Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005946.1 Hibiscus syriacus cultivar Beakdansim tig00013960_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: 2465359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2065405 original size:20 final size:19
Alignment explanation
Indices: 2065380--2065421 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
2065370 AATTTTTTTA
2065380 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAA-TTCCCAAT
*
2065400 TTCCCTCTAAATTCTCAAT
1 TTCCCTCTAAATTCCCAAT
2065419 TTC
1 TTC
2065422 ACTATATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.43
Consensus pattern (19 bp):
TTCCCTCTAAATTCCCAAT
Found at i:2065420 original size:19 final size:19
Alignment explanation
Indices: 2065351--2065421 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
2065341 ATAAAATCTC
*
2065351 AATTCTCAATTTCCCTCCA
1 AATTCTCAATTTCCCTCTA
***
2065370 AATT-TTTTTATTCCCTCTA
1 AATTCTCAAT-TTCCCTCTA
*
2065389 AATTTCCCAATTTCCCTCTA
1 AA-TTCTCAATTTCCCTCTA
2065409 AATTCTCAATTTC
1 AATTCTCAATTTC
2065422 ACTATATTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 2 0.05
19 24 0.60
20 13 0.32
21 1 0.03
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTCTCAATTTCCCTCTA
Found at i:2065628 original size:13 final size:13
Alignment explanation
Indices: 2065600--2065719 Score: 79
Period size: 13 Copynumber: 9.2 Consensus size: 13
2065590 ATATACTTTT
2065600 TATAGTTTATACATA
1 TATAGTTTAT--ATA
2065615 TATAGTTTATATA
1 TATAGTTTATATA
*
2065628 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
2065643 CATAATTTATATA
1 TATAGTTTATATA
**
2065656 TATAACTTATA-A
1 TATAGTTTATATA
2065668 TA-A--TTATATA
1 TATAGTTTATATA
* * *
2065678 GTTTA-TAATATAAA
1 -TATAGT-TTATATA
2065692 TATAGTTTATATA
1 TATAGTTTATATA
2065705 TATAGTTTATATA
1 TATAGTTTATATA
2065718 TA
1 TA
2065720 AACTTATATT
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
9 5 0.06
10 1 0.01
11 2 0.02
12 4 0.05
13 47 0.55
14 6 0.07
15 20 0.24
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:2065694 original size:18 final size:19
Alignment explanation
Indices: 2065673--2065708 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2065663 TATAATAATT
2065673 ATATAGTTTATA-ATATAA
1 ATATAGTTTATATATATAA
2065691 ATATAGTTTATATATATA
1 ATATAGTTTATATATATA
2065709 GTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
ATATAGTTTATATATATAA
Found at i:2065719 original size:30 final size:32
Alignment explanation
Indices: 2065648--2065739 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 32
2065638 ATAAACATAA
*
2065648 TTTAT-ATATATAACT-TATAATA-ATTATATAG
1 TTTATAATATA-AACTATATTATATA-TATATAG
2065679 TTTATAATATAAA-TATAGTT-TATATATATAG
1 TTTATAATATAAACTATA-TTATATATATATAG
2065710 TTTAT-ATATAAACTTATATTATATATATAT
1 TTTATAATATAAAC-TATATTATATATATAT
2065740 TATATTTTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
30 8 0.15
31 25 0.47
32 20 0.38
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (32 bp):
TTTATAATATAAACTATATTATATATATATAG
Found at i:2065731 original size:17 final size:16
Alignment explanation
Indices: 2065711--2065745 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2065701 TATATATAGT
2065711 TTATATATAAACTTATA
1 TTATATATAAA-TTATA
*
2065728 TTATATATATATTATA
1 TTATATATAAATTATA
2065744 TT
1 TT
2065746 TTTTTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATATAAATTATA
Found at i:2067793 original size:29 final size:31
Alignment explanation
Indices: 2067760--2067824 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
2067750 TAATCCCCTT
2067760 ATTTTAATCC-GTTTAGTACCTAAA-TTTCA
1 ATTTTAATCCAGTTTAGTACCTAAACTTTCA
* **
2067789 ATTTTAATCCATTTTAGTGTCTAAACTTTCA
1 ATTTTAATCCAGTTTAGTACCTAAACTTTCA
2067820 ATTTT
1 ATTTT
2067825 TTAAAATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 10 0.32
30 11 0.35
31 10 0.32
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.49
Consensus pattern (31 bp):
ATTTTAATCCAGTTTAGTACCTAAACTTTCA
Found at i:2082717 original size:22 final size:22
Alignment explanation
Indices: 2082692--2082746 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
2082682 ATACCTAATA
*
2082692 AGTCTTTATATTTTTCTTAAAT
1 AGTCTTAATATTTTTCTTAAAT
2082714 AGTC-TAATATTTTTCTTAAAT
1 AGTCTTAATATTTTTCTTAAAT
2082735 AGTC-TAATATTT
1 AGTCTTAATATTT
2082747 CGGTCCTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (22 bp):
AGTCTTAATATTTTTCTTAAAT
Found at i:2082724 original size:21 final size:21
Alignment explanation
Indices: 2082699--2082746 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
2082689 ATAAGTCTTT
2082699 ATATTTTTCTTAAATAGTCTA
1 ATATTTTTCTTAAATAGTCTA
2082720 ATATTTTTCTTAAATAGTCTA
1 ATATTTTTCTTAAATAGTCTA
2082741 ATATTT
1 ATATTT
2082747 CGGTCCTTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.54
Consensus pattern (21 bp):
ATATTTTTCTTAAATAGTCTA
Found at i:2082839 original size:2 final size:2
Alignment explanation
Indices: 2082832--2082891 Score: 65
Period size: 2 Copynumber: 32.0 Consensus size: 2
2082822 GGTTGTATCA
* * *
2082832 AT AT AT AT AT AC AT AT A- AT AC AC AT AT A- AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2082870 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2082892 TAACCTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
1 4 0.08
2 46 0.92
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2089571 original size:4 final size:4
Alignment explanation
Indices: 2089562--2089587 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2089552 CGCTAACTTG
2089562 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
2089588 TATGTTCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:2089777 original size:18 final size:19
Alignment explanation
Indices: 2089737--2089777 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
2089727 TGGCCTTTAC
2089737 CTTTTATTTAGTTAGTTTT
1 CTTTTATTTAGTTAGTTTT
2089756 -TTTTATTTCA-TTA-TTTT
1 CTTTTATTT-AGTTAGTTTT
2089773 CTTTT
1 CTTTT
2089778 TTTGTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.20
18 15 0.75
19 1 0.05
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.73
Consensus pattern (19 bp):
CTTTTATTTAGTTAGTTTT
Found at i:2090066 original size:26 final size:26
Alignment explanation
Indices: 2090012--2090068 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
2090002 AGGATTTTTC
* *
2090012 TTTTATTTATTTTATTTTATTTTCTG
1 TTTTATTTATTTTATTCTATTTTCGG
2090038 TTTTATTTAGTTTTGA-TCTATTTT-GG
1 TTTTATTTA-TTTT-ATTCTATTTTCGG
2090064 TTTTA
1 TTTTA
2090069 GGGTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 15 0.56
27 11 0.41
28 1 0.04
ACGTcount: A:0.16, C:0.04, G:0.09, T:0.72
Consensus pattern (26 bp):
TTTTATTTATTTTATTCTATTTTCGG
Found at i:2097558 original size:18 final size:18
Alignment explanation
Indices: 2097535--2097569 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2097525 ATGGATTATC
*
2097535 AGTGGTCTTTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
2097553 AGTGGTCATTCTGGACA
1 AGTGGTCATTCGGGACA
2097570 AATATTCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.31, T:0.31
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:2102933 original size:18 final size:18
Alignment explanation
Indices: 2102910--2102944 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2102900 AGGGATTATC
2102910 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
2102928 AGTGGTCCTTCAGGACA
1 AGTGGTCCTTCAGGACA
2102945 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:2105994 original size:20 final size:19
Alignment explanation
Indices: 2105969--2106018 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
2105959 TTTCATATTC
*
2105969 TTTATTATTCTTTACATTAT
1 TTTATTATT-TTGACATTAT
* *
2105989 TTTATTTAATTTGACATTTT
1 TTTA-TTATTTTGACATTAT
2106009 TTTATTATTT
1 TTTATTATTT
2106019 CATTCATTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 5 0.20
20 16 0.64
21 4 0.16
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTATTATTTTGACATTAT
Found at i:2107565 original size:22 final size:23
Alignment explanation
Indices: 2107540--2107609 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 23
2107530 ATTACACCTG
*
