Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009591.1 Hibiscus syriacus cultivar Beakdansim tig00116970_pilon, whole genome shotgun sequence
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: 2451160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1879984 original size:12 final size:13
Alignment explanation
Indices: 1879956--1879988 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1879946 TTTAGTTATC
*
1879956 CCCGCCCCGATTA
1 CCCGGCCCGATTA
1879969 CCCGGCCCGA-TA
1 CCCGGCCCGATTA
1879981 CCCGGCCC
1 CCCGGCCC
1879989 AATAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.12, C:0.58, G:0.21, T:0.09
Consensus pattern (13 bp):
CCCGGCCCGATTA
Found at i:1880078 original size:15 final size:15
Alignment explanation
Indices: 1880017--1880097 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
1880007 TTATTATATA
1880017 TATATATATATAATAT
1 TATATATATATAAT-T
* *
1880033 TA-ATAAATTTAATT
1 TATATATATATAATT
* * *
1880047 TAAAT-TA-AAAATA
1 TATATATATATAATT
1880060 TATATATA-AT-ATT
1 TATATATATATAATT
1880073 TATATAT-T-TAATT
1 TATATATATATAATT
*
1880086 TAAATATATATA
1 TATATATATATA
1880098 CTCGGCCCGA
Statistics
Matches: 49, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
12 1 0.02
13 25 0.51
14 8 0.16
15 13 0.27
16 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:1880278 original size:11 final size:11
Alignment explanation
Indices: 1880258--1880289 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1880248 AGGAACTAAT
1880258 ACCCGGCCCGA
1 ACCCGGCCCGA
*
1880269 ACCCGACCCGA
1 ACCCGGCCCGA
1880280 ACCCGGCCCG
1 ACCCGGCCCG
1880290 TTGCCATCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.56, G:0.25, T:0.00
Consensus pattern (11 bp):
ACCCGGCCCGA
Found at i:1885989 original size:17 final size:18
Alignment explanation
Indices: 1885946--1885986 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1885936 AAACTATATT
1885946 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1885963 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
1885981 ATTAAA
1 AGTAAA
1885987 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1886602 original size:59 final size:58
Alignment explanation
Indices: 1886522--1886677 Score: 197
Period size: 58 Copynumber: 2.7 Consensus size: 58
1886512 TCATTATCTC
* * * *
1886522 AAATTGGTCCTTAAACTTTTAAATATTCTAATTTAATCTTAAATTATGAATCTTATTCT
1 AAATTGGTCCTTAAACTTTTAAATGTTCTAATTT-ATCTCAAACTATGAATCTCATTCT
* * * *
1886581 AAATTAGTCCTTAAACATTTAAATGTTCTAATTTATCCCAAACTATGACTCTCATTCT
1 AAATTGGTCCTTAAACTTTTAAATGTTCTAATTTATCTCAAACTATGAATCTCATTCT
* *
1886639 AAATTGGTCCTCAAACTTTTGAATGTTC-AATTTCATCTC
1 AAATTGGTCCTTAAACTTTTAAATGTTCTAATTT-ATCTC
1886678 CAAATTCATC
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
57 5 0.06
58 47 0.57
59 31 0.37
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.43
Consensus pattern (58 bp):
AAATTGGTCCTTAAACTTTTAAATGTTCTAATTTATCTCAAACTATGAATCTCATTCT
Found at i:1886664 original size:58 final size:58
Alignment explanation
Indices: 1886500--1886681 Score: 208
Period size: 59 Copynumber: 3.1 Consensus size: 58
1886490 TCCAGTCATC
*
1886500 CCCAAACTATGATCATTA-TCTCAAATTGGTCCTTAAACTTTTAAATATTCTAATTTAAT
1 CCCAAACTATGATC-TTATTCT-AAATTGGTCCTTAAACTTTTAAATGTTCTAATTTAAT
** * * *
1886559 CTTAAATTATGAATCTTATTCTAAATTAGTCCTTAAACATTTAAATGTTCTAATTT-AT
1 CCCAAACTATG-ATCTTATTCTAAATTGGTCCTTAAACTTTTAAATGTTCTAATTTAAT
* * * *
1886617 CCCAAACTATGACTCTCATTCTAAATTGGTCCTCAAACTTTTGAATGTTC-AATTTCAT
1 CCCAAACTATGA-TCTTATTCTAAATTGGTCCTTAAACTTTTAAATGTTCTAATTTAAT
1886675 CTCCAAA
1 C-CCAAA
1886682 TTCATCCAAA
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
57 6 0.06
58 45 0.43
59 47 0.45
60 6 0.06
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (58 bp):
CCCAAACTATGATCTTATTCTAAATTGGTCCTTAAACTTTTAAATGTTCTAATTTAAT
Found at i:1889219 original size:63 final size:63
Alignment explanation
Indices: 1889112--1889230 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 63
1889102 ATAAGCGTTG
* * *
1889112 CCAGGATCCACAGGTTGTTCTTCTACAACCCCGCCACCTACTTCTTCATTTGGGTGTTCAATC
1 CCAGCATCCACAGGTTGTTCTTCGACAACCCCGCCACCTACTTCTTCATTCGGGTGTTCAATC
* * * * * *
1889175 CCAGCATCCACGGGTTGTTCTTCGACAACCCTGTCACTTGCTTCTTGATTCGGGTG
1 CCAGCATCCACAGGTTGTTCTTCGACAACCCCGCCACCTACTTCTTCATTCGGGTG
1889231 CTCGGCCTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 47 1.00
ACGTcount: A:0.17, C:0.32, G:0.19, T:0.32
Consensus pattern (63 bp):
CCAGCATCCACAGGTTGTTCTTCGACAACCCCGCCACCTACTTCTTCATTCGGGTGTTCAATC
Found at i:1889243 original size:63 final size:63
Alignment explanation
Indices: 1889112--1889250 Score: 145
Period size: 63 Copynumber: 2.2 Consensus size: 63
1889102 ATAAGCGTTG
* * * * * *
1889112 CCAGGATCCACAGGTTGTTCTTCTACAACCCCGCCACCTACTTCTTCATTTGGGTGTTCAATC
1 CCAGCATCCACGGGTTGTTCTTCGACAACCCCGCCACCTACTTCTTCATTCGGGTGCTCAAGC
* * * * * *
1889175 CCAGCATCCACGGGTTGTTCTTCGACAACCCTGTCACTTGCTTCTTGATTCGGGTGCTC-GGC
1 CCAGCATCCACGGGTTGTTCTTCGACAACCCCGCCACCTACTTCTTCATTCGGGTGCTCAAGC
*
1889237 CTCAGCATCGACGG
1 C-CAGCATCCACGG
1889251 TAACAGAATC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
62 2 0.03
63 60 0.97
ACGTcount: A:0.17, C:0.33, G:0.21, T:0.29
Consensus pattern (63 bp):
CCAGCATCCACGGGTTGTTCTTCGACAACCCCGCCACCTACTTCTTCATTCGGGTGCTCAAGC
Found at i:1898934 original size:14 final size:15
Alignment explanation
Indices: 1898915--1898947 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1898905 TCACCTTAAA
1898915 ATTTAAT-TTTTTTT
1 ATTTAATATTTTTTT
1898929 ATTTAATAATTTTTTT
1 ATTTAAT-ATTTTTTT
1898945 ATT
1 ATT
1898948 AAAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTAATATTTTTTT
Found at i:1910602 original size:20 final size:20
Alignment explanation
Indices: 1910579--1910635 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
1910569 TAGATTACTG
1910579 AAATTAGGATTAAATTAAAA
1 AAATTAGGATTAAATTAAAA
* * * **
1910599 AAATTAAAGTTTACATT-CTA
1 AAATT-AGGATTAAATTAAAA
1910619 AAATTAGGATTAAATTA
1 AAATTAGGATTAAATTA
1910636 TAAATTTTAA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
19 8 0.30
20 11 0.41
21 8 0.30
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (20 bp):
AAATTAGGATTAAATTAAAA
Found at i:1912343 original size:29 final size:30
Alignment explanation
Indices: 1912290--1912349 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1912280 TCTATCGATG
1912290 ATGCAACTGTTTTTGCATTCAAGATTAGGT
1 ATGCAACTGTTTTTGCATTCAAGATTAGGT
1912320 ATGCAACTGTTTTTGCATT-AAGATTAGGT
1 ATGCAACTGTTTTTGCATTCAAGATTAGGT
1912349 A
1 A
1912350 AGTCACCCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (30 bp):
ATGCAACTGTTTTTGCATTCAAGATTAGGT
Found at i:1913223 original size:19 final size:19
Alignment explanation
Indices: 1913196--1913253 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1913186 TTTGTTATTT
*
1913196 TATTTTTATTTAATTAAGA
1 TATTATTATTTAATTAAGA
* * *
1913215 TATTATTATTATTATTTATA
1 TATTATTATT-TAATTAAGA
1913235 T-TTA-TATTTAATTAAGA
1 TATTATTATTTAATTAAGA
1913252 TA
1 TA
1913254 CGATTACTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
17 7 0.23
18 4 0.13
19 12 0.40
20 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TATTATTATTTAATTAAGA
Found at i:1913283 original size:41 final size:37
Alignment explanation
Indices: 1913196--1913288 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
1913186 TTTGTTATTT
* ** *
1913196 TATTTTTATTTAATTAAGATATTATTATTATTATTTA
1 TATTTATATTTAATTAAGATACGATTATTATTATTAA
1913233 TATTTATATTTAATTAAGATACGATTACTTATTTATTAA
1 TATTTATATTTAATTAAGATACGATTA-TTA-TTATTAA
1913272 CT-TTTAAATATTTAATT
1 -TATTT--ATATTTAATT
1913289 GTTAAAATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
37 24 0.51
38 3 0.06
39 9 0.19
40 1 0.02
41 10 0.21
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (37 bp):
TATTTATATTTAATTAAGATACGATTATTATTATTAA
Found at i:1916870 original size:2 final size:2
Alignment explanation
Indices: 1916863--1916926 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1916853 GTAAATAATA
1916863 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
1916905 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1916927 CACACTCGGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1920132 original size:14 final size:14
Alignment explanation
Indices: 1920113--1920145 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1920103 ACTTATCAAA
1920113 TTCACATTCA-TAAG
1 TTCACATT-ATTAAG
1920127 TTCACATTATTAAG
1 TTCACATTATTAAG
1920141 TTCAC
1 TTCAC
1920146 TAGCCCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.06
14 17 0.94
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (14 bp):
TTCACATTATTAAG
Found at i:1920247 original size:23 final size:23
Alignment explanation
Indices: 1920221--1920289 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
1920211 CACCACAGCT
1920221 CGTATAATTGCACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
* * *
1920244 CGTATAATTGTA-CTAGAGTGCCG
1 CGTATAATTGCACCGA-AGTGCCA
** *
1920267 CGTCGAATTGCACCGTAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
1920290 TATAATAATG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
22 2 0.06
23 32 0.91
24 1 0.03
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:1920542 original size:30 final size:30
Alignment explanation
Indices: 1920501--1920569 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
1920491 CACATAGTTG
* * *
1920501 TATCACGTAGACATATTATTTTCATACCTT
1 TATCACATAGACATATCATTTCCATACCTT
1920531 TATCACATAGACATATCATTTCCATACCTT
1 TATCACATAGACATATCATTTCCATACCTT
1920561 TATCACATA
1 TATCACATA
1920570 ACTCATATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.39
Consensus pattern (30 bp):
TATCACATAGACATATCATTTCCATACCTT
Found at i:1921067 original size:63 final size:64
Alignment explanation
Indices: 1920954--1921092 Score: 151
Period size: 63 Copynumber: 2.2 Consensus size: 64
1920944 ATCCCTTAAC
* * * *
1920954 GGGTGCATCGATGCACTATCTATGCATCGGTGCATAAATCCCATTTGATGTTTGTA-TTT-AAT
1 GGGTGCATCGATGCACTATCTATGCATCGATACATAAATCACATTCGATGTTTGTATTTTAAAT
* * *
1921016 AGGGTGCATCGATGCACTA-CTTGTGCATCGATACACT-AATGACATTCGATGTTTTTATTTTAA
1 -GGGTGCATCGATGCACTATC-TATGCATCGATACA-TAAATCACATTCGATGTTTGTATTTTAA
1921079 AT
63 AT
*
1921081 GAGTGCATCGAT
1 GGGTGCATCGAT
1921093 ATACCTTGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
62 1 0.02
63 45 0.70
64 15 0.23
65 3 0.05
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (64 bp):
GGGTGCATCGATGCACTATCTATGCATCGATACATAAATCACATTCGATGTTTGTATTTTAAAT
Found at i:1922583 original size:38 final size:37
