Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 20 of 198
Found at i:5896781 original size:2 final size:2
Alignment explanation
Indices: 5896776--5896811 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5896766 AAAAAAATGA
*
5896776 AT AT AT AT AT AT AT AT AT AT CT 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
5896812 GTAGTAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5901145 original size:50 final size:50
Alignment explanation
Indices: 5901075--5901268 Score: 271
Period size: 50 Copynumber: 3.9 Consensus size: 50
5901065 ATTTGGGTAA
*
5901075 AGAGGTCCCATGTAACACCATGTCTGGGACATGGCGTTGACACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
* *
5901125 AGAGGTCCCATGAAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
** * * * *
5901175 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
** *
5901225 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGACAC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACAC
5901269 ATTTTTATCA
Statistics
Matches: 127, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 93 0.73
51 34 0.27
ACGTcount: A:0.26, C:0.25, G:0.30, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATG
Found at i:5905814 original size:12 final size:12
Alignment explanation
Indices: 5905797--5905823 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5905787 AAGTTAAGTG
5905797 AATGGGTCAATT
1 AATGGGTCAATT
5905809 AATGGGTCAATT
1 AATGGGTCAATT
5905821 AAT
1 AAT
5905824 TCTAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.33
Consensus pattern (12 bp):
AATGGGTCAATT
Found at i:5911106 original size:12 final size:12
Alignment explanation
Indices: 5911089--5911114 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5911079 TTTCAAACAC
5911089 TTAGAAAATGTT
1 TTAGAAAATGTT
5911101 TTAGAAAATGTT
1 TTAGAAAATGTT
5911113 TT
1 TT
5911115 CAATTTGTCC
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTAGAAAATGTT
Found at i:5919987 original size:24 final size:24
Alignment explanation
Indices: 5919960--5920011 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
5919950 AGTTAATGTC
* *
5919960 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
5919984 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATACT
5920008 AAAT
1 AAAT
5920012 CTTCTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:5923908 original size:15 final size:15
Alignment explanation
Indices: 5923888--5923918 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5923878 GTTATGTAAG
5923888 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
5923903 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
5923918 T
1 T
5923919 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:5928249 original size:15 final size:15
Alignment explanation
Indices: 5928229--5928259 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5928219 GTTATGTAAG
5928229 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
5928244 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
5928259 T
1 T
5928260 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:5930033 original size:13 final size:12
Alignment explanation
Indices: 5929994--5930038 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
5929984 CGAAACGATT
5929994 AAAAACTTGATG
1 AAAAACTTGATG
* *
5930006 AAAAATTTTATG
1 AAAAACTTGATG
5930018 AAAAGACTTGATG
1 AAAA-ACTTGATG
5930031 AAAAACTT
1 AAAAACTT
5930039 AAAAAGAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (12 bp):
AAAAACTTGATG
Found at i:5935297 original size:40 final size:40
Alignment explanation
Indices: 5935242--5935322 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
5935232 CTACACACAT
5935242 CCTCTTGTAGTCTATCCACGACCGTTACAGAAAGTACGAC
1 CCTCTTGTAGTCTATCCACGACCGTTACAGAAAGTACGAC
*
5935282 CCTCTTGTAGTCTATCCACGACCGTTACAGAAAGTATGAC
1 CCTCTTGTAGTCTATCCACGACCGTTACAGAAAGTACGAC
5935322 C
1 C
5935323 ACCTCTCATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (40 bp):
CCTCTTGTAGTCTATCCACGACCGTTACAGAAAGTACGAC
Found at i:5944226 original size:59 final size:59
Alignment explanation
Indices: 5944134--5944253 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
5944124 GTATATGTTA
5944134 TTATGTTTCTGGTTGAGGTCATTAAGTGGTTAATGAAAATTGTTTAGGAATTATTCTCT
1 TTATGTTTCTGGTTGAGGTCATTAAGTGGTTAATGAAAATTGTTTAGGAATTATTCTCT
5944193 TTATGTTTCTGGTTGAGGTCATTAAGTGGTTAATGAAAATTGTTTAGGAATTATTCTCT
1 TTATGTTTCTGGTTGAGGTCATTAAGTGGTTAATGAAAATTGTTTAGGAATTATTCTCT
5944252 TT
1 TT
5944254 CTCTCTCTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.47
Consensus pattern (59 bp):
TTATGTTTCTGGTTGAGGTCATTAAGTGGTTAATGAAAATTGTTTAGGAATTATTCTCT
Found at i:5947150 original size:2 final size:2
Alignment explanation
Indices: 5947143--5947176 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5947133 TCAGAGATAC
5947143 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
5947177 TAGATAAGGT
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):
AT
Found at i:5948440 original size:19 final size:18
Alignment explanation
Indices: 5948396--5948441 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5948386 GAGTTAAACG
* * *
5948396 AATCGAGTTATTCGAGTT
1 AATCGAATTATTCGAATC
5948414 AATCGAATTATTCGAATC
1 AATCGAATTATTCGAATC
5948432 AACTCGAATT
1 AA-TCGAATT
5948442 TTTTTTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (18 bp):
AATCGAATTATTCGAATC
Found at i:5948498 original size:9 final size:9
Alignment explanation
Indices: 5948481--5948517 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5948471 TGAGTTTTTG
5948481 AATTCGAAT
1 AATTCGAAT
*
5948490 AACTCGAAT
1 AATTCGAAT
5948499 AATTCGAAT
1 AATTCGAAT
5948508 AATTCGAAT
1 AATTCGAAT
5948517 A
1 A
5948518 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5948765 original size:30 final size:30
Alignment explanation
Indices: 5948731--5948788 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5948721 AAACCTTTTA
* *
5948731 TTTTCTCCC-AAAATTTTTACTCCTTTCCGC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCGC
*
5948761 TTTTCCCCTAAAACTTTTATTCCCTTCC
1 TTTTCCCCTAAAACTTTTACTCCCTTCC
5948789 CATCCCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.17, C:0.34, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCGC
Found at i:5950475 original size:21 final size:23
Alignment explanation
Indices: 5950434--5950491 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
5950424 AACTCTAAAT
5950434 TTTAA-AATTTTTTATGAATTTTG
1 TTTAATAA-TTTTTATGAATTTTG
*
5950457 TTT-ATAATTTTTATG-ATTTTT
1 TTTAATAATTTTTATGAATTTTG
*
5950478 TTTAATATTTTTTA
1 TTTAATAATTTTTA
5950492 AACTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 8 0.26
22 18 0.58
23 5 0.16
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TTTAATAATTTTTATGAATTTTG
Found at i:5951031 original size:15 final size:15
Alignment explanation
Indices: 5950998--5951032 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5950988 TTTAATGATA
* *
5950998 AAAAATAAAAATTAT
1 AAAAATAAAAATGAC
5951013 AAAAATAAAAATGAC
1 AAAAATAAAAATGAC
5951028 AAAAA
1 AAAAA
5951033 AAGATAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAAATAAAAATGAC
Found at i:5951032 original size:16 final size:15
Alignment explanation
Indices: 5950991--5951046 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
5950981 ACATTTCTTT
5950991 AATGATAAAAAATAAA
1 AATGA-AAAAAATAAA
* *
5951007 AATTATAAAAATAAA
1 AATGAAAAAAATAAA
5951022 AATGACAAAAAA-AGATA
1 AATGA-AAAAAATA-A-A
5951039 AATGAAAA
1 AATGAAAA
5951047 GAATTTAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 14 0.42
16 13 0.39
17 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (15 bp):
AATGAAAAAAATAAA
Found at i:5951408 original size:38 final size:40
Alignment explanation
Indices: 5951338--5951425 Score: 135