2107540 AAGAAAAGAAAAAA-ATTAAAAA
1 AAGAAAAGAAAAAAGAATAAAAA
* * *
2107562 AAGAGAGAGAAAAAAGAAGAAAAT
1 AAGA-AAAGAAAAAAGAATAAAAA
2107586 AAG-AAAGAAAAAAGAATAAAAA
1 AAGAAAAGAAAAAAGAATAAAAA
2107608 AA
1 AA
2107610 ACTGAAATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 22 0.56
23 9 0.23
24 8 0.21
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.06
Consensus pattern (23 bp):
AAGAAAAGAAAAAAGAATAAAAA
Found at i:2107574 original size:12 final size:10
Alignment explanation
Indices: 2107559--2107608 Score: 55
Period size: 10 Copynumber: 4.6 Consensus size: 10
2107549 AAAAAATTAA
2107559 AAAAAGAGAGAG
1 AAAAA-AGA-AG
2107571 AAAAAAGAAG
1 AAAAAAGAAG
2107581 AAAATAAGAAAG
1 AAAA-AAG-AAG
*
2107593 AAAAAAGAAT
1 AAAAAAGAAG
2107603 AAAAAA
1 AAAAAA
2107609 AACTGAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 14 0.40
11 9 0.26
12 12 0.34
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:2107609 original size:11 final size:11
Alignment explanation
Indices: 2107557--2107609 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
2107547 GAAAAAAATT
2107557 AAAAAAAGAGAG
1 AAAAAAAGA-AG
2107569 AGAAAAAAGAAG
1 A-AAAAAAGAAG
*
2107581 AAAATAAGAA-
1 AAAAAAAGAAG
*
2107591 AGAAAAAAGAAT
1 A-AAAAAAGAAG
2107603 AAAAAAA
1 AAAAAAA
2107610 ACTGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 1 0.03
11 22 0.61
12 5 0.14
13 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:2117867 original size:26 final size:26
Alignment explanation
Indices: 2117815--2117867 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2117805 ACAACCTGAT
* *
2117815 GTGGCAGTTTCTAAAAGGTCCAGTCA
1 GTGGCAGTTTCTAAAAGATCCACTCA
* *
2117841 GTGGCAGTTTCTAGAAGATCTACTCA
1 GTGGCAGTTTCTAAAAGATCCACTCA
2117867 G
1 G
2117868 CGCACCTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (26 bp):
GTGGCAGTTTCTAAAAGATCCACTCA
Found at i:2120970 original size:65 final size:66
Alignment explanation
Indices: 2120836--2121008 Score: 158
Period size: 65 Copynumber: 2.6 Consensus size: 66
2120826 AACATAAACC
* * * *
2120836 TTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCATTTGAGACAGTCTTCCTTAAGAGACAAACA
1 TTGAGATTGTTTTTCTTAAAACAAATTTCGTCTCACTTGAGACAGTCTTCCCTAAGAAACAAACA
2120901 T
66 T
* * *
2120902 TTGAGATTGTTTTT-TTTAAATAAATTTCGTCTCACTTGAGACA-TTTTCCCCTAA-AAACCCAA
1 TTGAGATTGTTTTTCTTAAAACAAATTTCGTCTCACTTGAGACAGTCTT-CCCTAAGAAA--CAA
*
2120964 A-TT
63 ACAT
* ** * *
2120967 TTGAAATTGTTTCACTTGAAACAAAATT-GATCTCACTTGAGA
1 TTGAGATTGTTTTTCTTAAAACAAATTTCG-TCTCACTTGAGA
2121009 TTGTTTTCCT
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
64 5 0.06
65 43 0.49
66 40 0.45
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (66 bp):
TTGAGATTGTTTTTCTTAAAACAAATTTCGTCTCACTTGAGACAGTCTTCCCTAAGAAACAAACA
T
Found at i:2122464 original size:29 final size:29
Alignment explanation
Indices: 2122432--2122500 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
2122422 TACATTTTAT
*
2122432 TTTATTTTATTTTTGACACC-CTGTT-TGCA
1 TTTATTTTATTTTGGACACCACT-TTCT-CA
* *
2122461 TTTATTTTAATTTGGCCACCACTTTCTCA
1 TTTATTTTATTTTGGACACCACTTTCTCA
2122490 TTTATTTTATT
1 TTTATTTTATT
2122501 ATTTTATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 31 0.91
30 3 0.09
ACGTcount: A:0.19, C:0.17, G:0.07, T:0.57
Consensus pattern (29 bp):
TTTATTTTATTTTGGACACCACTTTCTCA
Found at i:2123025 original size:16 final size:16
Alignment explanation
Indices: 2123006--2123036 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2122996 CTTTTTTTGT
*
2123006 TATTTAATTTTATGCA
1 TATTTAAATTTATGCA
2123022 TATTTAAATTTATGC
1 TATTTAAATTTATGC
2123037 TCTTTACCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
TATTTAAATTTATGCA
Found at i:2125626 original size:2 final size:2
Alignment explanation
Indices: 2125621--2125654 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2125611 TATGTGTGTG
2125621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2125655 ATTAGATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2126433 original size:10 final size:10
Alignment explanation
Indices: 2126418--2126466 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
2126408 GAGATAATGT
*
2126418 TTTTATTGAA
1 TTTTATTCAA
2126428 TTTTATTCATA
1 TTTTATTCA-A
*
2126439 TTTTATTCAT
1 TTTTATTCAA
*
2126449 TTTTATTGCAT
1 TTTTATT-CAA
2126460 TTTTATT
1 TTTTATT
2126467 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
10 15 0.43
11 20 0.57
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.67
Consensus pattern (10 bp):
TTTTATTCAA
Found at i:2126471 original size:10 final size:10
Alignment explanation
Indices: 2126417--2126474 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
2126407 CGAGATAATG
*
2126417 TTTTTATTGA
1 TTTTTATTCA
*
2126427 ATTTTATTCA
1 TTTTTATTCA
2126437 TATTTTATTCA
1 T-TTTTATTCA
2126448 TTTTTATTGCA
1 TTTTTATT-CA
*
2126459 TTTTTATTTA
1 TTTTTATTCA
2126469 TTTTTA
1 TTTTTA
2126475 AAAAAATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 22 0.52
11 20 0.48
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (10 bp):
TTTTTATTCA
Found at i:2126471 original size:21 final size:20
Alignment explanation
Indices: 2126417--2126474 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
2126407 CGAGATAATG
* *
2126417 TTTTTATTGAATTTTATTCA
1 TTTTTATTCATTTTTATTCA
2126437 TATTTTATTCATTTTTATTGCA
1 T-TTTTATTCATTTTTATT-CA
*
2126459 TTTTTATTTATTTTTA
1 TTTTTATTCATTTTTA
2126475 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.88
22 3 0.09
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTTATTCATTTTTATTCA
Found at i:2129564 original size:17 final size:17
Alignment explanation
Indices: 2129542--2129574 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2129532 CATAGTTATT
2129542 TTAAATATTT-TAAATAA
1 TTAAAT-TTTATAAATAA
2129559 TTAAATTTTATAAATA
1 TTAAATTTTATAAATA
2129575 TATATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAATTTTATAAATAA
Found at i:2131409 original size:125 final size:122
Alignment explanation
Indices: 2131172--2131419 Score: 318
Period size: 125 Copynumber: 2.0 Consensus size: 122
2131162 TTGATGCGTT
* * * * **
2131172 ATTCTAGTTTTTCAACCAAAGATGACCTAAATAAAGGCCATGAGAAGACGGTTTTAGCAAGGGAC
1 ATTCTAGCTTTTCAACCAAAGATGACCTAAATAAAGACCATGAGAAGACAGTGTTAGCAAAAGAC
* *
2131237 TTGGCCTTGTTGAGGAATCGTCTCATAAAGATGAGATGAAACCTAAGAGCAGAATGG
66 TTGGCCTTGTTGAGGAATCGTCTCATAAAGATGACAGGAAACCTAAGAGCAGAATGG
** * * *
2131294 ATTCTAGCTTTTCAACCAGTGATGACTTAAATAAAGACCGTGAGAA-ACAGTGTTGGCAAAAGAC
1 ATTCTAGCTTTTCAACCAAAGATGACCTAAATAAAGACCATGAGAAGACAGTGTTAGCAAAAGAC
* *
2131358 TTGGCGTTTCTTGTTGAGGAGTCGTCTCATGAAGATGACAGGAAACCTAAGAGCAGAATGG
66 TTGGC----CTTGTTGAGGAATCGTCTCATAAAGATGACAGGAAACCTAAGAGCAGAATGG
2131419 A
1 A
2131420 GCTTAAGAGG
Statistics
Matches: 107, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
121 18 0.17
122 40 0.37
125 49 0.46
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (122 bp):
ATTCTAGCTTTTCAACCAAAGATGACCTAAATAAAGACCATGAGAAGACAGTGTTAGCAAAAGAC
TTGGCCTTGTTGAGGAATCGTCTCATAAAGATGACAGGAAACCTAAGAGCAGAATGG
Found at i:2133878 original size:21 final size:19
Alignment explanation
Indices: 2133860--2133898 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
2133850 ATTGAAATTG
2133860 TTTTTAAACATAGAAAAATAT
1 TTTTTAAA-ATA-AAAAATAT
2133881 TTTTTAAAATAAAAAATA
1 TTTTTAAAATAAAAAATA
2133899 AATTAGCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTTTAAAATAAAAAATAT
Found at i:2134071 original size:2 final size:2
Alignment explanation
Indices: 2134062--2134094 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2134052 TCATATATGG
2134062 AT AT -T 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
2134095 TTAAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2138344 original size:21 final size:21
Alignment explanation
Indices: 2138318--2138387 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
2138308 AGTCCAAATT
2138318 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
** * *
2138339 CGTTGCGATTTTCCAAATT--
1 CGTTGCGATAGTCGAAGTTCG
*
2138358 TGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCGAAGTTCG
2138379 CGTTGCGAT
1 CGTTGCGAT
2138388 TTATTCCAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
