTATATAATTATAT
*
1614551 ATATATAATTATAT
1 TTATATAATTATAT
1614565 TTATAT
1 TTATAT
1614571 TATAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 8 0.31
13 4 0.15
14 14 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATATAATTATAT
Found at i:1614578 original size:14 final size:14
Alignment explanation
Indices: 1614525--1614578 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
1614515 TCACATCGAG
*
1614525 TTATATAATTATAT
1 TTATATAATAATAT
*
1614539 TTATATTATAATA-
1 TTATATAATAATAT
*
1614552 -TATATAATTATAT
1 TTATATAATAATAT
*
1614565 TTATATTATAATAT
1 TTATATAATAATAT
1614579 ATCAAGATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 10 0.31
14 22 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATATAATAATAT
Found at i:1614590 original size:32 final size:26
Alignment explanation
Indices: 1614526--1614580 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
1614516 CACATCGAGT
1614526 TATATAATTATATTTATATTATAATA
1 TATATAATTATATTTATATTATAATA
1614552 TATATAATTATATTTATATTATAATA
1 TATATAATTATATTTATATTATAATA
1614578 TAT
1 TAT
1614581 CAAGATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TATATAATTATATTTATATTATAATA
Found at i:1615291 original size:17 final size:17
Alignment explanation
Indices: 1615269--1615302 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1615259 TCAATTTGTT
*
1615269 AAATAATTTATTATAAA
1 AAATAATATATTATAAA
1615286 AAATAATATATTATAAA
1 AAATAATATATTATAAA
1615303 TTAATCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATATATTATAAA
Found at i:1615520 original size:14 final size:15
Alignment explanation
Indices: 1615501--1615530 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1615491 ATATAAAATG
1615501 AAATATTACT-AATT
1 AAATATTACTCAATT
1615515 AAATATTACTCAATT
1 AAATATTACTCAATT
1615530 A
1 A
1615531 TTTGTCACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATATTACTCAATT
Found at i:1616359 original size:61 final size:59
Alignment explanation
Indices: 1616150--1616349 Score: 193
Period size: 61 Copynumber: 3.3 Consensus size: 59
1616140 AACTATATAT
* ** * *
1616150 ACAAATTCATCAATTGGACTATAATCACCAATTTCAACTACTATTAGTGTAACTATATG
1 ACAAATTCATCAATTGGACTATAATCACCAATTTAAACTAGAATTAGTGTAAATACATG
* ** * * * *
1616209 TACAAATTTATCAATTGGACTAGTGGTAACCAATTTAAAGTAGAATAAGTGTAAATACATA
1 -ACAAATTCATCAATTGGACTA-TAATCACCAATTTAAACTAGAATTAGTGTAAATACATG
* ** * * *
1616270 ATAAAATTCATCAATTAAACTATTAATCACCAATTTGAATTAGAATTAGTGTAAGTACACTG
1 A-CAAATTCATCAATTGGACTA-TAATCACCAATTTAAACTAGAATTAGTGTAAATACA-TG
1616332 ACAAATTCATCAATTGGA
1 ACAAATTCATCAATTGGA
1616350 TGACTAATCA
Statistics
Matches: 109, Mismatches: 28, Indels: 5
0.77 0.20 0.04
Matches are distributed among these distances:
60 21 0.19
61 86 0.79
62 2 0.02
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (59 bp):
ACAAATTCATCAATTGGACTATAATCACCAATTTAAACTAGAATTAGTGTAAATACATG
Found at i:1616447 original size:25 final size:25
Alignment explanation
Indices: 1616419--1616469 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1616409 ACTACCAACT
*
1616419 ACCAATTTAAATTAGAAGT-AGTGTA
1 ACCAATTTAAAATAGAA-TAAGTGTA
1616444 ACCAATTTAAAATAGAATAAGTGTA
1 ACCAATTTAAAATAGAATAAGTGTA
1616469 A
1 A
1616470 ATATATATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (25 bp):
ACCAATTTAAAATAGAATAAGTGTA
Found at i:1616611 original size:68 final size:67
Alignment explanation
Indices: 1616519--1616644 Score: 166
Period size: 68 Copynumber: 1.9 Consensus size: 67
1616509 TTCAACTACT
* * * *
1616519 ATTAGTGTAACTATATGCATAAATTTA-ATAATTAGACTACTAATTACTAATTATTAATTTAAAG
1 ATTAGTGTAACTACATACATAAATTTATA-AATTAGACTACTAATCACCAATT-TTAATTTAAAG
1616583 TGGA
64 TGGA
*
1616587 ATTAGTGTAACTACATAC-TAAAATTTATAAATTAGACTATTAATCACCAATTTTAATT
1 ATTAGTGTAACTACATACAT-AAATTTATAAATTAGACTACTAATCACCAATTTTAATT
1616645 ACAATTAGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
67 7 0.14
68 43 0.84
69 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.40
Consensus pattern (67 bp):
ATTAGTGTAACTACATACATAAATTTATAAATTAGACTACTAATCACCAATTTTAATTTAAAGTG
GA
Found at i:1617884 original size:16 final size:16
Alignment explanation
Indices: 1617801--1617889 Score: 74
Period size: 16 Copynumber: 5.6 Consensus size: 16
1617791 TCCGAACCTG
* *
1617801 AAAATAACCCAAACCC
1 AAAATGACCCAAACTC
*
1617817 AAAATAACCCAAACTC
1 AAAATGACCCAAACTC
*
1617833 AAAATGACTCAAAAC-C
1 AAAATGAC-CCAAACTC
* *
1617849 AAAATGACCC-GAGTC
1 AAAATGACCCAAACTC
*
1617864 TGAAATGACCCAAACTC
1 -AAAATGACCCAAACTC
*
1617881 GAAATGACC
1 AAAATGACC
1617890 TGAACTTAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
14 1 0.02
15 2 0.03
16 49 0.82
17 8 0.13
ACGTcount: A:0.49, C:0.29, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAATGACCCAAACTC
Found at i:1618759 original size:20 final size:20
Alignment explanation
Indices: 1618734--1618807 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
1618724 GTAAAAAGAT
1618734 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
1618754 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
1618774 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
1618794 AAAATGTATCGATA
1 AGAATGTATCGATA
1618808 TATCTGGGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1618792 original size:40 final size:40
Alignment explanation
Indices: 1618737--1618901 Score: 141
Period size: 40 Copynumber: 3.9 Consensus size: 40
1618727 AAAAGATAGA
*
1618737 ATGTATCGATACATTGAAGAATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAAATGTATCGATACATTCATAC
* * *
1618777 ATGTATCGATACATTGAAAAATGTATCGATATATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACA--T---T-----CATA-C
* * * * *
1618828 ATATATCAACACATTGAAGAATGTATTGATACATTCATAC
1 ATGTATCGATACATTGAAAAATGTATCGATACATTCATAC
*
1618868 ATGTATCGATACATTGAAAAATGTAACGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACAT
1618902 CTTGGTAAAA
Statistics
Matches: 96, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
40 59 0.61
41 3 0.03
42 1 0.01
45 1 0.01
46 1 0.01
49 1 0.01
50 3 0.03
51 27 0.28
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (40 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATTCATAC
Found at i:1618842 original size:91 final size:91
Alignment explanation
Indices: 1618705--1618912 Score: 353
Period size: 91 Copynumber: 2.3 Consensus size: 91
1618695 TACATTATTC
* * *
1618705 AATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCGATACATTGAAGAATGTATCGATACA
1 AATGTATCGATACATCTGGGTAAAAAGATAGAATATATCAACACATTGAAGAATGTATCGATACA
1618770 TTCATACATGTATCGATACATTGAAA
66 TTCATACATGTATCGATACATTGAAA
* *
1618796 AATGTATCGATATATCTGGGTAAAAAGATAGAATATATCAACACATTGAAGAATGTATTGATACA
1 AATGTATCGATACATCTGGGTAAAAAGATAGAATATATCAACACATTGAAGAATGTATCGATACA
1618861 TTCATACATGTATCGATACATTGAAA
66 TTCATACATGTATCGATACATTGAAA
* *
1618887 AATGTAACGATACATCTTGGTAAAAA
1 AATGTATCGATACATCTGGGTAAAAA
1618913 TGTGACTTTT
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 109 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (91 bp):
AATGTATCGATACATCTGGGTAAAAAGATAGAATATATCAACACATTGAAGAATGTATCGATACA
TTCATACATGTATCGATACATTGAAA
Found at i:1618861 original size:20 final size:19
Alignment explanation
Indices: 1618838--1618901 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
1618828 ATATATCAAC
*
1618838 ACATTGAAGAATGTATTGAT
1 ACATTGAA-AATGTATCGAT
* *
1618858 ACATTCATACATGTATCGAT
1 ACATTGA-AAATGTATCGAT
*
1618878 ACATTGAAAAATGTAACGAT
1 ACATTG-AAAATGTATCGAT
1618898 ACAT
1 ACAT
1618902 CTTGGTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 34 0.94
21 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (19 bp):
ACATTGAAAATGTATCGAT
Found at i:1620724 original size:62 final size:61
Alignment explanation
Indices: 1620624--1620767 Score: 207
Period size: 62 Copynumber: 2.3 Consensus size: 61
1620614 TTTCTCTTTT
* * * * *
1620624 CACTTTTTAGTCCCCAAAGAGTAGGACGTCTTTTCCTTTCAAAGCCCACACAAGTTGGTGG
1 CACTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGG
* *
1620685 CATTTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CA-CTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGG
*
1620747 CACTTTCTAGTCCTCAAAGAG
1 CACTTTTTAGTCCTCAAAGAG
1620768 TAGGATGCTC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
61 19 0.26
62 54 0.74
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (61 bp):
CACTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:1621057 original size:117 final size:118
Alignment explanation
Indices: 1620786--1621462 Score: 719
Period size: 116 Copynumber: 5.8 Consensus size: 118
1620776 TCTTTCTTTT
* * * * *
1620786 CACCCTTTAGTCCTCAAAGCA-TAGGACGCCTTTT-AAAGCCCACACAAATTGGTGGCACTTTTT
1 CACCTTTTAGTCCTCAAAG-AGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
**
1620849 TAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTT-AAGCCCACACAAGTTGGTGG
