Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold158
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: 3161772
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 138004 characters in sequence are not A, C, G, or T
File 6 of 9
Found at i:1485386 original size:30 final size:31
Alignment explanation
Indices: 1485331--1485398 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
1485321 ACCGTTAAAA
** * **
1485331 TATTTACACTATTGGTCCTTCAAATTTTTCG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
1485362 TATTTACACT-TTAATCCCTCAAATTTTGAG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
1485392 TATTTAC
1 TATTTAC
1485399 TCTTGAGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.47
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTGAG
Found at i:1488591 original size:3 final size:3
Alignment explanation
Indices: 1488571--1488611 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1488561 TTAAGATATG
* *
1488571 ATA AGA ATA ATGA ATA ATA ATA ATA ATT ATA ATA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1488612 ACACCAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1490384 original size:51 final size:51
Alignment explanation
Indices: 1490260--1490444 Score: 160
Period size: 51 Copynumber: 3.6 Consensus size: 51
1490250 AGTTGCTAGG
* * * * * * *
1490260 TCACGTGTGTAGTACTATGTGCAGGTTACTACGTGTATCGGAATG-ATA-GG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGG-ATGAAAATGA
* * ***
1490310 TCGCATGTGTAGTACCATGTGCAGGCTACTATGCGTACCGGAT-AGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAAT-GA
* * * * * *
1490361 TCACGTGTGTAGTACTATTTGCAGGCTACTACGTGTATCGGATGAAAATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAATGA
*
1490412 TCACATGTGTAGTACTATGTGCAGGATACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1490445 TGAACCAGGT
Statistics
Matches: 105, Mismatches: 26, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
49 2 0.02
50 34 0.32
51 67 0.64
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATGAAAATGA
Found at i:1496812 original size:125 final size:124
Alignment explanation
Indices: 1496583--1497003 Score: 594
Period size: 125 Copynumber: 3.4 Consensus size: 124
1496573 CGTGGACGCA
* * * * *
1496583 AAGAATTTGTGAAATCGCGCCCTCCTGGACGCGATTTTGCTAAAGTTGGTCCTGGAAGAAATAAT
1 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCT-GAAAAAATAAT
*
1496648 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAG
65 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAG
* * ** *
1496708 AAGAATTTGTTAAATCGCGCCCACGTGGATGCGCTTTTGCTACA-TTATATCCTGAAAAAATTAT
1 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTT-GGTCCTGAAAAAATAAT
* * *
1496772 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGCTATT-TGAG
65 TTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCTACCAAGATGCT-TTATGAG
* * *
1496833 AAGAATTTTTGAAATTGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGAAAGAAATAAT
1 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGAAA-AAATAAT
* *
1496898 TTTGAGTTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAG
65 TTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAG
* *
1496958 AATAATTTGTGAAATTGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1497004 AGCATGTTTG
Statistics
Matches: 260, Mismatches: 30, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
124 43 0.17
125 179 0.69
126 38 0.15
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (124 bp):
AAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTTGGTCCTGAAAAAATAATT
TCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTTTATGAG
Found at i:1499957 original size:60 final size:60
Alignment explanation
Indices: 1499893--1500030 Score: 249
Period size: 60 Copynumber: 2.3 Consensus size: 60
1499883 AGTAGAATTC
*
1499893 TCAAATAATATCAAAATATTCAAAATATTTGTCCAAATTAATTAAGCTCATGTTATTACA
1 TCAAATAATATCAAAATATTCAAAATATTTGTACAAATTAATTAAGCTCATGTTATTACA
*
1499953 TCAAATAATATCAAAAAATTCAAAATATTTGTACAAATTAATTAAGCTCATGTTATTACA
1 TCAAATAATATCAAAATATTCAAAATATTTGTACAAATTAATTAAGCTCATGTTATTACA
*
1500013 CCAAATAATATCAAAATA
1 TCAAATAATATCAAAATA
1500031 ACTCAAAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 74 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (60 bp):
TCAAATAATATCAAAATATTCAAAATATTTGTACAAATTAATTAAGCTCATGTTATTACA
Found at i:1500073 original size:25 final size:25
Alignment explanation
Indices: 1500044--1500091 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1500034 CAAAAAATTT
*
1500044 TTCTATTTTATTATATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
*
1500069 TTCTATTTTATTACATTAAATAA
1 TTCTATTTTATTACATCAAATAA
1500092 TATCAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:1500123 original size:45 final size:45
Alignment explanation
Indices: 1500059--1500144 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
1500049 TTTTATTATA
* * *
1500059 TCAAATAAACTTCTATTTTATTACATTAAATAATATCAAAATAAC
1 TCAAAAAAACTTCTATTTTACTACATAAAATAATATCAAAATAAC
*
1500104 TCAAAAAAATTTCTATTTTACTACATAAAATAATATCAAAA
1 TCAAAAAAACTTCTATTTTACTACATAAAATAATATCAAAA
1500145 CATTCAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (45 bp):
TCAAAAAAACTTCTATTTTACTACATAAAATAATATCAAAATAAC
Found at i:1500774 original size:8 final size:8
Alignment explanation
Indices: 1500763--1500787 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1500753 GGTTGCCTTC
1500763 GTCGTCTT
1 GTCGTCTT
1500771 GTCGTCTT
1 GTCGTCTT
1500779 GTCGTCTT
1 GTCGTCTT
1500787 G
1 G
1500788 GATTTAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.28, T:0.48
Consensus pattern (8 bp):
GTCGTCTT
Found at i:1502477 original size:51 final size:51
Alignment explanation
Indices: 1502416--1502513 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
1502406 AATAATATAA
*
1502416 AAATAGGGATTTAAGAGAAAT-TT-AAGAAGAACTTGAGAGCAAGTTGAAATT
1 AAATAGGGATTTAAGAGAAATATTGAAG--GAACTTGAGAGCAAATTGAAATT
* * *
1502467 AAATATGGATTTGAGAGAAATATTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATATTGAAGGAACTTGAGAGCAAATTGA
1502514 GAGGAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 36 0.88
52 2 0.05
53 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.24, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATATTGAAGGAACTTGAGAGCAAATTGAAATT
Found at i:1502511 original size:12 final size:11
Alignment explanation
Indices: 1502475--1502529 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
1502465 TTAAATATGG
1502475 ATTTGAGAGAA
1 ATTTGAGAGAA
*
1502486 ATATTGA-AGGA
1 AT-TTGAGAGAA
1502497 ATTTGAGAGCAA
1 ATTTGAGAG-AA
1502509 A-TTGAGAGGAA
1 ATTTGAGA-GAA
1502520 ATTTGAGAGA
1 ATTTGAGAGA
1502530 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 4 0.11
11 20 0.54
12 13 0.35
ACGTcount: A:0.44, C:0.02, G:0.29, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:1502522 original size:23 final size:22
Alignment explanation
Indices: 1502475--1502529 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1502465 TTAAATATGG
1502475 ATTTGAGAGAAATATTGAAGGA
1 ATTTGAGAGAAATATTGAAGGA
*
1502497 ATTTGAGAGCAA-ATTGAGAGGAA
1 ATTTGAGAGAAATATTGA-AGG-A
1502520 ATTTGAGAGA
1 ATTTGAGAGA
1502530 GGATTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.17
22 14 0.48
23 10 0.34
ACGTcount: A:0.44, C:0.02, G:0.29, T:0.25
Consensus pattern (22 bp):
ATTTGAGAGAAATATTGAAGGA
Found at i:1503393 original size:10 final size:10
Alignment explanation
Indices: 1503378--1503427 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
1503368 TAAATATTAT
1503378 AAAAATATAA
1 AAAAATATAA
*
1503388 AAAAATCTAA
1 AAAAATATAA
*
1503398 CAAAATATAA
1 AAAAATATAA
* *
1503408 TAAATTATAA
1 AAAAATATAA
1503418 AAAAATATAA
1 AAAAATATAA
1503428 CATTAATAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAATATAA
Found at i:1503537 original size:32 final size:33
Alignment explanation
Indices: 1503475--1503537 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1503465 AAAGTATTAG
* *
1503475 AATTCTTAAAAAGATAATAAAAATTGTAAAACA
1 AATTATTAAAAAGATAATAAAAATTATAAAACA
* *
1503508 AATTATTAAAAA-ATATTAAAATTTATAAAA
1 AATTATTAAAAAGATAATAAAAATTATAAAA
1503538 TTTATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (33 bp):
AATTATTAAAAAGATAATAAAAATTATAAAACA
Found at i:1503562 original size:9 final size:10
Alignment explanation
Indices: 1503493--1503568 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 10
1503483 AAAAGATAAT
*
1503493 AAAAATTGTAA
1 AAAAATTAT-A
1503504 AACAAATTATTA
1 AA-AAATTA-TA
*
1503516 AAAAA-TATT
1 AAAAATTATA
*
1503525 AAAATTTAT-
1 AAAAATTATA
*
1503534 AAAATTTAT-
1 AAAAATTATA
1503543 AAAAATTATTAA
1 AAAAATTA-T-A
1503555 AAAAATTATA
1 AAAAATTATA
1503565 AAAA
1 AAAA
1503569 CTTGAACTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
9 21 0.38
10 11 0.20
11 6 0.11
12 16 0.29
13 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (10 bp):
AAAAATTATA
Found at i:1511692 original size:51 final size:51
Alignment explanation
Indices: 1511557--1511747 Score: 235
Period size: 51 Copynumber: 3.8 Consensus size: 51
1511547 GTTGAAAGTG
* * *
1511557 ATGGTCACTTGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* *
1511606 ATAGGTCCCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
* * ** * * *
1511657 TTCGATCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATTGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
1511709 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1511748 AACTGAACAT
Statistics
Matches: 119, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.34
51 75 0.63
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.34
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTA
Found at i:1511747 original size:26 final size:26
Alignment explanation
Indices: 1511667--1511747 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
1511657 TTCGATCATG
1511667 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
1511693 CGTGTA-T-CGGAT-TGTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
1511718 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
1511744 TGTG
1 TGTG
1511748 AACTGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 3 0.08
25 15 0.38
26 19 0.47
27 3 0.08
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:1511840 original size:45 final size:45
Alignment explanation
Indices: 1511754--1511842 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
1511744 TGTGAACTGA
* * * *
1511754 ACATCATTGATTAGTAAGGTGGTTGCTATGTGTTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTCAATCCACCGG
1511799 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTCAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTCAATCCACCG
1511843 AGCATCTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTCAATCCACCGG
Found at i:1528035 original size:2 final size:2
Alignment explanation
Indices: 1528028--1528058 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1528018 ATACATAAAA
*
1528028 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1528059 AAAAGGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1528854 original size:14 final size:14
Alignment explanation
Indices: 1528837--1528863 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1528827 CCTATTTTCC
1528837 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
1528851 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
1528864 CGCTGCTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (14 bp):
