Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 4 of 103
Found at i:1517470 original size:2 final size:2
Alignment explanation
Indices: 1517463--1517494 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1517453 TATGTATGAA
*
1517463 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1517495 TATTTCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1517804 original size:19 final size:19
Alignment explanation
Indices: 1517782--1517819 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1517772 TATTATATAA
1517782 AATTTTTAAAATTTTTTAT
1 AATTTTTAAAATTTTTTAT
*
1517801 AATTTTTATAATTTTTTAT
1 AATTTTTAAAATTTTTTAT
1517820 TTAGTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
AATTTTTAAAATTTTTTAT
Found at i:1517806 original size:8 final size:9
Alignment explanation
Indices: 1517782--1517816 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1517772 TATTATATAA
*
1517782 AATTTTTAA
1 AATTTTTAT
1517791 AATTTTTTAT
1 AA-TTTTTAT
1517801 AATTTTTAT
1 AATTTTTAT
1517810 AATTTTT
1 AATTTTT
1517817 TATTTAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
AATTTTTAT
Found at i:1517817 original size:10 final size:10
Alignment explanation
Indices: 1517784--1517819 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1517774 TTATATAAAA
*
1517784 TTTTTAAAAT
1 TTTTTATAAT
1517794 TTTTTATAA-
1 TTTTTATAAT
1517803 TTTTTATAAT
1 TTTTTATAAT
1517813 TTTTTAT
1 TTTTTAT
1517820 TTAGTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:1518568 original size:41 final size:41
Alignment explanation
Indices: 1518511--1518593 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
1518501 AAATCTAAAT
*
1518511 CTATCATAACATATTATATCTTAACAG-TCTAACCTAATAAC
1 CTATCATAACATATTATATCTTAACAGCTC-AACCCAATAAC
* *
1518552 CTATCATAATATATTATATCTTAATAGCTCAACCCAATAAC
1 CTATCATAACATATTATATCTTAACAGCTCAACCCAATAAC
1518593 C
1 C
1518594 CAATATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 36 0.95
42 2 0.05
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (41 bp):
CTATCATAACATATTATATCTTAACAGCTCAACCCAATAAC
Found at i:1533412 original size:2 final size:2
Alignment explanation
Indices: 1533405--1533434 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1533395 TCATCTCTAT
*
1533405 TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1533435 ACGCTTGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1535288 original size:15 final size:15
Alignment explanation
Indices: 1535242--1535289 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1535232 TATTTAAATT
* *
1535242 TAAAATAAATAATTA
1 TAAAAAAAATAATAA
* *
1535257 TAAAAACAATTATAA
1 TAAAAAAAATAATAA
*
1535272 TAAAAAAAATAACAA
1 TAAAAAAAATAATAA
1535287 TAA
1 TAA
1535290 CATCAAATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAAAAAATAATAA
Found at i:1540049 original size:2 final size:2
Alignment explanation
Indices: 1540042--1540071 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1540032 CTCTTTTTCC
1540042 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1540072 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1540264 original size:2 final size:2
Alignment explanation
Indices: 1540257--1540286 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1540247 CCTTCCTTTC
1540257 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1540287 TTCTGTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1542292 original size:2 final size:2
Alignment explanation
Indices: 1542285--1542330 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1542275 AGAAGCAATA
1542285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1542325 A- AT AT A
1 AT AT AT A
1542331 GTACTTAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1555143 original size:19 final size:19
Alignment explanation
Indices: 1555121--1555158 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1555111 TCACATAATT
*
1555121 ATATCATCATGTCA-TATTA
1 ATAT-ATCACGTCATTATTA
1555140 ATATATCACGTCATTATTA
1 ATATATCACGTCATTATTA
1555159 CGTCACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (19 bp):
ATATATCACGTCATTATTA
Found at i:1555256 original size:30 final size:28
Alignment explanation
Indices: 1555220--1555315 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 28
1555210 TCATGCACTC
1555220 TTATTTAATTTAAAGTAAAAATATAAAAAT
1 TTATTTAATTTAAA-T-AAAATATAAAAAT
* *
1555250 TTATTTAATTTTAAATAAATTACAAAAAT
1 TTATTTAA-TTTAAATAAAATATAAAAAT
*
1555279 TTAATTT-TTTATGAAATAAAA-ATAAAAAT
1 TT-ATTTAATT-T-AAATAAAATATAAAAAT
1555308 TTATTTAA
1 TTATTTAA
1555316 AATTTTTGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
28 6 0.11
29 23 0.42
30 20 0.36
31 6 0.11
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (28 bp):
TTATTTAATTTAAATAAAATATAAAAAT
Found at i:1569219 original size:31 final size:31
Alignment explanation
Indices: 1569160--1569221 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1569150 AAAGGCAAGT
*
1569160 AAGAAGAAGCTCACAACTTTCCTGCGGTGAC
1 AAGAAGAAGCTCACAACTTTCATGCGGTGAC
* * *
1569191 AAGAAGAAGCTCATAACTTTTATTCGGTGAC
1 AAGAAGAAGCTCACAACTTTCATGCGGTGAC
1569222 CAGGTCTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (31 bp):
AAGAAGAAGCTCACAACTTTCATGCGGTGAC
Found at i:1569470 original size:2 final size:2
Alignment explanation
Indices: 1569463--1569491 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1569453 AAGCGCCACC
1569463 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1569492 GTTAGCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1599484 original size:40 final size:40
Alignment explanation
Indices: 1599429--1599507 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
1599419 TTGGCTATTT
1599429 TTCACCTTAGTGGGGTTTTCAACCT-TGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCT-CCAAGATTGGTGA
*
1599469 TTCACCTTAGTGGGGTTTTCAACCTCTCCACGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCTCCAAGATTGGTG
1599508 TTTTTCATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCTCCAAGATTGGTGA
Found at i:1601360 original size:74 final size:74
Alignment explanation
Indices: 1601239--1601384 Score: 258
Period size: 74 Copynumber: 2.0 Consensus size: 74
1601229 TAAAGCACTC
*
1601239 ATCACTGTGCCTAGCTTAAGCAAAGCTTATTGTGAGTCAAACCATTTATG-TCTCTTATTAGTCT
1 ATCACTGTGCCTAGCTTAAGCAAAGCTTATTGTGAGTCAAACAATTTATGCTCTCTTATTAGTCT
1601303 CTAAAGNCTT
66 CTAAAG-CTT
1601313 ATCACTGTGCCTAGCTTAAGCAAAGCTTATTGTGAGTCAAACAATTTATGTCTCTCTTATTAGTC
1 ATCACTGTGCCTAGCTTAAGCAAAGCTTATTGTGAGTCAAACAATTTATG-CTCTCTTATTAGTC
1601378 TCTAAAG
65 TCTAAAG
1601385 AGAATAAAGT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
74 49 0.71
76 20 0.29
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (74 bp):
ATCACTGTGCCTAGCTTAAGCAAAGCTTATTGTGAGTCAAACAATTTATGCTCTCTTATTAGTCT
CTAAAGCTT
Found at i:1601859 original size:23 final size:24
Alignment explanation
Indices: 1601811--1601861 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1601801 AATTTAGTTG
* *
1601811 ATTTAAGATTATTTTCTTTATTTT
1 ATTTAAGATTATATTCTTTATCTT
1601835 ATTT-AGATTAGTATTCTTT-TCTT
1 ATTTAAGATTA-TATTCTTTATCTT
1601858 ATTT
1 ATTT
1601862 TTATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (24 bp):
ATTTAAGATTATATTCTTTATCTT
Found at i:1602226 original size:40 final size:40
Alignment explanation
Indices: 1602171--1602249 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
1602161 TTGGCTATTT
*
1602171 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
*
1602211 TTCACCTTAGTGGGGTTTTCAACCTCGCCACGATTGGTG
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTG
1602250 TTTTTCATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.34
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:1610194 original size:20 final size:20
Alignment explanation
Indices: 1610169--1610206 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1610159 TAAATTTTAA
1610169 AAATTATTAAA-AAAAATTTT
1 AAATTA-TAAATAAAAATTTT
1610189 AAATTATAAATAAAAATT
1 AAATTATAAATAAAAATT
1610207 CAAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTATAAATAAAAATTTT
Found at i:1610212 original size:20 final size:20
Alignment explanation
Indices: 1610168--1610212 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1610158 TTAAATTTTA
*
1610168 AAAATTATTAAAAAAAATTT
1 AAAATTATTAAAAAAAATTC
*
1610188 TAAATTA-TAAATAAAAATTC
1 AAAATTATTAAA-AAAAATTC
1610208 AAAAT
1 AAAAT
1610213 AATTCGATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTATTAAAAAAAATTC
Found at i:1613368 original size:27 final size:26
Alignment explanation
Indices: 1613338--1613416 Score: 91
Period size: 22 Copynumber: 3.3 Consensus size: 26
1613328 AGATTTTTTT
1613338 AATATTAATAATTTAAAATTTAATTAA
1 AATATTAATAATTTAAAATTTAATT-A
*
1613365 AATATTAATAA-TTAATA-TT--TTA
1 AATATTAATAATTTAAAATTTAATTA
1613387 AATATTAAT-ATTT--AATTTAATTA
1 AATATTAATAATTTAAAATTTAATTA
1613410 AATATTA
1 AATATTA
1613417 TTATGATCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
20 1 0.02
21 3 0.07
22 12 0.26
23 12 0.26
25 2 0.04
26 5 0.11
27 11 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATATTAATAATTTAAAATTTAATTA
Found at i:1613376 original size:15 final size:15
Alignment explanation