65 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
1620902 CACCTTCTAGTCCTTAAAGAGCAGGA--CACTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 CACCTTTTAGTCCTCAAAGAGCAGGATGC-CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * * * *
1620965 TATTCCTCAAAGAGTAGAACTCCTTTTCCTTTTAAAGCCCATAAAAGTTGGTGG
65 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* *
1621019 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTT-AAAGCCCACACAAGTTGGTAGCACTTTTTT
1 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCT
*
1621083 AGTCCTGAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
66 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
1621136 CA-TTTTTCAGTCCTCAAAGAACATGA--CACTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
1 CACCTTTT-AGTCCTCAAAGAGCAGGATGC-CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
*
1621197 CCAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGG
64 CTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
1621246 CA-TTTTTCAGTCTTCAAAGAGCAGGATGCTTTCTCTTTTCAAAGACCACACAAGTTGGTGGCAC
1 CACCTTTT-AGTCCTCAAAGAGCAGGATG----C-CTTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * * *
1621310 -CTTCCAGTCTTCAAAGAGCAAGACACCTTTT-CTTTGTAAAGGCCACACAAGTTGGTGG
60 TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT-TAAAGCCCACACAAGTTGGTGG
* * ** *
1621368 CACCTTTCAGTCCTCAAAGAGTAGGACACCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-
1 CACCTTTTAGTCCTCAAAGAGCAGG--A---TGCCTTTTCAAAGCCCACACAAGTTGGTGGCACT
*
1621432 TTTCTAGTCCTCAAAGAGCAAGACGCACTTT
61 TTTCTAGTCCTCAAAGAGCAGGACGC-CTTT
1621463 ATTTTCCTTT
Statistics
Matches: 478, Mismatches: 54, Indels: 51
0.82 0.09 0.09
Matches are distributed among these distances:
110 44 0.09
114 2 0.00
115 10 0.02
116 160 0.33
117 160 0.33
118 5 0.01
119 1 0.00
122 87 0.18
123 7 0.01
124 1 0.00
127 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (118 bp):
CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCT
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:1621468 original size:61 final size:59
Alignment explanation
Indices: 1620793--1621468 Score: 587
Period size: 61 Copynumber: 11.5 Consensus size: 59
1620783 TTTCACCCTT
* * *
1620793 TAGTCCTCAAAGCA-TAGGACGCC---TTTT-AAAGCCCACACAAATTGGTGGCACTTTTT
1 TAGTCCTCAAAG-AGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTC
* *
1620849 TAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTT--AAGCCCACACAAGTTGGTGGCACCTTC
1 TAGTCCTCAAAGAGCAGGACGCCTT---TTTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* *
1620909 TAGTCCTTAAAGAGCAGGAC-AC--TTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTC
* * * * * * *
1620965 TATTCCTCAAAGAGTAGAACTCCTTTTCCTTTTAAAGCCCATAAAAGTTGGTGGCACCTTT-
1 TAGTCCTCAAAGAGCAGGACGCCTTTT--TTTCAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * *
1621026 TAGTCCTCAAAGAGCAGGATGCC---TTTT-AAAGCCCACACAAGTTGGTAGCACTTTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTC
* * *
1621082 TAGTCCTGAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTT--TTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* * * *
1621142 TCAGTCCTCAAAGAACATGAC-AC---TTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 T-AGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* *
1621198 CAGTCCTCAAAGAGCAGGACGCC----TTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* * * * *
1621252 TCAGTCTTCAAAGAGCAGGATGCTTTCTCTTTTCAAAGACCACACAAGTTGGTGGCACCTTC
1 T-AGTCCTCAAAGAGCAGGACGCCTT-T-TTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* * * * * *
1621314 CAGTCTTCAAAGAGCAAGACACCTTTTCTTTGTAAAGGCCACACAAGTTGGTGGCACCTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTT-TTT-CAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * *
1621376 -AGTCCTCAAAGAGTAGGACACCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTC
1 TAGTCCTCAAAGAGCAGGACGCC-TTT-TTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
*
1621436 TAGTCCTCAAAGAGCAAGACGCACTTTATTTTC
1 TAGTCCTCAAAGAGCAGGACGC-CTTT-TTTTC
1621469 CTTTGTCTTC
Statistics
Matches: 516, Mismatches: 62, Indels: 79
0.79 0.09 0.12
Matches are distributed among these distances:
54 8 0.02
55 136 0.26
56 67 0.13
57 2 0.00
58 1 0.00
59 5 0.01
60 36 0.07
61 196 0.38
62 63 0.12
63 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (59 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
Found at i:1622102 original size:29 final size:29
Alignment explanation
Indices: 1622060--1622166 Score: 133
Period size: 29 Copynumber: 3.6 Consensus size: 29
1622050 CATTGTTCAT
*
1622060 TGTATCGATACATTTTGGGTTTACCCAAA
1 TGTATCGATACATTTTGGATTTACCCAAA
* * *
1622089 TGTATCGATACATTTTGCATTATATCGATACA
1 TGTATCGATACATTTTGGATT-TACCCA-A-A
*
1622121 TTGTATCGATACATTTTGGATTTACCCAGA
1 -TGTATCGATACATTTTGGATTTACCCAAA
1622151 TGTATCGATACATTTT
1 TGTATCGATACATTTT
1622167 ACAATGTATC
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
29 35 0.53
30 5 0.08
31 1 0.02
32 5 0.08
33 20 0.30
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (29 bp):
TGTATCGATACATTTTGGATTTACCCAAA
Found at i:1622127 original size:13 final size:13
Alignment explanation
Indices: 1622106--1622135 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1622096 ATACATTTTG
1622106 CATTATATCGATA
1 CATTATATCGATA
*
1622119 CATTGTATCGATA
1 CATTATATCGATA
1622132 CATT
1 CATT
1622136 TTGGATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:1622154 original size:62 final size:62
Alignment explanation
Indices: 1622057--1622184 Score: 211
Period size: 62 Copynumber: 2.1 Consensus size: 62
1622047 GTACATTGTT
* * *
1622057 CATTGTATCGATACATTTTGGGTTTACCCAAATGTATCGATACATTTTGCATTATATCGATA
1 CATTGTATCGATACATTTTGGATTTACCCAAATGTATCGATACATTTTACAATATATCGATA
* *
1622119 CATTGTATCGATACATTTTGGATTTACCCAGATGTATCGATACATTTTACAATGTATCGATA
1 CATTGTATCGATACATTTTGGATTTACCCAAATGTATCGATACATTTTACAATATATCGATA
1622181 CATT
1 CATT
1622185 CAGGCATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (62 bp):
CATTGTATCGATACATTTTGGATTTACCCAAATGTATCGATACATTTTACAATATATCGATA
Found at i:1624603 original size:51 final size:51
Alignment explanation
Indices: 1624483--1624603 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 51
1624473 TCCCGGTTCC
* ** * *
1624483 ATTTCCAAAACATCAATTTTTTCTTAATCGGGGATACTCCAACTCCAATTTT
1 ATTTCCAAAACATCAA-TTTATCGCAATCGAGGATACACCAACTCCAATTTT
** * * *
1624535 ATTTTTAAAGCGTCAATTTATCGCAATCGAGGATACACCAACTCCGATTTT
1 ATTTCCAAAACATCAATTTATCGCAATCGAGGATACACCAACTCCAATTTT
*
1624586 ATTTCCAAAACACCAATT
1 ATTTCCAAAACATCAATT
1624604 CTTCACAATT
Statistics
Matches: 54, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
51 42 0.78
52 12 0.22
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTATCGCAATCGAGGATACACCAACTCCAATTTT
Found at i:1624646 original size:28 final size:27
Alignment explanation
Indices: 1624614--1624687 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 27
1624604 CTTCACAATT
1624614 AGGGATACTCCAACCCCGTTATTTCATC-
1 AGGGATACTCCAACCCCGTTATTT--TCG
*
1624642 AGGGATACTCCAACCCCATTATTTTCG
1 AGGGATACTCCAACCCCGTTATTTTCG
1624669 AGGGGATACTCCAACCCCG
1 A-GGGATACTCCAACCCCG
1624688 GCTTTATATC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 39 0.93
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (27 bp):
AGGGATACTCCAACCCCGTTATTTTCG
Found at i:1624755 original size:108 final size:108
Alignment explanation
Indices: 1624567--1624843 Score: 322
Period size: 108 Copynumber: 2.6 Consensus size: 108
1624557 GCAATCGAGG
* * * * * * * **
1624567 ATACACCAACTCCGATTTTATTTCCAAAACACCAATTCTTCACAATTAGGGATACTCCAACCCCG
1 ATACTCCAACCCCGACTTTATATCTAAAATACCAATTTTTCACAATCGGGGATACTCCAACCCCG
* * *
1624632 TTATTTCATCAGGGATACTCCAACCCCATTATTTTC-GAGGGG
66 TTATGTCATCAGGGATACTCCAACCCCATTATTTTCTGAAGGA
* ** * * *
1624674 ATACTCCAACCCCGGCTTTATATCTAAAATATTGATTTTTTCATAATCGGGGGTACTCCAACCCC
1 ATACTCCAACCCCGACTTTATATCTAAAATA-CCAATTTTTCACAATCGGGGATACTCCAACCCC
* * *
1624739 GTTATGTCATCGGGGATACTCCAATCCCATTTTTTTCTGAAGGA
65 GTTATGTCATCAGGGATACTCCAACCCCATTATTTTCTGAAGGA
* * *
1624783 ATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1 ATACTCCAACCCCGACTTTATATCTAAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1624844 TCCGATTTTA
Statistics
Matches: 138, Mismatches: 30, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
107 24 0.17
108 83 0.60
109 31 0.22
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (108 bp):
ATACTCCAACCCCGACTTTATATCTAAAATACCAATTTTTCACAATCGGGGATACTCCAACCCCG
TTATGTCATCAGGGATACTCCAACCCCATTATTTTCTGAAGGA
Found at i:1624839 original size:51 final size:50
Alignment explanation
Indices: 1624783--1624896 Score: 174
Period size: 51 Copynumber: 2.2 Consensus size: 50
1624773 TTCTGAAGGA
* * *
1624783 ATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGG
1 ATACTCCAACCC-GATTTTATTTCCAAAACACCAATTTCTCACAATCGGGG