TTTTTTGTTTTTTT
Found at i:1532404 original size:20 final size:20
Alignment explanation
Indices: 1532375--1532430 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1532365 ATTTTAAAAT
* *
1532375 CAAGTGAAAATGATTTTAAC
1 CAAGTAAAAATGATTTCAAC
*
1532395 CAAGTAAAAATGATTTCAAT
1 CAAGTAAAAATGATTTCAAC
* *
1532415 CAAGTTAAAATCATTT
1 CAAGTAAAAATGATTT
1532431 AACACATCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (20 bp):
CAAGTAAAAATGATTTCAAC
Found at i:1546832 original size:23 final size:23
Alignment explanation
Indices: 1546785--1546833 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1546775 ACCTACTTTC
* * **
1546785 TTACTGTAGTAATTTTTGGGGTA
1 TTACAGTAGTAATTTTTAGAATA
1546808 TTACAGTAGTAATTTTTAGAATA
1 TTACAGTAGTAATTTTTAGAATA
1546831 TTA
1 TTA
1546834 TAGTTTTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (23 bp):
TTACAGTAGTAATTTTTAGAATA
Found at i:1563521 original size:44 final size:43
Alignment explanation
Indices: 1563448--1563578 Score: 183
Period size: 43 Copynumber: 3.0 Consensus size: 43
1563438 TTTTATCCTA
*
1563448 GAAAAAAAAATTTAGAAAA-AGGAGAAGATAATCTTGGGTTGTT
1 GAAAAAAGAATTTA-AAAAGAGGAGAAGATAATCTTGGGTTGTT
* * *
1563491 GAAAAAAGATTTTATAAAAGAGGAGGAGATAATCTTGAGTTGTT
1 GAAAAAAGAATTTA-AAAAGAGGAGAAGATAATCTTGGGTTGTT
* *
1563535 GAAAAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTT
1 GAAAAAAGAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT
1563578 G
1 G
1563579 GTTTTACCTT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 42 0.55
44 35 0.45
ACGTcount: A:0.47, C:0.02, G:0.25, T:0.25
Consensus pattern (43 bp):
GAAAAAAGAATTTAAAAAGAGGAGAAGATAATCTTGGGTTGTT
Found at i:1567796 original size:30 final size:30
Alignment explanation
Indices: 1567751--1567828 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
1567741 ATATGGATAT
*
1567751 ATTGATTCATGTATGGTTATACATTGCCGA
1 ATTGATTCATATATGGTTATACATTGCCGA
* ** * ** *
1567781 ATTGTTTGGTATATGGATATAGGTTGCTGA
1 ATTGATTCATATATGGTTATACATTGCCGA
1567811 ATTGATTCATATATGGTT
1 ATTGATTCATATATGGTT
1567829 GTTCATTGTT
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.44
Consensus pattern (30 bp):
ATTGATTCATATATGGTTATACATTGCCGA
Found at i:1569515 original size:39 final size:39
Alignment explanation
Indices: 1569472--1569616 Score: 200
Period size: 39 Copynumber: 3.7 Consensus size: 39
1569462 ACTCAATTTT
* *
1569472 AAGCATATATCCTATTACACATATAATCACCTAATGCTC
1 AAGCATATATCATAATACACATATAATCACCTAATGCTC
* * *** *
1569511 AAGCATATATCATAATACACATATAATCTCATAACATTT
1 AAGCATATATCATAATACACATATAATCACCTAATGCTC
* *
1569550 AAGCATATATCCTATTACACATATAATCACCTAATGCTC
1 AAGCATATATCATAATACACATATAATCACCTAATGCTC
1569589 AAGCATATATCATAATACACATATAATC
1 AAGCATATATCATAATACACATATAATC
1569617 TCATAACATT
Statistics
Matches: 88, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (39 bp):
AAGCATATATCATAATACACATATAATCACCTAATGCTC
Found at i:1569551 original size:78 final size:78
Alignment explanation
Indices: 1569469--1569638 Score: 340
Period size: 78 Copynumber: 2.2 Consensus size: 78
1569459 CATACTCAAT
1569469 TTTAAGCATATATCCTATTACACATATAATCACCTAATGCTCAAGCATATATCATAATACACATA
1 TTTAAGCATATATCCTATTACACATATAATCACCTAATGCTCAAGCATATATCATAATACACATA
1569534 TAATCTCATAACA
66 TAATCTCATAACA
1569547 TTTAAGCATATATCCTATTACACATATAATCACCTAATGCTCAAGCATATATCATAATACACATA
1 TTTAAGCATATATCCTATTACACATATAATCACCTAATGCTCAAGCATATATCATAATACACATA
1569612 TAATCTCATAACA
66 TAATCTCATAACA
1569625 TTTAAGCATATATC
1 TTTAAGCATATATC
1569639 TCAATACTCA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 92 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (78 bp):
TTTAAGCATATATCCTATTACACATATAATCACCTAATGCTCAAGCATATATCATAATACACATA
TAATCTCATAACA
Found at i:1569632 original size:39 final size:39
Alignment explanation
Indices: 1569469--1569638 Score: 196
Period size: 39 Copynumber: 4.4 Consensus size: 39
1569459 CATACTCAAT
* * * **
1569469 TTTAAGCATATATCCTATTACACATATAATCACCTAATG
1 TTTAAGCATATATCATAATACACATATAATCACATAACA
* * *
1569508 CTCAAGCATATATCATAATACACATATAATCTCATAACA
1 TTTAAGCATATATCATAATACACATATAATCACATAACA
* * * **
1569547 TTTAAGCATATATCCTATTACACATATAATCACCTAATG
1 TTTAAGCATATATCATAATACACATATAATCACATAACA
* * *
1569586 CTCAAGCATATATCATAATACACATATAATCTCATAACA
1 TTTAAGCATATATCATAATACACATATAATCACATAACA
1569625 TTTAAGCATATATC
1 TTTAAGCATATATC
1569639 TCAATACTCA
Statistics
Matches: 105, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 105 1.00
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (39 bp):
TTTAAGCATATATCATAATACACATATAATCACATAACA
Found at i:1571362 original size:50 final size:50
Alignment explanation
Indices: 1571273--1571558 Score: 286
Period size: 50 Copynumber: 5.6 Consensus size: 50
1571263 TTGTACTGCT
* * * * ** *
1571273 AATGCCATATCCCAGATATGGTCTTACAAGAGAGTTCTCATATAGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCC
* ** * *
1571323 CATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCT
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCC
*** * *
1571373 AACATCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCT
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCC
** * * * *
1571423 AACACTATGTCCCAGACATGGTCTT-CAATGGGACCCCTTATCTCGGTGCC
1 AATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTAGGTGCC
*
1571473 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCC
1 AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCT--A-GGTGCC
1571529 AATGCCATGTCCCAGACATGGTCTTACATG
1 AATGCCATGTCCCAGACATGGTCTTACATG
1571559 AGATCTCTTT
Statistics
Matches: 198, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.01
50 157 0.79
51 1 0.01
53 4 0.02
56 35 0.18
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCC
Found at i:1584043 original size:43 final size:44
Alignment explanation
Indices: 1583893--1584067 Score: 273
Period size: 44 Copynumber: 4.0 Consensus size: 44
1583883 TTTTATACTA
* *
1583893 GAAAAAAGAATTT-AAAAAGAGGAGAAGATAATATTGGATTGTT
1 GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
*
1583936 GAAAAAATAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
1 GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
*
1583980 GAAAAAAGAATTTCAAAAAGAGGAGAAGATATTCTTGGGTTGTT
1 GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
* * *
1584024 GAAAAAATAATTT-AAAAAGAGGAGAAGATAAACATGGGTTGTT
1 GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
1584067 G
1 G
1584068 GGTTGTTGGT
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
43 40 0.33
44 82 0.67
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (44 bp):
GAAAAAAGAATTTCAAAAAGAGGAGAAGATAATCTTGGGTTGTT
Found at i:1584050 original size:87 final size:87
Alignment explanation
Indices: 1583893--1584067 Score: 289
Period size: 87 Copynumber: 2.0 Consensus size: 87
1583883 TTTTATACTA
1583893 GAAAAAAGAATTTAAAAAGAGGAGAAGATAATATTGGATTGTTGAAAAAATAATTTCAAAAAGAG
1 GAAAAAAGAATTTAAAAAGAGGAGAAGATAATATTGGATTGTTGAAAAAATAATTTCAAAAAGAG
* *
1583958 GAGAAGATAATCTTGGGTTGTT
66 GAGAAGATAAACATGGGTTGTT
* * *
1583980 GAAAAAAGAATTTCAAAAAGAGGAGAAGATATTCTTGGGTTGTTGAAAAAATAATTT-AAAAAGA
1 GAAAAAAGAATTT-AAAAAGAGGAGAAGATAATATTGGATTGTTGAAAAAATAATTTCAAAAAGA
1584044 GGAGAAGATAAACATGGGTTGTT
65 GGAGAAGATAAACATGGGTTGTT
1584067 G
1 G
1584068 GGTTGTTGGT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
87 42 0.51
88 40 0.49
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (87 bp):
GAAAAAAGAATTTAAAAAGAGGAGAAGATAATATTGGATTGTTGAAAAAATAATTTCAAAAAGAG
GAGAAGATAAACATGGGTTGTT
Found at i:1594580 original size:48 final size:48
Alignment explanation
Indices: 1594500--1594657 Score: 235
Period size: 48 Copynumber: 3.3 Consensus size: 48
1594490 GGGAAGGATA
* * *
1594500 TGAAAAGAGTAAGTTAATATGACTCTTTATGTGATATATGTTACGTAT
1 TGAAATGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTAT
* * *
1594548 TGAAATGAGTAAGTTAATATGACCCTGCATGTGATATTTGTTATGTAT
1 TGAAATGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTAT
* *
1594596 TGAAATGAGTAAGTTAAAATGACTTTGTATGTGATATATGTTATGTAT
1 TGAAATGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTAT
*
1594644 TGAAATAAGTAAGT
1 TGAAATGAGTAAGT
1594658 GATAACTCTT
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 98 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.39
Consensus pattern (48 bp):
TGAAATGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTAT
Found at i:1605840 original size:19 final size:20
Alignment explanation
Indices: 1605792--1605840 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1605782 ATTCATCATG
1605792 TTAA-TATTTTTAAGATAAT
1 TTAATTATTTTTAAGATAAT
1605811 TTAATTA-TTTTATA-AT-AT
1 TTAATTATTTTTA-AGATAAT
1605829 TTAATTATTTTT
1 TTAATTATTTTT
1605841 TTGACAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.33
19 15 0.56
20 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTAATTATTTTTAAGATAAT
Found at i:1611708 original size:27 final size:27
Alignment explanation
Indices: 1611661--1611730 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
1611651 CATTTGACAC
* *
1611661 ATTTTACATCAGATTATAGAGCTTCAA
1 ATTTTACATCAGATTAGAGAGATTCAA
** *
1611688 ATTTTACATCATTTTAGAGAGATTTAA
1 ATTTTACATCAGATTAGAGAGATTCAA
1611715 ATTTTACATCAAGATT
1 ATTTTACATC-AGATT
1611731 TTCAATCAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (27 bp):
ATTTTACATCAGATTAGAGAGATTCAA
Found at i:1623563 original size:18 final size:17
Alignment explanation
Indices: 1623530--1623565 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1623520 CTCTGCATGA
1623530 GTTTCTTTGTTTTATTT
1 GTTTCTTTGTTTTATTT
*
1623547 GTTTCTTTTTCTTTATTT
1 GTTTCTTTGT-TTTATTT
1623565 G
1 G
1623566 ATTCGGGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.06, C:0.08, G:0.11, T:0.75
Consensus pattern (17 bp):
GTTTCTTTGTTTTATTT
Found at i:1633727 original size:106 final size:104
Alignment explanation
Indices: 1633535--1633742 Score: 296
Period size: 106 Copynumber: 2.0 Consensus size: 104
1633525 GTTACTCCAT
* *
1633535 CCCCTACCCTCAATATTGTATTAAAAAATTAAAAATATTATTAATGAGATCATTACTTATGGAAG
1 CCCCTACCCTCAATATTGTATTAAAAAATTAAAAATATTATTAATGAGATCATTACTAATAGAAG
*
1633600 ATATTATTAACTATTTCAACAAACTTTTATATACCAACA
66 ATATTATTAACTATTTCAACAAACTTTTACATACCAACA
* *
1633639 CCCCTACCC-CAATATTTTA-TAAAAAATGATACAAATTTATTATTAATGAGATCATTA-TAAAT
1 CCCCTACCCTCAATATTGTATTAAAAAAT--TA-AAA-ATATTATTAATGAGATCATTACT-AAT
*
1633701 ATAAGATATTATTAACTATTTCAACAAACTTTTACATACCAA
61 AGAAGATATTATTAACTATTTCAACAAACTTTTACATACCAA
1633743 TAGGTGTTGG
Statistics
Matches: 93, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
102 8 0.09
103 9 0.10
104 11 0.12
105 4 0.04
106 61 0.66
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (104 bp):
CCCCTACCCTCAATATTGTATTAAAAAATTAAAAATATTATTAATGAGATCATTACTAATAGAAG
ATATTATTAACTATTTCAACAAACTTTTACATACCAACA
Found at i:1637697 original size:82 final size:84
Alignment explanation
Indices: 1637538--1637705 Score: 286
Period size: 82 Copynumber: 2.0 Consensus size: 84
1637528 CAGACTAAAA
*
1637538 ATCTCTTCAATTTTAAAGTACAGAATCAAGGTTTTTTTTTTTTTAAGAACCAAAATCAGTCAATT
1 ATCTCTTCAATTTTAAAGTACAGAATCAAGG--TTTTTTTTTTAAAGAACCAAAATCAGTCAATT
1637603 GAAAACAAAATTAATCCCAAC
64 GAAAACAAAATTAATCCCAAC
1637624 ATCTCTTCAATTTTAAAGTACAGAATCAA-G-TTTTTTTTTAAAGAACCAAAATCAGTCAATTGA
1 ATCTCTTCAATTTTAAAGTACAGAATCAAGGTTTTTTTTTTAAAGAACCAAAATCAGTCAATTGA
*
1637687 AAACAGAATTAATCCCAAC
66 AAACAAAATTAATCCCAAC
1637706 CACTTGACAT