19 14 0.38
21 23 0.62
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCGAAGTTCG
Found at i:2138354 original size:40 final size:42
Alignment explanation
Indices: 2138310--2138412 Score: 183
Period size: 40 Copynumber: 2.5 Consensus size: 42
2138300 GTTGCAATAG
2138310 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-T
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
2138350 TCCAAATTTGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
2138392 TCCAAATTCGTTGCGATAGTC
1 TCCAAATTCGTTGCGATAGTC
2138413 TAAAATCGCA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 36 0.61
41 2 0.03
42 21 0.36
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:2138403 original size:21 final size:19
Alignment explanation
Indices: 2138291--2138412 Score: 109
Period size: 19 Copynumber: 6.1 Consensus size: 19
2138281 CAAATCAGTT
*
2138291 TCCAAATTCGTTGCAATAG
1 TCCAAATTCGTTGCGATAG
2138310 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * **
2138329 TCGAAGTTCGCGTTGCGATTT
1 TCCAAATT--CGTTGCGATAG
*
2138350 TCCAAATTTGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * *
2138369 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
2138392 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
2138411 TC
1 TC
2138413 TAAAATCGCA
Statistics
Matches: 80, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
19 42 0.52
21 30 0.38
23 8 0.10
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:2139023 original size:6 final size:6
Alignment explanation
Indices: 2139012--2139038 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2139002 TCTCGTCTCG
2139012 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
2139039 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2139193 original size:42 final size:42
Alignment explanation
Indices: 2139131--2139597 Score: 484
Period size: 42 Copynumber: 11.3 Consensus size: 42
2139121 TGCGATTTTG
* *
2139131 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2139173 GACTATCGCAACGAACTTGGAATAAATCTCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2139215 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2139257 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
2139299 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
2139341 GACTATCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTTG
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * * *
2139381 GAATAAATCGCAACGCGAACTTGGACT--ATCACAA--CGAATTTG
1 GACT--ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
* * * * *
2139423 GAATAAATCGCAACGTGAACTTCGACT--ATCGCAA--CGAATTTG
1 GACT--ATCGCAAC--GAACTTGGAATAAATCGCAACGCGAACTTC
** *
2139465 GAAAATCGCAACGAA-TTTGAA-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
2139505 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
2139545 GACTATCGCAACGCGAACTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTC
2139587 GACTATCGCAA
1 GACTATCGCAA
2139598 TGCGAATATG
Statistics
Matches: 382, Mismatches: 28, Indels: 30
0.87 0.06 0.07
Matches are distributed among these distances:
37 4 0.01
38 10 0.03
40 69 0.18
41 3 0.01
42 286 0.75
44 10 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:2139513 original size:40 final size:40
Alignment explanation
Indices: 2139469--2139597 Score: 195
Period size: 40 Copynumber: 3.2 Consensus size: 40
2139459 AATTTGGAAA
*
2139469 ATCGCAACGAATTTGAAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
2139509 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
* ** *
2139549 ATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTCGACT
2139591 ATCGCAA
1 ATCGCAA
2139598 TGCGAATATG
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 46 0.56
42 36 0.44
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.19
Consensus pattern (40 bp):
ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:2139552 original size:21 final size:21
Alignment explanation
Indices: 2139128--2139603 Score: 398
Period size: 21 Copynumber: 23.0 Consensus size: 21
2139118 CATTGCGATT
*
2139128 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
2139147 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
2139170 TTTGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
* *
2139189 TTGGAATAAATCTCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
2139212 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
2139231 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
2139254 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
2139273 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
2139296 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
2139315 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
2139338 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
2139359 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
2139378 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
2139401 TTGGACTATCACAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
2139420 TTGGAATAAATCGCAACGTGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
2139443 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
** *
2139462 TTGGAAAATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* **
2139481 TTGAAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
2139502 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
2139521 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
2139542 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
2139563 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
2139584 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
2139604 TATGTAAATC
Statistics
Matches: 371, Mismatches: 54, Indels: 62
0.76 0.11 0.13
Matches are distributed among these distances:
19 113 0.30
21 190 0.51
23 68 0.18
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:2144806 original size:31 final size:29
Alignment explanation
Indices: 2144771--2144828 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
2144761 TAATTTGAAT
2144771 ATTAACTATAATACATATATATATATATATC
1 ATTAACTATAATACA-ATATATAT-TATATC
* *
2144802 ATTAATTATAATATAATATATATTATA
1 ATTAACTATAATACAATATATATTATA
2144829 ATTTGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 8 0.32
31 13 0.52
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTAACTATAATACAATATATATTATATC
Found at i:2144826 original size:17 final size:17
Alignment explanation
Indices: 2144785--2144830 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2144775 ACTATAATAC
*
2144785 ATATATA-TATATATATC
1 ATATATATTATA-ATATA
2144802 AT-TA-ATTATAATATA
1 ATATATATTATAATATA
2144817 ATATATATTATAAT
1 ATATATATTATAAT
2144831 TTGAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 7 0.28
16 8 0.32
17 10 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATTATAATATA
Found at i:2146103 original size:29 final size:29
Alignment explanation
Indices: 2146045--2146153 Score: 112
Period size: 29 Copynumber: 3.7 Consensus size: 29
2146035 TTAACTTATT
* *
2146045 AAATATATTTTATTCTT-TTAGTAATCTAA
1 AAATATATTTTATTCTTATT-TTAATTTAA
* *
2146074 AAATACATTTTATTCTTATTTTTATTTAA
1 AAATATATTTTATTCTTATTTTAATTTAA
* * *
2146103 AAATATATTTTAATCTTATCTTAAATTAAA
1 AAATATATTTTATTCTTAT-TTTAATTTAA
2146133 AAATATATAATTTATTCTTAT
1 AAATATAT--TTTATTCTTAT
2146154 CATAACTTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
29 39 0.59
30 17 0.26
32 10 0.15
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.52
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAATTTAA
Found at i:2146232 original size:31 final size:31
Alignment explanation
Indices: 2146195--2146268 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
2146185 TATTTTAATT
*
2146195 TAAGATAAAAATATAATATAT-TTTGTATAGC
1 TAAGATAAAAATAAAATATATATTT-TATAGC
* *
2146226 TAAGATAAAAATAAAATATATATTTTGTAGT
1 TAAGATAAAAATAAAATATATATTTTATAGC
*
2146257 TAAAATAAAAAT
1 TAAGATAAAAAT
2146269 GTATTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 35 0.92
32 3 0.08
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.36
Consensus pattern (31 bp):
TAAGATAAAAATAAAATATATATTTTATAGC
Found at i:2146260 original size:26 final size:25
Alignment explanation
