Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 15 of 204
Found at i:5786097 original size:17 final size:17
Alignment explanation
Indices: 5786074--5786120 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
5786064 ATAGTTCAGA
*
5786074 TAATATTATTTTCTATT
1 TAATATTATTTTCTAAT
*
5786091 TATTATTATATTT-TAAT
1 TAATATTAT-TTTCTAAT
5786108 TAATATT-TTTTCT
1 TAATATTATTTTCT
5786121 GTTCAAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 17 0.68
18 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (17 bp):
TAATATTATTTTCTAAT
Found at i:5787473 original size:4 final size:4
Alignment explanation
Indices: 5787464--5787489 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5787454 AAAAACTGGG
5787464 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
5787490 GATTTATAGT
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:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:5793558 original size:21 final size:21
Alignment explanation
Indices: 5793533--5793586 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
5793523 GTACATTTTT
* * *
5793533 TATAAAAAAAATTTTACATCA
1 TATAAAAAAAATTTAAAATAA
**
5793554 TATAATTAAAATTTAAAATAA
1 TATAAAAAAAATTTAAAATAA
5793575 TATAATAAAAAA
1 TATAA-AAAAAA
5793587 AACTTAAATT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAAAAAAATTTAAAATAA
Found at i:5795237 original size:2 final size:2
Alignment explanation
Indices: 5795226--5795254 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5795216 GCATGGCTTT
5795226 TA TA -A 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
5795255 AGCATTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5796470 original size:2 final size:2
Alignment explanation
Indices: 5796463--5796497 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
5796453 TTACACGTAA
*
5796463 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5796498 TCTCAATCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:5813925 original size:19 final size:20
Alignment explanation
Indices: 5813877--5813932 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
5813867 TCAGTCTGCT
5813877 TTTATTATTT--AAATAATA
1 TTTATTATTTAAAAATAATA
*
5813895 TTTGTTACATTTAAAAATAA-A
1 TTTATT--ATTTAAAAATAATA
*
5813916 TTTATTATTTAATAATA
1 TTTATTATTTAAAAATA
5813933 TGAGCCATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 5 0.16
19 10 0.32
20 4 0.13
21 6 0.19
22 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTATTATTTAAAAATAATA
Found at i:5820010 original size:18 final size:19
Alignment explanation
Indices: 5819975--5820011 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5819965 CTATTTTTTT
*
5819975 TATAATTTTTTATTAAATC
1 TATAATTTTTTATAAAATC
5819994 TATAATTTTTTA-AAAATC
1 TATAATTTTTTATAAAATC
5820012 GAAAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAATTTTTTATAAAATC
Found at i:5825057 original size:26 final size:25
Alignment explanation
Indices: 5825012--5825079 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
5825002 CATCAAAATC
* *
5825012 TATTTTCTTTAGGAATATAAATTAATA
1 TATTTT-TTTAAGAAAAT-AATTAATA
* *
5825039 TATTTTTTTATGAAAATAATTATTA
1 TATTTTTTTAAGAAAATAATTAATA
*
5825064 -ATATTTTTAAGAAAAT
1 TATTTTTTTAAGAAAAT
5825080 GATTCATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 14 0.39
25 7 0.19
26 9 0.25
27 6 0.17
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (25 bp):
TATTTTTTTAAGAAAATAATTAATA
Found at i:5833286 original size:14 final size:13
Alignment explanation
Indices: 5833257--5833295 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
5833247 CTTTTATATG
5833257 TATTTTTTGGATTTT
1 TATTTTTT--ATTTT
5833272 TATATTTTTATTTT
1 TAT-TTTTTATTTT
5833286 TATTTTTTAT
1 TATTTTTTAT
5833296 AATTTTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 8 0.35
15 3 0.13
16 5 0.22
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:5839697 original size:15 final size:15
Alignment explanation
Indices: 5839688--5839721 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5839678 CAAATGCTAT
5839688 AATAATAAATACAAC
