Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1085
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: 1639209
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.20
Warning! 665865 characters in sequence are not A, C, G, or T
File 6 of 7
Found at i:1442339 original size:13 final size:13
Alignment explanation
Indices: 1442321--1442346 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1442311 ATTACTCAAC
1442321 GTATCGATACATT
1 GTATCGATACATT
1442334 GTATCGATACATT
1 GTATCGATACATT
1442347 ACTCAACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1442344 original size:33 final size:33
Alignment explanation
Indices: 1442302--1442380 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
1442292 CAAGGAAATA
*
1442302 TATCGATACATTACTCAACGTATCGATACATTG
1 TATCGATACATTACTCAACATATCGATACATTG
*
1442335 TATCGATACATTACTCAACATATCGATTCATTG
1 TATCGATACATTACTCAACATATCGATACATTG
*
1442368 TATCGATATATTA
1 TATCGATACATTA
1442381 ATCTTTGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (33 bp):
TATCGATACATTACTCAACATATCGATACATTG
Found at i:1443348 original size:20 final size:20
Alignment explanation
Indices: 1443301--1443367 Score: 100
Period size: 20 Copynumber: 3.3 Consensus size: 20
1443291 GTTAACAGCC
*
1443301 CATGATTCATGCATTT-TGAG
1 CATGTTTCATGCATTTATG-G
1443321 CTATGTTTCATGCATTTATGG
1 C-ATGTTTCATGCATTTATGG
1443342 CATGTTTCATGCATTTATGG
1 CATGTTTCATGCATTTATGG
1443362 CATGTT
1 CATGTT
1443368 CAGCACCTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
20 26 0.59
21 16 0.36
22 2 0.05
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (20 bp):
CATGTTTCATGCATTTATGG
Found at i:1446370 original size:20 final size:20
Alignment explanation
Indices: 1446345--1446382 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1446335 ATTTTAACTA
1446345 GAATAATGTATCGATACATC
1 GAATAATGTATCGATACATC
1446365 GAATAATGTATCGATACA
1 GAATAATGTATCGATACA
1446383 CCTGGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (20 bp):
GAATAATGTATCGATACATC
Found at i:1446446 original size:20 final size:20
Alignment explanation
Indices: 1446403--1446452 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1446393 AAGACAGAAT
* * *
1446403 GTATCGATACATTCATACAT
1 GTATCGATACATTCAAAAAA
*
1446423 GTATCGATACATTGAAAAAA
1 GTATCGATACATTCAAAAAA
1446443 GTATCGATAC
1 GTATCGATAC
1446453 CTCTGGGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
GTATCGATACATTCAAAAAA
Found at i:1446466 original size:71 final size:71
Alignment explanation
Indices: 1446349--1446524 Score: 210
Period size: 71 Copynumber: 2.5 Consensus size: 71
1446339 TAACTAGAAT
* * * * *
1446349 AATGTATCGATACATCGAATAATGTATCGATACACCTGGGTAAAAAGACAGAATGTATCGATACA
1 AATGTATCGATACATTGAAAAAAGTATCGATACACCTGGGTAAAAAGACAGAATATATCAATACA
*
1446414 TTCATA
66 TTCAAA
* *
1446420 CATGTATCGATACATTGAAAAAAGTATCGATAC-CTCTGGGTAAAAAGATAGAATATATCAATAC
1 AATGTATCGATACATTGAAAAAAGTATCGATACAC-CTGGGTAAAAAGACAGAATATATCAATAC
*
1446484 ATTGAAA
65 ATTCAAA
* * * * *
1446491 AATGTATCGTTACATTCATACATGTATCGATACA
1 AATGTATCGATACATTGAAAAAAGTATCGATACA
1446525 TTGAAAAATA
Statistics
Matches: 88, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
70 1 0.01
71 87 0.99
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (71 bp):
AATGTATCGATACATTGAAAAAAGTATCGATACACCTGGGTAAAAAGACAGAATATATCAATACA
TTCAAA
Found at i:1446504 original size:20 final size:20
Alignment explanation
Indices: 1446475--1446545 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1446465 AGATAGAATA
*
1446475 TATCAATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
* * * *
1446495 TATCGTTACATTCATACATG
1 TATCGATACATTGAAAAATG
*
1446515 TATCGATACATTGAAAAATA
1 TATCGATACATTGAAAAATG
*
1446535 TATCCATACAT
1 TATCGATACAT
1446546 CTGGGTAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (20 bp):
TATCGATACATTGAAAAATG
Found at i:1453386 original size:34 final size:34
Alignment explanation
Indices: 1453347--1453411 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
1453337 TTGATGACTT
1453347 CTATTCTATGGGGCATATTAATGATGATATTCTC
1 CTATTCTATGGGGCATATTAATGATGATATTCTC
1453381 CTATTCTATGGGGCATATTAATGATGATATT
1 CTATTCTATGGGGCATATTAATGATGATATT
1453412 TTATATTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (34 bp):
CTATTCTATGGGGCATATTAATGATGATATTCTC
Found at i:1454813 original size:23 final size:23
Alignment explanation
Indices: 1454787--1454833 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1454777 TAAGAATATG
1454787 AAAATATGACTCAAGTAAATAAA
1 AAAATATGACTCAAGTAAATAAA
* *
1454810 AAAATATGACTCGAGTGAATAAA
1 AAAATATGACTCAAGTAAATAAA
1454833 A
1 A
1454834 TGACCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.13, T:0.21
Consensus pattern (23 bp):
AAAATATGACTCAAGTAAATAAA
Found at i:1457436 original size:20 final size:20
Alignment explanation
Indices: 1457411--1457465 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1457401 AAAATGCTTG
*
1457411 AATGTATCGATACATTGTA-A
1 AATGTATCGATACAATG-AGA
*
1457431 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGAGA
1457451 AATGTATCGATACAA
1 AATGTATCGATACAA
1457466 ATTGTGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 31 0.97
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACAATGAGA
Found at i:1458578 original size:24 final size:24
Alignment explanation
Indices: 1458511--1458579 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
1458501 TACATTACTA
1458511 TTCATCAATGTTCATGTATCACTG
1 TTCATCAATGTTCATGTATCACTG
* * * *
1458535 TTCATCACTATTTATTTATCACTG
1 TTCATCAATGTTCATGTATCACTG
* *
1458559 TTTATCATTGTTCATGTATCA
1 TTCATCAATGTTCATGTATCA
1458580 ATACATTATA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.48
Consensus pattern (24 bp):
TTCATCAATGTTCATGTATCACTG
Found at i:1459114 original size:35 final size:36
Alignment explanation
Indices: 1459043--1459114 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
1459033 CTAAGTGACT
* *
1459043 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATTGGGA
1 GAGAGGTTCTATCTTAGCCTATGAAAAAGATAGGGA
1459079 GAGAGGTTCTATCTTAG-CTCATG-AAAAGATAGGGA
1 GAGAGGTTCTATCTTAGCCT-ATGAAAAAGATAGGGA
1459114 G
1 G
1459115 GTTTCTATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 14 0.42
36 19 0.58
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28
Consensus pattern (36 bp):
GAGAGGTTCTATCTTAGCCTATGAAAAAGATAGGGA
Found at i:1459139 original size:30 final size:31
Alignment explanation
Indices: 1459081--1459140 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
1459071 GATTGGGAGA
*
1459081 GAGGTTCTATCTTAGCTCATGAAAAGATAGG
1 GAGGTTCTATCATAGCTCATGAAAAGATAGG
*
1459112 GAGGTTTCTATCATAGC-CTTG-AAAGATAG
1 GAGG-TTCTATCATAGCTCATGAAAAGATAG
1459141 TGTTGTAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 7 0.27
32 11 0.42
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (31 bp):
GAGGTTCTATCATAGCTCATGAAAAGATAGG
Found at i:1463102 original size:16 final size:16
Alignment explanation
Indices: 1463081--1463111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1463071 GAGTTTGTAT
1463081 AAAATTCGTATTAAAG
1 AAAATTCGTATTAAAG
*
1463097 AAAATTTGTATTAAA
1 AAAATTCGTATTAAA
1463112 AGGGAGAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAATTCGTATTAAAG
Found at i:1464188 original size:24 final size:24
Alignment explanation
Indices: 1464128--1464225 Score: 115
Period size: 24 Copynumber: 4.0 Consensus size: 24
1464118 TTGATATATT
* *
1464128 ACTATTCATCAATGTTCATGTATC
1 ACTATTCATCACTATTCATGTATC
*
1464152 ATACTATTCATCACTATTTATGTATC
1 --ACTATTCATCACTATTCATGTATC
* * *
1464178 ACTATTTATCACTATCCATATATC
1 ACTATTCATCACTATTCATGTATC
*
1464202 ACTATTCATCACTGTTCATGTATC
1 ACTATTCATCACTATTCATGTATC
1464226 GATACATTTG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 40 0.66
26 21 0.34
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (24 bp):
ACTATTCATCACTATTCATGTATC
Found at i:1465251 original size:51 final size:51
Alignment explanation
Indices: 1465181--1465295 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
1465171 TCTCCCCCTT
* * *
1465181 TTTATTTC-AAAAATGATCTTCAAAAATAATCTCCCCCTATGTAAAACATG
1 TTTATTTCTAAAAATAATCTTCAAAAATAATCTCCCCCTATATAAAACAAG
* * * *
1465231 TTTATTTCTTAAAATAATCTTCAAAAATAATCTCTCCTTTTATAAAACAAG
1 TTTATTTCTAAAAATAATCTTCAAAAATAATCTCCCCCTATATAAAACAAG
*
1465282 TTTATTTCTCAAAA
1 TTTATTTCTAAAAA
1465296 CATCTCTCCC
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 8 0.14
51 48 0.86
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.39
Consensus pattern (51 bp):
TTTATTTCTAAAAATAATCTTCAAAAATAATCTCCCCCTATATAAAACAAG
Found at i:1467193 original size:13 final size:13
Alignment explanation
Indices: 1467175--1467204 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1467165 GCCCTTTATC
*
1467175 GATACAATGTATT
1 GATACAATATATT
1467188 GATACAATATATT
1 GATACAATATATT
1467201 GATA
1 GATA
1467205 TTAAGATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (13 bp):
GATACAATATATT
Found at i:1471068 original size:19 final size:17
Alignment explanation
Indices: 1470996--1471072 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 17
1470986 TAAAAAAACA
*
1470996 AATAAATATAAAAAA-T
1 AATAAATAGAAAAAATT
1471012 -AT-AATAAGAACAATAATT
1 AATAAAT-AGAA-AA-AATT
* *
1471030 AATTAAT-TAAAAAATT
1 AATAAATAGAAAAAATT
1471046 AATAAATAGAAAAAAGTT
1 AATAAATAGAAAAAA-TT
1471064 AAATAAATA
1 -AATAAATA
1471073 AATTAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
14 3 0.06
15 5 0.10
16 12 0.25
17 10 0.21
18 5 0.10
19 10 0.21
20 3 0.06
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (17 bp):
AATAAATAGAAAAAATT
Found at i:1471558 original size:103 final size:103
Alignment explanation
Indices: 1471441--1471656 Score: 378
Period size: 103 Copynumber: 2.1 Consensus size: 103
1471431 AAATTGATAC
1471441 AGCAATGAAGGAAGCAATGAATAGATGCAATTAAAGTTGCTGCAAATGGTAGCAATGAAGAGAGT
1 AGCAATGAAGGAAGCAATGAATAGATGCAATTAAAGTTGCTGCAAATGGTAGCAATGAAGAGAGT
* *
1471506 AACAGCTACTGGAAACCAAAACAAAAATGGTAGCAAGA
66 AACAGCTACTAGAAACCAAAACAAAAATGGCAGCAAGA
1471544 AGCAATGAAGGAAGCAATGAATAGATGCAATTAAAGTTGCTGCAAATGGTAGCAATGAAGAGAGT
1 AGCAATGAAGGAAGCAATGAATAGATGCAATTAAAGTTGCTGCAAATGGTAGCAATGAAGAGAGT
* * *
1471609 AATAGCTGCTAGAAACCAAAACAGAAATGGCAGCAAGA
66 AACAGCTACTAGAAACCAAAACAAAAATGGCAGCAAGA
*
1471647 AGTAATGAAG
1 AGCAATGAAG
1471657 AAAGAAACGA
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.46, C:0.12, G:0.25, T:0.17
Consensus pattern (103 bp):
AGCAATGAAGGAAGCAATGAATAGATGCAATTAAAGTTGCTGCAAATGGTAGCAATGAAGAGAGT
AACAGCTACTAGAAACCAAAACAAAAATGGCAGCAAGA
Found at i:1477250 original size:15 final size:16
Alignment explanation
Indices: 1477232--1477273 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1477222 GGGAGATGAT
1477232 AAAAAGAAAAAGCAAAA
1 AAAAAGAAAAAG-AAAA
1477249 AAAAA-AAAAAGAAAA
1 AAAAAGAAAAAGAAAA
*
1477264 AAAATGAAAA
1 AAAAAGAAAA
1477274 GAATGAAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 10 0.43
17 5 0.22
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAA
Found at i:1479862 original size:42 final size:42
Alignment explanation
Indices: 1479803--1481226 Score: 789
Period size: 42 Copynumber: 33.7 Consensus size: 42
1479793 TCCTACTTTC
* * * *
1479803 AGTCTGCCTGTCAGCTTTGACTTTGGATACTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * ** * **
1479845 AGTCTGCCTTTCGGCTTTGACCTTGGAGATTTTCTTACCCTTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCA-CCTAA
* *
1479888 AGTCTGCCTATCGGCTTTGACCTTGGAGACTGCCTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * ** * *
1479930 AGTCTGCCTGTCGGCTTGGA-CTCTGGAGATTTTCTTACCCT-C
1 AGTCTGCCTGTCGGCTTTGACCT-TGGAGACTGCCTCA-CCTAA
* * *
1479972 AGTCTGCTTGTCGGCTTTGACCTTGGAGACTGCCTTACCTTA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * * * * * **
1480014 AGTCTACCTGTCGACCTTGACCCTAGAGACTTTCCT-ACTTTC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCTCACCTAA
* * * *
1480056 AGTCTACCTGTTGGCTTTGACCTCGGAGACTGCCTTACCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* ** * **
1480098 AGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCTTTC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACC-TAA