Indices: 2146226--2146283 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
2146216 TTTGTATAGC
*
2146226 TAAGATAAAAATAAAATATATATTTT
1 TAAGTTAAAAATAAAA-ATATATTTT
*
2146252 GT-AGTT-AAAATAAAAATGTATTTT
1 -TAAGTTAAAAATAAAAATATATTTT
2146276 TAAGTTAA
1 TAAGTTAA
2146284 GATTAGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 1 0.04
24 12 0.44
25 10 0.37
26 3 0.11
27 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.40
Consensus pattern (25 bp):
TAAGTTAAAAATAAAAATATATTTT
Found at i:2146281 original size:24 final size:25
Alignment explanation
Indices: 2146233--2146283 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
2146223 AGCTAAGATA
2146233 AAAATAAAATATATATTTTGTAGTT
1 AAAATAAAATATATATTTTGTAGTT
*
2146258 AAAATAAAA-ATGTATTTT-TAAGTT
1 AAAATAAAATATATATTTTGT-AGTT
2146282 AA
1 AA
2146284 GATTAGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 14 0.58
25 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (25 bp):
AAAATAAAATATATATTTTGTAGTT
Found at i:2146352 original size:30 final size:30
Alignment explanation
Indices: 2146318--2146423 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 30
2146308 AGTTAAAATG
* * *
2146318 AGAATTAATTATATTTTATAATTTAAGGTA
1 AGAATTAAATATATTTAATAATTTAAGATA
*
2146348 AGAA-TAGAATATATTTAATAATTTAAGTTA
1 AGAATTA-AATATATTTAATAATTTAAGATA
* * * *
2146378 AGAA-AATAATTTATGTAATAAGTTAAGATA
1 AGAATTA-AATATATTTAATAATTTAAGATA
*
2146408 AGAATAAAATATATTT
1 AGAATTAAATATATTT
2146424 TTGTTAATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.03
30 59 0.94
31 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (30 bp):
AGAATTAAATATATTTAATAATTTAAGATA
Found at i:2146562 original size:18 final size:18
Alignment explanation
Indices: 2146530--2146578 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2146520 AAATATATTT
*
2146530 TTAATGTTAAGATGTAAAA
1 TTAAT-TTAATATGTAAAA
* *
2146549 TTAATTTAATATGTGAAT
1 TTAATTTAATATGTAAAA
*
2146567 TTAAGTTAATAT
1 TTAATTTAATAT
2146579 ATATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (18 bp):
TTAATTTAATATGTAAAA
Found at i:2147512 original size:16 final size:17
Alignment explanation
Indices: 2147476--2147514 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2147466 AGATGACGAG
*
2147476 TTTTAATAAAATCATAT
1 TTTTAATAAAATAATAT
2147493 TTTTAATAAAATAATAT
1 TTTTAATAAAATAATAT
2147510 TTTTA
1 TTTTA
2147515 TTCTAACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTAATAAAATAATAT
Found at i:2148541 original size:24 final size:26
Alignment explanation
Indices: 2148499--2148550 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
2148489 CTTTCGTGAA
2148499 CGTTCGATTATATGTTCATGTATGTT
1 CGTTCGATTATATGTTCATGTATGTT
*
2148525 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATGTATGTT
2148549 CG
1 CG
2148551 AACAGAGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.52
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATGTATGTT
Found at i:2148635 original size:20 final size:19
Alignment explanation
Indices: 2148587--2148635 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
2148577 GAAGATTATT
2148587 GAAGTTGTTTGGATTTCAA
1 GAAGTTGTTTGGATTTCAA
*
2148606 TAAGTTGTTTGGATTTCAA
1 GAAGTTGTTTGGATTTCAA
2148625 GAAGATTGTTT
1 GAAG-TTGTTT
2148636 TGTTGAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.45
Consensus pattern (19 bp):
GAAGTTGTTTGGATTTCAA
Found at i:2149051 original size:20 final size:20
Alignment explanation
Indices: 2149002--2149063 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
2148992 GTAAATTAAT
2149002 TATTTTATATAAAAT-TTATA
1 TATTTT-TATAAAATATTATA
* *
2149022 GT-TATGTATAAAATATTATA
1 -TATTTTTATAAAATATTATA
* *
2149042 TATTTTTATAAACTATAATA
1 TATTTTTATAAAATATTATA
2149062 TA
1 TA
2149064 ATAACATCGT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
19 9 0.27
20 23 0.70
21 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTTTATAAAATATTATA
Found at i:2150139 original size:12 final size:11
Alignment explanation
Indices: 2150116--2150146 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
2150106 TCATTTGTCA
2150116 TCTTCTTCCTC
1 TCTTCTTCCTC
2150127 TCTTCTATCCTC
1 TCTTCT-TCCTC
2150139 TCTTCTTC
1 TCTTCTTC
2150147 ATCCTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (11 bp):
TCTTCTTCCTC
Found at i:2151028 original size:23 final size:22
Alignment explanation
Indices: 2150985--2151028 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2150975 TTTTGTATCG
* *
2150985 GTGCTGAGGCACTTTAGTATTA
1 GTGCTAAGGCACTTCAGTATTA
*
2151007 GTGCTAAGGCAACTTCATTATT
1 GTGCTAAGGC-ACTTCAGTATT
2151029 TCATGGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (22 bp):
GTGCTAAGGCACTTCAGTATTA
Found at i:2152146 original size:29 final size:29
Alignment explanation
Indices: 2152105--2152166 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
2152095 TTTTGACCCA
* *
2152105 CCCC-AAAATTTTATAAGTTCAAGTTCGT
1 CCCCTAAAATTTTATAAGTTCAAATTCGC
2152133 CCCCTAAAATTTTATAAGTTCAAATTCGC
1 CCCCTAAAATTTTATAAGTTCAAATTCGC
2152162 CCCCT
1 CCCCT
2152167 CTAACATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (29 bp):
CCCCTAAAATTTTATAAGTTCAAATTCGC
Found at i:2152384 original size:26 final size:26
Alignment explanation
Indices: 2152337--2152387 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2152327 TAAAATTAGA
*
2152337 GTTTTCAAAATTTTAAGTTTTTTAAG
1 GTTTTCAAAATTTTAAGGTTTTTAAG
* **
2152363 GTTTTCAAATTTTTTGGGTTTTTAA
1 GTTTTCAAAATTTTAAGGTTTTTAA
2152388 TATAATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.25, C:0.04, G:0.14, T:0.57
Consensus pattern (26 bp):
GTTTTCAAAATTTTAAGGTTTTTAAG
Found at i:2157426 original size:13 final size:13
Alignment explanation
Indices: 2157408--2157437 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2157398 TTAATATATC
*
2157408 ATTAATTAGTTTA
1 ATTAATTAATTTA
2157421 ATTAATTAATTTA
1 ATTAATTAATTTA
2157434 ATTA
1 ATTA
2157438 GCTGACTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATTAATTAATTTA
Found at i:2157787 original size:25 final size:22
Alignment explanation
Indices: 2157735--2157787 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 22
2157725 GGTTAACACG
*
2157735 TTTTAATTTTTAATATATTATA
1 TTTTAATCTTTAATATATTATA
*
2157757 TATTAATCTTTAGATTATGATTATA
1 TTTTAATCTTTA-A-TAT-ATTATA
2157782 TTTTAA
1 TTTTAA
2157788 ATTGACTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 10 0.40
23 1 0.04
24 3 0.12
25 11 0.44
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (22 bp):
TTTTAATCTTTAATATATTATA
Found at i:2159693 original size:29 final size:28
Alignment explanation
Indices: 2159652--2159721 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
2159642 CCCTTTATAT
**
2159652 TTTTTTTGGTTTTCTTCAATTTATTT-TTA
1 TTTTTTTCTTTTTCTT--ATTTATTTATTA
*
2159681 TTTTTTTCTTTTTTCTTTTTTATTTATTA
1 TTTTTTTC-TTTTTCTTATTTATTTATTA
2159710 TTTATTTTCTTT
1 TTT-TTTTCTTT
2159722 GACTTGTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 7 0.20
29 16 0.46
30 12 0.34
ACGTcount: A:0.11, C:0.07, G:0.03, T:0.79
Consensus pattern (28 bp):
TTTTTTTCTTTTTCTTATTTATTTATTA
Found at i:2159749 original size:13 final size:13
Alignment explanation
Indices: 2159731--2159755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2159721 TGACTTGTTC
2159731 TTTCTTTTTTTAT
1 TTTCTTTTTTTAT
2159744 TTTCTTTTTTTA
1 TTTCTTTTTTTA
2159756 AAACTTATTT
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:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTCTTTTTTTAT
Found at i:2159802 original size:30 final size:30
Alignment explanation
Indices: 2159767--2159825 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2159757 AACTTATTTA
2159767 ATTTTTTTTA-TTTTTT-CTCTTGATTTATT
1 ATTTTTTTTATTTTTTTCCT-TTGATTTATT
2159796 ATTTTTTTTATTTTTTTCCTTTGATTTATT
1 ATTTTTTTTATTTTTTTCCTTTGATTTATT
2159826 TAATATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 10 0.36
30 16 0.57
31 2 0.07
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (30 bp):
ATTTTTTTTATTTTTTTCCTTTGATTTATT
Found at i:2159834 original size:29 final size:30
Alignment explanation
Indices: 2159760--2159837 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