1 AATAATAAATACAAC
*
5839703 AATAATAAATACATC
1 AATAATAAATACAAC
5839718 AATA
1 AATA
5839722 GCATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:5839746 original size:13 final size:14
Alignment explanation
Indices: 5839728--5839764 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5839718 AATAGCATAA
5839728 AAATAATATAAAC-
1 AAATAATATAAACG
5839741 AAATAA-ATAAACG
1 AAATAATATAAACG
5839754 AAATGAATATA
1 AAAT-AATATA
5839765 TATGAAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (14 bp):
AAATAATATAAACG
Found at i:5840278 original size:15 final size:15
Alignment explanation
Indices: 5840258--5840310 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
5840248 ACATGAAAAT
*
5840258 AATAATTACAATACC
1 AATAATAACAATACC
* *
5840273 AATAATAATAATACT
1 AATAATAACAATACC
* **
5840288 AATAATAATAATAAT
1 AATAATAACAATACC
5840303 AATAATAA
1 AATAATAA
5840311 TAAGAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAATAACAATACC
Found at i:5840279 original size:3 final size:3
Alignment explanation
Indices: 5840273--5840313 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
5840263 TTACAATACC
*
5840273 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5840314 GAAAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5841666 original size:132 final size:132
Alignment explanation
Indices: 5841488--5842399 Score: 1592
Period size: 132 Copynumber: 6.9 Consensus size: 132
5841478 CTGCAACTGG
* *
5841488 AGGGAGATAAGA-CTTACAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGC
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGC
* * * * *
5841552 TTCAATGTACTCCACTGTAACTACAGGGAGGTAAAACCCGCCATCTTCGATCTACTCCACTATTG
65 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
5841617 CTT
130 CTT
* * *
5841620 AGGGAGATAAAATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGTT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
5841685 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
5841750 TT
131 TT
*
5841752 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
*
5841817 TCAATGTACTCCACTATAACCACAAGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
5841882 TT
131 TT
* *
5841884 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTGGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
5841949 TCAATGTACTCCAGTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTAC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
5842014 TT
131 TT
*
5842016 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGACTTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* *
5842081 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
5842146 TT
131 TT
*
5842148 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCAAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
5842213 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
5842278 TT
131 TT
*
5842280 AGGGAGATAAGATCTGAAATCTTCAATCCATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
* * *
5842345 TCAATGTACTCCACTATAACCATAGGGAGGTAAAATCCGCCATATTTGATCTGCT
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
5842400 TCGCTGTCAA
Statistics
Matches: 746, Mismatches: 33, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
132 743 1.00
133 3 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:5847317 original size:47 final size:47
Alignment explanation
Indices: 5847259--5847599 Score: 479
Period size: 47 Copynumber: 7.3 Consensus size: 47
5847249 CAATAACATG
* * * * * *
5847259 CTCAAAA-TGGACAGCATTATACATCAAATTAGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* * * * * * *
5847305 CCCAAAATTGGACAGCATTATACATCAAATTAGACAGCTTAAATATA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
5847352 CTCACAATTGGACAGCATTATATATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
5847399 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
**
5847446 CTCAAAATTGGACAGCATTATACATTAAAATGGGTAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
5847493 CTCAAAATTGAACAGCATTACACATTAAAATGGACAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
