Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 6 of 120
Found at i:1773903 original size:28 final size:28
Alignment explanation
Indices: 1773872--1773926 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1773862 TAGAATTTAA
*
1773872 TTATTATAAAAATAGTTTA-AATTAAATT
1 TTATTAT-AAAATAATTTATAATTAAATT
*
1773900 TTATTATATAATAATTTATAATTAAAT
1 TTATTATAAAATAATTTATAATTAAAT
1773927 AGACGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TTATTATAAAATAATTTATAATTAAATT
Found at i:1774100 original size:20 final size:21
Alignment explanation
Indices: 1774055--1774111 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
1774045 CAAATTATTA
* **
1774055 AAAATAATAAAAATATTATTT
1 AAAATAATAATAATATTAGCT
1774076 AAAATAATAATAAT-TTAGCT
1 AAAATAATAATAATATTAGCT
*
1774096 AAAATAAAAAT-ATATT
1 AAAATAATAATAATATT
1774112 GAATAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.06
20 16 0.52
21 13 0.42
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATAATAATAATATTAGCT
Found at i:1775111 original size:27 final size:28
Alignment explanation
Indices: 1775058--1775119 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
1775048 TTTTTTTAGT
**
1775058 ATATTTTGGTAAATAAAAAAAAATTATA
1 ATATTTTAATAAATAAAAAAAAATTATA
1775086 ATATTTTAATAAAT-AAAAAAAATTATA
1 ATATTTTAATAAATAAAAAAAAATTATA
1775113 ATATTTT
1 ATATTTT
1775120 GGTTATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
ATATTTTAATAAATAAAAAAAAATTATA
Found at i:1777517 original size:31 final size:31
Alignment explanation
Indices: 1777456--1777526 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1777446 CCGACCCGAA
*
1777456 TATTATTTTCTTACCATTTTTTTTTGTTTTT
1 TATTATTTTCTTACCATTTTTTGTTGTTTTT
**
1777487 TATTATTTTCTTGTCATTTTCTTGTT-TTTTT
1 TATTATTTTCTTACCATTTT-TTGTTGTTTTT
* *
1777518 CACTATTTT
1 TATTATTTT
1777527 GCTACCAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (31 bp):
TATTATTTTCTTACCATTTTTTGTTGTTTTT
Found at i:1778336 original size:15 final size:15
Alignment explanation
Indices: 1778318--1778349 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1778308 GAAATTGTTC
*
1778318 TAGATGAATTATATA
1 TAGATGAATTACATA
1778333 TAGATGAATTACATA
1 TAGATGAATTACATA
1778348 TA
1 TA
1778350 ATATCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (15 bp):
TAGATGAATTACATA
Found at i:1778517 original size:7 final size:7
Alignment explanation
Indices: 1778507--1778531 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1778497 TACAATGTAC
1778507 AATATTT
1 AATATTT
1778514 AATATTT
1 AATATTT
1778521 AATATTT
1 AATATTT
1778528 AATA
1 AATA
1778532 GATATGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AATATTT
Found at i:1779255 original size:17 final size:16
Alignment explanation
Indices: 1779215--1779247 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1779205 AACATTTAGC
1779215 AAAAAGAGA-AAACCAA
1 AAAAAGA-ATAAACCAA
1779231 AAAAAGAATAAACCAA
1 AAAAAGAATAAACCAA
1779247 A
1 A
1779248 TTAAAGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.76, C:0.12, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAGAATAAACCAA
Found at i:1781103 original size:19 final size:19
Alignment explanation
Indices: 1781076--1781118 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1781066 ATATGTGTTT
* *
1781076 TAATTATAATAAAATAAAG
1 TAATAATAATAAAAGAAAG
1781095 TAATAATAATAAAAGAAAG
1 TAATAATAATAAAAGAAAG
1781114 -AATAA
1 TAATAA
1781119 AGAAAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (19 bp):
TAATAATAATAAAAGAAAG
Found at i:1787215 original size:23 final size:23
Alignment explanation
Indices: 1787188--1787231 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1787178 TTTGCTTATT
*
1787188 TATTTTTCTTAATATAAAAAAAC
1 TATTTTTATTAATATAAAAAAAC
1787211 TATTTTTATTAATATAAAAAA
1 TATTTTTATTAATATAAAAAA
1787232 CCAATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTTTTATTAATATAAAAAAAC
Found at i:1787238 original size:23 final size:23
Alignment explanation
Indices: 1787189--1787238 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1787179 TTGCTTATTT
* *
1787189 ATTTTTCTTAATATAAAAAAACT
1 ATTTTTATTAATATAAAAAAACA
*
1787212 ATTTTTATTAATATAAAAAACCA
1 ATTTTTATTAATATAAAAAAACA
1787235 ATTT
1 ATTT
1787239 AAAAAATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTTTATTAATATAAAAAAACA
Found at i:1788282 original size:13 final size:13
Alignment explanation
Indices: 1788250--1788283 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1788240 TTGTAATGAA
1788250 TTGAAATATTTTT
1 TTGAAATATTTTT
**
1788263 TAAAAATATTTTT
1 TTGAAATATTTTT
1788276 TTGAAATA
1 TTGAAATA
1788284 ATGAAAGAAT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (13 bp):
TTGAAATATTTTT
Found at i:1798084 original size:21 final size:21
Alignment explanation
Indices: 1798060--1798103 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1798050 TTAATATTGC
1798060 TATTATTATTATAACAT-TATA
1 TATTATTATTAT-ACATATATA
1798081 TATTATTATTATACATATATA
1 TATTATTATTATACATATATA
1798102 TA
1 TA
1798104 CACGTGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTATTATTATACATATATA
Found at i:1798319 original size:2 final size:2
Alignment explanation
Indices: 1798314--1798338 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1798304 ACATTTTTTA
1798314 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1798339 CATGCACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1802880 original size:4 final size:5
Alignment explanation
Indices: 1802863--1802896 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1802853 TGGACTTTAA
1802863 TATTT TATTT TA-TT TA-TT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
1802897 TTTGGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:1802905 original size:14 final size:14
Alignment explanation
Indices: 1802866--1802899 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1802856 ACTTTAATAT
1802866 TTTATTTTA-TTTA
1 TTTATTTTATTTTA
1802879 TTTATTTTATTTTA
1 TTTATTTTATTTTA
1802893 TTT-TTTT
1 TTTATTTT
1802900 GGTTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:1810300 original size:23 final size:21
Alignment explanation
Indices: 1810247--1810304 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
1810237 TATATTATAA
*
1810247 AATATTAAACTTGTTTTTATATT
1 AATATTAAA--TGATTTTATATT
1810270 AATATTAATATGATTTTATAATT
1 AATATTAA-ATGATTTTAT-ATT
1810293 AA-ACTTAAATGA
1 AATA-TTAAATGA
1810305 ACTTTTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 13 0.42
23 17 0.55
24 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (21 bp):
AATATTAAATGATTTTATATT
Found at i:1810875 original size:22 final size:22
Alignment explanation
Indices: 1810847--1810889 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1810837 ATTTTTAATC
1810847 AAATATATATATATATAATATT
1 AAATATATATATATATAATATT
* *
1810869 AAATATATATTTATTTAATAT
1 AAATATATATATATATAATAT
1810890 GGGCTAGGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATATATATATATATAATATT
Found at i:1815181 original size:15 final size:15
Alignment explanation
Indices: 1815148--1815185 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1815138 TAGGAAAATG
1815148 TTAATATATTATTAT
1 TTAATATATTATTAT
*
1815163 TTAATTTATTATTCA-
1 TTAATATATTATT-AT
1815178 TTAATATA
1 TTAATATA
1815186 CATTTTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATATATTATTAT
Found at i:1817314 original size:18 final size:19
Alignment explanation
Indices: 1817293--1817372 Score: 60
Period size: 21 Copynumber: 4.2 Consensus size: 19
1817283 GAAAAACCTT
1817293 AAAAATA-ATTAAAAATAA
1 AAAAATACATTAAAAATAA
* * *
1817311 AAAATTACA--AAGAATTA
1 AAAAATACATTAAAAATAA
*
1817328 AAAAATAACATTATAAAATTA
1 AAAAAT-ACATTA-AAAATAA
1817349 AAAAATA-ATATAAAATATAA
1 AAAAATACAT-TAAAA-ATAA
1817369 AAAA
1 AAAA
1817373 TTTACTAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
17 11 0.22
18 9 0.18
19 6 0.12
20 11 0.22
21 12 0.24
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (19 bp):
AAAAATACATTAAAAATAA
Found at i:1817381 original size:19 final size:18
Alignment explanation
Indices: 1817293--1817373 Score: 76
Period size: 18 Copynumber: 4.3 Consensus size: 18
1817283 GAAAAACCTT
*
1817293 AAAAATAAT-TAAAAATA
1 AAAAATAATATAAAATTA
* *
1817310 AAAAATTACA-AAGAATTA
1 AAAAATAATATAA-AATTA
1817328 AAAAATAACATTATAAAATTA
1 AAAAAT-A-A-TATAAAATTA
1817349 AAAAATAATATAAAATATA
1 AAAAATAATATAAAAT-TA
1817368 AAAAAT
1 AAAAAT
1817374 TTACTAAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
17 9 0.17
18 18 0.35
19 9 0.17
20 2 0.04
21 12 0.23
22 2 0.04
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (18 bp):
AAAAATAATATAAAATTA
Found at i:1817617 original size:26 final size:26
Alignment explanation
Indices: 1817583--1817634 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1817573 ATTATTTAAA
**
1817583 TAATGAAAATAATGTTATTTATTATT