* * * * * *
1480141 TGTCTACCTGTCGACTTTGACCTTAGAGAATGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
** * * * **
1480183 AGTCTGTTTGTCAGCTTTGACAC-TAGAGACTTTCC-CACCTTC
1 AGTCTGCCTGTCGGCTTTGAC-CTTGGAGAC-TGCCTCACCTAA
* *
1480225 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTACCTCACCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * * ** * **
1480267 AATTTGCTTGTCGGCTTTGACCTTAGAGACTTTCTTACCTTTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACC-TAA
* * * * *
1480310 AGTCTGCTTGTCGACTTTGACCTTGGAGACTACCTCACTTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* ** * **
1480352 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCTTACCTTC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * *
1480394 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTTACTTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * * * *
1480436 AGTCTGCCTGTCGGCTTTGATCTTAGAGACTTTCTTACCCCT-T
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCT-CACCTAA
* * * * * * *
1480479 AGTCTACTTATCGGCTTTGACCCTGGAGGCTGCCTTACCTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * * * *
1480521 AGTCTGCTTGTCGACTTTGACCCTAGAGACTTTCCT-ACCCT-T
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCTCA-CCTAA
* * * * *
1480563 AGTGTGCCTATCGGCTTTG-GCTCTAGAGACTGCCTCACCTCA
1 AGTCTGCCTGTCGGCTTTGACCT-TGGAGACTGCCTCACCTAA
** * ** * * * *
1480605 AGTCTTTCTATTTGCTTTGACCCTT-GAGACTTTCTTACCCCT-C
1 AGTCTGCCTGTCGGCTTTGA-CCTTGGAGAC-TGCCT-CACCTAA
* * *
1480648 AGTCTTCCTGTCGGCTTTGACCTTGGAGACTGCCTTACCTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * * ** * **
1480690 AGTCTGCCTATCAGCTTTAACCCTGGAGACTTTCTTACCCTTC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCA-CCTAA
* * ** * * * *
1480733 AGTCTACCTGTCAGCTTTGACCCCGAAGATTGCCTCATCGAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * * *
1480775 AGTCTGCTTGTCGGCTTTGACCCTGGAGACTTTCCT-ACCCAC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCTCACCTAA
* * * * * *
1480817 AGTTTGCCTATCGACTTTGAGCTTGGAGACTACCTCACCTTA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * ** * **
1480859 AGT-TGGGCTGTCGGCTTTGACCCTAGAGACTTTCTTACCCTTC
1 AGTCT-GCCTGTCGGCTTTGACCTTGGAGACTGCCTCA-CCTAA
* * *
1480902 AGTCTGCCTGTCGACTTTGACCTTGGAGATTGCCTTACCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * * * **
1480944 AGTCTGCATGTCGGCTTTGACCCTAGAGACTTTCCT-ACTTTC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCTCACCTAA
* *
1480986 AGTCTGCCTATCGGC-TTGACCTTGGAGACTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * * * * **
1481027 AGTTTGCCTATCGGCTTTGACTTTGGAAACTTTCCT-ACTTTC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCTCACCTAA
* * *
1481069 AGTCTGCCTGTCAGCTTTAACCTTGGAGACTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
* * * * * * * * *
1481111 CGTCTGCCTGTCAGTTTTGACCCTAGAGATTTTCC-AACCCTTCA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-CTGCCTCA-CC-TAA
* * * *
1481155 A-TCTGCCTGTTGGCTTTGA-CTCGGGAGACTGCTTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCT-TGGAGACTGCCTCACCTAA
*
1481196 AGTCTGCCTGTCGGCTTTGACCTTAGAGACT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACT
1481227 TTTCCACCTT
Statistics
Matches: 1039, Mismatches: 298, Indels: 90
0.73 0.21 0.06
Matches are distributed among these distances:
40 4 0.00
41 67 0.06
42 687 0.66
43 270 0.26
44 11 0.01
ACGTcount: A:0.17, C:0.29, G:0.20, T:0.35
Consensus pattern (42 bp):
AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAA
Found at i:1479946 original size:85 final size:85
Alignment explanation
Indices: 1479798--1481228 Score: 1382
Period size: 85 Copynumber: 16.9 Consensus size: 85
1479788 AACTTTCCTA
* * * * *
1479798 CTTTCAGTCTGCCTGTCAGCTTTGACTTTGGATACTGCCTCATCTAAAGTCTGCCTTTCGGCTTT
1 CTTT-AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTT
* * *
1479863 GACCTTGGAGATTTTCTTACC
65 GACCCTAGAGACTTTCTTACC
* * *
1479884 CTTTAGTCTGCCTATCGGCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTGTCGGCTTGG
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
* * *
1479949 ACTCTGGAGATTTTCTTACC
66 ACCCTAGAGACTTTCTTACC
* * * * * * *
1479969 C-TCAGTCTGCTTGTCGGCTTTGACCTTGGAGACTGCCTTACCTTAAGTCTACCTGTCGACCTTG
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
*
1480033 ACCCTAGAGACTTTCCTA--
66 ACCCTAGAGACTTTCTTACC
* * * * *
1480051 CTTTCAGTCTACCTGTTGGCTTTGACCTCGGAGACTGCCTTACCTAAAGTCTGCCTGTCGACTTT
1 CTTT-AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTT
* *
1480116 GACCTTGGAGACTTTCTTA-C
65 GACCCTAGAGACTTTCTTACC
* * * * * * ** *
1480136 CTTTCTGTCTACCTGTCGACTTTGACCTTAGAGAATGCCTCATCTAAAGTCTGTTTGTCAGCTTT
1 CTTT-AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTT
* **
1480201 GACACTAGAGACTTTCCCA-C
65 GACCCTAGAGACTTTCTTACC
* * * * * *
1480221 CTTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTACCTCACCTAAAATTTGCTTGTCGGCTTTG
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
*
1480286 ACCTTAGAGACTTTCTTACC
66 ACCCTAGAGACTTTCTTACC
* * * * * *
1480306 TTTTAGTCTGCTTGTCGACTTTGACCTTGGAGACTACCTCACTTCAAGTCTGCCTGTCGGCTTTG
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
*
1480371 ACCCTGGAGACTTTCTTA-C
66 ACCCTAGAGACTTTCTTACC
* * * *
1480390 CTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTTACTTCAAGTCTGCCTGTCGGCTTTG
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
* *
1480455 ATCTTAGAGACTTTCTTACC
66 ACCCTAGAGACTTTCTTACC
* * * * * * * * * *
1480475 CCTTAGTCTACTTATCGGCTTTGACCCTGGAGGCTGCCTTACCTCAAGTCTGCTTGTCGACTTTG
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
*
1480540 ACCCTAGAGACTTTCCTACC
66 ACCCTAGAGACTTTCTTACC
* * * * * ** * **
1480560 C-TTAGTGTGCCTATCGGCTTTG-GCTCTAGAGACTGCCTCACCTCAAGTCTTTCTATTTGCTTT
1 CTTTAGTCTGCCTGTCGGCTTTGACCT-TGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTT
*
1480623 GACCCTTGAGACTTTCTTACC
65 GACCCTAGAGACTTTCTTACC
* * * * * * * *
1480644 CCTCAGTCTTCCTGTCGGCTTTGACCTTGGAGACTGCCTTACCTCAAGTCTGCCTATCAGCTTTA
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
*
1480709 ACCCTGGAGACTTTCTTACC
66 ACCCTAGAGACTTTCTTACC
* * * ** * * * * *
1480729 CTTCAGTCTACCTGTCAGCTTTGACCCCGAAGATTGCCTCATCGAAAGTCTGCTTGTCGGCTTTG
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
* *
1480794 ACCCTGGAGACTTTCCTACC
66 ACCCTAGAGACTTTCTTACC
** * * * * * * *
1480814 C-ACAGTTTGCCTATCGACTTTGAGCTTGGAGACTACCTCACCTTAAGT-TGGGCTGTCGGCTTT
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCT-GCCTGTCGGCTTT
1480877 GACCCTAGAGACTTTCTTACC
65 GACCCTAGAGACTTTCTTACC
* * * * *
1480898 CTTCAGTCTGCCTGTCGACTTTGACCTTGGAGATTGCCTTACCTAAAGTCTGCATGTCGGCTTTG
1 CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
*
1480963 ACCCTAGAGACTTTCCTA--
66 ACCCTAGAGACTTTCTTACC
* * * *
1480981 CTTTCAGTCTGCCTATCGGC-TTGACCTTGGAGACTGCCTCATCTAAAGTTTGCCTATCGGCTTT
1 CTTT-AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTT
** * * *
1481045 GACTTTGGAAACTTTCCTA--
65 GACCCTAGAGACTTTCTTACC
* * * * * *
1481064 CTTTCAGTCTGCCTGTCAGCTTTAACCTTGGAGACTGCCTCATCTAACGTCTGCCTGTCAGTTTT
1 CTTT-AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTT
* **
1481129 GACCCTAGAGATTTTCCAACC
65 GACCCTAGAGACTTTCTTACC
* * * * * *
1481150 CTTCAATCTGCCTGTTGGCTTTGA-CTCGGGAGACTGCTTCATCTAAAGTCTGCCTGTCGGCTTT
1 CTTTAGTCTGCCTGTCGGCTTTGACCT-TGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTT
*
1481214 GACCTTAGAGACTTT
65 GACCCTAGAGACTTT
1481229 TCCACCTTTT
Statistics
Matches: 1112, Mismatches: 217, Indels: 33
0.82 0.16 0.02
Matches are distributed among these distances:
82 1 0.00
83 77 0.07
84 469 0.42
85 555 0.50
86 10 0.01
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (85 bp):
CTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTG
ACCCTAGAGACTTTCTTACC
Found at i:1480246 original size:169 final size:169
Alignment explanation
Indices: 1479789--1481257 Score: 1434
Period size: 169 Copynumber: 8.7 Consensus size: 169
1479779 AACAATATAA
* * * * *
1479789 ACTTTCCTA-CTTTCAGTCTGCCTGTCAGCTTTGACTTTGGATACTGCCTCATCTAAAGTCTGCC
1 ACTTTCTTACCTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCC
* * * * * * *
1479853 TTTCGGCTTTGACCTTGGAGATTTTCTTACCCTTTAGTCTGCCTATCGGCTTTGACCTTGGAGAC
66 TGTCGGCTTTGACCCTAGAGACTTTCCTA-CCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * *
1479918 TGCCTCACCTCAAGTCTGCCTGTCGGCTTGGA-CTCTGGAG
130 TGCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCT-TAGAG
* * * * * *
1479958 ATTTTCTTACC-CTCAGTCTGCTTGTCGGCTTTGACCTTGGAGACTGCCTTACCTTAAGTCTACC
1 ACTTTCTTACCTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCC
* * * * * *
1480022 TGTCGACCTTGACCCTAGAGACTTTCCTACTTTCAGTCTACCTGTTGGCTTTGACCTCGGAGACT
66 TGTCGGCTTTGACCCTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACT
* * *
1480087 GCCTTACCTAAAGTCTGCCTGTCGACTTTGACCTTGGAG
131 GCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCTTAGAG
* * * * * * **
1480126 ACTTTCTTACCTTTCTGTCTACCTGTCGACTTTGACCTTAGAGAATGCCTCATCTAAAGTCTGTT
1 ACTTTCTTACCTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCC
* * * *
1480191 TGTCAGCTTTGACACTAGAGACTTTCCCACCTTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACT
66 TGTCGGCTTTGACCCTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACT
* * * *
1480256 ACCTCACCTAAAATTTGCTTGTCGGCTTTGACCTTAGAG
131 GCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCTTAGAG
* * * * * *
1480295 ACTTTCTTACCTTTTAGTCTGCTTGTCGACTTTGACCTTGGAGACTACCTCACTTCAAGTCTGCC
1 ACTTTCTTACCTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCC
* *
1480360 TGTCGGCTTTGACCCTGGAGACTTTCTTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACT
66 TGTCGGCTTTGACCCTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACT
* * * *
1480425 GCCTTACTTCAAGTCTGCCTGTCGGCTTTGATCTTAGAG
131 GCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCTTAGAG
* * * * * * * *
1480464 ACTTTCTTACCCCTT-AGTCTACTTATCGGCTTTGACCCTGGAGGCTGCCTTACCTCAAGTCTGC
1 ACTTTCTTA-CCTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGC
* * * * * *
1480528 TTGTCGACTTTGACCCTAGAGACTTTCCTACCCTT-AGTGTGCCTATCGGCTTTG-GCTCTAGAG
65 CTGTCGGCTTTGACCCTAGAGACTTTCCTA-CCTTCAGTCTGCCTGTCGGCTTTGACCT-TGGAG
* ** * **
1480591 ACTGCCTCACCTCAAGTCTTTCTATTTGCTTTGACCCTT-GAG
128 ACTGCCTCACCTAAAGTCTGCCTGTCGGCTTTGA-CCTTAGAG
** * * *
1480633 ACTTTCTTACCCCTCAGTCTTCCTGTCGGCTTTGACCTTGGAGACTGCCTTACCTCAAGTCTGCC
1 ACTTTCTTACCTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCC
* * * * * * * ** * *
1480698 TATCAGCTTTAACCCTGGAGACTTTCTTACCCTTCAGTCTACCTGTCAGCTTTGACCCCGAAGAT
66 TGTCGGCTTTGACCCTAGAGACTTTCCTA-CCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * * * *
1480763 TGCCTCATCGAAAGTCTGCTTGTCGGCTTTGACCCTGGAG
130 TGCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCTTAGAG
* ** * * * * * * *
1480803 ACTTTCCTACC-CACAGTTTGCCTATCGACTTTGAGCTTGGAGACTACCTCACCTTAAGT-TGGG
1 ACTTTCTTACCTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCT-GC
* *
1480866 CTGTCGGCTTTGACCCTAGAGACTTTCTTACCCTTCAGTCTGCCTGTCGACTTTGACCTTGGAGA
65 CTGTCGGCTTTGACCCTAGAGACTTTCCTA-CCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGA
* * * *
1480931 TTGCCTTACCTAAAGTCTGCATGTCGGCTTTGACCCTAGAG
129 CTGCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCTTAGAG
* * * *
1480972 ACTTTCCTA-CTTTCAGTCTGCCTATCGGC-TTGACCTTGGAGACTGCCTCATCTAAAGTTTGCC
1 ACTTTCTTACCTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCC
* ** * * * * *
1481035 TATCGGCTTTGACTTTGGAAACTTTCCTACTTTCAGTCTGCCTGTCAGCTTTAACCTTGGAGACT
66 TGTCGGCTTTGACCCTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACT
* * * * *
1481100 GCCTCATCTAACGTCTGCCTGTCAGTTTTGACCCTAGAG
131 GCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCTTAGAG
* ** * * * * * *
1481139 ATTTTCCAACCCTTCAATCTGCCTGTTGGCTTTGA-CTCGGGAGACTGCTTCATCTAAAGTCTGC
1 ACTTTCTTACCTTTCAGTCTGCCTGTCGGCTTTGACCT-TGGAGACTGCCTCACCTAAAGTCTGC
* ** * *
1481203 CTGTCGGCTTTGACCTTAGAGACTTTTCC-ACCTTTTGTATGCCTGTTGGCTTTGA
65 CTGTCGGCTTTGACCCTAGAGAC-TTTCCTACCTTCAGTCTGCCTGTCGGCTTTGA
1481258 TCCGGGGGAA
Statistics
Matches: 1067, Mismatches: 215, Indels: 36
0.81 0.16 0.03
Matches are distributed among these distances:
167 71 0.07
168 148 0.14
169 776 0.73
170 71 0.07
171 1 0.00