* *
5847540 CTCAAAATTGGA-AGCATTACACATTAAAATGGGCAGCATCAATACA
1 CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
5847586 CTCAAAATTGGACA
1 CTCAAAATTGGACA
5847600 TCAAATTTGG
Statistics
Matches: 273, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
46 51 0.19
47 222 0.81
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (47 bp):
CTCAAAATTGGACAGCATTATACATTAAAATGGACAGCATCAATACA
Found at i:5847364 original size:94 final size:94
Alignment explanation
Indices: 5847218--5847599 Score: 466
Period size: 94 Copynumber: 4.1 Consensus size: 94
5847208 CAACTCTATT
* * * *
5847218 TTGGACAGCAATTATTCAACAAATTGGACAGCAATAACAT--GCTCAAAA-TGGACAGCATTATA
1 TTGGACAGC-ATTATACATCAAAATGGACAGC-ATAA-ATACACTCAAAATTGGACAGCATTATA
* * * * * * *
5847280 CATCAAATTAGACAGCTTAAATATACCCAAAA
63 CATTAAAATGGACAGCATCAATACACTCAAAA
* * * * * *
5847312 TTGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCACAATTGGACAGCATTATATAT
1 TTGGACAGCATTATACATCAAAATGGACAGCATAAATACACTCAAAATTGGACAGCATTATACAT
5847377 TAAAATGGACAGCATCAATACACTCAAAA
66 TAAAATGGACAGCATCAATACACTCAAAA
* *
5847406 TTGGACAGCATTATACATTAAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACAT
1 TTGGACAGCATTATACATCAAAATGGACAGCATAAATACACTCAAAATTGGACAGCATTATACAT
**
5847471 TAAAATGGGTAGCATCAATACACTCAAAA
66 TAAAATGGACAGCATCAATACACTCAAAA
* * * * *
5847500 TTGAACAGCATTACACATTAAAATGGACAGCATCAATACACTCAAAATTGGA-AGCATTACACAT
1 TTGGACAGCATTATACATCAAAATGGACAGCATAAATACACTCAAAATTGGACAGCATTATACAT
*
5847564 TAAAATGGGCAGCATCAATACACTCAAAA
66 TAAAATGGACAGCATCAATACACTCAAAA
5847593 TTGGACA
1 TTGGACA
5847600 TCAAATTTGG
Statistics
Matches: 256, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
91 2 0.01
92 3 0.01
93 70 0.27
94 181 0.71
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (94 bp):
TTGGACAGCATTATACATCAAAATGGACAGCATAAATACACTCAAAATTGGACAGCATTATACAT
TAAAATGGACAGCATCAATACACTCAAAA
Found at i:5847515 original size:22 final size:22
Alignment explanation
Indices: 5847238--5847599 Score: 173
Period size: 25 Copynumber: 15.5 Consensus size: 22
5847228 ATTATTCAAC
*
5847238 AAATTGGACAGCAATAACATGCTCA
1 AAATTGGACAGC-ATTACA--CTCA
*
5847263 AAA-TGGACAGCATTATACATC-
1 AAATTGGACAGCATTACAC-TCA
* * * *
5847284 AAATTAGACAGCTTAAATATACCCA
1 AAATTGGACAGC---ATTACACTCA
*
5847309 AAATTGGACAGCATTATACATC-
1 AAATTGGACAGCATTACAC-TCA
* * *
5847331 AAATTAGACAGCTTAAATATACTCA
1 AAATTGGACAGC---ATTACACTCA
* * * *
5847356 CAATTGGACAGCATTATATATTA
1 AAATTGGACAGCATTACA-CTCA
5847379 AAA-TGGACAGCATCAATACACTCA
1 AAATTGGACAGCAT---TACACTCA
* *
5847403 AAATTGGACAGCATTATACATTA
1 AAATTGGACAGCATTACAC-TCA
5847426 AAA-TGGACAGCATCAATACACTCA
1 AAATTGGACAGCAT---TACACTCA
* *
5847450 AAATTGGACAGCATTATACATTA
1 AAATTGGACAGCATTACAC-TCA
* * *
5847473 AAATGGGTAGCATCAATACACTCA
1 AAATTGG-A-CAGCATTACACTCA
* *
5847497 AAATTGAACAGCATTACACATTA
1 AAATTGGACAGCATTACAC-TCA
5847520 AAA-TGGACAGCATCAATACACTCA
1 AAATTGGACAGCAT---TACACTCA
*
5847544 AAATTGGA-AGCATTACACATTA
1 AAATTGGACAGCATTACAC-TCA
*
5847566 AAA-TGGGCAGCATCAATACACTCA
1 AAATTGGACAGCAT---TACACTCA
5847590 AAATTGGACA
1 AAATTGGACA
5847600 TCAAATTTGG
Statistics
Matches: 261, Mismatches: 41, Indels: 70
0.70 0.11 0.19
Matches are distributed among these distances:
21 12 0.05
22 87 0.33
23 28 0.11
24 44 0.17
25 90 0.34
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (22 bp):
AAATTGGACAGCATTACACTCA
Found at i:5847602 original size:22 final size:22
Alignment explanation
Indices: 5847389--5847603 Score: 134
Period size: 24 Copynumber: 9.3 Consensus size: 22
5847379 AAATGGACAG
5847389 CATCAATACACTCAAAATTGGA
1 CATCAATACACTCAAAATTGGA
* *
5847411 CAGCATTATACA-TTAAAA-TGGACA
1 CATCA--ATACACTCAAAATTGG--A
5847435 GCATCAATACACTCAAAATTGGA
1 -CATCAATACACTCAAAATTGGA
* * *
5847458 CAGCATTATACA-TTAAAATGGGTA
1 CATCA--ATACACTCAAAATTGG-A
*
5847482 GCATCAATACACTCAAAATTGAA
1 -CATCAATACACTCAAAATTGGA
* * *
5847505 CAGCATTACACATTAAAA-TGGACA
1 CATCAATACAC-TCAAAATTGG--A
5847529 GCATCAATACACTCAAAATTGGA
1 -CATCAATACACTCAAAATTGGA
* * * *
5847552 -AGCATTACACATTAAAATGGGCA