1 TAATGAAAATAACATTATTTATTATT
* *
1817609 TAATTAAAATAACATTATTTTTTATT
1 TAATGAAAATAACATTATTTATTATT
1817635 ATTTAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (26 bp):
TAATGAAAATAACATTATTTATTATT
Found at i:1824432 original size:19 final size:19
Alignment explanation
Indices: 1824408--1824444 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1824398 ATTATTTTAT
1824408 TTTATTAC-ACTTTAAAAAA
1 TTTATTACTAC-TTAAAAAA
1824427 TTTATTACTACTTAAAAA
1 TTTATTACTACTTAAAAA
1824445 GAAAATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTATTACTACTTAAAAAA
Found at i:1825887 original size:14 final size:16
Alignment explanation
Indices: 1825868--1825902 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1825858 AATAAAAGAA
1825868 ATAT-ATATAAACATAT
1 ATATAATATAAA-ATAT
1825884 ATATAATATAAAATAT
1 ATATAATATAAAATAT
1825900 ATA
1 ATA
1825903 AAAGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAATATAAAATAT
Found at i:1826278 original size:17 final size:18
Alignment explanation
Indices: 1826244--1826278 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1826234 TCATAAAAGC
*
1826244 TTAAAAAAATATATATAT
1 TTAAAAAAATATACATAT
1826262 TTAAAAAAA-ATACATAT
1 TTAAAAAAATATACATAT
1826279 ATATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAAAATATACATAT
Found at i:1826431 original size:18 final size:18
Alignment explanation
Indices: 1826386--1826434 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1826376 GATAATAACC
1826386 ATAATAATAAATAATATA
1 ATAATAATAAATAATATA
*
1826404 ACAATAATAAATAATGAT-
1 ATAATAATAAATAAT-ATA
*
1826422 ATAATGATAAATA
1 ATAATAATAAATA
1826435 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (18 bp):
ATAATAATAAATAATATA
Found at i:1826431 original size:21 final size:21
Alignment explanation
Indices: 1826369--1826425 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1826359 ATGAATATAG
*
1826369 AAATAATGATAATAACCATAAT
1 AAATAATGAT-ATAACAATAAT
*
1826391 -AATAAATAATATAACAATAAT
1 AAAT-AATGATATAACAATAAT
1826412 AAATAATGATATAA
1 AAATAATGATATAA
1826426 TGATAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (21 bp):
AAATAATGATATAACAATAAT
Found at i:1828081 original size:89 final size:89
Alignment explanation
Indices: 1827964--1828547 Score: 969
Period size: 89 Copynumber: 6.6 Consensus size: 89
1827954 TTAGGGAGAT
* *
1827964 AAGATCT-GTAATCT-TCGATCTACTTCACGGCAGTACATGAAGACAAGATCTATTTTCTTCGAT
1 AAGATCTGGT-ATCTCT-GATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGAT
* *
1828027 CTGCTTTGCCACCAGTATGGGAAGAC
64 CTGCTTCGCCACCAGTATGGGAAGGC
* * *
1828053 AAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTCGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
*
1828118 GCTTTGCCACCAGTATGGGAAGGC
66 GCTTCGCCACCAGTATGGGAAGGC
* *
1828142 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGATAAGATCTGCTTTT-TTTGATC
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCT-ATTTTCTTTGATC
1828206 TGCTTCGCCACCAGTATGGGAAGGC
65 TGCTTCGCCACCAGTATGGGAAGGC
1828231 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
*
1828296 GCTTCGCCACCGGTATGGG-AGGC
66 GCTTCGCCACCAGTATGGGAAGGC
1828319 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
* *
1828384 GCTTCGCCACCGGTATGGGAATGC
66 GCTTCGCCACCAGTATGGGAAGGC
1828408 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
* *
1828473 ACTTCGCCACCGGTATGGGAAGGC
66 GCTTCGCCACCAGTATGGGAAGGC
*
1828497 AAGATCTGGTATCACTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
1828548 GCTGCTTTTC
Statistics
Matches: 474, Mismatches: 16, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
88 92 0.19
89 376 0.79
90 6 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (89 bp):
AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
GCTTCGCCACCAGTATGGGAAGGC
Found at i:1828439 original size:266 final size:267
Alignment explanation
Indices: 1827964--1828547 Score: 969
Period size: 266 Copynumber: 2.2 Consensus size: 267
1827954 TTAGGGAGAT
*
1827964 AAGATCT-GTAATCT-TCGATCTACTTCACGGCAGTACATGAAGACAAGATCTATTTTCTTCGAT
1 AAGATCTGGT-ATCTCT-GATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTCGAT
* *
1828027 CTGCTTTGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATG
64 CTGCTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTCTGATCTACTTCACGCCAGTACATG
*
1828092 AAGACAAGATCTATTTTCTTCGATCTGCTTTGCCACCAGTATGGGAAGGCAAGATCTGGTATCTC
129 AAGACAAGATCTATTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTC
* * *
1828157 TGATCTACTTCACGCCAGTACATGAAGATAAGATCTGCTTTT-TTTGATCTGCTTCGCCACCAGT
194 TGATCTACTTCACGCCAGTACATGAAGACAAGATCT-ATTTTCTTTGATCTACTTCGCCACCAGT
1828221 ATGGGAAGGC
258 ATGGGAAGGC
*
1828231 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTCGATCT
* * *
1828296 GCTTCGCCACCGGTATGGG-AGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAA
66 GCTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTCTGATCTACTTCACGCCAGTACATGAA
* * *
1828360 GACAAGATCTATTTTCTTTGATCTGCTTCGCCACCGGTATGGGAATGCAAGATCTGGTATCTCTG
131 GACAAGATCTATTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTG
*
1828425 ATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCTACTTCGCCACCGGTATG
196 ATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCTACTTCGCCACCAGTATG
1828490 GGAAGGC
261 GGAAGGC
*
1828497 AAGATCTGGTATCACTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
1828548 GCTGCTTTTC
Statistics
Matches: 298, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
265 4 0.01
266 216 0.72
267 75 0.25
268 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (267 bp):
AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTCGATCT
GCTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTCTGATCTACTTCACGCCAGTACATGAA
GACAAGATCTATTTTCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTATCTCTG
ATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCTACTTCGCCACCAGTATG
GGAAGGC
Found at i:1831458 original size:16 final size:16
Alignment explanation
Indices: 1831437--1831568 Score: 92
Period size: 16 Copynumber: 8.4 Consensus size: 16
1831427 TTTGGTTGGC
*
1831437 TGTAATGAAATAGAGG
1 TGTAATGGAATAGAGG
*
1831453 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
1831469 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
* *****
1831485 CGTAATAGGTAATTCTTT
1 TGTAAT-GG-AATAGAGG
* * *
1831503 TGT-TTGG--TTGA-A
1 TGTAATGGAATAGAGG
*
1831515 TGGAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
1831531 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
1831547 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
1831563 CGTAAT
1 TGTAAT
1831569 AGGTAATTCT
Statistics
Matches: 88, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
12 2 0.02
13 5 0.06
15 3 0.03
16 70 0.80
17 3 0.03
18 5 0.06
ACGTcount: A:0.35, C:0.02, G:0.32, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:1831554 original size:78 final size:78
Alignment explanation
Indices: 1831425--1831615 Score: 328
Period size: 78 Copynumber: 2.4 Consensus size: 78
1831415 TTTAAGGGCA
** * *
1831425 TGTTTGGTTGGCTGTAATGAAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
1 TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
1831490 TAGGTAATTCTTT
66 TAGGTAATTCTTT
1831503 TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
1 TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
1831568 TAGGTAATTCTTT
66 TAGGTAATTCTTT
* *
1831581 TGTTTGGTTGAATGGAATGGAATAAAGGCGTAATG
1 TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATG
1831616 ATATTCTTGT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 107 1.00
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (78 bp):
TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
TAGGTAATTCTTT
Found at i:1831636 original size:44 final size:46
Alignment explanation
Indices: 1831550--1831638 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 46
1831540 ATAGATGTGT
* * *
1831550 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAAAGGCGTAATAGATAATTCTTGTGTTTGGTTGAATGG
1831596 AATGGAATAAAGGCGTAAT-GAT-ATTCTTGTGTTTGGTTGAATG
1 AATGGAATAAAGGCGTAATAGATAATTCTTGTGTTTGGTTGAATG
1831639 TAATAGAGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 20 0.50
45 2 0.05
46 18 0.45
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (46 bp):
AATGGAATAAAGGCGTAATAGATAATTCTTGTGTTTGGTTGAATGG
Found at i:1831638 original size:39 final size:44
Alignment explanation
Indices: 1831550--1831660 Score: 115
Period size: 46 Copynumber: 2.6 Consensus size: 44
1831540 ATAGATGTGT
* *
1831550 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGATAATTCTTGTGTTTGGTT--ATGG
*
1831596 AATGGAATAAAGGCGTAAT-GAT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGATAATTCTTGTGTTTGGTTATGG
* *
1831635 AATGTAATAGAGGTGTAATAGCATAA
1 AATGGAATAGAGGCGTAATAG-ATAA
1831661 GGAAAAAAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
39 17 0.30
40 2 0.04