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (169 bp):
ACTTTCTTACCTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTCTGCC
TGTCGGCTTTGACCCTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACT
GCCTCACCTAAAGTCTGCCTGTCGGCTTTGACCTTAGAG
Found at i:1482085 original size:17 final size:17
Alignment explanation
Indices: 1482034--1482095 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
1482024 TACATGTCAT
1482034 TGCATGCTTTTACTTTCA
1 TGCATGCTTTTAC-TTCA
* * * *
1482052 TGCATACCTTCATTTCA
1 TGCATGCTTTTACTTCA
1482069 TGCATGCTTTTACTTCA
1 TGCATGCTTTTACTTCA
1482086 TGCATGCTTT
1 TGCATGCTTT
1482096 CATGCAAATG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 27 0.75
18 9 0.25
ACGTcount: A:0.18, C:0.24, G:0.11, T:0.47
Consensus pattern (17 bp):
TGCATGCTTTTACTTCA
Found at i:1486209 original size:3 final size:3
Alignment explanation
Indices: 1486201--1486241 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1486191 CGAGTCAACT
1486201 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1486242 TTTGATGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:1487102 original size:20 final size:19
Alignment explanation
Indices: 1487064--1487102 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1487054 GTTTGAAGTA
*
1487064 ATGTTCGATACAATTCATC
1 ATGTTCGATACAATGCATC
*
1487083 ATGTATCGATATAATGCATC
1 ATGT-TCGATACAATGCATC
1487103 GATACAATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (19 bp):
ATGTTCGATACAATGCATC
Found at i:1487788 original size:22 final size:23
Alignment explanation
Indices: 1487763--1487807 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1487753 GGCTTTCATT
1487763 AAAAAAGTT-T-CCCTTTGATAA
1 AAAAAAGTTCTCCCCTTTGATAA
*
1487784 AAAAAATTTCTCCCCTTTGATAA
1 AAAAAAGTTCTCCCCTTTGATAA
1487807 A
1 A
1487808 TGGTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 1 0.05
23 12 0.57
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (23 bp):
AAAAAAGTTCTCCCCTTTGATAA
Found at i:1487817 original size:30 final size:31
Alignment explanation
Indices: 1487781--1487838 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1487771 TTCCCTTTGA
*
1487781 TAAAAAA-AATTTCTCCCCTTTGATAAATGG
1 TAAAAAAGAATTTCTCCCCATTGATAAATGG
*
1487811 TAAAAAAGATTTTCTCCCCATTGATAAA
1 TAAAAAAGAATTTCTCCCCATTGATAAA
1487839 AATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (31 bp):
TAAAAAAGAATTTCTCCCCATTGATAAATGG
Found at i:1489560 original size:22 final size:21
Alignment explanation
Indices: 1489525--1489574 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1489515 TTTATTGATG
*
1489525 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1489545 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1489566 AATTTGAAG
1 ATTTTGAAG
1489575 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1489571 original size:21 final size:22
Alignment explanation
Indices: 1489532--1489574 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1489522 ATGATTTTGA
* *
1489532 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1489554 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1489575 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1489701 original size:13 final size:13
Alignment explanation
Indices: 1489683--1489708 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1489673 TAGTAACCCT
1489683 TGTATCGATACAA
1 TGTATCGATACAA
1489696 TGTATCGATACAA
1 TGTATCGATACAA
1489709 AGAATATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1495816 original size:13 final size:13
Alignment explanation
Indices: 1495798--1495828 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1495788 CGTTTGAAGT
1495798 AATGTATCGATAC
1 AATGTATCGATAC
1495811 AATGTATCGATAC
1 AATGTATCGATAC
1495824 AATGT
1 AATGT
1495829 GCCATGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1495897 original size:19 final size:19
Alignment explanation
Indices: 1495873--1495909 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1495863 ACTACTAGTT
1495873 TCATGTATCGATACAATGA
1 TCATGTATCGATACAATGA
*
1495892 TCATGTATCGATATAATG
1 TCATGTATCGATACAATG
1495910 TATCGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:1497810 original size:19 final size:20
Alignment explanation
Indices: 1497786--1497831 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1497776 ATAATTCACT
*
1497786 ATGTATCGATACCAAG-AAC
1 ATGTATCGATACAAAGCAAC
* *
1497805 ATGTATTGATACAAAGCAAT
1 ATGTATCGATACAAAGCAAC
1497825 ATGTATC
1 ATGTATC
1497832 TTTACATCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAAC
Found at i:1499891 original size:20 final size:20
Alignment explanation
Indices: 1499866--1499916 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1499856 AAAGGAATTA
*
1499866 ATCGATACATTTA-CTTATGT
1 ATCGATACATTTATCATAT-T
1499886 ATCGATACATTTATCATATT
1 ATCGATACATTTATCATATT
*
1499906 ATCAATACATT
1 ATCGATACATT
1499917 CTGGATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
ATCGATACATTTATCATATT
Found at i:1500469 original size:23 final size:23
Alignment explanation
Indices: 1500428--1500478 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1500418 AAGCAACCAA
*
1500428 AAAACACTATTCCATTAGC-CTCC
1 AAAACACTATTCCAGTAGCTC-CC
* *
1500451 AAAACTCTATTCCCGTAGCTCCC
1 AAAACACTATTCCAGTAGCTCCC
1500474 AAAAC
1 AAAAC
1500479 CACAACCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.35, G:0.06, T:0.24
Consensus pattern (23 bp):
AAAACACTATTCCAGTAGCTCCC
Found at i:1506528 original size:20 final size:20
Alignment explanation
Indices: 1506492--1506529 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1506482 TATTATAACC
*
1506492 TTTCTTTGACATTACATTAA
1 TTTCTTTGACATCACATTAA
1506512 TTTCATTTGACA-CACATT
1 TTTC-TTTGACATCACATT
1506530 CCTGCATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.47
Consensus pattern (20 bp):
TTTCTTTGACATCACATTAA
Found at i:1509872 original size:30 final size:31
Alignment explanation
Indices: 1509829--1509892 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
1509819 AAAATCAAAA
* *
1509829 TTTTTCATAATTTACAATTTAGTCCCTATAT
1 TTTTTAATAATTTACAATTTAGTCCCTAAAT
* *
1509860 TTTTTAAT-ATTTACATTTTAGTCCTTAAAT
1 TTTTTAATAATTTACAATTTAGTCCCTAAAT
1509890 TTT
1 TTT
1509893 AAAATCTCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.56
Consensus pattern (31 bp):
TTTTTAATAATTTACAATTTAGTCCCTAAAT
Found at i:1511524 original size:9 final size:9
Alignment explanation
Indices: 1511510--1511554 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
1511500 TGTTTATGTA
1511510 TATATTTTT
1 TATATTTTT
*
1511519 TATATTTTC
1 TATATTTTT
*
1511528 T-TATTTTA
1 TATATTTTT
1511536 TACTATTTTT
1 TA-TATTTTT
1511546 TATATTTTT
1 TATATTTTT
1511555 ATTAATATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
8 7 0.23
9 16 0.52
10 8 0.26
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (9 bp):
TATATTTTT
Found at i:1511887 original size:5 final size:5
Alignment explanation
Indices: 1511877--1511924 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
1511867 AAGAAATAAA
* *
1511877 AAAAG AAAAG AAAAG AAAAATG AAAAA AAGAAG AAAAG AAAAA AAAAG
1 AAAAG AAAAG AAAAG -AAAA-G AAAAG AA-AAG AAAAG AAAAG AAAAG
1511925 CATGAAATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 23 0.64
6 12 0.33
7 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:1511903 original size:18 final size:17
Alignment explanation
Indices: 1511875--1511943 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
1511865 ATAAGAAATA
* *
1511875 AAAAAAGAAAAGAAAAG
1 AAAAATGAAAAAAAAAG
1511892 AAAAATGAAAAAAAGAAG
1 AAAAATGAAAAAAA-AAG
1511910 -AAAA-GAAAAAAAAAG
1 AAAAATGAAAAAAAAAG
* *
1511925 CATGAAATGAAAAATAAAG
1 -A-AAAATGAAAAAAAAAG
1511944 TGTAGATAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 3 0.07
16 8 0.19
17 16 0.37
18 6 0.14
19 10 0.23
ACGTcount: A:0.77, C:0.01, G:0.16, T:0.06
Consensus pattern (17 bp):
AAAAATGAAAAAAAAAG
Found at i:1511905 original size:15 final size:16
Alignment explanation
Indices: 1511877--1511921 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1511867 AAGAAATAAA
1511877 AAAAGAAAAGAAAAGAA-
1 AAAAG-AAA-AAAAGAAG
*
1511894 AAATGAAAAAAAGAAG
1 AAAAGAAAAAAAGAAG
1511910 AAAAGAAAAAAA
1 AAAAGAAAAAAA
1511922 AAGCATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAAAGAAG
Found at i:1511910 original size:23 final size:23
Alignment explanation
Indices: 1511870--1511923 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
1511860 TCTAAATAAG
1511870 AAATAAAAAAAGAAAAGAAAAGAA
1 AAATAAAAAAAG-AAAGAAAAGAA
1511894 AAATGAAAAAAAG-AAGAAAAGAA
1 AAAT-AAAAAAAGAAAGAAAAGAA
1511917 AAA-AAAA
1 AAATAAAA
1511924 GCATGAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
23 13 0.45
24 4 0.14
25 8 0.28
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (23 bp):
AAATAAAAAAAGAAAGAAAAGAA
Found at i:1511931 original size:19 final size:18
Alignment explanation
Indices: 1511877--1511943 Score: 59
Period size: 19 Copynumber: 3.8 Consensus size: 18
1511867 AAGAAATAAA
*
1511877 AAAAGAAAAGAAAAGAA-
1 AAAAGAAAAAAAAAGAAG
*
1511894 AAATG--AAAAAAAGAAG
1 AAAAGAAAAAAAAAGAAG
*
1511910 AAAAGAAAAAAAAAGCATG
1 AAAAGAAAAAAAAAG-AAG
* *
1511929 AAATGAAAAATAAAG
1 AAAAGAAAAAAAAAG
1511944 TGTAGATAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 9 0.22
16 4 0.10
17 4 0.10
18 8 0.20
19 15 0.38
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.06
Consensus pattern (18 bp):
AAAAGAAAAAAAAAGAAG
Found at i:1512752 original size:112 final size:113
Alignment explanation
Indices: 1512547--1512763 Score: 283
Period size: 112 Copynumber: 1.9 Consensus size: 113
1512537 AACTTGGAAG
* * * *
1512547 AACATCAAGTTTGTCTAATTTTCGAAGAAATTCCTATTTTATGCATTCCGATCCATTCATGCCTA
1 AACATCAAATTTGTCTAATTTTCGAAGAAATTCATATTTTATACATTCCGATCCATTCATCCCTA
* * * * * *
1512612 GGAAAATGGGGCGCGTATCCTATGAGTTTTGGAATTTTTAAAACCAAC
66 GGAAAATAGGGCACGTACCCAATCAGTTTTGAAATTTTTAAAACCAAC
* * * *
1512660 AACATCAAATTTGTTTGATTTTC-AAGAAATTCATATTTTATACATTTCGATCCATTCGTCCCTA
1 AACATCAAATTTGTCTAATTTTCGAAGAAATTCATATTTTATACATTCCGATCCATTCATCCCTA
* *
1512724 GGAAAATATGGCATGTACCCAATCAGTTTTGAAATTTTTA
66 GGAAAATAGGGCACGTACCCAATCAGTTTTGAAATTTTTA
1512764 GTCCAACCAA
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
112 68 0.77
113 20 0.23
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (113 bp):
AACATCAAATTTGTCTAATTTTCGAAGAAATTCATATTTTATACATTCCGATCCATTCATCCCTA
GGAAAATAGGGCACGTACCCAATCAGTTTTGAAATTTTTAAAACCAAC
Found at i:1513192 original size:72 final size:72
Alignment explanation
Indices: 1513103--1513238 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 72
1513093 CTACACTTTA
1513103 GATAACATTAGGATTTGCATCATTTCACATGCATTTGCCACTTTACT-AATGCTTACATTTGCAT
1 GATAACATTAGGATTTGCATCATTTCACATGCATTTGCCACTTTACTGAA-GCTTACATTTGCAT
1513167 CATTTCAT
65 CATTTCAT
* * *
1513175 GATAACATT-GGCATTTGCATCATTTCATATGCATTTGCCACTTTATTGAAGCTTATATTTGCAT
1 GATAACATTAGG-ATTTGCATCATTTCACATGCATTTGCCACTTTACTGAAGCTTACATTTGCAT
1513239 TGCTTCATAC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
71 2 0.03
72 55 0.93
73 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.41
Consensus pattern (72 bp):
GATAACATTAGGATTTGCATCATTTCACATGCATTTGCCACTTTACTGAAGCTTACATTTGCATC
ATTTCAT
Found at i:1514035 original size:41 final size:41
Alignment explanation
Indices: 1513985--1514596 Score: 192
Period size: 40 Copynumber: 15.3 Consensus size: 41
1513975 CTTTTAATTT
* *
1513985 GTTAACTTTATCAGTTTCACCCCGGTCAACCCTTCTAACTC
1 GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* * * * * *
1514026 GTTAGCTTTATC-GATTTCTCCCTGGCCAA-CTTTTTAATTG
1 GTTAGCTTTATCAG-TTTCACCCTGGTCAACCCTTCTAACTC
* * *
1514066 GTT-GACTTTATTAGTTTCACCCTAGTCAACCCTTCTAACCC
1 GTTAG-CTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* * * * * * * * *
1514107 GTTGGCTTTATCGGTTTCATCTTGGCCAA-CTTTTTAATTG
1 GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* * * * *
1514147 GTT-GAC-TTAT-GGCTTCACCTTGGTCAACCCTTCTATCCC
1 GTTAG-CTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* ** * *
1514186 GTTGGCTTTATCAGTTTTGCCTTGGCCAA-CC--CT-A-TC
1 GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* * * ** * * *