Alignment explanation
Indices: 1922532--1922624 Score: 123
Period size: 38 Copynumber: 2.4 Consensus size: 37
1922522 TAAACCATGT
* *
1922532 CCCGAAGGACCTATCATCCCGAAAGATGTCATCTGTGA
1 CCCGAA-GACCTATCATCACGAAAGATGTAATCTGTGA
* *
1922570 CCCGAATGACCTATCATCACGAAGGATGTAATCTGTGT
1 CCCGAA-GACCTATCATCACGAAAGATGTAATCTGTGA
1922608 CCCGAAGAACCTATCAT
1 CCCGAAG-ACCTATCAT
1922625 ATGTCTCGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
37 1 0.02
38 48 0.98
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (37 bp):
CCCGAAGACCTATCATCACGAAAGATGTAATCTGTGA
Found at i:1922849 original size:21 final size:19
Alignment explanation
Indices: 1922825--1922877 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
1922815 TGTATGTGTA
*
1922825 AACATCTATCTCATATCATAT
1 AACATATATCTCATAT-A-AT
* *
1922846 AACATGTATCACATATAAT
1 AACATATATCTCATATAAT
1922865 AACATATA-CTCAT
1 AACATATATCTCAT
1922878 GCACACATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 1 0.04
21 14 0.50
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (19 bp):
AACATATATCTCATATAAT
Found at i:1930332 original size:21 final size:19
Alignment explanation
Indices: 1930308--1930360 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
1930298 TGTATGTGTA
*
1930308 AACATCTATCTCATATCATAT
1 AACATATATCTCATAT-A-AT
* *
1930329 AACATGTATCACATATAAT
1 AACATATATCTCATATAAT
1930348 AACATATA-CTCAT
1 AACATATATCTCAT
1930361 GCACACATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 1 0.04
21 14 0.50
ACGTcount: A:0.43, C:0.21, G:0.02, T:0.34
Consensus pattern (19 bp):
AACATATATCTCATATAAT
Found at i:1932443 original size:9 final size:10
Alignment explanation
Indices: 1932428--1932486 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 10
1932418 GGCTTTGTAA
1932428 ATAATAATAT
1 ATAATAATAT
1932438 -TAATAATAT
1 ATAATAATAT
*
1932447 ATAATATTAT
1 ATAATAATAT
*
1932457 -TATTATATAT
1 ATAATA-ATAT
1932467 ATAATAACGTAT
1 ATAATAA--TAT
1932479 ATAA-AATA
1 ATAATAATA
1932487 AACATCACTC
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 15 0.38
10 12 0.30
11 6 0.15
12 7 0.17
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (10 bp):
ATAATAATAT
Found at i:1938757 original size:20 final size:21
Alignment explanation
Indices: 1938720--1938759 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1938710 ATTAAATTTT
*
1938720 ATATTCGGATCCGTTATCCGG
1 ATATTCGGATCCGATATCCGG
*
1938741 ATATTC-GATCTGATATCCG
1 ATATTCGGATCCGATATCCG
1938760 ATTTTTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (21 bp):
ATATTCGGATCCGATATCCGG
Found at i:1938822 original size:16 final size:17
Alignment explanation
Indices: 1938787--1938822 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1938777 ACAATTAGTA
**
1938787 TTTTAGATATCTTAATT
1 TTTTAGATATCCGAATT
1938804 TTTTAGATATCCGAATT
1 TTTTAGATATCCGAATT
1938821 TT
1 TT
1938823 CAGATCGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (17 bp):
TTTTAGATATCCGAATT
Found at i:1939623 original size:44 final size:44
Alignment explanation
Indices: 1939560--1939649 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
1939550 TCGTTGGTCT
1939560 AATCGTAGATTCAGATGTTAAATATAAGTTGGGATCGTATATGA
1 AATCGTAGATTCAGATGTTAAATATAAGTTGGGATCGTATATGA
1939604 AATCGTAGATTCAGATGTTAAATATAAGTTGGGATCGTATATGA
1 AATCGTAGATTCAGATGTTAAATATAAGTTGGGATCGTATATGA
1939648 AA
1 AA
1939650 CTTATCTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (44 bp):
AATCGTAGATTCAGATGTTAAATATAAGTTGGGATCGTATATGA
Found at i:1940429 original size:31 final size:31
Alignment explanation
Indices: 1940376--1940434 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
1940366 AGCCGACAGC
* *
1940376 TCGATAAAAGTAATAACTATTTTGTAATCAT
1 TCGATAAAAGTAATAACCATTTTATAATCAT
** *
1940407 TCGATAAATTTAATGACCATTTTATAAT
1 TCGATAAAAGTAATAACCATTTTATAAT
1940435 TTTTTAAAGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
TCGATAAAAGTAATAACCATTTTATAATCAT
Found at i:1941074 original size:120 final size:120
Alignment explanation
Indices: 1940861--1941101 Score: 464
Period size: 120 Copynumber: 2.0 Consensus size: 120
1940851 TATAATTTTC
1940861 AAATTTGGTGGGGTTTTATGCAAGTTTTCTTGTAGAAATTGCCCCATTGTCTCACATATTCAACA
1 AAATTTGGTGGGGTTTTATGCAAGTTTTCTTGTAGAAATTGCCCCATTGTCTCACATATTCAACA
* *
1940926 ATCCAAAAGGTCACTAGTGTTTAACAAAATATATGTATGACTAGGGATGGTAACA
66 ATCCAAAAGGTCACTAGTGTTTAACAAAATATATGTATGACTAAGGATGATAACA
1940981 AAATTTGGTGGGGTTTTATGCAAGTTTTCTTGTAGAAATTGCCCCATTGTCTCACATATTCAACA
1 AAATTTGGTGGGGTTTTATGCAAGTTTTCTTGTAGAAATTGCCCCATTGTCTCACATATTCAACA
1941046 ATCCAAAAGGTCACTAGTGTTTAACAAAATATATGTATGACTAAGGATGATAACA
66 ATCCAAAAGGTCACTAGTGTTTAACAAAATATATGTATGACTAAGGATGATAACA
1941101 A
1 A
1941102 GTCGGATTAG
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (120 bp):
AAATTTGGTGGGGTTTTATGCAAGTTTTCTTGTAGAAATTGCCCCATTGTCTCACATATTCAACA
ATCCAAAAGGTCACTAGTGTTTAACAAAATATATGTATGACTAAGGATGATAACA
Found at i:1941944 original size:20 final size:20
Alignment explanation
Indices: 1941896--1941947 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1941886 TTTTCCGACT
*
1941896 ATCGCAATACGAATATGTAA
1 ATCGCAATGCGAATATGTAA
1941916 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
1941936 ATCGCAATGCGA
1 ATCGCAATGCGA
1941948 TTCTGACTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:1941959 original size:20 final size:20
Alignment explanation
Indices: 1941936--1942003 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
1941926 GAATATGTAA
*
1941936 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1941956 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1941976 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1941996 GTCGCAAC
1 ATCGCAAC
1942004 ACTGAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1941960 original size:40 final size:40
Alignment explanation
Indices: 1941916--1942003 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
1941906 GAATATGTAA
* * *
1941916 ATCGCAATGCGAATATGTA-AATCGCAATGCGATTCTGACT
1 ATCGCAACGAGAATATG-ACAATCGCAACGCGATTCTGACT
* * *
1941956 ATCGCAACGAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGAGAATATGACAATCGCAACGCGATTCTGACT
*
1941996 GTCGCAAC
1 ATCGCAAC
1942004 ACTGAATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.03
40 39 0.98
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (40 bp):
ATCGCAACGAGAATATGACAATCGCAACGCGATTCTGACT
Found at i:1942874 original size:24 final size:24
Alignment explanation
Indices: 1942823--1942876 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1942813 ATATTCGAAA
*
1942823 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1942847 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1942871 TTTGAT
1 TTTGAT
1942877 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1945469 original size:140 final size:140
Alignment explanation
Indices: 1945217--1945486 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
1945207 AAACGTTGTA
1945217 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
* * *
1945282 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTTAATATCGCAACGCGAATTTGACTAT
66 TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
1945347 TATGTGTATT
131 TATGTGTATT
* *
1945357 TTATGTGTACACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
1945422 TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
1945487 CGCAACGCGA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:1945482 original size:20 final size:20
Alignment explanation
Indices: 1945457--1945755 Score: 285
Period size: 20 Copynumber: 15.8 Consensus size: 20
1945447 TTACACATTC
*
1945457 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1945477 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
1945497 ATTTAACTATCTCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
1945517 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
1945536 A----A-AAGCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1945551 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
1945571 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
1945590 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1945605 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1945625 ATTTGATTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
1945645 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
1945665 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1945679 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1945699 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
1945719 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
1945739 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
1945756 AGAAAATCGC
Statistics
Matches: 228, Mismatches: 31, Indels: 40
0.76 0.10 0.13
Matches are distributed among these distances:
14 30 0.13
15 6 0.03
16 1 0.00
18 1 0.00
19 6 0.03
20 183 0.80
21 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1945597 original size:34 final size:34
Alignment explanation
Indices: 1945559--1945735 Score: 151
Period size: 34 Copynumber: 4.9 Consensus size: 34
1945549 GAATTTGACT
* *
1945559 ATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* *
1945593 ATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-A
*
1945633 ATCGCAACG-GCTATTTGACTATCGCAACG-AGAAA
1 ATCGCAACGCG-AATTTGACTATCGCAACGCA-AAA
*
1945667 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGAGT
1 ATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-A
*
1945707 ATCGCAACGCGAATTTGATTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
1945736 GGTATTTGAC
Statistics
Matches: 117, Mismatches: 10, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
34 53 0.45
35 5 0.04
36 1 0.01
38 1 0.01
39 4 0.03
40 53 0.45
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:1945619 original size:74 final size:73
Alignment explanation
Indices: 1945541--1945735 Score: 284
Period size: 74 Copynumber: 2.6 Consensus size: 73
1945531 ACTCAAAAAG
*
1945541 CGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCA-AAAATCGCAACGCGA
1 CGCAACGCGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAACG-AGAAAATCGCAACGCGA
*
1945605 ATTTGTCTAT
64 ATTTGACTAT
* * *
1945615 CGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGCGAA
1 CGCAACGCGAATTTGACTATCGCAACCG-AATTTGACTATCGCAACGAGAAAATCGCAACGCGAA
1945680 TTTGACTAT
65 TTTGACTAT
* *
1945689 CGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAACG
1 CGCAACGCGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAACG
1945736 GGTATTTGAC
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