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
82 50 0.62
85 1 0.01
86 29 0.36
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (84 bp):
ATCTCTTCAATTTTAAAGTACAGAATCAAGGTTTTTTTTTTAAAGAACCAAAATCAGTCAATTGA
AAACAAAATTAATCCCAAC
Found at i:1650680 original size:18 final size:17
Alignment explanation
Indices: 1650652--1650685 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1650642 GACAAAGAAT
1650652 CAATAAATACAAATAAA
1 CAATAAATACAAATAAA
*
1650669 CAATACAATACACATAA
1 CAATA-AATACAAATAA
1650686 GAGCAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CAATAAATACAAATAAA
Found at i:1652973 original size:44 final size:44
Alignment explanation
Indices: 1652914--1653291 Score: 187
Period size: 44 Copynumber: 8.6 Consensus size: 44
1652904 CTGATGCGAT
* *
1652914 CCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAAC
1 CCACTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTTAAC
* * * * *
1652958 CCACTCCACTACAACTTCAAGGAGATAGGAT-TA-TAGGCTTAAAT
1 CCACTCCACTGCAACTTCAGGGAGATAAGATCTATTA--CTTTAAC
** * * *** **
1653002 CTTCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGA-
1 CCACTCCACTGCAACTTCAGGGAGATAAGATCTATTA-CTTTAAC
* ** * * * * *
1653046 TCGGTCCTACTGCAACTTCAGGGGGATAAGACCTA--A-TGTGAT
1 CCACTCC-ACTGCAACTTCAGGGAGATAAGATCTATTACTTTAAC
* *
1653088 CCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAAC
1 CCACTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTTAAC
* * * * * *
1653132 CCACTCCACTACAACTTCAGGGAAATAGGAT-TATCAGCTTCAAT
1 CCACTCCACTGCAACTTCAGGGAGATAAGATCTATTA-CTTTAAC
*** * * * *** * *
1653176 CTGTTCCACTACAACCTCAGGGAGATAAGATTTGCAATTTTCGA-
1 CCACTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTT-AAC
* ** * *
1653220 TCGGTCCCACTGCAACTTCAGAGAGATAAGATCTGTTACTTTAAC
1 CCACT-CCACTGCAACTTCAGGGAGATAAGATCTATTACTTTAAC
* *
1653265 CCATTCCACTACAACTTCAGGGAGATA
1 CCACTCCACTGCAACTTCAGGGAGATA
1653292 GGATTATCGG
Statistics
Matches: 245, Mismatches: 75, Indels: 28
0.70 0.22 0.08
Matches are distributed among these distances:
41 27 0.11
42 5 0.02
43 8 0.03
44 143 0.58
45 61 0.25
46 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (44 bp):
CCACTCCACTGCAACTTCAGGGAGATAAGATCTATTACTTTAAC
Found at i:1653094 original size:174 final size:174
Alignment explanation
Indices: 1652881--1653250 Score: 600
Period size: 174 Copynumber: 2.1 Consensus size: 174
1652871 GTCTGCTCCG
* *
1652881 CTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATC
1 CTGCAACTTCAGGGAGATAAGACCTAATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATC
*
1652946 TATTACTTTAACCCACTCCACTACAACTTCAAGGAGATAGGATTAT-AGGCTTAAATCT-TCTCC
66 TATTACTTTAACCCACTCCACTACAACTTCAAGGAAATAGGATTATCA-GCTTAAATCTGT-TCC
* * *
1653009 ACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGATCGGTCCTA
129 ACTACAACCTCAGGGAGATAAGATTTGCAATCTTCGATCGGTCCCA
* *
1653055 CTGCAACTTCAGGGGGATAAGACCTAATGTGATCCACTCTACTGCAACTTCAGAGAGATAAGATC
1 CTGCAACTTCAGGGAGATAAGACCTAATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATC
* *
1653120 TATTACTTTAACCCACTCCACTACAACTTCAGGGAAATAGGATTATCAGCTTCAATCTGTTCCAC
66 TATTACTTTAACCCACTCCACTACAACTTCAAGGAAATAGGATTATCAGCTTAAATCTGTTCCAC
*
1653185 TACAACCTCAGGGAGATAAGATTTGCAATTTTCGATCGGTCCCA
131 TACAACCTCAGGGAGATAAGATTTGCAATCTTCGATCGGTCCCA
*
1653229 CTGCAACTTCAGAGAGATAAGA
1 CTGCAACTTCAGGGAGATAAGA
1653251 TCTGTTACTT
Statistics
Matches: 181, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
174 179 0.99
175 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (174 bp):
CTGCAACTTCAGGGAGATAAGACCTAATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATC
TATTACTTTAACCCACTCCACTACAACTTCAAGGAAATAGGATTATCAGCTTAAATCTGTTCCAC
TACAACCTCAGGGAGATAAGATTTGCAATCTTCGATCGGTCCCA
Found at i:1653317 original size:44 final size:44
Alignment explanation
Indices: 1652925--1653340 Score: 165
Period size: 44 Copynumber: 9.5 Consensus size: 44
1652915 CACTCTACTG
* * * * **
1652925 CAACTTCAGAGAGATAAGATCTATTA-CTTTAACCCACTCCACTA
1 CAACTTCAGGGAGATAAGAT-TATCAGCTTCAATCTGCTCCACTA
* * * * *
1652969 CAACTTCAAGGAGATAGGATTAT-AGGCTTAAATCTTCTCCACTG
1 CAACTTCAGGGAGATAAGATTATCA-GCTTCAATCTGCTCCACTA
* * * * *
1653013 CAACCTCAGGGAGATAAGATT-TGCCATCTTCGATC-GGTCCTACTG
1 CAACTTCAGGGAGATAAGATTAT--CAGCTTCAATCTGCTCC-ACTA
* * * ** * *
1653058 CAACTTCAGGGGGATAAGACCTA--A--TGT-GATCCACTCTACTG
1 CAACTTCAGGGAGATAAGA-TTATCAGCT-TCAATCTGCTCCACTA
* * * * **
1653099 CAACTTCAGAGAGATAAGATCTATTA-CTTTAACCCACTCCACTA
1 CAACTTCAGGGAGATAAGAT-TATCAGCTTCAATCTGCTCCACTA
* * *
1653143 CAACTTCAGGGAAATAGGATTATCAGCTTCAATCTGTTCCACTA
1 CAACTTCAGGGAGATAAGATTATCAGCTTCAATCTGCTCCACTA
* ** * * *
1653187 CAACCTCAGGGAGATAAGATT-TGCAATTTTCGATC-GGTCCCACTG
1 CAACTTCAGGGAGATAAGATTAT-C-AGCTTCAATCTGCT-CCACTA
* * * * * ***
1653232 CAACTTCAGAGAGATAAGATCTGTTA-CTTTAACCCATTCCACTA
1 CAACTTCAGGGAGATAAGAT-TATCAGCTTCAATCTGCTCCACTA
* * *
1653276 CAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTG
1 CAACTTCAGGGAGATAAGATTATCAGCTTCAATCTGCTCCACTA
* **
1653320 CAACCTCAGAAAGATAAGATT
1 CAACTTCAGGGAGATAAGATT
1653341 TGCCATATTC
Statistics
Matches: 278, Mismatches: 71, Indels: 46
0.70 0.18 0.12
Matches are distributed among these distances:
41 28 0.10
42 4 0.01
43 14 0.05
44 169 0.61
45 59 0.21
46 3 0.01
47 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (44 bp):
CAACTTCAGGGAGATAAGATTATCAGCTTCAATCTGCTCCACTA
Found at i:1653383 original size:133 final size:133
Alignment explanation
Indices: 1653095--1653372 Score: 448
Period size: 133 Copynumber: 2.1 Consensus size: 133
1653085 GATCCACTCT
*
1653095 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCACTCCACTACAACTTCAGGGAAATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTTACTTTAACCCACTCCACTACAACTTCAGGGAAATAG
* ** *
1653160 GATTATCAGCTTCAATCTGTTCCACTACAACCTCAGGGAGATAAGATTTGCAATTTTCGATCGGT
66 GATTATCAGCTTCAATCTGCTCCACTACAACCTCAGAAAGATAAGATTTGCAATATTCGATCGGT
1653225 CCC
131 CCC
* *
1653228 ACTGCAACTTCAGAGAGATAAGATCTGTTACTTTAACCCATTCCACTACAACTTCAGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTGTTACTTTAACCCACTCCACTACAACTTCAGGGAAATAG
* * *
1653293 GATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGAAAGATAAGATTTGCCATATTCGATCGGT
66 GATTATCAGCTTCAATCTGCTCCACTACAACCTCAGAAAGATAAGATTTGCAATATTCGATCGGT
*
1653358 TCC
131 CCC
*
1653361 ACTGTAACTTCA
1 ACTGCAACTTCA
1653373 AGGGGATAAG
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (133 bp):
ACTGCAACTTCAGAGAGATAAGATCTGTTACTTTAACCCACTCCACTACAACTTCAGGGAAATAG
GATTATCAGCTTCAATCTGCTCCACTACAACCTCAGAAAGATAAGATTTGCAATATTCGATCGGT
CCC
Found at i:1653411 original size:89 final size:89
Alignment explanation
Indices: 1653308--1653830 Score: 311
Period size: 89 Copynumber: 5.9 Consensus size: 89
1653298 TCGGCTTCAA
* * ** * *
1653308 TCTGCTCCACTGCAACCTCAGAAAGATAAGATTTGCCATATTCGATCGGTTCCACTGTAACTTCA
1 TCTGCTCCACTGCAACCTCAGAAAGATAAGACTTGCCATATCCGATCGGCCCCACTGCAACCTCA
1653373 AGGGGATAAGACCTGCTTACTCAG
66 AGGGGATAAGACCTGCTTACTCAG
* * * * * *
1653397 TCTGTTCCACTGCAACCTCAGAGAGATAAGACTTGTCTTCTCCGATCTGCCCCACTGCAACCTCA
1 TCTGCTCCACTGCAACCTCAGAAAGATAAGACTTGCCATATCCGATCGGCCCCACTGCAACCTCA
*
1653462 GGGGGATAAGACCTGCTTACTCAG
66 AGGGGATAAGACCTGCTTACTCAG
* * * * * * *
1653486 TCTGCTCCAC-GACAACCTCA-AAGAGATAAGAATTGTCTTCTCAG-TCTGCTCCACTGCAACCT
1 TCTGCTCCACTG-CAACCTCAGAA-AGATAAGACTTGCCATATCCGATCGGCCCCACTGCAACCT
* * *
1653548 C-AGGGAGATAAGACCTG-ATGC-GA-
64 CAAGGG-GATAAGACCTGCTTACTCAG
** * ** * * *** * * * * * *
1653571 TCCACTCTACTGCAAATTCAGAGAGATAAGA--T-CTATTACTTTAATCCGCTCCAATACAGCTT
1 TCTGCTCCACTGCAACCTCAGAAAGATAAGACTTGCCA-TA-TCCGATCGGCCCCACTGCAACCT
* * * *
1653633 C-AGGGAGATAGGATTATCGGC-T--TCAA
64 CAAGGG-GATA--A-GACCTGCTTACTCAG
* ** * * * *
1653659 TCTGTTCCACTGCAACCTCAGGGAGATATGATTTGCCATCTTCGATCTGG-CCCACTGCAACCTC
1 TCTGCTCCACTGCAACCTCAGAAAGATAAGACTTGCCATATCCGATC-GGCCCCACTGCAACCTC
*
1653723 AGGGGGATAAGACCTGCTTACTCAG
65 AAGGGGATAAGACCTGCTTACTCAG
* ** * * * * *
1653748 TCTGCTCCACTGCAACCTTAGGGAGATAAGACTTGTCTTCTCTGATCTGCCCCACTGCAACCTCA
1 TCTGCTCCACTGCAACCTCAGAAAGATAAGACTTGCCATATCCGATCGGCCCCACTGCAACCTCA
*
1653813 GGGGGATAAGACCTGCTT
66 AGGGGATAAGACCTGCTT
1653831 GAAAAACTTA
Statistics
Matches: 335, Mismatches: 76, Indels: 46
0.73 0.17 0.10
Matches are distributed among these distances:
83 2 0.01
84 1 0.00
85 44 0.13
86 7 0.02
87 9 0.03
88 59 0.18
89 205 0.61
90 6 0.02
91 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (89 bp):
TCTGCTCCACTGCAACCTCAGAAAGATAAGACTTGCCATATCCGATCGGCCCCACTGCAACCTCA
AGGGGATAAGACCTGCTTACTCAG
Found at i:1653425 original size:44 final size:44
Alignment explanation
Indices: 1653308--1653830 Score: 304
Period size: 44 Copynumber: 11.9 Consensus size: 44
1653298 TCGGCTTCAA
** ** * *
1653308 TCTGCTCCACTGCAACCTCAGAAAGATAAGATTTGCCATATTC-G
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTG-CTTACTCAG
* * * *
1653352 ATCGGTTCCACTGTAACTTCAAGGG-GATAAGACCTGCTTACTCAG
1 -TCTGCTCCACTGCAACCTC-AGGGAGATAAGACCTGCTTACTCAG
* * * *
1653397 TCTGTTCCACTGCAACCTCAGAGAGATAAGACTTGTCTT-CTCCG
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTG-CTTACTCAG
* *
1653441 ATCTGCCCCACTGCAACCTCAGGGGGATAAGACCTGCTTACTCAG
1 -TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCTTACTCAG
** **
1653486 TCTGCTCCAC-GACAACCTCAAAGAGATAAGAATTGTCTT-CTCAG
1 TCTGCTCCACTG-CAACCTCAGGGAGATAAGACCTG-CTTACTCAG
* * *
1653530 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTG-ATGC-GA-
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCTTACTCAG
** * ** * * * * *
1653571 TCCACTCTACTGCAAATTCAGAGAGATAAGATCT-ATTACTTTAA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCTTAC-TCAG
* * * * * * * * *
1653615 TCCGCTCCAATACAGCTTCAGGGAGATAGGATTATCGGC-T--TCAA
1 TCTGCTCCACTGCAACCTCAGGGAGATA--A-GACCTGCTTACTCAG
* * ** *
1653659 TCTGTTCCACTGCAACCTCAGGGAGATATGATTTGC-CATCTTC-G
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCTTA-C-TCAG
*
1653703 ATCTGGC-CCACTGCAACCTCAGGGGGATAAGACCTGCTTACTCAG
1 -TCT-GCTCCACTGCAACCTCAGGGAGATAAGACCTGCTTACTCAG
* * *
1653748 TCTGCTCCACTGCAACCTTAGGGAGATAAGACTTGTCTT-CTCTG
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTG-CTTACTCAG
* *
1653792 ATCTGCCCCACTGCAACCTCAGGGGGATAAGACCTGCTT
1 -TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCTT
1653831 GAAAAACTTA
Statistics
Matches: 368, Mismatches: 81, Indels: 59
0.72 0.16 0.12
Matches are distributed among these distances:
41 33 0.09
42 2 0.01
43 8 0.02
44 183 0.50
45 133 0.36
46 5 0.01
47 4 0.01
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (44 bp):
TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGCTTACTCAG
Found at i:1655058 original size:7 final size:7
Alignment explanation
Indices: 1655039--1655083 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
1655029 TTAGCCTCTC
1655039 CATTTTT
1 CATTTTT
1655046 -ACTTTTT
1 CA-TTTTT
1655053 CATTTTTT
1 CA-TTTTT
1655061 CATTTTT
1 CATTTTT
1655068 CA-TTTT
1 CATTTTT
1655074 CATTTTT
1 CATTTTT
1655081 CAT
1 CAT
1655084 CATTTTTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
6 7 0.21
7 19 0.56
8 8 0.24
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:1655066 original size:15 final size:15
Alignment explanation
Indices: 1655039--1655083 Score: 60
Period size: 13 Copynumber: 3.2 Consensus size: 15
1655029 TTAGCCTCTC
*
1655039 CATTTTTAC-TTTTT
1 CATTTTTTCATTTTT
1655053 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
1655068 CA--TTTTCATTTTT