Period size: 38 Copynumber: 2.2 Consensus size: 40
5951328 TAAAAAATAT
* * *
5951338 TTATATTAAAAACATTACCATAAATCTAATAAATATTTTA
1 TTATATTAAAAACATCACAATAAATATAATAAATATTTTA
5951378 TTATATTAAAAACA-CA-AATAAATATAATAAATATTTTA
1 TTATATTAAAAACATCACAATAAATATAATAAATATTTTA
5951416 TTATATTAAA
1 TTATATTAAA
5951426 TATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 30 0.67
39 1 0.02
40 14 0.31
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAACATCACAATAAATATAATAAATATTTTA
Found at i:5951624 original size:10 final size:9
Alignment explanation
Indices: 5951609--5951679 Score: 52
Period size: 10 Copynumber: 7.1 Consensus size: 9
5951599 AAGAGTAATT
5951609 AAAAATTGTA
1 AAAAATT-TA
*
5951619 AAAAATTATT
1 AAAAATT-TA
*
5951629 TAAAATTTA
1 AAAAATTTA
5951638 AAAAATTTAAA
1 AAAAATTT--A
*
5951649 AAAAATTGTT
1 AAAAATT-TA
5951659 AAAAATTATA
1 AAAAATT-TA
5951669 AAAATATTTA
1 AAAA-ATTTA
5951679 A
1 A
5951680 TTTTTTTAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
9 8 0.16
10 29 0.59
11 11 0.22
12 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (9 bp):
AAAAATTTA
Found at i:5951635 original size:20 final size:20
Alignment explanation
Indices: 5951609--5951672 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
5951599 AAGAGTAATT
*
5951609 AAAAATTGTAAAAAATTATT
1 AAAAATTGTAAAAAATTATA
* *
5951629 TAAAATT-TAAAAAATTTAAA
1 AAAAATTGTAAAAAA-TTATA
*
5951649 AAAAATTGTTAAAAATTATA
1 AAAAATTGTAAAAAATTATA
5951669 AAAA
1 AAAA
5951673 TATTTAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 7 0.19
20 23 0.64
21 6 0.17
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAATTGTAAAAAATTATA
Found at i:5951652 original size:30 final size:32
Alignment explanation
Indices: 5951618--5951679 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
5951608 TAAAAATTGT
*
5951618 AAAAAATTATTTAAAATT-TAAAAA-ATTTAA
1 AAAAAATTATTAAAAATTATAAAAATATTTAA
*
5951648 AAAAAATTGTTAAAAATTATAAAAATATTTAA
1 AAAAAATTATTAAAAATTATAAAAATATTTAA
5951680 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.57
31 6 0.21
32 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (32 bp):
AAAAAATTATTAAAAATTATAAAAATATTTAA
Found at i:5951710 original size:9 final size:9
Alignment explanation
Indices: 5951607--5951737 Score: 66
Period size: 9 Copynumber: 13.8 Consensus size: 9
5951597 GTAAGAGTAA
5951607 TTAAAAATT
1 TTAAAAATT
*
5951616 GTAAAAAATT
1 -TTAAAAATT
*
5951626 ATTTAAAATT
1 -TTAAAAATT
*
5951636 TAAAAAATT
1 TTAAAAATT
*
5951645 TAAAAAAAATT
1 T--TAAAAATT
5951656 GTTAAAAATT
1 -TTAAAAATT
*
5951666 ATAAAAATAT
1 TTAAAAAT-T
***
5951676 TTAATTTTT
1 TTAAAAATT
*
5951685 TTAAACAATCA
1 TTAAA-AAT-T
5951696 TTAAAAATT
1 TTAAAAATT
*
5951705 TTAAAAATG
1 TTAAAAATT
* *
5951714 ATGAAAA-T
1 TTAAAAATT
*
5951722 TAAAAAATT
1 TTAAAAATT
5951731 TTAAAAA
1 TTAAAAA
5951738 ATTCAAAATT
Statistics
Matches: 89, Mismatches: 25, Indels: 15
0.69 0.19 0.12
Matches are distributed among these distances:
8 4 0.04
9 40 0.45
10 31 0.35
11 13 0.15
12 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (9 bp):
TTAAAAATT
Found at i:5952262 original size:40 final size:40
Alignment explanation
Indices: 5952183--5952265 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
5952173 AAAAATAATA
* ** *
5952183 TTTAATACAATAAAATATTTATTATATTTATTTTTGTGTT
1 TTTAATACAATAAAACATTTATTATATTTATGATAGTGTT
*
5952223 TTTAATATAATAAAACATTTATTATATTTATGATAGTGTT
1 TTTAATACAATAAAACATTTATTATATTTATGATAGTGTT
5952263 TTT
1 TTT
5952266 TAATGTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (40 bp):
TTTAATACAATAAAACATTTATTATATTTATGATAGTGTT
Found at i:5954048 original size:12 final size:12
Alignment explanation
Indices: 5954031--5954061 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5954021 ATTCCAACAC
5954031 CCTATTCTATTG
1 CCTATTCTATTG
5954043 CCTATTCTATTG
1 CCTATTCTATTG
*
5954055 TCTATTC
1 CCTATTC
5954062 CAACACCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.06, T:0.52
Consensus pattern (12 bp):
CCTATTCTATTG
Found at i:5954112 original size:16 final size:17
Alignment explanation
Indices: 5954093--5954134 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5954083 TTTTATTCGA
5954093 TTTTCATTTTTCCA-TT
1 TTTTCATTTTTCCAGTT
* *
5954109 TTTTCCTTTTTCTAGTT
1 TTTTCATTTTTCCAGTT
*
5954126 TTTTTATTT
1 TTTTCATTT
5954135 GTTTGTCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTTCATTTTTCCAGTT
Found at i:5954175 original size:27 final size:26
Alignment explanation
Indices: 5954124--5954183 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
5954114 CTTTTTCTAG
5954124 TTTTTTT-ATTTGTTTGTCCTTTTTA
1 TTTTTTTAATTTGTTTGTCCTTTTTA
* *
5954149 TTTTTTTAATTTGTTTTTCTTTATTTA
1 TTTTTTTAATTTGTTTGTCCTT-TTTA
*
5954176 CTTTTTTA
1 TTTTTTTA
5954184 GTTTTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 7 0.23
26 12 0.40
27 11 0.37
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.77
Consensus pattern (26 bp):
TTTTTTTAATTTGTTTGTCCTTTTTA
Found at i:5954228 original size:22 final size:21
Alignment explanation
Indices: 5954203--5954261 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
5954193 TTATTTTTCC
5954203 TTTATTATTTATTTTATAATGT
1 TTTATTATTTATTTTA-AATGT
* * *
5954225 TTTAATGTATATTTTAAATGT
1 TTTATTATTTATTTTAAATGT
*
5954246 TTTATAATATTATTTT
1 TTTATTAT-TTATTTT
5954262 TTAAAAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTATTATTTATTTTAAATGT
Found at i:5954272 original size:24 final size:24
Alignment explanation
Indices: 5954236--5954287 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5954226 TTAATGTATA
**
5954236 TTTTAAATGTTTTATAA-TATTATT
1 TTTTAAAAATTTTA-AATTATTATT
5954260 TTTTAAAAATTTTAAATTATTATT
1 TTTTAAAAATTTTAAATTATTATT
5954284 TTTT
1 TTTT
5954288 TAATATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTAAAAATTTTAAATTATTATT
Found at i:5954299 original size:24 final size:24
Alignment explanation
Indices: 5954253--5954299 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
5954243 TGTTTTATAA
*
5954253 TATTATTTTTTAAAAATTTTAAAT
1 TATTATTTTTTAAAAATTATAAAT
* *
5954277 TATTATTTTTTTAATATTATAAA
1 TATTATTTTTTAAAAATTATAAA
5954300 ACATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTATTTTTTAAAAATTATAAAT
Found at i:5954387 original size:22 final size:20
Alignment explanation
Indices: 5954350--5954424 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 20
5954340 ATTTATTATT
*
5954350 TATTTTATAATATTTTAAATC
1 TATTTT-TAAAATTTTAAATC
5954371 TATATTTTAAAACTTTTAAA-C
1 TAT-TTTTAAAA-TTTTAAATC
*
5954392 ATTATTTTTTAAAATTTTAAATT
1 --TA-TTTTTAAAATTTTAAATC
5954415 TATTTTTAAA
1 TATTTTTAAA
5954425 GATATTCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
20 8 0.17
21 10 0.22
22 17 0.37
23 10 0.22
24 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATTTTAAATC
Found at i:5954421 original size:21 final size:21
Alignment explanation
Indices: 5954347--5954421 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
5954337 CAAATTTATT
* *
5954347 ATTTATTTTATAATATTTTAA
1 ATTTATTTTTTAAAATTTTAA
* *
5954368 ATCTATATTTTAAAACTTTTAA
1 ATTTATTTTTTAAAA-TTTTAA
*
5954390 ACATTATTTTTTAAAATTTTAA
1 A-TTTATTTTTTAAAATTTTAA
5954412 ATTTATTTTT
1 ATTTATTTTT
5954422 AAAGATATTC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.43
22 14 0.32
23 11 0.25
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTATTTTTTAAAATTTTAA
Found at i:5960670 original size:19 final size:19
Alignment explanation
Indices: 5960648--5960692 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
5960638 AAGTCATTGT
5960648 TTTTTTAACAAATAAATAA
1 TTTTTTAACAAATAAATAA
*
5960667 TTTTTTAACAAATAAATCA
1 TTTTTTAACAAATAAATAA
5960686 TTTTTTA
1 TTTTTTA
5960693 TTTTTTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTTAACAAATAAATAA
Found at i:5960968 original size:15 final size:15
Alignment explanation
Indices: 5960944--5961006 Score: 62
Period size: 15 Copynumber: 4.5 Consensus size: 15
5960934 AGACAAATAA
*
5960944 AAATATAGAAAAAAC
1 AAATAAAGAAAAAAC
5960959 AAATAAAG-AAAAAC
1 AAATAAAGAAAAAAC
5960973 AAAT--A-AAAAAAC
1 AAATAAAGAAAAAAC
* * *
5960985 AAATAAAGGACAAAT
1 AAATAAAGAAAAAAC
5961000 AAATAAA
1 AAATAAA
5961007 AATATATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 11 0.28
14 11 0.28
15 18 0.45
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.11
Consensus pattern (15 bp):
AAATAAAGAAAAAAC
Found at i:5960998 original size:37 final size:34
Alignment explanation
Indices: 5960957--5961080 Score: 95
Period size: 35 Copynumber: 3.5 Consensus size: 34
5960947 TATAGAAAAA
5960957 ACAAATAAAGAAAAACAAATAAAAAAACAAATAAAGG
1 ACAAATAAA-AAAAA-AAATAAAAAAACAAA-AAAGG
* * * *
5960994 ACAAATAAATAAAAATATATAAAAACGAAAAAGG
1 ACAAATAAAAAAAAAAATAAAAAAACAAAAAAGG
* * * ** *
5961028 ACAAACAAATAAAAAATTAGAAAAAGGAAAAAATG
1 ACAAATAAAAAAAAAAATA-AAAAAACAAAAAAGG
* * *
5961063 AAAAACAAATAAAAAAAT
1 ACAAATAAAAAAAAAAAT
5961081 CAGGAAAAGG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
34 21 0.29
35 38 0.53
36 4 0.06
37 9 0.12
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.11
Consensus pattern (34 bp):
ACAAATAAAAAAAAAAATAAAAAAACAAAAAAGG
Found at i:5961003 original size:27 final size:26
Alignment explanation
Indices: 5960952--5961008 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
5960942 AAAAATATAG
5960952 AAAAAACAAATAAAGAAAAACAAATA
1 AAAAAACAAATAAAGAAAAACAAATA
* *
5960978 AAAAAACAAATAAAGGACAAATAAATA
1 AAAAAACAAATAAA-GAAAAACAAATA
5961005 AAAA
1 AAAA
5961009 TATATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.79, C:0.07, G:0.05, T:0.09
Consensus pattern (26 bp):
AAAAAACAAATAAAGAAAAACAAATA
Found at i:5961043 original size:35 final size:34
Alignment explanation
Indices: 5960979--5961078 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 34
5960969 AAACAAATAA
* * *
5960979 AAAAACAAATAAAGGACAAATAAAT-AAAAATATAT
1 AAAAACGAA-AAAGGACAAACAAATAAAAAAT-TAG
5961014 AAAAACGAAAAAGGACAAACAAATAAAAAATTAG
1 AAAAACGAAAAAGGACAAACAAATAAAAAATTAG
* * *
5961048 AAAAAGGAAAAAATGAAAAACAAATAAAAAA
1 AAAAACG-AAAAAGGACAAACAAATAAAAAA
5961079 ATCAGGAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 22 0.39
35 35 0.61
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.11
Consensus pattern (34 bp):
AAAAACGAAAAAGGACAAACAAATAAAAAATTAG
Found at i:5961089 original size:36 final size:35
Alignment explanation
Indices: 5960989--5961090 Score: 100
Period size: 34 Copynumber: 2.9 Consensus size: 35
5960979 AAAAACAAAT
* * * *
5960989 AAAGGACAAATAAATAAAAATAT-ATAAAAACG-AA
1 AAAGGAAAAACAAATAAAAA-ATCAGAAAAAGGAAA
* *
5961023 AAAGGACAAACAAATAAAAAATTAGAAAAAGGAAA
1 AAAGGAAAAACAAATAAAAAATCAGAAAAAGGAAA
* *
5961058 AAATGAAAAACAAATAAAAAAATCAGGAAAAGG
1 AAAGGAAAAACAAAT-AAAAAATCAGAAAAAGG
5961091 GTGTTGGAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
33 2 0.03
34 26 0.45
35 15 0.26
36 15 0.26
ACGTcount: A:0.71, C:0.06, G:0.13, T:0.11
Consensus pattern (35 bp):
AAAGGAAAAACAAATAAAAAATCAGAAAAAGGAAA
Found at i:5963340 original size:2 final size:2
Alignment explanation
Indices: 5963333--5963363 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5963323 CTAACATGTA
5963333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5963364 ATAACACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5964414 original size:23 final size:23
Alignment explanation
Indices: 5964385--5964461 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
5964375 ATAAGTGCCA
* *
5964385 CACTGATATGTTGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
5964408 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
5964431 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
5964454 CACTGATA
1 CACTGATA
5964462 ATTAACACTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:5973454 original size:146 final size:146
Alignment explanation
Indices: 5973190--5973462 Score: 501
Period size: 146 Copynumber: 1.9 Consensus size: 146
5973180 AAAGTTAGTA
* *
5973190 TTAAAGTTTCGTTAAGAAATTTTAAAGTTCCGATAATTAATTGAACAAAAAGGACTAAATTGTAA
1 TTAAAATTTCGTTAAGAAATTTTAAAGTTCCGATAATTAATTGAACAAAAAAGACTAAATTGTAA
*
5973255 TAAATGCAAAATTATGGGAAATGATTAAATAGCTTAAATGATAAAAGGAAGAGGGCTTAAAAACT
66 TAAATGCAAAATTATGGAAAATGATTAAATAGCTTAAATGATAAAAGGAAGAGGGCTTAAAAACT
5973320 GTATAAACCAGAAGGC
131 GTATAAACCAGAAGGC
* *
5973336 TTAAAATTTCGTTAAGAAATTTTAAAGTTCTGATAATTAATTGAACAAAAAAGACTAAATTGTTA
1 TTAAAATTTCGTTAAGAAATTTTAAAGTTCCGATAATTAATTGAACAAAAAAGACTAAATTGTAA
5973401 TAAATGCAAAATTATGGAAAATGATTAAATAGCTTAAATGATAAAAGGAAGAGGGCTTAAAA
66 TAAATGCAAAATTATGGAAAATGATTAAATAGCTTAAATGATAAAAGGAAGAGGGCTTAAAA
5973463 GGAAAATAGA
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
146 122 1.00
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (146 bp):
TTAAAATTTCGTTAAGAAATTTTAAAGTTCCGATAATTAATTGAACAAAAAAGACTAAATTGTAA
TAAATGCAAAATTATGGAAAATGATTAAATAGCTTAAATGATAAAAGGAAGAGGGCTTAAAAACT
GTATAAACCAGAAGGC
Found at i:5975547 original size:44 final size:44
Alignment explanation
Indices: 5975484--5975647 Score: 229
Period size: 44 Copynumber: 3.6 Consensus size: 44
5975474 TTTGAGTACT
5975484 TCTAATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTAATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
5975528 TCTAATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTAATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
5975572 TCTGATCAGTGACAAGTAACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCT-A--A-T--C-AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
5975623 TCTGATCAGGGACAAGTGACAAGTG
1 TCTAATCAGTGACAAGTGATAAGTG
5975648 ATAAATGTGA
Statistics
Matches: 108, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
44 62 0.57
45 2 0.02
47 2 0.02
48 2 0.02
50 1 0.01
51 39 0.36
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (44 bp):
TCTAATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:5975594 original size:51 final size:51
Alignment explanation
Indices: 5975539--5975651 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
5975529 CTAATCAGTG
*
5975539 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTA
*
5975590 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTA
5975641 ACAAGTGATAA
1 ACAAGTGATAA
5975652 ATGTGATCCG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (51 bp):
ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTA
Found at i:5977830 original size:23 final size:23
Alignment explanation
Indices: 5977804--5977971 Score: 309
Period size: 23 Copynumber: 7.3 Consensus size: 23
5977794 ATAAGTGCCA
*
5977804 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
5977827 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
5977850 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
*
5977873 CACTGATATGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
5977896 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
*
5977919 CACTAATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
5977942 CACTGATACGTAGCCGAAGCTAC
1 CACTGATACGTAGCCGAAGCTAC
5977965 CACTGAT
1 CACTGAT
5977972 CAATAACACT
Statistics
Matches: 140, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 140 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (23 bp):
CACTGATACGTAGCCGAAGCTAC
Found at i:5978223 original size:18 final size:17
Alignment explanation
Indices: 5978197--5978235 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5978187 ATTTTCCTTC
5978197 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
5978214 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
5978232 CACA
1 CACA