1624834 ATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGG
1 ATACTCCAAC-CCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGG
*
1624885 ATACTCTAACCC
1 ATACTCCAACCC
1624897 CGTTATTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
50 2 0.03
51 54 0.93
52 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.32
Consensus pattern (50 bp):
ATACTCCAACCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGG
Found at i:1624922 original size:79 final size:78
Alignment explanation
Indices: 1624831--1625055 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
1624821 TTCACAATCG
*
1624831 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA-TTTCTCACAATCGGGGATACTCTAAC
1 GGGATACTCCAAC-CCGATTTTATTTCCAAAACACCAATTTTC-CACAATCGGGGATACTCCAAC
*
1624895 CCCGTTATTTTC-AC
64 CCCGTTATTTTCGAA
** ** * * *
1624909 GGAGATACTCCAACCCCGACCTTATTTTTAAAGCATCAATTTTCCACAATCAGGGATACTCCAAC
1 GG-GATACTCCAA-CCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAAC
1624974 CCCGTTATTTTCGAA
64 CCCGTTATTTTCGAA
* * * * * *
1624989 GGGATACTCTAACCCTGATTTTATTTCCAAAATACCGATTTTCCATAATCGAGGATACTCCAGCC
1 GGGATACTCCAACCC-GATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACC
1625054 CC
65 CC
1625056 ATTGTTATCT
Statistics
Matches: 120, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
78 5 0.04
79 107 0.89
80 8 0.07
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (78 bp):
GGGATACTCCAACCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCC
CGTTATTTTCGAA
Found at i:1627228 original size:20 final size:20
Alignment explanation
Indices: 1627205--1627271 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
1627195 TACATCCAAA
1627205 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
1627225 TGTATCGAT--A-TA----T
1 TGTATCGATACATTATGCTT
*
1627238 TGTATCGACACATTATGCTT
1 TGTATCGATACATTATGCTT
1627258 TGTATCGATACATT
1 TGTATCGATACATT
1627272 GTATCGATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 9 0.24
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
20 23 0.61
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:1627251 original size:33 final size:33
Alignment explanation
Indices: 1627205--1627278 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
1627195 TACATCCAAA
* *
1627205 TGTATCGATACATTATGCTTTGTATCGATATAT
1 TGTATCGACACATTATGCTTTGTATCGATACAT
1627238 TGTATCGACACATTATGCTTTGTATCGATACAT
1 TGTATCGACACATTATGCTTTGTATCGATACAT
1627271 TGTATCGA
1 TGTATCGA
1627279 TATCTGTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGACACATTATGCTTTGTATCGATACAT
Found at i:1627716 original size:20 final size:20
Alignment explanation
Indices: 1627693--1627765 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1627683 ACAATTCAAA
1627693 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1627713 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
1627734 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1627754 GTATCGATACAT
1 GTATCGATACAT
1627766 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1627736 original size:21 final size:21
Alignment explanation
Indices: 1627710--1627786 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1627700 TACATGTTGC
1627710 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
1627731 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
1627751 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
1627771 GGATGTATCGATACAT
1 -AATGTATCGATACAT
1627787 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:1627744 original size:41 final size:41
Alignment explanation
Indices: 1627693--1627786 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1627683 ACAATTCAAA
1627693 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
1627734 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
1627775 GTATCGATACAT
1 GTATCGATACAT
1627787 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:1627843 original size:13 final size:13
Alignment explanation
Indices: 1627825--1627850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1627815 TACAGCAAGT
1627825 ATGTATCGATACA
1 ATGTATCGATACA
1627838 ATGTATCGATACA
1 ATGTATCGATACA
1627851 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1631321 original size:20 final size:20
Alignment explanation
Indices: 1631280--1631333 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1631270 TTCTACAATT
**
1631280 TGTATCGATACAATTGGTGAA
1 TGTATCGATAC-ATAAGTGAA
1631301 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
1631321 TGTATCGATACAT
1 TGTATCGATACAT
1631334 GTCTTAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:1631342 original size:20 final size:20
Alignment explanation
Indices: 1631297--1631350 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1631287 ATACAATTGG
*
1631297 TGAATGTATCGATACATAAG
1 TGAATGTATCGATACATAAC
**
1631317 TGAATGTATCGATACATGTC
1 TGAATGTATCGATACATAAC
*
1631337 TTAATGTATCGATA
1 TGAATGTATCGATA
1631351 TAGGACCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (20 bp):
TGAATGTATCGATACATAAC
Found at i:1633343 original size:26 final size:27
Alignment explanation
Indices: 1633309--1633378 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
1633299 AAAAAAAAAT
* *
1633309 CGGGATTGGAGTATCCTTC-GAAATAA
1 CGGGGTTGGAGTATCCCTCGGAAATAA
*
1633335 CGGGGTTGGAGTATCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCTCGGAAATAA
1633362 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
1633379 CGATGAGATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 17 0.43
27 23 0.57
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCGGAAATAA
Found at i:1633602 original size:51 final size:51
Alignment explanation
Indices: 1633393--1633615 Score: 221
Period size: 52 Copynumber: 4.3 Consensus size: 51
1633383 GAGATAACGA
* * * * *
1633393 GGTTAGAGTAATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGT-ATCCCCGATTATGAAAAATTAGTA-TTTTGGAAATAAAACCGG
** * * * * *
1633446 AATTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTATTTTGGAAATAAAACCGG
* * * *
1633498 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTTGGAAATAAAACCGG
* * * **
1633550 GGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAACCGG
1633601 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1633616 CCGAAAATAA
Statistics
Matches: 139, Mismatches: 29, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
51 37 0.27
52 86 0.62
53 16 0.12
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAACCGG
Found at i:1633632 original size:28 final size:26
Alignment explanation
Indices: 1633598--1633669 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
1633588 GAAATAAAGT
*
1633598 CGGGGTTGGAGTATCCCCCCGAAAATAA
1 CGGGGTTGGAGTATCCCCACG--AATAA
* * *
1633626 CGGGGTTGGAGTATCCCAATGATTAA
1 CGGGGTTGGAGTATCCCCACGAATAA
1633652 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
1633670 GATTGTGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 21 0.54
28 18 0.46
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCACGAATAA
Found at i:1633723 original size:55 final size:52
Alignment explanation
Indices: 1633656--1633787 Score: 151
Period size: 51 Copynumber: 2.5 Consensus size: 52
1633646 GATTAACGGG
* * *
1633656 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTG----TCTTGAAAATAAAATCGGA
* *
1633711 GTTTGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTCTTGAAAATAAAATCGGA
*
1633762 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
1633788 TTGAGAACTC
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
51 34 0.52
53 4 0.06
54 1 0.02
55 27 0.41
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTCTTGAAAATAAAATCGGA
Found at i:1635038 original size:63 final size:64
Alignment explanation
Indices: 1634966--1635089 Score: 189
Period size: 63 Copynumber: 2.0 Consensus size: 64
1634956 TCGTTTCACG
* *
1634966 TTTTTAGTCCCCAAAGAGCAGGACGGCTG-T-TCCTTTCAAAGCCCACACAAGTTGGTGGCATTT
1 TTTTTAGTCCCCAAAGAGCAAGACGCCTGCTCTCCTTTCAAAGCCCACACAA-TTGGTGGCATTT
* *
1635029 TTTTTAGTCCTCAAAGAGCAAGACGCCTGCTCTCCTTTTAAAGCCCACACAATTGGTGGCA
1 TTTTTAGTCCCCAAAGAGCAAGACGCCTGCTCTCCTTTCAAAGCCCACACAATTGGTGGCA
1635090 CTTTCTAGTC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
63 26 0.47
64 10 0.18
65 19 0.35
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (64 bp):
TTTTTAGTCCCCAAAGAGCAAGACGCCTGCTCTCCTTTCAAAGCCCACACAATTGGTGGCATTT
Found at i:1635368 original size:124 final size:118
Alignment explanation
Indices: 1635136--1635573 Score: 380
Period size: 120 Copynumber: 3.7 Consensus size: 118
1635126 CACCCTTTAG
* * *
1635136 TCCTCAAA-GCATAGGACGCCTTTTAAAGCCCACAAAAATTGGTGGCACTTTTTTAGTCCTCAAA
1 TCCTCAAAGGCA-A-GACACCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTTTAGTCCTCAAA
**
1635200 GAGCAGGACGCC--TTCGCC-TTTT-AAGCCCACACAAGTTGGTGGCACCTTCTAG-
63 GAGCAGGACGCCTTTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCTAGT
* * * *
1635252 TCCTTAAAGAGCAGGACACTTTTTAAGAAAGCCCACACAAGTTGGTGGCACGTTTTCTATTCCTC
1 TCCTCAAAG-GCAAGACACCTTTT---AAAGCCCACACAAGTTGGTGGCAC-TTTT-TAGTCCTC
* * * * * *
1635317 AAAGAGTAGAACTCCTTTTTTCCTTTTTAAAGCCCATAAAAGTTGGTGGCACTTTTAGT
60 AAAGAGCAGGACGCCTTTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCTAGT
** * *
1635376 TCCTCAAAGGCAAGATGCCTTTTAAAGCCCACACAAGTTGGTAGCACACTTTTTAGTCCTGAAAG
1 TCCTCAAAGGCAAGACACCTTTTAAAGCCCACACAAGTTGGT-G-GCACTTTTTAGTCCTCAAAG
* * *
1635441 AGCAGGACGCCTTTCTT--TTTTTAAAGCCCACACAAGTTGGTGGGCATTTTTTTCAG-
64 AGCAGGACGCCTTTTTTCCTTTTTAAAGCCCACACAAGTTGGT-GGCA--CTTCT-AGT
* * *
1635497 TCCTCAAAGAACATGACA-CTTTTCAAAG-CCACACAAG-TGGTGGGCA-TTTTCCAGTCCTCAA
1 TCCTCAAAG-GCAAGACACCTTTT-AAAGCCCACACAAGTTGGT-GGCACTTTT-TAGTCCTCAA
1635558 AGAGCAGGACGCCTTT
62 AGAGCAGGACGCCTTT
1635574 CAAAAGCCCA
Statistics
Matches: 263, Mismatches: 39, Indels: 37
0.78 0.12 0.11
Matches are distributed among these distances:
116 15 0.06
118 29 0.11
119 56 0.21
120 66 0.25
121 32 0.12
122 17 0.06
123 20 0.08
124 28 0.11
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (118 bp):
TCCTCAAAGGCAAGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAG
CAGGACGCCTTTTTTCCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCTAGT
Found at i:1635503 original size:185 final size:182
Alignment explanation
Indices: 1635156--1635506 Score: 419
Period size: 185 Copynumber: 1.9 Consensus size: 182
1635146 ATAGGACGCC
*
1635156 TTTTAAAGCCCACAAAAATTGGTGGCACTTTTTTAGTCCTCAAAGAGCAGGACGCCTTCGCCTTT
1 TTTTAAAGCCCACAAAAATTGGTGGCAC-TTTTTAGTCCTCAAAGAGCA-GACG-CATCGCCTTT
* *
1635221 TAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTTAAAGAGCAGGACACTTTTTAAGAAAGCCC
63 TAAGCCCACACAAGTTGGTAGCACCTTCTAGTCCTGAAAGAGCAGGACACTTTTTAAGAAAGCCC
*
1635286 ACACAAGTTGGTGGCACGTTTTCTATTCCTCAAAGAGTAGAACTCCTTTTTTCCT
128 ACACAAGTTGGTGGCACGTTTTCTAGTCCTCAAAGAGTAGAACTCCTTTTTTCCT
* *
1635341 TTTTAAAGCCCATAAAAGTTGGTGGCAC-TTTTAGTTCCTCAAAG-GCA-A-G-AT-GCCTTTTA
1 TTTTAAAGCCCACAAAAATTGGTGGCACTTTTTAG-TCCTCAAAGAGCAGACGCATCGCCTTTT-
* * ***
1635400 AAGCCCACACAAGTTGGTAGCACACTTTTTAGTCCTGAAAGAGCAGGACGCCTTTCTTTTTTTAA
64 AAGCCCACACAAGTTGGTAGCAC-C-TTCTAGTCCTGAAAGAGCAGGAC-AC--T-TTTTAAGAA
* *
1635465 AGCCCACACAAGTTGGTGGGCA-TTTTTTTCAGTCCTCAAAGA
123 AGCCCACACAAGTTGGT-GGCACGTTTTCT-AGTCCTCAAAGA
1635507 ACATGACACT
Statistics
Matches: 143, Mismatches: 13, Indels: 20
0.81 0.07 0.11
Matches are distributed among these distances:
177 7 0.05
178 23 0.16
179 1 0.01
180 22 0.15
181 2 0.01
183 10 0.07
184 37 0.26
185 41 0.29
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (182 bp):
TTTTAAAGCCCACAAAAATTGGTGGCACTTTTTAGTCCTCAAAGAGCAGACGCATCGCCTTTTAA
GCCCACACAAGTTGGTAGCACCTTCTAGTCCTGAAAGAGCAGGACACTTTTTAAGAAAGCCCACA
CAAGTTGGTGGCACGTTTTCTAGTCCTCAAAGAGTAGAACTCCTTTTTTCCT
Found at i:1635573 original size:119 final size:119
Alignment explanation
Indices: 1635155--1635816 Score: 440
Period size: 124 Copynumber: 5.5 Consensus size: 119
1635145 CATAGGACGC
* * ** ***
1635155 CTTTT-AAAGCCCACAAAAATTGGTGGCACTTTTTTAGTCCTCAAAGAGCAGGACGCC-TTCGCC
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCTTT
* * * * *
1635218 TTTT-AAGCCCACACAAGTTGGTGGCACCTTCT-AGTCCTTAAAGAGCAGGACA
66 TTTTAAAGCCCACACAAGTTGGTGGCATCTTTTCAGTCCTCAAAGAACATGACA
* * * * * *
1635270 CTTTTTAAGAAAGCCCACACAAGTTGGTGGCACGTTTTCTATTCCTCAAAGAGTAGAACTCCTTT
1 C-TTTT--CAAAGCCCACACAAGTTGGTGGCAC-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTT
* * * *
1635335 TTTCCTTTTTAAAGCCCATAAAAGTTGGTGGCA-CTTTT-AGTTCCTCAAAGGCAAGATG-C-
62 CTT--TTTTTAAAGCCCACACAAGTTGGTGGCATCTTTTCAG-TCCTCAAA-G-AACATGACA
* * *
1635394 CTTTT-AAAGCCCACACAAGTTGGTAGCACACTTTT-TAGTCCTGAAAGAGCAGGACGCCTTTCT
1 CTTTTCAAAGCCCACACAAGTTGGT-G-GCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCT
*
1635457 TTTTTTAAAGCCCACACAAGTTGGTGGGCATTTTTTTCAGTCCTCAAAGAACATGACA
64 TTTTTTAAAGCCCACACAAGTTGGT-GGCA-TCTTTTCAGTCCTCAAAGAACATGACA
1635515 CTTTTCAAAG-CCACACAAG-TGGTGGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTC--
1 CTTTTCAAAGCCCACACAAGTTGGT-GGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCTT
* * * * *
1635575 ----AAAAGCCCA-ACACAGTTGGTGGCAT-TGTTTCAGTCTTCAAAGAGCAGGATGCTTTCT
65 TTTTTAAAGCCCACACA-AGTTGGTGGCATCT-TTTCAGTCCTCAAAGA--A-CATG---ACA
* * * * *
1635632 CTCTTTCAAAGACCACACAAGTTGGTGGCAC-CTTCCAG-CTTCAAAGAGCAAGACACCTTT-TT
1 CT-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCTT
* * * * ** *
1635694 CTTTGTAAAGGCCACACAAGTTGGTGGGCAACCTTTCAGTCCTCAAAGAGTAGGACA
65 -TTTTTAAAGCCCACACAAGTTGGT-GGCATCTTTTCAGTCCTCAAAGAACATGACA
* * *
1635751 CCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-TTTCTAGTCCTC-AAGAGCAAGACGCAC
1 ------CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGC-C
1635814 TTT
59 TTT
1635817 ATTTCCTTTG
Statistics
Matches: 437, Mismatches: 58, Indels: 94
0.74 0.10 0.16
Matches are distributed among these distances:
110 1 0.00
111 16 0.04
112 7 0.02
113 16 0.04
114 3 0.01
115 1 0.00
116 4 0.01
117 3 0.01
118 53 0.12
119 78 0.18
120 76 0.17
121 33 0.08
122 11 0.03
123 14 0.03
124 85 0.19
125 33 0.08
126 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (119 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCTTT
TTTTAAAGCCCACACAAGTTGGTGGCATCTTTTCAGTCCTCAAAGAACATGACA
Found at i:1635615 original size:57 final size:56
Alignment explanation
Indices: 1635463--1635755 Score: 211
Period size: 57 Copynumber: 5.0 Consensus size: 56
1635453 TTCTTTTTTT
* * *
1635463 AAAGCCCACACAAGTTGGTGGGCATTTTTTTCAGTCCTCAAAGAACATGACACTTTTC
1 AAAGCCCACACAAGTTGGTGGGCA--TTTTTCAGTCCTCAAAGAGCAGGACACCTTTC
* *
1635521 AAAG-CCACACAAG-TGGTGGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTC
1 AAAGCCCACACAAGTTGGTGGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTTTC
* *
1635575 AAAAGCCCA-ACACAGTTGGT-GGCATTGTTTCAGTCTTCAAAGAGCAGGATGCTTTCTCTCTTT
1 -AAAGCCCACACA-AGTTGGTGGGCATT-TTTCAGTCCTCAAAGAGCAGGA------CAC-CTTT
1635638 C
56 C
* ** * * *
1635639 AAAGACCACACAAGTTGGT-GGCACCTTCCAG-CTTCAAAGAGCAAGACACCTTTTTC
1 AAAGCCCACACAAGTTGGTGGGCATTTTTCAGTCCTCAAAGAGCAGGACACC--TTTC
* ** *
1635695 TTTGTAAAGGCCACACAAGTTGGTGGGCAACCTTTCAGTCCTCAAAGAGTAGGACACCTTT
1 -----AAAGCCCACACAAGTTGGTGGGC-ATTTTTCAGTCCTCAAAGAGCAGGACACCTTT
1635756 TCTTTTCAAA
Statistics
Matches: 193, Mismatches: 19, Indels: 42
0.76 0.07 0.17
Matches are distributed among these distances:
54 28 0.15
55 9 0.05
56 24 0.12
57 33 0.17
58 4 0.02
61 32 0.17
62 11 0.06
63 28 0.15
64 24 0.12
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (56 bp):
AAAGCCCACACAAGTTGGTGGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTTTC
Found at i:1635680 original size:61 final size:62
Alignment explanation
Indices: 1635570--1635805 Score: 214
Period size: 61 Copynumber: 3.8 Consensus size: 62
1635560 AGCAGGACGC
* ** * **
1635570 CTTTCAAAAGCCCA-ACACAGTTGGTGGCATTGTTTCAGTCTTCAAAGAGCAGGA-TGCTTTCTC
1 CTTTC-AAAGACCACACA-AGTTGGTGGCA-CCTTCCAGTCTTCAAAGAGCAGGACACCTTT-TC
1635633 T
62 T
*
1635634 CTTTCAAAGACCACACAAGTTGGTGGCACCTTCCAG-CTTCAAAGAGCAAGACACCTTTT-T
1 CTTTCAAAGACCACACAAGTTGGTGGCACCTTCCAGTCTTCAAAGAGCAGGACACCTTTTCT
* * * * *
1635694 CTTTGTAAAGGCCACACAAGTTGGTGGGCAACCTTTCAGTCCTCAAAGAGTAGGACACCTTTTCT
1 CTTT-CAAAGACCACACAAGTTGGT-GGC-ACCTTCCAGTCTTCAAAGAGCAGGACACCTTTTCT
* * * * *
1635759 -TTTCAAAGCCCACACGAGTTGGTGGCACTTTCTAGTCCTC-AAGAGCA
1 CTTTCAAAGACCACACAAGTTGGTGGCACCTTCCAGTCTTCAAAGAGCA
1635806 AGACGCACTT
Statistics
Matches: 145, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
60 11 0.08
61 44 0.30
62 15 0.10
63 43 0.30
64 31 0.21
65 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (62 bp):
CTTTCAAAGACCACACAAGTTGGTGGCACCTTCCAGTCTTCAAAGAGCAGGACACCTTTTCT
Found at i:1639090 original size:28 final size:27
Alignment explanation
Indices: 1639058--1639130 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
1639048 TCTCACAATT
1639058 AGGGATACTCCAACCCCGTTATTTCATC-
1 AGGGATACTCCAACCCCGTTATTT--TCG
*
1639086 AGGGATACTCCAA-CCCATTATTTTCG
1 AGGGATACTCCAACCCCGTTATTTTCG
1639112 AGGGATATCTCCAACCCCG
1 AGGGATA-CTCCAACCCCG
1639131 GCTTATATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 2 0.05
26 7 0.17
27 15 0.38
28 16 0.40
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (27 bp):
AGGGATACTCCAACCCCGTTATTTTCG
Found at i:1639123 original size:27 final size:26
Alignment explanation
Indices: 1639058--1639128 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 26
1639048 TCTCACAATT
*
1639058 AGGGATACTCCAACCCCGTTATTTCATC
1 AGGGATACTCCAA-CCCATTATTT-ATC
1639086 AGGGATACTCCAACCCATTATTT-TC
1 AGGGATACTCCAACCCATTATTTATC
1639111 GAGGGATATCTCCAACCC
1 -AGGGATA-CTCCAACCC
1639129 CGGCTTATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
25 2 0.05