1 CATTTTTTCATTTTT
1655081 CAT
1 CAT
1655084 CATTTTTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 13 0.46
14 8 0.29
15 7 0.25
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (15 bp):
CATTTTTTCATTTTT
Found at i:1656024 original size:47 final size:47
Alignment explanation
Indices: 1655940--1656082 Score: 196
Period size: 47 Copynumber: 3.0 Consensus size: 47
1655930 CCATTTTTCC
** * *
1655940 CTTTCTTCTCTCTTTTTTCATTTTCATTTTAACTTTGATTTTGATTTTT
1 CTTT-TTCT-TCTTTTTTGTTTTTCATTTTGATTTTGATTTTGATTTTT
* *
1655989 CTTTTTCTTCTTTTTTGTTTTTTATTTTGATTTTGATTTTGATTTTG
1 CTTTTTCTTCTTTTTTGTTTTTCATTTTGATTTTGATTTTGATTTTT
* *
1656036 ATTTTTCTTCTTTTTTGTTTTTGATTTTGATTTTGATTTTGATTTTT
1 CTTTTTCTTCTTTTTTGTTTTTCATTTTGATTTTGATTTTGATTTTT
1656083 TTTGGGGATT
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 77 0.91
48 4 0.05
49 4 0.05
ACGTcount: A:0.10, C:0.09, G:0.08, T:0.72
Consensus pattern (47 bp):
CTTTTTCTTCTTTTTTGTTTTTCATTTTGATTTTGATTTTGATTTTT
Found at i:1656076 original size:53 final size:53
Alignment explanation
Indices: 1655954--1656081 Score: 170
Period size: 53 Copynumber: 2.4 Consensus size: 53
1655944 CTTCTCTCTT
* * * *
1655954 TTTTCATTTTCATTTTAACTTTGATTTTGATTTTTCTTTTTCTTCTTTTTTGT
1 TTTTCATTTTGATTTTGATTTTGATTTTGATTTTTCTTTTTCTTCTTTTTTGA
*
1656007 TTTTTATTTTGATTTTGATTTTGATTTTGATTTTTCTTCTTT-TT-TGTTTTTGA
1 TTTTCATTTTGATTTTGATTTTGATTTTGATTTTTCTT-TTTCTTCT-TTTTTGA
*
1656060 TTTTGATTTTGATTTTGATTTT
1 TTTTCATTTTGATTTTGATTTT
1656082 TTTTGGGGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
52 1 0.01
53 63 0.94
54 3 0.04
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.73
Consensus pattern (53 bp):
TTTTCATTTTGATTTTGATTTTGATTTTGATTTTTCTTTTTCTTCTTTTTTGA
Found at i:1660239 original size:18 final size:17
Alignment explanation
Indices: 1660211--1660244 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1660201 GACAAAGAAT
1660211 CAATAAATACAAATAAA
1 CAATAAATACAAATAAA
*
1660228 CAATACAATACACATAA
1 CAATA-AATACAAATAA
1660245 GAGCAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CAATAAATACAAATAAA
Found at i:1664603 original size:19 final size:19
Alignment explanation
Indices: 1664565--1664604 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1664555 CATTTGTTTG
*
1664565 CACTTTGGTGCTTCTTTTA
1 CACTTTGGTGCTTCTATTA
1664584 CACTTTGGTG-TCTCTATTA
1 CACTTTGGTGCT-TCTATTA
1664603 CA
1 CA
1664605 GTTCAGTGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (19 bp):
CACTTTGGTGCTTCTATTA
Found at i:1668354 original size:25 final size:24
Alignment explanation
Indices: 1668321--1668375 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
1668311 TTGGTTTATT
*
1668321 TTTAATTATA-TTTAAAATATTTTAA
1 TTTATTTATACTTT-AAA-ATTTTAA
*
1668346 TTTATTTATACTTTTAAATTTTAA
1 TTTATTTATACTTTAAAATTTTAA
1668370 TTTATT
1 TTTATT
1668376 AACATTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 13 0.48
25 11 0.41
26 3 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTATTTATACTTTAAAATTTTAA
Found at i:1669472 original size:21 final size:23
Alignment explanation
Indices: 1669448--1669490 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1669438 AAACATAAAA
1669448 TAAA-TAAATATATTTT-ATAAT
1 TAAATTAAATATATTTTCATAAT
*
1669469 TAAATTAAATATTTTTTCATAA
1 TAAATTAAATATATTTTCATAA
1669491 ATACTAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAATTAAATATATTTTCATAAT
Found at i:1670501 original size:6 final size:6
Alignment explanation
Indices: 1670490--1670527 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
1670480 TACGTTCTTC
*
1670490 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTCCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
1670528 CTTCACTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:1671532 original size:14 final size:14
Alignment explanation
Indices: 1671513--1671539 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1671503 GTATGCTTAT
1671513 ATCTATATCTGTAC
1 ATCTATATCTGTAC
1671527 ATCTATATCTGTA
1 ATCTATATCTGTA
1671540 TTGGGGCTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (14 bp):
ATCTATATCTGTAC
Found at i:1679963 original size:56 final size:56
Alignment explanation
Indices: 1679872--1680070 Score: 277
Period size: 56 Copynumber: 3.7 Consensus size: 56
1679862 ATTTGGGTAA
*
1679872 AGAGATCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
1679928 AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
* *
1679984 AGAGGTCCCATGTAAGACCATGTC-TAGGACACGGCATTGGCA-C--CGAG---ATG
1 AGAGGTCCCATGTAAGACCATGTCTTA-GACATGGCATTGGCATCATTGAGATTATG
* * **
1680034 AGAGGTCCCCTGTAAGACCATATCTGGGACATGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCAT
1680071 GGCCACCGAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
50 34 0.26
53 3 0.02
55 3 0.02
56 93 0.70
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (56 bp):
AGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATG
Found at i:1680035 original size:50 final size:53
Alignment explanation
Indices: 1679872--1680126 Score: 258
Period size: 56 Copynumber: 4.8 Consensus size: 53
1679862 ATTTGGGTAA
* *
1679872 AGAGATCCCATGTAAGACCATGTCTTA-GACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTC-TAGGACATGGCATTGGCATCA-CGAG--TATG
*
1679928 AGAGGTCCCATGTAAGACCATGTCTTA-GACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTC-TAGGACATGGCATTGGCATCA-CGAG--TATG
*
1679984 AGAGGTCCCATGTAAGACCATGTCTAGGACACGGCATTGGCA-C-CGAG-ATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCACGAGTATG
* * *
1680034 AGAGGTCCCCTGTAAGACCATATCTGGGACATGGCA-TGGC--CACCGA-TATG
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCA-CGAGTATG
** * * *
1680084 AGAACTCCCATGTAAGACCATATCTGGGACATGGCTTTGGCAT
1 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCAT
1680127 GTTATTATCA
Statistics
Matches: 181, Mismatches: 11, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
48 1 0.01
49 4 0.02
50 73 0.40
51 4 0.02
53 3 0.02
55 3 0.02
56 93 0.51
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (53 bp):
AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCACGAGTATG
Found at i:1680124 original size:100 final size:104
Alignment explanation
Indices: 1679925--1680125 Score: 248
Period size: 100 Copynumber: 2.0 Consensus size: 104
1679915 CATTGAGATT
* * * **
1679925 ATGAGAGGTCCCATGTAAGACCATGTCTTAGACATGGCATTGGCATCATTGAGATTATGAGAGGT
1 ATGAGAGGTCCCATGTAAGACCATATCTGAGACATGGCATTGGCA-CA-TCAGATTATGAGAACT
*
1679990 CCCATGTAAGACCATGTCTAGGACACGGCATTGGCACCGAG
64 CCCATGTAAGACCATATCTAGGACACGGCATTGGCACCGAG
* * *
1680031 ATGAGAGGTCCCCTGTAAGACCATATCTGGGACATGGCA-TGGC-CA-CCGA-TATGAGAACTCC
1 ATGAGAGGTCCCATGTAAGACCATATCTGAGACATGGCATTGGCACATCAGATTATGAGAACTCC
* * *
1680092 CATGTAAGACCATATCTGGGACATGGCTTTGGCA
66 CATGTAAGACCATATCTAGGACACGGCATTGGCA
1680126 TGTTATTATC
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
100 40 0.48
101 2 0.02
103 2 0.02
105 4 0.05
106 35 0.42
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (104 bp):
ATGAGAGGTCCCATGTAAGACCATATCTGAGACATGGCATTGGCACATCAGATTATGAGAACTCC
CATGTAAGACCATATCTAGGACACGGCATTGGCACCGAG
Found at i:1685981 original size:302 final size:302
Alignment explanation
Indices: 1685434--1686043 Score: 1150
Period size: 302 Copynumber: 2.0 Consensus size: 302
1685424 AGAACCGGTA
1685434 AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTATTCTG
1 AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTATTCTG
1685499 GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACACAA
66 GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACACAA
*
1685564 ATCTCTTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCTA
131 ATCTCCTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCTA
*
1685629 GATTTTGGGCCTAGTCGGAACAGTGGTTTCGGGACCACAAATCCGATGAGGAAAAATTTATCTTT
196 GATTTTGGGCCTAGTCGGAACAGTGGTTTCGAGACCACAAATCCGATGAGGAAAAATTTATCTTT
1685694 ACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
261 ACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
*
1685736 AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTGTTCTG
1 AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTATTCTG
*
1685801 GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACCCAA
66 GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACACAA
1685866 ATCTCCTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCTC
131 ATCTCCTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCT-
**
1685931 A-ATTTTGGGCCTAGTCGGAACAGTGGTTTCGAGACCACAAATTTGATGAGGAAAAATTTATCTT
195 AGATTTTGGGCCTAGTCGGAACAGTGGTTTCGAGACCACAAATCCGATGAGGAAAAATTTATCTT
1685995 TACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
260 TACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
1686038 AAAATT
1 AAAATT
1686044 TCGACGTTTG
Statistics
Matches: 301, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
302 300 1.00
303 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (302 bp):
AAAATTCTAGATAGAGAGATCAAGCAACTAAGGAACAAGAGTATTGCACTTGTGCGAGTATTCTG
GAATAGGCATGGGGTTGATGAGGTTACATGGGAGCCCGAAGAGGCTATGCGAAAACAATACACAA
ATCTCCTCACAGGTAAGATTTTCGCGGACGAAAATCCCTAAAAGGGGGGAGAAATGTAACATCTA
GATTTTGGGCCTAGTCGGAACAGTGGTTTCGAGACCACAAATCCGATGAGGAAAAATTTATCTTT
ACTATATTTTTATGGCCTACAATTTCACGGAATGATTTCGTG
Found at i:1687189 original size:56 final size:53
Alignment explanation
Indices: 1687098--1687401 Score: 322
Period size: 50 Copynumber: 5.8 Consensus size: 53
1687088 ATATGGGTAA
* * *
1687098 AGAGATCCCATGTAAGACTATGTCTAGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA--GAGA-TATG
*
1687154 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-AG--ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGAGATATG
* * * *
1687204 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGACATTGGAATCATTGACATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCA--GAGA-TATG
* * * *
1687260 AGAGGTCCCATGTAAAACCATGTGTGGGACATGGCGTTGGCA-CCGAG--ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGAGATATG
* *
1687310 AGAGGTTCCC-TCTAAGACCATGTCTGGGACATGGCATGGGCATC---GATATG
1 AGAGG-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGAGATATG
* * *
1687360 AGAAGTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1687402 GTACAAGAAT
Statistics
Matches: 210, Mismatches: 27, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
48 1 0.00
49 4 0.02
50 114 0.54
51 5 0.02
53 5 0.02
55 1 0.00
56 80 0.38
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (53 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAGAGATATG
Found at i:1687293 original size:106 final size:104
Alignment explanation
Indices: 1687098--1687401 Score: 400
Period size: 106 Copynumber: 2.9 Consensus size: 104
1687088 ATATGGGTAA
* * * *
1687098 AGAGATCCCATGTAAGACTATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCC
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATTGG-ATCATTGA-ATTATGAGAGGTCCC
1687163 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
64 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
*
1687204 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGACATTGGAATCATTGACATTATGAGAGGTCCC
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATTGG-ATCATTGA-ATTATGAGAGGTCCC
* * * *
1687269 ATGTAAAACCATGTGTGGGACATGGCGTTGGCACCGAGATG
64 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* * * * *
1687310 AGAGGTTCCCTCTAAGACCATGTCTGGGACATGGCA-TGG-GCATCG-A-TATGAGAAGTCCCAT