73 2 0.02
74 106 0.97
75 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (73 bp):
CGCAACGCGAATTTGACTATCGCAACCGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAAT
TTGACTAT
Found at i:1945639 original size:94 final size:93
Alignment explanation
Indices: 1945541--1945767 Score: 280
Period size: 94 Copynumber: 2.4 Consensus size: 93
1945531 ACTCAAAAAG
* * *
1945541 CGCAACGCGAATTTGACTATCGCAAC-ACGAATAT-GACTATCGC-AACGCAAAAATCGCAACGC
1 CGCAACG-GTATTTGACTATCGCAACGA-GAAAATCG-C-AACGCGAACGCAAAAATCGCAACGC
*
1945603 GAATTTGTCTATCGCAACGCGAATTTGATTAT
62 GAATTTGACTATCGCAACGCGAATTTGATTAT
**** **
1945635 CGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATCGCAACGCGAA
1 CGCAACGG-TATTTGACTATCGCAACGAGAAAATCGCAACGCGAACGCAAAAATCGCAACGCGAA
*
1945700 TTTGAGTATCGCAACGCGAATTTGATTAT
65 TTTGACTATCGCAACGCGAATTTGATTAT
1945729 CGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAA
1 CGCAAC-GGTATTTGACTATCGCAACGAGAAAATCGCAA
1945768 AGCGTATTAG
Statistics
Matches: 117, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
93 5 0.04
94 108 0.92
95 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (93 bp):
CGCAACGGTATTTGACTATCGCAACGAGAAAATCGCAACGCGAACGCAAAAATCGCAACGCGAAT
TTGACTATCGCAACGCGAATTTGATTAT
Found at i:1945766 original size:54 final size:54
Alignment explanation
Indices: 1945485--1945799 Score: 253
Period size: 54 Copynumber: 5.7 Consensus size: 54
1945475 GAATTTGACT
* * * * *
1945485 ATCGCAACGCGAATTTAACTATCTCAATGCGAATTTGATTATCGCAACTCA-AAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAAC-GAGAAA
* * *
1945539 AGCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCA-AAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG-AGAAA
* * **
1945593 ATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTGATTATCGCAACG-GCTA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAA
* * * *** ** *
1945646 TTTGACTATCGC-AACGAGAAAATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGA
1 ATCG-C-AACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAA----A
* * *
1945705 GTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAA
1 --ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAA
* * * *
1945761 ATCGCAAAGCGTATTAGACTATCGCAATGCGAA-TTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACT
1945800 TTCGTGTTGC
Statistics
Matches: 204, Mismatches: 45, Indels: 25
0.74 0.16 0.09
Matches are distributed among these distances:
53 9 0.04
54 147 0.72
55 5 0.02
56 1 0.00
59 5 0.02
60 35 0.17
61 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAA
Found at i:1945781 original size:94 final size:94
Alignment explanation
Indices: 1945593--1945799 Score: 344
Period size: 94 Copynumber: 2.2 Consensus size: 94
1945583 CAACGCAAAA
*
1945593 ATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
* *
1945658 AACGAGAAAATCGCAACGCGAATTTGACT
66 AACGAGAAAATCGCAAAGCGAATTAGACT
* *
1945687 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
*
1945752 AACGAGAAAATCGCAAAGCGTATTAGACT
66 AACGAGAAAATCGCAAAGCGAATTAGACT
*
1945781 ATCGCAATGCGAA-TTGACT
1 ATCGCAACGCGAATTTGACT
1945800 TTCGTGTTGC
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
93 5 0.05
94 100 0.95
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
AACGAGAAAATCGCAAAGCGAATTAGACT
Found at i:1946011 original size:14 final size:14
Alignment explanation
Indices: 1945950--1946011 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
1945940 CACAAATACG
*
1945950 AATTATTTACACATC
1 AATT-TTTACAAATC
**
1945965 AATATTAAACAAATC
1 AAT-TTTTACAAATC
* *
1945980 AACTTTTACAAATT
1 AATTTTTACAAATC
*
1945994 AATTTTTATAAATC
1 AATTTTTACAAATC
1946008 AATT
1 AATT
1946012 AAACAAGCAA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 12 0.33
16 1 0.03
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:1947433 original size:21 final size:21
Alignment explanation
Indices: 1947403--1947504 Score: 98
Period size: 21 Copynumber: 4.9 Consensus size: 21
1947393 TTGGAGGGAT
* *
1947403 CTCTTCAACGATGATAGTGGC
1 CTCTTGAACGATGATAGGGGC
* ** *
1947424 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGATGATAGGGGC
**
1947445 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGATAGGGGC
**
1947466 CTCTTGAACGAT-AGGGGAGGC
1 CTCTTGAACGATGATAGG-GGC
1947487 CTCTTGAACGATGATAGG
1 CTCTTGAACGATGATAGG
1947505 TGAGTCGGGC
Statistics
Matches: 61, Mismatches: 18, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 55 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGATAGGGGC
Found at i:1947491 original size:42 final size:42
Alignment explanation
Indices: 1947395--1947504 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
1947385 CTAGAATGTT
* * *
1947395 GGAG-GGATCTCTTCAACGATGATAGTGGCCTCTTGAACGGTG
1 GGAGAGGA-CTCTTGAACGATGATAGGGGCCTCTTGAACGATG
* **
1947437 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAG
1 GGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGAT-G
*
1947480 GG-GAGGCCTCTTGAACGATGATAGG
1 GGAGAGGACTCTTGAACGATGATAGG
1947505 TGAGTCGGGC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
42 51 0.89
43 6 0.11
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.23
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGATG
Found at i:1948024 original size:20 final size:20
Alignment explanation
Indices: 1947999--1948054 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1947989 TCGCAACACG
1947999 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
1948019 AATGACTATCGCAACACGAA
1 AATGACTATCGCAACGCGAA
**
1948039 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
1948055 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:1948295 original size:18 final size:18
Alignment explanation
Indices: 1948272--1948321 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1948262 TTTACTAAGC
1948272 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
1948290 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
1948308 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
1948322 TACAAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:1950106 original size:20 final size:19
Alignment explanation
Indices: 1950070--1950130 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
1950060 CGTAACACGA
1950070 AAATGACTATCGCAACGCG
1 AAATGACTATCGCAACGCG
* *
1950089 AATTTGACTATCGCAACGTG
1 AA-ATGACTATCGCAACGCG
**
1950109 AAATGAAAATCGCAACGCG
1 AAATGACTATCGCAACGCG
1950128 AAA
1 AAA
1950131 CTAAAATTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:1950137 original size:19 final size:19
Alignment explanation
Indices: 1950034--1950130 Score: 77
Period size: 20 Copynumber: 4.9 Consensus size: 19
1950024 TCTGAAACTT
*
1950034 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACGCG--AAATG
* *
1950055 AAAATCGTAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
1950075 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
** *
1950095 ACTATCGCAACGTGAAATG
1 AAAATCGCAACGCGAAATG
1950114 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
1950131 CTAAAATTGC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 18 0.28
20 33 0.52
21 13 0.20
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1950760 original size:20 final size:20
Alignment explanation
Indices: 1950723--1950836 Score: 147
Period size: 20 Copynumber: 5.7 Consensus size: 20
1950713 GCGCTTTGAA
* *
1950723 AATCGCATTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
1950743 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
1950763 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
1950783 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* * *
1950803 AATCGCATTACGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
1950823 AATCGCATTGCGAT
1 AATCGCGTTGCGAT
1950837 TTACATATTC
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:1950836 original size:40 final size:40
Alignment explanation
Indices: 1950723--1950918 Score: 162
Period size: 40 Copynumber: 4.8 Consensus size: 40
1950713 GCGCTTTGAA
* * *
1950723 AATCGCATTGTGATAGTCAGCATCGCGTTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAG
* *
1950763 AATCGCGTTGCGATAGTCAGAATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAG
* * * * *
1950803 AATCGCATTACGATAGTCATAATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGT-CAG
* * *** * * *
1950843 ATTCGCATTGCGATAGTCGGAAAATCGCAACGCGA-ATTTGGAA
1 AATCGCATTGCGATAGTC--AGAATCGCGTTGCGATA-GT-CAG
*
1950886 AATCGCAATGCGATAGTCAGAATCGCGTTGCGA
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGA
1950919 ATCTGGAAAC
Statistics
Matches: 125, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
39 1 0.01
40 82 0.66
41 11 0.09
42 12 0.10
43 19 0.15
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.26
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAGAATCGCGTTGCGATAGTCAG
Found at i:1950854 original size:60 final size:60
Alignment explanation
Indices: 1950723--1950860 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
1950713 GCGCTTTGAA
* * * * *
1950723 AATCGCATTGTGATAGTCAGCATCGCGTTGCGACAGTCAGAATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGCATTACGACAGTCAGAATCGCATTGCGATAGTCAG
* * * * * *
1950783 AATCTCGTTGCGATAGTCAGAATCGCATTACGATAGTCATAATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGTCAGAATCGCATTACGACAGTCAGAATCGCATTGCGATAGT-CAG
*
1950843 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
1950861 GGAAAATCGC
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
59 1 0.02
60 62 0.98
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAGAATCGCATTACGACAGTCAGAATCGCATTGCGATAGTCAG
Found at i:1955786 original size:3 final size:3
Alignment explanation
Indices: 1955778--1955803 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1955768 TTCAACAAAA
1955778 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1955804 ATAGAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1961071 original size:63 final size:63
Alignment explanation
Indices: 1961003--1961126 Score: 221
Period size: 63 Copynumber: 2.0 Consensus size: 63
1960993 AAGGTGGGTT
* *
1961003 GGGTTAGGGTGTGTCACCTTATAAAAGAAGAAGCTACTTTATGATGGATTATAAAGTTTTAAA
1 GGGTTAGGGGGTGTCACCTTATAAAAGAAGAAGCTACTTTATGATGGATTATAAAATTTTAAA
*
1961066 GGGTTAGGGGGTGTCACCTTATACAAGAAGAAGCTACTTTATGATGGATTATAAAATTTTA
1 GGGTTAGGGGGTGTCACCTTATAAAAGAAGAAGCTACTTTATGATGGATTATAAAATTTTA
1961127 TTAAAACTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (63 bp):
GGGTTAGGGGGTGTCACCTTATAAAAGAAGAAGCTACTTTATGATGGATTATAAAATTTTAAA
Found at i:1963575 original size:14 final size:14