41 2 0.04
42 1 0.02
43 1 0.02
44 13 0.23
45 2 0.04
46 18 0.32
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGATAATTCTTGTGTTTGGTTATGG
Found at i:1831823 original size:18 final size:17
Alignment explanation
Indices: 1831802--1831835 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1831792 TTATTATTAA
*
1831802 ATATATTTTAATTAAAAC
1 ATATAATTTAA-TAAAAC
1831820 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
1831836 TTCTTAATAA
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:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAC
Found at i:1831848 original size:15 final size:16
Alignment explanation
Indices: 1831828--1831857 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1831818 ACATATAATT
1831828 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
1831843 TAATAAATATTCTTA
1 TAATAAATATTCTTA
1831858 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:1836618 original size:16 final size:16
Alignment explanation
Indices: 1836598--1836666 Score: 120
Period size: 16 Copynumber: 4.3 Consensus size: 16
1836588 TTGGTTCGCT
*
1836598 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
1836614 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
1836630 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
1836646 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
1836662 GTAAT
1 GTAAT
1836667 AGGTAATTCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.04, G:0.35, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:1836735 original size:44 final size:46
Alignment explanation
Indices: 1836648--1836740 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
1836638 ATAGATGCGT
*
1836648 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
1836694 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
1836738 AAT
1 AAT
1836741 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 24 0.52
45 3 0.07
46 19 0.41
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:1836736 original size:39 final size:44
Alignment explanation
Indices: 1836648--1836753 Score: 141
Period size: 39 Copynumber: 2.5 Consensus size: 44
1836638 ATAGATGCGT
*
1836648 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
1836694 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
*
1836733 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
1836754 CATAAGTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
39 19 0.33
40 2 0.04
43 1 0.02
44 13 0.23
45 3 0.05
46 19 0.33
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:1837020 original size:25 final size:25
Alignment explanation
Indices: 1836975--1837044 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 25
1836965 ACTAAAATCA
* *
1836975 TAATATATAATACTATAAAATATAATT
1 TAATA-ATAATATTATTAAATATAA-T
1837002 TAA-AATAATATTATTAAATATAAT
1 TAATAATAATATTATTAAATATAAT
*
1837026 TAATAAAAATATATATTAA
1 TAATAATAATAT-TATTAA
1837045 TAAAATTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 4 0.11
25 24 0.63
26 7 0.18
27 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATAATAATATTATTAAATATAAT
Found at i:1837035 original size:15 final size:16
Alignment explanation
Indices: 1837017--1837049 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1837007 TAATATTATT
1837017 AAATATA-ATTAATAA
1 AAATATATATTAATAA
1837032 AAATATATATTAATAA
1 AAATATATATTAATAA
1837048 AA
1 AA
1837050 TTCTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATATATTAATAA
Found at i:1837050 original size:15 final size:13
Alignment explanation
Indices: 1836974--1837050 Score: 59
Period size: 15 Copynumber: 5.5 Consensus size: 13
1836964 TACTAAAATC
*
1836974 ATAATATATAATACT
1 ATAAAATATAAT--T
1836989 ATAAAATATAATT
1 ATAAAATATAATT
1837002 -TAAAATA-ATATT
1 ATAAAATATA-ATT
*
1837014 ATTAAATATAATT
1 ATAAAATATAATT
1837027 AATAAAAATATATATT
1 -AT-AAAATATA-ATT
1837043 AATAAAAT
1 -ATAAAAT
1837051 TCTTAATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
11 1 0.02
12 10 0.19
13 10 0.19
14 3 0.06
15 23 0.43
16 6 0.11
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAAAATATAATT
Found at i:1837051 original size:25 final size:29
Alignment explanation
Indices: 1836989--1837051 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 29
1836979 ATATAATACT
*
1836989 ATAAAATATAATTTAAAATAATATTATTAA
1 ATAAAAT-TAATTAAAAATAATATTATTAA
*
1837019 ATATAATTAA-TAAAAAT-ATA-TATT-A
1 ATAAAATTAATTAAAAATAATATTATTAA
1837044 ATAAAATT
1 ATAAAATT
1837052 CTTAATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 8 0.27
26 4 0.13
27 3 0.10
28 6 0.20
29 3 0.10
30 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
ATAAAATTAATTAAAAATAATATTATTAA
Found at i:1837097 original size:115 final size:118
Alignment explanation
Indices: 1836880--1837113 Score: 379
Period size: 115 Copynumber: 2.0 Consensus size: 118
1836870 TTAATCATAT
* *
1836880 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1836945 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAAT-CTATAAAA-ATAA
1837000 TTTAAAATAA-TATTATTAAATATAA-TTAATAAAAATATAT-A-TTAATAAAATTCTTAATA-T
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
1837060 AATTATTCTTATATGAATTTACTAAAATCATATTATATAATCTATAAAAATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATCTATAAAAATAA
1837113 T
1 T
1837114 ATATAATCTA
Statistics
Matches: 110, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
113 5 0.05
114 8 0.07
115 40 0.36
116 17 0.15
117 1 0.01
118 15 0.14
119 15 0.14
120 9 0.08
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (118 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATCTATAAAAATAA
Found at i:1838818 original size:4 final size:4
Alignment explanation
Indices: 1838809--1838839 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1838799 GATGTTCATA
*
1838809 TATG TATG TATG TATG CATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
1838840 TTGGTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:1849156 original size:27 final size:26
Alignment explanation
Indices: 1849116--1849166 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1849106 TTTAAAATAC
*
1849116 TTTAAAAATATTTTTATTTTTATTTT
1 TTTAAAAATATTTTTATGTTTATTTT
* *
1849142 TTTAAAATATTTTTTTGTGTTTATT
1 TTTAAAA-ATATTTTTATGTTTATT
1849167 AAAAATCAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTAAAAATATTTTTATGTTTATTTT
Found at i:1849878 original size:13 final size:15
Alignment explanation
Indices: 1849848--1849880 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1849838 TTCTCCATAT
1849848 TTTTATTTTTATAAA
1 TTTTATTTTTATAAA
1849863 TTTTA-TTTTA-AAA
1 TTTTATTTTTATAAA
1849876 TTTTA
1 TTTTA
1849881 GTTCAACTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 5 0.28
15 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTATTTTTATAAA
Found at i:1850988 original size:17 final size:18
Alignment explanation
Indices: 1850954--1850995 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1850944 AAATTTTAAA
*
1850954 ATTAAAAATATATGAATT
1 ATTAAAAATAAATGAATT
1850972 ATTAAAAATAAAT-AATT
1 ATTAAAAATAAATGAATT
1850989 ATTAAAA
1 ATTAAAA
1850996 TTATTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTAAAAATAAATGAATT
Found at i:1851057 original size:17 final size:17
Alignment explanation
Indices: 1851035--1851068 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1851025 AAAAGAATAA
1851035 TTTAAAA-TAATTTAATT
1 TTTAAAATTAA-TTAATT
1851052 TTTAAAATTAATTAATT
1 TTTAAAATTAATTAATT
1851069 GCTAACGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAATTAATTAATT
Found at i:1852065 original size:46 final size:46
Alignment explanation
Indices: 1851964--1852125 Score: 269
Period size: 46 Copynumber: 3.6 Consensus size: 46
1851954 TACGTATGAT
1851964 CACTTATCACTTGTC-C-C-TGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTT-TCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
1852007 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
1852053 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1852099 CACTTATCACTTTCTCACTTGATCAGA
1 CACTTATCACTTTCTCACTTGATCAGA
1852126 AGTACTCAAA
Statistics
Matches: 112, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
42 1 0.01
43 13 0.12
44 1 0.01
45 19 0.17
46 78 0.70
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:1858255 original size:2 final size:2
Alignment explanation
Indices: 1858250--1858279 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1858240 TTATTATCTG
1858250 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
1858280 TTGAATGACT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1863525 original size:44 final size:44
Alignment explanation
Indices: 1863457--1863894 Score: 216
Period size: 44 Copynumber: 9.8 Consensus size: 44
1863447 AGTGTCTTCC
* *
1863457 ATCTGCTCCGCTATAA-TCTCAGGGAGATAAGATCCTAAATTTTA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCCTAAATTTTA
* * * *
1863501 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATTATCGGCTTCAATCTGATGTG
1 ATCTGCTCCACTGTAACTTCAGGGAGATA--A-GATC--C-TAAAT-T--T-TA
* * * **
1863555 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTAAATTTTA
* * * * *
1863599 ATCCGCTCCACTGTAATTTCAGGGAGATAGGAT--TATTATCTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTA-AAT-TTTA
* * * *
1863643 ATCTGCTCCGCTGTAATCTT-AGAGAGATAAGA-CCTGAATTTCTTCG
1 ATCTGCTCCACTGTAA-CTTCAGGGAGATAAGATCCT-AAATT-TT-A
* * * * ***
1863689 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CC-AGA-TGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTAAATTTTA
* * * *
1863730 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTAAATTTTA
* * ** * **
1863774 AGCCGCTCCACTGTAACTTCAGGGAGATAAGATAGT--GTCTTGG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTAAAT-TTTA
* *** *
1863817 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCT-GGCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATC-CTAAATTTTA
*
1863861 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATC
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATC
1863895 TGAAATTCTT
Statistics
Matches: 298, Mismatches: 68, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
41 30 0.10
42 5 0.02
43 36 0.12
44 144 0.48
45 10 0.03
46 28 0.09
47 4 0.01
48 3 0.01
49 2 0.01
50 4 0.01
51 4 0.01
52 1 0.00
53 1 0.00
54 26 0.09
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCCTAAATTTTA
Found at i:1863801 original size:131 final size:131
Alignment explanation
Indices: 1863647--1863894 Score: 290
Period size: 131 Copynumber: 1.9 Consensus size: 131
1863637 TCTTCAATCT
* *
1863647 GCTCCGCTGTAATCTTAGAGAGATAAGACCTGAATTTCTTCGG-TCTACTCCACTGTAACCTCAG
1 GCTCCACTGTAATCTTAGAGAGATAAGA--T-AATGTCTT-GGATCTACTCCACTGTAACCTCAG
* *
1863711 GGAGATAAGA-C-C-AGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTT
62 GGAGATAAGATCTCTAGATGCAATCTACTCCACTGTAACCTCAGAGAGATAAGATCCTAAATTTT
1863773 AAGCC
127 AAGCC
* * * * *
1863778 GCTCCACTGTAA-CTTCAGGGAGATAAGATAGTGTCTTGGATCTGCTCCGCTGTAATCTCAGGGA
1 GCTCCACTGTAATCTT-AGAGAGATAAGATAATGTCTTGGATCTACTCCACTGTAACCTCAGGGA
* * * * *
1863842 GATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATC
65 GATAAGATCTCTAGATGCAATCTACTCCACTGTAACCTCAGAGAGATAAGATC
1863895 TGAAATTCTT
Statistics
Matches: 98, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
127 2 0.02
128 34 0.35
129 2 0.02
130 4 0.04
131 56 0.57
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (131 bp):
GCTCCACTGTAATCTTAGAGAGATAAGATAATGTCTTGGATCTACTCCACTGTAACCTCAGGGAG
ATAAGATCTCTAGATGCAATCTACTCCACTGTAACCTCAGAGAGATAAGATCCTAAATTTTAAGC
C
Found at i:1863844 original size:87 final size:87
Alignment explanation
Indices: 1863565--1863892 Score: 274
Period size: 87 Copynumber: 3.8 Consensus size: 87
1863555 ATCTACTCTA
** * ** *
1863565 CTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATTTCAGGGAGATAG
1 CTGTAATC-TCAGAGAGATAAGATCCTAAATTTTAAGCCGCTCCACTGTAACCTCAGGGAGATAA
* * * *
1863629 GATTATTATCTTCAATCTGCTCCG
65 GACTAGTGTCTT-GATCTGCTCCG
* * ** **
1863653 CTGTAATCTTAGAGAGATAAGA-CCTGAATTTCTTCGGTCTACTCCACTGTAACCTCAGGGAGAT
1 CTGTAATCTCAGAGAGATAAGATCCT-AAATT-TTAAG-CCGCTCCACTGTAACCTCAGGGAGAT
* * **
1863717 AAGACCAGATG-C--GATCTACTCTA
63 AAGACTAG-TGTCTTGATCTGCTCCG
* *
1863740 CTGTAACCTCAGAGAGATAAGATCCTAAATTTTAAGCCGCTCCACTGTAACTTCAGGGAGATAAG
1 CTGTAATCTCAGAGAGATAAGATCCTAAATTTTAAGCCGCTCCACTGTAACCTCAGGGAGATAAG
1863805 A-TAGTGTCTTGGATCTGCTCCG
66 ACTAGTGTCTT-GATCTGCTCCG
* *** * * *
1863827 CTGTAATCTCAGGGAGATAAGATCTCT-GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAA
1 CTGTAATCTCAGAGAGATAAGATC-CTAAATTTTAAGCCGCTCCACTGTAACCTCAGGGAGATAA
1863891 GA
65 GA
1863893 TCTGAAATTC
Statistics
Matches: 188, Mismatches: 41, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
83 2 0.01
84 3 0.02
85 27 0.14
86 3 0.02
87 96 0.51
88 26 0.14
89 3 0.02
90 27 0.14
91 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (87 bp):
CTGTAATCTCAGAGAGATAAGATCCTAAATTTTAAGCCGCTCCACTGTAACCTCAGGGAGATAAG
ACTAGTGTCTTGATCTGCTCCG
Found at i:1877190 original size:22 final size:24
Alignment explanation
Indices: 1877152--1877200 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
1877142 GTGTATATGT
*
1877152 ATATGTATTTACTAAAA-TA-AAA
1 ATATGTATGTACTAAAAGTATAAA
1877174 ATATGTATGTA-TAAAAAGTATAAA
1 ATATGTATGTACT-AAAAGTATAAA
1877198 ATA
1 ATA
1877201 CAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 2 0.09
24 6 0.26
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATGTATGTACTAAAAGTATAAA
Found at i:1880447 original size:12 final size:12
Alignment explanation
Indices: 1880430--1880455 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1880420 AAGGATGATA
1880430 CCATTAGAGTTC
1 CCATTAGAGTTC
1880442 CCATTAGAGTTC
1 CCATTAGAGTTC
1880454 CC
1 CC
1880456 GAGCTAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (12 bp):
CCATTAGAGTTC
Found at i:1883095 original size:31 final size:31
Alignment explanation
Indices: 1883057--1883126 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
1883047 GTTAGAAGCC
*
1883057 CTCAAATGTAATTTATATATTGCATCAAATG
1 CTCAAATGTAATCTATATATTGCATCAAATG
1883088 CTCAAATGTAATCTATATATTGCATCAAATG
1 CTCAAATGTAATCTATATATTGCATCAAATG
1883119 CTCAAATG
1 CTCAAATG
1883127 CATCCTTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.36
Consensus pattern (31 bp):
CTCAAATGTAATCTATATATTGCATCAAATG
Found at i:1885347 original size:37 final size:39
Alignment explanation
Indices: 1885289--1885391 Score: 101
Period size: 37 Copynumber: 2.7 Consensus size: 39
1885279 AAAAATAATT
* * *
1885289 TTATTTTAATAGTTTAATATTAAATTTGAT-TT-AA-TAC
1 TTATCTTAATAGTTTAATATT-AATTTAATATTAAAGTAA
*
1885326 TTATCTTAATAGTATT-TTATTAATTTAATATTAAAGTAA
1 TTATCTTAATAGT-TTAATATTAATTTAATATTAAAGTAA
*
1885365 TTATCTTAATA-TTAAAT-TTAATTTAAT
1 TTATCTTAATAGTTTAATATTAATTTAAT
1885392 GTTTATCTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
36 7 0.13
37 29 0.53
38 6 0.11
39 13 0.24
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (39 bp):
TTATCTTAATAGTTTAATATTAATTTAATATTAAAGTAA
Found at i:1885439 original size:62 final size:59
Alignment explanation
Indices: 1885370--1885486 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
1885360 AGTAATTATC
* * * *
1885370 TTAATATTAAATTTAATTTAATGTTTATCTTGTTGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-TT-ATAAATATTATATTAATTTAATAAGAT
1885432 TTAATATTAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATA
1885487 TTAAAATGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 21 0.41
60 2 0.04
61 1 0.02
62 27 0.53
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATAAGAT
Found at i:1887796 original size:20 final size:20
Alignment explanation
Indices: 1887765--1887818 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1887755 TTTTATAATG
1887765 AAATATTAAAAATATTTAAATT
1 AAATA-TAAAAATA-TTAAATT
*
1887787 AAA-ATAAAAATATTAATTT
1 AAATATAAAAATATTAAATT
*
1887806 AAATTTAAAAATA
1 AAATATAAAAATA
1887819 CCTTATTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.31
20 16 0.55
21 1 0.03
22 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATAAAAATATTAAATT
Found at i:1889398 original size:33 final size:33
Alignment explanation
Indices: 1889346--1889425 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1889336 TCATCACCCA
* *
1889346 GTAGAAGGTTTTTATACCCTTCTTCTTTCTCCC
1 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
1889379 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
1 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
*
1889412 GAAGAAGGTGTTTA
1 GTAGAAGGTGTTTA
1889426 TTTATACCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (33 bp):
GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
Found at i:1893673 original size:18 final size:17
Alignment explanation
Indices: 1893634--1893677 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1893624 AAATTTTTCA
1893634 AAAAATT-TTAAAAAAT
1 AAAAATTATTAAAAAAT
1893650 AAAAATTATTAAAAAAT
1 AAAAATTATTAAAAAAT
*
1893667 AGGAAATTATT
1 A-AAAATTATT
1893678 TTAAATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 7 0.28
17 10 0.40
18 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAAATTATTAAAAAAT
Found at i:1895575 original size:24 final size:24
Alignment explanation
Indices: 1895476--1895586 Score: 122
Period size: 24 Copynumber: 4.7 Consensus size: 24
1895466 ATTGGTGTTA
1895476 TATTATTTT-AAGTTCATTATGTA-
1 TATTATTTTAAAGTT-ATTATGTAT
* *
1895499 TGTTGTTTTAAA-TCTATTATGTAT
1 TATTATTTTAAAGT-TATTATGTAT
* * *
1895523 TATTGTTTTAAAATTATTGTGTAT
1 TATTATTTTAAAGTTATTATGTAT
*
1895547 TATTATTTTAAAGTTACTATGTAT
1 TATTATTTTAAAGTTATTATGTAT
1895571 TATTA-TTTAAAGTTAT
1 TATTATTTTAAAGTTAT
1895587 CTCATATTTA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
23 26 0.35
24 48 0.64