Indices: 1613338--1613379 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1613328 AGATTTTTTT
*
1613338 AATATTAATAATTTA
1 AATATTAATAATTAA
1613353 AA-ATT--TAATTAA
1 AATATTAATAATTAA
1613365 AATATTAATAATTAA
1 AATATTAATAATTAA
1613380 TATTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 3 0.13
15 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATATTAATAATTAA
Found at i:1613387 original size:15 final size:15
Alignment explanation
Indices: 1613358--1613399 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1613348 ATTTAAAATT
* *
1613358 TAATTAAAATATTAA
1 TAATTAATATTTTAA
1613373 TAATTAATATTTTAA
1 TAATTAATATTTTAA
1613388 -ATATTAATATTT
1 TA-ATTAATATTT
1613400 AATTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTAATATTTTAA
Found at i:1613981 original size:26 final size:26
Alignment explanation
Indices: 1613940--1613994 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
1613930 NNNNNNNNNN
*
1613940 TATAATTTAAATATTAATATTTTATT
1 TATAATTTAAATATTAATATTTTAAT
1613966 TATAATTT-AATCATTAATATTTTAAT
1 TATAATTTAAAT-ATTAATATTTTAAT
1613992 TAT
1 TAT
1613995 TAATAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TATAATTTAAATATTAATATTTTAAT
Found at i:1613991 original size:15 final size:14
Alignment explanation
Indices: 1613941--1614004 Score: 62
Period size: 15 Copynumber: 4.6 Consensus size: 14
1613931 NNNNNNNNNT
1613941 ATAATTTAAATATTA
1 ATAATTT-AATATTA
*
1613956 AT-ATTT--TATTT
1 ATAATTTAATATTA
1613967 ATAATTTAATCATTA
1 ATAATTTAAT-ATTA
*
1613982 ATATTTTAATTATTA
1 ATAATTTAA-TATTA
1613997 ATAATTTA
1 ATAATTTA
1614005 TTTAATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
11 6 0.15
12 4 0.10
14 5 0.12
15 24 0.60
16 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
ATAATTTAATATTA
Found at i:1614024 original size:41 final size:41
Alignment explanation
Indices: 1613945--1614019 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1613935 NNNNNTATAA
*
1613945 TTTAAATATTAATATTTTATTTATAATTTAATCATTAATAT
1 TTTAAATATTAATAATTTATTTATAATTTAATCATTAATAT
*
1613986 TTTAATTATTAATAATTTA-TT-TAATTTAAT-ATTA
1 TTTAAATATTAATAATTTATTTATAATTTAATCATTA
1614020 TTAATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
38 4 0.12
39 9 0.28
40 2 0.06
41 17 0.53
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (41 bp):
TTTAAATATTAATAATTTATTTATAATTTAATCATTAATAT
Found at i:1614046 original size:26 final size:25
Alignment explanation
Indices: 1613983--1614047 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
1613973 TAATCATTAA
1613983 TATTTTA-ATTATTAATAATTTATT
1 TATTTTATATTATTAATAATTTATT
*
1614007 TAATTTAATATTATTAATTAATTGT-TT
1 T-ATTTTATATTATTAA-TAATT-TATT
*
1614034 TATTTTATTTTATT
1 TATTTTATATTATT
1614048 TTTTAAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 1 0.03
25 5 0.15
26 19 0.56
27 8 0.24
28 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TATTTTATATTATTAATAATTTATT
Found at i:1614231 original size:22 final size:21
Alignment explanation
Indices: 1614194--1614272 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 21
1614184 TAAATTATTT
* * *
1614194 TATTAATAATTGATAACTTAAA
1 TATTAATATTTTATAA-TTTAA
1614216 TATTAATATTTTATAATATTAA
1 TATTAATATTTTATAAT-TTAA
*
1614238 TATT-TTA-TTTATAATTTAA
1 TATTAATATTTTATAATTTAA
1614257 TATTAAATATTATTAT
1 TATT-AATATT-TTAT
1614273 TTATAATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.17
20 8 0.17
21 5 0.11
22 22 0.47
23 4 0.09
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (21 bp):
TATTAATATTTTATAATTTAA
Found at i:1614233 original size:16 final size:16
Alignment explanation
Indices: 1614214--1614245 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1614204 TGATAACTTA
1614214 AATATTAATATTTTAT
1 AATATTAATATTTTAT
1614230 AATATTAATATTTTAT
1 AATATTAATATTTTAT
1614246 TTATAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATATTAATATTTTAT
Found at i:1614269 original size:20 final size:19
Alignment explanation
Indices: 1614214--1614287 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
1614204 TGATAACTTA
1614214 AATATTAATATTTTATAATATT
1 AATATTAA-A-TTTATAAT-TT
**
1614236 AATATTTTATTTATAATTT
1 AATATTAAATTTATAATTT
*
1614255 AATATTAAATATTATTATTT
1 AATATTAAAT-TTATAATTT
1614275 -ATAATTAAATTTA
1 AAT-ATTAAATTTA
1614288 AAAATGTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.33
20 23 0.51
21 1 0.02
22 6 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTAAATTTATAATTT
Found at i:1614288 original size:26 final size:26
Alignment explanation
Indices: 1614230--1614289 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
1614220 AATATTTTAT
*
1614230 AATATT-AATATTTTATTTATAATTT
1 AATATTAAATATTTTATTTATAATTA
1614255 AATATTAAATATTATTATTTATAATTA
1 AATATTAAATATT-TTATTTATAATTA
1614282 AAT-TTAAA
1 AATATTAAA
1614290 AATGTTGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 6 0.19
26 11 0.34
27 15 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AATATTAAATATTTTATTTATAATTA
Found at i:1629242 original size:116 final size:116
Alignment explanation
Indices: 1629033--1629270 Score: 467
Period size: 116 Copynumber: 2.1 Consensus size: 116
1629023 AAGTTTATGA
*
1629033 AGCTGAAAAAACACCAATTCCATCATTGGTAGCATCCTGGTGAAATACTTATCACATAAAACACA
1 AGCTAAAAAAACACCAATTCCATCATTGGTAGCATCCTGGTGAAATACTTATCACATAAAACACA
1629098 AAAAGGTTCTCCTTGCAATCACTGTTAATATGCTAAGCAGCCAAAAACTAG
66 AAAAGGTTCTCCTTGCAATCACTGTTAATATGCTAAGCAGCCAAAAACTAG
1629149 AGCTAAAAAAACACCAATTCCATCATTGGTAGCATCCTGGTGAAATACTTATCACATAAAACACA
1 AGCTAAAAAAACACCAATTCCATCATTGGTAGCATCCTGGTGAAATACTTATCACATAAAACACA
1629214 AAAAGGTTCTCCTTGCAATCACTGTTAATATGCTAAGCAGCCAAAAACTAG
66 AAAAGGTTCTCCTTGCAATCACTGTTAATATGCTAAGCAGCCAAAAACTAG
1629265 AGCTAA
1 AGCTAA
1629271 CATGACGAAT
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 121 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (116 bp):
AGCTAAAAAAACACCAATTCCATCATTGGTAGCATCCTGGTGAAATACTTATCACATAAAACACA
AAAAGGTTCTCCTTGCAATCACTGTTAATATGCTAAGCAGCCAAAAACTAG
Found at i:1636754 original size:21 final size:21
Alignment explanation
Indices: 1636728--1636774 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1636718 AGCATGGAAG
1636728 GCCCTTAGACACAAAAACATA
1 GCCCTTAGACACAAAAACATA
* *
1636749 GCCCTTAGACACAAACACATG
1 GCCCTTAGACACAAAAACATA
1636770 GCCCT
1 GCCCT
1636775 GAAGGTCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.34, G:0.13, T:0.15
Consensus pattern (21 bp):
GCCCTTAGACACAAAAACATA
Found at i:1638005 original size:36 final size:36
Alignment explanation
Indices: 1637952--1638064 Score: 163
Period size: 36 Copynumber: 3.1 Consensus size: 36
1637942 TCAACTCAGC
*
1637952 TCATGTGCACTCTCACACCGCACATAGTTATTATCG
1 TCATGTGCACTCCCACACCGCACATAGTTATTATCG
* * * *
1637988 TTATGTGCACTCCCACACTGCACATAATTATCATCG
1 TCATGTGCACTCCCACACCGCACATAGTTATTATCG
* *
1638024 TCATATGCACTCCCACACCGCACATAGTTATTATCA
1 TCATGTGCACTCCCACACCGCACATAGTTATTATCG
1638060 TCATG
1 TCATG
1638065 AGCTTCCATA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.30
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCGCACATAGTTATTATCG
Found at i:1638811 original size:22 final size:20
Alignment explanation
Indices: 1638763--1638812 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
1638753 AATGTGAAAA
1638763 TTATTT-TTATTTTATTTAT
1 TTATTTATTATTTTATTTAT
1638782 TT-TATTATTATATATTATTTAT
1 TTAT-TTATTAT-T-TTATTTAT
1638804 TTATTTATT
1 TTATTTATT
1638813 TTAATTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.04
19 4 0.15
20 4 0.15
21 1 0.04
22 15 0.58
23 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTATTATTTTATTTAT
Found at i:1647218 original size:20 final size:21
Alignment explanation
Indices: 1647195--1647233 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1647185 AATAAATATT
*
1647195 CTATTTAAAAAAT-ATAAACA
1 CTATTAAAAAAATAATAAACA
1647215 CTATTAAAAAAATAATAAA
1 CTATTAAAAAAATAATAAA
1647234 ATAACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (21 bp):
CTATTAAAAAAATAATAAACA
Found at i:1647403 original size:23 final size:22
Alignment explanation
Indices: 1647371--1647415 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1647361 CTTTGATTTT
* *
1647371 TTTTTTAAATTATATAATAATAA
1 TTTTTAAAATTA-ATAAAAATAA
1647394 TTTTTAAAATTAATAAAAATAA
1 TTTTTAAAATTAATAAAAATAA
1647416 AATTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTTAAAATTAATAAAAATAA
Found at i:1648442 original size:13 final size:13
Alignment explanation
Indices: 1648424--1648463 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1648414 CATATCTTAC
1648424 TCTCTTTTTTTTT
1 TCTCTTTTTTTTT
* *
1648437 TCTCTTTCTCTTT
1 TCTCTTTTTTTTT
*
1648450 TCTGTTTTTTTTT
1 TCTCTTTTTTTTT
1648463 T
1 T
1648464 TTTTTTACTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (13 bp):
TCTCTTTTTTTTT
Found at i:1654367 original size:3 final size:3
Alignment explanation
Indices: 1654359--1654386 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1654349 ATATTTTCAG
1654359 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1654387 TGTAGGACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1655185 original size:12 final size:12
Alignment explanation
Indices: 1655162--1655206 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