1 CATCAATACAC-TCAAAATTGG-A
5847575 GCATCAATACACTCAAAATTGGA
1 -CATCAATACACTCAAAATTGGA
5847598 CATCAA
1 CATCAA
5847604 ATTTGGCAGC
Statistics
Matches: 146, Mismatches: 26, Indels: 42
0.68 0.12 0.20
Matches are distributed among these distances:
21 8 0.05
22 36 0.25
23 33 0.23
24 38 0.26
25 31 0.21
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.23
Consensus pattern (22 bp):
CATCAATACACTCAAAATTGGA
Found at i:5851238 original size:15 final size:15
Alignment explanation
Indices: 5851229--5851262 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5851219 CAAATGCTAT
5851229 AATAATAAATACAAC
1 AATAATAAATACAAC
*
5851244 AATAATAAATACATC
1 AATAATAAATACAAC
5851259 AATA
1 AATA
5851263 GCATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:5851287 original size:13 final size:14
Alignment explanation
Indices: 5851269--5851305 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5851259 AATAGCATAA
5851269 AAATAATATAAAC-
1 AAATAATATAAACG
5851282 AAATAA-ATAAACG
1 AAATAATATAAACG
5851295 AAATGAATATA
1 AAAT-AATATA
5851306 TATGAAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (14 bp):
AAATAATATAAACG
Found at i:5851812 original size:3 final size:3
Alignment explanation
Indices: 5851806--5851838 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5851796 TTACAATACC
5851806 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5851839 GAGAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5855918 original size:27 final size:27
Alignment explanation
Indices: 5855894--5855946 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
5855884 AGAATGGCGG
5855894 CACCAATGGTGCCATTCTCATTGGCAC
1 CACCAATGGTGCCATTCTCATTGGCAC
*
5855921 CACCAATGGTGCCTTTCTCATTGGCA
1 CACCAATGGTGCCATTCTCATTGGCA
5855947 TCACTAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.28
Consensus pattern (27 bp):
CACCAATGGTGCCATTCTCATTGGCAC
Found at i:5873133 original size:14 final size:15
Alignment explanation
Indices: 5873097--5873133 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
5873087 CAAACATTTG
5873097 TCAACATTAATTATT
1 TCAACATTAATTATT
*
5873112 T-AATATTAATTATT
1 TCAACATTAATTATT
5873126 TCAA-ATTA
1 TCAACATTA
5873134 TATTTTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (15 bp):
TCAACATTAATTATT
Found at i:5873213 original size:61 final size:61
Alignment explanation
Indices: 5873148--5873335 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
5873138 TTATAGTATC
5873148 ATATATTATGATTTTAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTTAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * ** * *
5873209 ATATATTTTAATTATAATATATTTA-ATAATAAT-TATG-TTA--AATTATCTTT-TATAGTATC
1 ATATATTATGATTTTAATAAATTCATATAAGAATAT-TGATTATTAAGAAT-TTTAT-TA-AATT
* *
5873268 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTTAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
5873329 ATATATT
1 ATATATT
5873336 TTAATTATAA
Statistics
Matches: 95, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
57 5 0.05
58 5 0.05
59 24 0.25
60 18 0.19
61 33 0.35
62 5 0.05
63 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTTAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:5873230 original size:16 final size:16
Alignment explanation
Indices: 5873209--5873254 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5873199 TTATTAAATT
5873209 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
5873225 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
5873240 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
5873255 CTTTTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:5873321 original size:120 final size:120
Alignment explanation
Indices: 5873104--5873372 Score: 470
Period size: 120 Copynumber: 2.2 Consensus size: 120
5873094 TTGTCAACAT
* *
5873104 TAAT-TATTTAATATTAATTAT-TTCAAATTATATTTTATAGTATCATATATTATGATTTTAATA
1 TAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTATCATATATTATGATTTGAATA
5873167 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTA
65 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTA
* *
5873223 TAATATATTTAATAATAATTATGTTAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAA
1 TAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAATAA
5873288 ATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTA
66 ATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTA
5873343 TAATATATTTAATAATAATTATGTTTAAAT
1 TAATATATTTAATAATAATTATG-TTAAAT
5873373 ATGATTAAAT
Statistics
Matches: 143, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
119 4 0.03
120 131 0.92
121 8 0.06
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
TAATATATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAATAA
ATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTA
Found at i:5873332 original size:59 final size:59
Alignment explanation
Indices: 5873149--5873332 Score: 150
Period size: 57 Copynumber: 3.1 Consensus size: 59
5873139 TATAGTATCA
*
5873149 TATATTATGATTTTAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 TATATTATGATTTAAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
* * * * *
5873208 TATA-TAT--TTTAATTATAATAT-ATTTAATAATAATT-A-TGTTAA-ATTATCTTT-TATAGT
1 TATATTATGATTTAAATA-AAT-TCATATAAGAAT-ATTGATTATTAAGA--AT-TTTAT-TA-A
5873265 AT
58 AT
* *
5873267 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
5873328 TATAT
1 TATAT
5873333 ATTTTAATTA
Statistics
Matches: 95, Mismatches: 12, Indels: 36
0.66 0.08 0.25
Matches are distributed among these distances:
55 1 0.01
56 11 0.12
57 15 0.16
58 12 0.13
59 11 0.12
61 6 0.06
62 12 0.13
63 15 0.16
64 11 0.12
65 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (59 bp):
TATATTATGATTTAAATAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAAT
Found at i:5873350 original size:16 final size:16
Alignment explanation
Indices: 5873329--5873370 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
5873319 TTATTAAATT
*
5873329 ATATATTTTAATTATA
1 ATATATTTTAATAATA
5873345 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
5873360 AT-TATGTTTAA
1 ATATAT-TTTAA
5873371 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:5873355 original size:15 final size:15
Alignment explanation
Indices: 5873320--5873361 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5873310 TTAAGAATTT
*
5873320 TATTAAATTAT-ATA
1 TATTTAATTATAATA
5873334 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
5873348 TATTTAATAATAAT
1 TATTTAATTATAAT
5873362 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:5873605 original size:16 final size:16
Alignment explanation
Indices: 5873584--5873616 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5873574 TTGATTTGCT
*
5873584 ATTACGCCTCTGTTCC
1 ATTACGCCTCTATTCC
5873600 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
5873616 A
1 A
5873617 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:5878144 original size:19 final size:20
Alignment explanation
Indices: 5878114--5878154 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
5878104 AAATTTTGAG
*
5878114 AAATTATTATTTATTTTTTA
1 AAATTATTATTTATCTTTTA
5878134 AAATT-TTATTTATCTTTTA
1 AAATTATTATTTATCTTTTA
5878153 AA
1 AA
5878155 GAAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTATTTATCTTTTA
Found at i:5881085 original size:82 final size:82
Alignment explanation
Indices: 5880998--5881161 Score: 292
Period size: 82 Copynumber: 2.0 Consensus size: 82
5880988 TTAGTACATA
*
5880998 AAACACATTAAATTATAAATAATGGTTAAAAATGTCACTTGACTTTAAATATGTTTTTTCCAAGG
1 AAACACATTAAATTATAAATAATGGTTAAAAATGTCACTTGACTTTAAATATGTATTTTCCAAGG
5881063 ATTCAAAAGCATTTTCT
66 ATTCAAAAGCATTTTCT
* *
5881080 AAACACATTAAATTATAAATAATGGTTAAAAATGTGACTTGACTTTAAGTATGTATTTTCCAAGG
1 AAACACATTAAATTATAAATAATGGTTAAAAATGTCACTTGACTTTAAATATGTATTTTCCAAGG
*
5881145 ATTCAAAAGCTTTTTCT
66 ATTCAAAAGCATTTTCT
5881162 TACTTCTGAA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (82 bp):
AAACACATTAAATTATAAATAATGGTTAAAAATGTCACTTGACTTTAAATATGTATTTTCCAAGG
ATTCAAAAGCATTTTCT
Found at i:5883920 original size:10 final size:11
Alignment explanation