Alignment explanation
Indices: 1963556--1963583 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1963546 AATACATTCA
1963556 TTGCATTTGCATTT
1 TTGCATTTGCATTT
1963570 TTGCATTTGCATTT
1 TTGCATTTGCATTT
1963584 ACATTTACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
TTGCATTTGCATTT
Found at i:1969156 original size:55 final size:55
Alignment explanation
Indices: 1969027--1969595 Score: 251
Period size: 53 Copynumber: 10.5 Consensus size: 55
1969017 GTTTTTTAGG
* * * * * *
1969027 AACTACGTCTGATTTTCATAGGTTTCTTGACATGGTATTTTT-AATTAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTG--AT--TATTTTTAAATGAGATTTCAAAGA
* * *
1969085 AACTAAGTCTGATTTTCGGAAGTTTCTTGATTATTTTTAAATGAGCTTTCACAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAAGA
** * * *
1969140 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATTAGATTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAAGA
* *
1969195 AACTAAGTCTGATTTTCATAACTTTCTTG-TTGATTTTTAAAAT-A-ACTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATT-ATTTTT-AAATGAGA-TTTCAAAGA
* ** * ** * * *
1969250 AATTAAACCTAACTTTT-AGGGGGTTCTTGA-TATTTTCAAATGA-ATTTGAAAGA
1 AACTAAGTCTGA-TTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAAGA
* * * * ** * * * * *
1969303 AATTAAGCCTAATTTTTAGGGGTTTCTTGA-TGTTTTAAAAT-AAATTTTAAAAAA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGA-TTTCAAAGA
* ** * * *
1969357 AACTAAG-CTTGATTTTTAGGGGTTTCTTGA-TGTTTTCAAATGA-ATTTGAAAGA
1 AACTAAGTC-TGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAAGA
* * * ** * * * *
1969410 AA-TGAAGCCTAATTTTTAGGGGTTTCTCGA-TGTTTTCAAATGA-ATTTGAAAGA
1 AACT-AAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAAGA
* * ** * * * * *
1969463 AGCTAAG-CATGATTTTTAGGGGTTTC-TCAATGTTTTCAAATGA-ATTTGAAAGA
1 AACTAAGTC-TGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAAGA
* * * ** * * * *
1969516 AGCTAAGCCTGATTTTTAGGGGTTTCTCGA-TGTTTTCAAATGA-ATTTGAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAAGA
* *
1969569 AACTAAGTCTAATTTTCAGGAGTTTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCT
1969596 CAATGTCTTC
Statistics
Matches: 435, Mismatches: 57, Indels: 43
0.81 0.11 0.08
Matches are distributed among these distances:
52 8 0.02
53 212 0.49
54 63 0.14
55 117 0.27
56 10 0.02
58 25 0.06
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (55 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGATTTCAAAGA
Found at i:1969211 original size:110 final size:111
Alignment explanation
Indices: 1969027--1969235 Score: 289
Period size: 110 Copynumber: 1.9 Consensus size: 111
1969017 GTTTTTTAGG
* * * * *
1969027 AACTACGTCTGATTTTCATAGGTTTCTTGACATGGTATTTTTAATTAGTTTTTAAAGAAACTAAG
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACA--GTATTTTAAATTAGATTTTAAAGAAACTAAG
* *
1969092 TCTGATTTTCGGAAGTTTCTTGATT-ATTTTTAAATGAGCTTTCACAGA
64 TCTGATTTTCAGAACTTTCTTG-TTGATTTTTAAATGAGCTTTCACAGA
1969140 AACTAAGTCTGATTTTCAGAAGTTTCTTGAC-G-ATTTTCAAATTAGATTTTAAAGAAACTAAGT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACAGTATTTT-AAATTAGATTTTAAAGAAACTAAGT
*
1969203 CTGATTTTCATAACTTTCTTGTTGATTTTTAAA
65 CTGATTTTCAGAACTTTCTTGTTGATTTTTAAA
1969236 ATAACTTTCA
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
109 7 0.08
110 51 0.59
113 28 0.33
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.44
Consensus pattern (111 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGACAGTATTTTAAATTAGATTTTAAAGAAACTAAGTC
TGATTTTCAGAACTTTCTTGTTGATTTTTAAATGAGCTTTCACAGA
Found at i:1969277 original size:110 final size:109
Alignment explanation
Indices: 1969069--1969318 Score: 265
Period size: 110 Copynumber: 2.3 Consensus size: 109
1969059 TGGTATTTTT
* * * *
1969069 AATTAGTTTTTAAAGAAACTAAGTCTGATTTTCGGAAGTTTCTTGATTATTTTTAAATGAGCTTT
1 AATTAGATTTTAAAGAAACTAAGTCTGATTTTCAGAACTTTCTTGATTATTTTTAAATGAACTTT
* ** * *
1969134 CACAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCA
66 CAAAGAAACTAAACCTAATTTTCAGAAGGTTCTTGA-GATTTTCA
*
1969179 AATTAGATTTTAAAGAAACTAAGTCTGATTTTCATAACTTTCTTG-TTGATTTTTAAAAT-AACT
1 AATTAGATTTTAAAGAAACTAAGTCTGATTTTCAGAACTTTCTTGATT-ATTTTT-AAATGAACT
* ** *
1969242 TTCAAAGAAATTAAACCTAACTTTT-AGGGGGTTCTTGATATTTTCA
64 TTCAAAGAAACTAAACCTAA-TTTTCAGAAGGTTCTTGAGATTTTCA
* * * * *
1969288 AATGA-ATTTGAAAGAAATTAAGCCTAATTTT
1 AATTAGATTTTAAAGAAACTAAGTCTGATTTT
1969319 TAGGGGTTTC
Statistics
Matches: 118, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
108 22 0.19
109 13 0.11
110 75 0.64
111 8 0.07
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (109 bp):
AATTAGATTTTAAAGAAACTAAGTCTGATTTTCAGAACTTTCTTGATTATTTTTAAATGAACTTT
CAAAGAAACTAAACCTAATTTTCAGAAGGTTCTTGAGATTTTCA
Found at i:1969306 original size:53 final size:53
Alignment explanation
Indices: 1969137--1969651 Score: 521
Period size: 53 Copynumber: 9.6 Consensus size: 53
1969127 GAGCTTTCAC
* * * ** * * *
1969137 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTCAAATTAGATTTTAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
* * * **** * * *
1969192 AGAAACTAAGTCTGATTTTCATAACTTTCTTGTTGATTTTTAAAAT-AACTTTCAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG--TTTTCAAATGAA-TTTGAA
* * * * *
1969247 AGAAATTAAACCTAACTTTTAGGGGGTTCTTGATATTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
* * * *
1969300 AGAAATTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTAAAATAAATTTTAAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA-TTTGAA
* * *
1969354 AAAAACTAAGCTTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
*
1969407 AGAAA-TGAAGCCTAATTTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTGAA
1 AGAAACT-AAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
* * * **
1969460 AGAAGCTAAGCATGATTTTTAGGGGTTTCTCAATGTTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
* * *
1969513 AGAAGCTAAGCCTGATTTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
* * * ** *
1969566 AGAAACTAAGTCTAATTTTCAGGAGTTTCTCAATGTCTTCAAATGAATTTGAA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
* * *
1969619 TGGAGCTAAGCCTAATTTTTAGGGGTTTCTTGA
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGA
1969652 CAATTAAGAA
Statistics
Matches: 393, Mismatches: 61, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
52 1 0.00
53 275 0.70
54 50 0.13
55 59 0.15
56 8 0.02
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (53 bp):
AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
Found at i:1970038 original size:144 final size:145
Alignment explanation
Indices: 1969778--1970075 Score: 393
Period size: 144 Copynumber: 2.1 Consensus size: 145
1969768 AGCAAGATGA
* * * * *
1969778 TAAGTCCTTCGAGCCATCTATAAGACCTTCGGATAGGATGTTTTCAACATTTCCTTTGCTCGATT
1 TAAGTCCTTCGAGCCACCCATAAGACCTTCGGACAGGATATTTTCAACATTTCATTTGCTCGATT
* * * *
1969843 TACAACACTTTAAATCAACAACACCCCACTATAGGGATTAACATTTCATATTGCTCGATTCAC-A
66 CACAACACTTCAAATCAACAACACCCCACCAGAGGGATTAACATTTCATATTGCTCGATTCACAA
*
1969907 CACTTCGAATCAGCT
131 CACTTCGAATAAGCT
* * *
1969922 TAAGTTCTTCGGGCCACCCATAAGACCTTCGGGCAGGATATTTTCAACATTTCATTTGCTCGATT
1 TAAGTCCTTCGAGCCACCCATAAGACCTTCGGACAGGATATTTTCAACATTTCATTTGCTCGATT
* * * * *
1969987 CACAAGACTTCGAATCAGCAACGCCTCACCAGA-GGAGTTAACATTTCATATTGCTCGATTCACA
66 CACAACACTTCAAATCAACAACACCCCACCAGAGGGA-TTAACATTTCATATTGCTCGATTCACA
*
1970051 ATACTTCGAATAAGCT
130 ACACTTCGAATAAGCT
*
1970067 GAAGTCCTT
1 TAAGTCCTT
1970076 TAGGCCATCA
Statistics
Matches: 131, Mismatches: 21, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
143 3 0.02
144 107 0.82
145 21 0.16
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (145 bp):
TAAGTCCTTCGAGCCACCCATAAGACCTTCGGACAGGATATTTTCAACATTTCATTTGCTCGATT
CACAACACTTCAAATCAACAACACCCCACCAGAGGGATTAACATTTCATATTGCTCGATTCACAA
CACTTCGAATAAGCT
Found at i:1971191 original size:64 final size:64
Alignment explanation
Indices: 1971090--1971280 Score: 196
Period size: 64 Copynumber: 3.0 Consensus size: 64
1971080 ATCCACCAAT
* * * * *
1971090 CCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGTATTTCATGCATCGATGCACTT
1 CCATGCATCGATGCACTCAGGCATT---TTGAAACATCGAATGCATTTGATGCATCGATGCACTC
1971153 A-
63 AG
*
1971154 CCATGCA-CTGATGCACTGAGG-ATTTATGAAAACATCGAATGCATTTGATGCATCGATGCAC-C
1 CCATGCATC-GATGCACTCAGGCATTT-TG-AAACATCGAATGCATTTGATGCATCGATGCACTC
1971216 AG
63 AG
* * *
1971218 CCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATACACTC
1 CCATGCATCGATGCACTCAGGC-ATTTTGAAACATCGAATGCATTTGATGCATCGATGCACTC
1971281 TTAGTGCACC
Statistics
Matches: 108, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
61 1 0.01
62 2 0.02
63 2 0.02
64 93 0.86
65 6 0.06
66 4 0.04
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (64 bp):
CCATGCATCGATGCACTCAGGCATTTTGAAACATCGAATGCATTTGATGCATCGATGCACTCAG
Found at i:1973109 original size:32 final size:32
Alignment explanation
Indices: 1973073--1973146 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
1973063 TAAGCATGTT
1973073 TTATGTATTAGATATTTATTTCACTTACATTA
1 TTATGTATTAGATATTTATTTCACTTACATTA
* *
1973105 TTATGTACTAGATATTTATTTCACTTATATTA
1 TTATGTATTAGATATTTATTTCACTTACATTA
*
1973137 TTATATATTA
1 TTATGTATTA
1973147 CTTTATTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (32 bp):
TTATGTATTAGATATTTATTTCACTTACATTA
Found at i:1973160 original size:19 final size:19
Alignment explanation
Indices: 1973127--1973163 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1973117 TATTTATTTC
1973127 ACTTATATTATTATATATT
1 ACTTATATTATTATATATT
1973146 ACTT-TATTATATATATAT
1 ACTTATATTAT-TATATAT
1973164 ATAAATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
ACTTATATTATTATATATT
Found at i:1977228 original size:29 final size:28
Alignment explanation
Indices: 1977180--1977238 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
1977170 AAATATTAAA
*
1977180 TATTTTTTAAAATATACTTTTATAAATT
1 TATTTTTTAAAATATACTTTAATAAATT
*
1977208 TATTGTTTTAAAATA-ATCTTTAATGAATT
1 TATT-TTTTAAAATATA-CTTTAATAAATT
1977237 TA
1 TA
1977239 GATCTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (28 bp):
TATTTTTTAAAATATACTTTAATAAATT
Found at i:1986380 original size:13 final size:13
Alignment explanation
Indices: 1986364--1986388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1986354 TATATATTTT
1986364 AAACATATAATAA
1 AAACATATAATAA
1986377 AAACATATAATA
1 AAACATATAATA
1986389 TCACATTATT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (13 bp):
AAACATATAATAA
Found at i:1988551 original size:18 final size:18
Alignment explanation
Indices: 1988528--1988570 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1988518 GAGATGATGT