5978236 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:5979761 original size:14 final size:14
Alignment explanation
Indices: 5979750--5979778 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5979740 ATAAAATGTT
5979750 TTCCT-GAAAATGA
1 TTCCTAGAAAATGA
5979763 TTCCTAGAAAATGA
1 TTCCTAGAAAATGA
5979777 TT
1 TT
5979779 TACTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (14 bp):
TTCCTAGAAAATGA
Found at i:5981222 original size:32 final size:32
Alignment explanation
Indices: 5981179--5981261 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
5981169 TGTCAATCAT
* *
5981179 TTCAATATCCAACAAGCTTAAAGCATAATAGA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
5981211 TTCAATGTCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
* **
5981243 TTCAGTATTTAACAAGCTT
1 TTCAATATCCAACAAGCTT
5981262 CAATATCTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:5985155 original size:17 final size:17
Alignment explanation
Indices: 5985133--5985165 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5985123 TCATAATGTC
5985133 ATTAAT-TAGTCTAAATG
1 ATTAATATAGT-TAAATG
5985150 ATTAATATAGTTAAAT
1 ATTAATATAGTTAAAT
5985166 TTTTTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (17 bp):
ATTAATATAGTTAAATG
Found at i:5985724 original size:19 final size:18
Alignment explanation
Indices: 5985688--5985742 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
5985678 AATGGTTTTC
5985688 ATAATTTTTCA-AATAAAAGT
1 ATAATTTTT-ATAA-AAAA-T
5985708 ATAATTTTTATAAAAAAT
1 ATAATTTTTATAAAAAAT
5985726 A-AATTTCTTTATAAAAA
1 ATAA-TT-TTTATAAAAA
5985743 CAATTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.06
18 4 0.12
19 15 0.47
20 11 0.34
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
ATAATTTTTATAAAAAAT
Found at i:5987079 original size:18 final size:19
Alignment explanation
Indices: 5987056--5987102 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5987046 CTAAAAATTT
5987056 ATAAAATAATATTC-AAAA
1 ATAAAATAATATTCAAAAA
5987074 ATAAAAATAA-ATTCAAAAA
1 AT-AAAATAATATTCAAAAA
*
5987093 ATTAAATAAT
1 ATAAAATAAT
5987103 TAATATATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAAAATAATATTCAAAAA
Found at i:5991856 original size:13 final size:13
Alignment explanation
Indices: 5991838--5991863 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5991828 GTTTCTGTAA
5991838 TTACAACATTTTT
1 TTACAACATTTTT
5991851 TTACAACATTTTT
1 TTACAACATTTTT
5991864 CTAATGCAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTACAACATTTTT
Found at i:6000100 original size:15 final size:16
Alignment explanation
Indices: 6000080--6000113 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6000070 AAAAGCATAG
6000080 CATAAAAA-TATCAAA
1 CATAAAAAGTATCAAA
*
6000095 CATAAAAAGTATCACA
1 CATAAAAAGTATCAAA
6000111 CAT
1 CAT
6000114 TAGTTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.59, C:0.18, G:0.03, T:0.21
Consensus pattern (16 bp):
CATAAAAAGTATCAAA
Found at i:6002354 original size:12 final size:11
Alignment explanation
Indices: 6002337--6002370 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
6002327 AATGCAAATG
6002337 AATTTATATATA
1 AATTTATATA-A
6002349 AATTTATA-AA
1 AATTTATATAA
6002359 AATTTATATAA
1 AATTTATATAA
6002370 A
1 A
6002371 CAAAATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.43
11 4 0.19
12 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTATATAA
Found at i:6002640 original size:18 final size:18
Alignment explanation
Indices: 6002612--6002664 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
6002602 AGTTTGAAAA
*
6002612 AAATAATAATACATATGT
1 AAATAAAAATACATATGT
* * *
6002630 ACATAAAAATATACATGT
1 AAATAAAAATACATATGT
*
6002648 AAATAATAATTACATAT
1 AAATAA-AAATACATAT
6002665 AAAAATTAAA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.32
Consensus pattern (18 bp):
AAATAAAAATACATATGT
Found at i:6002702 original size:22 final size:22
Alignment explanation
Indices: 6002652--6002696 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
6002642 ACATGTAAAT
6002652 AATAATTACATATAAAAATTAA
1 AATAATTACATATAAAAATTAA
* *
6002674 AAAAATTACATTATTAAAATTAA
1 AATAATTACA-TATAAAAATTAA
6002697 TTAATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAATTACATATAAAAATTAA
Found at i:6005010 original size:12 final size:12
Alignment explanation
Indices: 6004995--6005036 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
6004985 TAAGGTATGT
6004995 TTTATTCCATTA
1 TTTATTCCATTA
* *
6005007 TTTATT-TAATA
1 TTTATTCCATTA
6005018 TTTTATTCCATTA
1 -TTTATTCCATTA
6005031 TTTATT
1 TTTATT
6005037 TAATGTCAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTATTCCATTA
Found at i:6005026 original size:24 final size:24
Alignment explanation
Indices: 6004994--6005040 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
6004984 GTAAGGTATG
6004994 TTTTATTCCATTATTTATTTAATA
1 TTTTATTCCATTATTTATTTAATA
6005018 TTTTATTCCATTATTTATTTAAT
1 TTTTATTCCATTATTTATTTAAT
6005041 GTCAAGAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATTCCATTATTTATTTAATA
Found at i:6011212 original size:2 final size:2
Alignment explanation
Indices: 6011205--6011240 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6011195 TTGTGGAGTG
6011205 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
6011241 GTTTTCCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6011364 original size:36 final size:36
Alignment explanation
Indices: 6011321--6011420 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 36
6011311 TAAGTTGGGC
6011321 TAGCTCTTCA-CAGCCATT-GTGTGTTTTCGAATGGAT
1 TAGCTCTT-ATCAG-CATTGGTGTGTTTTCGAATGGAT
* * *
6011357 TAGCTCTTATGAGCATTGGTGTGTTTTTGGATGGAT
1 TAGCTCTTATCAGCATTGGTGTGTTTTCGAATGGAT
* *
6011393 TAGCTCTTATGAGTATCTGGTGTGTTTT
1 TAGCTCTTATCAGCAT-TGGTGTGTTTT
6011421 GGTTGGAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
35 5 0.09
36 41 0.72
37 11 0.19
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.44
Consensus pattern (36 bp):
TAGCTCTTATCAGCATTGGTGTGTTTTCGAATGGAT
Found at i:6011421 original size:36 final size:35
Alignment explanation
Indices: 6011335--6011427 Score: 125
Period size: 36 Copynumber: 2.6 Consensus size: 35
6011325 TCTTCACAGC
*
6011335 CATT-GTGTGTTTTCGAATGGATTAGCTCTTATGAG
1 CATTGGTGTGTTTT-GGATGGATTAGCTCTTATGAG
6011370 CATTGGTGTGTTTTTGGATGGATTAGCTCTTATGAG
1 CATTGGTGTG-TTTTGGATGGATTAGCTCTTATGAG
* *
6011406 TATCTGGTGTGTTTTGGTTGGA
1 CAT-TGGTGTGTTTTGGATGGA
6011428 ATAACAATGT
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
35 4 0.08
36 37 0.71
37 11 0.21
ACGTcount: A:0.16, C:0.09, G:0.30, T:0.45
Consensus pattern (35 bp):
CATTGGTGTGTTTTGGATGGATTAGCTCTTATGAG
Found at i:6013229 original size:2 final size:2
Alignment explanation
Indices: 6013211--6013247 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
6013201 AACCTTTATG
* *
6013211 TA TA TT TA TA AA 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 TA T
6013248 GAACCTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6022306 original size:17 final size:17
Alignment explanation
Indices: 6022266--6022306 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
6022256 AGTCCCCAAA
6022266 TTATTTTCTTTTTCTTT
1 TTATTTTCTTTTTCTTT
*
6022283 TTCTTTTCTTTTT-TTAT
1 TTATTTTCTTTTTCTT-T
6022300 TTATTTT
1 TTATTTT
6022307 GATTTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (17 bp):
TTATTTTCTTTTTCTTT
Found at i:6022311 original size:6 final size:6
Alignment explanation
Indices: 6022302--6022329 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6022292 TTTTTTATTT
6022302 ATTTTG ATTTTG ATTTTG ATTTTG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTT
6022330 ATTTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (6 bp):
ATTTTG
Found at i:6023482 original size:22 final size:22