1514222 GTTGGCTTTATCGGTTTCAGCCTAATCAACCGTTTTAACCC
1 GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* * ** *** * * * * * *
1514263 ATTGGCTTTATTTGTTTCTTTCTAG-CAAACTTTTTAATTG
1 GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
1514303 GTT-GACTTTATC-GATTTCACCCTGGTCAACCCTTCTAAC-C
1 GTTAG-CTTTATCAG-TTTCACCCTGGTCAACCCTTCTAACTC
* * * * * * *
1514343 GTTGGCTTTATC-GATTTCACCTTGG-CTAA-CTTTTTCATTG
1 GTTAGCTTTATCAG-TTTCACCCTGGTC-AACCCTTCTAACTC
* * * * * *
1514383 GTTAGCTTTATCAGTTTCGCCTTGGTTAATCTTTCTAACTT
1 GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* * * * * *
1514424 GTTGGCTTTATCAATTTCGCCTTAGCCAACCCTTCTAAC-C
1 GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* * * ** * *
1514464 TATTGGCTTTATCGGTTTTGCCCTGGTCAA-CCTTCTAATTG
1 -GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* * *
1514505 GTT-GACTTTATCAGGTTCACCCTGGTCAACCTTTCT-ACCC
1 GTTAG-CTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
* ** * *
1514545 GTTGGCTTTATGGGTTTCACCTTGGTCAACCCTTTTAA-TCC
1 GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACT-C
*
1514586 ATTAGCTTTAT
1 GTTAGCTTTAT
1514597 TGGTTTTGCC
Statistics
Matches: 414, Mismatches: 126, Indels: 62
0.69 0.21 0.10
Matches are distributed among these distances:
36 22 0.05
37 1 0.00
38 16 0.04
39 25 0.06
40 178 0.43
41 171 0.41
42 1 0.00
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (41 bp):
GTTAGCTTTATCAGTTTCACCCTGGTCAACCCTTCTAACTC
Found at i:1514115 original size:81 final size:81
Alignment explanation
Indices: 1513976--1514453 Score: 426
Period size: 81 Copynumber: 6.0 Consensus size: 81
1513966 AGATATAACC
* * * * *
1513976 TTTTAATTTGTTAACTTTATCAGTTTCACCCCGGTCAACCCTTCTAACTCGTTAGCTTTATCGAT
1 TTTTAATTGGTTGACTTTATCAGTTTCACCCTGGTCAACCCTTCTAACCCGTTGGCTTTATCGAT
*
1514041 TTCTCCCTGGCCAACT
66 TTCTCCTTGGCCAACT
* * *
1514057 TTTTAATTGGTTGACTTTATTAGTTTCACCCTAGTCAACCCTTCTAACCCGTTGGCTTTATCGGT
1 TTTTAATTGGTTGACTTTATCAGTTTCACCCTGGTCAACCCTTCTAACCCGTTGGCTTTATCGAT
1514122 TTCAT-CTTGGCCAACT
66 TTC-TCCTTGGCCAACT
* * * *
1514138 TTTTAATTGGTTGAC-TTAT-GGCTTCACCTTGGTCAACCCTTCTATCCCGTTGGCTTTATC-AG
1 TTTTAATTGGTTGACTTTATCAGTTTCACCCTGGTCAACCCTTCTAACCCGTTGGCTTTATCGA-
1514200 TTT-TGCCTTGGCCAAC-
65 TTTCT-CCTTGGCCAACT
** * * * * ** * * * *
1514216 -CCT-A-TCGTTGGCTTTATCGGTTTCAGCCTAATCAACCGTTTTAACCCATTGGCTTTATTTG-
1 TTTTAATTGGTTGACTTTATCAGTTTCACCCTGGTCAACCCTTCTAACCCGTTGGCTTTA-TCGA
* * *
1514277 TTTCT-TTCTAGCAAACT
65 TTTCTCCT-TGGCCAACT
1514294 TTTTAATTGGTTGACTTTATC-GATTTCACCCTGGTCAACCCTTCTAA-CCGTTGGCTTTATCGA
1 TTTTAATTGGTTGACTTTATCAG-TTTCACCCTGGTCAACCCTTCTAACCCGTTGGCTTTATCGA
* *
1514357 TTTCACCTTGGCTAACT
65 TTTCTCCTTGGCCAACT
* * * * * * ** *
1514374 TTTTCATTGGTT-AGCTTTATCAGTTTCGCCTTGGTTAATCTTTCTAACTTGTTGGCTTTATCAA
1 TTTTAATTGGTTGA-CTTTATCAGTTTCACCCTGGTCAACCCTTCTAACCCGTTGGCTTTATCGA
* *
1514438 TTTCGCCTTAGCCAAC
65 TTTCTCCTTGGCCAAC
1514454 CCTTCTAACC
Statistics
Matches: 318, Mismatches: 59, Indels: 40
0.76 0.14 0.10
Matches are distributed among these distances:
75 6 0.02
76 6 0.02
77 41 0.13
78 2 0.01
79 53 0.17
80 65 0.20
81 144 0.45
82 1 0.00
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (81 bp):
TTTTAATTGGTTGACTTTATCAGTTTCACCCTGGTCAACCCTTCTAACCCGTTGGCTTTATCGAT
TTCTCCTTGGCCAACT
Found at i:1514602 original size:121 final size:122
Alignment explanation
Indices: 1514303--1514610 Score: 284
Period size: 121 Copynumber: 2.5 Consensus size: 122
1514293 TTTTTAATTG
* * * * * * * * ** *
1514303 GTTGACTTTATCGATTTCACCCTGGTCAACCCTTCTAACC-GTTGGCTTTATCGATTTCACCTTG
1 GTTGGCTTTATCAATTTCACCTTAGCCAACCCTTCTAACCTATTAGCTTTATCGGTTTTGCCCTG
* * * * * * * * **
1514367 G-CTAACTTTTTCATTGGTTAGCTTTATCAGTTTCGCCTTGGTTAATCTTTCTAACTT
66 GTC-AACCTTCTAATTGGTTAGCTTTATCAGGTTCACCCTGGTCAACCTTTCTAACCC
* *
1514424 GTTGGCTTTATCAATTTCGCCTTAGCCAACCCTTCTAACCTATTGGCTTTATCGGTTTTGCCCTG
1 GTTGGCTTTATCAATTTCACCTTAGCCAACCCTTCTAACCTATTAGCTTTATCGGTTTTGCCCTG
1514489 GTCAACCTTCTAATTGGTT-GACTTTATCAGGTTCACCCTGGTCAACCTTTCT-ACCC
66 GTCAACCTTCTAATTGGTTAG-CTTTATCAGGTTCACCCTGGTCAACCTTTCTAACCC
*** * * * *
1514545 GTTGGCTTTATGGGTTTCACCTTGGTCAACCCTTTTAATCC-ATTAGCTTTATTGGTTTTGCCCT
1 GTTGGCTTTATCAATTTCACCTTAGCCAACCCTTCTAA-CCTATTAGCTTTATCGGTTTTGCCCT
1514609 GG
65 GG
1514611 CCAAATTCTA
Statistics
Matches: 153, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
121 91 0.59
122 61 0.40
123 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (122 bp):
GTTGGCTTTATCAATTTCACCTTAGCCAACCCTTCTAACCTATTAGCTTTATCGGTTTTGCCCTG
GTCAACCTTCTAATTGGTTAGCTTTATCAGGTTCACCCTGGTCAACCTTTCTAACCC
Found at i:1514903 original size:42 final size:42
Alignment explanation
Indices: 1514857--1515086 Score: 137
Period size: 42 Copynumber: 5.5 Consensus size: 42
1514847 AAGTAAATCC
*
1514857 TTTTATCCTTTGTTGACTTCTCGGTTCAATCCCGGTCAACTT
1 TTTTATCCTTTGTTGACTTATCGGTTCAATCCCGGTCAACTT
* * * *
1514899 TTTTATCCTTTGTTTACTTATCGGGTT-AGTCCTGGGT-AAATCT
1 TTTTATCCTTTGTTGACTTATC-GGTTCAATCC-CGGTCAACT-T
* * * ** *
1514942 TTTTATCCTTTATTGACTTGTCAGTTCAATCTTGGTCAAC-C
1 TTTTATCCTTTGTTGACTTATCGGTTCAATCCCGGTCAACTT
* * * ** * * ** *
1514983 TTTTATCCTTTGTTTACCTGTCTATTTAGTTCCAAGT-AAATCT
1 TTTTATCCTTTGTTGACTTATCGGTTCA-ATCCCGGTCAACT-T
* * *
1515026 TTTTATCCTTTGTTGACTTATCAGTTCAATCTCGGTTAAAC-T
1 TTTTATCCTTTGTTGACTTATCGGTTCAATCCCGG-TCAACTT
* *
1515068 TTCTATCCTTTGTTTACTT
1 TTTTATCCTTTGTTGACTT
1515087 GTTGACTTAG
Statistics
Matches: 139, Mismatches: 39, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
41 24 0.17
42 58 0.42
43 55 0.40
44 2 0.01
ACGTcount: A:0.18, C:0.20, G:0.13, T:0.49
Consensus pattern (42 bp):
TTTTATCCTTTGTTGACTTATCGGTTCAATCCCGGTCAACTT
Found at i:1514969 original size:85 final size:85
Alignment explanation
Indices: 1514771--1515267 Score: 459
Period size: 85 Copynumber: 5.9 Consensus size: 85
1514761 TCAAGTATAG
* * * * * *
1514771 CTTTTTATCTTTTGTTAACTTGTCAGTTCATTCTCGATTAACTTTTATATCCTTTGTTTACCTGT
1 CTTTTTATCCTTTGTTGACTTGTCAGTTCAATCTCGGTCAACTTTTTTATCCTTTGTTTACCTGT
* *
1514836 C-GCTTAATCTTAAGTAAAT
66 CGGCTTAGTCCTAAGTAAAT
* * * * * *
1514855 CCTTTTATCCTTTGTTGACTTCTCGGTTCAATCCCGGTCAACTTTTTTATCCTTTGTTTACTTAT
1 CTTTTTATCCTTTGTTGACTTGTCAGTTCAATCTCGGTCAACTTTTTTATCCTTTGTTTACCTGT
* **
1514920 CGGGTTAGTCCTGGGTAAAT
66 CGGCTTAGTCCTAAGTAAAT
* * *
1514940 CTTTTTATCCTTTATTGACTTGTCAGTTCAATCTTGGTCAAC-CTTTTATCCTTTGTTTACCTGT
1 CTTTTTATCCTTTGTTGACTTGTCAGTTCAATCTCGGTCAACTTTTTTATCCTTTGTTTACCTGT
***
1515004 CTATTTAGTTCC-AAGTAAAT
66 CGGCTTAG-TCCTAAGTAAAT
* * * *
1515024 CTTTTTATCCTTTGTTGACTTATCAGTTCAATCTCGGTTAAAC-TTTCTATCCTTTGTTTACTTG
1 CTTTTTATCCTTTGTTGACTTGTCAGTTCAATCTCGG-TCAACTTTTTTATCCTTTGTTTACCTG
* * * **
1515088 TTGACTTAGTACTGGGTAAAT
65 TCGGCTTAGTCCTAAGTAAAT
* * * * * * *
1515109 CTTTTTA-CCTTTTTTTGACTTGTCAGTTTAATCCCAGTCAACCTTTTTATCCTTTATTTACCTA
1 CTTTTTATCC-TTTGTTGACTTGTCAGTTCAATCTCGGTCAACTTTTTTATCCTTTGTTTACCTG
1515173 TCGGCTTAGTCCCT-AGTAAAT
65 TCGGCTTAGT-CCTAAGTAAAT
* * * * * * * * *
1515194 CATTTTATTCTTTGTTGACTTGTTAGTTTAATCTCAGTCAA-TTTTGTATCTTTTATTTACTTGT
1 CTTTTTATCCTTTGTTGACTTGTCAGTTCAATCTCGGTCAACTTTTTTATCCTTTGTTTACCTGT
**
1515258 TAGCTTAGTC
66 CGGCTTAGTC
1515268 TCGGGTAACC
Statistics
Matches: 335, Mismatches: 70, Indels: 17
0.79 0.17 0.04
Matches are distributed among these distances:
83 1 0.00
84 151 0.45
85 180 0.54
86 3 0.01
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.49
Consensus pattern (85 bp):
CTTTTTATCCTTTGTTGACTTGTCAGTTCAATCTCGGTCAACTTTTTTATCCTTTGTTTACCTGT
CGGCTTAGTCCTAAGTAAAT
Found at i:1515055 original size:169 final size:168
Alignment explanation
Indices: 1514771--1515255 Score: 519
Period size: 169 Copynumber: 2.9 Consensus size: 168
1514761 TCAAGTATAG
* * * * * * *
1514771 CTTTTTATCTTTTGTTAACTTGTCAGTTCATTCTCGATTAACTTTTATATCCTTTGTTTACCTGT
1 CTTTTTATCCTTTATTGACTTGTCAGTTCAATCTCGGTCAACCTTT-TATCCTTTGTTTACCTGT
* * * * * *
1514836 CGCTTA-ATCTTAAGTAAATCCTTTTATCCTTTGTTGACTTCTCGGTTCAATCCCGGTCAACTTT
65 CGCTTAGTTC-CAAGTAAATCATTTTATCCTTTGTTGACTTATCAGTTCAATCTCGGTCAACTTT
* ** *
1514900 TTTATCCTTTGTTTACTTATCGGGTTAGTCCTGGGTAAAT
129 TCTATCCTTTGTTTACTTATCGACTTAGTACTGGGTAAAT
*
1514940 CTTTTTATCCTTTATTGACTTGTCAGTTCAATCTTGGTCAACCTTTTATCCTTTGTTTACCTGTC
1 CTTTTTATCCTTTATTGACTTGTCAGTTCAATCTCGGTCAACCTTTTATCCTTTGTTTACCTGTC
** * *
1515005 TATTTAGTTCCAAGTAAATCTTTTTATCCTTTGTTGACTTATCAGTTCAATCTCGGTTAAAC-TT
66 -GCTTAGTTCCAAGTAAATCATTTTATCCTTTGTTGACTTATCAGTTCAATCTCGG-TCAACTTT
* *
1515069 TCTATCCTTTGTTTACTTGTTGACTTAGTACTGGGTAAAT
129 TCTATCCTTTGTTTACTTATCGACTTAGTACTGGGTAAAT
* * * * * *
1515109 CTTTTTA-CCTTTTTTTGACTTGTCAGTTTAATCCCAGTCAACCTTTTTATCCTTTATTTACCTA
1 CTTTTTATCC-TTTATTGACTTGTCAGTTCAATCTCGGTCAACC-TTTTATCCTTTGTTTACCTG
* * * * * * *
1515173 TCGGCTTAGTCCCTAGTAAATCATTTTATTCTTTGTTGACTTGTTAGTTTAATCTCAGTCAA-TT
64 TC-GCTTAGTTCCAAGTAAATCATTTTATCCTTTGTTGACTTATCAGTTCAATCTCGGTCAACTT
* * *
1515237 TTGTATCTTTTATTTACTT
128 TTCTATCCTTTGTTTACTT
1515256 GTTAGCTTAG
Statistics
Matches: 265, Mismatches: 45, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
168 21 0.08
169 173 0.65
170 71 0.27
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.49
Consensus pattern (168 bp):
CTTTTTATCCTTTATTGACTTGTCAGTTCAATCTCGGTCAACCTTTTATCCTTTGTTTACCTGTC
GCTTAGTTCCAAGTAAATCATTTTATCCTTTGTTGACTTATCAGTTCAATCTCGGTCAACTTTTC
TATCCTTTGTTTACTTATCGACTTAGTACTGGGTAAAT
Found at i:1515685 original size:4 final size:5
Alignment explanation
Indices: 1515658--1515687 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1515648 AATTTTTAAA
1515658 TATTT TATTT TATTT TATTT TA-TT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT T
1515688 TTTCAACTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:1515688 original size:15 final size:15
Alignment explanation
Indices: 1515658--1515687 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1515648 AATTTTTAAA
1515658 TATTTTATTTTATTT
1 TATTTTATTTTATTT
1515673 TATTTTA-TTTATTT
1 TATTTTATTTTATTT
1515687 T
1 T
1515688 TTTCAACTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TATTTTATTTTATTT
Found at i:1517410 original size:155 final size:155
Alignment explanation
Indices: 1517199--1517480 Score: 426
Period size: 155 Copynumber: 1.8 Consensus size: 155
1517189 ACTAGGTCCA
* *
1517199 CTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCTATCTATAATCCTTTTTAAGTCTTTT
1 CTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
1517264 AAAAGTATTAG-GCACTTCTAAGTCA-AAGGTATCCCCTAAAG-GTATTTTCATAATTTTCTAGA
66 AAAAGTA-TAGAGCACTTCTAAGT-AGAAGGTAT-CCCTAAAGTGTATTTTCATAATTTTCTAGA
1517326 ACCGAGTCCTAGGTTTTCACGAAGTTCG
128 ACCGAGTCCTAGGTTTTCACGAAGTTCG
* *
1517354 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTACGTCCTTT
1 CTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
*** * * *
1517419 AGGGGTATCGAGCATTTCTAAGTAGAAGGTATCCCTTAAGTGTATTTTCATAATTTTCTAGA
66 AAAAGTATAGAGCACTTCTAAGTAGAAGGTATCCCTAAAGTGTATTTTCATAATTTTCTAGA
1517481 GTCACCGAGT
Statistics
Matches: 114, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
154 10 0.09
155 104 0.91
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (155 bp):
CTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTT
AAAAGTATAGAGCACTTCTAAGTAGAAGGTATCCCTAAAGTGTATTTTCATAATTTTCTAGAACC
GAGTCCTAGGTTTTCACGAAGTTCG
Found at i:1517810 original size:155 final size:155
Alignment explanation
Indices: 1517651--1518020 Score: 449
Period size: 155 Copynumber: 2.4 Consensus size: 155
1517641 CTAGGTCTGC
* *
1517651 TTTTATGTTGAAGGTGGGTGTCTAGGATAGGTTCATCCCATTTATAATTTTTTTAAGTCCGTTAG
1 TTTTATGTTGAAGGTGGGTATCTAGGATAGGTTCATCCCATTTATAATTTTTTTAAGTCCGTTAA
* * * * * *
1517716 GGTTATC-AGGATACCTTCGCGTCAAAGATATATCCTAGGGGCATTTTTGTAATTTTTTAAAACT
66 GGTTATCGA-GATACCTTCACATCAAAGATATATCCTAGAGGCATTTTCGTAATTTTCTAAAACC
1517780 AAGTCCTAGGCTGTCATTGGCTTCGT
130 AAGTCCTAGGCTGTCATTGGCTTCGT
* **
1517806 TTTTATGTTGAAGGTGGGTATTTAGGATAGGTTCATCCCATTTATAATTTTTTTAAGTCTTTTAA
1 TTTTATGTTGAAGGTGGGTATCTAGGATAGGTTCATCCCATTTATAATTTTTTTAAGTCCGTTAA
* * * *
1517871 GGTTATCGAGATACCTTCACATTAAAGGTATATCCTAGAGGCATTTTCGTAATTTTCTAGAACCG
66 GGTTATCGAGATACCTTCACATCAAAGATATATCCTAGAGGCATTTTCGTAATTTTCTAAAACCA
* * *
1517936 AGTCCTAGGTTGTCATTGGGATAC--