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATTGGATCATTGAATTATGAGAGGTCCCAT
* *
1687371 GTAAGACCATATCTGGGATATGGCATTGGCA
66 GTAAGACCATGTCTGGGACATGGCATTGGCA
1687402 GTACAAGAAT
Statistics
Matches: 176, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
100 40 0.23
101 1 0.01
103 4 0.02
105 3 0.02
106 128 0.73
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (104 bp):
AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATTGGATCATTGAATTATGAGAGGTCCCAT
GTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:1691394 original size:61 final size:61
Alignment explanation
Indices: 1691299--1691426 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
1691289 GAGTCCAGTC
* * *
1691299 CGTGTGGCTCCAAACAAGGTCGTGTGGTTAACCTACACACCGATGTGCGACCTCACATGCA
1 CGTGTGGCTCCAAAAAAGGTCGTGTGGTTAACCTACACACCCATGTACGACCTCACATGCA
* * * *
1691360 CGTGTGGCTCCAAAAAAGGTCGTGTGGTTAACCTATACGCCCATGTACGACCTTACATGCC
1 CGTGTGGCTCCAAAAAAGGTCGTGTGGTTAACCTACACACCCATGTACGACCTCACATGCA
1691421 CGTGTG
1 CGTGTG
1691427 CATGGATTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (61 bp):
CGTGTGGCTCCAAAAAAGGTCGTGTGGTTAACCTACACACCCATGTACGACCTCACATGCA
Found at i:1700617 original size:12 final size:12
Alignment explanation
Indices: 1700600--1700629 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1700590 CCATACACAC
1700600 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
1700612 CCGTGTGCTAGG
1 CCGTGTGCCAGG
1700624 CCGTGT
1 CCGTGT
1700630 AACAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:1701708 original size:25 final size:25
Alignment explanation
Indices: 1701680--1701759 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
1701670 ATGCTCATGT
*
1701680 GAGCTATGGATCGGTATGCTCTCAC
1 GAGCTATGGATCGGTAAGCTCTCAC
1701705 GAGC--TGGAAATCGGTAAGCTCAT-AC
1 GAGCTATGG--ATCGGTAAGCTC-TCAC
* * *
1701730 GAGCTAAGAATCGGTAAGCTCTCAT
1 GAGCTATGGATCGGTAAGCTCTCAC
1701755 GAGCT
1 GAGCT
1701760 GGTGTGTCTG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
23 3 0.07
24 1 0.02
25 39 0.87
26 1 0.02
27 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (25 bp):
GAGCTATGGATCGGTAAGCTCTCAC
Found at i:1705660 original size:13 final size:13
Alignment explanation
Indices: 1705629--1705713 Score: 63
Period size: 13 Copynumber: 6.4 Consensus size: 13
1705619 AGGCAACCCA
1705629 ATTT-TTATT-TT
1 ATTTATTATTATT
*
1705640 AGTTATTATTATT
1 ATTTATTATTATT
1705653 ATTTATTATT-TT
1 ATTTATTATTATT
1705665 ATTTTATT-TTATTT
1 A-TTTATTATTA-TT
1705679 ACTTTATTTATTACTTT
1 A-TTTA-TTATTA--TT
1705696 ATTTTATT-TTATT
1 A-TTTATTATTATT
1705709 ATTTA
1 ATTTA
1705714 CTACTTATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 15
0.77 0.05 0.19
Matches are distributed among these distances:
11 3 0.05
12 14 0.23
13 20 0.32
14 7 0.11
15 5 0.08
16 5 0.08
17 8 0.13
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (13 bp):
ATTTATTATTATT
Found at i:1705668 original size:5 final size:5
Alignment explanation
Indices: 1705631--1705708 Score: 68
Period size: 5 Copynumber: 14.4 Consensus size: 5
1705621 GCAACCCAAT
1705631 TTTTA TTTTA GTTATTA TTATTA TTTATTA TTTTA TTTTA TTTTA -TTTA
1 TTTTA TTTTA -TT-TTA TT-TTA -TT-TTA TTTTA TTTTA TTTTA TTTTA
* *
1705680 CTTTA TTTATTA CTTTA TTTTA TTTTA TT
1 TTTTA -TT-TTA TTTTA TTTTA TTTTA TT
1705709 ATTTACTACT
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
4 4 0.06
5 36 0.56
6 12 0.19
7 12 0.19
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:1705677 original size:31 final size:30
Alignment explanation
Indices: 1705631--1705712 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 30
1705621 GCAACCCAAT
*
1705631 TTTTATTTTA-GTTATTATTATTATTTATTA
1 TTTTATTTTATTTTATTATT-TTATTTATTA
*
1705661 TTTTATTTTATTTTATTTACTTTATTTATTA
1 TTTTATTTTATTTTA-TTATTTTATTTATTA
*
1705692 CTTTATTTTATTTTATTATTT
1 TTTTATTTTATTTTATTATTT
1705713 ACTACTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
30 15 0.33
31 27 0.59
32 4 0.09
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.73
Consensus pattern (30 bp):
TTTTATTTTATTTTATTATTTTATTTATTA
Found at i:1706939 original size:101 final size:100
Alignment explanation
Indices: 1706751--1706939 Score: 231
Period size: 101 Copynumber: 1.9 Consensus size: 100
1706741 GAACATGTTA
* ** * * *
1706751 GGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTTTCTTCGTGTGAAAAGGTTCGATGTGTT
1 GGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATGTC
*
1706816 CTTAAGAAAAAATTATAGTAAATTAGGAGTGTGCTG
66 CTAAAGAAAAAA-TATAGTAAATTAGGAGTGTGCTG
* *
1706852 GGCTGAGTAATCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCAGTATAT-
1 GGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTC-G-ATATG
1706916 TCCTAAAGCATAAAAA-ATA-TAAAT
64 TCCTAAAG-A-AAAAATATAGTAAAT
1706940 AATAAATAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
101 56 0.75
102 10 0.13
103 4 0.05
104 5 0.07
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (100 bp):
GGCTGAGTAACCGGGGTGAGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATGTC
CTAAAGAAAAAATATAGTAAATTAGGAGTGTGCTG
Found at i:1707558 original size:15 final size:15
Alignment explanation
Indices: 1707533--1707567 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1707523 AACTCTATTT
*
1707533 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
1707547 TAATTAATATTAAGA
1 TAATTAATATTAAGA
1707562 TAATTA
1 TAATTA
1707568 TTAATGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:1709106 original size:22 final size:22
Alignment explanation
Indices: 1709081--1709127 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1709071 AATCACAAGC
1709081 AAAGTAGAACTATTACCAAGAT
1 AAAGTAGAACTATTACCAAGAT
1709103 AAAGTAGAACTATTACCAAGAT
1 AAAGTAGAACTATTACCAAGAT
1709125 AAA
1 AAA
1709128 CATATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.21
Consensus pattern (22 bp):
AAAGTAGAACTATTACCAAGAT
Found at i:1711429 original size:12 final size:12
Alignment explanation
Indices: 1711412--1711436 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1711402 CTGTGTCAGA
1711412 GGCTTCATCAAT
1 GGCTTCATCAAT
1711424 GGCTTCATCAAT
1 GGCTTCATCAAT
1711436 G
1 G
1711437 ATTTCTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (12 bp):
GGCTTCATCAAT
Found at i:1716646 original size:21 final size:22
Alignment explanation
Indices: 1716609--1716649 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1716599 GCACCCTAGG
*
1716609 CTTTTATTTTATGATTCCTTTC
1 CTTTTATTTAATGATTCCTTTC
1716631 CTTTTATTTAAT-ATTCCTT
1 CTTTTATTTAATGATTCCTT
1716650 AAAAAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (22 bp):
CTTTTATTTAATGATTCCTTTC
Found at i:1718604 original size:41 final size:41
Alignment explanation
Indices: 1718547--1718666 Score: 116
Period size: 41 Copynumber: 2.9 Consensus size: 41
1718537 TGATCGAATG
* * * *
1718547 TAATTCAGACTTATTGTCCAGGAGGCTTGATGCCGGTGATA
1 TAATTCAGACTCATTGTCCAGCAGGCTTAATGCCAGTGATA
* *
1718588 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGAAA
1 TAATTCAGACTCATTGTCCAGCAGGCTTAATGCCAGTGATA
* * * * * *
1718629 TTATTCGGACT-ATAAGTCTAGCAGGCTAAAAGCCAGTG
1 TAATTCAGACTCAT-TGTCCAGCAGGCTTAATGCCAGTG
1718667 TATTAAATCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
40 2 0.03
41 65 0.97
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (41 bp):
TAATTCAGACTCATTGTCCAGCAGGCTTAATGCCAGTGATA
Found at i:1722603 original size:12 final size:13
Alignment explanation
Indices: 1722586--1722617 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1722576 GTGGCTATGC
1722586 AAGGGAAA-GGAA
1 AAGGGAAATGGAA
1722598 AAGGGAAATGGAA
1 AAGGGAAATGGAA
1722611 AAGGGAA
1 AAGGGAA
1722618 TGATAGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.03
Consensus pattern (13 bp):
AAGGGAAATGGAA
Found at i:1723131 original size:21 final size:22
Alignment explanation
Indices: 1723093--1723140 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1723083 ATTATGAATA
*
1723093 TTAATTCATAATATAATTAATT
1 TTAATTCATAATACAATTAATT
* *
1723115 TTAATT-ATAATCCAATTTATT
1 TTAATTCATAATACAATTAATT
1723136 TTAAT
1 TTAAT
1723141 CCAATTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATTCATAATACAATTAATT
Found at i:1729530 original size:106 final size:106
Alignment explanation
Indices: 1729220--1729518 Score: 517
Period size: 106 Copynumber: 2.8 Consensus size: 106
1729210 ATACATACGA
* *
1729220 ATAGGTTTATCCCGGATCAATCAAAGCAGTAACATTAGTGTCAATGATAGAAAAAGTACTAGTAA
1 ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAATGATAGAAAAAGTACTAGTAA
1729285 TAACATCTGGAGCAGAAGCTTCCTATCGTGCACGAATCTAG
66 TAACATCTGGAGCAGAAGCTTCCTATCGTGCACGAATCTAG
1729326 ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAATGATAGAAAAAGTACTAGTAA
1 ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAATGATAGAAAAAGTACTAGTAA
1729391 TAACATCTGGAGCAGAAGCTTCCTATCGTGCACGAATCTAG
66 TAACATCTGGAGCAGAAGCTTCCTATCGTGCACGAATCTAG
* * * *
1729432 ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAAAGATAGAAAAACTCCCAGTAA
1 ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAATGATAGAAAAAGTACTAGTAA
* * *
1729497 AAATATTTGGAGCAGAAGCTTC
66 TAACATCTGGAGCAGAAGCTTC
1729519 ATCTTGTGCA
Statistics
Matches: 184, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 184 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.24
Consensus pattern (106 bp):
ATAGGTTGATCCCGAATCAATCAAAGCAGTAACATTAGTGTCAATGATAGAAAAAGTACTAGTAA
TAACATCTGGAGCAGAAGCTTCCTATCGTGCACGAATCTAG
Found at i:1734125 original size:45 final size:45
Alignment explanation
Indices: 1734076--1734196 Score: 154
Period size: 45 Copynumber: 2.7 Consensus size: 45
1734066 ACCGGAAATG
* * *
1734076 AATAAGAACATAGTTGAAAGACACTATGGCACTAT-TATAGAAACA
1 AATAAGACCATAGTTGAAAGACACTATGGCAATATGT-CAGAAACA
* *
1734121 AATAAGACCATAGTTGAAAGACACTATGGCAATATGTCGGAAATA
1 AATAAGACCATAGTTGAAAGACACTATGGCAATATGTCAGAAACA
* * *
1734166 AATAAGACCATGGCTAAAAGACACTATGGCA
1 AATAAGACCATAGTTGAAAGACACTATGGCA
1734197 TACTTAAACA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 66 0.99
46 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (45 bp):
AATAAGACCATAGTTGAAAGACACTATGGCAATATGTCAGAAACA
Found at i:1750146 original size:45 final size:45
Alignment explanation
Indices: 1750095--1750180 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
1750085 TATGAACCGA
* * * *
1750095 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCAGCGG
1 ACATCATTGATTAATAAGGTGATTGCTATGTACTGAATCCAGCGG
1750140 ACATCATTGATTAATAAGGTGATTGCTATGTACTGAATCCA
1 ACATCATTGATTAATAAGGTGATTGCTATGTACTGAATCCA
1750181 CCGAGTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGATTGCTATGTACTGAATCCAGCGG
Found at i:1761410 original size:22 final size:23
Alignment explanation
Indices: 1761382--1761438 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
1761372 CTGTGGTGTA
1761382 GTGGCAAGG-TGGCGTCACAGGT
1 GTGGCAAGGATGGCGTCACAGGT
*
1761404 GTGGCAAGGATATGGTGTCACAGGT
1 GTGGCAAGG--ATGGCGTCACAGGT
*
1761429 GTGGTAAGGA
1 GTGGCAAGGA
1761439 GAGGTTCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 9 0.30
23 1 0.03
25 20 0.67
ACGTcount: A:0.23, C:0.12, G:0.44, T:0.21
Consensus pattern (23 bp):
GTGGCAAGGATGGCGTCACAGGT
Found at i:1762627 original size:19 final size:19
Alignment explanation
Indices: 1762598--1762640 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1762588 TGTTATGAGC
1762598 CTCGT-TGGGCCGAAATGGG
1 CTCGTGTGGGCC-AAATGGG
*
1762617 C-CGTGTGGGCCTAATGGG
1 CTCGTGTGGGCCAAATGGG