Indices: 5883903--5883931 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
5883893 ACTAGCCCTT
5883903 TATTATTATTA
1 TATTATTATTA
5883914 T-TTATTATTA
1 TATTATTATTA
5883924 TATTATTA
1 TATTATTA
5883932 GATATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTATTATTA
Found at i:5885345 original size:19 final size:20
Alignment explanation
Indices: 5885315--5885355 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
5885305 AAATTTTGAG
*
5885315 AAATTATTATTTATTTTTTA
1 AAATTATTATTTATCTTTTA
*
5885335 AAATT-TTATTTCTCTTTTA
1 AAATTATTATTTATCTTTTA
5885354 AA
1 AA
5885356 GTTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTATTTATCTTTTA
Found at i:5887290 original size:30 final size:29
Alignment explanation
Indices: 5887251--5887317 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
5887241 ACCAAAAAAA
5887251 GCCACTTTTTTTAAAAAATTACCGAAATGG
1 GCCA-TTTTTTTAAAAAATTACCGAAATGG
* ** * *
5887281 GCCAGTTTTTTAATTATTTACCGGAATGG
1 GCCATTTTTTTAAAAAATTACCGAAATGG
5887310 GCCATTTT
1 GCCATTTT
5887318 CCCCGAAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (29 bp):
GCCATTTTTTTAAAAAATTACCGAAATGG
Found at i:5890108 original size:18 final size:17
Alignment explanation
Indices: 5890085--5890229 Score: 89
Period size: 19 Copynumber: 8.1 Consensus size: 17
5890075 CGTGATCTGA
5890085 TTGAAACACGAGAATTTT
1 TTGAAACACGA-AATTTT
*
5890103 TTGAAAACACGAAAATTT
1 TTG-AAACACGAAATTTT
* *
5890121 TTGAAACAAGAAAACTTT
1 TTGAAACACG-AAATTTT
*
5890139 TTGAAAACACGAATTTTTTT
1 TTG-AAACACGAA--ATTTT
* * *
5890159 TTAAAAAAAACAAAATTTT
1 TT--GAAACACGAAATTTT
*
5890178 TT-AAACACTAGAATTTT
1 TTGAAACACGA-AATTTT
* *
5890195 TTGAAAATACGAAA-GTT
1 TTG-AAACACGAAATTTT
5890212 TTGAAACACG-AATTTT
1 TTGAAACACGAAATTTT
5890228 TT
1 TT
5890230 AAAAAAAAAC
Statistics
Matches: 99, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
15 2 0.02
16 16 0.16
17 19 0.19
18 24 0.24
19 26 0.26
20 5 0.05
21 7 0.07
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (17 bp):
TTGAAACACGAAATTTT
Found at i:5890156 original size:17 final size:17
Alignment explanation
Indices: 5890096--5890233 Score: 70
Period size: 17 Copynumber: 7.8 Consensus size: 17
5890086 TGAAACACGA
5890096 GAATTTTTTGAAAACAC
1 GAATTTTTTGAAAACAC
* *
5890113 GAAAATTTTTG-AAACAA
1 G-AATTTTTTGAAAACAC
*
5890130 GAAAACTTTTTGAAAACAC
1 G--AATTTTTTGAAAACAC
* *
5890149 GAATTTTTTTTTAAAAAAAAC
1 GAA---TTTTTT-GAAAACAC
*
5890170 AAAATTTTTT--AAACAC
1 -GAATTTTTTGAAAACAC
*
5890186 TAGAATTTTTTGAAAATAC
1 --GAATTTTTTGAAAACAC
**
5890205 GAAAGTTTTG-AAACAC
1 GAATTTTTTGAAAACAC
5890221 GAATTTTTT-AAAA
1 GAATTTTTTGAAAA
5890234 AAAAACATGA
Statistics
Matches: 93, Mismatches: 16, Indels: 25
0.69 0.12 0.19
Matches are distributed among these distances:
16 20 0.22
17 26 0.28
18 17 0.18
19 17 0.18
20 5 0.05
21 6 0.06
22 2 0.02
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (17 bp):
GAATTTTTTGAAAACAC
Found at i:5890184 original size:37 final size:36
Alignment explanation
Indices: 5890100--5890269 Score: 98
Period size: 37 Copynumber: 4.6 Consensus size: 36
5890090 ACACGAGAAT
* * * * * *
5890100 TTTTTGAAAACACGAAAATTTTTGAAACAAGA-AAAC
1 TTTTTG-AAACACGGAATTTTTTTAAAAAAAACAAAA
5890136 TTTTTGAAAACAC-GAATTTTTTTTTAAAAAAAACAAAA
1 TTTTTG-AAACACGGAA--TTTTTTTAAAAAAAACAAAA
* * * * *
5890174 TTTTTTAAACACTAGAA-TTTTTT-GAAAATACGAAA
1 TTTTTGAAACAC-GGAATTTTTTTAAAAAAAACAAAA
* *
5890209 GTTTTGAAACAC-GAATTTTTTAAAAAAAAACATGAAA
1 TTTTTGAAACACGGAATTTTTTTAAAAAAAACA--AAA
* *
5890246 ATTTTGAAAGACGGGAATTTTTTT
1 TTTTTGAAACAC-GGAATTTTTTT
5890270 TGAAAACACA
Statistics
Matches: 104, Mismatches: 19, Indels: 19
0.73 0.13 0.13
Matches are distributed among these distances:
33 3 0.03
34 5 0.05
35 27 0.26
36 19 0.18
37 30 0.29
38 8 0.08
39 12 0.12
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (36 bp):
TTTTTGAAACACGGAATTTTTTTAAAAAAAACAAAA
Found at i:5890358 original size:55 final size:54
Alignment explanation
Indices: 5890237--5890346 Score: 132
Period size: 55 Copynumber: 2.0 Consensus size: 54
5890227 TTTAAAAAAA