2159750 TTTTTAAAAC
* *
2159760 TTATTTAATTTTTTTTATTTTTTCTCTTGAT
1 TTATTTAATTTTTATT-TTTTTCCTCTTGAT
**
2159791 TTATTATTTTTTTTATTTTTTTCCT-TTGAT
1 TTATT-TAATTTTTATTTTTTTCCTCTTGAT
*
2159821 TTATTTAATATTTATTT
1 TTATTTAATTTTTATTT
2159838 ATTATTATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 9 0.23
30 10 0.26
31 12 0.31
32 8 0.21
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (30 bp):
TTATTTAATTTTTATTTTTTTCCTCTTGAT
Found at i:2164468 original size:24 final size:24
Alignment explanation
Indices: 2164441--2164528 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
2164431 ATTTCCAACT
* *
2164441 TGAATTCTGTTATGATATATGACC
1 TGAATTCTGTTCTGATATATGATC
* *
2164465 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATATGATC
* *
2164489 TGGATTCTGTTCTGATATATGTTC
1 TGAATTCTGTTCTGATATATGATC
*
2164513 TGAATTCTGTTTTGAT
1 TGAATTCTGTTCTGAT
2164529 TTCTAATATC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATATGATC
Found at i:2164484 original size:12 final size:12
Alignment explanation
Indices: 2164464--2164532 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 12
2164454 GATATATGAC
*
2164464 CTGAATTCTGTT
1 CTGATTTCTGTT
*
2164476 CTGATTTCTGAT
1 CTGATTTCTGTT
2164488 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
2164500 CTGATATATGTT
1 CTGATTTCTGTT
*
2164512 CTGAATTCTGTT
1 CTGATTTCTGTT
*
2164524 TTGATTTCT
1 CTGATTTCT
2164533 AATATCTTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.52
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:2168443 original size:29 final size:29
Alignment explanation
Indices: 2168408--2168468 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
2168398 CTCTGTTAAC
2168408 TTTCTGAAAGTTAAAACACATTTTAAGTG
1 TTTCTGAAAGTTAAAACACATTTTAAGTG
2168437 TTTCTGAAAGTTAAAACACATTTTAAGTG
1 TTTCTGAAAGTTAAAACACATTTTAAGTG
2168466 TTT
1 TTT
2168469 TTAGCTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (29 bp):
TTTCTGAAAGTTAAAACACATTTTAAGTG
Found at i:2168678 original size:23 final size:21
Alignment explanation
Indices: 2168645--2168694 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
2168635 TCCTCTAAGT
2168645 TTTA-TTTTATTTTATCATTATTA
1 TTTATTTTTA-TTTAT--TTATTA
2168668 -TTATTTTTATTTATTTATTA
1 TTTATTTTTATTTATTTATTA
2168688 TTTATTT
1 TTTATTT
2168695 CTCCATATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 6 0.24
21 6 0.24
22 8 0.32
23 5 0.20
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTATTTTTATTTATTTATTA
Found at i:2170076 original size:43 final size:44
Alignment explanation
Indices: 2169994--2170090 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
2169984 TTTACTTTTT
* * * *
2169994 TAAGCTCGATCGAGTTTTACTTTTAAAGTTTAAAAAACTCGATC
1 TAAGCTTGATCAAGTTTCACTTTAAAAGTTTAAAAAACTCGATC
*
2170038 TAAGCTTGATCAAGTTTCACTTTAAAAGTTT-AAGAACTCGATC
1 TAAGCTTGATCAAGTTTCACTTTAAAAGTTTAAAAAACTCGATC
*
2170081 -GAGCTTGATC
1 TAAGCTTGATC
2170091 CAAAATAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 9 0.19
43 11 0.23
44 27 0.57
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (44 bp):
TAAGCTTGATCAAGTTTCACTTTAAAAGTTTAAAAAACTCGATC
Found at i:2184149 original size:6 final size:6
Alignment explanation
Indices: 2184123--2184160 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2184113 ATCAGGGAAG
* *
2184123 GGGA-A GGGACG GGGACG GGGACA GGGACA GGGACA GGG
1 GGGACA GGGACA GGGACA GGGACA GGGACA GGGACA GGG
2184161 GTGGGGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.26, C:0.13, G:0.61, T:0.00
Consensus pattern (6 bp):
GGGACA
Found at i:2184149 original size:12 final size:12
Alignment explanation
Indices: 2184115--2184161 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2184105 GCGATGGCAT
*
2184115 CAGGGAAGGGGA
1 CAGGGACGGGGA
2184127 -AGGGACGGGGA
1 CAGGGACGGGGA
* *
2184138 CGGGGACAGGGA
1 CAGGGACGGGGA
2184150 CAGGGACAGGGG
1 CAGGGAC-GGGG
2184162 TGGGGGATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 10 0.36
12 15 0.54
13 3 0.11
ACGTcount: A:0.28, C:0.13, G:0.60, T:0.00
Consensus pattern (12 bp):
CAGGGACGGGGA
Found at i:2184150 original size:18 final size:17
Alignment explanation
Indices: 2184115--2184161 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
2184105 GCGATGGCAT
*
2184115 CAGGGAAGGGGAAGGGA
1 CAGGGACGGGGAAGGGA
*
2184132 CGGGGACGGGGACAGGGA
1 CAGGGACGGGGA-AGGGA
2184150 CAGGGACAGGGG
1 CAGGGAC-GGGG
2184162 TGGGGGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.40
18 11 0.44
19 4 0.16
ACGTcount: A:0.28, C:0.13, G:0.60, T:0.00
Consensus pattern (17 bp):
CAGGGACGGGGAAGGGA
Found at i:2186994 original size:44 final size:44
Alignment explanation
Indices: 2186935--2187145 Score: 302
Period size: 44 Copynumber: 4.7 Consensus size: 44
2186925 GATAGACTTG
* *
2186935 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAACTATCGACT
1 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGACT
*
2186979 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAACT
1 TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGACT
*
2187023 TTTTATTTATTTTGTTT-TTAATATTTTTATTATTTAATTATGGA-T
1 TTTTATTTATTTTGTTTCTT-A-ATGTTT-TTATTTAATTATGGACT
*
2187068 TTTTATTTATTTTATTTCTTAATGTTTTTATTATTTAATTATGGAC-
1 TTTTATTTATTTTGTTTCTTAATG--TTT-TTATTTAATTATGGACT
2187114 TTTTATTTATTTTGTTTCTTAATGTTTTTATT
1 TTTTATTTATTTTGTTTCTTAATGTTTTTATT
2187146 ATTTAATTGT
Statistics
Matches: 152, Mismatches: 8, Indels: 15
0.87 0.05 0.09
Matches are distributed among these distances:
43 7 0.05
44 64 0.42
45 23 0.15
46 58 0.38
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (44 bp):
TTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGGACT
Found at i:2187058 original size:16 final size:14
Alignment explanation
Indices: 2187022--2187153 Score: 57
Period size: 16 Copynumber: 8.6 Consensus size: 14
2187012 AATTATGAAC
* *
2187022 TTTTTATTTATTTTG
1 TTTTTAATT-TTTTA
2187037 TTTTTAATATTTTTA
1 TTTTTAAT-TTTTTA
* **
2187052 TTATTTAATTATGGA
1 TT-TTTAATTTTTTA
*
2187067 TTTTTATTTATTTTA
1 TTTTTAATT-TTTTA
2187082 TTTCTTAATGTTTTTA
1 TTT-TTAAT-TTTTTA
* **
2187098 TTATTTAATTATGGA
1 TT-TTTAATTTTTTA
* * *
2187113 CTTTTATTTATTTTG
1 TTTTTAATT-TTTTA
2187128 TTTCTTAATGTTTTTA
1 TTT-TTAAT-TTTTTA
2187144 TTATTTAATT
1 TT-TTTAATT
2187154 GTTTGAATTG
Statistics
Matches: 85, Mismatches: 22, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
14 12 0.14
15 31 0.36
16 38 0.45
17 4 0.05
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTTTAATTTTTTA
Found at i:2187077 original size:22 final size:22
Alignment explanation
Indices: 2187045--2187125 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
2187035 TGTTTTTAAT
2187045 ATTTTTA-TTATTTAATTATGG
1 ATTTTTATTTATTTAATTATGG
* * **
2187066 ATTTTTATTTATTTTATTTCTTA
1 ATTTTTATTTA-TTTAATTATGG
2187089 ATGTTTT-TATTATTTAATTATGG
1 AT-TTTTAT-TTATTTAATTATGG
*
2187112 ACTTTTATTTATTT
1 ATTTTTATTTATTT
2187126 TGTTTCTTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
21 7 0.15
22 13 0.28
23 19 0.41
24 7 0.15
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (22 bp):
ATTTTTATTTATTTAATTATGG
Found at i:2187090 original size:46 final size:47
Alignment explanation
Indices: 2186935--2187153 Score: 303
Period size: 46 Copynumber: 4.9 Consensus size: 47
2186925 GATAGACTTG
* * *
2186935 TTTTATTTATTTTGTTTCTT-A-ATGTTT-TTATTTAACTATCGACT
1 TTTTATTTATTTTGTTTCTTAATATTTTTATTATTTAATTATGGACT
* *
2186979 TTTTATTTATTTTGTTTCTT-A-ATGTTT-TTATTTAATTATGAACT
1 TTTTATTTATTTTGTTTCTTAATATTTTTATTATTTAATTATGGACT
2187023 TTTTATTTATTTTGTTT-TTAATATTTTTATTATTTAATTATGGA-T
1 TTTTATTTATTTTGTTTCTTAATATTTTTATTATTTAATTATGGACT
* *
2187068 TTTTATTTATTTTATTTCTTAATGTTTTTATTATTTAATTATGGAC-
1 TTTTATTTATTTTGTTTCTTAATATTTTTATTATTTAATTATGGACT
*
2187114 TTTTATTTATTTTGTTTCTTAATGTTTTTATTATTTAATT
1 TTTTATTTATTTTGTTTCTTAATATTTTTATTATTTAATT
2187154 GTTTGAATTG
Statistics
Matches: 162, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
43 2 0.01
44 59 0.36
45 22 0.14
46 79 0.49
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.67
Consensus pattern (47 bp):
TTTTATTTATTTTGTTTCTTAATATTTTTATTATTTAATTATGGACT
Found at i:2187101 original size:24 final size:25
Alignment explanation