25 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.57
Consensus pattern (24 bp):
TATTATTTTAAAGTTATTATGTAT
Found at i:1895597 original size:24 final size:24
Alignment explanation
Indices: 1895520--1895598 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
1895510 ATCTATTATG
* * * * *
1895520 TATTATTGTTTTAAAATTATTGTG
1 TATTATTATTTTAAAGTTACTATA
*
1895544 TATTATTATTTTAAAGTTACTATG
1 TATTATTATTTTAAAGTTACTATA
1895568 TATTATTA-TTTAAAGTTATCTCATA
1 TATTATTATTTTAAAGTTA-CT-ATA
1895593 T-TTATT
1 TATTATT
1895599 TTATTGTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 10 0.21
24 35 0.73
25 3 0.06
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.57
Consensus pattern (24 bp):
TATTATTATTTTAAAGTTACTATA
Found at i:1899384 original size:43 final size:43
Alignment explanation
Indices: 1899292--1899434 Score: 187
Period size: 50 Copynumber: 3.1 Consensus size: 43
1899282 TTTGAGTACT
* *
1899292 TCTGATCAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATTAGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTA
1899336 TCTGATTAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATTAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
1899379 TCTGATAAGTGACAAGTAACAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGAT---T----AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
1899429 TCTGAT
1 TCTGAT
1899435 CAGAGATAAT
Statistics
Matches: 89, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
43 19 0.21
44 28 0.31
46 1 0.01
50 41 0.46
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (43 bp):
TCTGATTAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:1899456 original size:50 final size:50
Alignment explanation
Indices: 1899347--1899460 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 50
1899337 CTGATTAGTG
* *
1899347 ACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATAAGTGACAAGTA
1 ACAAATGATAAGTGGTAGCTTAGCTACACTTATCTGATAAGAGACAAGTA
* * *
1899397 ACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGAGATAA-TA
1 ACAAATGATAAGTGGTAGCTTAGCTACACTTATCTGATAAGAGACAAGTA
*
1899446 GATAAATGATAAGTG
1 -ACAAATGATAAGTG
1899461 ATTCCGTGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 2 0.03
50 56 0.97
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (50 bp):
ACAAATGATAAGTGGTAGCTTAGCTACACTTATCTGATAAGAGACAAGTA
Found at i:1902136 original size:17 final size:16
Alignment explanation
Indices: 1902093--1902136 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
1902083 GAAAGTAAAA
*
1902093 AAAAGAAACAAAGAAG
1 AAAAGAAACAGAGAAG
1902109 AAAAGAAACAGAGAAG
1 AAAAGAAACAGAGAAG
*
1902125 CAAACGAAACAG
1 -AAAAGAAACAG
1902137 GGGAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.68, C:0.11, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAGAAACAGAGAAG
Found at i:1902917 original size:12 final size:11
Alignment explanation
Indices: 1902892--1902986 Score: 52
Period size: 11 Copynumber: 8.7 Consensus size: 11
1902882 ATTTTTTTAA
*
1902892 TTTTAAAATAT
1 TTTTAAAAAAT
1902903 TTTTAAAAAACT
1 TTTTAAAAAA-T
***
1902915 TTTT-TTTAA-
1 TTTTAAAAAAT
*
1902924 TTTTAAAATAT
1 TTTTAAAAAAT
*
1902935 TTTTAAAATACT
1 TTTTAAAA-AAT
*
1902947 TTTTAAAATAT
1 TTTTAAAAAAT
**
1902958 TTTTTTAAAA-
1 TTTTAAAAAAT
* *
1902968 TTTTAATATAT
1 TTTTAAAAAAT
1902979 TTTTAAAA
1 TTTTAAAA
1902987 TACTTTTTTA
Statistics
Matches: 59, Mismatches: 20, Indels: 10
0.66 0.22 0.11
Matches are distributed among these distances:
9 4 0.07
10 7 0.12
11 34 0.58
12 14 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAAAAT
Found at i:1902924 original size:32 final size:32
Alignment explanation
Indices: 1902883--1902950 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
1902873 CTTTTTAAAA
1902883 TTTTTTTAATTTTAAAATATTTTTAAAAAACT
1 TTTTTTTAATTTTAAAATATTTTTAAAAAACT
*
1902915 TTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTTAATTTTAAAATATTTTTAAAAAACT
1902947 TTTT
1 TTTT
1902951 AAAATATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTTTTTAATTTTAAAATATTTTTAAAAAACT
Found at i:1902970 original size:44 final size:43
Alignment explanation
Indices: 1902892--1903019 Score: 156
Period size: 44 Copynumber: 3.0 Consensus size: 43
1902882 ATTTTTTTAA
*
1902892 TTTTAAAATA-TTTTTAAAAAACTTTTTTT-TAATTTTAAAATAT
1 TTTTAAAATACTTTTT-AAAAA-TTTTTTTAAAATTTTAAAATAT
*
1902935 TTTTAAAATACTTTTTAAAATATTTTTTTAAAATTTTAATATAT
1 TTTTAAAATACTTTTTAAAA-ATTTTTTTAAAATTTTAAAATAT
* *
1902979 TTTTAAAATACTTTTT--TAATTTTTTTATAATTTTTAAAATA
1 TTTTAAAATACTTTTTAAAAATTTTTTTA-AAATTTTAAAATA
1903020 AAAATGGGCC
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
41 9 0.12
42 12 0.16
43 21 0.28
44 34 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (43 bp):
TTTTAAAATACTTTTTAAAAATTTTTTTAAAATTTTAAAATAT
Found at i:1902987 original size:32 final size:32
Alignment explanation
Indices: 1902935--1903019 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
1902925 TTTAAAATAT
* *
1902935 TTTTAAAATACTTTTTAAAATATTTTTTTAAAA
1 TTTTAATATA-TTTTTAAAATACTTTTTTAAAA
**
1902968 TTTTAATATATTTTTAAAATACTTTTTTAATT
1 TTTTAATATATTTTTAAAATACTTTTTTAAAA
*
1903000 TTTTTATA-ATTTTTAAAATA
1 TTTTAATATATTTTTAAAATA
1903020 AAAATGGGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 12 0.26
32 26 0.55
33 9 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (32 bp):
TTTTAATATATTTTTAAAATACTTTTTTAAAA
Found at i:1903312 original size:3 final size:3
Alignment explanation
Indices: 1903304--1903338 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1903294 GGTAAGTATA
1903304 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1903339 GAGTGAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1903451 original size:29 final size:30
Alignment explanation
Indices: 1903390--1903467 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
1903380 AAATTGTTTG
*** *
1903390 TTGATTGAAAAAT-AATTAGTGATTTGAAT
1 TTGATTGAAAAATGAATTAAAAATATGAAT
1903419 TTGATTGAAAAATGAATTAAAAATATGAA-
1 TTGATTGAAAAATGAATTAAAAATATGAAT
* *
1903448 TTGAAT-AAAAGTGAATTAAA
1 TTGATTGAAAAATGAATTAAA
1903468 TTATGATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 13 0.31
29 18 0.43
30 11 0.26
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (30 bp):
TTGATTGAAAAATGAATTAAAAATATGAAT
Found at i:1906657 original size:39 final size:39
Alignment explanation
Indices: 1906603--1906730 Score: 238
Period size: 39 Copynumber: 3.3 Consensus size: 39
1906593 CAACTTCGGC
*
1906603 TCTACTCCATCGACAGCTCCTGGCTTCGGCTTTTCATCT
1 TCTACTTCATCGACAGCTCCTGGCTTCGGCTTTTCATCT
1906642 TCTACTTCATCGACAGCTCCTGGCTTCGGCTTTTCATCT
1 TCTACTTCATCGACAGCTCCTGGCTTCGGCTTTTCATCT
1906681 TCTACTTCATCGACAGCTCCTGGCTTCGGCTTTTCATCT
1 TCTACTTCATCGACAGCTCCTGGCTTCGGCTTTTCATCT
*
1906720 TCTACTACATC
1 TCTACTTCATC
1906731 ATTCGGCTCT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.14, C:0.34, G:0.14, T:0.38
Consensus pattern (39 bp):
TCTACTTCATCGACAGCTCCTGGCTTCGGCTTTTCATCT
Found at i:1913664 original size:33 final size:33
Alignment explanation
Indices: 1913612--1913731 Score: 183
Period size: 33 Copynumber: 3.7 Consensus size: 33
1913602 TCATCACCCA
*
1913612 GTAGAAGGTTTTTATACCCTTCTTCTTTCTCCC
1 GTAGAAGGTGTTTATACCCTTCTTCTTTCTCCC
*
1913645 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
1 GTAGAAGGTGTTTATACCCTTCTTCTTTCTCCC
1913678 GT---AGGTGTTTATACCCTTCTTCTTTCTCCC
1 GTAGAAGGTGTTTATACCCTTCTTCTTTCTCCC
* *
1913708 GTAGAAGGTATTTATACCCATCTT
1 GTAGAAGGTGTTTATACCCTTCTT
1913732 TCTAACTTTC
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
30 29 0.37
33 50 0.63
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.42
Consensus pattern (33 bp):
GTAGAAGGTGTTTATACCCTTCTTCTTTCTCCC
Found at i:1913684 original size:30 final size:30
Alignment explanation
Indices: 1913617--1913711 Score: 145
Period size: 30 Copynumber: 3.1 Consensus size: 30
1913607 ACCCAGTAGA
*
1913617 AGGTTTTTATACCCTTCTTCTTTCTCCCGT
1 AGGTGTTTATACCCTTCTTCTTTCTCCCGT
*
1913647 AGAAGGTGTTTAAACCCTTCTTCTTTCTCCCGT
1 ---AGGTGTTTATACCCTTCTTCTTTCTCCCGT
1913680 AGGTGTTTATACCCTTCTTCTTTCTCCCGT
1 AGGTGTTTATACCCTTCTTCTTTCTCCCGT
1913710 AG
1 AG
1913712 AAGGTATTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
30 31 0.53
33 28 0.47
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.44
Consensus pattern (30 bp):
AGGTGTTTATACCCTTCTTCTTTCTCCCGT
Found at i:1921944 original size:25 final size:25
Alignment explanation
Indices: 1921911--1921963 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1921901 TAAAAAACGA
*
1921911 AAAAGTAAAATATTTTATATTAATT
1 AAAAGTAAAATATTATATATTAATT
* * *
1921936 AAAATTAAAATATTATATTTTCATT
1 AAAAGTAAAATATTATATATTAATT
1921961 AAA
1 AAA
1921964 GGCAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAAAGTAAAATATTATATATTAATT
Found at i:1925443 original size:19 final size:17
Alignment explanation