26 7 0.17
27 18 0.45
28 13 0.32
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (26 bp):
AGGGATACTCCAACCCATTATTTATC
Found at i:1641750 original size:30 final size:33
Alignment explanation
Indices: 1641682--1641752 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 33
1641672 TACATCCAAA
* *
1641682 TGTATCGATACATTATGCTTTGTATCGAATAGT
1 TGTATCGACACATTATGCTTTGTATCGAATAAT
1641715 TGTATCGACAC-TTATGCTTT-T-TCG-ATACAT
1 TGTATCGACACATTATGCTTTGTATCGAATA-AT
1641745 TGTATCGA
1 TGTATCGA
1641753 TATCTGTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 3 0.09
30 12 0.34
31 1 0.03
32 9 0.26
33 10 0.29
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGACACATTATGCTTTGTATCGAATAAT
Found at i:1642226 original size:20 final size:20
Alignment explanation
Indices: 1642164--1642235 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1642154 ACAATTCAAA
1642164 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1642184 GGTATCGATACAT-AAAAAAT
1 -GTATCGATACATGTTGCAAT
1642204 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1642224 GTATCGATACAT
1 GTATCGATACAT
1642236 AAAAAGGATG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.29
20 18 0.43
21 12 0.29
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1642250 original size:40 final size:40
Alignment explanation
Indices: 1642164--1642240 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
1642154 ACAATTCAAA
1642164 GTATCGATACATGTTGCAATGGTATCGATACATAAAAAAT
1 GTATCGATACATGTTGCAATGGTATCGATACATAAAAAAT
1642204 GTATCGATACATGTTGCAAT-GTATCGATACATAAAAA
1 GTATCGATACATGTTGCAATGGTATCGATACATAAAAA
1642241 GGATGATCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 17 0.46
40 20 0.54
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (40 bp):
GTATCGATACATGTTGCAATGGTATCGATACATAAAAAAT
Found at i:1645762 original size:20 final size:21
Alignment explanation
Indices: 1645737--1645788 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1645727 CTCTACAATT
**
1645737 TGTATCG-TACAATTGGTGAA
1 TGTATCGATACAATAAGTGAA
1645757 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
1645777 TGTATCGATACA
1 TGTATCGATACA
1645789 TGTCTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.33
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:1645789 original size:20 final size:20
Alignment explanation
Indices: 1645752--1645789 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1645742 CGTACAATTG
1645752 GTGAATGTATCGATACATAA
1 GTGAATGTATCGATACATAA
1645772 GTGAATGTATCGATACAT
1 GTGAATGTATCGATACAT
1645790 GTCTTAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
GTGAATGTATCGATACATAA
Found at i:1645798 original size:20 final size:20
Alignment explanation
Indices: 1645753--1645806 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1645743 GTACAATTGG
*
1645753 TGAATGTATCGATACATAAG
1 TGAATGTATCGATACATAAC
**
1645773 TGAATGTATCGATACATGTC
1 TGAATGTATCGATACATAAC
*
1645793 TTAATGTATCGATA
1 TGAATGTATCGATA
1645807 TAGGACCATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (20 bp):
TGAATGTATCGATACATAAC
Found at i:1646672 original size:16 final size:16
Alignment explanation
Indices: 1646590--1646677 Score: 81
Period size: 16 Copynumber: 5.6 Consensus size: 16
1646580 TCCGAACCTG
* *
1646590 AAAATAACCCAAACCC
1 AAAATGACCCAAACTC
*
1646606 AAAATAACCCAAACTC
1 AAAATGACCCAAACTC
*
1646622 AAAATGACTCAAAC-C
1 AAAATGACCCAAACTC
* *
1646637 AAAATGACCC-GAGTC
1 AAAATGACCCAAACTC
*
1646652 TGAAATGACCCAAACTC
1 -AAAATGACCCAAACTC
*
1646669 GAAATGACC
1 AAAATGACC
1646678 TGAACTTAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
14 1 0.02
15 11 0.18
16 45 0.75
17 3 0.05
ACGTcount: A:0.49, C:0.30, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAATGACCCAAACTC
Found at i:1647545 original size:20 final size:20
Alignment explanation
Indices: 1647520--1647593 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
1647510 GTAAAAAGAT
1647520 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
1647540 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
1647560 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
1647580 AAAATGTATCGATA
1 AGAATGTATCGATA
1647594 TATCTGGGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1647578 original size:40 final size:40
Alignment explanation
Indices: 1647523--1647688 Score: 134
Period size: 40 Copynumber: 3.9 Consensus size: 40
1647513 AAAAGATAGA
*
1647523 ATGTATCGATACATTGAAGAATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAAATGTATCGATACATTCATAC
* * *
1647563 ATGTATCGATACATTGAAAAATGTATCGATATATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACA--T---T-----CATA-C
* * * * *
1647614 ATATATCAACACATTGAAGAATGTATTGATACATTCATAC
1 ATGTATCGATACATTGAAAAATGTATCGATACATTCATAC
*
1647654 ATGTATCGATACATTGAAAAATGTAACGATTACAT
1 ATGTATCGATACATTGAAAAATGTATCGA-TACAT
1647689 CTTGGTAAAA
Statistics
Matches: 96, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
40 54 0.56
41 8 0.08
42 1 0.01
45 1 0.01
46 1 0.01
49 1 0.01
50 3 0.03
51 27 0.28
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (40 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATTCATAC
Found at i:1647628 original size:91 final size:91
Alignment explanation
Indices: 1647491--1647699 Score: 346
Period size: 91 Copynumber: 2.3 Consensus size: 91
1647481 TACATTATTC
* * *
1647491 AATGTATCGATACATCTGGGTAAAAAGATAGAATGTATCGATACATTGAAGAATGTATCGATACA
1 AATGTATCGATACATCTGGGTAAAAAGATAGAATATATCAACACATTGAAGAATGTATCGATACA
1647556 TTCATACATGTATCGATACATTGAAA
66 TTCATACATGTATCGATACATTGAAA
* *
1647582 AATGTATCGATATATCTGGGTAAAAAGATAGAATATATCAACACATTGAAGAATGTATTGATACA
1 AATGTATCGATACATCTGGGTAAAAAGATAGAATATATCAACACATTGAAGAATGTATCGATACA
1647647 TTCATACATGTATCGATACATTGAAA
66 TTCATACATGTATCGATACATTGAAA
* *
1647673 AATGTAACGATTACATCTTGGTAAAAA
1 AATGTATCGA-TACATCTGGGTAAAAA
1647700 TGTGACTTTT
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 95 0.87
92 14 0.13
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (91 bp):
AATGTATCGATACATCTGGGTAAAAAGATAGAATATATCAACACATTGAAGAATGTATCGATACA
TTCATACATGTATCGATACATTGAAA
Found at i:1647647 original size:20 final size:19
Alignment explanation
Indices: 1647624--1647688 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
1647614 ATATATCAAC
*
1647624 ACATTGAAGAATGTATTGAT
1 ACATTGAA-AATGTATCGAT
* *
1647644 ACATTCATACATGTATCGAT
1 ACATTGA-AAATGTATCGAT
*
1647664 ACATTGAAAAATGTAACGATT
1 ACATTG-AAAATGTATCGA-T
1647685 ACAT
1 ACAT
1647689 CTTGGTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
20 29 0.81
21 7 0.19
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (19 bp):
ACATTGAAAATGTATCGAT
Found at i:1649507 original size:62 final size:61
Alignment explanation
Indices: 1649407--1649550 Score: 216
Period size: 62 Copynumber: 2.3 Consensus size: 61
1649397 TTTCTCTTTT
* * * *
1649407 CACTTTTTAGTCCCCAAAGAGCAGGACGTCTTTTCCTTTCAAAGCCCACACAAGTTGGTGG
1 CACTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGG
* *
1649468 CATTTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGG
1 CA-CTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGG
*
1649530 CACTTTCTAGTCCTCAAAGAG
1 CACTTTTTAGTCCTCAAAGAG
1649551 TAGGATGCTC
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
61 19 0.26
62 55 0.74
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (61 bp):
CACTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:1649840 original size:117 final size:118
Alignment explanation
Indices: 1649569--1650245 Score: 719
Period size: 116 Copynumber: 5.8 Consensus size: 118
1649559 TCTTTCTTTT
* * * * *
1649569 CACCCTTTAGTCCTCAAAGCA-TAGGACGCCTTTT-AAAGCCCACACAAATTGGTGGCACTTTTT
1 CACCTTTTAGTCCTCAAAG-AGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
**
1649632 TAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTT-AAGCCCACACAAGTTGGTGG
65 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
1649685 CACCTTCTAGTCCTTAAAGAGCAGGA--CACTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 CACCTTTTAGTCCTCAAAGAGCAGGATGC-CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * * * *
1649748 TATTCCTCAAAGAGTAGAACTCCTTTTCCTTTTAAAGCCCATAAAAGTTGGTGG
65 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* *
1649802 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTT-AAAGCCCACACAAGTTGGTAGCACTTTTTT
1 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCT
*
1649866 AGTCCTGAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
66 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
1649919 CA-TTTTTCAGTCCTCAAAGAACATGA--CACTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
1 CACCTTTT-AGTCCTCAAAGAGCAGGATGC-CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
*
1649980 CCAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGG
64 CTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