* * * *
5890237 AACATGAAAATTTTGAAAGACGGGAATTTTTTTTGAAAACACAAAAAAATTTTTT
1 AACACGAAAATTTTGAAACACGAGAATTTTTTCTGAAAACAC-AAAAAATTTTTT
* * * *
5890292 AACACAAAAATTTTGAAACACTAGAATTTTTTCTGAAAACAC-TAAATTTTTTT
1 AACACGAAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAAAAATTTTTT
5890345 AA
1 AA
5890347 AATACGAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 11 0.23
55 36 0.77
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.35
Consensus pattern (54 bp):
AACACGAAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAAAAATTTTTT
Found at i:5891149 original size:12 final size:11
Alignment explanation
Indices: 5891132--5891180 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 11
5891122 ATATATAATT
5891132 TTTTCTTTTGTC
1 TTTTCTTTT-TC
5891144 TTTTCTTTTTC
1 TTTTCTTTTTC
5891155 TTCTT-TCTTTTC
1 TT-TTCT-TTTTC
5891167 TTTCTCTTTTTC
1 TTT-TCTTTTTC
5891179 TT
1 TT
5891181 CTTCGAGCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 6 0.18
12 26 0.79
13 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:5891154 original size:18 final size:17
Alignment explanation
Indices: 5891131--5891180 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 17
5891121 TATATATAAT
5891131 TTTTTCTTTTGTCTTTTC
1 TTTTTCTTTT-TCTTTTC
5891149 TTTTTCTTCTTTCTTTTC
1 TTTTTCTT-TTTCTTTTC
*
5891167 TTTCTCTTTTTCTT
1 TTTTTCTTTTTCTT
5891181 CTTCGAGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.20
18 22 0.73
19 2 0.07
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTC
Found at i:5891179 original size:24 final size:25
Alignment explanation
Indices: 5891133--5891183 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
5891123 TATATAATTT
5891133 TTTCTTTTGTCTTTTCTTTTTCTTC
1 TTTCTTTTGTCTTTTCTTTTTCTTC
5891158 TTTC-TTT-TCTTTCTCTTTTTCTTC
1 TTTCTTTTGTCTTT-TCTTTTTCTTC
5891182 TT
1 TT
5891184 CGAGCCGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 4 0.16
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTCTTTTGTCTTTTCTTTTTCTTC
Found at i:5892168 original size:24 final size:23
Alignment explanation
Indices: 5892136--5892185 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
5892126 TTAATTAAAT
* *
5892136 TTTATAAATAATTAATATTTATTA
1 TTTAAAAATAATTAAAATTTA-TA
*
5892160 TTTAAAAATATTTAAAATTTATA
1 TTTAAAAATAATTAAAATTTATA
5892183 TTT
1 TTT
5892186 CATATATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAAAAATAATTAAAATTTATA
Found at i:5893353 original size:19 final size:18
Alignment explanation
Indices: 5893311--5893354 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
5893301 CGTTACCCAT
5893311 GGTTTTTCCCTCTTTGAG
1 GGTTTTTCCCTCTTTGAG
5893329 GGTTTTTCCCTCTTTGAG
1 GGTTTTTCCCTCTTTGAG
5893347 GGTTTTTC
1 GGTTTTTC
5893355 GCGTGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.05, C:0.20, G:0.23, T:0.52
Consensus pattern (18 bp):
GGTTTTTCCCTCTTTGAG
Found at i:5893824 original size:24 final size:24
Alignment explanation
Indices: 5893792--5893837 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5893782 TTAATTAAAT
* *
5893792 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
5893816 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
5893838 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:5894584 original size:21 final size:22
Alignment explanation
Indices: 5894555--5894599 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
5894545 ATATATTTGA
*
5894555 ACCACAATTAAGGTTTCA-TTAT
1 ACCACAATTAAAGTTT-ATTTAT
5894577 ACCA-AATTAAAGTTTATTTAT
1 ACCACAATTAAAGTTTATTTAT
5894598 AC
1 AC
5894600 AATCACACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 16 0.76
22 4 0.19
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (22 bp):
ACCACAATTAAAGTTTATTTAT
Found at i:5898306 original size:23 final size:22
Alignment explanation
Indices: 5898248--5898307 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
5898238 TTTTCCAAAA
* * *
5898248 GGCAAAACGGTAGAAATGTAGG
1 GGCAAAAAGGTAAAAATATAGG
* *
5898270 GACAAAATGGTAAAAATATAGG
1 GGCAAAAAGGTAAAAATATAGG
5898292 GGCAAAAAGGATAAAA