*
1988528 TATTATTATTTAATAAAA
1 TATTATTATTTAAGAAAA
* *
1988546 TATTATAATTTGAGAAAA
1 TATTATTATTTAAGAAAA
*
1988564 AATTATT
1 TATTATT
1988571 GTCATTAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
TATTATTATTTAAGAAAA
Found at i:1989559 original size:5 final size:5
Alignment explanation
Indices: 1989549--1989586 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
1989539 AGAATATCTA
1989549 TAACG TAACG TAACG TAACG TAACG TAACG TAACG TAA
1 TAACG TAACG TAACG TAACG TAACG TAACG TAACG TAA
1989587 TAATACTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (5 bp):
TAACG
Found at i:1989635 original size:18 final size:19
Alignment explanation
Indices: 1989596--1989641 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1989586 ATAATACTAT
1989596 TTAATTTA-ATTTAATTAA
1 TTAATTTATATTTAATTAA
**
1989614 TTAATTTATATTT-ATTTC
1 TTAATTTATATTTAATTAA
1989632 TTAATTTATA
1 TTAATTTATA
1989642 ATTTTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAATTTATATTTAATTAA
Found at i:1991067 original size:111 final size:111
Alignment explanation
Indices: 1990934--1991146 Score: 300
Period size: 111 Copynumber: 1.9 Consensus size: 111
1990924 TAATTTGAAG
* * * *
1990934 ATTAAATTAAATTTATTAAAATTATGACTAAATTAATAGAATCTATAAGTAAAAGTGACCAAATA
1 ATTAAATTAAATTTATTAAAATTACGACTAAATTAATAGAATATAAAAGTAAAAGTGACAAAATA
* * *
1990999 TGTAATCATGTCAATTTTATTAAATTTTAAAAGTTAATTATTATAA
66 TGTAATCATATCAATTTAATTAAATTTTAAAAATTAATTATTATAA
* * * * * *
1991045 ATTAATTTTAATTTTTTAAAATTACGACTAAATTGATAGAATATAAAAGTATAAGTGACAAAATG
1 ATTAAATTAAATTTATTAAAATTACGACTAAATTAATAGAATATAAAAGTAAAAGTGACAAAATA
*
1991110 TGTAATTATATCAATTTAATTAAATTTTAAAAATTAA
66 TGTAATCATATCAATTTAATTAAATTTTAAAAATTAA
1991147 GATGGGGTGA
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
111 88 1.00
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (111 bp):
ATTAAATTAAATTTATTAAAATTACGACTAAATTAATAGAATATAAAAGTAAAAGTGACAAAATA
TGTAATCATATCAATTTAATTAAATTTTAAAAATTAATTATTATAA
Found at i:1991181 original size:128 final size:128
Alignment explanation
Indices: 1991048--1991278 Score: 383
Period size: 128 Copynumber: 1.8 Consensus size: 128
1991038 ATTATAAATT
* *
1991048 AATTTTAATTTTTTAAAATTACGACTAAATTGATAGAATATAAAAGT-ATAAGTGACAAAATGTG
1 AATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATAAAAGTCA-AACTGACAAAATGTG
1991112 TAATTATATCAATTTAATTAAATTTTAAAAATTAAGATGGGGTGAGAGATAAAAAATATAAAGC
65 TAATTATATCAATTTAATTAAATTTTAAAAATTAAGATGGGGTGAGAGATAAAAAATATAAAGC
* * *
1991176 AATTTTAATTTATTAAAATTATGACTAAATTGATAGAATATATAAGTCAAACTGACCAAATGTGT
1 AATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATAAAAGTCAAACTGACAAAATGTGT
* *
1991241 AATTATATCAATTTGATTAAATTTTAAAAGTTAAGATG
66 AATTATATCAATTTAATTAAATTTTAAAAATTAAGATG
1991279 ATATAAAAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
128 94 0.99
129 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (128 bp):
AATTTTAATTTATTAAAATTACGACTAAATTGATAGAATATAAAAGTCAAACTGACAAAATGTGT
AATTATATCAATTTAATTAAATTTTAAAAATTAAGATGGGGTGAGAGATAAAAAATATAAAGC
Found at i:1991303 original size:30 final size:29
Alignment explanation
Indices: 1991268--1991414 Score: 101
Period size: 30 Copynumber: 5.1 Consensus size: 29
1991258 TAAATTTTAA
*
1991268 AAGTTAAGATGATATAAAAAATATATTTTT
1 AAGTTAAGATAATA-AAAAAATATATTTTT
1991298 AAGTT-AGATAATAATAAAAA-ATTATTTTTT
1 AAGTTAAGATAATAA-AAAAATA-TA-TTTTT
* *
1991328 AA--TAA-ATAACAATAAAAATATA-TTTC
1 AAGTTAAGATAATAA-AAAAATATATTTTT
* ** * * *
1991354 AATTTAATTTGATAATAAAATATATTTAAT
1 AAGTTAAGATAATAAAAAAATATATTT-TT
1991384 AAGTTAAGATAA-AAATAAAATATATTTTT
1 AAGTTAAGATAATAAA-AAAATATATTTTT
1991413 AA
1 AA
1991415 ACTTAAAATA
Statistics
Matches: 91, Mismatches: 15, Indels: 23
0.71 0.12 0.18
Matches are distributed among these distances:
26 5 0.05
28 28 0.31
29 27 0.30
30 31 0.34
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.39
Consensus pattern (29 bp):
AAGTTAAGATAATAAAAAAATATATTTTT
Found at i:1993791 original size:2 final size:2
Alignment explanation
Indices: 1993784--1993818 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1993774 GCAACAAAAG
1993784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1993819 CATCATTATC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1994117 original size:21 final size:21
Alignment explanation
Indices: 1994093--1994176 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
1994083 CATATAGAAT
1994093 TGTCCCGAAGGACCACATATA
1 TGTCCCGAAGGACCACATATA
* * *
1994114 TGTCCCGAAGGACCTCGTAGAA
1 TGTCCCGAAGGACCACATA-TA
* **
1994136 TTATCCCGAATAACCACATATA
1 -TGTCCCGAAGGACCACATATA
*
1994158 TGTCCCGAAGGACCTCATA
1 TGTCCCGAAGGACCACATA
1994177 GAGCCCTCAA
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
21 32 0.67
22 2 0.04
23 14 0.29
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:1994137 original size:44 final size:44
Alignment explanation
Indices: 1994086--1994178 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
1994076 TGAGTACCAT
* *
1994086 ATAGAATTGTCCCGAAGGACCACATATATGTCCCGAAGGACCTC
1 ATAGAATTATCCCGAAGAACCACATATATGTCCCGAAGGACCTC
* *
1994130 GTAGAATTATCCCGAATAACCACATATATGTCCCGAAGGACCTC
1 ATAGAATTATCCCGAAGAACCACATATATGTCCCGAAGGACCTC
1994174 ATAGA
1 ATAGA
1994179 GCCCTCAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (44 bp):
ATAGAATTATCCCGAAGAACCACATATATGTCCCGAAGGACCTC
Found at i:2011060 original size:111 final size:111
Alignment explanation
Indices: 2010931--2011142 Score: 334
Period size: 111 Copynumber: 1.9 Consensus size: 111
2010921 GGTGCCACTA
* ** * *
2010931 ATGAAAGTTATAGATCGATTTTGTTTAATGTATAATGGTGCATTTACGGTATAAAAGGTGCTACC
1 ATGAAAGTTATAGATCGATTTTGTTTAATGCATAACAGTGCATTTACGGCATAAAAGGTGCCACC
* *
2010996 CATGGTATTCATAAAAGGTGAATTACCATTTCGGAATACTTTGTGT
66 CACGGTATTCATAAAAGGTGAATGACCATTTCGGAATACTTTGTGT
* * *
2011042 ATGAAAGTTATCGATCGATTTTGTTTAATGCATAACAGTGCATTTTCGGCATAAAAGGTGCCACT
1 ATGAAAGTTATAGATCGATTTTGTTTAATGCATAACAGTGCATTTACGGCATAAAAGGTGCCACC
2011107 CACGGTATTCATAAAAGGTGAATGACCATTTCGGAA
66 CACGGTATTCATAAAAGGTGAATGACCATTTCGGAA
2011143 CTTTGGTGCA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 91 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (111 bp):
ATGAAAGTTATAGATCGATTTTGTTTAATGCATAACAGTGCATTTACGGCATAAAAGGTGCCACC
CACGGTATTCATAAAAGGTGAATGACCATTTCGGAATACTTTGTGT
Found at i:2015716 original size:22 final size:22
Alignment explanation
Indices: 2015688--2015750 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
2015678 AGTCGAAGGT
2015688 TACATAGGTCATTCGGGACATA
1 TACATAGGTCATTCGGGACATA
*
2015710 TACATAGGTCTTTCGGG--ATA
1 TACATAGGTCATTCGGGACATA
*
2015730 TATATGAGGTCATTCGGGACA
1 TACAT-AGGTCATTCGGGACA
2015751 AATTTCATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 7 0.20
21 11 0.31
22 16 0.46
23 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (22 bp):
TACATAGGTCATTCGGGACATA
Found at i:2018926 original size:18 final size:17
Alignment explanation
Indices: 2018903--2018937 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2018893 TGGTTAAATG
2018903 ATGTGACATTCTTTGGAA
1 ATGTGA-ATTCTTTGGAA
*
2018921 ATGTGATTTCTTTGGAA
1 ATGTGAATTCTTTGGAA
2018938 GGAATTCGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (17 bp):
ATGTGAATTCTTTGGAA
Found at i:2026363 original size:108 final size:108
Alignment explanation
Indices: 2026156--2026356 Score: 332
Period size: 108 Copynumber: 1.9 Consensus size: 108
2026146 GCCACTAATG
2026156 AAGTTATCGATGATTTTGTTTAATGCATAACGCTGCATTTACGACATAAAAGGTGCCACCCATGA
1 AAGTTATCGATGATTTTGTTTAATGCATAACGCTGCATTTACGACATAAAAGGTGCCACCCATGA
*
2026221 TATTCATAAAAGGTGAATTACCATTTCGACACTTCATGTATGA
66 TATTCATAAAAGGTGAATGACCATTTCGACACTTCATGTATGA
* * * *
2026264 AAGTTA-CGATCGATTTTGTTTAATGCATAACGGTGCATTTTCGGCATAAAAGGTGCCACTCATG
1 AAGTTATCGAT-GATTTTGTTTAATGCATAACGCTGCATTTACGACATAAAAGGTGCCACCCATG
*
2026328 GTATTCATAAAAGGTGAATGACCATTTCG
65 ATATTCATAAAAGGTGAATGACCATTTCG
2026357 GAACTTCGGT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
107 4 0.05
108 82 0.95
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (108 bp):
AAGTTATCGATGATTTTGTTTAATGCATAACGCTGCATTTACGACATAAAAGGTGCCACCCATGA
TATTCATAAAAGGTGAATGACCATTTCGACACTTCATGTATGA
Found at i:2033117 original size:21 final size:20
Alignment explanation
Indices: 2033092--2033136 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
2033082 ATATGATAAC
*
2033092 ATATTAAAATATTTAATTTTT
1 ATATTAAAATA-TTAACTTTT
2033113 ATATT-AAATATTAACTTTT
1 ATATTAAAATATTAACTTTT
2033132 A-ATTA
1 ATATTA
2033137 TCATATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 9 0.41
20 5 0.23
21 5 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTAAAATATTAACTTTT
Found at i:2034993 original size:20 final size:19
Alignment explanation
Indices: 2034959--2034998 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2034949 ATATTATACG
2034959 TATACATATACATTTTCATA
1 TATACATATACA-TTTCATA
**
2034979 TATACATATGGATTTCATA
1 TATACATATACATTTCATA
2034998 T
1 T
2034999 TTTTTGGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (19 bp):
TATACATATACATTTCATA
Found at i:2041524 original size:23 final size:21
Alignment explanation
Indices: 2041469--2041527 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 21
2041459 CAAACGTGAG
2041469 AATAATAAATAAAACAAGAAAA
1 AATAATAAA-AAAACAAGAAAA
* *
2041491 AATGAAAAAAAAAACACGTAAAA
1 AAT-AATAAAAAAACAAG-AAAA
2041514 AATAATTAAAAAAA
1 AATAA-TAAAAAAA
2041528 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (21 bp):
AATAATAAAAAAACAAGAAAA
Found at i:2041928 original size:15 final size:15
Alignment explanation
Indices: 2041891--2041976 Score: 70
Period size: 15 Copynumber: 5.6 Consensus size: 15
2041881 ATACATATAT
*
2041891 ATATATATAATGATATA
1 ATATATATAAT-A-AAA
*
2041908 AGATATATAATAAAA
1 ATATATATAATAAAA
2041923 ATATATAT-ATAAAA
1 ATATATATAATAAAA
* *
2041937 A-AAAGGA-ATATAAAA
1 ATATA-TATA-ATAAAA
2041952 ATATATATAATTAAAA
1 ATATATATAA-TAAAA
2041968 ATATATATA
1 ATATATATA
2041977 GGGGACGAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
13 2 0.04
14 8 0.14
15 18 0.32
16 18 0.32
17 10 0.18
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
ATATATATAATAAAA
Found at i:2041930 original size:17 final size:17
Alignment explanation
Indices: 2041910--2041976 Score: 65
Period size: 16 Copynumber: 4.3 Consensus size: 17
2041900 ATGATATAAG
2041910 ATATATAATAAAAATAT
1 ATATATAATAAAAATAT
2041927 ATATATAA-AAAAA-A-
1 ATATATAATAAAAATAT
**
2041941 GGA-AT-ATAAAAATAT
1 ATATATAATAAAAATAT
*
2041956 ATATA-ATTAAAAATAT
1 ATATATAATAAAAATAT
2041972 ATATA