Indices: 2187067--2187149 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 25
2187057 TAATTATGGA
2187067 TTTTTATTTATTTTATTTCTTAATG
1 TTTTTATTTATTTTATTTCTTAATG
* * **
2187092 TTTTTA-TTA-TTTAATTATGGA--
1 TTTTTATTTATTTTATTTCTTAATG
* *
2187113 CTTTTATTTATTTTGTTTCTTAATG
1 TTTTTATTTATTTTATTTCTTAATG
2187138 TTTTTA-TTATTT
1 TTTTTATTTATTT
2187150 AATTGTTTGA
Statistics
Matches: 43, Mismatches: 11, Indels: 9
0.68 0.17 0.14
Matches are distributed among these distances:
21 5 0.12
22 3 0.07
23 15 0.35
24 9 0.21
25 11 0.26
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (25 bp):
TTTTTATTTATTTTATTTCTTAATG
Found at i:2195525 original size:39 final size:39
Alignment explanation
Indices: 2195476--2195561 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
2195466 GTGCTTATAC
*
2195476 TTTCATTTGTTTCAAAATCATACCTAATGCTTACTTTGT
1 TTTCGTTTGTTTCAAAATCATACCTAATGCTTACTTTGT
2195515 TTTCGTTTGTTTCAAAATCATACCTAATGCTTACTTTGT
1 TTTCGTTTGTTTCAAAATCATACCTAATGCTTACTTTGT
2195554 TTTCGTTT
1 TTTCGTTT
2195562 TGGTGTCGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.51
Consensus pattern (39 bp):
TTTCGTTTGTTTCAAAATCATACCTAATGCTTACTTTGT
Found at i:2204075 original size:2 final size:2
Alignment explanation
Indices: 2204068--2204105 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2204058 ACGTAGTTTA
2204068 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
2204106 TATGCAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2204763 original size:60 final size:59
Alignment explanation
Indices: 2204649--2204766 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
2204639 GGGGTTTAGG
* * *
2204649 GATGAAATTAAAATATTTAAAAGTTTAAGAACTAATTTAAAATGAGACTCATAATTTAA
1 GATGAAATAAAAATATTTAAAAGTTTAAAAACTAATTTAAAATAAGACTCATAATTTAA
* * *
2204708 GATGAAATCAAAAATATTTAGAAGTTTAAAAATTAATTTAAAATAATGA-TTATAATTTA
1 GATGAAAT-AAAAATATTTAAAAGTTTAAAAACTAATTTAAAATAA-GACTCATAATTTA
2204767 GAAACATATG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 8 0.16
60 41 0.80
61 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (59 bp):
GATGAAATAAAAATATTTAAAAGTTTAAAAACTAATTTAAAATAAGACTCATAATTTAA
Found at i:2210868 original size:93 final size:93
Alignment explanation
Indices: 2210709--2210881 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 93
2210699 AAAATCAATT
* ** *
2210709 AAATAATCCTTCATTCCCTCATTAGCACATGCATTCTTACAACAATTCCTGTTATCATCTTCTGC
1 AAATAATCCTTCATTCCCTCAATAGCACATGCAAACATACAACAATTCCTGTTATCATCTTCTGC
*
2210774 CTCTCTTTCCGCATGATCCAGCATTATA
66 CTCTCTCTCCGCATGATCCAGCATTATA
* * ** * *
2210802 AAATAATCCTTCCTTCCCTCAATAGCACGTGCAAACATACAACTTTTCCTGTTGTCATTTTCTGC
1 AAATAATCCTTCATTCCCTCAATAGCACATGCAAACATACAACAATTCCTGTTATCATCTTCTGC
2210867 CTCTCTCTCCGCATG
66 CTCTCTCTCCGCATG
2210882 CTCTAGCACA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.24, C:0.31, G:0.09, T:0.36
Consensus pattern (93 bp):
AAATAATCCTTCATTCCCTCAATAGCACATGCAAACATACAACAATTCCTGTTATCATCTTCTGC
CTCTCTCTCCGCATGATCCAGCATTATA
Found at i:2241344 original size:160 final size:158
Alignment explanation
Indices: 2241119--2241431 Score: 430
Period size: 160 Copynumber: 2.0 Consensus size: 158
2241109 AAAAGAGTGA
* * * *
2241119 CTTAAAATAAATCAAAAAATGAAGGAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAA
1 CTTAAAATAAATCAAAAAATGAAGAAATAAGGAGACTATGAAAAATTGAAAGACTAAACTGAAAA
* * * *
2241184 ATAAAAAATATATTATCAAAAAGAGGAATTGAAAGTACACGTGTATTCTACTATGGTTTAGGATG
66 ATAAAAAATATATTATAAAAAAGAGGAATTGAAAATACAC--GTATTCTACTATGATTGAGGA-G
2241249 -ATGTGGCTCAAATTTAGTAAAAAAAAGGGG
128 CATGTGGCTCAAATTTAGTAAAAAAAAGGGG
* * * * * *
2241279 CTTAAAATAAATGACAAATTGAAGAAATAAGGAGACTATGAAAGATTTAAATACTAAACTGAAAA
1 CTTAAAATAAATCAAAAAATGAAGAAATAAGGAGACTATGAAAAATTGAAAGACTAAACTGAAAA
* *
2241344 ATAAAAAATTTGTTATAAAAAAGAGGAATTGAAAATACACGTATTCTACTATGATTGAGGAGCAT
66 ATAAAAAATATATTATAAAAAAGAGGAATTGAAAATACACGTATTCTACTATGATTGAGGAGCAT
* *
2241409 GTGGTTCAAATTTGGTAAAAAAA
131 GTGGCTCAAATTTAGTAAAAAAA
2241432 TAGACTTAAA
Statistics
Matches: 134, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
157 1 0.01
158 42 0.31
160 91 0.68
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (158 bp):
CTTAAAATAAATCAAAAAATGAAGAAATAAGGAGACTATGAAAAATTGAAAGACTAAACTGAAAA
ATAAAAAATATATTATAAAAAAGAGGAATTGAAAATACACGTATTCTACTATGATTGAGGAGCAT
GTGGCTCAAATTTAGTAAAAAAAAGGGG
Found at i:2243176 original size:7 final size:7
Alignment explanation
Indices: 2243164--2243205 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
2243154 AATCATCATT
2243164 TTTTTTA
1 TTTTTTA
2243171 TTTTTTA
1 TTTTTTA
2243178 TTTTTTTA
1 -TTTTTTA
*
2243186 CTTTTTA
1 TTTTTTA
2243193 TTTTTTA
1 TTTTTTA
2243200 TTTTTT
1 TTTTTT
2243206 TATATTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 25 0.78
8 7 0.22
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:2243190 original size:22 final size:22
Alignment explanation
Indices: 2243165--2243207 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2243155 ATCATCATTT
2243165 TTTTTATTTTTTATTTTTTTAC
1 TTTTTATTTTTTATTTTTTTAC
2243187 TTTTTATTTTTTATTTTTTTA
1 TTTTTATTTTTTATTTTTTTA
2243208 TATTATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTATTTTTTATTTTTTTAC
Found at i:2243208 original size:15 final size:15
Alignment explanation
Indices: 2243163--2243205 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2243153 AAATCATCAT
2243163 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
*
2243178 TTTTTTTACTTTTTA
1 TTTTTTTATTTTTTA
2243193 -TTTTTTATTTTTT
1 TTTTTTTATTTTTT
2243206 TATATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:2243507 original size:2 final size:2
Alignment explanation
Indices: 2243500--2243537 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2243490 ATTCTTCTAA
2243500 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
2243538 GTCGATTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2244519 original size:24 final size:25
Alignment explanation
Indices: 2244472--2244519 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2244462 ATTTTAATAT
* *
2244472 GTCATTTATCATTTATTTTATTTTG
1 GTCATTGATCATTTATGTTATTTTG
*
2244497 GTCATTGAT-ATTTATGTTGTTTT
1 GTCATTGATCATTTATGTTATTTT
2244520 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (25 bp):
GTCATTGATCATTTATGTTATTTTG
Found at i:2246602 original size:17 final size:17
Alignment explanation
Indices: 2246575--2246613 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2246565 AATTTACAAT
2246575 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
2246591 TAATTATAAATAATATC
1 TAATTATAAATAATATC
2246608 TAATTA
1 TAATTA
2246614 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:2249518 original size:85 final size:85
Alignment explanation
Indices: 2249408--2249581 Score: 348
Period size: 85 Copynumber: 2.0 Consensus size: 85
2249398 CTAAAATAAA
2249408 ATCATGCGTTTGTCCTTGAACAAATGGATTATGATGACTATAACGATTCATTATTTTTAGTTTTG
1 ATCATGCGTTTGTCCTTGAACAAATGGATTATGATGACTATAACGATTCATTATTTTTAGTTTTG
2249473 ATCGATAGTCATAATCGATT
66 ATCGATAGTCATAATCGATT
2249493 ATCATGCGTTTGTCCTTGAACAAATGGATTATGATGACTATAACGATTCATTATTTTTAGTTTTG
1 ATCATGCGTTTGTCCTTGAACAAATGGATTATGATGACTATAACGATTCATTATTTTTAGTTTTG
2249558 ATCGATAGTCATAATCGATT
66 ATCGATAGTCATAATCGATT
2249578 ATCA
1 ATCA
2249582 GACAATTGTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (85 bp):
ATCATGCGTTTGTCCTTGAACAAATGGATTATGATGACTATAACGATTCATTATTTTTAGTTTTG
ATCGATAGTCATAATCGATT
Found at i:2250822 original size:23 final size:23
Alignment explanation
Indices: 2250789--2250840 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
2250779 AGGGAGAAAA
*
2250789 AATTCGGTTAATGAAATTTGGGT
1 AATTCGATTAATGAAATTTGGGT
2250812 AATTCGATTAATGAAATTTGGGT
1 AATTCGATTAATGAAATTTGGGT
2250835 AATTCG
1 AATTCG
2250841 GTTCAGTCGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (23 bp):
AATTCGATTAATGAAATTTGGGT
Found at i:2256363 original size:21 final size:21
Alignment explanation
Indices: 2256311--2256354 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2256301 CGAGCGACGT
2256311 AAAAGACTATCCACAAATACA
1 AAAAGACTATCCACAAATACA
2256332 AAAAGACTATCCACAAATACA
1 AAAAGACTATCCACAAATACA
2256353 AA
1 AA