Alignment explanation
Indices: 6023457--6023505 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
6023447 GTGCTTGGGC
*
6023457 GCAGGGATAAGGGT-GGTTGGCT
1 GCAGGAAT-AGGGTAGGTTGGCT
*
6023479 GCAGGAATAGGGTAGTTTGGCT
1 GCAGGAATAGGGTAGGTTGGCT
6023501 GCAGG
1 GCAGG
6023506 CATTCTGGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.20, C:0.10, G:0.47, T:0.22
Consensus pattern (22 bp):
GCAGGAATAGGGTAGGTTGGCT
Found at i:6023685 original size:22 final size:22
Alignment explanation
Indices: 6023660--6023721 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
6023650 CCAAATAAGT
*
6023660 AATAAATAATAAAATAAAATAA
1 AATAAATAATAAAATAAAAGAA
*
6023682 AAT-AATAAATAAAGT-AAAGAA
1 AATAAAT-AATAAAATAAAAGAA
6023703 AATAAATAA-ATAAATAAAA
1 AATAAATAATA-AAATAAAA
6023722 ATTGGGTTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
20 1 0.03
21 16 0.48
22 16 0.48
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (22 bp):
AATAAATAATAAAATAAAAGAA
Found at i:6023686 original size:18 final size:17
Alignment explanation
Indices: 6023663--6023716 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
6023653 AATAAGTAAT
6023663 AAATAATAAAATAAAATA
1 AAATAAT-AAATAAAATA
*
6023681 AAATAATAAATAAAGTA
1 AAATAATAAATAAAATA
*
6023698 AAGAAAATAAAT-AAATA
1 AA-ATAATAAATAAAATA
6023715 AA
1 AA
6023717 TAAAAATTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (17 bp):
AAATAATAAATAAAATA
Found at i:6023694 original size:4 final size:4
Alignment explanation
Indices: 6023660--6023720 Score: 54
Period size: 4 Copynumber: 14.5 Consensus size: 4
6023650 CCAAATAAGT
*
6023660 AATA AAT- AATAA AATAA AATA AA-A TAATA AATA AAGTA AAGAA AATA
1 AATA AATA AAT-A AAT-A AATA AATA -AATA AATA AA-TA AA-TA AATA
6023707 AATA AATA AATA AA
1 AATA AATA AATA AA
6023721 AATTGGGTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
3 4 0.08
4 29 0.58
5 17 0.34
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:6023722 original size:18 final size:18
Alignment explanation
Indices: 6023652--6023723 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
6023642 ATTAATATCC
*
6023652 AAATAAGTAATAAAT-AAT
1 AAATAAATAA-AAATAAAT
6023670 AAAATAAAATAAAATAATAAAT
1 -AAAT-AAAT-AAA-AATAAAT
*
6023692 AAAGTAAA-GAAAATAAAT
1 AAA-TAAATAAAAATAAAT
6023710 AAATAAATAAAAAT
1 AAATAAATAAAAAT
6023724 TGGGTTGCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
17 4 0.09
18 15 0.34
19 6 0.14
20 4 0.09
21 11 0.25
22 4 0.09
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (18 bp):
AAATAAATAAAAATAAAT
Found at i:6027676 original size:15 final size:14
Alignment explanation
Indices: 6027655--6027690 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
6027645 ATAATCCTTA
*
6027655 ATAATTATCTTAAT
1 ATAATTATCCTAAT
6027669 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
6027684 ATAATTA
1 ATAATTA
6027691 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:6029085 original size:6 final size:6
Alignment explanation
Indices: 6029076--6029102 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6029066 AATATAAATT
6029076 TTTATA TTTATA TTTATA TTTATA TTT
1 TTTATA TTTATA TTTATA TTTATA TTT
6029103 TTTAAACAAT
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATA
Found at i:6031575 original size:11 final size:11
Alignment explanation
Indices: 6031555--6031592 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
6031545 GGCCCGACCC
6031555 ATATTAAATAT
1 ATATTAAATAT
*
6031566 ATATTTAATAT
1 ATATTAAATAT
*
6031577 ATATAAAATAT
1 ATATTAAATAT
6031588 ATATT
1 ATATT
6031593 TGATTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:6031585 original size:22 final size:22
Alignment explanation
Indices: 6031555--6031670 Score: 85
Period size: 22 Copynumber: 5.1 Consensus size: 22
6031545 GGCCCGACCC
*
6031555 ATATTAAATATATATTTAATAT
1 ATATAAAATATATATTTAATAT
* *
6031577 ATATAAAATATATATTTGATTAA
1 ATATAAAATATATATTT-AATAT
* *
6031600 AAATAAAAATATATATTTGAT-T
1 ATAT-AAAATATATATTTAATAT
* * *
6031622 AAATATATATATATATGATTAA-AA
1 ATATA-AAATATATAT--TTAATAT
6031646 ATA-AAATATATATATTTAATAT
1 ATATAAA-ATATATATTTAATAT
6031668 ATA
1 ATA
6031671 ATCCGGGCTG
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
21 5 0.07
22 34 0.47
23 16 0.22
24 18 0.25
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (22 bp):
ATATAAAATATATATTTAATAT
Found at i:6031633 original size:44 final size:46
Alignment explanation
Indices: 6031560--6031668 Score: 159
Period size: 44 Copynumber: 2.4 Consensus size: 46
6031550 GACCCATATT
* *
6031560 AAATATATATTTAATATATATAAAATATATATTTGATTAAAAATAA
1 AAATATATATTTAATATAAATAAAATATATATATGATTAAAAATAA
* *
6031606 AAATATATATTTGAT-TAAAT-ATATATATATATGATTAAAAATAA
1 AAATATATATTTAATATAAATAAAATATATATATGATTAAAAATAA
6031650 AATATATATATTTAATATA
1 AA-ATATATATTTAATATA
6031669 TAATCCGGGC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 24 0.43
45 16 0.29
46 16 0.29
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (46 bp):
AAATATATATTTAATATAAATAAAATATATATATGATTAAAAATAA
Found at i:6032600 original size:20 final size:20
Alignment explanation
Indices: 6032575--6032613 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
6032565 ATAGATTGCA
6032575 GTTAAAAAATTAATAAATCG
1 GTTAAAAAATTAATAAATCG
6032595 GTTAAAAAATTAATAAATC
1 GTTAAAAAATTAATAAATC
6032614 TATCAATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (20 bp):
GTTAAAAAATTAATAAATCG
Found at i:6033373 original size:20 final size:18
Alignment explanation
Indices: 6033340--6033403 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 18
6033330 CTTTACATCT
*
6033340 TAAAAAATTATAAAGAAAC
1 TAAAAAA-TATAAAAAAAC
*
6033359 TAAAGAATATATAAAAAAAT
1 TAAA-AA-ATATAAAAAAAC
6033379 TAAAAAATATAAAAAAAC
1 TAAAAAATATAAAAAAAC
6033397 TCAAAAA
1 T-AAAAA
6033404 CCCTAAACCC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 12 0.31
19 11 0.28
20 15 0.38
21 1 0.03
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (18 bp):
TAAAAAATATAAAAAAAC
Found at i:6033402 original size:18 final size:18
Alignment explanation
Indices: 6033340--6033403 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
6033330 CTTTACATCT
*
6033340 TAAAAAATTATAAAGAAAC
1 TAAAAAA-TATAAAAAAAC
*
6033359 TAAAGAATATATAAAAAAAT
1 TAAA-AA-ATATAAAAAAAC
6033379 TAAAAAATATAAAAAAAC
1 TAAAAAATATAAAAAAAC
*
6033397 TCAAAAA
1 TAAAAAA
6033404 CCCTAAACCC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
18 17 0.44
19 6 0.15
20 15 0.38
21 1 0.03
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (18 bp):
TAAAAAATATAAAAAAAC
Found at i:6034994 original size:27 final size:27
Alignment explanation
Indices: 6034976--6035032 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
6034966 ACTAAAATGT
6034976 TATA-AATTTTTTTATTTACCAAAATA
1 TATATAATTTTTTTATTTACCAAAATA
6035002 TATATAATTTTTTTATTTACCAAAATA
1 TATATAATTTTTTTATTTACCAAAATA
6035029 TATA
1 TATA
6035033 AAAAAACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (27 bp):
TATATAATTTTTTTATTTACCAAAATA
Found at i:6035053 original size:16 final size:16
Alignment explanation
Indices: 6035032--6035072 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
6035022 CAAAATATAT
*
6035032 AAAAAAACTAAAAAAC
1 AAAAAAAATAAAAAAC
6035048 AAAAAAAATAAAAAAC
1 AAAAAAAATAAAAAAC
6035064 AGAAAAAAA
1 A-AAAAAAA
6035073 ACCTGAACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.85, C:0.07, G:0.02, T:0.05
Consensus pattern (16 bp):
AAAAAAAATAAAAAAC
Found at i:6037544 original size:17 final size:17
Alignment explanation
Indices: 6037522--6037558 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
6037512 ATGGGATAAG
6037522 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
6037539 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
6037556 ATG
1 ATG