Indices: 1925419--1925467 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
1925409 TTTTATAATT
1925419 TTTAAAATTTTACAAAAAA
1 TTTAAAATTTT--AAAAAA
1925438 TTTAAAAGTTATTAAAAAA
1 TTTAAAA-TT-TTAAAAAA
*
1925457 TTTAACATTTT
1 TTTAAAATTTT
1925468 TATATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 19 0.70
20 2 0.07
21 2 0.07
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAAATTTTAAAAAA
Found at i:1926583 original size:2 final size:2
Alignment explanation
Indices: 1926576--1926610 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1926566 AATTATGTAA
1926576 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1926611 AACTTAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1927732 original size:24 final size:23
Alignment explanation
Indices: 1927704--1927752 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1927694 ATGGAACAAT
* *
1927704 ATTTTATGCACCGTCGGTGTAATA
1 ATTTTATGCACCATCAGTG-AATA
*
1927728 ATTTTATGTACCATCAGTGAATA
1 ATTTTATGCACCATCAGTGAATA
1927751 AT
1 AT
1927753 AACATGTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (23 bp):
ATTTTATGCACCATCAGTGAATA
Found at i:1929377 original size:24 final size:21
Alignment explanation
Indices: 1929333--1929373 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1929323 CAGGGTAAGG
1929333 AGCAGCATAATGTGGAGGTGC
1 AGCAGCATAATGTGGAGGTGC
*
1929354 AGCAGCATACTGTGGAGGTG
1 AGCAGCATAATGTGGAGGTG
1929374 GTGCCATCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.39, T:0.20
Consensus pattern (21 bp):
AGCAGCATAATGTGGAGGTGC
Found at i:1929396 original size:78 final size:78
Alignment explanation
Indices: 1929267--1929410 Score: 261
Period size: 78 Copynumber: 1.8 Consensus size: 78
1929257 AACCAGGCCT
*
1929267 TGGAGGTGGAGCAGCATACTGTGGAGGTGGTGCCATCACTGGGGGATAACCTTGAGCAGGGTAAG
1 TGGAGGTGCAGCAGCATACTGTGGAGGTGGTGCCATCACTGGGGGATAACCTTGAGCAGGGTAAG
1929332 GAGCAGCATAATG
66 GAGCAGCATAATG
* *
1929345 TGGAGGTGCAGCAGCATACTGTGGAGGTGGTGCCATCGCTGGGGGATAACCTTGAGGAGGGTAAG
1 TGGAGGTGCAGCAGCATACTGTGGAGGTGGTGCCATCACTGGGGGATAACCTTGAGCAGGGTAAG
1929410 G
66 G
1929411 GTCAGGACAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.24, C:0.15, G:0.42, T:0.19
Consensus pattern (78 bp):
TGGAGGTGCAGCAGCATACTGTGGAGGTGGTGCCATCACTGGGGGATAACCTTGAGCAGGGTAAG
GAGCAGCATAATG
Found at i:1931280 original size:99 final size:98
Alignment explanation
Indices: 1931135--1931332 Score: 360
Period size: 99 Copynumber: 2.0 Consensus size: 98
1931125 CCGTCACTAT
* *
1931135 TGAAGATTCATAATTGATATATTAGGAAATTATCGTGAGTTTGTTTTATTCTTATGGTTATGAAG
1 TGAAGATTCATAATTGATATATTAGGAAATTATCGTGAATTTGTTTTATTCTTATGGTTATAAAG
1931200 TATCTTTGACTTTTCCCTTTTGCATCTCCAACAA
66 TATCTTTGACTTTTCCCTTTT-CATCTCCAACAA
1931234 TGAAGATTCATAATTGATATATTAGGAAATTATCGTGAATTTGTTTTATTCTTATGGTTATAAAG
1 TGAAGATTCATAATTGATATATTAGGAAATTATCGTGAATTTGTTTTATTCTTATGGTTATAAAG
*
1931299 TATCTTTGACTTTTCTCTTTTCATCTCCAACAA
66 TATCTTTGACTTTTCCCTTTTCATCTCCAACAA
1931332 T
1 T
1931333 CTGCCATCCA
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
98 13 0.14
99 83 0.86
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (98 bp):
TGAAGATTCATAATTGATATATTAGGAAATTATCGTGAATTTGTTTTATTCTTATGGTTATAAAG
TATCTTTGACTTTTCCCTTTTCATCTCCAACAA
Found at i:1948342 original size:2 final size:2
Alignment explanation
Indices: 1948335--1948383 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1948325 CATTGCCAAC
1948335 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
1948377 AT AT AT A
1 AT AT AT A
1948384 CACATGATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1950260 original size:17 final size:17
Alignment explanation
Indices: 1950210--1950272 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 17
1950200 TGATCCGATT
1950210 AAAACACGATAATTTTTG
1 AAAACACGA-AATTTTTG
*
1950228 AAAACATGAAACTTTTTG
1 AAAACACGAAA-TTTTTG
1950246 -AAACACGAGAA-TTTTG
1 AAAACACGA-AATTTTTG
1950262 AAAACACGAAA
1 AAAACACGAAA
1950273 AATTTTCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 7 0.17
17 17 0.43
18 16 0.40
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (17 bp):
AAAACACGAAATTTTTG
Found at i:1950278 original size:18 final size:18
Alignment explanation
Indices: 1950210--1950278 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
1950200 TGATCCGATT
* *
1950210 AAAACACGATAATTTTTG
1 AAAACACGAAAAATTTTG
* **
1950228 AAAACATGAAACTTTTTG
1 AAAACACGAAAAATTTTG
*
1950246 -AAACACG-AGAATTTTG
1 AAAACACGAAAAATTTTG
1950262 AAAACACGAAAAATTTT
1 AAAACACGAAAAATTTT
1950279 CCGATTTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 6 0.15
17 13 0.32
18 22 0.54
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (18 bp):
AAAACACGAAAAATTTTG
Found at i:1950808 original size:10 final size:10
Alignment explanation
Indices: 1950787--1950828 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1950777 CCCCTTTTTA
1950787 TTTTTTCT-T
1 TTTTTTCTCT
1950796 TTTTTTCTCT
1 TTTTTTCTCT
*
1950806 TTTTTCCTCT
1 TTTTTTCTCT
1950816 TCTTTTT-TCT
1 T-TTTTTCTCT
1950826 TTT
1 TTT
1950829 CTTTTTCTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 10 0.34
10 15 0.52
11 4 0.14
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:1950895 original size:23 final size:23
Alignment explanation
Indices: 1950869--1950927 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
1950859 GCTTGGAGGC
1950869 CTGCTGGCCTGCTAGGGGCTGGG
1 CTGCTGGCCTGCTAGGGGCTGGG
*
1950892 CTGCTGGCCTGTTAGGGGCTGGG
1 CTGCTGGCCTGCTAGGGGCTGGG
*
1950915 CTGCTGGCTTGCT
1 CTGCTGGCCTGCT
1950928 GGGCTGCCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.03, C:0.25, G:0.44, T:0.27
Consensus pattern (23 bp):
CTGCTGGCCTGCTAGGGGCTGGG
Found at i:1951066 original size:21 final size:21
Alignment explanation
Indices: 1951041--1951112 Score: 108
Period size: 21 Copynumber: 3.3 Consensus size: 21
1951031 GGGTTGCTGT
1951041 TCGGGTCGGATCGTTGGTGGG
1 TCGGGTCGGATCGTTGGTGGG
*
1951062 TCGGGTCGGATCGTCGGTGGG
1 TCGGGTCGGATCGTTGGTGGG
1951083 TCGGGTCGGATCGATTCGGTCGGG
1 TCGGGTCGGATCG-TT-GGT-GGG
1951107 TCGGGT
1 TCGGGT
1951113 TGACCCGACT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 33 0.72
22 1 0.02
23 3 0.07
24 9 0.20
ACGTcount: A:0.06, C:0.18, G:0.50, T:0.26
Consensus pattern (21 bp):
TCGGGTCGGATCGTTGGTGGG
Found at i:1951594 original size:29 final size:29
Alignment explanation
Indices: 1951527--1951673 Score: 109
Period size: 30 Copynumber: 5.0 Consensus size: 29
1951517 TAAATGCAGC
* *
1951527 AAAAGTTTTGGGG-CTAAAACATAATTTTGA
1 AAAAGTTTAGGGGTC-AAAATATAATTTT-A
** * *
1951557 GGAAGTTTATGGGTCAAAATGTAATTTTA
1 AAAAGTTTAGGGGTCAAAATATAATTTTA
*** * *
1951586 AAAAGTTTATATGTTAAAATGTAATTTTA
1 AAAAGTTTAGGGGTCAAAATATAATTTTA
* * *
1951615 GGAAAA-TTTAGGGGTTAAAATACAATTTCA
1 --AAAAGTTTAGGGGTCAAAATATAATTTTA
1951645 AAAAGTTTAGGGGGTCAAAATATAATTTT
1 AAAAGTTTA-GGGGTCAAAATATAATTTT
1951674 TTATTTTTTG
Statistics
Matches: 92, Mismatches: 20, Indels: 10
0.75 0.16 0.08
Matches are distributed among these distances:
28 4 0.04
29 29 0.32
30 54 0.59
31 5 0.05
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (29 bp):
AAAAGTTTAGGGGTCAAAATATAATTTTA
Found at i:1951604 original size:59 final size:59
Alignment explanation
Indices: 1951541--1951653 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
1951531 GTTTTGGGGC
* * ** *
1951541 TAAAACATAATTTTGAGG-AAGTTTATGGGTCAAAATGTAATTTTAAAAAGTTTATATGT
1 TAAAACATAATTTT-AGGAAAATTTAGGGGTCAAAATACAATTTCAAAAAGTTTATATGT
** *
1951600 TAAAATGTAATTTTAGGAAAATTTAGGGGTTAAAATACAATTTCAAAAAGTTTA
1 TAAAACATAATTTTAGGAAAATTTAGGGGTCAAAATACAATTTCAAAAAGTTTA
1951654 GGGGGTCAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
58 3 0.07
59 42 0.93
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (59 bp):
TAAAACATAATTTTAGGAAAATTTAGGGGTCAAAATACAATTTCAAAAAGTTTATATGT
Found at i:1951634 original size:30 final size:30
Alignment explanation
Indices: 1951548--1951635 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 30
1951538 GGCTAAAACA
* *
1951548 TAATTTTGAGG-AAGTTTATGGGTCAAAATG
1 TAATTTT-AGGAAAATTTATGGGTTAAAATG
**
1951578 TAATTTTA--AAAAGTTTATATGTTAAAATG
1 TAATTTTAGGAAAA-TTTATGGGTTAAAATG
*
1951607 TAATTTTAGGAAAATTTAGGGGTTAAAAT
1 TAATTTTAGGAAAATTTATGGGTTAAAAT
1951636 ACAATTTCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
28 2 0.04
29 22 0.47
30 19 0.40
31 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.40
Consensus pattern (30 bp):
TAATTTTAGGAAAATTTATGGGTTAAAATG
Found at i:1951687 original size:9 final size:8
Alignment explanation
Indices: 1951670--1951712 Score: 50
Period size: 8 Copynumber: 4.9 Consensus size: 8
1951660 CAAAATATAA
1951670 TTTTTTAT
1 TTTTTTAT
1951678 TTTTTGTAT
1 TTTTT-TAT
1951687 TTTTTTAT
1 TTTTTTAT
1951695 TTTTATATAT
1 TTTT-T-TAT
1951705 ATTTTTTA
1 -TTTTTTA
1951713 AAAAAAGCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 12 0.39
9 11 0.35
10 4 0.13