1 ATATA
2041977 GGGGACGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
12 1 0.03
13 7 0.17
14 2 0.05
15 2 0.05
16 20 0.50
17 8 0.20
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
ATATATAATAAAAATAT
Found at i:2043485 original size:110 final size:110
Alignment explanation
Indices: 2043337--2043535 Score: 294
Period size: 110 Copynumber: 1.8 Consensus size: 110
2043327 AACTGGGAAA
*
2043337 TTGTTTGTTGACAGCCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT-TCAAT
1 TTGTTTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCT-AAT
* *
2043401 A-TCATTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTAAAAAG
65 ATTC-CTCGCTGTGAAGTTAAAATTGACTTTGAATGAAACTAAAAAG
* ** * *
2043447 TTGTTTGTTGACAATCAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCTAATA
1 TTGTTTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATA
2043512 TTCCTCGCTGTGAAGTTAAAATTG
66 TTCCTCGCTGTGAAGTTAAAATTG
2043536 GCTCTGAAAC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
110 76 0.96
111 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (110 bp):
TTGTTTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATA
TTCCTCGCTGTGAAGTTAAAATTGACTTTGAATGAAACTAAAAAG
Found at i:2044372 original size:67 final size:65
Alignment explanation
Indices: 2044256--2044438 Score: 215
Period size: 65 Copynumber: 2.8 Consensus size: 65
2044246 AAGATATCTG
* * * * **
2044256 TTGTTTCATGA-AAACAGTCTCAATGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGA-
2044320 TT
64 TT
*
2044322 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
2044387 T
65 T
* * * * * *
2044388 TTGTTTCAAGGGAAACTGTCTTAAGAGAGACGAAATTTGTTTCAAGAGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
2044439 CTGTCTCAAG
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
65 43 0.43
66 4 0.04
67 34 0.34
68 20 0.20
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:2044439 original size:36 final size:36
Alignment explanation
Indices: 2044387--2044555 Score: 149
Period size: 36 Copynumber: 4.9 Consensus size: 36
2044377 ATTCAAAGAT
*
2044387 TTTGTTTCAAGGGAAACTGTCTTAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
2044423 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * * *
2044459 TTTATTTCAAGGGAAA-TGTTTTC-----A-ATG--T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACGAAA
* * *
2044487 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* *
2044524 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
2044556 TAAAATCTTC
Statistics
Matches: 105, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.02
29 15 0.14
30 4 0.04
31 1 0.01
34 1 0.01
35 3 0.03
36 51 0.49
37 26 0.25
38 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
Found at i:2044441 original size:101 final size:102
Alignment explanation
Indices: 2044324--2044561 Score: 300
Period size: 101 Copynumber: 2.3 Consensus size: 102
2044314 GAAGATTTTG
* * * *
2044324 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATAAATTCAAAG-TTT
* * *
2044389 -TGTTTCAAGGGAAACTGTCTTAAGAGAGACGAAA-TT
65 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *** *
2044425 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATAAATTCAAAGTTTA
*
2044490 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * *
2044527 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
2044562 CTTCTTTTTA
Statistics
Matches: 117, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
100 3 0.03
101 82 0.70
102 32 0.27
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAATAAATTCAAAGTTTA
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:2044541 original size:37 final size:37
Alignment explanation
Indices: 2044490--2044561 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
2044480 TCAATGTTTA
* *
2044490 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
* *
2044527 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
2044562 CTTCTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTT
Found at i:2046255 original size:26 final size:25
Alignment explanation
Indices: 2046213--2046272 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
2046203 TTTTTCTTCA
* *
2046213 ATTTTC-CTTTGTTTTTTCTCTTTTT
1 ATTTTCTCTTTGCTTTTTCTC-TCTT
*
2046238 ATTTTCTCTTTGCTTTTTTTCTCTT
1 ATTTTCTCTTTGCTTTTTCTCTCTT
2046263 -TTTTCTCTTT
1 ATTTTCTCTTT
2046273 TTGTTCCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.32
25 9 0.29
26 12 0.39
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (25 bp):
ATTTTCTCTTTGCTTTTTCTCTCTT
Found at i:2046257 original size:15 final size:13
Alignment explanation
Indices: 2046214--2046266 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
2046204 TTTTCTTCAA
*
2046214 TTTTC-CTTTGTT
1 TTTTCTCTTTTTT
*
2046226 TTTTCTCTTTTTA
1 TTTTCTCTTTTTT
2046239 TTTTCTCTTTGCTTT
1 TTTTCTCTTT--TTT
2046254 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
2046267 CTCTTTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 5 0.14
13 18 0.51
15 12 0.34
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:2046261 original size:28 final size:25
Alignment explanation
Indices: 2046213--2046265 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 25
2046203 TTTTTCTTCA
2046213 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
2046238 ATTTTCTCTTTGCTTTTTTTCTCTTTTT
1 ATTTTC-CTTTG--TTTTTTCTCTTTTT
2046266 TCTCTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
28 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:2049492 original size:18 final size:17
Alignment explanation
Indices: 2049460--2049506 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
2049450 TATTAATGGA
2049460 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
* *
2049477 GTAAAAGAAATTAAAAAT
1 GTAAAA-AAATAAAAAAG
2049495 G-AATAAAAATAA
1 GTAA-AAAAATAA
2049507 TGTGTACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:2049573 original size:36 final size:36
Alignment explanation
Indices: 2049532--2049636 Score: 108
Period size: 36 Copynumber: 2.9 Consensus size: 36
2049522 TAGTATTTAC
2049532 TAAAACAAATAAAAATAATAAATATATAATACTAAG
1 TAAAACAAATAAAAATAATAAATATATAATACTAAG
* *
2049568 TAAAACAAATAAAAAATAA-AGATATACATAATATTAAG
1 TAAAACAAAT-AAAAATAATA-A-ATATATAATACTAAG
* *
2049606 -AAAAAAAAT-AAAATAAAGTAAAAATATAATA
1 TAAAACAAATAAAAAT-AA-TAAATATATAATA
2049637 TATATAAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
35 5 0.09
36 21 0.36
37 18 0.31
38 14 0.24
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (36 bp):
TAAAACAAATAAAAATAATAAATATATAATACTAAG
Found at i:2049715 original size:16 final size:16
Alignment explanation
Indices: 2049625--2049704 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
2049615 AAAATAAAGT
2049625 AAAAATATAATATAT-
1 AAAAATATAATATATA
* * *
2049640 ATAAATA-AATAAAAA
1 AAAAATATAATATATA
*
2049655 CAAAAATAGAATAT-TA
1 -AAAAATATAATATATA
2049671 AGAAAATAT-ATATATA
1 A-AAAATATAATATATA
*
2049687 AAAACATATAAAATATA
1 AAAA-ATATAATATATA
2049704 A
1 A
2049705 TATTAAGAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
14 5 0.10
15 14 0.28
16 20 0.40
17 11 0.22
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAATATAATATATA
Found at i:2049817 original size:18 final size:19
Alignment explanation
Indices: 2049773--2049850 Score: 58
Period size: 18 Copynumber: 4.2 Consensus size: 19
2049763 ATATAATGAT
2049773 ATAAG-ATATAATATAAAA
1 ATAAGAATATAATATAAAA
*
2049791 ATAATAATATAA-ATAAAA
1 ATAAGAATATAATATAAAA
*
2049809 A-AAGGAATATAGTA-AATAA
1 ATAA-GAATATAATATAA-AA
*
2049828 ATAAAAAAATATAAT-TAAAA
1 AT--AAGAATATAATATAAAA
2049848 ATA
1 ATA
2049851 TATATATGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
17 2 0.04
18 20 0.43
19 10 0.21
20 4 0.09
21 9 0.19
22 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
ATAAGAATATAATATAAAA
Found at i:2051246 original size:42 final size:43
Alignment explanation
Indices: 2051172--2051257 Score: 147
Period size: 42 Copynumber: 2.0 Consensus size: 43
2051162 CAAATTAACT
2051172 CCCCAAAAGTATAGTTTGTACTCACCCATTATGATTTGATGAC
1 CCCCAAAAGTATAGTTTGTACTCACCCATTATGATTTGATGAC
**
2051215 CCCCAAAAGTATAG-TTGTACTCGTCCATTATGATTTGATGAC
1 CCCCAAAAGTATAGTTTGTACTCACCCATTATGATTTGATGAC
2051257 C
1 C
2051258 TCTAATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 27 0.66
43 14 0.34
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (43 bp):
CCCCAAAAGTATAGTTTGTACTCACCCATTATGATTTGATGAC
Found at i:2053489 original size:59 final size:58
Alignment explanation
Indices: 2053378--2053489 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 58
2053368 TATGATTATC
* * * *
2053378 ATTCTAAATTATCCTCAAACTTTGACCATTTTATTTTCATCCCCAAACTATGTCATTT
1 ATTCTAAATTAGCCTCAAACTTTGAACATTTAAATTTCATCCCCAAACTATGTCATTT
*
2053436 ATTCTAAGTTAGCCTTCAAACTTTGTCAACATTTAAATTTCAT-CCCAAA-TATGT
1 ATTCTAAATTAGCC-TCAAACTTTG--AACATTTAAATTTCATCCCCAAACTATGT
2053490 ATATACTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 12 0.26
59 15 0.33
60 6 0.13
61 13 0.28
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.41
Consensus pattern (58 bp):
ATTCTAAATTAGCCTCAAACTTTGAACATTTAAATTTCATCCCCAAACTATGTCATTT
Found at i:2056359 original size:44 final size:45
Alignment explanation
Indices: 2056310--2056399 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 45
2056300 ACAGACATGT
2056310 CAATAG-AT-ATTAATATGTTGATTTTATCGCATTTCGAGCTTAGA
1 CAATAGAATCATTAATATG-TGATTTTATCGCATTTCGAGCTTAGA
2056354 CAATAGATATCATTAATATGTGATTTTATCGCATTTCGAGCTTAGA
1 CAATAGA-ATCATTAATATGTGATTTTATCGCATTTCGAGCTTAGA
2056400 AGACTGTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
44 6 0.14
46 28 0.65
47 9 0.21
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (45 bp):
CAATAGAATCATTAATATGTGATTTTATCGCATTTCGAGCTTAGA
Found at i:2056895 original size:6 final size:6
Alignment explanation
Indices: 2056884--2057700 Score: 1170
Period size: 6 Copynumber: 140.2 Consensus size: 6
2056874 ATAAACACTC
2056884 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATAC--
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
2056930 ATACAT ATACAT ATACAT ATACAT ATAACAT ATACAT ATACAT ATACATAT
1 ATACAT ATACAT ATACAT ATACAT AT-ACAT ATACAT ATACAT ATAC--AT
*
2056981 ATACAT ATACAT AT-CAT ATACAT ATTACAT ATAAAT ATACAT AT-CAT
1 ATACAT ATACAT ATACAT ATACAT A-TACAT ATACAT ATACAT ATACAT
2057028 ATACAT ATACAT ATACAT ATACAT -TACAT ATACAT ATACAT ATAC-T
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
2057074 ATAC-- ATACAT -TACAT ATACAT ATACAT ATACAT AT-CAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
*