1655152 TATTTTTTTT
*
1655162 CAACAATTTCAA
1 CAACATTTTCAA
*
1655174 CAATATTTTCAA
1 CAACATTTTCAA
* *
1655186 TAACACTTTCAA
1 CAACATTTTCAA
1655198 CAACATTTT
1 CAACATTTT
1655207 TAATAAAGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (12 bp):
CAACATTTTCAA
Found at i:1655190 original size:24 final size:24
Alignment explanation
Indices: 1655163--1655212 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1655153 ATTTTTTTTC
*
1655163 AACAATTTCAACAATATTTTCAAT
1 AACAATTTCAACAACATTTTCAAT
* *
1655187 AACACTTTCAACAACATTTTTAAT
1 AACAATTTCAACAACATTTTCAAT
1655211 AA
1 AA
1655213 AGATAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (24 bp):
AACAATTTCAACAACATTTTCAAT
Found at i:1655426 original size:17 final size:17
Alignment explanation
Indices: 1655404--1655436 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1655394 TTTTGTTGGG
*
1655404 AAAAAAAAGGAAAGAAT
1 AAAAAAAAGAAAAGAAT
1655421 AAAAAAAAGAAAAGAA
1 AAAAAAAAGAAAAGAA
1655437 AATTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAAAAGAAAAGAAT
Found at i:1660549 original size:26 final size:27
Alignment explanation
Indices: 1660520--1660598 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 27
1660510 AAATTTGATG
1660520 ATATTTGAGTTGAAAGGTTTTATCTT-
1 ATATTTGAGTTGAAAGGTTTTATCTTA
* * ** *
1660546 ATATTTGTGAATTCAAA--TTCCAACTTA
1 ATA-TT-TGAGTTGAAAGGTTTTATCTTA
1660573 ATATTTGAGTTGAAAGGTTTTATCTT
1 ATATTTGAGTTGAAAGGTTTTATCTT
1660599 GTGTTCGTGA
Statistics
Matches: 38, Mismatches: 10, Indels: 9
0.67 0.18 0.16
Matches are distributed among these distances:
25 8 0.21
26 11 0.29
27 11 0.29
28 8 0.21
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (27 bp):
ATATTTGAGTTGAAAGGTTTTATCTTA
Found at i:1660578 original size:53 final size:53
Alignment explanation
Indices: 1660520--1660624 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
1660510 AAATTTGATG
*
1660520 ATATTTGAGTTGAAAGGTTTTATCTTATATTTGTGAATTCAAATTCCAACTTA
1 ATATTTGAGTTGAAAGGTTTTATCTTATATTCGTGAATTCAAATTCCAACTTA
* * *
1660573 ATATTTGAGTTGAAAGGTTTTATCTTGTGTTCGTGAATTCAGATTCCAACTT
1 ATATTTGAGTTGAAAGGTTTTATCTTATATTCGTGAATTCAAATTCCAACTT
1660625 TCCATGGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (53 bp):
ATATTTGAGTTGAAAGGTTTTATCTTATATTCGTGAATTCAAATTCCAACTTA
Found at i:1667940 original size:21 final size:19
Alignment explanation
Indices: 1667908--1667949 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
1667898 ATAAAAATTT
1667908 ATTTAAAATTTTTAAAATA
1 ATTTAAAATTTTTAAAATA
*
1667927 ATTTAAAAACTTTTTCAAATA
1 ATTT-AAAA-TTTTTAAAATA
1667948 AT
1 AT
1667950 ATCCCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAAATTTTTAAAATA
Found at i:1668387 original size:13 final size:13
Alignment explanation
Indices: 1668369--1668396 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1668359 CAAAAATTAT
1668369 AACTTATAAAAAA
1 AACTTATAAAAAA
1668382 AACTTATAAAAAA
1 AACTTATAAAAAA
1668395 AA
1 AA
1668397 TTTACCAAAC
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:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
AACTTATAAAAAA
Found at i:1672774 original size:122 final size:122
Alignment explanation
Indices: 1672518--1672794 Score: 522
Period size: 122 Copynumber: 2.3 Consensus size: 122
1672508 CCTTTTTGAC
* *
1672518 TTGACCCATTCTTTAAAACTTGACCATATCCAAAAGAACTGATTAACAAGTTTGTATATAAAAAA
1 TTGACCCATTTTTTTAAACTTGACCATATCCAAAAGAACTGATTAACAAGTTTGTATATAAAAAA
1672583 GTTCAATTGATGTACAATTTTTTTTTATGTGCCAATATAATACAAAGTTTATTCAAT
66 GTTCAATTGATGTACAATTTTTTTTTATGTGCCAATATAATACAAAGTTTATTCAAT
1672640 TTGACCCATTTTTTTAAACTTGACCATATCCAAAAGAACTGATTAACAAGTTTGTATATAAAAAA
1 TTGACCCATTTTTTTAAACTTGACCATATCCAAAAGAACTGATTAACAAGTTTGTATATAAAAAA
1672705 GTTCAATTGATGTACAA-TTTTTTTTATGTGCCAATATAATACAAAGTTTATTCAAT
66 GTTCAATTGATGTACAATTTTTTTTTATGTGCCAATATAATACAAAGTTTATTCAAT
1672761 TTGACCCATTTTTTTAAACTTGACCATAT-CAAAA
1 TTGACCCATTTTTTTAAACTTGACCATATCCAAAA
1672795 TTCCTTCAAT
Statistics
Matches: 153, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
120 5 0.03
121 68 0.44
122 80 0.52
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.38
Consensus pattern (122 bp):
TTGACCCATTTTTTTAAACTTGACCATATCCAAAAGAACTGATTAACAAGTTTGTATATAAAAAA
GTTCAATTGATGTACAATTTTTTTTTATGTGCCAATATAATACAAAGTTTATTCAAT
Found at i:1683845 original size:21 final size:20
Alignment explanation
Indices: 1683813--1683855 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1683803 AATTTCTATG
*
1683813 AATGGTGATAAAATTACACA
1 AATGGTCATAAAATTACACA
* *
1683833 AATGGTCACTAAATTTTCACA
1 AATGGTCA-TAAAATTACACA
1683854 AA
1 AA
1683856 ATTTTCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (20 bp):
AATGGTCATAAAATTACACA
Found at i:1697334 original size:2 final size:2
Alignment explanation
Indices: 1697322--1697368 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1697312 ATTTCCTTCA
* * * *
1697322 TC TC CC TC TC TC TC TC TC TC TC TC TC TG TC TC TG TC TC TG TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1697364 TC TC T
1 TC TC T
1697369 GTGCTTATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.45, G:0.06, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1711141 original size:2 final size:2
Alignment explanation
Indices: 1711134--1711187 Score: 67
Period size: 2 Copynumber: 27.5 Consensus size: 2
1711124 CCCAAGGTCC
**
1711134 CT CT CT CT CT CT CT CT NA C- CGT C- CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT CT CT
1711175 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
1711188 AAAATTCAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.04
2 43 0.93
3 1 0.02
ACGTcount: A:0.02, C:0.50, G:0.02, T:0.44
Consensus pattern (2 bp):
CT
Found at i:1731001 original size:55 final size:55
Alignment explanation
Indices: 1730878--1731001 Score: 133
Period size: 55 Copynumber: 2.3 Consensus size: 55
1730868 TATAGAGTGC
* * **
1730878 AATAACTAATTTTTTTAATATAACATATAATAATTAAATCTTCAACATGGCATAT
1 AATAATTAAATTTTTTAATATAACATATAATAATTAAATCTTCAACATAACATAT
* * * * * * *
1730933 AA-CATTAACATTTTTTAATATGACGTATAATAATTAAATTTTTAATATAATATAT
1 AATAATTAA-ATTTTTTAATATAACATATAATAATTAAATCTTCAACATAACATAT
1730988 AATAATTAAATTTT
1 AATAATTAAATTTT
1731002 CAACATGATA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
54 4 0.07
55 46 0.84
56 5 0.09
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (55 bp):
AATAATTAAATTTTTTAATATAACATATAATAATTAAATCTTCAACATAACATAT
Found at i:1731012 original size:27 final size:27
Alignment explanation
Indices: 1730900--1731009 Score: 105
Period size: 27 Copynumber: 4.0 Consensus size: 27
1730890 TTTTAATATA
*
1730900 ACATATAATAATTAAATCTTCAACATG
1 ACATATAATAATTAAATTTTCAACATG
* * * *
1730927 GCATATAA-CATTAACATTTTTTAATATG
1 ACATATAATAATTAA-A-TTTTCAACATG
* * * *
1730955 ACGTATAATAATTAAATTTTTAATATA
1 ACATATAATAATTAAATTTTCAACATG
*
1730982 ATATATAATAATTAAATTTTCAACATG
1 ACATATAATAATTAAATTTTCAACATG
1731009 A
1 A
1731010 TATGTAACTA
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
26 5 0.08
27 41 0.62
28 15 0.23
29 5 0.08
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (27 bp):
ACATATAATAATTAAATTTTCAACATG
Found at i:1732372 original size:29 final size:29
Alignment explanation
Indices: 1732340--1732411 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
1732330 ATTATTAATT
** *
1732340 ATAAAATTTAAAAGTTTATTTGACTCAAA
1 ATAAAATACAAAAGCTTATTTGACTCAAA
* *
1732369 ATAAAAATACAAAAGCTTATTTGATTTAAA
1 AT-AAAATACAAAAGCTTATTTGACTCAAA
1732399 ATAAAAATACAAA
1 AT-AAAATACAAA
1732412 GTCTTAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.32
Consensus pattern (29 bp):
ATAAAATACAAAAGCTTATTTGACTCAAA
Found at i:1732383 original size:30 final size:29
Alignment explanation
Indices: 1732349--1732449 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
1732339 TATAAAATTT
1732349 AAAAGTTTATTTGACTCAAAATAAAAATAC
1 AAAAGTTTATTTGA-TCAAAATAAAAATAC
* *
1732379 AAAAGCTTATTTGATTTAAAATAAAAATAC
1 AAAAGTTTATTTGA-TCAAAATAAAAATAC
* * *
1732409 -AAAGTCTTAATTGAACATAATAAAAATA-
1 AAAAGT-TTATTTGATCAAAATAAAAATAC
*
1732437 TAAAGATTTATTT
1 AAAAG-TTTATTT
1732450 AAATATTTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
29 24 0.41
30 35 0.59
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (29 bp):
AAAAGTTTATTTGATCAAAATAAAAATAC
Found at i:1734607 original size:18 final size:18
Alignment explanation
Indices: 1734584--1734625 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1734574 GTGCCATTTG
1734584 TTAATTTGGCAAGACTAA
1 TTAATTTGGCAAGACTAA
1734602 TTAATTTGGCAAGACTAA
1 TTAATTTGGCAAGACTAA
1734620 TTAATT
1 TTAATT
1734626 ATCTTGTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (18 bp):
TTAATTTGGCAAGACTAA
Found at i:1741392 original size:16 final size:17
Alignment explanation
Indices: 1741366--1741400 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1741356 TTGTTTTTTT
1741366 TTTTTTAATTATTATTA
1 TTTTTTAATTATTATTA
*
1741383 TTTTTT-ATTATTGTTA
1 TTTTTTAATTATTATTA
1741399 TT
1 TT
1741401 GCTATCATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTAATTATTATTA
Found at i:1750345 original size:13 final size:12
Alignment explanation