6037559 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:6038535 original size:14 final size:14
Alignment explanation
Indices: 6038516--6038544 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6038506 TTTTTGTATC
6038516 AATTTAATTATTCT
1 AATTTAATTATTCT
6038530 AATTTAATTATTCT
1 AATTTAATTATTCT
6038544 A
1 A
6038545 TTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:6041000 original size:18 final size:18
Alignment explanation
Indices: 6040974--6041011 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6040964 ATCCCAATGA
* *
6040974 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
6040992 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
6041010 TC
1 TC
6041012 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:6041018 original size:18 final size:18
Alignment explanation
Indices: 6040977--6041018 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
6040967 CCAATGATCG
* *
6040977 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
6040995 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
6041013 CCACCA
1 CCACCA
6041019 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:6041768 original size:3 final size:3
Alignment explanation
Indices: 6041760--6041830 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
6041750 AGTAACATCT
6041760 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6041808 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
6041831 CTATAAAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6042162 original size:27 final size:27
Alignment explanation
Indices: 6042143--6042222 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
6042133 TGGTTGGCAG
6042143 GACTGGTGCCGCCAACCTGGTTCCCTA
1 GACTGGTGCCGCCAACCTGGTTCCCTA
* * *
6042170 GACTGGTGCCGCCAACCTGCTTCCTTT
1 GACTGGTGCCGCCAACCTGGTTCCCTA
** *
6042197 GTTTGGTGCCGCCAACCTGCTTCCCT
1 GACTGGTGCCGCCAACCTGGTTCCCT
6042223 CCATTCAGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.11, C:0.38, G:0.24, T:0.28
Consensus pattern (27 bp):
GACTGGTGCCGCCAACCTGGTTCCCTA
Found at i:6042280 original size:15 final size:17
Alignment explanation
Indices: 6042255--6042290 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
6042245 AGTTTAGGTT
6042255 TTTTTTCTGTTTTTTA-
1 TTTTTTCTGTTTTTTAG
6042271 TTTTTT-TGTTTTTTAG
1 TTTTTTCTGTTTTTTAG
6042287 TTTT
1 TTTT
6042291 ATTTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.06, C:0.03, G:0.08, T:0.83
Consensus pattern (17 bp):
TTTTTTCTGTTTTTTAG
Found at i:6042324 original size:27 final size:28
Alignment explanation
Indices: 6042294--6042363 Score: 108
Period size: 27 Copynumber: 2.5 Consensus size: 28
6042284 TAGTTTTATT
6042294 TATATATTTTGGTAAAT-AAAAAAATTA
1 TATATATTTTGGTAAATAAAAAAAATTA
6042321 TATATATTTTGGTAAATAAAAAAAAATTA
1 TATATATTTTGGTAAAT-AAAAAAAATTA
*
6042350 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
6042364 TTTTTATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 17 0.43
28 11 0.28
29 12 0.30
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (28 bp):
TATATATTTTGGTAAATAAAAAAAATTA
Found at i:6046422 original size:59 final size:57
Alignment explanation
Indices: 6046358--6046490 Score: 187
Period size: 59 Copynumber: 2.3 Consensus size: 57
6046348 TTGTTATTAA
* *
6046358 ATTTTAATA-AGATTATTACTAAATACAATTTAGTAAAAATAATGATATAATTTAATAAT
1 ATTTTAATATA-ATTATTACTAAATACAATTTAAT-AAAATAAT-ATATAATTTAATAAC
* *
6046417 ATTTTAACATAATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTACTAAATACAATTTAATAAAATAATATATAATTTAATAAC
6046474 ATTCTTAATATAATTAT
1 ATT-TTAATATAATTAT
6046491 GTTTAAAATA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
57 17 0.25
58 20 0.30
59 29 0.43
60 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (57 bp):
ATTTTAATATAATTATTACTAAATACAATTTAATAAAATAATATATAATTTAATAAC
Found at i:6046497 original size:58 final size:59
Alignment explanation
Indices: 6046369--6046524 Score: 185
Period size: 59 Copynumber: 2.6 Consensus size: 59
6046359 TTTTAATAAG
* * *
6046369 ATTATTACTAAATACAATTTAGTAAAAATAATGATATAATTTAATAATATTTTAACATA
1 ATTATTATTAAATACAATTTAATAAAAATAATGATATAATTTAATAACATTTTAACATA
*
6046428 ATTATTATTAAATACAATTTAAT-AAAATAAT-ATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATACAATTTAATAAAAATAATGATATAATTTAATAACATT-TTAACATA
* * *
6046486 ATTATGT-TTAAAATATGAA-TTAATAAAAATTATAATATA
1 ATTAT-TATT-AAATA-CAATTTAATAAAAATAATGATATA
6046525 TAATATTTAA
Statistics
Matches: 85, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
57 17 0.20
58 22 0.26
59 32 0.38
60 9 0.11
61 5 0.06
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.42
Consensus pattern (59 bp):
ATTATTATTAAATACAATTTAATAAAAATAATGATATAATTTAATAACATTTTAACATA
Found at i:6047327 original size:54 final size:54
Alignment explanation
Indices: 6047260--6047363 Score: 199
Period size: 54 Copynumber: 1.9 Consensus size: 54
6047250 CGTTGAATAT
6047260 CAATGACACAGGAAAAATCAAAACCACAAAATAATGATCCTATTATCATGATAG
1 CAATGACACAGGAAAAATCAAAACCACAAAATAATGATCCTATTATCATGATAG
*
6047314 CAATGACAGAGGAAAAATCAAAACCACAAAATAATGATCCTATTATCATG
1 CAATGACACAGGAAAAATCAAAACCACAAAATAATGATCCTATTATCATG
6047364 CAAAGCAGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20
Consensus pattern (54 bp):
CAATGACACAGGAAAAATCAAAACCACAAAATAATGATCCTATTATCATGATAG
Found at i:6051231 original size:7 final size:7
Alignment explanation
Indices: 6051219--6051250 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
6051209 TAGTCGATTG
6051219 GTATTTA
1 GTATTTA
6051226 GTATTTA
1 GTATTTA
6051233 GTATTTA
1 GTATTTA
6051240 GTATTTA
1 GTATTTA
6051247 GTAT
1 GTAT
6051251 ATAACTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTTA
Found at i:6053920 original size:13 final size:13
Alignment explanation
Indices: 6053902--6054032 Score: 135
Period size: 13 Copynumber: 10.2 Consensus size: 13
6053892 ATTTTTAATG
6053902 TAATATACTGTTT
1 TAATATACTGTTT
*
6053915 TAATATACTGTTA
1 TAATATACTGTTT
6053928 TAA-A-A-T-TTT
1 TAATATACTGTTT
6053937 TAATATACTGTTT
1 TAATATACTGTTT
*
6053950 TAATATACTATTAT
1 TAATATACTGTT-T
* *
6053964 AAATATACTTTTT
1 TAATATACTGTTT
* *
6053977 TGATATATTGTTT
1 TAATATACTGTTT
6053990 TAATATACTGTTAT
1 TAATATACTGTT-T
* *
6054004 AAATATATTGTTT
1 TAATATACTGTTT
*
6054017 TAATATAATGTTT
1 TAATATACTGTTT
6054030 TAA
1 TAA
6054033 CTTTTAATAT
Statistics
Matches: 97, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
9 5 0.05
10 2 0.02
11 2 0.02
12 2 0.02
13 64 0.66
14 22 0.23
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.53
Consensus pattern (13 bp):
TAATATACTGTTT
Found at i:6053936 original size:40 final size:37
Alignment explanation
Indices: 6053902--6054032 Score: 158
Period size: 40 Copynumber: 3.4 Consensus size: 37
6053892 ATTTTTAATG
6053902 TAATATACTGTTTTAATATACTGTTATAAAA--TTTT
1 TAATATACTGTTTTAATATACTGTTATAAAATTTTTT
*
6053937 TAATATACTGTTTTAATATACTATTATAAATATACTTTTT
1 TAATATACTGTTTTAATATACTGTTATAAA-AT--TTTTT
* *
6053977 TGATATATTGTTTTAATATACTGTTATAAATATATTGTTT
1 TAATATACTGTTTTAATATACTGTTATAAA-AT-TT-TTT
*
6054017 TAATATAATGTTTTAA
1 TAATATACTGTTTTAA
6054033 CTTTTAATAT
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
35 29 0.35
36 1 0.01
39 2 0.02
40 51 0.61
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.53
Consensus pattern (37 bp):
TAATATACTGTTTTAATATACTGTTATAAAATTTTTT
Found at i:6053968 original size:27 final size:26
Alignment explanation
Indices: 6053902--6054032 Score: 135
Period size: 27 Copynumber: 5.1 Consensus size: 26
6053892 ATTTTTAATG
* *
6053902 TAATATACTGTTTTAATATACTGTTA
1 TAATATATTGTTTTAATATACTGTTT
6053928 TAA-A-A-T-TTTTAATATACTGTTT
1 TAATATATTGTTTTAATATACTGTTT
* * * *
6053950 TAATATACTATTATAAATATACTTTTT
1 TAATATATTGTT-TTAATATACTGTTT
*
6053977 TGATATATTGTTTTAATATACTGTTAT