2256355 TCGGGTATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.23, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAAGACTATCCACAAATACA
Found at i:2259667 original size:18 final size:18
Alignment explanation
Indices: 2259644--2259688 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
2259634 TTCTAGATTT
2259644 GCTATTTAAGAGTATGAA
1 GCTATTTAAGAGTATGAA
2259662 GCTATTTAAGAGTATGAA
1 GCTATTTAAGAGTATGAA
2259680 GCTATTTAA
1 GCTATTTAA
2259689 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (18 bp):
GCTATTTAAGAGTATGAA
Found at i:2260101 original size:30 final size:30
Alignment explanation
Indices: 2260065--2260144 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 30
2260055 GTAAATTACC
* *
2260065 AAAATAACAGCTTACTAATAATGAGTTAAT
1 AAAATAAAAACTTACTAATAATGAGTTAAT
* * * * *
2260095 AAAATAAAACCTTAATAATGATGGGTTACT
1 AAAATAAAAACTTACTAATAATGAGTTAAT
2260125 AAAATAAAAACTTACTAATA
1 AAAATAAAAACTTACTAATA
2260145 TTGCTGCTGT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.53, C:0.10, G:0.09, T:0.29
Consensus pattern (30 bp):
AAAATAAAAACTTACTAATAATGAGTTAAT
Found at i:2260191 original size:17 final size:16
Alignment explanation
Indices: 2260171--2260203 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2260161 TGATATTATT
2260171 AATTAATTGAGTAAAAA
1 AATTAATTGAG-AAAAA
2260188 AATTAATTGAGAAAAA
1 AATTAATTGAGAAAAA
2260204 TAAGATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (16 bp):
AATTAATTGAGAAAAA
Found at i:2262019 original size:23 final size:24
Alignment explanation
Indices: 2261977--2262028 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2261967 AATACAAACT
* * *
2261977 AAGAACCAACCAAACAAAACTGAG
1 AAGACCCAACAAAACAAAACTGAA
2262001 AAGACCCAACAAAAC-AAACTGAA
1 AAGACCCAACAAAACAAAACTGAA
2262024 AAGAC
1 AAGAC
2262029 AAAGCAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.60, C:0.25, G:0.12, T:0.04
Consensus pattern (24 bp):
AAGACCCAACAAAACAAAACTGAA
Found at i:2265002 original size:24 final size:24
Alignment explanation
Indices: 2264949--2265003 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
2264939 TGTGTTAACA
2264949 GTAAATTTATAAAATATTATAAGG
1 GTAAATTTATAAAATATTATAAGG
2264973 GATAAATTTATAAAAGT-TTA-AAGG
1 G-TAAATTTATAAAA-TATTATAAGG
2264997 TGTAAAT
1 -GTAAAT
2265004 AGATTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 10 0.36
25 17 0.61
26 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (24 bp):
GTAAATTTATAAAATATTATAAGG
Found at i:2265614 original size:14 final size:14
Alignment explanation
Indices: 2265595--2265626 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2265585 TTAATGTCAG
2265595 TTTAGGGCTTAGGA
1 TTTAGGGCTTAGGA
*
2265609 TTTAGGGTTTAGGA
1 TTTAGGGCTTAGGA
2265623 TTTA
1 TTTA
2265627 TAATACTTAT
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:0.22, C:0.03, G:0.31, T:0.44
Consensus pattern (14 bp):
TTTAGGGCTTAGGA
Found at i:2271183 original size:20 final size:20
Alignment explanation
Indices: 2271121--2271184 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
2271111 CAATGGAAGG
*
2271121 GTTCATAATGAGAAGAGCTT
1 GTTCATAATGAGAAGAACTT
* * ***
2271141 G-TC-CAATGAGGGAGAAAAA
1 GTTCATAATGA-GAAGAACTT
2271160 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
2271180 GTTCA
1 GTTCA
2271185 ACCTTGGCTT
Statistics
Matches: 30, Mismatches: 11, Indels: 6
0.64 0.23 0.13
Matches are distributed among these distances:
18 5 0.17
19 7 0.23
20 13 0.43
21 5 0.17
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:2271219 original size:116 final size:113
Alignment explanation
Indices: 2270988--2271204 Score: 276
Period size: 116 Copynumber: 1.9 Consensus size: 113
2270978 GATAGACCAT
* * * * *
2270988 TCAACATTTCTAATGGAGGGGTTCATAATAAGAACTCGTTCGATGAGGGAGAAGAAGTTCCTAAT
1 TCAACATTTCTAATGGAAGGGTTCATAATAAGAACTCGTCCAATGAGGGAGAAAAAGTTCATAAT
* *
2271053 GATAAGAACTTGCTCAACCTTGGTTCACCCATCGCAGAAGAAGGTGGA
66 GAGAAGAACTTGCTCAACCTTGGTTCACCCATCACAGAAGAAGGTGGA
* *
2271101 TCAACATTT-TCAATGGAAGGGTTCATAATGAGAAGAGCTTGTCCAATGAGGGAGAAAAAGTTCA
1 TCAACATTTCT-AATGGAAGGGTTCATAAT---AAGAACTCGTCCAATGAGGGAGAAAAAGTTCA
* *
2271165 TAATGAGAAGAACTTGTTCAACCTTGGCTT-ATCCATCACA
62 TAATGAGAAGAACTTGCTCAACCTTGG-TTCACCCATCACA
2271205 AAAAGAGTTG
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
112 1 0.01
113 26 0.30
116 59 0.67
117 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (113 bp):
TCAACATTTCTAATGGAAGGGTTCATAATAAGAACTCGTCCAATGAGGGAGAAAAAGTTCATAAT
GAGAAGAACTTGCTCAACCTTGGTTCACCCATCACAGAAGAAGGTGGA
Found at i:2271243 original size:42 final size:42
Alignment explanation
Indices: 2271195--2271309 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 42
2271185 ACCTTGGCTT
* * * *
2271195 ATCCATCACAAAAAGAGTTGGATCAGCATCAACATTTCGTTC
1 ATCCATCACATAAGGAGTTGGATCAACATCAACATTTCGCTC
* * * *
2271237 GTCCATCACATAAGGAATTGGATCAACATTAACATTTTGCTC
1 ATCCATCACATAAGGAGTTGGATCAACATCAACATTTCGCTC
**
2271279 ATCCATCACATAAGGAGTTTCATCAACATCA
1 ATCCATCACATAAGGAGTTGGATCAACATCA
2271310 TTTCGCTTGA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (42 bp):
ATCCATCACATAAGGAGTTGGATCAACATCAACATTTCGCTC
Found at i:2272383 original size:42 final size:42
Alignment explanation
Indices: 2272293--2272418 Score: 155
Period size: 42 Copynumber: 3.0 Consensus size: 42
2272283 CATCCATAAC
* * * *
2272293 ATAAAGAGTAAGATCAGCATCACCATTTCACTTAATTCCATCGT
1 ATAAGGAGTTAGATCAGCATCACC-TTT-ACTTGATTCCATTGT
*
2272337 ATAAGGAGTTAGATCAGCATCACCTTTGCTTGATTCCATTGT
1 ATAAGGAGTTAGATCAGCATCACCTTTACTTGATTCCATTGT
**
2272379 ATAAGGAGTTCA-ATCAGTGTCACCTTTACTTGATTCCATT
1 ATAAGGAGTT-AGATCAGCATCACCTTTACTTGATTCCATT
2272419 ACAGAATGAG
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
42 47 0.64
43 4 0.05
44 22 0.30
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (42 bp):
ATAAGGAGTTAGATCAGCATCACCTTTACTTGATTCCATTGT
Found at i:2273224 original size:16 final size:16
Alignment explanation
Indices: 2273203--2273234 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2273193 AACTGAGCCC
2273203 GGATCCACACTCTCGG
1 GGATCCACACTCTCGG
2273219 GGATCCACACTCTCGG
1 GGATCCACACTCTCGG
2273235 CGTTGTAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.38, G:0.25, T:0.19
Consensus pattern (16 bp):
GGATCCACACTCTCGG
Found at i:2278145 original size:2 final size:2
Alignment explanation
Indices: 2278138--2278183 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2278128 TATAAGACTA
2278138 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
2278180 AT AT
1 AT AT
2278184 TTGGGTTAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2278407 original size:2 final size:2
Alignment explanation
Indices: 2278400--2278431 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2278390 TAAGTGGATC
2278400 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
2278432 TCTAGATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2279452 original size:13 final size:13
Alignment explanation
Indices: 2279434--2279458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2279424 TATTAAAAAT
2279434 AATAATTTATTTA
1 AATAATTTATTTA
2279447 AATAATTTATTT
1 AATAATTTATTT
2279459 GTTTAAAATT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATAATTTATTTA
Found at i:2280963 original size:32 final size:33
Alignment explanation
Indices: 2280921--2280985 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
2280911 CCACCTTTGT
* *
2280921 GCAAATCAATTGAAACACA-CGGGGGCGCCGGC
1 GCAAACCAATTGAAACACAGAGGGGGCGCCGGC
* *
2280953 GCAAACCAATTGGAACACAGAGGGGGTGCCGGC
1 GCAAACCAATTGAAACACAGAGGGGGCGCCGGC
2280986 TAACCTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.31, C:0.26, G:0.34, T:0.09
Consensus pattern (33 bp):
GCAAACCAATTGAAACACAGAGGGGGCGCCGGC
Found at i:2281701 original size:22 final size:22
Alignment explanation
Indices: 2281671--2281712 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2281661 ATTTTTAATA
*
2281671 ATTATAAAT-TAATTATAATTAT
1 ATTAAAAATATAATTA-AATTAT
2281693 ATTAAAAATATAATTAAATT
1 ATTAAAAATATAATTAAATT
2281713 TTAATTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAAAAATATAATTAAATTAT
Found at i:2281707 original size:27 final size:28
Alignment explanation