131 AGTCCTAGGCTGTCATT-GGCTTCGT
*** * * * * * *
1517960 TTTTATGCCAAAAGTGAGTATTTAGGATAGGTTCATCCTATCTATAATCCTTTTTAAGTCC
1 TTTTATGTTGAAGGTGGGTATCTAGGATAGGTTCATCCCATTTATAAT-TTTTTTAAGTCC
1518021 TTTAGGGGTA
Statistics
Matches: 185, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
154 41 0.22
155 139 0.75
156 5 0.03
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (155 bp):
TTTTATGTTGAAGGTGGGTATCTAGGATAGGTTCATCCCATTTATAATTTTTTTAAGTCCGTTAA
GGTTATCGAGATACCTTCACATCAAAGATATATCCTAGAGGCATTTTCGTAATTTTCTAAAACCA
AGTCCTAGGCTGTCATTGGCTTCGT
Found at i:1528676 original size:21 final size:21
Alignment explanation
Indices: 1528650--1528701 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1528640 ATGATTAATA
1528650 TATCGATACACTTTAAACAGG
1 TATCGATACACTTTAAACAGG
1528671 TATCGATACACTTTAAACAGG
1 TATCGATACACTTTAAACAGG
1528692 TATCGATACA
1 TATCGATACA
1528702 TTTTCTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.29
Consensus pattern (21 bp):
TATCGATACACTTTAAACAGG
Found at i:1528794 original size:20 final size:21
Alignment explanation
Indices: 1528769--1528820 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1528759 CATTTCAAGC
1528769 ATGTATCGATACATTTACT-T
1 ATGTATCGATACATTTACTAT
* *
1528789 ATGTATCGGTATATTTACTAT
1 ATGTATCGATACATTTACTAT
*
1528810 TTGTATCGATA
1 ATGTATCGATA
1528821 TAAATTATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (21 bp):
ATGTATCGATACATTTACTAT
Found at i:1530088 original size:63 final size:63
Alignment explanation
Indices: 1529989--1530148 Score: 277
Period size: 63 Copynumber: 2.5 Consensus size: 63
1529979 AATACAATTC
* * *
1529989 TTCATGTATCGATACAATGTGCCATGTATCGATATAAATAGTGGTAGGGTAGTTATTGCCAGT
1 TTCATGTATCGATACAATGTGCCATGTATCGATATAAACAGTGGTAGGGTAGCTACTGCCAGT
1530052 TTCATGTATCGATACAATGTGCCATGTATCGATATAAACAGTGGTAGGGTAGCTACTGCCAGT
1 TTCATGTATCGATACAATGTGCCATGTATCGATATAAACAGTGGTAGGGTAGCTACTGCCAGT
1530115 TTCATGTATCGATACAATCGTG-CATGTATCGATA
1 TTCATGTATCGATACAAT-GTGCCATGTATCGATA
1530149 CAATGAACAT
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
63 90 0.97
64 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (63 bp):
TTCATGTATCGATACAATGTGCCATGTATCGATATAAACAGTGGTAGGGTAGCTACTGCCAGT
Found at i:1532570 original size:21 final size:21
Alignment explanation
Indices: 1532546--1532601 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1532536 CGATCTGAAA
1532546 TTGAAGAAATTTGAAATTGAT
1 TTGAAGAAATTTGAAATTGAT
1532567 TTGAAGAAATTTGAAATTGAT
1 TTGAAGAAATTTGAAATTGAT
1532588 TTGAAGAAATTTGA
1 TTGAAGAAATTTGA
1532602 TGAAAGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.38
Consensus pattern (21 bp):
TTGAAGAAATTTGAAATTGAT
Found at i:1538389 original size:20 final size:20
Alignment explanation
Indices: 1538344--1538389 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1538334 GTTAACAGCC
*
1538344 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
1538364 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
1538385 CATGT
1 CATGT
1538390 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:1540568 original size:15 final size:15
Alignment explanation
Indices: 1540548--1540580 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1540538 CGTTGCGACA
1540548 ATCATTATCATCATC
1 ATCATTATCATCATC
*
1540563 ATCATTATCTTCATC
1 ATCATTATCATCATC
1540578 ATC
1 ATC
1540581 TTTGACGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (15 bp):
ATCATTATCATCATC
Found at i:1542303 original size:19 final size:20
Alignment explanation
Indices: 1542259--1542314 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1542249 TTACCAGTTT
*
1542259 CATGTATCGATACAATCATG
1 CATGTATCGATACAATCATA
*
1542279 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATCATA
*
1542298 CATGTATCGATATAATC
1 CATGTATCGATACAATC
1542315 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATCATA
Found at i:1543158 original size:62 final size:62
Alignment explanation
Indices: 1543060--1543569 Score: 610
Period size: 63 Copynumber: 8.1 Consensus size: 62
1543050 TTTGAAAAGG
* * * * * * *
1543060 AAAAAAAAGAAAGGTGTCCTACTCTTTGAGGACTAAAAGGTGCCATCAGCTTGTATGGACTTT
1 AAAAAGAA-AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* * * * * *
1543123 AAAAAGAAAGAGGCGTCTTGCTTTTTGAGGACTAAAAAGTGCCACTAGCTTGTGTGGGCTTT
1 AAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* * * *
1543185 AAAAAGAAAGAA-GCGACCTGCTATTTAAGGACTAAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAAGAAA-AAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* *
1543247 -AAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTATGTGCTTT
1 AAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* * * *
1543308 AAAAAAAGAAAAGGCATCCTGCTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTGGGCTCT
1 AAAAAGA-AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* * * * * *
1543371 AAAGAAGGAAAAGGCCTCATGTTCTTTGAAGACTAAAAGGTGCCACCAACTTGTGTAGGCTTT
1 AAA-AAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
* *
1543434 AAAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTTGTGTGGGTTTCT
1 -AAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTT-T
* *
1543498 AAAAAGAAAAAAGACGTCCTGCTCTTTGAGGACTAAAAAGGAGTGCCACCAACTTGTGTGGACTT
1 AAAAAG-AAAAAGGCGTCCTGCTCTTTGAGGACT-AAAA-G-GTGCCACCAACTTGTGTGGGCTT
1543563 T
62 T
*
1543564 TAAAAG
1 AAAAAG
1543570 GGATGTCACT
Statistics
Matches: 386, Mismatches: 50, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
60 2 0.01
61 52 0.13
62 102 0.26
63 167 0.43
64 32 0.08
65 4 0.01
66 6 0.02
67 21 0.05
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (62 bp):
AAAAAGAAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:1544759 original size:10 final size:10
Alignment explanation
Indices: 1544744--1544775 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1544734 CTTACCAAGA
1544744 TTTTTTGTTG
1 TTTTTTGTTG
*
1544754 TTTTTTGTTT
1 TTTTTTGTTG
1544764 TTTTTTGTTG
1 TTTTTTGTTG
1544774 TT
1 TT
1544776 GAAAAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (10 bp):
TTTTTTGTTG
Found at i:1549100 original size:156 final size:155
Alignment explanation
Indices: 1548545--1549378 Score: 631
Period size: 155 Copynumber: 5.4 Consensus size: 155
1548535 GGTGCAAGAG
* * * * *
1548545 TGACAACCTAGGACTTGATCCTAGAAAAATTATGAAAATGCCCTTATGAGG-TACCTTCGACGTA
1 TGACAACCTAGGACTCGATTCTAAAAAAATTATGAAAATACCCTTA-GAGGATACCTTCGACATA
* * * * *
1548609 GAAGTACCTGATACCCCCCCTAAAAGACTTGAAAAGGATTATAGATGGGATGAACCTATCCTAAA
65 GAAGTGCCCGATA----CCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAGA
* * * * *
1548674 TACCTACCTTTGGCATGAAAG-TATCCCAA
126 TACCCACCTTTGGCATAAAAGCAAACCCGA
* * * * *
1548703 TGACAACCTAGGACTCAATTCT-AAGAAATTACGAAAATA-CCTCTAGTGTATACCTTCGACAT-
1 TGACAACCTAGGACTCGATTCTAAAAAAATTATGAAAATACCCT-TAGAGGATACCTTCGACATA
* * *
1548765 GAAAGTATCCCGGTAACCCTAAAGGACTTAAAAAAGATTATAGATGGGATGAACCTATCCTAGAT
65 G-AAGT-GCCCGAT-ACCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAGAT
* * ** * ** *
1548830 A-CCTCTTTTAACATAAAAGCAGACTTGG
127 ACCCACCTTTGGCATAAAAGCAAACCCGA
* * * * * *
1548858 TGACAACCTAGGACTCGATT-TTAAAAAATTATGAAAATGCCCTTAAAGTATACCTCCAACAT-G
1 TGACAACCTAGGACTCGATTCTAAAAAAATTATGAAAATACCCTTAGAGGATACCTTCGACATAG
* * * * *
1548921 AAGGTAGCTCGGTAACCCTAAAGGATTTAAAAAAGATTATAGATGGGATAAACCTATCCTAGATA
66 AA-GT-GCCCGAT-ACCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAGATA
*
1548986 CCCATCTTTGGCATAAAAGCAAACCCGA
128 CCCACCTTTGGCATAAAAGCAAACCCGA
* ** * * *
1549014 TGACAACCAAGGACTTAATTTTAAAAAAATTATGAAAATACCCTTAGAGGATACGTTCGACCTAG
1 TGACAACCTAGGACTCGATTCTAAAAAAATTATGAAAATACCCTTAGAGGATACCTTCGACATAG
* * * * * *
1549079 AAGTGCCCAATACCTTTAAAGGACTTAGAAAGGATTATAGATGGGATAAACTTATCCTAGATAGC
66 AAGTGCCCGATACC-CTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAGATACC
** ***
1549144 CACCTTCAGCATAAAAGTGGACCCTG-
130 CACCTTTGGCATAAAAGCAAACCC-GA
* * * * * * *
1549170 TGACAATCTAAGACTCGGTTCTAAAAAAATTATGAAAATACCCCTA-AGG-GA--TT-AACTTAG
1 TGACAACCTAGGACTCGATTCTAAAAAAATTATGAAAATACCCTTAGAGGATACCTTCGACATAG
** * * * * *
1549230 AAGTGCCTAATACTCCTAAAGGACTTAAAAGGGGTTATAGATAGGATGAACCTATCCTAAATGCC
66 AAGTGCCCGATAC-CCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAGATACC
* * * ** *
1549295 CACCTTCGGCATAAAAGCGATCTTGG
130 CACCTTTGGCATAAAAGCAAACCCGA
* * * * * *
1549321 TGA-AACATAAGACTCGGTTCT-GAAAAATTATAAAAATACCCCTA-AGGTATACCTTCGA
1 TGACAACCTAGGACTCGATTCTAAAAAAATTATGAAAATACCCTTAGAGG-ATACCTTCGA
1549379 TTTAAAAGTA
Statistics
Matches: 544, Mismatches: 111, Indels: 46
0.78 0.16 0.07
Matches are distributed among these distances:
149 24 0.04
150 17 0.03
151 79 0.15
152 3 0.01
153 2 0.00
154 17 0.03
155 160 0.29
156 148 0.27
157 67 0.12
158 26 0.05
159 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (155 bp):
TGACAACCTAGGACTCGATTCTAAAAAAATTATGAAAATACCCTTAGAGGATACCTTCGACATAG
AAGTGCCCGATACCCTAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAGATACCC
ACCTTTGGCATAAAAGCAAACCCGA
Found at i:1549137 original size:311 final size:312
Alignment explanation
Indices: 1548626--1549208 Score: 703
Period size: 311 Copynumber: 1.9 Consensus size: 312
1548616 CTGATACCCC
* * * * *
1548626 CCCTAAAAGACTTGAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCTACCTTTGGCATG
1 CCCTAAAAGACTTAAAAAAGATTATAGATGGGATAAACCTATCCTAAATACCCACCTTTGGCATA
* * * * * *
1548691 AAAGTATCCCAATGACAACCTAGGACTCAATTCTAAGAAATTACGAAAATACCTCTAGTGTATAC
66 AAAGAAACCCAATGACAACCAAGGACTCAATTCTAAAAAATTACGAAAATACCTCTAGAGGATAC
* ** *
1548756 CTTCGACATGAAAGTATCCCGGTAACCCTAAAGGACTTAAAAAAGATTATAGATGGGATGAACCT
131 CTTCGACATGAAAGTAGCCCAATAACCCTAAAGGACTTAAAAAAGATTATAGATGGGATAAACCT
* * * * * *
1548821 ATCCTAGATA-CCTCTTTTAACATAAAAGCAGA-CTTGGTGACAACCTAGGACTCGATT-TTAAA
196 ATCCTAGATAGCCACCTTCAACATAAAAGCAGACCCT-GTGACAACCTAAGACTCGATTCTAAAA
1548883 AAATTATGAAAATGCCCTTAAAGTATACCTCCAACATGAAGGTAGCTCGGTAA
260 AAATTATGAAAATGCCCTTAAAGTATACCTCCAACATGAAGGTAGCTCGGTAA
* * * *
1548936 CCCTAAAGGATTTAAAAAAGATTATAGATGGGATAAACCTATCCTAGATACCCATCTTTGGCATA
1 CCCTAAAAGACTTAAAAAAGATTATAGATGGGATAAACCTATCCTAAATACCCACCTTTGGCATA
* * * *
1549001 AAAGCAAACCCGATGACAACCAAGGACTTAATTTTAAAAAAATTATGAAAATACC-CTTAGAGGA
66 AAAG-AAACCCAATGACAACCAAGGACTCAATTCT-AAAAAATTACGAAAATACCTC-TAGAGGA
* * * * *
1549065 TACGTTCGACCT-AGAAGT-GCCCAAT-ACCTTTAAAGGACTTAGAAAGGATTATAGATGGGATA
128 TACCTTCGACATGA-AAGTAGCCCAATAACC-CTAAAGGACTTAAAAAAGATTATAGATGGGATA
* * ** * *
1549127 AACTTATCCTAGATAGCCACCTTCAGCATAAAAGTGGACCCTGTGACAATCTAAGACTCGGTTCT
191 AACCTATCCTAGATAGCCACCTTCAACATAAAAGCAGACCCTGTGACAACCTAAGACTCGATTCT
1549192 AAAAAAATTATGAAAAT
256 AAAAAAATTATGAAAAT
1549209 ACCCCTAAGG
Statistics
Matches: 225, Mismatches: 40, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
310 63 0.28
311 73 0.32
312 70 0.31
313 19 0.08
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (312 bp):
CCCTAAAAGACTTAAAAAAGATTATAGATGGGATAAACCTATCCTAAATACCCACCTTTGGCATA
AAAGAAACCCAATGACAACCAAGGACTCAATTCTAAAAAATTACGAAAATACCTCTAGAGGATAC
CTTCGACATGAAAGTAGCCCAATAACCCTAAAGGACTTAAAAAAGATTATAGATGGGATAAACCT
ATCCTAGATAGCCACCTTCAACATAAAAGCAGACCCTGTGACAACCTAAGACTCGATTCTAAAAA
AATTATGAAAATGCCCTTAAAGTATACCTCCAACATGAAGGTAGCTCGGTAA
Found at i:1549298 original size:151 final size:153
Alignment explanation
Indices: 1548783--1549367 Score: 392
Period size: 156 Copynumber: 3.8 Consensus size: 153
1548773 CCCGGTAACC
* * * * * * * * *
1548783 CTAAAGGACTTAAAAAAGATTATAGATGGGATGAACCTATCCTAGATA-CCTCTTTTAACATAAA
1 CTAAAGGACTTAGAAAGGATTATAGATAGGATAAACCTATCCTAAATAGCCACCTTCAGCATAAA
* * * * * * * * *
1548847 AGCAGA-CTTGGTGACAACCTAGGACTCGATT-TTAAAAAATTATGAAAATGCCCTTAAAGTATA
66 AGC-GACCCTGGTGA-AACATAAGACTCGGTTCTAAAAAAATTATGAAAATACCCCT-AAGGAGA
* * * **
1548910 CCTCCAACAT-GAAGGTAGCTCGGTAACC-
128 -CTTCAACCTAGAA-GT-GCCCAAT-ACCT
* * * * * * * **
1548938 CTAAAGGATTTAAAAAAGATTATAGATGGGATAAACCTATCCTAGATACCCATCTTTGGCATAAA
1 CTAAAGGACTTAGAAAGGATTATAGATAGGATAAACCTATCCTAAATAGCCACCTTCAGCATAAA
* * * *** * * *
1549003 AGCAAACCC-GATGACAACCA-AGGACTTAATTTTAAAAAAATTATGAAAATACCCTTAGAGGAT
66 AGC-GACCCTGGTGA-AA-CATAAGACTCGGTTCTAAAAAAATTATGAAAATACCCCTA-AGGAG
*
1549066 ACGTTCGACCTAGAAGTGCCCAATACCT