11 4 0.13
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1951692 original size:17 final size:19
Alignment explanation
Indices: 1951664--1951712 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
1951654 GGGGGTCAAA
1951664 ATATA-ATTTTTTATTTTT
1 ATATATATTTTTTATTTTT
*
1951682 -TGTAT-TTTTTTATTTTT
1 ATATATATTTTTTATTTTT
1951699 ATATATATTTTTTA
1 ATATATATTTTTTA
1951713 AAAAAAGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 15 0.58
18 4 0.15
19 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
ATATATATTTTTTATTTTT
Found at i:1952017 original size:75 final size:75
Alignment explanation
Indices: 1951891--1952045 Score: 256
Period size: 75 Copynumber: 2.1 Consensus size: 75
1951881 TGATTCCCCC
* * * * * *
1951891 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCCTTGGTGGTTGTTAAGTGCTGATTCCACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATCCCACCGTAAC
1951956 TTGAATGTGA
66 TTGAATGTGA
1951966 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATCCCACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATCCCACCGTAAC
1952031 TTGAATGTGA
66 TTGAATGTGA
1952041 AAGGG
1 AAGGG
1952046 ATCCCACCGT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATCCCACCGTAAC
TTGAATGTGA
Found at i:1952057 original size:28 final size:28
Alignment explanation
Indices: 1952017--1952073 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1952007 GCTAACTGCT
1952017 GATCCCACCGTAACTTGAATGTGAAAGG
1 GATCCCACCGTAACTTGAATGTGAAAGG
1952045 GATCCCACCGTAACTTGAATGTGAAAGG
1 GATCCCACCGTAACTTGAATGTGAAAGG
1952073 G
1 G
1952074 GTTGCTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (28 bp):
GATCCCACCGTAACTTGAATGTGAAAGG
Found at i:1952065 original size:103 final size:103
Alignment explanation
Indices: 1951946--1952148 Score: 388
Period size: 103 Copynumber: 2.0 Consensus size: 103
1951936 AGTGCTGATT
1951946 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
1 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
1952011 ACTGCTGATCCCACCGTAACTTGAATGTGAAAGGGATC
66 ACTGCTGATCCCACCGTAACTTGAATGTGAAAGGGATC
1952049 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
1 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
* *
1952114 AGTGCTGATCCTACCGTAACTTGAATGTGAAAGGG
66 ACTGCTGATCCCACCGTAACTTGAATGTGAAAGGG
1952149 GTTGCTAAGT
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (103 bp):
CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
ACTGCTGATCCCACCGTAACTTGAATGTGAAAGGGATC
Found at i:1952136 original size:75 final size:74
Alignment explanation
Indices: 1952049--1952278 Score: 329
Period size: 75 Copynumber: 3.1 Consensus size: 74
1952039 GAAAGGGATC
*
1952049 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
1 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATCGGTGGTTGCTA
1952114 AGTGCTGAT
66 AGTGCTGAT
* * *
1952123 CCTACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTTATTCGCCGAATCATTGGTGGTTGCT
1 CC-ACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATCGGTGGTTGCT
*
1952188 AAGT-TTGATT
65 AAGTGCTGA-T
* *
1952198 CCACCGTATCTTCGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA-CTAGTGGTTGC
1 CCACCGTAACTT-GAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATC-GGTGGTTGC
*
1952262 GAAGTGCTGAAT
64 TAAGTGCTG-AT
1952274 CCACC
1 CCACC
1952279 AAATAACGGT
Statistics
Matches: 138, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
74 14 0.10
75 115 0.83
76 8 0.06
77 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (74 bp):
CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATCGGTGGTTGCTA
AGTGCTGAT
Found at i:1952217 original size:178 final size:178
Alignment explanation
Indices: 1951891--1952223 Score: 526
Period size: 178 Copynumber: 1.9 Consensus size: 178
1951881 TGATTCCCCC
* * * *
1951891 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCCTTGGTGGTTGTTAAGTGCTGATTCCACCGTAAC
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
1951956 TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATC
66 TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATC
1952021 CCACCGTAACTTGAATGTGAAAGGGATCCCACCGTAACTTGAATGTGA
131 CCACCGTAACTTGAATGTGAAAGGGATCCCACCGTAACTTGAATGTGA
1952069 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGA-TCCTACCGTAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCC-ACCGTAA
* * * * * *
1952133 CTTGAATGTGAAAGGGGTTGCTAAGTGCTTATTCGCCGAATCATTGGTGGTTGCTAAGT-TTGAT
65 CTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGAT
* *
1952197 TCCACCGTATCTTCGAATGTGAAAGGG
130 CCCACCGTAACTT-GAATGTGAAAGGG
1952224 GTTGCTAAGT
Statistics
Matches: 141, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
177 18 0.13
178 123 0.87
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (178 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTAAC
TTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTGATC
CCACCGTAACTTGAATGTGAAAGGGATCCCACCGTAACTTGAATGTGA
Found at i:1965962 original size:17 final size:17
Alignment explanation
Indices: 1965912--1965974 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 17
1965902 TGATCTGATT
1965912 AAAACACGATAATTTTTG
1 AAAACACGA-AATTTTTG
*
1965930 AAAACATGAAACTTTTTG
1 AAAACACGAAA-TTTTTG
1965948 -AAACACGAGAA-TTTTG
1 AAAACACGA-AATTTTTG
1965964 AAAACACGAAA
1 AAAACACGAAA
1965975 AATTTTTCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 7 0.17
17 17 0.43
18 16 0.40
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (17 bp):
AAAACACGAAATTTTTG
Found at i:1965980 original size:18 final size:18
Alignment explanation
Indices: 1965912--1965980 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
1965902 TGATCTGATT
* *
1965912 AAAACACGATAATTTTTG
1 AAAACACGAAAAATTTTG
* **
1965930 AAAACATGAAACTTTTTG
1 AAAACACGAAAAATTTTG
*
1965948 -AAACACG-AGAATTTTG
1 AAAACACGAAAAATTTTG
1965964 AAAACACGAAAAATTTT
1 AAAACACGAAAAATTTT
1965981 TCGATTTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 6 0.15
17 13 0.32
18 22 0.54
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (18 bp):
AAAACACGAAAAATTTTG
Found at i:1965981 original size:35 final size:35
Alignment explanation
Indices: 1965913--1965981 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
1965903 GATCTGATTA
* * *
1965913 AAACACGATAATTTTTGAAAACATGAAACTTTTTG
1 AAACACGAGAATTTTTGAAAACACGAAAATTTTTG
1965948 AAACACGAGAA-TTTTGAAAACACGAAAAATTTTT
1 AAACACGAGAATTTTTGAAAACACG-AAAATTTTT
1965982 CGATTTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (35 bp):
AAACACGAGAATTTTTGAAAACACGAAAATTTTTG
Found at i:1966122 original size:20 final size:21
Alignment explanation
Indices: 1966084--1966126 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1966074 CGTTACCTTA
1966084 TTTTTGAAAACACGAGAAAATT
1 TTTTTGAAAACAC-AGAAAATT
*
1966106 TTTTTGAAGACAC-GAAAATT
1 TTTTTGAAAACACAGAAAATT
1966126 T
1 T
1966127 CAAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (21 bp):
TTTTTGAAAACACAGAAAATT
Found at i:1966163 original size:17 final size:19
Alignment explanation
Indices: 1966141--1966181 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
1966131 ACCCGAGGAT
1966141 TTTTTTTGAA-A-ATACAA
1 TTTTTTTGAATATATACAA
*
1966158 TTTTTTTGAATATTTACAA
1 TTTTTTTGAATATATACAA
1966177 TTTTT
1 TTTTT
1966182 AAAAGGACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 1 0.05
19 10 0.48
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTTTTGAATATATACAA
Found at i:1967321 original size:28 final size:28
Alignment explanation
Indices: 1967281--1967337 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1967271 GCTAACTGCT
1967281 GATCCCACCGTAACTTGAATGTGAAAGG
1 GATCCCACCGTAACTTGAATGTGAAAGG
1967309 GATCCCACCGTAACTTGAATGTGAAAGG
1 GATCCCACCGTAACTTGAATGTGAAAGG
1967337 G
1 G
1967338 GTTGCTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (28 bp):
GATCCCACCGTAACTTGAATGTGAAAGG
Found at i:1967396 original size:103 final size:103
Alignment explanation
Indices: 1967217--1967412 Score: 374
Period size: 103 Copynumber: 1.9 Consensus size: 103
1967207 NNNNNNNNNN
1967217 AACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTG
1 AACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTG
1967282 ATCCCACCGTAACTTGAATGTGAAAGGGATCCCACCGT
66 ATCCCACCGTAACTTGAATGTGAAAGGGATCCCACCGT
*
1967320 AACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTG
1 AACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTG
*
1967385 ATCCTACCGTAACTTGAATGTGAAAGGG
66 ATCCCACCGTAACTTGAATGTGAAAGGG
1967413 GTTGCTAAGT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 91 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (103 bp):
AACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAACTGCTG
ATCCCACCGTAACTTGAATGTGAAAGGGATCCCACCGT
Found at i:1967400 original size:75 final size:74
Alignment explanation
Indices: 1967313--1967531 Score: 316
Period size: 75 Copynumber: 2.9 Consensus size: 74