Indices: 1750325--1750360 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1750315 TGGAGTTGGG
1750325 TTTTTTTTTTTC
1 TTTTTTTTTTTC
* *
1750337 TTCTTTTTTTCC
1 TTTTTTTTTTTC
1750349 TTTTTTTTTTTC
1 TTTTTTTTTTTC
1750361 GAATTTTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:1751000 original size:157 final size:156
Alignment explanation
Indices: 1750784--1751071 Score: 384
Period size: 157 Copynumber: 1.8 Consensus size: 156
1750774 GTATAAAGAG
* * *
1750784 ATAAAATAAACACTACAAAAAAGAAATTTACCATATTAGGTATCTAGAAAAATACTTGTTATAAG
1 ATAAAATAAAAACTACAAAAAAGAAATTTA-CATATTAGGTATCCAGAAAAATAATTGTTATAAG
* * *
1750849 ATTCTT-TGCTTGTTCGGTGTAGAATTGAAATACCCTATTATTTATTTATTTTTAAAACATTTGA
65 ATTCTTCTACTTGTTCGGTGCAAAATTGAAATACCCTA-TATTTA-TT-TTTTTAAAACATTTGA
1750913 CATGATATGATCGAGTATAAATAAAATAAA
127 CATGATATGATCGAGTATAAATAAAATAAA
* *
1750943 ATAAAATAAAAATTACAAAAAAG-ACTTGT-CATATTAGGTATCCAGAAAAATAATTGTTATAAG
1 ATAAAATAAAAACTACAAAAAAGAAATT-TACATATTAGGTATCCAGAAAAATAATTGTTATAAG
* * ** * *
1751006 ATTTTTCTATTTGTTCGGTGCAAAATTGAAATATTCTATGTTTATTTTTTTAAAGCATTTGACAT
65 ATTCTTCTACTTGTTCGGTGCAAAATTGAAATACCCTATATTTATTTTTTTAAAACATTTGACAT
1751071 G
130 G
1751072 CAAAATTGAA
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
155 19 0.17
156 2 0.02
157 42 0.37
158 28 0.25
159 22 0.19
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (156 bp):
ATAAAATAAAAACTACAAAAAAGAAATTTACATATTAGGTATCCAGAAAAATAATTGTTATAAGA
TTCTTCTACTTGTTCGGTGCAAAATTGAAATACCCTATATTTATTTTTTTAAAACATTTGACATG
ATATGATCGAGTATAAATAAAATAAA
Found at i:1768314 original size:26 final size:23
Alignment explanation
Indices: 1768273--1768319 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 23
1768263 TTTAAGAAAA
1768273 AAAAAAAAAGAAGAAAAAAGGAG
1 AAAAAAAAAGAAGAAAAAAGGAG
1768296 AAAAAAAAAGCAAATGAAAAAAGG
1 AAAAAAAAAG--AA-GAAAAAAGG
1768320 GTAGTACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
25 2 0.10
26 9 0.43
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAGAAGAAAAAAGGAG
Found at i:1773647 original size:128 final size:127
Alignment explanation
Indices: 1773373--1773630 Score: 401
Period size: 128 Copynumber: 2.0 Consensus size: 127
1773363 ACTCTTATTT
* * *
1773373 GAATCCGACTGATCTTAATAGTTACATTCGAATCGATCATATCCTTTTTTATATTTGATCTGAAT
1 GAATCAGACTGATCTTAATAGTTACATTCGAATCGATCATATCCTTTTTGATATTCGATCTGAAT
* * *
1773438 ATGAAAAATATATATATATAACCTCACATCCAACTTGACTCGACTTGAAATTACTCTTATTT
66 ATGAAAAATATATATATATAACCTCACATCCAACTTGACTCGACTTGAAATTAATCTTAATA
*
1773500 GAATCCGACTGATCCTTAATAGTTACATTCGAATCGATCATATCCTTTTTGATATTCGATCTGAA
1 GAATCAGACTGAT-CTTAATAGTTACATTCGAATCGATCATATCCTTTTTGATATTCGATCTGAA
*
1773565 TCTGAAAAATATATATATATATAACCTCACATCCAACTTGACTCGACTTGAAATTTAAT-TTAAT
65 TATG-AAAA-ATATATATATATAACCTCACATCCAACTTGACTCGACTTGAAA-TTAATCTTAAT
1773629 A
127 A
1773630 G
1 G
1773631 TTATAGTTTA
Statistics
Matches: 121, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
127 13 0.11
128 52 0.43
129 4 0.03
130 48 0.40
131 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (127 bp):
GAATCAGACTGATCTTAATAGTTACATTCGAATCGATCATATCCTTTTTGATATTCGATCTGAAT
ATGAAAAATATATATATATAACCTCACATCCAACTTGACTCGACTTGAAATTAATCTTAATA
Found at i:1778749 original size:51 final size:51
Alignment explanation
Indices: 1778671--1778778 Score: 207
Period size: 51 Copynumber: 2.1 Consensus size: 51
1778661 GGTTTTCCTT
1778671 TCTCTTCTCAGTCTCACTCGCGTGCCTCTCCCTCACGCCCCAACTGTCAGA
1 TCTCTTCTCAGTCTCACTCGCGTGCCTCTCCCTCACGCCCCAACTGTCAGA
*
1778722 TNTCTTCTCAGTCTCACTCGCGTGCCTCTCCCTCACGCCCCAACTGTCAGA
1 TCTCTTCTCAGTCTCACTCGCGTGCCTCTCCCTCACGCCCCAACTGTCAGA
1778773 TCTCTT
1 TCTCTT
1778779 TCTCTCTCTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.13, C:0.44, G:0.13, T:0.30
Consensus pattern (51 bp):
TCTCTTCTCAGTCTCACTCGCGTGCCTCTCCCTCACGCCCCAACTGTCAGA
Found at i:1778849 original size:2 final size:2
Alignment explanation
Indices: 1778842--1778867 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1778832 CCCCCTCTTC
1778842 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1778868 ATCTGCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1778968 original size:2 final size:2
Alignment explanation
Indices: 1778961--1778999 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1778951 TGTGCGTATC
*
1778961 TG TG TG TG TG TG TG TG TG TG TG TG TG TG AG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1779000 TTGGGGAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.03, C:0.00, G:0.49, T:0.49
Consensus pattern (2 bp):
TG
Found at i:1779769 original size:15 final size:15
Alignment explanation
Indices: 1779749--1779779 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1779739 CACCCAAATC
1779749 TGTTGATCAATAGGT
1 TGTTGATCAATAGGT
1779764 TGTTGATCAATAGGT
1 TGTTGATCAATAGGT
1779779 T
1 T
1779780 ATACGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.42
Consensus pattern (15 bp):
TGTTGATCAATAGGT
Found at i:1783028 original size:54 final size:54
Alignment explanation
Indices: 1782946--1783055 Score: 193
Period size: 54 Copynumber: 2.0 Consensus size: 54
1782936 ACCCAAATCT
* *
1782946 TTTAATGTCCAATGTCCTGGTGATTCTTTTTCTTTGCTTTGCAAGATTTTACCA
1 TTTAATGACCAATGTCCTAGTGATTCTTTTTCTTTGCTTTGCAAGATTTTACCA
*
1783000 TTTAATGACCAATGTCTTAGTGATTCTTTTTCTTTGCTTTGCAAGATTTTACCA
1 TTTAATGACCAATGTCCTAGTGATTCTTTTTCTTTGCTTTGCAAGATTTTACCA
1783054 TT
1 TT
1783056 GTAAATCCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (54 bp):
TTTAATGACCAATGTCCTAGTGATTCTTTTTCTTTGCTTTGCAAGATTTTACCA
Found at i:1783476 original size:27 final size:27
Alignment explanation
Indices: 1783446--1783534 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
1783436 TCCAGCTCGA
1783446 GCTTGTTGCTCATGTTGTTGCCTTGTG
1 GCTTGTTGCTCATGTTGTTGCCTTGTG
* * * *
1783473 GCTTGCT-CATCATTTTCTTG-TTTAGCTCG
1 GCTTGTTGC-TCATGTTGTTGCCTT-G-T-G
* *
1783502 AGCTGGTTGCTCATGTTGTTGCCTTATG
1 -GCTTGTTGCTCATGTTGTTGCCTTGTG
1783530 GCTTG
1 GCTTG
1783535 CTCATCATTT
Statistics
Matches: 44, Mismatches: 11, Indels: 14
0.64 0.16 0.20
Matches are distributed among these distances:
26 3 0.07
27 20 0.45
28 2 0.05
29 2 0.05
30 14 0.32
31 3 0.07
ACGTcount: A:0.08, C:0.20, G:0.26, T:0.46
Consensus pattern (27 bp):
GCTTGTTGCTCATGTTGTTGCCTTGTG
Found at i:1783488 original size:57 final size:57
Alignment explanation
Indices: 1783395--1783576 Score: 319
Period size: 57 Copynumber: 3.2 Consensus size: 57
1783385 CATAGATGTA
*
1783395 TGCTTATGTTGTTGCCTTGTGGCTTGCTCATCATTTTCTTGTCCAGCTCGAGCTTGT
1 TGCTCATGTTGTTGCCTTGTGGCTTGCTCATCATTTTCTTGTCCAGCTCGAGCTTGT
** *
1783452 TGCTCATGTTGTTGCCTTGTGGCTTGCTCATCATTTTCTTGTTTAGCTCGAGCTGGT
1 TGCTCATGTTGTTGCCTTGTGGCTTGCTCATCATTTTCTTGTCCAGCTCGAGCTTGT
*
1783509 TGCTCATGTTGTTGCCTTATGGCTTGCTCATCATTTTCTTGTCCAGCTCGAGCTTGT
1 TGCTCATGTTGTTGCCTTGTGGCTTGCTCATCATTTTCTTGTCCAGCTCGAGCTTGT
1783566 TGCTCATGTTG
1 TGCTCATGTTG
1783577 CTACCCTATG
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 117 1.00
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (57 bp):
TGCTCATGTTGTTGCCTTGTGGCTTGCTCATCATTTTCTTGTCCAGCTCGAGCTTGT
Found at i:1783564 original size:30 final size:30
Alignment explanation
Indices: 1783416--1783564 Score: 91
Period size: 30 Copynumber: 5.2 Consensus size: 30
1783406 TTGCCTTGTG
1783416 GCTTGCTCATCATTTTCTTGTCCAGCTCGA
1 GCTTGCTCATCATTTTCTTGTCCAGCTCGA
* * * *
1783446 GCTTGTTGC-TCATGTTGTTG-CCTTG-T-G-
1 GCTTGCT-CATCATTTTCTTGTCC-AGCTCGA
**
1783473 GCTTGCTCATCATTTTCTTGTTTAGCTCGA
1 GCTTGCTCATCATTTTCTTGTCCAGCTCGA
* * * * ***
1783503 GCTGGTTGC-TCATGTTGTTG-CCTTAT-G-
1 GCTTGCT-CATCATTTTCTTGTCCAGCTCGA
1783530 GCTTGCTCATCATTTTCTTGTCCAGCTCGA
1 GCTTGCTCATCATTTTCTTGTCCAGCTCGA
1783560 GCTTG
1 GCTTG
1783565 TTGCTCATGT
Statistics
Matches: 81, Mismatches: 26, Indels: 24
0.62 0.20 0.18
Matches are distributed among these distances:
26 2 0.02
27 30 0.37
28 6 0.07
29 6 0.07
30 35 0.43
31 2 0.02
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (30 bp):
GCTTGCTCATCATTTTCTTGTCCAGCTCGA
Found at i:1786239 original size:93 final size:93
Alignment explanation
Indices: 1785986--1786427 Score: 361
Period size: 93 Copynumber: 4.7 Consensus size: 93
1785976 CATTCTCCGA
* * * * ** * * **
1785986 GTTTTGTTTAGCTTTTCCGTTATCAGATCCTTTTAGCGATGTTGAATCACTAGTATATGCCATTT
1 GTTTTCTTCAGCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATTT
** * * * * *
1786051 TGGGCTATCAAGCACCATCACTTTTTAAA
66 TGGTTTGTCAAGCATCACCA-TTTTTCAG
* * * * * * **
1786080 ATTTT-TTCAGCTTTTCCCCTATCATATTCTTTTCCTGGTGTTGAATCACCAACATTTGCCATTT
1 GTTTTCTTCAGCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATTT
1786144 TGGTTTGTCAAGCATCACCATTTTTCAG
66 TGGTTTGTCAAGCATCACCATTTTTCAG
* * * *
1786172 GTTTTCTTCAGC-TTTCTCCTTATCAAATTCTTTTCCCGGTGTTGAATCACCATTATCCGCCACT
1 GTTTTCTTCAGCTTTTC-CCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATT
* * *
1786236 TTGGTTATCTGTCGAA-CACCATCACTTTTTGAG
65 TTGG-T-T-TGTC-AAGCATCACCA-TTTTTCAG
* * * * * *
1786269 GTTTTCTTCAACCTTGT-CCTTATTAGATTCTTTTACCGATGTTGAATCACCAGTATCTGCCATT
1 GTTTTCTTC-AGCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATT
* ** ** * *
1786333 TTAGTTTGTTGAGCATTGCCATGTTCCAG
65 TTGGTTTGTCAAGCATCACCATTTTTCAG
* *