127 AC-TTCAACCTAGAAGTGCCCAATACCT
* * * *
1549094 TTAAAGGACTTAGAAAGGATTATAGATGGGATAAACTTATCCTAGATAGCCACCTTCAGCATAAA
1 CTAAAGGACTTAGAAAGGATTATAGATAGGATAAACCTATCCTAAATAGCCACCTTCAGCATAAA
*
1549159 AGTGGACCCT-GTGACAATC-TAAGACTCGGTTCTAAAAAAATTATGAAAATACCCCTAAGG-GA
66 AG-CGACCCTGGTGA-AA-CATAAGACTCGGTTCTAAAAAAATTATGAAAATACCCCTAAGGAGA
* *
1549221 -TT-AACTTAGAAGTGCCTAATA-CT
128 CTTCAACCTAGAAGTGCCCAATACCT
* * *
1549244 CCTAAAGGACTTA-AAAGGGGTTATAGATAGGATGAACCTATCCTAAAT-GCCCACCTTCGGCAT
1 -CTAAAGGACTTAGAAA-GGATTATAGATAGGATAAACCTATCCTAAATAG-CCACCTTCAGCAT
* * * *
1549307 AAAAGCGATCTTGGTGAAACATAAGACTCGGTTCT-GAAAAATTATAAAAATACCCCTAAGG
63 AAAAGCGACCCTGGTGAAACATAAGACTCGGTTCTAAAAAAATTATGAAAATACCCCTAAGG
1549368 TATACCTTCG
Statistics
Matches: 357, Mismatches: 57, Indels: 38
0.79 0.13 0.08
Matches are distributed among these distances:
149 25 0.07
150 26 0.07
151 74 0.21
152 2 0.01
154 1 0.00
155 52 0.15
156 138 0.39
157 36 0.10
158 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (153 bp):
CTAAAGGACTTAGAAAGGATTATAGATAGGATAAACCTATCCTAAATAGCCACCTTCAGCATAAA
AGCGACCCTGGTGAAACATAAGACTCGGTTCTAAAAAAATTATGAAAATACCCCTAAGGAGACTT
CAACCTAGAAGTGCCCAATACCT
Found at i:1550900 original size:13 final size:13
Alignment explanation
Indices: 1550882--1550908 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1550872 GATACAATTC
1550882 ATAATGTATCGAT
1 ATAATGTATCGAT
1550895 ATAATGTATCGAT
1 ATAATGTATCGAT
1550908 A
1 A
1550909 CATTGTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
ATAATGTATCGAT
Found at i:1553480 original size:13 final size:13
Alignment explanation
Indices: 1553462--1553489 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1553452 AAATAGTACC
1553462 CAATGTATCGATA
1 CAATGTATCGATA
1553475 CAATGTATCGATA
1 CAATGTATCGATA
1553488 CA
1 CA
1553490 TGTCTCTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1553604 original size:19 final size:19
Alignment explanation
Indices: 1553569--1553620 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 19
1553559 CTATAGTCCC
*
1553569 TAATTCATATCAAACAAACA
1 TAATTCA-ATCATACAAACA
1553589 TAATTCAATCATAC-AACA
1 TAATTCAATCATACAAACA
1553607 TAA--CAATCAT-CAAA
1 TAATTCAATCATACAAA
1553621 ATTCATTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.03
16 9 0.30
18 7 0.23
19 6 0.20
20 7 0.23
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (19 bp):
TAATTCAATCATACAAACA
Found at i:1559622 original size:13 final size:13
Alignment explanation
Indices: 1559604--1559634 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1559594 ACATTTCTTC
1559604 ATGTATCGATACA
1 ATGTATCGATACA
1559617 ATGTATCGATACA
1 ATGTATCGATACA
*
1559630 TTGTA
1 ATGTA
1559635 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1559622 original size:33 final size:33
Alignment explanation
Indices: 1559584--1559650 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
1559574 GTTACAAGCT
1559584 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
1559617 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
1559650 A
1 A
1559651 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:1559724 original size:19 final size:19
Alignment explanation
Indices: 1559679--1559735 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1559669 CTGCCAGTTT
**
1559679 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
1559700 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1559719 CATGTATCGATATAATG
1 CATGTATCGATACAATG
1559736 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1561097 original size:163 final size:167
Alignment explanation
Indices: 1560924--1561276 Score: 513
Period size: 163 Copynumber: 2.1 Consensus size: 167
1560914 ATGGGAGTCT
** *
1560924 AATGACAATATTTGATGAATTTTAAAAATTTTAAATCGAGAAAAATCCTT-TCGAAAAAATTTAT
1 AATGACAATATTAAATAAATTTTAAAAATTTTAAATCGAGAAAAATCCTTCT-GAAAAAATTTAT
* * *
1560988 AGAATAGAAAACTCAG-TTTTCGAGAATAGGGAAACTTT-ATG-AAAAAATGAAAAACTGATGAA
65 AGAATAGAAAACTCAGTTTTTCAAGAATAGGGAAACTTTAAGGAAAAAAATGAAAAACTCATGAA
*
1561050 AATAAATGAATTTTTCAAAAC-AATTTACTA-TGAATTA
130 AATAAATGAATTTTTCAAAACTAATTTAATAGT-AATTA
* *
1561087 AATGACAATATTAAATAAATTTTAAAAATTTTAAATTGAGAAAAATCCTTCTGAAAACATTTATA
1 AATGACAATATTAAATAAATTTTAAAAATTTTAAATCGAGAAAAATCCTTCTGAAAAAATTTATA
*
1561152 GAATAGAAAACTCAGTTTTTCAAGAATAGGGAAATTTTAAGGAAAAAAATGAAAAACTCATGAAA
66 GAATAGAAAACTCAGTTTTTCAAGAATAGGGAAACTTTAAGGAAAAAAATGAAAAACTCATGAAA
*
1561217 ATAAATGAATTTTTTAAAACTAATTTAATAGTAATTA
131 ATAAATGAATTTTTCAAAACTAATTTAATAGTAATTA
* *
1561254 AATGATAATTTATAAAT-AATTTT
1 AATGACAATAT-TAAATAAATTTT
1561277 GAAGTTAGAA
Statistics
Matches: 170, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
163 73 0.43
164 21 0.12
165 2 0.01
166 40 0.24
167 28 0.16
168 6 0.04
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (167 bp):
AATGACAATATTAAATAAATTTTAAAAATTTTAAATCGAGAAAAATCCTTCTGAAAAAATTTATA
GAATAGAAAACTCAGTTTTTCAAGAATAGGGAAACTTTAAGGAAAAAAATGAAAAACTCATGAAA
ATAAATGAATTTTTCAAAACTAATTTAATAGTAATTA
Found at i:1564153 original size:22 final size:22
Alignment explanation
Indices: 1564123--1564167 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1564113 CCTAATTCAT
*
1564123 ATCTTTCCCTCAACTATCCTAC
1 ATCTGTCCCTCAACTATCCTAC
*
1564145 ATCTGTCCCTCAATTATCCTAC
1 ATCTGTCCCTCAACTATCCTAC
1564167 A
1 A
1564168 GTGTCCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.02, T:0.36
Consensus pattern (22 bp):
ATCTGTCCCTCAACTATCCTAC
Found at i:1569106 original size:20 final size:20
Alignment explanation
Indices: 1569059--1569133 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1569049 AAAAAGACAT
*
1569059 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1569078 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1569099 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1569119 AATGTATCGATACAT
1 AATGTATCGATACAT
1569134 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1569127 original size:40 final size:39
Alignment explanation
Indices: 1569056--1569133 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1569046 GGTAAAAAGA
* *
1569056 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1569095 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1569134 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1570969 original size:630 final size:627
Alignment explanation
Indices: 1569689--1571299 Score: 2545
Period size: 630 Copynumber: 2.6 Consensus size: 627
1569679 TTTTTTAAAA
* ** *
1569689 AAAATGTGCCACT-AGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTCGAA
1 AAAAGGTGCCACTGA-CTTGTG--GGCTTTGAAAAAAG-TGCCACTG--ATTTGTGGGCTTTGAA
* ** * *
1569753 AAGAGTGTTACTGACTTGCGTGGGCTTTAAAAGG-GTGCCACTGACTTGCGTGGGCTTTGAAAGG
60 AAAAGTGCCACTGACTT--GTGGGCTTTGAAAGGAGTGCCATTGACTT--GTGGGCTTTGAAAGG
* * *
1569817 ATGCCACTGACTCGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTG
121 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTG
* * *
1569881 ACTCGTGGGCTTTGAAAAG-GTACCACTGACTCGTGGGC-TTGAAAGGGTGCCACTGACTTGTGG
186 ACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG
* *
1569944 GCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACTTACTTGCGTGGGCTTTG
251 GCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTG
* *
1570008 AAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGA
314 AAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAAGATGCCACTAACTCGTGGGCTTTGAAAGGA
* *
1570073 TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGA
377 TGCCACTGACTCGTGGGCTTTGAAAGAGTACCACTGACTCGTGGGCTTTGAAAAGGTACCACTGA
*
1570138 CTTGCGTGAGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAACGGGTGCCACTGACTTG
442 CTTGCGTGAGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTG
* *
1570203 TGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTCGCAATGGTGCCACTGACCTGTGGGCTTCG
507 TGGGCTTTGAAAAAGTGCCACTAAATTGTGGGCTTCGCAATGGTGCCACTGACCTATGGGCTTCG
1570268 AAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTG
572 AAAGGGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTG
* * *
1570324 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGTTTTGAAAAAAGT
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAAAGTGCCACTGATTTGTGGGCTTTGAAAAAAGT
1570389 GCCACTGACTTGTGGGCTTTGAAAGGAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAA
66 GCCACTGACTTGTGGGCTTTGAAAGGAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAA
*
1570454 CTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGG
131 CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG-GTGCCACTGACTTGTGG
* * *
1570519 GCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGAGCTTTGAA
194 GCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-A
* * *
1570584 AAGAGTGCCACTCATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTG
258 AAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTG
* *
1570649 CCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC
323 CCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTCGTGGGCTTTGAAAGGA-TGCCACTGAC
*
1570713 TCGTGGGCTTTGAAATG-GTACCACTGACTCGTGGGCTTTGAAATGGTACCACTGACTTGCGTGA
387 TCGTGGGCTTTGAAA-GAGTACCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGA
1570777 GCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG
451 GCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
1570842 AAAAAGTGCCACTGAATTGTGGGCTTCGCAATGGTGCCACTGACTTATGGGCTTCGAAAGGGTGC
516 AAAAAGTGCCACTAAATTGTGGGCTTCGCAATGGTGCCACTGACCTATGGGCTTCGAAAGGGTGC
1570907 CACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTG
581 CACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTG
* * *
1570954 AAAAGGTGTCACTGACTTGTGGGCTTTGAAAATAGTGCCACTGATTTATGGGCTTTGAAAAAAGT
1 AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAAAGTGCCACTGATTTGTGGGCTTTGAAAAAAGT
*
1571019 GCCACTAACTTGTGGGCTTTGAAAGGAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAA
66 GCCACTGACTTGTGGGCTTTGAAAGGAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAA
*
1571084 CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGCGCTTTGAAAGGGTGCCACTGACTTGTGGG
131 CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACTTGTGGG
*
1571149 CTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAA
195 CTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
* ** *
1571214 GGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGTTTTGTGGGCTTTGAAAGGAGTACC
260 GAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCC
1571279 ACTGACTTGTGGGCTTTGAAA
325 ACTGACTTGTGGGCTTTGAAA
1571300 GGGATGAACA
Statistics
Matches: 906, Mismatches: 58, Indels: 31
0.91 0.06 0.03
Matches are distributed among these distances:
627 35 0.04
628 123 0.14
629 97 0.11
630 496 0.55
631 19 0.02
632 64 0.07
633 42 0.05
634 12 0.01
635 17 0.02
636 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (627 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTGAAAAAAGTGCCACTGATTTGTGGGCTTTGAAAAAAGT
GCCACTGACTTGTGGGCTTTGAAAGGAGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAA
CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGTGCCACTGACTTGTGGGC
TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
AGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCA
CTGACTTGTGGGCTTTGAAAAGATGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTCGT
GGGCTTTGAAAGAGTACCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGCGTGAGCTTT
AAAAGGAGTGCCACTGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAA
GTGCCACTAAATTGTGGGCTTCGCAATGGTGCCACTGACCTATGGGCTTCGAAAGGGTGCCACTG
ACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTG
Found at i:1571300 original size:29 final size:29
Alignment explanation
Indices: 1569694--1571301 Score: 1978
Period size: 28 Copynumber: 56.0 Consensus size: 29
1569684 TAAAAAAAAT
**
1569694 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAA
1 GTGCCACTGA-CTTGTG--GGCTTTGAAAGGA
* * *
1569725 GTTGCCACTGACACATGTGGGCTTCGAAAAGA
1 G-TGCCACTG--ACTTGTGGGCTTTGAAAGGA
** *
1569757 GTGTTACTGACTTGCGTGGGCTTTAAAAGG-
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
1569787 GTGCCACTGACTTGCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
*