1762635 CTCGTG
1 CTCGTG
1762641 AGCCCCTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23
Consensus pattern (19 bp):
CTCGTGTGGGCCAAATGGG
Found at i:1762891 original size:27 final size:27
Alignment explanation
Indices: 1762851--1763537 Score: 565
Period size: 27 Copynumber: 25.7 Consensus size: 27
1762841 AAAAGGTAGT
* * *
1762851 TAAATTTACCGAAACACCCTCGATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
*
1762878 TAAGATTATCGAAATACTCC-CGATGGG
1 TAAAATTATCGAAATAC-CCTCGATGGG
* * * *
1762905 TAATATTACCGAAATACCCCCGAAGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* * * *
1762932 TAAAATTATTGAAATACCCCCAAAGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* * *
1762959 TAAAACTATTGAAATACCCCCGATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* *
1762986 TAAAATTA-CTAAAATACCCTTGATGGG
1 TAAAATTATC-GAAATACCCTCGATGGG
*
1763013 TTAAATTA-CTGAAATACCCTCGATGGG
1 TAAAATTATC-GAAATACCCTCGATGGG
** * *
1763040 TAAAATTATTAAAATACCC-CGAAGCG
1 TAAAATTATCGAAATACCCTCGATGGG
* * *
1763066 TAAAATTA-CTAAAATA-CCTCTGAAGCG
1 TAAAATTATC-GAAATACCCTC-GATGGG
* *
1763093 TAAAATTACCAAAATACCC-CTGATGGG
1 TAAAATTATCGAAATACCCTC-GATGGG
* * *
1763120 TAATATTA-CTGAAATACCCCCGAAGGG
1 TAAAATTATC-GAAATACCCTCGATGGG
* *
1763147 TAAAATTA-CTGACATA-CCT-GCACAGGG
1 TAAAATTATC-GAAATACCCTCG-A-TGGG
1763174 TAAAATTA-CGAAAATACCCTCGATGGG
1 TAAAATTATCG-AAATACCCTCGATGGG
* * * *
1763201 TAAAATGATTGAAATGCCCT-AATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
1763227 TAAAATTATCGAAATACCCTCGATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* *
1763254 TAAAATTACCGAAATACTCTCGATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* * *
1763281 TAAAATTACCAAAATA-TCT-GATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* *
1763306 TAAAATTATCGAAATACCCCCGAAGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* *
1763333 TAAAATTA-CTGACATA-CCT-GCACAGGG
1 TAAAATTATC-GAAATACCCTCG-A-TGGG
1763360 TAAAATTA-CGAAAATACCCTCGATGGG
1 TAAAATTATCG-AAATACCCTCGATGGG
* * * *
1763387 TAAAATGATTGAAATGCCCT-AATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
1763413 TAAAATTATCGAAATACCCTCGATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* *
1763440 TAAAATTACCGAAATACTCTCGATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* * *
1763467 TAAAATTACCAAAATA-TCT-GATGGG
1 TAAAATTATCGAAATACCCTCGATGGG
* *
1763492 TAAAATTATCGAAATACCCCCGAAGGG
1 TAAAATTATCGAAATACCCTCGATGGG
1763519 TAAAATTA-CTGAAATACCC
1 TAAAATTATC-GAAATACCC
1763538 CCATAGGGTA
Statistics
Matches: 555, Mismatches: 74, Indels: 62
0.80 0.11 0.09
Matches are distributed among these distances:
25 44 0.08
26 85 0.15
27 408 0.74
28 16 0.03
29 2 0.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.24
Consensus pattern (27 bp):
TAAAATTATCGAAATACCCTCGATGGG
Found at i:1763128 original size:107 final size:106
Alignment explanation
Indices: 1762866--1763538 Score: 580
Period size: 107 Copynumber: 6.3 Consensus size: 106
1762856 TTACCGAAAC
* * * *
1762866 ACCCTCGATGGGTAAGATTATCGAAATACTCCC-GATGGGTAATATTACCGAAATACCCCCGAAG
1 ACCCT-GATGGGTAAAATTATCGAAATAC-CCCTGATGGGTAAAATTACTGAAATACCCTCGAAG
* * * * *
1762930 GGTAAAATTATTGAAATACCCCCAAAGGGTAAAACTATTGAAAT
64 GGTAAAATTACTGAAATA-CCCCGAAGGGTAAAATTACTAAAAT
* * * * *
1762974 ACCCCCGATGGGTAAAATTA-CTAAAATACCCTTGATGGGTTAAATTACTGAAATACCCTCGATG
1 A-CCCTGATGGGTAAAATTATC-GAAATACCCCTGATGGGTAAAATTACTGAAATACCCTCGAAG
* * *
1763038 GGTAAAATTATTAAAATACCCCGAAGCGTAAAATTACTAAAAT
64 GGTAAAATTACTGAAATACCCCGAAGGGTAAAATTACTAAAAT
* * * * * *
1763081 ACCTCTGAAGCGTAAAATTACCAAAATACCCCTGATGGGTAATATTACTGAAATACCCCCGAAGG
1 ACC-CTGATGGGTAAAATTATCGAAATACCCCTGATGGGTAAAATTACTGAAATACCCTCGAAGG
* * *
1763146 GTAAAATTACTGACATA-CCTGCACAGGGTAAAATTACGAAAAT
65 GTAAAATTACTGAAATACCCCG-A-AGGGTAAAATTACTAAAAT
* * * * *
1763189 ACCCTCGATGGGTAAAATGATTGAAAT-GCCCTAATGGGTAAAATTA-TCGAAATACCCTCGATG
1 ACCCT-GATGGGTAAAATTATCGAAATACCCCTGATGGGTAAAATTACT-GAAATACCCTCGAAG
* * * *
1763252 GGTAAAATTACCGAAATACTCTCGATGGGTAAAATTACCAAAAT
64 GGTAAAATTACTGAAATAC-CCCGAAGGGTAAAATTACTAAAAT
* * * *
1763296 A-TCTGATGGGTAAAATTATCGAAATACCCCCGAAGGGTAAAATTACTGACATA-CCT-GCACAG
1 ACCCTGATGGGTAAAATTATCGAAATACCCCTGATGGGTAAAATTACTGAAATACCCTCG-A-AG
* * * *
1763358 GGTAAAATTAC-GAAAATACCCTCGATGGGTAAAATGATTGAAAT
64 GGTAAAATTACTG-AAATACCC-CGAAGGGTAAAATTACTAAAAT
* * * * *
1763402 GCCCTAATGGGTAAAATTATCGAAATA-CCCTCGATGGGTAAAATTACCGAAATACTCTCGATGG
1 ACCCTGATGGGTAAAATTATCGAAATACCCCT-GATGGGTAAAATTACTGAAATACCCTCGAAGG
** * * * *
1763466 GTAAAATTACCAAAATA-TCTGATGGGTAAAATTA-TCGAAAT
65 GTAAAATTACTGAAATACCCCGAAGGGTAAAATTACT-AAAAT
* *
1763507 ACCCCCGAAGGGTAAAATTA-CTGAAATACCCC
1 A-CCCTGATGGGTAAAATTATC-GAAATACCCC
1763539 CATAGGGTAA
Statistics
Matches: 462, Mismatches: 77, Indels: 53
0.78 0.13 0.09
Matches are distributed among these distances:
104 2 0.00
105 44 0.10
106 89 0.19
107 218 0.47
108 103 0.22
109 6 0.01
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (106 bp):
ACCCTGATGGGTAAAATTATCGAAATACCCCTGATGGGTAAAATTACTGAAATACCCTCGAAGGG
TAAAATTACTGAAATACCCCGAAGGGTAAAATTACTAAAAT
Found at i:1763360 original size:186 final size:187
Alignment explanation
Indices: 1762851--1763536 Score: 945
Period size: 186 Copynumber: 3.7 Consensus size: 187
1762841 AAAAGGTAGT
* * * * * * * *
1762851 TAAATTTACCGAAACACCCTCGATGGGTAAGATTATCGAAATACTCCCGATGGGTAATATTACCG
1 TAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACTCTCGATGGGTAAAATTACCA
* * * * * * *
1762916 AAATACCCCCGAAGGGTAAAATTATTGAAATACCCCCAAAGGGTAAAACTATTGAAATACC--CC
66 AAATA-CCCTGATGGGTAAAATTATCGAAATACCCCCGAAGGGTAAAATTACTGAAATACCTGCA
* * * * * * *
1762979 CGATGGGTAAAATTACTAAAATACCCTTGATGGGTTAAATTACTGAAATACCCTCGATGGG
130 C-A-GGGTAAAATTACGAAAATACCCTCGATGGGTAAAATGATTGAAATGCCCT-AATGGG
** * * ** * *
1763040 TAAAATTATTAAAATACCC-CGAAGCGTAAAATTACTAAAATAC-CTCTGAAGCGTAAAATTACC
1 TAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACTCTC-GATGGGTAAAATTACC
* *
1763103 AAAATACCCCTGATGGGTAATATTA-CTGAAATACCCCCGAAGGGTAAAATTACTGACATACCTG
65 AAAATA-CCCTGATGGGTAAAATTATC-GAAATACCCCCGAAGGGTAAAATTACTGAAATACCTG
1763167 CACAGGGTAAAATTACGAAAATACCCTCGATGGGTAAAATGATTGAAATGCCCTAATGGG
128 CACAGGGTAAAATTACGAAAATACCCTCGATGGGTAAAATGATTGAAATGCCCTAATGGG
1763227 TAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACTCTCGATGGGTAAAATTACCA
1 TAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACTCTCGATGGGTAAAATTACCA
* *
1763292 AAATA-TCTGATGGGTAAAATTATCGAAATACCCCCGAAGGGTAAAATTACTGACATACCTGCAC
66 AAATACCCTGATGGGTAAAATTATCGAAATACCCCCGAAGGGTAAAATTACTGAAATACCTGCAC
1763356 AGGGTAAAATTACGAAAATACCCTCGATGGGTAAAATGATTGAAATGCCCTAATGGG
131 AGGGTAAAATTACGAAAATACCCTCGATGGGTAAAATGATTGAAATGCCCTAATGGG
1763413 TAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACTCTCGATGGGTAAAATTACCA
1 TAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACTCTCGATGGGTAAAATTACCA
*
1763478 AAATA-TCTGATGGGTAAAATTATCGAAATACCCCCGAAGGGTAAAATTACTGAAATACC
66 AAATACCCTGATGGGTAAAATTATCGAAATACCCCCGAAGGGTAAAATTACTGAAATACC
1763537 CCCATAGGGT
Statistics
Matches: 447, Mismatches: 43, Indels: 17
0.88 0.08 0.03
Matches are distributed among these distances:
186 235 0.53
187 25 0.06
188 167 0.37
189 18 0.04
190 2 0.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.24
Consensus pattern (187 bp):
TAAAATTATCGAAATACCCTCGATGGGTAAAATTACCGAAATACTCTCGATGGGTAAAATTACCA
AAATACCCTGATGGGTAAAATTATCGAAATACCCCCGAAGGGTAAAATTACTGAAATACCTGCAC
AGGGTAAAATTACGAAAATACCCTCGATGGGTAAAATGATTGAAATGCCCTAATGGG
Found at i:1765277 original size:25 final size:25
Alignment explanation
Indices: 1765249--1765302 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
1765239 TGTAGTGGCA
* *
1765249 AGGTGGCGTCACAGGTGTGGCAAGG
1 AGGTGGCGTCACAAGTGTGGCAAAG
* *
1765274 AGGTGGTGTCACAAGTGTGGTAAAG
1 AGGTGGCGTCACAAGTGTGGCAAAG
1765299 AGGT
1 AGGT
1765303 TAGAGGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.44, T:0.20
Consensus pattern (25 bp):
AGGTGGCGTCACAAGTGTGGCAAAG
Found at i:1767093 original size:10 final size:10
Alignment explanation
Indices: 1767078--1767104 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1767068 CTAAGGTATT
1767078 GAAGAGATGC
1 GAAGAGATGC
1767088 GAAGAGATGC
1 GAAGAGATGC
1767098 GAAGAGA
1 GAAGAGA
1767105 CGAATCTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.07, G:0.41, T:0.07
Consensus pattern (10 bp):
GAAGAGATGC
Found at i:1776822 original size:32 final size:32
Alignment explanation
Indices: 1776786--1776849 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1776776 TTAAGCCGAA
1776786 AATCTTTGTTTGCTCTACGTGCAATGAATACT
1 AATCTTTGTTTGCTCTACGTGCAATGAATACT
1776818 AATCTTTGTTTGCTCTACGTGCAATGAATACT
1 AATCTTTGTTTGCTCTACGTGCAATGAATACT
1776850 CAGTTGACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (32 bp):
AATCTTTGTTTGCTCTACGTGCAATGAATACT
Found at i:1779525 original size:50 final size:49
Alignment explanation
Indices: 1779407--1779535 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 49
1779397 GATAATAACA
* * *
1779407 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTTCTAGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAAATGGGATGTTTCTAGTAC
* * *
1779456 TGCCAATGCCATATCCCAGATATGGTCTTAAATGGG-TGTTCTCATA-TTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAAATGGGATGTT-TC-TAGTAC
*
1779505 GTGCCCATGCCATGTCCCAGACATGGTCTTA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTA
1779536 CGGGGGACCT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
48 4 0.06
49 35 0.51
50 29 0.43
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTAAATGGGATGTTTCTAGTAC
Found at i:1779549 original size:50 final size:50
Alignment explanation
Indices: 1779407--1779588 Score: 172
Period size: 50 Copynumber: 3.7 Consensus size: 50
1779397 GATAATAACA
* * ** * *
1779407 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATGTTTC-TAGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA-TTCG
* * * ***
1779456 TGCCAATGCCATATCCCAGATATGGTCTTAAATGGGTGTTCTCATATTCG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATTCG
* ** *
1779506 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCAT-CTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATTC-G
*
1779556 TGCCAACGCCATGTCCCAGACATGGTCTTACAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
1779589 NNNNNNNNNN
Statistics
Matches: 106, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
49 38 0.36
50 68 0.64
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATTCG
Found at i:1796368 original size:13 final size:13
Alignment explanation
Indices: 1796350--1796385 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1796340 CCATTTGTTA
*
1796350 TGTCACCATACTT
1 TGTCACCAAACTT
1796363 TGTCACCAAACTT
1 TGTCACCAAACTT
*
1796376 TGCCACCAAA
1 TGTCACCAAA
1796386 TCATTCCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.28
Consensus pattern (13 bp):
TGTCACCAAACTT
Found at i:1818541 original size:37 final size:37
Alignment explanation
Indices: 1818491--1818567 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
1818481 AATTTCCTAA
1818491 CTTATGAACATACTTACCTACCAAAATCCATTTATCT
1 CTTATGAACATACTTACCTACCAAAATCCATTTATCT
1818528 CTTATGAACATACTTACCTACCAAAATCCATTTATCT
1 CTTATGAACATACTTACCTACCAAAATCCATTTATCT
1818565 CTT
1 CTT
1818568 GACTATATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (37 bp):
CTTATGAACATACTTACCTACCAAAATCCATTTATCT
Found at i:1823604 original size:30 final size:30