Indices: 2281648--2281719 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
2281638 ATAAATTACT
* *
2281648 TAAATTAATTATTATT-TTTAATAATTA
1 TAAATTAATTATAATTATTTAATAAATA
2281675 TAAATTAATTATAATTATATTAA-AAATA
1 TAAATTAATTATAATTAT-TTAATAAATA
*
2281703 T-AATTAAATTTTAATTA
1 TAAATT-AATTATAATTA
2281720 ATGATAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 19 0.49
28 16 0.41
29 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TAAATTAATTATAATTATTTAATAAATA
Found at i:2282544 original size:23 final size:23
Alignment explanation
Indices: 2282513--2282562 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
2282503 TCATATTCTT
2282513 TCTTACATAATTTCTTTCTTCCC
1 TCTTACATAATTTCTTTCTTCCC
*
2282536 TCTTCCATAATTTCTTTCTTCCC
1 TCTTACATAATTTCTTTCTTCCC
2282559 TCTT
1 TCTT
2282563 TCATTCCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.32, G:0.00, T:0.54
Consensus pattern (23 bp):
TCTTACATAATTTCTTTCTTCCC
Found at i:2289218 original size:42 final size:41
Alignment explanation
Indices: 2289154--2289239 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 41
2289144 TTCCCCAAAA
* *
2289154 TCCCGTGTTTATTTTACGTAATT-TATTTTCCGAAAAATGTTT
1 TCCCGTGTTTATTTCACGTAATTCT-TTTTCAG-AAAATGTTT
* *
2289196 TCCCTTGTTTGTTTCACGTAATTCGTTTTTCAGAAAATGTTT
1 TCCCGTGTTTATTTCACGTAATTC-TTTTTCAGAAAATGTTT
2289238 TC
1 TC
2289240 TAGTGTTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 31 0.82
43 6 0.16
44 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.50
Consensus pattern (41 bp):
TCCCGTGTTTATTTCACGTAATTCTTTTTCAGAAAATGTTT
Found at i:2289495 original size:25 final size:29
Alignment explanation
Indices: 2289449--2289503 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 29
2289439 TTAATCAAAA
2289449 TATTAATTATTAAAATATTTAAATATATT
1 TATTAATTATTAAAATATTTAAATATATT
2289478 TATTAA-TATT-AAA-A-TTAAATATATT
1 TATTAATTATTAAAATATTTAAATATATT
2289503 T
1 T
2289504 TAAGTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 12 0.46
26 1 0.04
27 3 0.12
28 4 0.15
29 6 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTAATTATTAAAATATTTAAATATATT
Found at i:2289857 original size:19 final size:20
Alignment explanation
Indices: 2289835--2289877 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2289825 AAATTGTTAC
2289835 TAAAATATT-ATATTAATAT
1 TAAAATATTAATATTAATAT
* * *
2289854 TAAACTATTAATTTTTATAT
1 TAAAATATTAATATTAATAT
2289874 TAAA
1 TAAA
2289878 TTGATACACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATATTAATATTAATAT
Found at i:2292184 original size:17 final size:18
Alignment explanation
Indices: 2292162--2292201 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2292152 TAATAGTGGG
2292162 TTATTATAA-GATATATT
1 TTATTATAATGATATATT
*
2292179 TTATTATAATTATATATT
1 TTATTATAATGATATATT
2292197 TTATT
1 TTATT
2292202 TGTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTATTATAATGATATATT
Found at i:2292966 original size:10 final size:10
Alignment explanation
Indices: 2292951--2293015 Score: 50
Period size: 10 Copynumber: 6.7 Consensus size: 10
2292941 CATTTAATAA
2292951 ATAAACGAAC
1 ATAAACGAAC
2292961 ATAAACGAAC
1 ATAAACGAAC
2292971 ----ACGAAC
1 ATAAACGAAC
2292977 ATAAACGAAC
1 ATAAACGAAC
**
2292987 ACGAACGTAA-
1 ATAAACG-AAC
2292997 ATGAACACGAAC
1 AT-AA-ACGAAC
2293009 ATAAACG
1 ATAAACG
2293016 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 4, Indels: 16
0.68 0.06 0.25
Matches are distributed among these distances:
6 6 0.14
10 25 0.58
11 7 0.16
12 5 0.12
ACGTcount: A:0.55, C:0.22, G:0.14, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2292976 original size:16 final size:16
Alignment explanation
Indices: 2292955--2293015 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
2292945 TAATAAATAA
2292955 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2292971 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
2292987 ACGAACGTAAATGAAC
1 ACGAACATAAACGAAC
2293003 ACGAACATAAACG
1 ACGAACATAAACG
2293016 TTGGAGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.54, C:0.23, G:0.15, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2294512 original size:53 final size:51
Alignment explanation
Indices: 2294455--2294555 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 51
2294445 ATATTTACAC
* * *
2294455 TTATATATGAATCATATCAATTTAAACTATGATAAATTGAAAAAAATATATTA
1 TTATATATGAATCAAATCAATTTAAACTATAATAAAAT--AAAAAATATATTA
*
2294508 TTATATATGAATTAAATCAATTTAAACTATAATAAAATAAAAAATATA
1 TTATATATGAATCAAATCAATTTAAACTATAATAAAATAAAAAATATA
2294556 AAAAAATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 10 0.23
53 34 0.77
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (51 bp):
TTATATATGAATCAAATCAATTTAAACTATAATAAAATAAAAAATATATTA
Found at i:2294571 original size:16 final size:17
Alignment explanation
Indices: 2294552--2294585 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2294542 AAATAAAAAA
*
2294552 TATAA-AAAAATATAAT
1 TATAATAAAAACATAAT
2294568 TATAATAAAAACATAAT
1 TATAATAAAAACATAAT
2294585 T
1 T
2294586 TATATAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
TATAATAAAAACATAAT
Found at i:2294592 original size:17 final size:18
Alignment explanation
Indices: 2294551--2294592 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2294541 AAAATAAAAA
2294551 ATATAAAAAAATATAATT
1 ATATAAAAAAATATAATT
* *
2294569 ATAATAAAAACATA-ATTT
1 AT-ATAAAAAAATATAATT
2294587 ATATAA
1 ATATAA
2294593 CTAACTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 10 0.48
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAAAAAAATATAATT
Found at i:2294664 original size:13 final size:13
Alignment explanation
Indices: 2294646--2294670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2294636 TTTTTAAATA
2294646 ATTAAAAATAATT
1 ATTAAAAATAATT
2294659 ATTAAAAATAAT
1 ATTAAAAATAAT
2294671 AAATTATTTT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTAAAAATAATT
Found at i:2296947 original size:32 final size:33
Alignment explanation
Indices: 2296906--2296983 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
2296896 TTTAAATAGT
* *
2296906 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
2296938 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
2296971 TATTATTTATTTA
1 TATTATTT-TTTA
2296984 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:2297144 original size:17 final size:17
Alignment explanation
Indices: 2297122--2297175 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
2297112 AATGTTAATA
2297122 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
2297139 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
2297156 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
2297173 TTT
1 TTT
2297176 TATAATGTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:2298782 original size:21 final size:21
Alignment explanation
Indices: 2298756--2298849 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
2298746 TATGCCATCT
* *
2298756 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
2298777 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
2298798 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
2298819 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
2298840 CCGCAGGGTT
1 CCGCAGGGTT
2298850 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:2299430 original size:33 final size:34
Alignment explanation
Indices: 2299371--2299467 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
2299361 AAATGTTTTT
*
2299371 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
2299405 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
2299438 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
2299468 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:2299474 original size:34 final size:33
Alignment explanation
Indices: 2299369--2299474 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
2299359 ATAAATGTTT
*
2299369 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
2299403 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
2299435 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
2299470 TTAAA
1 TTAAA
2299475 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Done.