1569818 -TGCCACTGACTCGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1569845 GTGCCACTGACTTGTGGGCTTTGAAA-G-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1569872 GTGCCACTGACTCGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1569900 GTACCACTGACTCGTGGGC-TTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1569927 GTGCCACTGACTTGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1569955 GTGCCACTGACTCGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1569983 GTGCCACTTACTTGCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
1570014 GTGCCACTGACTTGTGTGGGCTTTGAAAGG-
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGA
* *
1570044 GTGCCACTAACTCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1570073 -TGCCACTGACTTGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1570100 GTGCCACTGACTCGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
1570128 GTACCACTGACTTGCGTGAGCTTTAAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
1570159 GTGCCACTGACTTGTGTGGGCTTT-AAACGG-
1 GTGCCACTGAC-T-TGTGGGCTTTGAAA-GGA
1570189 GTGCCACTGACTTGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * * *
1570217 GTGCCACTAAATTGTGGGCTTCGCAATG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1570245 GTGCCACTGACCTGTGGGCTTCGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1570273 GTGCCACTGACTTGTGGGCTCTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1570301 GTGCCACTAACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1570329 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * **
1570358 GTGCCACTGATTTGTGGGTTTTGAAAAAA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1570387 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1570416 GTGCCATTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1570444 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1570473 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1570502 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1570531 GTGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
1570559 GTGCCATTGACTTGTGAGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1570588 GTGCCACTCATTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1570617 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1570646 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1570675 -TGCCACTGACTTGTGGGCTTTGAAA-GA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1570702 GTGCCACTGACTCGTGGGCTTTGAAATG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
1570730 GTACCACTGACTCGTGGGCTTTGAAATG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
1570758 GTACCACTGACTTGCGTGAGCTTTAAAAGGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAGGA
*
1570789 GTGCCACTGACTTGTGTGGGCTTTAAAAGG-
1 GTGCCACTGAC-T-TGTGGGCTTTGAAAGGA
*
1570819 GTGCCACTGACTTGTGGGCTTTGAAA-AA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * * *
1570847 GTGCCACTGAATTGTGGGCTTCGCAATG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1570875 GTGCCACTGACTTATGGGCTTCGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1570903 GTGCCACTGACTTGTGGGCTCTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1570931 GTGCCACTAACTTGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* **
1570959 GTGTCACTGACTTGTGGGCTTTGAAAATA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* * **
1570988 GTGCCACTGATTTATGGGCTTTGAAAAAA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1571017 GTGCCACTAACTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1571046 GTGCCATTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
* *
1571074 GTGCCACTAACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1571103 GTGCCACTGACTTGTGCGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1571131 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
1571160 GTGCCACTGACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1571188 GTGCCACTAACTTGTGGGCTTTGAAAGG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1571216 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
**
1571245 GTGCCACTGTTTTGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGGA
*
1571274 GTACCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGG
1571302 GATGAACATT
Statistics
Matches: 1398, Mismatches: 134, Indels: 92
0.86 0.08 0.06
Matches are distributed among these distances:
27 57 0.04
28 681 0.49
29 430 0.31
30 111 0.08
31 88 0.06
32 22 0.02
33 3 0.00
34 5 0.00
35 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:1572532 original size:1 final size:1
Alignment explanation
Indices: 1572528--1572587 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
1572518 TTTTTTGCTA
* ** * * * *
1572528 TTTTTTTCTTTTTTTTTGGTTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1572588 GGGTGTAAAG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (1 bp):
T
Found at i:1572573 original size:24 final size:24
Alignment explanation
Indices: 1572531--1572587 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 24
1572521 TTTGCTATTT
1572531 TTTTCTTTTTTTTTGGTTTTTTTTG
1 TTTT-TTTTTTTTTGGTTTTTTTTG
1572556 TTTTGTTTTTTTTT-GTTTTTTTTG
1 TTTT-TTTTTTTTTGGTTTTTTTTG
1572580 TTTTTTTT
1 TTTTTTTT
1572588 GGGTGTAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 4 0.13
24 14 0.45
25 13 0.42
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.88
Consensus pattern (24 bp):
TTTTTTTTTTTTTGGTTTTTTTTG
Found at i:1572586 original size:10 final size:10
Alignment explanation
Indices: 1572518--1572587 Score: 62
Period size: 10 Copynumber: 7.5 Consensus size: 10
1572508 GACCCTTCTA
*
1572518 TTTTTTGCTAT
1 TTTTTTG-TTT
*
1572529 TTTTTTCTTT
1 TTTTTTGTTT
*
1572539 TTTTTTGGTT
1 TTTTTTGTTT
1572549 TTTTTTG---
1 TTTTTTGTTT
1572556 --TTTTGTTT
1 TTTTTTGTTT
1572564 TTTTTTG-TT
1 TTTTTTGTTT
1572573 TTTTTTGTTT
1 TTTTTTGTTT
1572583 TTTTT
1 TTTTT
1572588 GGGTGTAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
5 5 0.10
9 9 0.18
10 29 0.59
11 6 0.12
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:1572588 original size:9 final size:9
Alignment explanation
Indices: 1572518--1572588 Score: 67
Period size: 9 Copynumber: 7.8 Consensus size: 9
1572508 GACCCTTCTA
1572518 TTTTTTGCTAT
1 TTTTTTG-T-T
*
1572529 TTTTTTCTTT
1 TTTTTT-GTT
1572539 TTTTTTGGTT
1 TTTTTT-GTT
1572549 TTTTTTG--
1 TTTTTTGTT
*
1572556 TTTTGT-TT
1 TTTTTTGTT
1572564 TTTTTTGTT
1 TTTTTTGTT
1572573 TTTTTTGTT
1 TTTTTTGTT
1572582 TTTTTTG
1 TTTTTTG
1572589 GGTGTAAAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
7 5 0.10
8 5 0.10
9 19 0.37
10 15 0.29
11 7 0.14
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:1582319 original size:23 final size:23
Alignment explanation
Indices: 1582293--1582337 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1582283 ATAATGGGAA
*
1582293 TGAATAGCAAAAAAAAAAAAAAT
1 TGAACAGCAAAAAAAAAAAAAAT
* **
1582316 TGAACATCAATCAAAAAAAAAA
1 TGAACAGCAAAAAAAAAAAAAA
1582338 GTGGCCCTTC
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:0.71, C:0.09, G:0.07, T:0.13
Consensus pattern (23 bp):
TGAACAGCAAAAAAAAAAAAAAT
Found at i:1586617 original size:20 final size:20
Alignment explanation
Indices: 1586570--1586644 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1586560 AAAAAGACAT
*
1586570 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1586589 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1586610 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1586630 AATGTATCGATACAT
1 AATGTATCGATACAT
1586645 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1586638 original size:40 final size:39
Alignment explanation
Indices: 1586567--1586644 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1586557 GGTAAAAAGA
* *
1586567 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1586606 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1586645 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1593450 original size:28 final size:28
Alignment explanation
Indices: 1593401--1593456 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1593391 ATATTACAAG
**
1593401 TTACATAAAACATTACGTTTACATATAA
1 TTACATAAAACATTACAATTACATATAA
1593429 TTACATAAAA-ATTACAAATTACATATAA
1 TTACATAAAACATTAC-AATTACATATAA
1593457 ATACTCTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.34
Consensus pattern (28 bp):
TTACATAAAACATTACAATTACATATAA
Found at i:1593481 original size:54 final size:55
Alignment explanation
Indices: 1593413--1593516 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 55
1593403 ACATAAAACA
*
1593413 TTACGTTTACATATAATTACATAAAA-ATTACAAATTACATATAAATACTCTTGG
1 TTACATTTACATATAATTACATAAAATATTACAAATTACATATAAATACTCTTGG
* **
1593467 TTACATTTACATATAATTACATAAAATATTATAAATTATGTATAAATACT
1 TTACATTTACATATAATTACATAAAATATTACAAATTACATATAAATACT
1593517 ATCAATTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 25 0.56
55 20 0.44
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (55 bp):
TTACATTTACATATAATTACATAAAATATTACAAATTACATATAAATACTCTTGG
Found at i:1593526 original size:55 final size:54
Alignment explanation
Indices: 1593412--1593527 Score: 151
Period size: 55 Copynumber: 2.1 Consensus size: 54
1593402 TACATAAAAC
* * **
1593412 ATTACGTTTACATATAATTACATAAAAATTACAAATTACATATAAATACTCTTG
1 ATTACATTTACATATAATTACATAAAAATTACAAATTACATATAAATACTATCA
* * **
1593466 GTTACATTTACATATAATTACATAAAATATTATAAATTATGTATAAATACTATCA
1 ATTACATTTACATATAATTACATAAAA-ATTACAAATTACATATAAATACTATCA
1593521 ATTACAT
1 ATTACAT
1593528 AAAATATTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
54 25 0.48
55 27 0.52
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (54 bp):
ATTACATTTACATATAATTACATAAAAATTACAAATTACATATAAATACTATCA
Found at i:1593594 original size:20 final size:20
Alignment explanation
Indices: 1593569--1593624 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1593559 ATGTTATAAA
*
1593569 TTACATATAAACTTTACAAG
1 TTACATATAAACATTACAAG
*
1593589 TTACATGTAAACATTACAAG
1 TTACATATAAACATTACAAG
*
1593609 TTACATA-AAAAATTAC
1 TTACATATAAACATTAC
1593625 CTTTACATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 8 0.25
20 24 0.75
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.32
Consensus pattern (20 bp):
TTACATATAAACATTACAAG
Found at i:1593724 original size:66 final size:67
Alignment explanation
Indices: 1593567--1593731 Score: 199
Period size: 66 Copynumber: 2.5 Consensus size: 67
1593557 AAATGTTATA
* * * *
1593567 AATTACATATAAACTTTACAAGTTACATG-TAAACATTACAAGTTACATAAAAAATTACCTTTAC
1 AATTACATA-AAACATTACAAATTATA-GATAAGCATTACAAGTTACATAAAAAATTACCTTTAC
1593631 ATGT
64 ATGT
* * *
1593635 AATTACATAAAACATTACCAATTATAGATAAGCATTACAAGTTATATAAAACA-TACCTTTACAT
1 AATTACATAAAACATTACAAATTATAGATAAGCATTACAAGTTACATAAAAAATTACCTTTACAT
1593699 GT
66 GT
** * *
1593701 AATTACATAAATTATTAGAAATTATATATAA
1 AATTACATAAAACATTACAAATTATAGATAA
1593732 ATAATAATAG
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
66 40 0.48
67 35 0.42
68 9 0.11
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (67 bp):
AATTACATAAAACATTACAAATTATAGATAAGCATTACAAGTTACATAAAAAATTACCTTTACAT
GT
Found at i:1593744 original size:66 final size:67
Alignment explanation
Indices: 1593567--1593756 Score: 188
Period size: 66 Copynumber: 2.8 Consensus size: 67
1593557 AAATGTTATA
* * * * *
1593567 AATTACATATAAACTTTACAAGTTACATG-TAAACATTACAAGTTACATAAAAAATTACCTTTAC
1 AATTACATA-AAACATTACAAATTATA-GATAAACAATACAAGTTATATAAAAAATTACCTTTAC
1593631 ATGT
64 ATGT
* * * *
1593635 AATTACATAAAACATTACCAATTATAGATAAGCATTACAAGTTATATAAAACA-TACCTTTACAT
1 AATTACATAAAACATTACAAATTATAGATAAACAATACAAGTTATATAAAAAATTACCTTTACAT
1593699 GT
66 GT
** * * * *
1593701 AATTACATAAATTATTAGAAATTATATATAAATAATA-ATAGTTACATATAAAAATT
1 AATTACATAAAACATTACAAATTATAGATAAACAATACA-AGTTATATA-AAAAATT
1593757 TCTTTAACTG
Statistics
Matches: 101, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
65 1 0.01
66 51 0.50
67 39 0.39
68 10 0.10
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (67 bp):
AATTACATAAAACATTACAAATTATAGATAAACAATACAAGTTATATAAAAAATTACCTTTACAT
GT
Found at i:1600749 original size:19 final size:19
Alignment explanation
Indices: 1600706--1600760 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