1786362 GTTTTCTTCATCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCACCATTT
1 GTTTTCTTCAGCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATTT
1786427 T
66 T
1786428 AGACTATTGA
Statistics
Matches: 278, Mismatches: 59, Indels: 23
0.77 0.16 0.06
Matches are distributed among these distances:
92 19 0.07
93 169 0.61
94 12 0.04
95 2 0.01
96 11 0.04
97 61 0.22
98 2 0.01
99 2 0.01
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (93 bp):
GTTTTCTTCAGCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATTT
TGGTTTGTCAAGCATCACCATTTTTCAG
Found at i:1786457 original size:93 final size:93
Alignment explanation
Indices: 1786081--1786491 Score: 300
Period size: 93 Copynumber: 4.4 Consensus size: 93
1786071 CTTTTTAAAA
* * * * * * **
1786081 TTTT-TTCAGCTTTTCCCCTATCATATTCTTTTCCTGGTGTTGAATCACCAACATTTGCCATTTT
1 TTTTCTTCATCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATTTT
* ** * *
1786145 GGTTTG-TCAA-GCATCACCATTTTTCAGG
66 AGACTGTTGAACGC--CATCATTTTTCAGG
* * * * *
1786173 TTTTCTTCAGC-TTTCTCCTTATCAAATTCTTTTCCCGGTGTTGAATCACCATTATCCGCCACTT
1 TTTTCTTCATCTTTTC-CCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATTT
* * * *
1786237 TGGTTATCTGTCGAACACCATCACTTTTTGAGG
65 TAG--A-CTGTTGAACGCCATCA-TTTTTCAGG
* * * * * *
1786270 TTTTCTTCAACCTTGT-CCTTATTAGATTCTTTTACCGATGTTGAATCACCAGTATCTGCCATTT
1 TTTTCTTC-ATCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATTT
** * *
1786334 TAGTTTGTTG-A-G-CATTGCCATGTTCCAGG
65 TAGACTGTTGAACGCCA-T--CATTTTTCAGG
*
1786363 TTTTCTTCATCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCACCATTTT
1 TTTTCTTCATCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATTTT
* * *
1786428 AGACTATTGAACGCCATCTTTTTTTAGG
66 AGACTGTTGAACGCCATCATTTTTCAGG
* * *
1786456 TTTCCTTTAGT-TTTTTCCTTATCAGATTCTTTTCCC
1 TTTTCTTCA-TCTTTTCCCTTATCAGATTCTTTTCCC
1786492 TGCCATTTGA
Statistics
Matches: 252, Mismatches: 49, Indels: 35
0.75 0.15 0.10
Matches are distributed among these distances:
91 2 0.01
92 14 0.06
93 152 0.60
94 8 0.03
95 2 0.01
96 8 0.03
97 61 0.24
98 3 0.01
99 2 0.01
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.45
Consensus pattern (93 bp):
TTTTCTTCATCTTTTCCCTTATCAGATTCTTTTCCCGATGTTGAATCACCAATATCCGCCATTTT
AGACTGTTGAACGCCATCATTTTTCAGG
Found at i:1788861 original size:13 final size:13
Alignment explanation
Indices: 1788829--1788870 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
1788819 AGTATAGAAT
1788829 TATTTTTATG-CA
1 TATTTTTATGACA
1788841 TATTTTTATGACA
1 TATTTTTATGACA
1788854 -ATTGTTTATGA-A
1 TATT-TTTATGACA
1788866 TATTT
1 TATTT
1788871 GTTGCAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (13 bp):
TATTTTTATGACA
Found at i:1789876 original size:2 final size:2
Alignment explanation
Indices: 1789871--1789912 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1789861 CTCTATATTT
* *
1789871 TG TG TG TG TG TG TG TG TG TG TG TG TT TG CG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1789913 GGCGTGCATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.02, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1790973 original size:249 final size:246
Alignment explanation
Indices: 1790507--1791217 Score: 1036
Period size: 249 Copynumber: 2.9 Consensus size: 246
1790497 CTTTAAAGCC
* * *
1790507 TATATATATATAAACACATGATGTAACACTCATTCAGAAAGCTGCAAAAAAGAAGCCAAAGCTAA
1 TATATATATATAAACACATGATGTAACACTCATTTAGAAAGCTGCAAAAGAGAAACCAAAGCTAA
* * * *
1790572 GTTATTACATCGATAGCATGCTTACCTCAGAATGTTCTCCATGTTGACATTGATCACTCTTAGCA
66 GTTATTACATCGATAGCATGCTCACCTTAGAATGCTCTCCATGTTGACATTGATCATTCTTAGCA
* * * * * * * *
1790637 TCAATACTAAAAGCCAATGTTATTTTTTTCGAAA-AGTTTGCTTGGTTAAACTCAGAACCTAAAG
131 TCAGTATTAAGAGCCAATGTTA-TTTTCTCCAAAGGGTTTGCTTGGTCAAACTCAGAACCTGAAG
*
1790701 CTACTTGCTTCCTCTTTCTCCCACGTCTCTTTGAAGCCTACATATATATATA
195 CTACTTGCTTCTTCTTTCTCCCACGTCTCTTTGAAGCCTACATATATATATA
* * *
1790753 TATATATATATAAATACATGATGTAACACTCATTTAGAAAACTGCAATAGAGAAACCACAA-CTA
1 TATATATATATAAACACATGATGTAACACTCATTTAGAAAGCTGCAAAAGAGAAACCA-AAGCTA
* *
1790817 AGTTATTACATCGATAGCATGCTCACCTTAGACTGCTCTCCATGTTGATATTGAATATCATTCTT
65 AGTTATTACATCGATAGCATGCTCACCTTAGAATGCTCTCCATGTTGACATTG---ATCATTCTT
1790882 AGCATCAGTATTAAGAGCCAATGTTATTTTCTCCAAAGGGTTTGCTTGGTCAAACTCAGAACCTG
127 AGCATCAGTATTAAGAGCCAATGTTATTTTCTCCAAAGGGTTTGCTTGGTCAAACTCAGAACCTG
* *
1790947 AAGCAACTTGCTTCTTCTTTCTCCCACGTCTCTTTGAAGCCTACATATATGTATA
192 AAGCTACTTGCTTCTTCTTTCTCCCACGTCTCTTTGAAGCCTACATATATATATA
* * * *
1791002 TATATATA-A-AAACACATGATGTAGCACTCATTTAGAAAGTTGCAACAGA-AAAGCCAAAGCCA
1 TATATATATATAAACACATGATGTAACACTCATTTAGAAAGCTGCAAAAGAGAAA-CCAAAGCTA
**
1791064 AGTTATTACATCGATAGCATGCTCACCTTAGGTTGCTCTCCATGTTGACATTGATCATTCTTAGC
65 AGTTATTACATCGATAGCATGCTCACCTTAGAATGCTCTCCATGTTGACATTGATCATTCTTAGC
* * *
1791129 ATTAGTATTAAGAGCCAATGTTATTTTCTCCGAAGGGTTTGCTTGGTCAAACTCAGAACTTGAAG
130 ATCAGTATTAAGAGCCAATGTTATTTTCTCCAAAGGGTTTGCTTGGTCAAACTCAGAACCTGAAG
*
1791194 CTACTTGCTTTTTCTTTCTCCCAC
195 CTACTTGCTTCTTCTTTCTCCCAC
1791218 ATTTGTTTTT
Statistics
Matches: 421, Mismatches: 37, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
244 96 0.23
246 108 0.26
247 92 0.22
248 10 0.02
249 115 0.27
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (246 bp):
TATATATATATAAACACATGATGTAACACTCATTTAGAAAGCTGCAAAAGAGAAACCAAAGCTAA
GTTATTACATCGATAGCATGCTCACCTTAGAATGCTCTCCATGTTGACATTGATCATTCTTAGCA
TCAGTATTAAGAGCCAATGTTATTTTCTCCAAAGGGTTTGCTTGGTCAAACTCAGAACCTGAAGC
TACTTGCTTCTTCTTTCTCCCACGTCTCTTTGAAGCCTACATATATATATA
Found at i:1791267 original size:2 final size:2
Alignment explanation
Indices: 1791260--1791286 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1791250 TTCGAAGCCT
1791260 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1791287 TAATGCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1791512 original size:269 final size:265
Alignment explanation
Indices: 1791050--1791645 Score: 732
Period size: 269 Copynumber: 2.2 Consensus size: 265
1791040 GTTGCAACAG
* * **
1791050 AAAAGCCAAAGCCAAGTTATTACATCGATAGCATGCTCACCTTAGGTTGCTCTCCATGTTGACAT
1 AAAAGCCAAAGCTAAGTTATTACATCGATAGCATGCTCACCTCAAATTGCTCTCCATGTTGACAT
* * * * * *
1791115 TGATCATTCTTAGCATTAGTATTAAGAGCCAATGTTATTTTCTCCGAAGGGTTTGCTTGGTCAAA
66 CGATCATTCTCAACATCAGTATTAAGAACCAATGTTATTTTCTCCGAAGGGTTTGCATGGTCAAA
** *
1791180 CTCAGAACTTGAAGCTACTTGCTTTTTCTTTCTCCCACATTTGTTTTTCACTATTTGCCCTTTGG
131 CTCAGAACCCGAAGCTACTTGCTTTTTCTTTCTCCCACATTTGTTTTTCAATATTTGCCCTTTGG
* * *
1791245 AGCT-TTTCGAAGCCTACACACACACACACACACACACACACATAATGCAACACTTGTTTAGAAA
196 AGCTCTTT-GAAACCT--ACACACACACACACACA-A-ACACATAATGCAACACTCGTTCAGAAA
* *
1791309 ACTGCAGTAG
256 ACTGCAATAA
* * * * * *
1791319 AGATGCCAAAGTTAGGTTATTACATCGATAGCATGCTTACCTCAAACTGCTCTCCATGTTGACAT
1 AAAAGCCAAAGCTAAGTTATTACATCGATAGCATGCTCACCTCAAATTGCTCTCCATGTTGACAT
* *
1791384 CGATCATTCTCAACATCAGTGTTAAGAACTAATGTTATTTTCT-C-AAGAGGATTTGCATGGTCA
66 CGATCATTCTCAACATCAGTATTAAGAACCAATGTTATTTTCTCCGAAG-GG-TTTGCATGGTCA
* * * * *
1791447 AACTCATAACCCGAAGCTGCTTGCTTCTTT-TTTCTCCCACGTTTGTTTTTTAATATTTTCCCTT
129 AACTCAGAACCCGAAGCTACTTGCTT-TTTCTTTCTCCCACATTTGTTTTTCAATATTTGCCCTT
* * * * * *
1791511 TGGAGCTCTTTGAAACCTACACACATATATATATAAACACATAATGCAACACTCGTTCAGAAAGC
193 TGGAGCTCTTTGAAACCTACACACACACACACACAAACACATAATGCAACACTCGTTCAGAAAAC
1791576 TGCAATAA
258 TGCAATAA
* * *
1791584 AAAAGCCAAAGCTAAGTTATTATATCAATAGCATGCTCACCTCAAATTGCTCTCCCTGTTGA
1 AAAAGCCAAAGCTAAGTTATTACATCGATAGCATGCTCACCTCAAATTGCTCTCCATGTTGA
1791646 TTTATTACCT
Statistics
Matches: 277, Mismatches: 46, Indels: 12
0.83 0.14 0.04
Matches are distributed among these distances:
265 85 0.31
266 1 0.00
267 15 0.05
268 3 0.01
269 167 0.60
270 6 0.02
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (265 bp):
AAAAGCCAAAGCTAAGTTATTACATCGATAGCATGCTCACCTCAAATTGCTCTCCATGTTGACAT
CGATCATTCTCAACATCAGTATTAAGAACCAATGTTATTTTCTCCGAAGGGTTTGCATGGTCAAA
CTCAGAACCCGAAGCTACTTGCTTTTTCTTTCTCCCACATTTGTTTTTCAATATTTGCCCTTTGG
AGCTCTTTGAAACCTACACACACACACACACAAACACATAATGCAACACTCGTTCAGAAAACTGC
AATAA
Found at i:1791774 original size:57 final size:57
Alignment explanation
Indices: 1791672--1791831 Score: 144
Period size: 57 Copynumber: 2.8 Consensus size: 57
1791662 TGTGCTTATC
* * * * **
1791672 TTGTTGCCTTGTGACTTGCTTATCATTTTCTTG-ACTAGCACGAGCTAATAACTCATA
1 TTGTTGCATTGTGGCTTGCTCATCATTTTCTTGTAC-AACTTGAGCTAATAACTCATA
* * * * ** *
1791729 TTGTT-CTTTTGTGGTTTGCTCATCATTTTCTTGTCCAACTTGAGCTAGTTGCTCATG
1 TTGTTGC-ATTGTGGCTTGCTCATCATTTTCTTGTACAACTTGAGCTAATAACTCATA
* * *
1791786 TTGTTGCATTGTGGCTTGTTCATTATTTTCTTGTACAGCTTGAGCT
1 TTGTTGCATTGTGGCTTGCTCATCATTTTCTTGTACAACTTGAGCT
1791832 TGTTGCTCAT
Statistics
Matches: 82, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
56 1 0.01
57 79 0.96
58 2 0.02
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.46
Consensus pattern (57 bp):
TTGTTGCATTGTGGCTTGCTCATCATTTTCTTGTACAACTTGAGCTAATAACTCATA
Found at i:1791837 original size:57 final size:57
Alignment explanation
Indices: 1791737--1791849 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
1791727 TATTGTTCTT
* *
1791737 TTGTGGTTTGCTCATCATTTTCTTGTCCAACTTGAGCTAGTTGCTCATGTTGTTGCA
1 TTGTGGCTTGCTCATCATTTTCTTGTACAACTTGAGCTAGTTGCTCATGTTGTTGCA