Alignment explanation
Indices: 1823545--1823606 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1823535 TTTTTTTGAA
* * * *
1823545 AATATTTACAAAAAGAGGCATCTAGTTTTT
1 AATATTTACAAAAAGAGGAACCAAATTTTT
*
1823575 AATATTTACAAAAAGAGTAACCAAATTTTT
1 AATATTTACAAAAAGAGGAACCAAATTTTT
1823605 AA
1 AA
1823607 AAATAATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGAACCAAATTTTT
Found at i:1832456 original size:22 final size:22
Alignment explanation
Indices: 1832431--1832487 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
1832421 AATTTAGCCA
1832431 TTTTT-TATTTTAATTTTAATAT
1 TTTTTATATTTTAATTTTAAT-T
*
1832453 TTTTTGT-TTTTAA-TTTAATT
1 TTTTTATATTTTAATTTTAATT
*
1832473 TTTTTATATTCTAAT
1 TTTTTATATTTTAAT
1832488 ATTCTATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 7 0.23
21 11 0.37
22 11 0.37
23 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTTATATTTTAATTTTAATT
Found at i:1839317 original size:3 final size:3
Alignment explanation
Indices: 1839311--1839387 Score: 52
Period size: 3 Copynumber: 25.7 Consensus size: 3
1839301 CTCCCCTTAT
* * *
1839311 TTA TTA TTA TATA TT- TT- TTA TTA TTA CTA TTA TTA CTA ATA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1839355 TTA TT- CTA TTTA TTA TATG TTG TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA T-TA TTA TTA TTA TTA TT
1839388 TGTTTAGTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
2 5 0.08
3 48 0.80
4 7 0.12
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1840407 original size:37 final size:37
Alignment explanation
Indices: 1840358--1840434 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
1840348 ATGATGCACA
*
1840358 CTTTCTTTGGAGCACGGCGATGCGACCCCAATTTGAT
1 CTTTCTTTGGAGCACAGCGATGCGACCCCAATTTGAT
*
1840395 CTTTCTTTGGAGCACAGCGATGCGGCCCCAATTTGAT
1 CTTTCTTTGGAGCACAGCGATGCGACCCCAATTTGAT
1840432 CTT
1 CTT
1840435 GCATATTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.31
Consensus pattern (37 bp):
CTTTCTTTGGAGCACAGCGATGCGACCCCAATTTGAT
Found at i:1853335 original size:42 final size:42
Alignment explanation
Indices: 1853273--1853371 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
1853263 CCACATGCCT
* *
1853273 GTGTGCCAGGCCATGTACCCTTCGAAGTAGTCTCACACGCTC
1 GTGTGCCAGGCCATGCACCCTTCGAAGTAGCCTCACACGCTC
** *
1853315 GTGTGCCAGGCTGTGCACCCTTCGAAGTAGCCTTACACGC-C
1 GTGTGCCAGGCCATGCACCCTTCGAAGTAGCCTCACACGCTC
* *
1853356 TATGTGCTAGGCCATG
1 -GTGTGCCAGGCCATG
1853372 TACTAGGCCA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.24
Consensus pattern (42 bp):
GTGTGCCAGGCCATGCACCCTTCGAAGTAGCCTCACACGCTC
Found at i:1854641 original size:43 final size:43
Alignment explanation
Indices: 1854394--1854656 Score: 294
Period size: 43 Copynumber: 6.1 Consensus size: 43
1854384 TAAAAAAATA
* * *
1854394 CCGCTAAAGATAATGGCCTTTAGCGGCGCTTCTTCCACAAACG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
* * ** * *
1854437 CCGCTAAAGATCATGGCCTTTAGTGGCGCTTCTTTCGCAAACA
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
* *
1854480 CCGCTAAAGATTATGAGCTTTAGCGGCGCTTCTACCACAAACG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
** *
1854523 CCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTACCACAAACG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
* * * * ** *
1854566 TCGCTAAAAAT-ATGACCTTTAGTGACATTTCTACCACAAATG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
* ** *
1854608 CCGCTAAAGATCATGACCTTTAGCGGTGCTTCTATTACAAATG
1 CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
1854651 CCGCTA
1 CCGCTA
1854657 TAAAAATGAA
Statistics
Matches: 183, Mismatches: 36, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
42 32 0.17
43 151 0.83
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
CCGCTAAAGATCATGACCTTTAGCGGCGCTTCTACCACAAACG
Found at i:1871639 original size:7 final size:7
Alignment explanation
Indices: 1871627--1871653 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1871617 ATTTTGATAT
1871627 TTTAAAA
1 TTTAAAA
1871634 TTTAAAA
1 TTTAAAA
1871641 TTTAAAA
1 TTTAAAA
1871648 TTTAAA
1 TTTAAA
1871654 TATAAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAA
Found at i:1871849 original size:31 final size:31
Alignment explanation
Indices: 1871799--1871882 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
1871789 GAATATATTA
** * *
1871799 TTGGGTGATTAAAACGAAAGTGACCTAG-GAT
1 TTGGGTGACCAAAACGAAAGTGA-CTAGCAAG
* * *
1871830 TTGGGTGACCAAAATGAAAGTCACTTGCAAG
1 TTGGGTGACCAAAACGAAAGTGACTAGCAAG
1871861 TTGGGTGACCAAAACGAAAGTG
1 TTGGGTGACCAAAACGAAAGTG
1871883 CAAGCATGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
30 3 0.07
31 40 0.93
ACGTcount: A:0.36, C:0.13, G:0.29, T:0.23
Consensus pattern (31 bp):
TTGGGTGACCAAAACGAAAGTGACTAGCAAG
Found at i:1880185 original size:25 final size:25
Alignment explanation
Indices: 1880141--1880284 Score: 177
Period size: 25 Copynumber: 5.8 Consensus size: 25
1880131 CGGACACACA
*
1880141 ATAGCTCGT-ATGAGCTTACCAATTT
1 ATAGCTCGTGA-GAGCATACCAATTT
*
1880166 ATAGCTTGTGA-ATGCATACCAATTT
1 ATAGCTCGTGAGA-GCATACCAATTT
1880191 ATAGCTCGTGAGAGCATACCAATTT
1 ATAGCTCGTGAGAGCATACCAATTT
*
1880216 ATAGCTCGTGAGAGCATACCGATTT
1 ATAGCTCGTGAGAGCATACCAATTT
* * *
1880241 ATAGCTCGAGAGAGCATACCGATTC
1 ATAGCTCGTGAGAGCATACCAATTT
*
1880266 ACAGCTCGT-ATGAGCATAC
1 ATAGCTCGTGA-GAGCATAC
1880285 ATGTACAGGA
Statistics
Matches: 107, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.02
25 103 0.96
26 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (25 bp):
ATAGCTCGTGAGAGCATACCAATTT
Found at i:1886988 original size:25 final size:24
Alignment explanation
Indices: 1886920--1887000 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
1886910 TATGCTCATA
* *
1886920 CGAGCTATGAATCGGTATGGT-TACT
1 CGAGCTATGAAT-TGTATGCTCT-CT
1886945 CGAGCTAT-AGATTGATATGCTCTCT
1 CGAGCTATGA-ATTG-TATGCTCTCT
* *
1886970 CGAGCTATGAATTAGTATGCTCACA
1 CGAGCTATGAATT-GTATGCTCTCT
1886995 CGAGCT
1 CGAGCT
1887001 GTGGGTCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
24 2 0.04
25 42 0.89
26 3 0.06
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (24 bp):
CGAGCTATGAATTGTATGCTCTCT
Found at i:1894647 original size:25 final size:25
Alignment explanation
Indices: 1894580--1894674 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 25
1894570 TCCATGTACA
* * * *
1894580 TGTATGCTCAAACGAGCTGTGAACC
1 TGTATACTCACACGAGCTGTAAATC
* * * * * *
1894605 GGTATGCTCACTCAAGCTGTAGATT
1 TGTATACTCACACGAGCTGTAAATC
* *
1894630 TGTATACTCTCACGAGCTATAAATC
1 TGTATACTCACACGAGCTGTAAATC
*
1894655 TGTATGCTCACACGAGCTGT
1 TGTATACTCACACGAGCTGT
1894675 GGGTCAGAAC
Statistics
Matches: 51, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (25 bp):
TGTATACTCACACGAGCTGTAAATC
Found at i:1896315 original size:27 final size:27
Alignment explanation
Indices: 1896285--1896353 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
1896275 CCATACAAAA
1896285 TACGCCACAAAGGCTATAT-ATAAAGAG
1 TACGCCACAAAGGCTAT-TCATAAAGAG
** ** **
1896312 TACGCCGTAAAGATTATTCATTTAGAG
1 TACGCCACAAAGGCTATTCATAAAGAG
1896339 TACGCCACAAAGGCT
1 TACGCCACAAAGGCT
1896354 GACAGGATGC
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (27 bp):
TACGCCACAAAGGCTATTCATAAAGAG
Found at i:1897224 original size:72 final size:72
Alignment explanation
Indices: 1897117--1897261 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
1897107 CTATACACCT
* * *
1897117 ACACGTATACGCCAAAATAATAGTTTTGGAGGATAACACCACACCAAATAGACTGTTTACTGCTA
1 ACACGTATACGCCAAAATAATAGTTTAGGAGGATAACACCACACCAAACAGACTGTTTACTACTA
1897182 TACGTCC
66 TACGTCC
* * ** *
1897189 ACACTTATACGCCAAAATAATCA-TTTAGGTGGATAACACCACGTCAGACAGACTGTTTACTACT
1 ACACGTATACGCCAAAATAAT-AGTTTAGGAGGATAACACCACACCAAACAGACTGTTTACTACT
*
1897253 ATACTTCC
65 ATACGTCC
1897261 A
1 A
1897262 AAACCTTAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 62 0.98
73 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (72 bp):
ACACGTATACGCCAAAATAATAGTTTAGGAGGATAACACCACACCAAACAGACTGTTTACTACTA
TACGTCC
Found at i:1903344 original size:15 final size:15
Alignment explanation
Indices: 1903324--1903355 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1903314 GAGATTGGCC
1903324 GTGGTAGAGGTGATG
1 GTGGTAGAGGTGATG
*
1903339 GTGGTAGAGGTGCTG
1 GTGGTAGAGGTGATG
1903354 GT
1 GT
1903356 TAGAGTGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.03, G:0.53, T:0.28
Consensus pattern (15 bp):
GTGGTAGAGGTGATG
Found at i:1905339 original size:25 final size:25
Alignment explanation
Indices: 1905311--1905362 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1905301 TTTTATGTCG
1905311 CTTGTGTATTCCAGAGGACAAGGAT
1 CTTGTGTATTCCAGAGGACAAGGAT
1905336 CTTGTGTATTCCAGAGGACAAGGAT
1 CTTGTGTATTCCAGAGGACAAGGAT
1905361 CT
1 CT
1905363 GAGGCGCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (25 bp):
CTTGTGTATTCCAGAGGACAAGGAT
Found at i:1908044 original size:13 final size:13
Alignment explanation
Indices: 1908026--1908050 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1908016 TTAGAAGCTT
1908026 AATTAATTATTAC
1 AATTAATTATTAC
1908039 AATTAATTATTA
1 AATTAATTATTA
1908051 TGGTTGAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAATTATTAC
Found at i:1911993 original size:18 final size:19
Alignment explanation
Indices: 1911959--1911996 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1911949 TATACTTTAT
*
1911959 ATTTTATATATACATATAC
1 ATTTTATATACACATATAC
1911978 ATTTTATA-ACACATATAC
1 ATTTTATATACACATATAC
1911996 A
1 A
1911997 CTTTCCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTTATATACACATATAC
Found at i:1916427 original size:155 final size:155
Alignment explanation
Indices: 1916134--1916449 Score: 578
Period size: 155 Copynumber: 2.0 Consensus size: 155
1916124 TCGTGGAGCC
1916134 TGTAGCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
1 TGTAGCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
* *
1916199 CCTATCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTGAACTTCTGT
66 CCTATCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTAAACTTCTGC
* *
1916264 AGTGCCTGGTTTAGGATTAAGTATG
131 AGTACCTGGTTTAGGATTAAGGATG
*
1916289 TGTATCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
1 TGTAGCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
*
1916354 CCTGTCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTAAACTTCTGC
66 CCTATCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTAAACTTCTGC
1916419 AGTACCTGGTTTAGGATTAAGGATG
131 AGTACCTGGTTTAGGATTAAGGATG
1916444 TGTAGC
1 TGTAGC
1916450 GGATAGTTAA
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
155 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (155 bp):
TGTAGCTCAATGCCTATACTCATCAATTGTCCAGTTTGATTGAGGCTTGCTATGTGATCATAAAT
CCTATCAATATATATATCCAATTCTTTTTAGCTTGTGGAAAATTCCTAGATCATTAAACTTCTGC
AGTACCTGGTTTAGGATTAAGGATG
Found at i:1920032 original size:104 final size:104
Alignment explanation
Indices: 1919852--1920167 Score: 614
Period size: 104 Copynumber: 3.0 Consensus size: 104
1919842 TTTAAGAATT
1919852 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGAT
1 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGAT
1919917 CGTCAGTTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
66 CGTCAGTTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
1919956 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGAT
1 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGAT
1920021 CGTCAGTTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
66 CGTCAGTTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
*
1920060 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCCTTAGGGAT
1 AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGAT
*
1920125 CGTCAATTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
66 CGTCAGTTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
1920164 AAAT
1 AAAT
1920168 GTGCATAGAC
Statistics
Matches: 210, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 210 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (104 bp):
AAATATACAACTAAAGAAGCTACTTGATAGATATTTCAAAAGACCAGGTGTGTCTCATTAGGGAT
CGTCAGTTCTATTTGTGAAGAAAAAATATGGTAGTTTAA
Found at i:1930893 original size:26 final size:27
Alignment explanation
Indices: 1930864--1930920 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1930854 TAAAACGATA
**
1930864 ATTTTACCCTTGGA-GGTATTTTGGTC
1 ATTTTACCCTTGGAGGGTATTTCAGTC
* *
1930890 ATTTTACCTTTTGAGGGTATTTCAGTC
1 ATTTTACCCTTGGAGGGTATTTCAGTC
1930917 ATTT
1 ATTT
1930921 AACCACCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.49
Consensus pattern (27 bp):
ATTTTACCCTTGGAGGGTATTTCAGTC
Found at i:1935362 original size:39 final size:39
Alignment explanation
Indices: 1935308--1935426 Score: 238
Period size: 39 Copynumber: 3.1 Consensus size: 39
1935298 ACACGAATGC
1935308 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
1 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
1935347 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
1 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
1935386 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
1 GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
1935425 GT
1 GT
1935427 TTCCAAACTC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.29
Consensus pattern (39 bp):
GTATTTACTAAGTAAAGGATTCCGAAAGGACCTAATGTG
Found at i:1943744 original size:19 final size:20
Alignment explanation
Indices: 1943702--1943753 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
1943692 TTAAAGGATG
1943702 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGA-ATA
1943723 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
1943742 TGCAATCTTAGA
1 TGCAATCTTAGA
1943754 ACATGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:1944138 original size:26 final size:26
Alignment explanation
Indices: 1944109--1944163 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
1944099 TTTGTTTTAA
1944109 ATTCATTTAAATTTTATTACACGAAT
1 ATTCATTTAAATTTTATTACACGAAT
* *
1944135 ATTCTTTTAAATTTTATTACACGAGT
1 ATTCATTTAAATTTTATTACACGAAT
1944161 ATT
1 ATT
1944164 TTGGACTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (26 bp):
ATTCATTTAAATTTTATTACACGAAT
Found at i:1951025 original size:14 final size:14
Alignment explanation
Indices: 1951003--1951040 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1950993 TTCAAAATAT
1951003 AAAAAAAAAGAG-C
1 AAAAAAAAAGAGCC
*
1951016 AAAAATAAAATAGCC
1 AAAAA-AAAAGAGCC
1951031 AAAAAAAAAG
1 AAAAAAAAAG
1951041 GAAAGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 5 0.24
14 10 0.48
15 6 0.29
ACGTcount: A:0.76, C:0.08, G:0.11, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAGAGCC
Found at i:1952416 original size:88 final size:88
Alignment explanation
Indices: 1952267--1953031 Score: 899
Period size: 88 Copynumber: 8.7 Consensus size: 88
1952257 AACAGATCAT
* *
1952267 TGAAGATAGTAGATCTTGCCTTCCTGTACTGACA-CTGGAGCAGATCGAAGACACCAGTCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGC-GAAGCAGATCGAAGACACCAGTCTTGCC
*
1952331 TCCCTAGGTTGTAGTGGAGCAGAC
65 TCCCTAGGTTGCAGTGGAGCAGAC
* *
1952355 TGAAGATAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * *
1952420 CCCTAGGTTGTACTGGAACAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * * * *
1952443 TGTAGATAGTAGATCTTGCCTTCATATACTGACAGCGAAGCAGATCAAAGACAGCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
1952508 CCCTAGGTTGTAGTGGAGCAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * *
1952531 TGAAGACAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATC-AAGGACACCAGCCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA-GACACCAGTCTTGCC
* * **
1952595 TCCCTGGGTTGCAGCGGAGCAGGT
65 TCCCTAGGTTGCAGTGGAGCAGAC
* * ** *
1952619 TGAAAATAGCAGATCTTGCCTTCCTATACTGACAGCGAATTAGATCGAAGACACCAGTCTTGCGT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
1952684 CCCTAGGTTGCAGTGGAGCAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * *
1952707 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCAAAGCAGATCAAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
** **
1952772 CCCT-GGATTGCAGCAGAGCAGGT
66 CCCTAGG-TTGCAGTGGAGCAGAC
* * * * *
1952795 TGAAAATAGTAGATCTTGCCTTACTGTACTGACAGCGAAGCAGATTGAAGACAACAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
1952860 TCCTAGGTTGCAGTGGAGCAGAC
66 CCCTAGGTTGCAGTGGAGCAGAC
* * * * * * * * * * * *
1952883 TTAAGATAGCAGATCTTACCTTCTTGTTCCGGCAGTGAAGCAGATCAAAAACTCCAGCCTTGTCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
** * **
1952948 CCCT-GAGCAGCAGTGGAGTAGGT
66 CCCTAG-GTTGCAGTGGAGCAGAC
* * * * *
1952971 TGAAAATAGCAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACATCAGTCTT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTT
1953032 ATTGCCTTGA
Statistics
Matches: 569, Mismatches: 102, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
87 5 0.01
88 559 0.98
89 5 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
CCCTAGGTTGCAGTGGAGCAGAC
Found at i:1953248 original size:117 final size:116
Alignment explanation
Indices: 1953058--1953409 Score: 578
Period size: 117 Copynumber: 3.0 Consensus size: 116
1953048 AATGAAAAAT
* *
1953058 ATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAATGGAGCG
1 ATTGAAGCCACGACG-CGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCG
*
1953123 GATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAACAG
65 GATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
*
1953175 ATTGAAGCCACAACAGCGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCG
1 ATTGAAGCCACGAC-GCGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCG
* *
1953240 GATTAAAGCCGAGGGTAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
65 GATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
* * *
1953292 ATTGAAGCTACGACGGCAAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTAAAGTGGAGCG
1 ATTGAAGCCACGAC-GCGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCG
* *
1953357 GATTAAAGCTGAGGGCAACGAATCCTATCTCTTTGGCATTGTAGTGGAGCAG
65 GATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
1953409 A
1 A
1953410 CTGAGTAAAA
Statistics
Matches: 219, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
117 218 1.00
118 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (116 bp):
ATTGAAGCCACGACGCGAATCTTATCTTCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCGG
ATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCAG
Found at i:1953976 original size:19 final size:20
Alignment explanation
Indices: 1953934--1953985 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
1953924 TTCAAGGATG
1953934 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGA-ATA
1953955 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
1953974 TGCAATCTTAGA
1 TGCAATCTTAGA
1953986 AGATGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:1954236 original size:23 final size:23
Alignment explanation
Indices: 1954192--1954236 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1954182 TCTTATTTTG
* *
1954192 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
1954215 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
1954237 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:1959461 original size:15 final size:15
Alignment explanation
Indices: 1959443--1959473 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1959433 CACCACGCTA
1959443 ACCAGCACCTCTACC
1 ACCAGCACCTCTACC
*
1959458 ACCATCACCTCTACC
1 ACCAGCACCTCTACC
1959473 A
1 A
1959474 TGGCCTCTAC
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:0.29, C:0.52, G:0.03, T:0.16
Consensus pattern (15 bp):
ACCAGCACCTCTACC
Found at i:1997881 original size:58 final size:58
Alignment explanation
Indices: 1997811--1997926 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
1997801 AGTAATTTTA
*
1997811 AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATGTTGAAAGATCCGT
1 AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATATTGAAAGATCCGT
1997869 AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATATTGAAAGATCCGT
1 AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATATTGAAAGATCCGT
1997927 TCCAGTTTGT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.31
Consensus pattern (58 bp):
AGTCTGTTAATTTTCCAATGGCTAGTGTGGAAAGTGGAAGGAATATTGAAAGATCCGT
Found at i:1998364 original size:17 final size:17
Alignment explanation
Indices: 1998342--1998374 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1998332 GTATTGATTT
1998342 TGACAAC-CTTATGTCAA
1 TGACAACACTT-TGTCAA
1998359 TGACAACACTTTGTCA
1 TGACAACACTTTGTCA
1998375 TCAATCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (17 bp):
TGACAACACTTTGTCAA
Found at i:2003588 original size:41 final size:41
Alignment explanation
Indices: 2003477--2003593 Score: 168
Period size: 38 Copynumber: 2.9 Consensus size: 41
2003467 AAGAATATTG
2003477 CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* * *
2003518 ATAAATTG--C-TACGTGCCCCTGTTTGTACTTCGTTACCC
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* *
2003556 CTGAATTGCACATACGTGCCCCTATTTCTACTTCGGTA
1 CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA
2003594 ATTCTAAACT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
38 34 0.52
39 1 0.02
40 1 0.02
41 29 0.45
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (41 bp):
CTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
Found at i:2010776 original size:41 final size:41
Alignment explanation
Indices: 2010420--2010787 Score: 335
Period size: 41 Copynumber: 9.0 Consensus size: 41
2010410 AAGAATATTG
* * * *
2010420 CTGAATTGCACATGCGTGCCCC-AGTTTGTACTCCGGTACTC
1 CTGAATTGCACATACGTGCCCCTA-TTTGTACTTCGATACCC
* * * * * *
2010461 CTAAATTGCACATACGTGCCTCGATTTATTCTTCGGTACCC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* *
2010502 TTAAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * * * * * *
2010543 CTAAATTGCACATACATGCCCGTGTCTATGCTTCGATACCC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * * ** *
2010584 TTAAATTGCACATATGTGCCCCTGCTTGTAGTTCGATA-CC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* *
2010624 CTGAAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
1 CTG-AATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * *
2010666 CTGAATTACACATACGTGTCCCTATTTGTACTTTGATACCC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * * * * *
2010707 CTGAAATGCATATATGCGCCCCTATTTGTACTTCAATACTC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
* * * * *
2010748 CTGAATTGCACATATGTGCACCTTTTTGTACATCGGTACC
1 CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACC
2010788 TCTGGATGTA
Statistics
Matches: 266, Mismatches: 58, Indels: 6
0.81 0.18 0.02
Matches are distributed among these distances:
40 3 0.01
41 257 0.97
42 6 0.02
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (41 bp):
CTGAATTGCACATACGTGCCCCTATTTGTACTTCGATACCC
Done.