1 TAATATATTGTTTTAATATACTGTT-T
* *
6054004 AAATATATTGTTTTAATATAATGTTT
1 TAATATATTGTTTTAATATACTGTTT
6054030 TAA
1 TAA
6054033 CTTTTAATAT
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
22 18 0.21
23 2 0.02
24 2 0.02
25 2 0.02
26 19 0.22
27 44 0.51
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.53
Consensus pattern (26 bp):
TAATATATTGTTTTAATATACTGTTT
Found at i:6054203 original size:72 final size:72
Alignment explanation
Indices: 6054124--6054272 Score: 289
Period size: 72 Copynumber: 2.1 Consensus size: 72
6054114 TCAAATATTA
*
6054124 AAAATATTTAAATCTAAAATAATTACTTACTGTTTTTAATAAAATACTAGAAAACTATGTCTTTA
1 AAAATATTTAAATCTAAAATAATTACTTACCGTTTTTAATAAAATACTAGAAAACTATGTCTTTA
6054189 ATTGCCC
66 ATTGCCC
6054196 AAAATATTTAAATCTAAAATAATTACTTACCGTTTTTAATAAAATACTAGAAAACTATGTCTTTA
1 AAAATATTTAAATCTAAAATAATTACTTACCGTTTTTAATAAAATACTAGAAAACTATGTCTTTA
6054261 ATTGCCC
66 ATTGCCC
6054268 AAAAT
1 AAAAT
6054273 GAAATTTAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (72 bp):
AAAATATTTAAATCTAAAATAATTACTTACCGTTTTTAATAAAATACTAGAAAACTATGTCTTTA
ATTGCCC
Found at i:6056561 original size:9 final size:9
Alignment explanation
Indices: 6056547--6056601 Score: 92
Period size: 9 Copynumber: 6.1 Consensus size: 9
6056537 GGTTGCAAAA
6056547 AGGACGATG
1 AGGACGATG
6056556 AGGACGATG
1 AGGACGATG
6056565 AGGACGATG
1 AGGACGATG
*
6056574 ATGACGATG
1 AGGACGATG
6056583 AGGACGATG
1 AGGACGATG
*
6056592 AGGATGATG
1 AGGACGATG
6056601 A
1 A
6056602 CGTTTCTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.35, C:0.09, G:0.42, T:0.15
Consensus pattern (9 bp):
AGGACGATG
Found at i:6058514 original size:12 final size:12
Alignment explanation
Indices: 6058497--6058521 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6058487 GGTGTTCATT
6058497 CGGTTAACCGAC
1 CGGTTAACCGAC
6058509 CGGTTAACCGAC
1 CGGTTAACCGAC
6058521 C
1 C
6058522 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:6058694 original size:9 final size:9
Alignment explanation
Indices: 6058683--6058776 Score: 118
Period size: 9 Copynumber: 10.4 Consensus size: 9
6058673 TTTGGTTAAA
*
6058683 AATTAACCA
1 AATTAACCG
6058692 AATTAACCG
1 AATTAACCG
*
6058701 AATTACCCG
1 AATTAACCG
6058710 AATT-ACTCG
1 AATTAAC-CG
6058719 AATTAACCG
1 AATTAACCG
*
6058728 AATTACCCG
1 AATTAACCG
*
6058737 AATTAACTG
1 AATTAACCG
*
6058746 AATTACCCG
1 AATTAACCG
6058755 AATTAACCG
1 AATTAACCG
*
6058764 AATTAACCA
1 AATTAACCG
6058773 AATT
1 AATT
6058777 GAATCACTAC
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
8 1 0.01
9 70 0.96
10 2 0.03
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:6058926 original size:18 final size:18
Alignment explanation
Indices: 6058883--6058926 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
6058873 TAATTTTATG
* *
6058883 ATTGGGTTGGGTTGAGTA
1 ATTGGGTTGGGTTAAATA
*
6058901 ATTAGGTTGGGTTAAATA
1 ATTGGGTTGGGTTAAATA
*
6058919 CTTGGGTT
1 ATTGGGTT
6058927 TAGATTGGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.36, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTAAATA
Found at i:6062231 original size:127 final size:127
Alignment explanation
Indices: 6061830--6062371 Score: 885
Period size: 127 Copynumber: 4.3 Consensus size: 127
6061820 AGCCAAACAT
* * *
6061830 GAGCTACTGTAGCAAAAGCGTGTACACG-GTGGAGCTTCTTTTAGTACTTTTGCTGACAAAGCAT
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTG-GGAGCTTCTTTCAGTACTTTTGCTGACAAAGCAT
* *
6061894 CTTGCTTAAAGC-TTTTTTGACACTATTTGCTCAGAAACGTCTTCTTGAAATTATTTTTTCAG
65 CCTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAG
* * *
6061956 GAGCTATTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGATAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
* *
6062021 CTGCTTAAAGCGTTTTTTG--ACTATTTGCTCAGAAACGTCTTCTTGAAATTATTTTTCCAG
66 CTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAG
6062081 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
*
6062146 CTGCTTAAAGTGTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAG
66 CTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAG
* *
6062208 AAGCTACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
* * *
6062273 TTGCTTAAAGCATTTTTTGACACTATTTGCTCAGAAACGTCTTTTCGAAATTATTTTTTCAG
66 CTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAG
* *
6062335 GAGCTACTGTAGCAAAAGTGCGTCCACATGGGAGCTT
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTT
6062372 TTTTAAATTA
Statistics
Matches: 388, Mismatches: 24, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
125 120 0.31
126 67 0.17
127 201 0.52
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (127 bp):
GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
CTGCTTAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAG
Found at i:6062280 original size:252 final size:252
Alignment explanation
Indices: 6061830--6062371 Score: 901
Period size: 252 Copynumber: 2.1 Consensus size: 252
6061820 AGCCAAACAT
* * *
6061830 GAGCTACTGTAGCAAAAGCGTGTACACG-GTGGAGCTTCTTTTAGTACTTTTGCTGACAAAGCAT
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTG-GGAGCTTCTTTCAGTACTTTTGCTGACAAAGCAT
* * *
6061894 CTTGCTTAAAGCTTTTTTGACACTATTTGCTCAGAAACGTCTTCTTGAAATTATTTTTTCAGGAG
65 CCTGCTTAAAGCTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAGAAG
* *
6061959 CTATTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGATAAAGCATCCTG
130 CTACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTG
*
6062024 CTTAAAGCGTTTTTTG-ACTATTTGCTCAGAAACGTCTTCTT-GAAATTATTTTTCCAG
195 CTTAAAGCATTTTTTGAACTATTTGCTCAGAAACGTCTT-TTCGAAATTATTTTTCCAG
6062081 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
*
6062146 CTGCTTAAAGTGTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAGAAG
66 CTGCTTAAAG-CTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAGAAG
*
6062211 CTACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCTTG
130 CTACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTG
*
6062276 CTTAAAGCATTTTTTGACACTATTTGCTCAGAAACGTCTTTTCGAAATTATTTTTTCAG
195 CTTAAAGCATTTTTTGA-ACTATTTGCTCAGAAACGTCTTTTCGAAATTATTTTTCCAG
* *
6062335 GAGCTACTGTAGCAAAAGTGCGTCCACATGGGAGCTT
1 GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTT
6062372 TTTTAAATTA
Statistics
Matches: 272, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
251 69 0.25
252 129 0.47
253 2 0.01
254 72 0.26
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (252 bp):
GAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATC
CTGCTTAAAGCTTTTTTGACACTATTTGCTCAGAAACGTCTTCTCGAAATTATTTTTTCAGAAGC
TACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGCATCCTGC
TTAAAGCATTTTTTGAACTATTTGCTCAGAAACGTCTTTTCGAAATTATTTTTCCAG
Found at i:6062588 original size:15 final size:14
Alignment explanation
Indices: 6062563--6062618 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 14
6062553 TTTTTTTCTT
*
6062563 TAAAACTCTAAACC
1 TAAAACCCTAAACC
6062577 TAAAAACCCT-AACC
1 T-AAAACCCTAAACC
* *
6062591 TTAAACCCTAAAAC
1 TAAAACCCTAAACC
*
6062605 -AAAACCCAAAACC
1 TAAAACCCTAAACC
6062618 T
1 T
6062619 TAACCAGCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 17 0.52
14 9 0.27
15 7 0.21
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (14 bp):
TAAAACCCTAAACC
Found at i:6062635 original size:23 final size:23
Alignment explanation
Indices: 6062605--6062650 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
6062595 ACCCTAAAAC
*
6062605 AAAACCCAAAACCTTAACCAGCA
1 AAAACCCAAAACCCTAACCAGCA
6062628 AAAACCCAAAACCCTAACCAGCA
1 AAAACCCAAAACCCTAACCAGCA
6062651 GGAGACACGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.52, C:0.37, G:0.04, T:0.07
Consensus pattern (23 bp):
AAAACCCAAAACCCTAACCAGCA
Found at i:6068546 original size:17 final size:18
Alignment explanation