* * * *
1791794 TTGTGGCTTGTTCATTATTTTCTTGTACAGCTTGAGCTTGTTGCTCATGTTGTTGC
1 TTGTGGCTTGCTCATCATTTTCTTGTACAACTTGAGCTAGTTGCTCATGTTGTTGC
1791850 CCTGTGACTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (57 bp):
TTGTGGCTTGCTCATCATTTTCTTGTACAACTTGAGCTAGTTGCTCATGTTGTTGCA
Found at i:1792796 original size:277 final size:275
Alignment explanation
Indices: 1792223--1792840 Score: 610
Period size: 277 Copynumber: 2.2 Consensus size: 275
1792213 TACATACATT
* * * *
1792223 CATGACTTTCACGAAAGATTTGGAATCTTTTTGTAGAATTGAAATGATTTGCGAATTAATT-A-A
1 CATGACTTTCA-GAAAGATTTGAAATCTTTTTGCATAATTGAAATGATTTGCGTATTAATTAACA
* * * * ** * * *
1792286 CATACTTCCCTATGATTATTTTCTTTTCAGGTGTTGATGATTTCATAATCATTAATTGATGTAAA
65 CATAATTCCCTATGATAATTTTATTTTCAAGTACTAATGATGTCATAATCATTAATGGATGTAAA
* * * * *
1792351 CAGGAAAAATGAAAAAATGAGTTACATACCTAGGCATGCATGCACATGTGTGCATGCATGCTCGT
130 CAAGAAAAATGAAAAAATAAGTTACATACCTAGGCATACATGCACATGTGCGCATGAATGC-CG-
* * *
1792416 ACACATATATTAATATATTCATGACAACATACATGTATATATGTTTGTGAGATATTATGACAAAA
193 ACACATATATTAATATATTCAGGACAACATACATGTATATATGTGTATGAGATATTATGACAAAA
* * * * *
1792481 TTACTACAAATATATGTG
258 TAACGACAAACAGATATG
*
1792499 CATGACTTTC-GCATAAGATTTGAAATCTTTTTGCATAATTTAAATGATTTGCGTATTAATTAAC
1 CATGACTTTCAG-A-AAGATTTGAAATCTTTTTGCATAATTGAAATGATTTGCGTATTAATTAAC
* * *
1792563 ATCATAATTCCTTTTATGATAATTTTATTTTTAAGTACTAATGATGTCATGATCATTTAATGGAT
64 A-CATAATTCC--CTATGATAATTTTATTTTCAAGTACTAATGATGTCATAATCA-TTAATGGAT
* * * * * *
1792628 GATAAATAAGAGAAATG-AAAAATAAGTTACATA-CTAGGTATACGTGCATATGTGCGCGTGAAT
125 G-TAAACAAGAAAAATGAAAAAATAAGTTACATACCTAGGCATACATGCACATGTGCGCATGAAT
* * * * * * *
1792691 G-C-ACGCGTATATTAATATATTCAGGACAACGTGA-GTGTGTATGTGTGTATGTGATATTATGA
189 GCCGACACATATATTAATATATTCAGGACAACAT-ACATGTATATATGTGTATGAGATATTATGA
*
1792753 CAAAATAACGACAAACAGATATT
253 CAAAATAACGACAAACAGATATG
* *
1792776 TATGACTTTCATGAAAGATTT-ATAAT-TTTTT-CATAAAATTGAAATGATTTACGTATTAATTA
1 CATGACTTTCA-GAAAGATTTGA-AATCTTTTTGCAT--AATTGAAATGATTTGCGTATTAATTA
1792838 ACA
62 ACA
1792841 ACGTGTGTAT
Statistics
Matches: 280, Mismatches: 47, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
274 1 0.00
275 4 0.01
276 58 0.21
277 112 0.40
278 3 0.01
279 10 0.04
281 56 0.20
282 24 0.09
283 12 0.04
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (275 bp):
CATGACTTTCAGAAAGATTTGAAATCTTTTTGCATAATTGAAATGATTTGCGTATTAATTAACAC
ATAATTCCCTATGATAATTTTATTTTCAAGTACTAATGATGTCATAATCATTAATGGATGTAAAC
AAGAAAAATGAAAAAATAAGTTACATACCTAGGCATACATGCACATGTGCGCATGAATGCCGACA
CATATATTAATATATTCAGGACAACATACATGTATATATGTGTATGAGATATTATGACAAAATAA
CGACAAACAGATATG
Found at i:1794864 original size:93 final size:93
Alignment explanation
Indices: 1794703--1795147 Score: 418
Period size: 93 Copynumber: 4.8 Consensus size: 93
1794693 ATTGATCTTA
* * *
1794703 GGCTGTTGAGCACCATCACTTT-TCGGGTTTTCTAT-AGCTTTTCCCTTATCAGATTCTTTT--T
1 GGCTGTCGAGCACCATCACTTTCT-AGGTTTTCT-TCAGCTTTTTCCTTATCAGATTCTTTTCCT
* * ** *
1794764 GAGGTGTTGAATTATCAGTATCCGTCACTTTG
64 -A-GTGTTGAATCACCAGTATCCACCATTTTG
* * * *
1794796 GGCTGTCGAGCACCATCACTTTCCAAGTTTTCTTCAGTTTTTTCCTTATCAGATCCTTTTCCTAG
1 GGCTGTCGAGCACCATCACTTTCTAGGTTTTCTTCAGCTTTTTCCTTATCAGATTCTTTTCCTAG
*
1794861 TGTTGAATCACCGGTATCCACCATTTTG
66 TGTTGAATCACCAGTATCCACCATTTTG
* *
1794889 GTGATCTG-CTGAGCACCATCACTTTCTAGGTTTTCTTCAGCCTTGTCCTTATCAGATTCTTTT-
1 G-G--CTGTC-GAGCACCATCACTTTCTAGGTTTTCTTCAGCTTTTTCCTTATCAGATTCTTTTC
* * * *
1794952 ATCGATGTTGAATCCCCAGAATCCACCATTTTG
62 CTAG-TGTTGAATCACCAGTATCCACCATTTTG
* * * * * * * * * *
1794985 GTCTTTCGAGCATCACCACTTTCTTGGTTTTTTTCAGCTTTTCCCTTATCAAATTTTTTTCCTAA
1 GGCTGTCGAGCACCATCACTTTCTAGGTTTTCTTCAGCTTTTTCCTTATCAGATTCTTTTCCTAG
* **
1795050 TGTTGAAACACCAGTATCCACTGTTTTG
66 TGTTGAATCACCAGTATCCACCATTTTG
* * * * *
1795078 GTCTGTTGAGCACCATC-CTTTTCTAGGTTTCCTTCATCTTTTTCCTTATCAGATTCTTTTCGTA
1 GGCTGTCGAGCACCATCAC-TTTCTAGGTTTTCTTCAGCTTTTTCCTTATCAGATTCTTTTCCTA
1795142 GTGTTG
65 GTGTTG
1795148 GACCATCGAT
Statistics
Matches: 284, Mismatches: 56, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
92 2 0.01
93 198 0.70
94 4 0.01
95 4 0.01
96 76 0.27
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.43
Consensus pattern (93 bp):
GGCTGTCGAGCACCATCACTTTCTAGGTTTTCTTCAGCTTTTTCCTTATCAGATTCTTTTCCTAG
TGTTGAATCACCAGTATCCACCATTTTG
Found at i:1795034 original size:189 final size:185
Alignment explanation
Indices: 1794709--1795147 Score: 456
Period size: 189 Copynumber: 2.3 Consensus size: 185
1794699 CTTAGGCTGT
*
1794709 TGAGCACCATCACTTT-TCGGGTTTTCTAT-AG-CTTTTCCCTTATCAGATTCTTTTTGAGGTGT
1 TGAGCACCATCACTTTCT-AGGTTTTCT-TCAGCCTTTT-CCTTATCAGATTCTTTTTGA-GTGT
* * * ** * *
1794771 TGAATTATCAGTATCCGTCACTTTGGGCTGTCGAGCACCATCACTTTCCAAGTTTTCTTCAGTTT
62 TGAATCACCAGAATCCACCACTTTGGGCTGTCGAGCACCACCACTTTCCAAGTTTTCTTCAGCTT
* * * * *
1794836 TTTCCTTATCAGATCCTTTTCCTAGTGTTGAATCACCGGTATCCACCATTTTGGTGATCTGC
127 TTCCCTTATCAAATCCTTTTCCTAATGTTGAAACACCAGTATCCACCATTTT-G-G-TCTGC
*
1794898 TGAGCACCATCACTTTCTAGGTTTTCTTCAGCCTTGTCCTTATCAGATTCTTTTATCGA-TGTTG
1 TGAGCACCATCACTTTCTAGGTTTTCTTCAGCCTTTTCCTTATCAGATTCTTTT-T-GAGTGTTG
* * * * * *** *
1794962 AATCCCCAGAATCCACCATTTTGGTCTTTCGAGCATCACCACTTTCTTGGTTTTTTTCAGCTTTT
64 AATCACCAGAATCCACCACTTTGGGCTGTCGAGCACCACCACTTTCCAAGTTTTCTTCAGCTTTT
** ** *
1795027 CCCTTATCAAATTTTTTTCCTAATGTTGAAACACCAGTATCCACTGTTTTGGTCTGT
129 CCCTTATCAAATCCTTTTCCTAATGTTGAAACACCAGTATCCACCATTTTGGTCTGC
* * * *
1795084 TGAGCACCATC-CTTTTCTAGGTTTCCTTCATCTTTTTCCTTATCAGATTCTTTTCGTAGTGTTG
1 TGAGCACCATCAC-TTTCTAGGTTTTCTTCAGCCTTTTCCTTATCAGATTCTTTTTG-AGTGTTG
1795148 GACCATCGAT
Statistics
Matches: 209, Mismatches: 33, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
184 1 0.00
185 2 0.01
186 57 0.27
187 1 0.00
188 2 0.01
189 138 0.66
190 6 0.03
191 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (185 bp):
TGAGCACCATCACTTTCTAGGTTTTCTTCAGCCTTTTCCTTATCAGATTCTTTTTGAGTGTTGAA
TCACCAGAATCCACCACTTTGGGCTGTCGAGCACCACCACTTTCCAAGTTTTCTTCAGCTTTTCC
CTTATCAAATCCTTTTCCTAATGTTGAAACACCAGTATCCACCATTTTGGTCTGC
Found at i:1798599 original size:75 final size:76
Alignment explanation
Indices: 1798508--1798649 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 76
1798498 TGAGTAGTTC
* * *
1798508 TATATGGAATATCACCATA-TACACCTCATGT-TTTTCATTGGTATGCCTTCTATATTGGTAGAA
1 TATATGGAATAGCACCATAGTACACCTCATGTATTTT-ATTGGTATGCCTTATATATTAGTAGAA
1798571 AAACGATTTTCT
65 AAACGATTTTCT
* * * *
1798583 TATATGGAATAGCACCATAGTGCGCCTTATGTATTTTATTGGTATGCCTTATATTTTAGTAGAAA
1 TATATGGAATAGCACCATAGTACACCTCATGTATTTTATTGGTATGCCTTATATATTAGTAGAAA
1798648 AA
66 AA
1798650 TGCTTCAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
75 18 0.31
76 36 0.62
77 4 0.07
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (76 bp):
TATATGGAATAGCACCATAGTACACCTCATGTATTTTATTGGTATGCCTTATATATTAGTAGAAA
AACGATTTTCT
Found at i:1798822 original size:33 final size:33
Alignment explanation
Indices: 1798780--1798849 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
1798770 TTTCATGGCA
1798780 ACTTTTAGGTGTTGATTGTAAATGAAAATGTCT
1 ACTTTTAGGTGTTGATTGTAAATGAAAATGTCT
1798813 ACTTTTAGGTGTTGATTGTAAATGAAAATGTCT
1 ACTTTTAGGTGTTGATTGTAAATGAAAATGTCT
1798846 ACTT
1 ACTT
1798850 GTCAATCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (33 bp):
ACTTTTAGGTGTTGATTGTAAATGAAAATGTCT
Found at i:1811068 original size:23 final size:23
Alignment explanation
Indices: 1811045--1811087 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1811035 CTTTAGTTTA
*
1811045 AATTA-AATAAATTTTTATGATT
1 AATTATAATAAATTGTTATGATT
*
1811067 AATTATAATTAATTGTTATGA
1 AATTATAATAAATTGTTATGA
1811088 ATCAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (23 bp):
AATTATAATAAATTGTTATGATT
Found at i:1816530 original size:32 final size:33
Alignment explanation
Indices: 1816483--1816547 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1816473 ATGTGTCAAT
* *
1816483 CCTTTACTTAAAATGTTCTACTTTATGATCAAAC
1 CCTTTAC-TAAAATGTTCTACGTTATAATCAAAC
1816517 CCTTTAC-AAAATGTTCTACGTTATAATCAAA
1 CCTTTACTAAAATGTTCTACGTTATAATCAAA
1816548 TTTTTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 22 0.76
34 7 0.24
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.38
Consensus pattern (33 bp):
CCTTTACTAAAATGTTCTACGTTATAATCAAAC
Found at i:1821890 original size:55 final size:55
Alignment explanation
Indices: 1821829--1821937 Score: 164
Period size: 55 Copynumber: 2.0 Consensus size: 55
1821819 GTCAGTCAAG
* * *
1821829 AAGACATCCTAAACATTTATTATATAACATAATTACCATAGGATCAAGGTTATTT
1 AAGACATCCTAAACATTAATTAGATAACATAATTACCACAGGATCAAGGTTATTT
* * *
1821884 AAGACATCCTTAATATTAATTAGATAACATGATTACCACAGGATCAAGGTTATT
1 AAGACATCCTAAACATTAATTAGATAACATAATTACCACAGGATCAAGGTTATT
1821938 CATCACTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (55 bp):
AAGACATCCTAAACATTAATTAGATAACATAATTACCACAGGATCAAGGTTATTT
Found at i:1825635 original size:39 final size:37
Alignment explanation
Indices: 1825587--1825659 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 37
1825577 AAATATTGTT
1825587 TTAAATATAATTT-TGAACTTATAATTTACTTTTTATGAA
1 TTAAATATAATTTATGAA-TT-TAATTTA-TTTTTATGAA
* *
1825626 TTAATTATAATTTATTAATTTAATTTATTTTTAT