1600696 GCCAGTTTCG
**
1600706 TGTATCGATACAATTTGTCCA
1 TGTATCGATACAA--TGAACA
1600727 TGTATCGATACAATGAACA
1 TGTATCGATACAATGAACA
1600746 TGTATCGATACAATG
1 TGTATCGATACAATG
1600761 TATCGATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 19 0.59
21 13 0.41
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAATGAACA
Found at i:1600763 original size:13 final size:13
Alignment explanation
Indices: 1600745--1600771 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1600735 TACAATGAAC
1600745 ATGTATCGATACA
1 ATGTATCGATACA
1600758 ATGTATCGATACA
1 ATGTATCGATACA
1600771 A
1 A
1600772 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1600786 original size:33 final size:32
Alignment explanation
Indices: 1600726--1600790 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1600716 CAATTTGTCC
*
1600726 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
1600758 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
1600791 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1601329 original size:16 final size:17
Alignment explanation
Indices: 1601308--1601342 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1601298 GTTTTCGTTT
1601308 TTCT-CCCCTTAAAAAA
1 TTCTCCCCCTTAAAAAA
*
1601324 TTCTCCCCCTTAAACAA
1 TTCTCCCCCTTAAAAAA
1601341 TT
1 TT
1601343 ATCTTCTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (17 bp):
TTCTCCCCCTTAAAAAA
Found at i:1602623 original size:19 final size:19
Alignment explanation
Indices: 1602588--1602639 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 19
1602578 CTATAGACCC
*
1602588 TAATTCATATCAAACAAACA
1 TAATTCA-ATCATACAAACA
1602608 TAATTCAATCATAC-AACA
1 TAATTCAATCATACAAACA
1602626 TAA--CAATCAT-CAAA
1 TAATTCAATCATACAAA
1602640 ATTCATTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 1 0.03
16 9 0.30
18 7 0.23
19 6 0.20
20 7 0.23
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (19 bp):
TAATTCAATCATACAAACA
Found at i:1607965 original size:17 final size:18
Alignment explanation
Indices: 1607939--1607973 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1607929 GAATTTTTCC
*
1607939 AAATTTGAAAGA-AAAAT
1 AAATTCGAAAGACAAAAT
1607956 AAATTCGAAAGACAAAAT
1 AAATTCGAAAGACAAAAT
1607974 GAAGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.63, C:0.06, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATTCGAAAGACAAAAT
Found at i:1608629 original size:20 final size:20
Alignment explanation
Indices: 1608604--1608656 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1608594 GTTACAAGCT
1608604 ATGTATCGATACATT-T-CTTC
1 ATGTATCGATACATTGTAC--C
1608624 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
1608644 ATGTATCGATACA
1 ATGTATCGATACA
1608657 AATAGTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:1608731 original size:19 final size:20
Alignment explanation
Indices: 1608686--1608739 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
1608676 CTGCTAGTTT
**
1608686 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA-TTGAA
1608707 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
1608726 CATGTATTGATACA
1 CATGTATCGATACA
1608740 TTGCATCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1608753 original size:32 final size:33
Alignment explanation
Indices: 1608712--1608773 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1608702 TTGTCCATGT
* *
1608712 ATCGATACAATG-AACATGTATTGATACATTGC
1 ATCGATACAAAGCAACATGTATCGATACATTGC
*
1608744 ATCGATACAAAGCAGCATGTATCGATACAT
1 ATCGATACAAAGCAACATGTATCGATACAT
1608774 CTGGGTGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (33 bp):
ATCGATACAAAGCAACATGTATCGATACATTGC
Found at i:1611939 original size:20 final size:20
Alignment explanation
Indices: 1611914--1611960 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1611904 GAAGGTGCTG
1611914 AACATGCTGT-AAATGCATGA
1 AACATGCT-TAAAATGCATGA
1611934 AACATGGCTTAAAATGCATGA
1 AACAT-GCTTAAAATGCATGA
*
1611955 ATCATG
1 AACATG
1611961 GGCTGTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (20 bp):
AACATGCTTAAAATGCATGA
Found at i:1612995 original size:32 final size:32
Alignment explanation
Indices: 1612954--1613022 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
1612944 CTTTGTAGCA
1612954 ATACATTGTATCGAAACAACACTTATGTATCG
1 ATACATTGTATCGAAACAACACTTATGTATCG
*
1612986 ATACATTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGAAACAACACTTATGTATCG
1613018 ATACA
1 ATACA
1613023 GTTACTGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (32 bp):
ATACATTGTATCGAAACAACACTTATGTATCG
Found at i:1612997 original size:13 final size:13
Alignment explanation
Indices: 1612979--1613003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1612969 ACAACACTTA
1612979 TGTATCGATACAT
1 TGTATCGATACAT
1612992 TGTATCGATACA
1 TGTATCGATACA
1613004 ACACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1613019 original size:19 final size:19
Alignment explanation
Indices: 1612960--1613022 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
1612950 AGCAATACAT
*
1612960 TGTATCGAAACAACACTTA
1 TGTATCGATACAACACTTA
1612979 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1612992 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1613011 TGTATCGATACA
1 TGTATCGATACA
1613023 GTTACTGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 20 0.54
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1615191 original size:22 final size:24
Alignment explanation
Indices: 1615161--1615205 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1615151 CCTCTCAATC
*
1615161 TCTTCAAGA-ATTATACCCCAAAT
1 TCTTCAAGAGATTATAACCCAAAT
*
1615184 TCTT-AAGAGATTGTAACCCAAA
1 TCTTCAAGAGATTATAACCCAAA
1615206 GTTAAATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (24 bp):
TCTTCAAGAGATTATAACCCAAAT
Found at i:1615741 original size:13 final size:13
Alignment explanation
Indices: 1615723--1615747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1615713 GCCAAGATCA
1615723 TGTATCGATACAG
1 TGTATCGATACAG
1615736 TGTATCGATACA
1 TGTATCGATACA
1615748 AAGTAATAAG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1619549 original size:21 final size:21
Alignment explanation
Indices: 1619523--1619565 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1619513 GTTATGTGTA
1619523 TACTTAAATCAACCTATCTTT
1 TACTTAAATCAACCTATCTTT
1619544 TACTTAAATCAACCTATCTTT
1 TACTTAAATCAACCTATCTTT
1619565 T
1 T
1619566 TTATCTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (21 bp):
TACTTAAATCAACCTATCTTT
Found at i:1622745 original size:11 final size:11
Alignment explanation
Indices: 1622716--1622776 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
1622706 TATTAATTTT
1622716 AAATATAATATA
1 AAATATAATA-A
*
1622728 ATTATATAATAA
1 A-AATATAATAA
*
1622740 AAATATAATTA
1 AAATATAATAA
* *
1622751 AATTAAAATATA
1 AAATATAATA-A
1622763 AAATAATAATAA
1 AAAT-ATAATAA
1622775 AA
1 AA
1622777 TAACATCACA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 15 0.39
12 10 0.26
13 13 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATAATAA
Found at i:1622747 original size:24 final size:24
Alignment explanation
Indices: 1622716--1622777 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
1622706 TATTAATTTT
1622716 AAATATAATAT-AATTATATAATA-A
1 AAATATAATATAAATTA-A-AATATA
1622740 AAATATAAT-TAAATTAAAATATA
1 AAATATAATATAAATTAAAATATA
1622763 AAATAATAATA-AAAT
1 AAAT-ATAATATAAAT
1622778 AACATCACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
22 4 0.12
23 7 0.21
24 23 0.68
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AAATATAATATAAATTAAAATATA
Found at i:1622760 original size:40 final size:41
Alignment explanation
Indices: 1622702--1622779 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
1622692 TATCTCAATT
* * * * *
1622702 TATATATTAATTTTAAATATAATATAATTATATAATAAAAA
1 TATATATTAAATTAAAATATAAAATAATAATAAAATAAAAA
1622743 TATA-ATTAAATTAAAATATAAAATAATAATAAAATAA
1 TATATATTAAATTAAAATATAAAATAATAATAAAATAA
1622780 CATCACATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (41 bp):
TATATATTAAATTAAAATATAAAATAATAATAAAATAAAAA
Found at i:1622881 original size:18 final size:18
Alignment explanation
Indices: 1622858--1622897 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1622848 TTATTATAAT
* *
1622858 TAATAAAAAATATAATTA
1 TAATAAAAAATAAAAATA
1622876 TAATAAAAAATAAAAATA
1 TAATAAAAAATAAAAATA
1622894 TAAT
1 TAAT
1622898 CTTATCCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATAAAAAATAAAAATA
Found at i:1630589 original size:29 final size:28
Alignment explanation
Indices: 1630556--1630615 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
1630546 AAATTTAAAA
1630556 ATAAT-TTTTCTTACTT-TTTTAAAGTTTAG
1 ATAATATTTT-TT-CTTCTTTTAAAGTTT-G
*
1630585 ATAATATTTTTTTTTCTTTTAAAGTTTG
1 ATAATATTTTTTCTTCTTTTAAAGTTTG
1630613 ATA
1 ATA
1630616 TAAAATGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 6 0.21
29 18 0.64
30 4 0.14
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (28 bp):
ATAATATTTTTTCTTCTTTTAAAGTTTG
Found at i:1630594 original size:31 final size:29
Alignment explanation
Indices: 1630539--1630615 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 29
1630529 TATATTATGA
* *
1630539 TTTTTTAAAATTTA-AAAATAATTTTTCTT
1 TTTTTTAAAGTTTAGATAATAATTTTT-TT
1630568 ACTTTTTTAAAGTTTAGATAAT-ATTTTTTT
1 --TTTTTTAAAGTTTAGATAATAATTTTTTT
1630598 TTCTTTTAAAGTTT-GATA
1 TT-TTTTAAAGTTTAGATA
1630616 TAAAATGTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 6 0.14
29 11 0.26
30 2 0.05
31 19 0.45
32 4 0.10
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTTTTAAAGTTTAGATAATAATTTTTTT
Found at i:1630640 original size:32 final size:29
Alignment explanation
Indices: 1630572--1630641 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1630562 TTTCTTACTT
* * *
1630572 TTTTAAAGTTTAGATAATATTTTTTTTTC
1 TTTTAAAGTTTAGATAAAATTGTTTTATC
*
1630601 TTTTAAAGTTTGATATAAAATGTGTTTTATC
1 TTTTAAAGTTT-AGATAAAAT-TGTTTTATC
1630632 TCTTTAAAGT
1 T-TTTAAAGT
1630642 ATTACTTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.32
30 7 0.21
31 8 0.24
32 8 0.24
ACGTcount: A:0.30, C:0.04, G:0.10, T:0.56
Consensus pattern (29 bp):
TTTTAAAGTTTAGATAAAATTGTTTTATC
Found at i:1631241 original size:14 final size:14
Alignment explanation
Indices: 1631219--1631264 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1631209 TAATTAATTA
1631219 ATTTAAATAAATAT
1 ATTTAAATAAATAT
*
1631233 ATTTTAATAAATAT
1 ATTTAAATAAATAT
*
1631247 ATTTCAAAGTTAATAT
1 ATTT-AAA-TAAATAT
1631263 AT
1 AT
1631265 AATTAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 17 0.63
15 2 0.07
16 8 0.30
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTTAAATAAATAT
Found at i:1632041 original size:23 final size:21
Alignment explanation
Indices: 1632005--1632062 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
1631995 CAAAATCATT
*
1632005 AAAATA-AAATTATTCAAAAATA
1 AAAATATATATTATT-AAAAA-A
1632027 AAAATATATATTATTAAAAAA
1 AAAATATATATTATTAAAAAA
1632048 ATAAA-ATATATTATT
1 A-AAATATATATTATT
1632063 TTTATTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 12 0.36
22 14 0.42
23 7 0.21
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATATATATTATTAAAAAA
Found at i:1632045 original size:21 final size:21
Alignment explanation
Indices: 1632004--1632062 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
1631994 TCAAAATCAT
*
1632004 TAAAATAAAATTATTCAAAAATAA
1 TAAAAT-ATATTATT-AAAAA-AA
1632028 -AAATATATATTATTAAAAAAA
1 TAAA-ATATATTATTAAAAAAA
1632049 TAAAATATATTATT
1 TAAAATATATTATT
1632063 TTTATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 12 0.38
22 8 0.25
23 10 0.31
24 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAATATATTATTAAAAAAA
Found at i:1634726 original size:17 final size:17
Alignment explanation
Indices: 1634704--1634739 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1634694 CATTTCATAT
* *
1634704 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
1634721 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
1634738 TT
1 TT
1634740 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Done.