1650029 CA-TTTTTCAGTCTTCAAAGAGCAGGATGCTTTCTCTTTTCAAAGACCACACAAGTTGGTGGCAC
1 CACCTTTT-AGTCCTCAAAGAGCAGGATG----C-CTTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * * *
1650093 -CTTCCAGTCTTCAAAGAGCAAGACACCTTTT-CTTTGTAAAGGCCACACAAGTTGGTGG
60 TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT-TAAAGCCCACACAAGTTGGTGG
* * ** *
1650151 CACCTTTCAGTCCTCAAAGAGTAGGACACCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-
1 CACCTTTTAGTCCTCAAAGAGCAGG--A---TGCCTTTTCAAAGCCCACACAAGTTGGTGGCACT
*
1650215 TTTCTAGTCCTCAAAGAGCAAGACGCACTTT
61 TTTCTAGTCCTCAAAGAGCAGGACGC-CTTT
1650246 ATTTTCCTTT
Statistics
Matches: 478, Mismatches: 54, Indels: 51
0.82 0.09 0.09
Matches are distributed among these distances:
110 44 0.09
114 2 0.00
115 10 0.02
116 160 0.33
117 160 0.33
118 5 0.01
119 1 0.00
122 87 0.18
123 7 0.01
124 1 0.00
127 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (118 bp):
CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCT
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:1650251 original size:61 final size:59
Alignment explanation
Indices: 1649576--1650251 Score: 587
Period size: 61 Copynumber: 11.5 Consensus size: 59
1649566 TTTCACCCTT
* * *
1649576 TAGTCCTCAAAGCA-TAGGACGCC---TTTT-AAAGCCCACACAAATTGGTGGCACTTTTT
1 TAGTCCTCAAAG-AGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTC
* *
1649632 TAGTCCTCAAAGAGCAGGACGCCTTCGCCTTTT--AAGCCCACACAAGTTGGTGGCACCTTC
1 TAGTCCTCAAAGAGCAGGACGCCTT---TTTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* *
1649692 TAGTCCTTAAAGAGCAGGAC-AC--TTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTC
* * * * * * *
1649748 TATTCCTCAAAGAGTAGAACTCCTTTTCCTTTTAAAGCCCATAAAAGTTGGTGGCACCTTT-
1 TAGTCCTCAAAGAGCAGGACGCCTTTT--TTTCAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * *
1649809 TAGTCCTCAAAGAGCAGGATGCC---TTTT-AAAGCCCACACAAGTTGGTAGCACTTTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTC
* * *
1649865 TAGTCCTGAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTT--TTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* * * *
1649925 TCAGTCCTCAAAGAACATGAC-AC---TTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
1 T-AGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* *
1649981 CAGTCCTCAAAGAGCAGGACGCC----TTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
1 TAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* * * * *
1650035 TCAGTCTTCAAAGAGCAGGATGCTTTCTCTTTTCAAAGACCACACAAGTTGGTGGCACCTTC
1 T-AGTCCTCAAAGAGCAGGACGCCTT-T-TTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
* * * * * *
1650097 CAGTCTTCAAAGAGCAAGACACCTTTTCTTTGTAAAGGCCACACAAGTTGGTGGCACCTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTT-TTT-CAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * *
1650159 -AGTCCTCAAAGAGTAGGACACCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTC
1 TAGTCCTCAAAGAGCAGGACGCC-TTT-TTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
*
1650219 TAGTCCTCAAAGAGCAAGACGCACTTTATTTTC
1 TAGTCCTCAAAGAGCAGGACGC-CTTT-TTTTC
1650252 CTTTGTCTTC
Statistics
Matches: 516, Mismatches: 62, Indels: 79
0.79 0.09 0.12
Matches are distributed among these distances:
54 8 0.02
55 136 0.26
56 67 0.13
57 2 0.00
58 1 0.00
59 5 0.01
60 36 0.07
61 196 0.38
62 63 0.12
63 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (59 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTTTTCAAAGCCCACACAAGTTGGTGGCACTTTC
Found at i:1650885 original size:29 final size:29
Alignment explanation
Indices: 1650843--1650949 Score: 133
Period size: 29 Copynumber: 3.6 Consensus size: 29
1650833 CATTGTTCAT
*
1650843 TGTATCGATACATTTTGGGTTTACCCAAA
1 TGTATCGATACATTTTGGATTTACCCAAA
* * *
1650872 TGTATCGATACATTTTGCATTATATCGATACA
1 TGTATCGATACATTTTGGATT-TACCCA-A-A
*
1650904 TTGTATCGATACATTTTGGATTTACCCAGA
1 -TGTATCGATACATTTTGGATTTACCCAAA
1650934 TGTATCGATACATTTT
1 TGTATCGATACATTTT
1650950 ACAATGTATC
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
29 35 0.53
30 5 0.08
31 1 0.02
32 5 0.08
33 20 0.30
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (29 bp):
TGTATCGATACATTTTGGATTTACCCAAA
Found at i:1650910 original size:13 final size:13
Alignment explanation
Indices: 1650889--1650918 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1650879 ATACATTTTG
1650889 CATTATATCGATA
1 CATTATATCGATA
*
1650902 CATTGTATCGATA
1 CATTATATCGATA
1650915 CATT
1 CATT
1650919 TTGGATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:1650937 original size:62 final size:62
Alignment explanation
Indices: 1650840--1650967 Score: 211
Period size: 62 Copynumber: 2.1 Consensus size: 62
1650830 GTACATTGTT
* * *
1650840 CATTGTATCGATACATTTTGGGTTTACCCAAATGTATCGATACATTTTGCATTATATCGATA
1 CATTGTATCGATACATTTTGGATTTACCCAAATGTATCGATACATTTTACAATATATCGATA
* *
1650902 CATTGTATCGATACATTTTGGATTTACCCAGATGTATCGATACATTTTACAATGTATCGATA
1 CATTGTATCGATACATTTTGGATTTACCCAAATGTATCGATACATTTTACAATATATCGATA
1650964 CATT
1 CATT
1650968 CAGGCATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (62 bp):
CATTGTATCGATACATTTTGGATTTACCCAAATGTATCGATACATTTTACAATATATCGATA
Found at i:1653429 original size:28 final size:27
Alignment explanation
Indices: 1653397--1653470 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 27
1653387 CTTCACAATT
1653397 AGGGATACTCCAACCCCGTTATTTCATC-
1 AGGGATACTCCAACCCCGTTATTT--TCG
*
1653425 AGGGATACTCCAACCCCATTATTTTCG
1 AGGGATACTCCAACCCCGTTATTTTCG
1653452 AGGGGATACTCCAACCCCG
1 A-GGGATACTCCAACCCCG
1653471 GCTTTATATC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 39 0.93
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (27 bp):
AGGGATACTCCAACCCCGTTATTTTCG
Found at i:1653538 original size:108 final size:108
Alignment explanation
Indices: 1653375--1653626 Score: 317
Period size: 108 Copynumber: 2.3 Consensus size: 108
1653365 TTTATTTCCA
* * ** *
1653375 AAAACACCAATTCTTCACAATTAGGGATACTCCAACCCCGTTATTTCATCAGGGATACTCCAACC
1 AAAATACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATGTCATCAGGGATACTCCAACC
* * *
1653440 CCATTATTTTC-GAGGGGATACTCCAACCCCGGCTTTATATCT
66 CCATTATTTTCTGAAGGAATACTCCAACCCCGACTTTATATCT
** * * * * *
1653482 AAAATATTGATTTTTTCATAATCGGGGGTACTCCAACCCCGTTATGTCATCGGGGATACTCCAAT
1 AAAATA-CCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATGTCATCAGGGATACTCCAAC
* * * *
1653547 CCCATTTTTTTCTGAAGGAATACTCCAACCCTGATTTTATTTCT
65 CCCATTATTTTCTGAAGGAATACTCCAACCCCGACTTTATATCT
1653591 AAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1 AAAATACCAATTTTTCACAATCGGGGATACTCCAAC
1653627 TCCGATTTTA
Statistics
Matches: 119, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
107 5 0.04
108 83 0.70
109 31 0.26
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (108 bp):
AAAATACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATGTCATCAGGGATACTCCAACC
CCATTATTTTCTGAAGGAATACTCCAACCCCGACTTTATATCT
Found at i:1653622 original size:51 final size:50
Alignment explanation
Indices: 1653566--1653679 Score: 174
Period size: 51 Copynumber: 2.2 Consensus size: 50
1653556 TTCTGAAGGA
* * *
1653566 ATACTCCAACCCTGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGG
1 ATACTCCAACCC-GATTTTATTTCCAAAACACCAATTTCTCACAATCGGGG
1653617 ATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGG
1 ATACTCCAAC-CCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGG
*
1653668 ATACTCTAACCC
1 ATACTCCAACCC
1653680 CGTTATTTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
50 2 0.03
51 54 0.93
52 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.32
Consensus pattern (50 bp):
ATACTCCAACCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGG
Found at i:1653705 original size:79 final size:78
Alignment explanation
Indices: 1653614--1653838 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 78
1653604 TTCACAATCG
*
1653614 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA-TTTCTCACAATCGGGGATACTCTAAC
1 GGGATACTCCAAC-CCGATTTTATTTCCAAAACACCAATTTTC-CACAATCGGGGATACTCCAAC
*
1653678 CCCGTTATTTTC-AC
64 CCCGTTATTTTCGAA
** ** * * *
1653692 GGAGATACTCCAACCCCGACCTTATTTTTAAAGCATCAATTTTCCACAATCAGGGATACTCCAAC
1 GG-GATACTCCAA-CCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAAC
1653757 CCCGTTATTTTCGAA
64 CCCGTTATTTTCGAA
* * * * * *
1653772 GGGATACTCTAACCCTGATTTTATTTCCAAAATACCGATTTTCCATAATCGAGGATACTCCAGCC
1 GGGATACTCCAACCC-GATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACC
1653837 CC
65 CC
1653839 ATTGTTATCT
Statistics
Matches: 120, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
78 5 0.04
79 107 0.89
80 8 0.07
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (78 bp):
GGGATACTCCAACCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCC
CGTTATTTTCGAA
Found at i:1656011 original size:20 final size:20
Alignment explanation