Indices: 6068524--6068562 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
6068514 TTAATTAGCG
*
6068524 GAGAA-TGTGGGTTTGGT
1 GAGAATTGTGGGTTTGAT
6068541 GAGAATTTGTGGGTTTGAT
1 GAGAA-TTGTGGGTTTGAT
6068560 GAG
1 GAG
6068563 GGTAGAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
19 14 0.74
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.36
Consensus pattern (18 bp):
GAGAATTGTGGGTTTGAT
Found at i:6074583 original size:2 final size:2
Alignment explanation
Indices: 6074578--6074610 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6074568 TTAAATATTA
6074578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6074611 ATAAGTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6074816 original size:33 final size:33
Alignment explanation
Indices: 6074757--6074837 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
6074747 TAAATACATC
* *
6074757 ATTTTTTTAATT-ACATGACTATCAAGTGAGCAA
1 ATTTTTTTATTTCA-ATGACTACCAAGTGAGCAA
* * *
6074790 ATTTTTTTATTTCAATGGCTACCAAGTGAGTAT
1 ATTTTTTTATTTCAATGACTACCAAGTGAGCAA
*
6074823 TTTTTTTTATTTCAA
1 ATTTTTTTATTTCAA
6074838 AATATCACAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 40 0.98
34 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (33 bp):
ATTTTTTTATTTCAATGACTACCAAGTGAGCAA
Found at i:6075558 original size:4 final size:4
Alignment explanation
Indices: 6075549--6075578 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
6075539 GAAATAGTGA
6075549 AAAT AAAT AAAT AAAT AAAT AAAT -AAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
6075579 AGGGCAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:6082484 original size:3 final size:3
Alignment explanation
Indices: 6082476--6082505 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6082466 ACAGACATTG
6082476 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6082506 CTCGTTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6084478 original size:21 final size:19
Alignment explanation
Indices: 6084441--6084479 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
6084431 TAAATAAGAA
*
6084441 ATATATTATATTTTAATAT
1 ATATATTATATTATAATAT
6084460 ATATATATATATTGATAATA
1 ATATAT-TATATT-ATAATA
6084480 ATTAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
ATATATTATATTATAATAT
Found at i:6085553 original size:17 final size:16
Alignment explanation
Indices: 6085512--6085553 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
6085502 AATTCAATTT
*
6085512 TAATATAAATATTCAA
1 TAATATAAAAATTCAA
6085528 T-ATACTAAACAATTCAA
1 TAATA-TAAA-AATTCAA
6085545 TAATATAAA
1 TAATATAAA
6085554 TAATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 3 0.14
16 5 0.23
17 11 0.50
18 3 0.14
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATATAAAAATTCAA
Found at i:6092095 original size:41 final size:41
Alignment explanation
Indices: 6092038--6092118 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
6092028 ATGATGACTG
6092038 AGTCACTTCCTATAACCAAGTTTGAGCATTGCTTAGACTTA
1 AGTCACTTCCTATAACCAAGTTTGAGCATTGCTTAGACTTA
6092079 AGTCACTTCCTATAACCAAGTTTGAGCATTGCTTAGACTT
1 AGTCACTTCCTATAACCAAGTTTGAGCATTGCTTAGACTT
6092119 GGTCAAACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (41 bp):
AGTCACTTCCTATAACCAAGTTTGAGCATTGCTTAGACTTA
Found at i:6097191 original size:5 final size:5
Alignment explanation
Indices: 6097183--6097213 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
6097173 TTTTCTTTTT
*
6097183 TCACC TCACC TCACC TCACC TCACA TCACC T
1 TCACC TCACC TCACC TCACC TCACC TCACC T
6097214 TCCCTTCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.55, G:0.00, T:0.23
Consensus pattern (5 bp):
TCACC
Found at i:6097451 original size:15 final size:16
Alignment explanation
Indices: 6097425--6097455 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6097415 GTCTATTTTT
6097425 ATTTTTATTTTATTTG
1 ATTTTTATTTTATTTG
6097441 ATTTTTA-TTTATTTG
1 ATTTTTATTTTATTTG
6097456 CTTATTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (16 bp):
ATTTTTATTTTATTTG
Found at i:6097504 original size:19 final size:20
Alignment explanation
Indices: 6097477--6097517 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
6097467 TTCTTGTTTA
* *
6097477 TCCTTTATTTTTA-TATTAT
1 TCCTCTATTCTTATTATTAT
6097496 TCCTCTATTCTTATTATTAT
1 TCCTCTATTCTTATTATTAT
6097516 TC
1 TC
6097518 TTTATTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (20 bp):
TCCTCTATTCTTATTATTAT
Found at i:6097531 original size:19 final size:18
Alignment explanation
Indices: 6097474--6097532 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
6097464 TCTTTCTTGT
* *
6097474 TTATCCTTTATTTTTATA
1 TTATTCTTTATTTTTTTA
* *
6097492 TTATTCCTCTATTCTTATTA
1 TTATT-CTTTATT-TTTTTA
6097512 TTATTCTTTATTTGTTTTA
1 TTATTCTTTATTT-TTTTA
6097531 TT
1 TT
6097533 CTGCTTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 5 0.16
19 18 0.56
20 9 0.28
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATTCTTTATTTTTTTA
Found at i:6099140 original size:6 final size:6
Alignment explanation
Indices: 6099124--6099167 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
6099114 AGTCTATTTG
*
6099124 TTTTA- TTTTAT TTTTAT TTTTAT TTTTAT GTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
6099168 CTTAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:6100552 original size:9 final size:9
Alignment explanation
Indices: 6100538--6100564 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6100528 CCTTAAGCAC
6100538 TTTGAGTGA
1 TTTGAGTGA
6100547 TTTGAGTGA
1 TTTGAGTGA
6100556 TTTGAGTGA
1 TTTGAGTGA
6100565 ATCTTCAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (9 bp):
TTTGAGTGA
Found at i:6102607 original size:17 final size:16
Alignment explanation
Indices: 6102593--6102627 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6102583 GTCATTACTG
6102593 ATATTCTATTTTTACA
1 ATATTCTATTTTTACA
*
6102609 ATGTTCTATTTTTA-A
1 ATATTCTATTTTTACA
6102624 ATAT
1 ATAT
6102628 AGTATTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (16 bp):
ATATTCTATTTTTACA
Found at i:6104817 original size:18 final size:19
Alignment explanation
Indices: 6104780--6104816 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6104770 TTTTTAAAAA
*
6104780 TATAAA-ATTTGGAATTTT
1 TATAAATATTTAGAATTTT
6104798 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
6104817 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:6105689 original size:12 final size:12
Alignment explanation
Indices: 6105645--6105692 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
6105635 GAGCACAAGC
*
6105645 CCGACACCGTCA
1 CCGACACCGGCA
** *
6105657 CCCTCACCAGCA
1 CCGACACCGGCA
*
6105669 CCGGCACCGGCA
1 CCGACACCGGCA
6105681 CCGACACCGGCA
1 CCGACACCGGCA
6105693 TACACAAATC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.23, C:0.52, G:0.21, T:0.04
Consensus pattern (12 bp):
CCGACACCGGCA
Found at i:6109165 original size:23 final size:23
Alignment explanation
Indices: 6109110--6109167 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
6109100 AAAACATCGT
* *
6109110 CGAAGCGAATAATAGAACACCGC
1 CGAAGCGGATAATAGAACAACGC
* *
6109133 CAAAGTGGATAATAGAACAACGC
1 CGAAGCGGATAATAGAACAACGC
*
6109156 TGAAGCGGATAA
1 CGAAGCGGATAA
6109168 ACAAAGAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (23 bp):
CGAAGCGGATAATAGAACAACGC
Found at i:6112886 original size:21 final size:20
Alignment explanation
Indices: 6112862--6112920 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
6112852 GTTTATTAGG
* *
6112862 AATTTTAGAGTTTTTCTGAAA
1 AATTTTAGA-ATTTTATGAAA
*
6112883 AATTATAGAATTTTATGAAAA
1 AATTTTAGAATTTTATG-AAA
*
6112904 AATTTAAGAATTTTATG
1 AATTTTAGAATTTTATG
6112921 TTTTTTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (20 bp):
AATTTTAGAATTTTATGAAA
Done.