2057118 ATACAT ATACCT ATACAT ATAC-- ATAC-T ATACATAT ATACAT ATAC-T
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATAC--AT ATACAT ATACAT
*
2057164 ATACAT ATACAT ATACAT ATACAT ATACAT ATGCAT ATAC-- ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
2057210 ATAC-- ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
2057256 -TACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATATAT ACATAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
2057303 ATACAT ATACAT ATAACAT ATACAT ATACAT ATACAT ATACAT CATACAT
1 ATACAT ATACAT AT-ACAT ATACAT ATACAT ATACAT ATACAT -ATACAT
2057353 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
2057401 ATACAT ATAC-- ATAC-T ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
2057446 AT--AT AT-CAT ATACAT AT--AT ATACAT -TACAT ATACATAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATAC--AT ATACAT
2057490 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT AT--A- ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
2057535 ATACAT ATACAT ATACAT ATACAT -TACAT ATACAT ATACAT ATA-AT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
*
2057581 ATATAT ACATACAT ATAC-T A-ACAT ATACAT ATACAT ATAACAT ATACAT
1 ATACAT --ATACAT ATACAT ATACAT ATACAT ATACAT AT-ACAT ATACAT
2057630 ATACAT ATACAT ATAACAT ATACAT ATACAT ATACAT ATAC-T ATACAT
1 ATACAT ATACAT AT-ACAT ATACAT ATACAT ATACAT ATACAT ATACAT
*
2057678 ATA-AT AAACAT ATACAT A-ACAT A
1 ATACAT ATACAT ATACAT ATACAT A
2057701 CATAAGACAC
Statistics
Matches: 751, Mismatches: 13, Indels: 95
0.87 0.02 0.11
Matches are distributed among these distances:
3 2 0.00
4 35 0.05
5 86 0.11
6 570 0.76
7 36 0.05
8 22 0.03
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
ATACAT
Found at i:2058023 original size:12 final size:12
Alignment explanation
Indices: 2058006--2058038 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2057996 ATGATAAGCT
2058006 GTGGTGGTGGCG
1 GTGGTGGTGGCG
2058018 GTGGTGGTGGCG
1 GTGGTGGTGGCG
*
2058030 GCGGTGGTG
1 GTGGTGGTG
2058039 AGTTGGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.09, G:0.67, T:0.24
Consensus pattern (12 bp):
GTGGTGGTGGCG
Found at i:2058026 original size:15 final size:15
Alignment explanation
Indices: 2058006--2058038 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2057996 ATGATAAGCT
*
2058006 GTGGTGGTGGCGGTG
1 GTGGTGGCGGCGGTG
2058021 GTGGTGGCGGCGGTG
1 GTGGTGGCGGCGGTG
2058036 GTG
1 GTG
2058039 AGTTGGTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.67, T:0.24
Consensus pattern (15 bp):
GTGGTGGCGGCGGTG
Found at i:2060990 original size:20 final size:20
Alignment explanation
Indices: 2060965--2061031 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
2060955 CGATATACCA
2060965 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
*
2060985 GATAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
*
2061005 GGTAACAAA-ATGATAAAGCC
1 GGTAA-AAATATGATAAAACC
2061025 GGTAAAA
1 GGTAAAA
2061032 CGTTACCAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.05
20 38 0.88
21 3 0.07
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.18
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:2061159 original size:200 final size:201
Alignment explanation
Indices: 2060810--2061208 Score: 574
Period size: 200 Copynumber: 2.0 Consensus size: 201
2060800 ACCTGTATTG
* * * *
2060810 AAATGATAAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATC
1 AAATGATAAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTAATATAAGGATC
* *
2060875 GACATTTCGTGAATTTAAAAGAGAAACAGTTTTAAATCCTATAAAGTGTCGATACTTTTAAAAAA
66 GACATTTCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAA
* *
2060940 TGTATCGATTCAAAACGATATACCAGGTAAAAATATGATAAAACC-G-ATAAAAATATGATAAAA
131 TATATCGATTCAAAACGATATAACAGGTAAAAATATGATAAAACCAGTAT-AAAA-ATGAT-AAA
2061003 CCGGTAACA
193 CCGGTAACA
* * *
2061012 AAATGATAAAGCCGGTAAAACGTTACCAGATATATTGAAAGTGTCGATACTTT-ATATAAGGATC
1 AAATGATAAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTAATATAAGGATC
* ** *
2061076 GACACTTT-GTGAATTTAAAAGAGAAGCAG-TTTAGCGCCTATAATGTGTCGATACTTTAAAAAA
66 GACA-TTTCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAA
* *
2061139 ATATATCGATTCACAACGATATAACAGGTAAAAATATGATAAAACCAGTATTAAAATGATAAACC
130 ATATATCGATTCAAAACGATATAACAGGTAAAAATATGATAAAACCAGTATAAAAATGATAAACC
2061204 GGTAA
195 GGTAA
2061209 AATGATACCG
Statistics
Matches: 177, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
199 10 0.06
200 77 0.44
201 39 0.22
202 51 0.29
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (201 bp):
AAATGATAAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTAATATAAGGATC
GACATTTCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAA
TATATCGATTCAAAACGATATAACAGGTAAAAATATGATAAAACCAGTATAAAAATGATAAACCG
GTAACA
Found at i:2062092 original size:19 final size:19
Alignment explanation
Indices: 2062068--2062116 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2062058 AATGTAGGGT
2062068 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2062087 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
2062106 TAATTTTGTAT
1 TAATTTTGTAT
2062117 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2062827 original size:197 final size:200
Alignment explanation
Indices: 2062226--2062972 Score: 1145
Period size: 197 Copynumber: 3.8 Consensus size: 200
2062216 AAATTTACAT
* * * *
2062226 ATGGCAAACATGGTGTAACCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCTCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
**
2062289 CGAAACCCAAAAG--TAATGTAATAGGTAATTTTTCAATCTATTCGGTACAAGTATA-CGG-TTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
2062350 AT--GAGAATATGTCTAAATAATGTATCG--ACTTTTGTAGTTTGTGTCGATA-TTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
2062410 AATGA
196 AATGA
* *
2062415 ATGGCAAATA-GGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
2062479 CGAAACCCAAAAGTATAATGTAAT-GTGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
66 CGAAACCCAAAAGTATAATGTAATAG-GTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
* * *
2062543 TATGAGAGAATAGGTCTAAATAATATGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTACA
130 TATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCA
*
2062608 AAATGA
195 GAATGA
2062614 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
2062679 CGAAACCCATAAGTATAATGTAATAGGTAA-TTTTCAATATAACTGGTACAAGTATACC-G-TTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
2062741 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
2062806 AATGA
196 AATGA
2062811 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
2062876 CGAAACCCATAAGTATAATGTAATAGGTAA--TTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
2062939 ATGAGAGAATTGGTATATAAT-ATGTATGGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTATCGACACT
2062973 GTTTAATGTT
Statistics
Matches: 516, Mismatches: 25, Indels: 25
0.91 0.04 0.04
Matches are distributed among these distances:
188 23 0.04
189 9 0.02
190 40 0.08
191 1 0.00
192 38 0.07
193 3 0.01
194 5 0.01
196 47 0.09
197 165 0.32
198 52 0.10
199 52 0.10
200 80 0.16
201 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:2064479 original size:12 final size:12
Alignment explanation
Indices: 2064457--2064496 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2064447 CAAGCGGTCA
*
2064457 ATGAAGATGAAG
1 ATGACGATGAAG
*
2064469 CTGACGATGAAG
1 ATGACGATGAAG
*
2064481 ATGACGATGATG
1 ATGACGATGAAG
2064493 ATGA
1 ATGA
2064497 TCCAAACAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:2064495 original size:18 final size:18
Alignment explanation
Indices: 2064457--2064496 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2064447 CAAGCGGTCA
*
2064457 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGATGACG
* *
2064475 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
2064493 ATGA
1 ATGA
2064497 TCCAAACAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:2065445 original size:15 final size:14
Alignment explanation
Indices: 2065425--2065463 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2065415 TTGAACATTC
2065425 TTGTGTATGTATATT
1 TTGTGTAT-TATATT
2065440 TTGTGTGATTATATT
1 TTGTGT-ATTATATT
*
2065455 GTGTGTATT
1 TTGTGTATT
2065464 TTCATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 17 0.77
16 2 0.09
ACGTcount: A:0.18, C:0.00, G:0.23, T:0.59
Consensus pattern (14 bp):
TTGTGTATTATATT
Found at i:2066140 original size:182 final size:182
Alignment explanation
Indices: 2065620--2066217 Score: 955
Period size: 181 Copynumber: 3.3 Consensus size: 182
2065610 AAATTTTCAG
* * *
2065620 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTTCA
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCTTGTCA
* * *
2065685 AAAAGTG-CG--ATTGAAAAAACATCAGAACCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 AAAAGTGTCGACATT---TACACATCGGAACCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
2065747 AA-CGGTATAAATATACCTG-TTTATGAGCGAATAGGTCTACAACCTATATCGAC
128 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
2065800 AC-TTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAAGAAAAATGTGTCG-TACCTTGTC
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATT-GAAAGAAAAATGTGTCGATACCTTGTC
*
2065863 AAAAAGTGTCAACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAA-TTTGTAATATA
65 AAAAAGTGTCGACATTTACACATCGGAA-CCAGAATTATAATGTAATAGATAATTTTGTAATATA
*
2065927 ACCGGTATAAATATACTGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
129 ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
* *
2065981 ACTTTTTAATA-TGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTATTGATACCTTGTCA
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCTTGTCA
2066045 AAAAGTGTCGACATTTACACATCGGAACCAAGAATTATAATGTAATAGATAATTTTGTAATATAA
66 AAAAGTGTCGACATTTACACATCGGAACC-AGAATTATAATGTAATAGATAATTTTGTAATATAA
*
2066110 CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCAAC
130 CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
2066163 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATT-AGAAGAAAAATGTGTCGA
1 ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGA-AAGAAAAATGTGTCGA
2066218 CATATATATT
Statistics
Matches: 389, Mismatches: 16, Indels: 23
0.91 0.04 0.05
Matches are distributed among these distances:
179 70 0.18
180 75 0.19
181 119 0.31
182 86 0.22
183 39 0.10
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (182 bp):
ACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCTTGTCA
AAAAGTGTCGACATTTACACATCGGAACCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGAC
Found at i:2066491 original size:23 final size:23
Alignment explanation
Indices: 2066460--2066532 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2066450 ATAGGTAAAA
* *
2066460 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
2066483 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
2066506 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
2066529 ATAT
1 ATAT
2066533 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2074313 original size:68 final size:69
Alignment explanation
Indices: 2074166--2074330 Score: 316
Period size: 68 Copynumber: 2.4 Consensus size: 69
2074156 TTGTTGTCTC
2074166 CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTATTTTTTTTTTCTGTTTTGTTTGTTGTCG
1 CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTATTTTTTTTTTCTGTTTTGTTTGTTGTCG
2074231 TCCT
66 TCCT
2074235 CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTA-TTTTTTTTTCTGTTTTGTTTGTTGTCG
1 CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTATTTTTTTTTTCTGTTTTGTTTGTTGTCG
2074299 TCCT
66 TCCT
2074303 CTGTTGCTCTCTGTGGCTGTCCT-CTTTC
1 CTGTTGCTCTCTGTGGCTGTCCTCCTTTC
2074331 TTTCTTGCAG
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
67 5 0.05
68 54 0.56
69 37 0.39
ACGTcount: A:0.01, C:0.24, G:0.18, T:0.57
Consensus pattern (69 bp):
CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTATTTTTTTTTTCTGTTTTGTTTGTTGTCG
TCCT
Found at i:2074804 original size:3 final size:3
Alignment explanation
Indices: 2074796--2074914 Score: 148
Period size: 3 Copynumber: 39.0 Consensus size: 3
2074786 TTATTTATTA
*
2074796 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * * *
2074843 AAT TAT TAT AAT AAT ACT AAT ACT AAT AAT AAT AAT AAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
2074891 AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
2074915 TTTAAATGAA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
3 94 0.94
4 6 0.06
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2075205 original size:76 final size:76
Alignment explanation
Indices: 2075046--2076067 Score: 1715
Period size: 76 Copynumber: 13.4 Consensus size: 76
2075036 GAAATGTTGA
* * * *
2075046 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTTGTAAATATCAAAAAGTTCCCG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
2075111 AAGGCTTTTTGG
65 AAGGCTTTTTGG
2075123 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2075188 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2075199 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2075264 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2075275 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2075340 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2075351 AAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2075415 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2075426 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTTGTAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
2075491 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
2075503 AAACATCATGCACTGAAGGGCTTACAGATGA-CCGAAGGCTTTTGTAAATATCAAAAAGTTCCCG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
2075567 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
2075579 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTTGTAAATATCAAAAAGTTCCCG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
2075644 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
2075656 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
2075721 AGGCTTTTAGG
66 AGGCTTTTTGG
*
2075732 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2075797 AGGCTTTTTGG
66 AGGCTTTTTGG
*
2075808 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
2075873 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
2075884 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
2075949 AGGCTTTTAGG
66 AGGCTTTTTGG
* * * *
2075960 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTTGTAAATATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
2076025 AAGGCTTTTTTGG
65 AAGGC-TTTTTGG
*
2076038 AAATATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
2076068 TGGGAAATAG
Statistics
Matches: 908, Mismatches: 32, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
75 74 0.08
76 585 0.64
77 215 0.24
78 34 0.04
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:2079556 original size:92 final size:92
Alignment explanation
Indices: 2079354--2079682 Score: 579
Period size: 92 Copynumber: 3.6 Consensus size: 92
2079344 TGATTTTAGA
* * * *
2079354 GTTCATACCAAATCATATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT-GT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
* *
2079418 CTTCCAAATTCAATGATTGGTTCTGTG
66 CTTCCAAATTCAATAACTGGTTCTGTG
2079445 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
2079510 CTTCCAAATTCAATAACTGGTTCTGTG
66 CTTCCAAATTCAATAACTGGTTCTGTG
*
2079537 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAGCACATTCCT
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
*
2079602 CTTCTAAATTCAATAACTGGTTCTGTG
66 CTTCCAAATTCAATAACTGGTTCTGTG
2079629 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
2079683 GGTCTCCTTA
Statistics
Matches: 228, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
91 59 0.26
92 169 0.74
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (92 bp):
GTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCT
CTTCCAAATTCAATAACTGGTTCTGTG
Found at i:2082251 original size:2 final size:2
Alignment explanation
Indices: 2082244--2082269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2082234 ACAACAAAGG
2082244 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
2082270 TAAAGGATAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2086610 original size:18 final size:17
Alignment explanation
Indices: 2086562--2086612 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
2086552 AAATACTTGC
*
2086562 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
2086580 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
2086598 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
2086613 TTGACAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:2088452 original size:68 final size:69
Alignment explanation
Indices: 2088305--2088469 Score: 316
Period size: 68 Copynumber: 2.4 Consensus size: 69
2088295 TTGTTGTCTC
2088305 CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTATTTTTTTTTTCTGTTTTGTTTGTTGTCG
1 CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTATTTTTTTTTTCTGTTTTGTTTGTTGTCG
2088370 TCCT
66 TCCT
2088374 CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTA-TTTTTTTTTCTGTTTTGTTTGTTGTCG
1 CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTATTTTTTTTTTCTGTTTTGTTTGTTGTCG
2088438 TCCT
66 TCCT
2088442 CTGTTGCTCTCTGTGGCTGTCCT-CTTTC
1 CTGTTGCTCTCTGTGGCTGTCCTCCTTTC
2088470 TTTCTTGCAG
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
67 5 0.05
68 54 0.56
69 37 0.39
ACGTcount: A:0.01, C:0.24, G:0.18, T:0.57
Consensus pattern (69 bp):
CTGTTGCTCTCTGTGGCTGTCCTCCTTTCGTTTTCTATTTTTTTTTTCTGTTTTGTTTGTTGTCG
TCCT
Found at i:2088944 original size:3 final size:3
Alignment explanation
Indices: 2088936--2089060 Score: 169
Period size: 3 Copynumber: 41.0 Consensus size: 3
2088926 TTATTTATTA
*
2088936 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * *
2088983 AAT AAT TAT TAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
2089031 AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2089061 TTTAAATGAA
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
3 102 0.94
4 6 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2093934 original size:10 final size:10
Alignment explanation
Indices: 2093914--2093942 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2093904 ATCATTGGAG
2093914 AAGAG-AAAA
1 AAGAGAAAAA
2093923 AAGAGAAAAA
1 AAGAGAAAAA
2093933 AAGAGAAAAA
1 AAGAGAAAAA
2093943 CATCGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAGAGAAAAA
Found at i:2098503 original size:15 final size:14
Alignment explanation
Indices: 2098481--2098512 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2098471 TATATACAGA
*
2098481 GATTTTTTCGCAGG
1 GATTTTTTTGCAGG
2098495 GATTTTTTTGCAGG
1 GATTTTTTTGCAGG
2098509 GATT
1 GATT
2098513 ACTATCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.09, G:0.28, T:0.47
Consensus pattern (14 bp):
GATTTTTTTGCAGG
Found at i:2107321 original size:23 final size:23
Alignment explanation
Indices: 2107295--2107382 Score: 108
Period size: 23 Copynumber: 3.8 Consensus size: 23
2107285 AGCTCATATA
2107295 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
2107318 AATTTGTC-CCGAAG-GACCGCGTAG
1 AA-TTG-CACCGAAGTG-CCACGTAG
*
2107342 AAATGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
2107365 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
2107383 TATAAGATTG
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 1 0.02
23 34 0.62
24 19 0.35
25 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:2108728 original size:12 final size:12
Alignment explanation
Indices: 2108711--2108736 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2108701 AGATGACAAG
2108711 TAAAATTCAACT
1 TAAAATTCAACT
2108723 TAAAATTCAACT
1 TAAAATTCAACT
2108735 TA
1 TA
2108737 TCAATTCTAT
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:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAAATTCAACT
Found at i:2113956 original size:23 final size:23
Alignment explanation
Indices: 2113930--2114017 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
2113920 AGCTCATATA
2113930 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
2113953 AATTTGTC-CCGAAG-GACCGCGTAA
1 AA-TTG-CACCGAAGTG-CCACGTAG
*
2113977 AAATGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
2114000 AATTGCATCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
2114018 TATAAGATTG
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 18 0.35
25 1 0.02
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:2115084 original size:34 final size:35
Alignment explanation
Indices: 2115041--2115108 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 35
2115031 TTTTATTTAG
2115041 GGGGAATCGATACCCCCCA-GGGGAATCTATTCCT
1 GGGGAATCGATACCCCCCAGGGGGAATCTATTCCT
*
2115075 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTATTCC
2115109 CCCTGCACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 19 0.59
35 13 0.41
ACGTcount: A:0.22, C:0.29, G:0.29, T:0.19
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGGGAATCTATTCCT
Done.