Indices: 1655988--1656054 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
1655978 TACATCCAAA
1655988 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
1656008 TGTATCGAT--A-TA----T
1 TGTATCGATACATTATGCTT
*
1656021 TGTATCGACACATTATGCTT
1 TGTATCGATACATTATGCTT
1656041 TGTATCGATACATT
1 TGTATCGATACATT
1656055 GTATCGATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 9 0.24
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
20 23 0.61
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:1656034 original size:33 final size:33
Alignment explanation
Indices: 1655988--1656061 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
1655978 TACATCCAAA
* *
1655988 TGTATCGATACATTATGCTTTGTATCGATATAT
1 TGTATCGACACATTATGCTTTGTATCGATACAT
1656021 TGTATCGACACATTATGCTTTGTATCGATACAT
1 TGTATCGACACATTATGCTTTGTATCGATACAT
1656054 TGTATCGA
1 TGTATCGA
1656062 TATCTGTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGACACATTATGCTTTGTATCGATACAT
Found at i:1656499 original size:20 final size:20
Alignment explanation
Indices: 1656476--1656548 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1656466 ACAATTCAAA
1656476 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1656496 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
1656517 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1656537 GTATCGATACAT
1 GTATCGATACAT
1656549 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1656519 original size:21 final size:21
Alignment explanation
Indices: 1656493--1656569 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1656483 TACATGTTGC
1656493 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
1656514 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
1656534 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
1656554 GGATGTATCGATACAT
1 -AATGTATCGATACAT
1656570 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:1656527 original size:41 final size:41
Alignment explanation
Indices: 1656476--1656569 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1656466 ACAATTCAAA
1656476 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
1656517 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
1656558 GTATCGATACAT
1 GTATCGATACAT
1656570 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:1656626 original size:13 final size:13
Alignment explanation
Indices: 1656608--1656633 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1656598 TACAGCAAGT
1656608 ATGTATCGATACA
1 ATGTATCGATACA
1656621 ATGTATCGATACA
1 ATGTATCGATACA
1656634 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1660110 original size:20 final size:20
Alignment explanation
Indices: 1660069--1660122 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1660059 TTCTACAATT
**
1660069 TGTATCGATACAATTGGTGAA
1 TGTATCGATAC-ATAAGTGAA
1660090 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
1660110 TGTATCGATACAT
1 TGTATCGATACAT
1660123 GTCTTAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:1662133 original size:28 final size:27
Alignment explanation
Indices: 1662097--1662199 Score: 111
Period size: 28 Copynumber: 3.8 Consensus size: 27
1662087 AAAAAAAAAT
*
1662097 CGGGATTGGAGTATCCCTTCGAAAATAA
1 CGGGGTTGGAGTATCCC-TCGAAAATAA
* *
1662125 CGGGGTTGGAGTATCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCTCGAAAATAA
*
1662152 CGGGGTTGGAGTATCCC-CGATGAGATAA
1 CGGGGTTGGAGTATCCCTCGA--AAATAA
* *
1662180 CGAGGTTAGAGTAT-CCTCGA
1 CGGGGTTGGAGTATCCCTCGA
1662200 TTGTGAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.03
27 27 0.42
28 35 0.55
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.23
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCGAAAATAA
Found at i:1662160 original size:27 final size:28
Alignment explanation
Indices: 1662097--1662168 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
1662087 AAAAAAAAAT
*
1662097 CGGGATTGGAGTATCCCTTCGAAAATAA
1 CGGGGTTGGAGTATCCCTTCGAAAATAA
* *
1662125 CGGGGTTGGAGTATCCC-TCGGAAGTAA
1 CGGGGTTGGAGTATCCCTTCGAAAATAA
1662152 CGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCC
1662169 CGATGAGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAA
Found at i:1662247 original size:52 final size:51
Alignment explanation
Indices: 1662183--1662569 Score: 231
Period size: 52 Copynumber: 7.4 Consensus size: 51
1662173 GAGATAACGA
* * * * * *
1662183 GGTTAGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGT-GTTTTGGAAATAAAACCGG
** * * * *
1662235 AATTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
1662287 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * **
1662339 GGTTGGAGTATCCTCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
** *** * * * **** *
1662390 GGTTGGAGTATCCCCCCGAAAAT-AACGGGGTTGGAGTATCCCCAATGATTAA-CGG
1 GGTTGGAGTAT--CCCCGATTATGAA--AAATTAGTGTTTTGGAAAT-A-AAACCGG
* * *
1662445 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTG----TTTTGGAAATAAAACCGG
* * * * *
1662500 AGTTTGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAACCGG
* *
1662551 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
1662570 GTGGAGAATT
Statistics
Matches: 253, Mismatches: 67, Indels: 31
0.72 0.19 0.09
Matches are distributed among these distances:
51 67 0.26
52 99 0.39
53 24 0.09
54 11 0.04
55 46 0.18
56 6 0.02
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:1662442 original size:27 final size:26
Alignment explanation
Indices: 1662387--1662461 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
1662377 GAAATAAAGT
1662387 CGGGGTTGGAGTATCCCCCCGAAAATAA
1 CGGGGTTGGAGTAT--CCCCGAAAATAA
*
1662415 CGGGGTTGGAGTATCCCC-AATGATTAA
1 CGGGGTTGGAGTATCCCCGAA--AATAA
1662442 CGGGGTTGGAGTATCCCCGA
1 CGGGGTTGGAGTATCCCCGA
1662462 TTGTGAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
25 2 0.05
26 4 0.09
27 22 0.51
28 15 0.35
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGAAAATAA
Found at i:1662509 original size:55 final size:52
Alignment explanation
Indices: 1662446--1662577 Score: 151
Period size: 51 Copynumber: 2.5 Consensus size: 52
1662436 GATTAACGGG
* * *
1662446 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTG----TCTTGAAAATAAAATCGGA
* *
1662501 GTTTGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTCTTGAAAATAAAATCGGA
*
1662552 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
1662578 TTGAGAAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
51 34 0.52
53 4 0.06
54 1 0.02
55 27 0.41
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAGAAAATTAGTGTCTTGAAAATAAAATCGGA
Found at i:1664964 original size:13 final size:13
Alignment explanation
Indices: 1664946--1664971 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1664936 ACAAAGATCC
1664946 ATGTATCGATACA
1 ATGTATCGATACA
1664959 ATGTATCGATACA
1 ATGTATCGATACA
1664972 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1664967 original size:33 final size:33
Alignment explanation
Indices: 1664925--1664991 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1664915 AAAATTTCCA
***
1664925 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1664958 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1664991 A
1 A
1664992 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1665075 original size:32 final size:32
Alignment explanation
Indices: 1665014--1665076 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1665004 TAGCTAATTA
* * ** *
1665014 TGTATCGATATAATACTTATTTATTGATACAT
1 TGTATCGATACAAAACTTAAGTATCGATACAT
1665046 TGTATCGATACAAAACTTAAGTATCGATACA
1 TGTATCGATACAAAACTTAAGTATCGATACA
1665077 AATTGTTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (32 bp):
TGTATCGATACAAAACTTAAGTATCGATACAT
Found at i:1665956 original size:55 final size:54
Alignment explanation
Indices: 1665872--1666064 Score: 246
Period size: 55 Copynumber: 3.4 Consensus size: 54
1665862 ATAAAGTGTA
*
1665872 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
1665927 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTAAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
*
1665982 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT--AAAAGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
1666043 TCCTGCTCTTTGAGGACTAAAA
1 TCCTGCTCTTTGAGGACTAAAA
1666065 AGCGGAAGGA
Statistics
Matches: 123, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
54 6 0.05
55 86 0.70
57 4 0.03
59 4 0.03
61 21 0.17
62 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:1679579 original size:28 final size:28
Alignment explanation
Indices: 1679548--1679613 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
1679538 ATCGGGATTA
*
1679548 GAGTATCCCTTCGAAAATAACGGCGTTG
1 GAGTATCCCCTCGAAAATAACGGCGTTG
* * *
1679576 GAGTATCCCCTCGGAAGTAACGGGGTTG
1 GAGTATCCCCTCGAAAATAACGGCGTTG
1679604 GAGTATCCCC
1 GAGTATCCCC