1967303 GAAAGGGATC
*
1967313 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTA
1 CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATCGGTGGTTGCTA
1967378 AGTGCTGAT
66 AGTGCTGAT
* * *
1967387 CCTACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTTATTCGCCGAATCATTGGTGGTTGCT
1 CC-ACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATCGGTGGTTGCT
*
1967452 AAGT-TTGATT
65 AAGTGCTGA-T
* *
1967462 CCACCGTATCTTCGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCA-CTAGTGGTTGC
1 CCACCGTAACTT-GAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATC-GGTGGTTGC
*
1967526 GAAGTG
64 TAAGTG
1967532 NNNNNNNNNN
Statistics
Matches: 129, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
74 14 0.11
75 115 0.89
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (74 bp):
CCACCGTAACTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATCGGTGGTTGCTA
AGTGCTGAT
Found at i:1968464 original size:19 final size:18
Alignment explanation
Indices: 1968436--1968472 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1968426 TTCATTTATT
*
1968436 TTTATTTTATTTGTTTAA
1 TTTATTTTATTTCTTTAA
1968454 TTTATTATTATTTCTTTAA
1 TTTATT-TTATTTCTTTAA
1968473 ATTTTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTATTTTATTTCTTTAA
Found at i:1970568 original size:24 final size:24
Alignment explanation
Indices: 1970530--1970599 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 24
1970520 AAATTAAAAC
1970530 AAAATTAAAAA-TATTTT-AAATT
1 AAAATTAAAAAGTATTTTAAAATT
1970552 AAAAATTAAAAAGTATTTTAAAAATT
1 -AAAATTAAAAAGTATTTT-AAAATT
* *
1970578 AAATTTAAAAAGTATTTAAAAA
1 AAAATTAAAAAGTATTTTAAAA
1970600 GTATTTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 11 0.26
24 10 0.24
25 16 0.38
26 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (24 bp):
AAAATTAAAAAGTATTTTAAAATT
Found at i:1970591 original size:25 final size:26
Alignment explanation
Indices: 1970512--1970599 Score: 96
Period size: 24 Copynumber: 3.4 Consensus size: 26
1970502 ACCAAAAATT
1970512 TATTTTAAAAATTAAAACAAAATTAAAAA-
1 TATTTTAAAAATT---A-AAAATTAAAAAG
1970541 TATTTT--AAATTAAAAATTAAAAAG
1 TATTTTAAAAATTAAAAATTAAAAAG
*
1970565 TATTTTAAAAATT-AAATTTAAAAAG
1 TATTTTAAAAATTAAAAATTAAAAAG
1970590 TA-TTTAAAAA
1 TATTTTAAAAA
1970600 GTATTTAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
23 11 0.20
24 15 0.27
25 13 0.24
26 5 0.09
27 5 0.09
29 6 0.11
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (26 bp):
TATTTTAAAAATTAAAAATTAAAAAG
Found at i:1970596 original size:11 final size:11
Alignment explanation
Indices: 1970557--1970608 Score: 68
Period size: 11 Copynumber: 4.5 Consensus size: 11
1970547 AAATTAAAAA
1970557 TTAAAAAGTATT
1 TTAAAAAGTA-T
*
1970569 TTAAAAATTAAAT
1 TTAAAAAGT--AT
1970582 TTAAAAAGTAT
1 TTAAAAAGTAT
1970593 TTAAAAAGTAT
1 TTAAAAAGTAT
1970604 TTAAA
1 TTAAA
1970609 TTAAAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
11 18 0.50
12 8 0.22
13 9 0.25
14 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (11 bp):
TTAAAAAGTAT
Found at i:1973681 original size:18 final size:18
Alignment explanation
Indices: 1973655--1973703 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
1973645 TGTAATTTAT
*
1973655 AATTTAATATTTATAAAA
1 AATTAAATATTTATAAAA
*
1973673 AATTAAATAATTTTATAAAT
1 AATTAAAT-A-TTTATAAAA
1973693 AATTAAA-ATTT
1 AATTAAATATTT
1973704 TATTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.11
18 8 0.30
19 1 0.04
20 15 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAAATATTTATAAAA
Found at i:1973689 original size:20 final size:21
Alignment explanation
Indices: 1973659--1973699 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1973649 ATTTATAATT
1973659 TAATATTTATAAAAAATTAAA
1 TAATATTTATAAAAAATTAAA
*
1973680 TAAT-TTTATAAATAATTAAA
1 TAATATTTATAAAAAATTAAA
1973700 ATTTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATATTTATAAAAAATTAAA
Found at i:1975248 original size:39 final size:39
Alignment explanation
Indices: 1975205--1975281 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
1975195 AGCAGAAGTT
1975205 ACAAGGCTCCA-CAGAAGCCAAACAAGCTGGGTGAATGTG
1 ACAAGGCT-CAGCAGAAGCCAAACAAGCTGGGTGAATGTG
* * * * *
1975244 ACAAGGGTTAGCAGAAGCTAAACCAGTTGGGTGAATGT
1 ACAAGGCTCAGCAGAAGCCAAACAAGCTGGGTGAATGT
1975282 TAGTGATTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (39 bp):
ACAAGGCTCAGCAGAAGCCAAACAAGCTGGGTGAATGTG
Found at i:1978878 original size:18 final size:17
Alignment explanation
Indices: 1978836--1978872 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
1978826 TGGTTTTTAA
1978836 TTATTTTTAAATATATT
1 TTATTTTTAAATATATT
1978853 TTATTTTT-AATATATT
1 TTATTTTTAAATATATT
1978869 TTAT
1 TTAT
1978873 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTTTTAAATATATT
Found at i:1986212 original size:59 final size:60
Alignment explanation
Indices: 1986134--1986257 Score: 164
Period size: 59 Copynumber: 2.1 Consensus size: 60
1986124 CAAGTCAGTT
* * * *
1986134 AACTATTTCCCATTTTCTTTTTTGGTCACTCAATTAT-AATTTTTTTAATTTGA-TCACCC
1 AACTATTTCCCACTTTCTTTTTTGGTCACCCAACTATCAATTTTTCTAATTT-ACTCACCC
*
1986193 AACTATTGTCCC-CTTTCTTTTTTGGTCACCCAACTATCAATTTTTCTAATTTACTCATCC
1 AACTATT-TCCCACTTTCTTTTTTGGTCACCCAACTATCAATTTTTCTAATTTACTCACCC
1986253 AACTA
1 AACTA
1986258 ATCAAGATTG
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
59 30 0.53
60 27 0.47
ACGTcount: A:0.24, C:0.24, G:0.05, T:0.47
Consensus pattern (60 bp):
AACTATTTCCCACTTTCTTTTTTGGTCACCCAACTATCAATTTTTCTAATTTACTCACCC
Found at i:1986662 original size:4 final size:4
Alignment explanation
Indices: 1986653--1986677 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1986643 GCTACTGCTA
1986653 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
1986678 GACCGCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1986861 original size:29 final size:31
Alignment explanation
Indices: 1986778--1986861 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 31
1986768 TGATATTGAT
*
1986778 TAGTTGAGTGACGAAAAAAAAAAAAAGAGTTAA
1 TAGTTGAATGA-G-AAAAAAAAAAAAGAGTTAA
* * ** *
1986811 TAGTTGAGTGAGCAAATTAAAAAA-A-TTGA
1 TAGTTGAATGAGAAAAAAAAAAAAGAGTTAA
*
1986840 TAGTTGAATGATAAAAAAAAAA
1 TAGTTGAATGAGAAAAAAAAAA
1986862 TAATAATTGG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
29 20 0.48
30 1 0.02
31 9 0.21
32 1 0.02
33 11 0.26
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.23
Consensus pattern (31 bp):
TAGTTGAATGAGAAAAAAAAAAAAGAGTTAA
Found at i:1986944 original size:19 final size:21
Alignment explanation
Indices: 1986922--1986962 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
1986912 AGTAGTTGAA
1986922 AGAGAAATGGA-AGTG-GTGG
1 AGAGAAATGGAGAGTGAGTGG
*
1986941 AGAGAAGTGGAGAGTGAGTGG
1 AGAGAAATGGAGAGTGAGTGG
1986962 A
1 A
1986963 CTGATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 4 0.21
21 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.49, T:0.15
Consensus pattern (21 bp):
AGAGAAATGGAGAGTGAGTGG
Found at i:1990476 original size:61 final size:60
Alignment explanation
Indices: 1990401--1990521 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 60
1990391 AAGTATCCCC
1990401 CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAAGGTAGCATCCATTGAAACAATCA
1 CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAA-GTAGCATCCATTGAAACAATCA
1990462 CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAAGTAGCATCCATTGAAACAATCA
1 CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAAGTAGCATCCATTGAAACAATCA
1990522 TTCTTTTTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 22 0.37
61 38 0.63
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (60 bp):
CTGAAGATGAGATCTAAAGAAAAGTTGGATTCAAAGAAGTAGCATCCATTGAAACAATCA
Found at i:2004999 original size:26 final size:26
Alignment explanation
Indices: 2004970--2005021 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2004960 TAATAAATTT
2004970 GAATTTTCTATTAATATA-CTGAAAAG
1 GAATTTTCTATTAATATATC-GAAAAG
*
2004996 GAATTTTCTGTTAATATATCGAAAAG
1 GAATTTTCTATTAATATATCGAAAAG
2005022 AAAAGAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (26 bp):
GAATTTTCTATTAATATATCGAAAAG
Found at i:2015290 original size:45 final size:45
Alignment explanation
Indices: 2015239--2015346 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
2015229 GATGTGGAAA
** *
2015239 AACCACTAATCGGTGCAGATAAAAGCTGTTAATACGAA-GTGGATT
1 AACCACTAATCGGTGCAGATAAAAGCTACTAATAC-AATGTAGATT
* * *
2015284 GACCACTAAAT-GATACAGATAAAAGCTACTAATACAATGTAGATT
1 AACCACT-AATCGGTGCAGATAAAAGCTACTAATACAATGTAGATT
*
2015329 AACCACTAAACGGTGCAG
1 AACCACTAATCGGTGCAG
2015347 GCAAGCTGCT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
44 4 0.08
45 43 0.86
46 3 0.06
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.22
Consensus pattern (45 bp):
AACCACTAATCGGTGCAGATAAAAGCTACTAATACAATGTAGATT
Done.