1 TTAAATATAATTTATGAATTTAATTTATTTTTAT
1825660 TTTAATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 7 0.23
38 7 0.23
39 14 0.45
40 3 0.10
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (37 bp):
TTAAATATAATTTATGAATTTAATTTATTTTTATGAA
Found at i:1825651 original size:13 final size:14
Alignment explanation
Indices: 1825625--1825654 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1825615 CTTTTTATGA
1825625 ATTAATTATAATTT
1 ATTAATTATAATTT
1825639 ATTAATT-TAATTT
1 ATTAATTATAATTT
1825652 ATT
1 ATT
1825655 TTTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTAATTATAATTT
Found at i:1828367 original size:3 final size:3
Alignment explanation
Indices: 1828354--1828383 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1828344 CTTCCCACCT
1828354 TTC TCTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TT
1828384 GTCTTCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1838076 original size:17 final size:16
Alignment explanation
Indices: 1838050--1838083 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1838040 CCTGTTTGGT
1838050 TTGATTTTTTTTTAAC
1 TTGATTTTTTTTTAAC
1838066 TTGATTTTTTTTTAAC
1 TTGATTTTTTTTTAAC
1838082 TT
1 TT
1838084 AAAACTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (16 bp):
TTGATTTTTTTTTAAC
Found at i:1838276 original size:18 final size:18
Alignment explanation
Indices: 1838242--1838275 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1838232 TAAAAAGTAT
1838242 TTAATAAATAACTTTTTA
1 TTAATAAATAACTTTTTA
*
1838260 TTAATAACTAA-TTTTT
1 TTAATAAATAACTTTTT
1838276 TTGTTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATAAATAACTTTTTA
Found at i:1838403 original size:18 final size:16
Alignment explanation
Indices: 1838380--1838424 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
1838370 TCTTTAGTAG
1838380 TTTTTTTTTAAACTTCTT
1 TTTTTTTTTAAA-TT-TT
1838398 TTTTTTTTT-AATTTT
1 TTTTTTTTTAAATTTT
*
1838413 TGTTTTTTTAAA
1 TTTTTTTTTAAA
1838425 AAAAGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 10 0.40
16 4 0.16
17 2 0.08
18 9 0.36
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTTTTTTAAATTTT
Found at i:1838531 original size:13 final size:13
Alignment explanation
Indices: 1838515--1838539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1838505 CTCTTTAGAG
1838515 TTTTTTTTTAAAC
1 TTTTTTTTTAAAC
1838528 TTTTTTTTTAAA
1 TTTTTTTTTAAA
1838540 AATTTTGTTT
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:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTAAAC
Found at i:1838535 original size:15 final size:14
Alignment explanation
Indices: 1838515--1838557 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1838505 CTCTTTAGAG
*
1838515 TTTTTTTTTAAACT
1 TTTTTTTTTAAAAT
*
1838529 TTTTTTTTAAAAATT
1 TTTTTTTTTAAAA-T
1838544 TTGTTTTTTTAAAA
1 TT-TTTTTTTAAAA
1838558 AAAGTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.46
15 3 0.12
16 10 0.42
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTTTTTTTAAAAT
Found at i:1838550 original size:18 final size:17
Alignment explanation
Indices: 1838528--1838573 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1838518 TTTTTTAAAC
*
1838528 TTTTTTTTT-AAAAATT
1 TTTTTTTTTAAAAAAGT
1838544 TTGTTTTTTTAAAAAAAGT
1 TT-TTTTTTT-AAAAAAGT
1838563 TTTTTTTTTAA
1 TTTTTTTTTAA
1838574 GAGCTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 9 0.35
18 7 0.27
19 8 0.31
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTTTTTTTAAAAAAGT
Found at i:1838552 original size:19 final size:18
Alignment explanation
Indices: 1838528--1838573 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1838518 TTTTTTAAAC
*
1838528 TTTTTTTTT--AAAAATT
1 TTTTTTTTTAAAAAAAGT
1838544 TTGTTTTTTTAAAAAAAGT
1 TT-TTTTTTTAAAAAAAGT
1838563 TTTTTTTTTAA
1 TTTTTTTTTAA
1838574 GAGCTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 7 0.27
18 9 0.35
19 8 0.31
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTTTTTTTAAAAAAAGT
Found at i:1838578 original size:133 final size:135
Alignment explanation
Indices: 1838344--1838614 Score: 458
Period size: 133 Copynumber: 2.0 Consensus size: 135
1838334 TATAAANTTT
**
1838344 TTAAAAAAAGAAGAAAAAAAAACTCCTCTTTAGTAGTTTTTTTTTAAACTTCTTTTTTTTTTTAA
1 TTAAAAAAAGAAGAAAAAAAAACTCCTCTTTAGTAGTTTTTTTTTAAA--TCTTTTTTTTTAAAA
*
1838409 TTTTTGTTTTTTTAAAAAAAGTTTTTTTTTAAGAGCTTTTCAAAAAATTGACTTTTACTTTTAAG
64 ATTTTGTTTTTTTAAAAAAAGTTTTTTTTTAAGAGCTTTTCAAAAAATTGACTTTTACTTTTAAG
1838474 AGATAGA
129 AGATAGA
*
1838481 TTAAAAAAAG-AGAAAAAAAAGCTCCTCTTTAG-AGTTTTTTTTTAAA-CTTTTTTTTTAAAAAT
1 TTAAAAAAAGAAGAAAAAAAAACTCCTCTTTAGTAGTTTTTTTTTAAATCTTTTTTTTTAAAAAT
1838543 TTTGTTTTTTTAAAAAAAGTTTTTTTTTTAAGAGCTTTTCAAAAAATTGACTTTTACTTTTAAGA
66 TTTGTTTTTTTAAAAAAAG-TTTTTTTTTAAGAGCTTTTCAAAAAATTGACTTTTACTTTTAAGA
1838608 GATAGA
130 GATAGA
1838614 T
1 T
1838615 AAGCTGAAAA
Statistics
Matches: 129, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
132 32 0.25
133 52 0.40
135 14 0.11
136 21 0.16
137 10 0.08
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (135 bp):
TTAAAAAAAGAAGAAAAAAAAACTCCTCTTTAGTAGTTTTTTTTTAAATCTTTTTTTTTAAAAAT
TTTGTTTTTTTAAAAAAAGTTTTTTTTTAAGAGCTTTTCAAAAAATTGACTTTTACTTTTAAGAG
ATAGA
Found at i:1841258 original size:13 final size:14
Alignment explanation
Indices: 1841240--1841268 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1841230 TACCATTATG
1841240 AAAAGAAAAG-AAA
1 AAAAGAAAAGTAAA
1841253 AAAAGAAAAGTAAA
1 AAAAGAAAAGTAAA
1841267 AA
1 AA
1841269 CCTGCCTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAGTAAA
Found at i:1851772 original size:20 final size:20
Alignment explanation
Indices: 1851747--1851786 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1851737 AAAAATACCA
*
1851747 TTTATTAATATTTAATTATT
1 TTTATTAATATTTAAATATT
* *
1851767 TTTATTTATTTTTAAATATT
1 TTTATTAATATTTAAATATT
1851787 AATAATTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATTAATATTTAAATATT
Found at i:1851812 original size:8 final size:8
Alignment explanation
Indices: 1851778--1851826 Score: 50
Period size: 7 Copynumber: 6.2 Consensus size: 8
1851768 TTATTTATTT
1851778 TTAAAT-A
1 TTAAATAA
1851785 TT-AATAA
1 TTAAATAA
1851792 TTATAATTAA
1 TTA-AA-TAA
1851802 TTAAATAA
1 TTAAATAA
1851810 TT-AATAA
1 TTAAATAA
*
1851817 TTTAATAA
1 TTAAATAA
1851825 TT
1 TT
1851827 TAAGATATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
6 3 0.08
7 12 0.32
8 12 0.32
9 4 0.11
10 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TTAAATAA
Found at i:1851822 original size:24 final size:23
Alignment explanation
Indices: 1851778--1851905 Score: 90
Period size: 24 Copynumber: 5.6 Consensus size: 23
1851768 TTATTTATTT
1851778 TTAAATATTAATAATTATAATTAA
1 TTAAATATTAATAATT-TAATTAA
1851802 TTAAATAATTAATAATTTAA-TAA
1 TTAAAT-ATTAATAATTTAATTAA
* *
1851825 TTTAAGATATCAATATTTTAATATAA
1 -TTAA-ATATTAATAATTTAAT-TAA
* * *
1851851 TTTAATTACTAATATTTTAATTAA
1 -TTAAATATTAATAATTTAATTAA
*
1851875 -T-AATATT--TTATTT-A-TAA
1 TTAAATATTAATAATTTAATTAA
1851892 TTTAAATATTAATA
1 -TTAAATATTAATA
1851906 TTTTTAAGTT
Statistics
Matches: 84, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
17 3 0.04
18 1 0.01
19 5 0.06
20 6 0.07
21 4 0.05
22 2 0.02
23 3 0.04
24 27 0.32
25 25 0.30
26 8 0.10
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (23 bp):
TTAAATATTAATAATTTAATTAA
Found at i:1851827 original size:8 final size:8
Alignment explanation
Indices: 1851785--1851829 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
1851775 TTTTTAAATA
1851785 TTAATAAT
1 TTAATAAT
1851793 TATAATTAAT
1 T-TAA-TAAT
*
1851803 TAAATAA-
1 TTAATAAT
1851810 TTAATAAT
1 TTAATAAT
1851818 TTAATAAT
1 TTAATAAT
1851826 TTAA
1 TTAA
1851830 GATATCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 6 0.19
8 16 0.50
9 5 0.16
10 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TTAATAAT
Found at i:1851864 original size:41 final size:41
Alignment explanation
Indices: 1851819--1851905 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
1851809 ATTAATAATT
*
1851819 TAATAATTTAAGAT-ATCAATATTTTA-ATATAATTTAATTAC
1 TAATAATTTAA-ATAAT-AATATTTTATATATAATTTAAATAC
* * * *
1851860 TAATATTTTAATTAATAATATTTTATTTATAATTTAAATAT
1 TAATAATTTAAATAATAATATTTTATATATAATTTAAATAC
1851901 TAATA
1 TAATA
1851906 TTTTTAAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
40 10 0.26
41 29 0.74
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (41 bp):
TAATAATTTAAATAATAATATTTTATATATAATTTAAATAC
Found at i:1851867 original size:14 final size:14
Alignment explanation
Indices: 1851850--1851993 Score: 52
Period size: 15 Copynumber: 10.2 Consensus size: 14
1851840 TTTTAATATA
*
1851850 ATTTAATTACTAAT
1 ATTTAATTAATAAT
1851864 ATTTTAATTAATAAT
1 A-TTTAATTAATAAT
* *
1851879 ATTTTATTTATAAT
1 ATTTAATTAATAAT
*
1851893 -TTAAATATTAAT-AT
1 ATT-TA-ATTAATAAT
*
1851907 TTTTAAGTTAA-AAT
1 ATTTAA-TTAATAAT
1851921 AGTTTAAATTAAATAAT
1 A-TTT-AATT-AATAAT
* **
1851938 -TTTATTTTTTAAT
1 ATTTAATTAATAAT
*
1851951 A-TTCATTAA-AA-
1 ATTTAATTAATAAT
*
1851962 ATTTAATATATTAAT
1 ATTTAAT-TAATAAT
*
1851977 ATTATAAATAA-AAT
1 ATT-TAATTAATAAT
1851991 ATT
1 ATT
1851994 AATAGTTTAA
Statistics