1679614 GATGAGATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (28 bp):
GAGTATCCCCTCGAAAATAACGGCGTTG
Found at i:1679624 original size:28 final size:27
Alignment explanation
Indices: 1679563--1679644 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 27
1679553 TCCCTTCGAA
* ***
1679563 AATAACGGCGTTGGAGTATCCCCTCGG
1 AATAACGGGGTTGGAGTATCCCCGATG
1679590 AAGTAACGGGGTTGGAGTATCCCCGATG
1 AA-TAACGGGGTTGGAGTATCCCCGATG
* *
1679618 AGATAACGAGGTTGGAGTATCCTCGAT
1 A-ATAACGGGGTTGGAGTATCCCCGAT
1679645 TATGAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
27 2 0.04
28 44 0.94
29 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (27 bp):
AATAACGGGGTTGGAGTATCCCCGATG
Found at i:1679779 original size:52 final size:52
Alignment explanation
Indices: 1679627--1679901 Score: 322
Period size: 52 Copynumber: 5.3 Consensus size: 52
1679617 GAGATAACGA
* * * * *
1679627 GGTTGGAGTATCCTCGATTAT-GAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGT-GTTTTAGAAATAAAACCGG
** * *
1679679 AATTGGAGTATCCCCGATTAAAGGAAAAATTGGTGTTTT-GAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAAATTAGTGTTTTAG-AAATAAAACCGG
* *
1679732 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGAAATAAAACCGG
* * *
1679784 GGTTGGAGTATCCCTGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGAAATAAAACCGG
* * * * **
1679836 GGTTGGAGTATCCCCGATTAT-GAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGAAATAAAACCGG
1679887 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1679902 TCGGAAATAA
Statistics
Matches: 197, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
51 38 0.19
52 114 0.58
53 34 0.17
54 11 0.06
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:1679845 original size:104 final size:104
Alignment explanation
Indices: 1679627--1679901 Score: 356
Period size: 105 Copynumber: 2.6 Consensus size: 104
1679617 GAGATAACGA
* * **
1679627 GGTTGGAGTATCCTCGATTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTA-TTTTGGAAATAAAATCGGGGTTGGAGTATCC
*
1679692 CCGATTAAAGGAAAAATTGGTGTTTTGAAAATAAAACCGG
65 CCGATTAAAGGAAAAATTAGTGTTTTGAAAATAAAACCGG
* * * * *
1679732 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTATTTTGGAAATAAAATCGGGGTTGGAGTATCC
* ** *
1679797 CTGATT-GTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG
65 CCGATTAAAGGAAAAATTAGTGTTTTGA-AAATAAAACCGG
* * *
1679836 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGGGGTTGGAGTATCCC
1679901 C
66 C
1679902 TCGGAAATAA
Statistics
Matches: 145, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
103 38 0.26
104 47 0.32
105 50 0.34
106 10 0.07
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (104 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTGGAAATAAAATCGGGGTTGGAGTATCCC
CGATTAAAGGAAAAATTAGTGTTTTGAAAATAAAACCGG
Found at i:1679947 original size:27 final size:28
Alignment explanation
Indices: 1679884--1679959 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
1679874 GAAATAAAGT
***
1679884 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1679912 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1679939 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1679960 TGTGAAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1680042 original size:161 final size:158
Alignment explanation
Indices: 1679572--1680062 Score: 468
Period size: 161 Copynumber: 3.1 Consensus size: 158
1679562 AAATAACGGC
* *
1679572 GTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAGATAACGAGGTTGGAGTA
1 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT--GATAACGGGGTTGGAGTA
* * * *
1679637 TCCTCGATTATGAAAAATTG-GTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAA
64 TCCCCGATTGTGAAAAATTGTGT-TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA
* * *
1679701 GGAAAAATTGGTGTTTTGAAAATAAAACCGGG
128 -GAAAAATTAGAGTTTTGAAAATAAAATCGGG
* * * * *** * *
1679733 GTTGGAGTATCCCCGATTGTGGAAA-AA-----TTAGTGTTTTAGCAAT-AAAACCGGGGTTGGA
1 GTTGGAGTATCCCC---T-CGGAAATAACGGGGTTGGAGTATCCCCGATGATAA-CGGGGTTGGA
* * * * *
1679791 GTATCCCTGATTGTGGAAAAATTAGTG--TTTTAGCAATAAAACCGGGGTTGGAGTATCCCCGAT
61 GTATCCCCGATTGT-GAAAAATT-GTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGAT
* * * *
1679854 TAT-GAAAAATCA-ATATTTTGGAAATAAAGTCGGG
124 TATAGAAAAATTAGA-GTTTTGAAAATAAAATCGGG
1679888 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTAT
1 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGA-TAACGGGGTTGGAGTAT
*
1679953 CCCCGATTGTGAAAATTTGGTGTTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAT
65 CCCCGATTGTGAAAAATT-GTG--TTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAT
* *
1680018 AG-AAAATTAGAGTCTTGAAAATAAAATCGGA
127 AGAAAAATTAGAGTTTTGAAAATAAAATCGGG
*
1680049 GTTGGAATATCCCC
1 GTTGGAGTATCCCC
1680063 AATTGTGGAG
Statistics
Matches: 257, Mismatches: 50, Indels: 46
0.73 0.14 0.13
Matches are distributed among these distances:
151 5 0.02
152 3 0.01
155 37 0.14
156 3 0.01
157 72 0.28
158 32 0.12
159 12 0.05
160 1 0.00
161 83 0.32
162 2 0.01
164 3 0.01
165 4 0.02
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (158 bp):
GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATAACGGGGTTGGAGTATC
CCCGATTGTGAAAAATTGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAA
AAATTAGAGTTTTGAAAATAAAATCGGG
Found at i:1680870 original size:13 final size:13
Alignment explanation
Indices: 1680852--1680877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1680842 AATTTTTTTG
1680852 TGTATCGATACAT
1 TGTATCGATACAT
1680865 TGTATCGATACAT
1 TGTATCGATACAT
1680878 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1680960 original size:20 final size:21
Alignment explanation
Indices: 1680916--1680968 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1680906 CTGCCAAGAA
***
1680916 ATGTATCGATACATCTTTTAC
1 ATGTATCGATACATCTGCAAC
1680937 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTGCAAC
1680957 ATGTATCGATAC
1 ATGTATCGATAC
1680969 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (21 bp):
ATGTATCGATACATCTGCAAC
Found at i:1681616 original size:21 final size:21
Alignment explanation
Indices: 1681575--1681618 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1681565 CTCCCCTTTA
* *
1681575 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1681596 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1681617 TC
1 TC
1681619 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1683437 original size:13 final size:13
Alignment explanation
Indices: 1683419--1683457 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1683409 ATAATCACCC
1683419 TGTATCGATACAA
1 TGTATCGATACAA
1683432 TGTATCGATACAA
1 TGTATCGATACAA
1683445 TGTATCGATACAA
1 TGTATCGATACAA
1683458 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1685556 original size:15 final size:15
Alignment explanation
Indices: 1685536--1685566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1685526 ATTTCGTTTG
*
1685536 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1685551 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1685566 G
1 G
1685567 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1687398 original size:21 final size:21
Alignment explanation
Indices: 1687369--1687413 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1687359 AAGTTTTCAT
*
1687369 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1687389 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1687411 TTT
1 TTT
1687414 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1689660 original size:13 final size:13
Alignment explanation
Indices: 1689642--1689667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1689632 AATTTTTTTG
1689642 TGTATCGATACAT
1 TGTATCGATACAT
1689655 TGTATCGATACAT
1 TGTATCGATACAT
1689668 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1692415 original size:20 final size:20
Alignment explanation
Indices: 1692388--1692442 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1692378 TAAAATTTCC
*
1692388 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
1692408 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
1692428 AAATGTATCGATACA
1 AAATGTATCGATACA
1692443 TTTCCTTAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:1692486 original size:19 final size:18
Alignment explanation
Indices: 1692462--1692529 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1692452 CAGTAGCTAA
1692462 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1692481 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1692496 TTA--TATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1692513 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1692530 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 9 0.21
15 3 0.07
16 2 0.05
17 3 0.07
18 3 0.07
19 23 0.53
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Done.