Matches: 95, Mismatches: 19, Indels: 32
0.65 0.13 0.22
Matches are distributed among these distances:
11 1 0.01
12 6 0.06
13 13 0.14
14 32 0.34
15 33 0.35
16 7 0.07
17 3 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTAATTAATAAT
Found at i:1851870 original size:49 final size:48
Alignment explanation
Indices: 1851777--1851871 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 48
1851767 TTTATTTATT
* *
1851777 TTTAAATATTAATAATTATAATTAATTAAATAATTAATAATTTAATAA
1 TTTAAATATCAATAATTATAATTAATTAAATAACTAATAATTTAATAA
* * * *
1851825 TTTAAGATATCAAT-ATTTTAATATAATTTAATTACTAATATTTTAAT
1 TTTAA-ATATCAATAATTATAAT-TAATTAAATAACTAATAATTTAAT
1851872 TAATAATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
48 12 0.31
49 27 0.69
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (48 bp):
TTTAAATATCAATAATTATAATTAATTAAATAACTAATAATTTAATAA
Found at i:1851871 original size:15 final size:15
Alignment explanation
Indices: 1851842--1851884 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1851832 TATCAATATT
*
1851842 TTAAT-ATAATTTAA
1 TTAATAATATTTTAA
*
1851856 TTACTAATATTTTAA
1 TTAATAATATTTTAA
1851871 TTAATAATATTTTA
1 TTAATAATATTTTA
1851885 TTTATAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAATAATATTTTAA
Found at i:1851906 original size:41 final size:41
Alignment explanation
Indices: 1851836--1851927 Score: 116
Period size: 41 Copynumber: 2.2 Consensus size: 41
1851826 TTAAGATATC
*
1851836 AATATTTTAATATAATTTAATTACTAATA-TTTTAA-TTAA
1 AATATTTTAATATAATTTAAATACTAATATTTTTAAGTTAA
* *
1851875 TAATATTTTATTTATAATTTAAATATTAATATTTTTAAGTTAA
1 -AATATTTTA-ATATAATTTAAATACTAATATTTTTAAGTTAA
*
1851918 AATAGTTTAA
1 AATATTTTAA
1851928 ATTAAATAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
40 9 0.20
41 17 0.39
42 14 0.32
43 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (41 bp):
AATATTTTAATATAATTTAAATACTAATATTTTTAAGTTAA
Found at i:1851975 original size:26 final size:27
Alignment explanation
Indices: 1851928--1851987 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
1851918 AATAGTTTAA
* * *
1851928 ATTAAATAATTTTATTTTTTAATATTC
1 ATTAAATAATTTAATATATTAATATTC
1851955 ATTAAA-AATTTAATATATTAATATT-
1 ATTAAATAATTTAATATATTAATATTC
1851980 A-TAAATAA
1 ATTAAATAA
1851988 AATATTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 4 0.14
25 3 0.10
26 16 0.55
27 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
ATTAAATAATTTAATATATTAATATTC
Found at i:1851985 original size:22 final size:22
Alignment explanation
Indices: 1851955--1852022 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 22
1851945 TTTAATATTC
*
1851955 ATTAAAAATTTAATATATTAAT
1 ATTATAAATTTAATATATTAAT
*
1851977 ATTATAAA--TAAAATATTAAT
1 ATTATAAATTTAATATATTAAT
1851997 AGTT-TAAAATATTAATAT-TTAAT
1 A-TTAT-AAAT-TTAATATATTAAT
1852020 ATT
1 ATT
1852023 TTAATCATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 13 0.34
21 5 0.13
22 9 0.24
23 6 0.16
24 5 0.13
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (22 bp):
ATTATAAATTTAATATATTAAT
Found at i:1852073 original size:15 final size:15
Alignment explanation
Indices: 1851959--1852073 Score: 71
Period size: 15 Copynumber: 7.9 Consensus size: 15
1851949 ATATTCATTA
1851959 AAAAT-TTAATATAT
1 AAAATATTAATATAT
* *
1851973 -TAATATT-ATAAAT
1 AAAATATTAATATAT
*
1851986 AAAATATTAATAGTTT
1 AAAATATTAATA-TAT
*
1852002 AAAATATTAATATTT
1 AAAATATTAATATAT
* *
1852017 AATATTTTAATCATAT
1 AAAATATTAAT-ATAT
* *
1852033 -TAATATTAATAATGT
1 AAAATATTAAT-ATAT
**
1852048 TTAA-ATT-ATATAT
1 AAAATATTAATATAT
1852061 AAAATATTAATAT
1 AAAATATTAATAT
1852074 TCTAAATTTT
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
13 13 0.17
14 13 0.17
15 32 0.42
16 19 0.25
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (15 bp):
AAAATATTAATATAT
Found at i:1852113 original size:8 final size:8
Alignment explanation
Indices: 1852100--1852132 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1852090 AATTTATTCC
1852100 TTTTT-TT
1 TTTTTCTT
1852107 TTTTT-TT
1 TTTTTCTT
1852114 TTTTTCTT
1 TTTTTCTT
1852122 TTTTTCTT
1 TTTTTCTT
1852130 TTT
1 TTT
1852133 CATGGGCCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 12 0.48
8 13 0.52
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1852475 original size:2 final size:2
Alignment explanation
Indices: 1852468--1852510 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1852458 AATGAAACTA
1852468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1852510 A
1 A
1852511 GGTCTAGGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1854143 original size:7 final size:7
Alignment explanation
Indices: 1854131--1854157 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1854121 GTTCTATTGC
1854131 AGTTTCT
1 AGTTTCT
1854138 AGTTTCT
1 AGTTTCT
1854145 AGTTTCT
1 AGTTTCT
1854152 AGTTTC
1 AGTTTC
1854158 GATTTCGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
AGTTTCT
Found at i:1857968 original size:2 final size:2
Alignment explanation
Indices: 1857963--1857995 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1857953 TATATATAAT
1857963 AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1857996 TGAAAAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1858055 original size:2 final size:2
Alignment explanation
Indices: 1858048--1858087 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1858038 TCTTTTACTT
1858048 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1858088 GGTAGTTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1862939 original size:15 final size:15
Alignment explanation
Indices: 1862915--1862945 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1862905 CGATGAGTGA
*
1862915 AGGGAGTTTAACCCC
1 AGGGAATTTAACCCC
1862930 AGGGAATTTAACCCC
1 AGGGAATTTAACCCC
1862945 A
1 A
1862946 CTTCATCCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (15 bp):
AGGGAATTTAACCCC
Found at i:1877124 original size:3 final size:3
Alignment explanation
Indices: 1877116--1877149 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1877106 GCCACCTCTA
*
1877116 GGT GGT GGT GGT GGT GGT GGC GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
1877150 ATGGACCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.68, T:0.29
Consensus pattern (3 bp):
GGT
Found at i:1882752 original size:15 final size:16
Alignment explanation
Indices: 1882732--1882763 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1882722 TGTTATAATG
1882732 ATTA-TTTATTTTTAA
1 ATTATTTTATTTTTAA
1882747 ATTATTTTATTTTTAA
1 ATTATTTTATTTTTAA
1882763 A
1 A
1882764 CATTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTATTTTATTTTTAA
Found at i:1882807 original size:34 final size:32
Alignment explanation
Indices: 1882759--1882827 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 32
1882749 TATTTTATTT
* *
1882759 TTAAACATTAATAATTTATAATTTATTTAAAATA
1 TTAAAAATTAATAATTTA-AATAT-TTTAAAATA
* *
1882793 TTAAAAATTGATAATTTAAANATTTTAAAATA
1 TTAAAAATTAATAATTTAAATATTTTAAAATA
1882825 TTA
1 TTA
1882828 TATTTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 12 0.39
33 3 0.10
34 16 0.52
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.45
Consensus pattern (32 bp):
TTAAAAATTAATAATTTAAATATTTTAAAATA
Found at i:1882832 original size:23 final size:22
Alignment explanation
Indices: 1882782--1882832 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
1882772 ATTTATAATT
1882782 TATTTAAAATATTAAAAATTGA
1 TATTTAAAATATTAAAAATTGA
*
1882804 TAATTTAAANATTTTAAAATATT-A
1 T-ATTTAAA-ATATTAAAA-ATTGA
1882828 TATTT
1 TATTT
1882833 TTATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 1 0.04
23 11 0.44
24 10 0.40
25 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTTAAAATATTAAAAATTGA
Found at i:1882840 original size:127 final size:124
Alignment explanation
Indices: 1882683--1883028 Score: 411
Period size: 127 Copynumber: 2.8 Consensus size: 124
1882673 ATCTAATCAT
**
1882683 TAATATTACAAAATATTGATATTTTATTTATAATTTAAATGTTATAATGATTATTTATTTTTAAA
1 TAATATTTTAAAATATT-ATATTTTATTTATAATTTAAATGTTATAATGATTATTTATTTTTAAA
1882748 TTATTTTATTTTTAAACATTAATAATTTATAATTTATTTAAAATATTAAAAATTGATAATT-TA
65 TTATTTTATTTTTAAACATTAATAATTTATAA--TA-TTAAAATA-TAAAAATTGATAATTATA
*
1882811 -AANATTTTAAAATATTATATTTTTATTTATAATTTAAATGTTATAATGATTATTTATTTTTAAA
1 TAATATTTTAAAATATTATA-TTTTATTTATAATTTAAATGTTATAATGATTATTTATTTTTAAA
* *
1882875 TTTTTTTATTTTTTAAACATTAATAA-TTATAATATTAAAATATAAAAATTGATATTTATA
65 TTATTTTA-TTTTTAAACATTAATAATTTATAATATTAAAATATAAAAATTGATAATTATA
* * * **
1882935 TTAATATTTT---AT-TTATACTTTAATCATTAATATTAAATGTTATTGTGATTATTTA-TTTTA
1 -TAATATTTTAAAATATTATATTTTATTTA-TAAT-TTAAATGTTATAATGATTATTTATTTTTA
** *
1882995 TTTTATTTTATCTTTTAAATATTAATCAATTTAT
63 AATTATTTTAT-TTTTAAACATTAAT-AATTTAT
1883029 TTTTTAAATA
Statistics
Matches: 193, Mismatches: 15, Indels: 24
0.83 0.06 0.10
Matches are distributed among these distances:
121 7 0.04
122 34 0.18
123 39 0.20
124 14 0.07
125 2 0.01
126 10 0.05
127 70 0.36
128 17 0.09
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (124 bp):
TAATATTTTAAAATATTATATTTTATTTATAATTTAAATGTTATAATGATTATTTATTTTTAAAT
TATTTTATTTTTAAACATTAATAATTTATAATATTAAAATATAAAAATTGATAATTATA
Done.