1 GGCAAAAAGG-TAAAA
5898308 TTCTATAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.52, C:0.07, G:0.28, T:0.13
Consensus pattern (22 bp):
GGCAAAAAGGTAAAAATATAGG
Found at i:5900014 original size:3 final size:3
Alignment explanation
Indices: 5900006--5900036 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5899996 GAAAAACAGT
5900006 TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
5900037 TGGAGAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:5902610 original size:33 final size:33
Alignment explanation
Indices: 5902563--5902626 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
5902553 GGGTGGAGGC
5902563 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
1 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
* * * *
5902596 GGTGGAGTCTGCATGGTTTTTGGAGGTGGAG
1 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAG
5902627 GCGGCAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.16, C:0.09, G:0.47, T:0.28
Consensus pattern (33 bp):
GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
Found at i:5908243 original size:30 final size:30
Alignment explanation
Indices: 5908201--5908270 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
5908191 GAATTACTAT
5908201 CAAATTCAACAGATTCTTTTGAGTAATTCCA
1 CAAATT-AACAGATTCTTTTGAGTAATTCCA
5908232 CAAATTAACAGATTCTTTTGAGTAATTCCA
1 CAAATTAACAGATTCTTTTGAGTAATTCCA
5908262 CAAATTAAC
1 CAAATTAAC
5908271 TCTTTAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
30 33 0.85
31 6 0.15
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.34
Consensus pattern (30 bp):
CAAATTAACAGATTCTTTTGAGTAATTCCA
Found at i:5930287 original size:17 final size:17
Alignment explanation
Indices: 5930264--5930301 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5930254 AAAGATGAAA
5930264 ATAAAAAATAA-AACGTAT
1 ATAAAAAA-AACAA-GTAT
5930282 ATAAAAAAAACAAGTAT
1 ATAAAAAAAACAAGTAT
5930299 ATA
1 ATA
5930302 TACATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (17 bp):
ATAAAAAAAACAAGTAT
Found at i:5941590 original size:10 final size:10
Alignment explanation
Indices: 5941558--5941595 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
5941548 TTGATTAATG
*
5941558 TTTTAAAAAT
1 TTTTTAAAAT
*
5941568 ATTTTAAAA-
1 TTTTTAAAAT
5941577 TTTTTAAAAT
1 TTTTTAAAAT
5941587 TTTTTAAAA
1 TTTTTAAAA
5941596 ATTTAATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:5943132 original size:27 final size:28
Alignment explanation
Indices: 5943102--5943160 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
5943092 ACACACCCGG
**
5943102 AATAATAT-AAATCCTCCTTAACACACC
1 AATAATATCAAATCCTCCCAAACACACC
* *
5943129 AAT-ATGTCATATCCTCCCAAACACACC
1 AATAATATCAAATCCTCCCAAACACACC
5943156 AATAA
1 AATAA
5943161 GGCATTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 3 0.12
27 22 0.85
28 1 0.04
ACGTcount: A:0.44, C:0.31, G:0.02, T:0.24
Consensus pattern (28 bp):
AATAATATCAAATCCTCCCAAACACACC
Found at i:5949247 original size:9 final size:9
Alignment explanation
Indices: 5949235--5949331 Score: 65
Period size: 9 Copynumber: 10.4 Consensus size: 9
5949225 AAATTAGAAA
5949235 AAAAATTAT
1 AAAAATTAT
5949244 AAAAATCGTA-
1 AAAAAT--TAT
*
5949254 AAAAAATAT
1 AAAAATTAT
*
5949263 AAAAAATTGT
1 -AAAAATTAT
*
5949273 AAAATTTTAT
1 AAAA-ATTAT
*
5949283 AAAAATCAT
1 AAAAATTAT
5949292 AAAAA-TAT
1 AAAAATTAT
5949300 ATAAAATATAT
1 A-AAAAT-TAT
*
5949311 AGAAA-TAT
1 AAAAATTAT
*
5949319 GAAAATTAT
1 AAAAATTAT
5949328 AAAA
1 AAAA
5949332 TTTTATAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
8 11 0.16
9 28 0.42
10 22 0.33
11 6 0.09
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5949247 original size:21 final size:19
Alignment explanation
Indices: 5949217--5949267 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
5949207 AAAAAATTCT
5949217 AATATTAAAAATTAGAAAAAA
1 AATA-TAAAAA-TAGAAAAAA
* *
5949238 AATTATAAAAATCGTAAAAA
1 AA-TATAAAAATAGAAAAAA
5949258 AATATAAAAA
1 AATATAAAAA
5949268 ATTGTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
20 9 0.33
21 8 0.30
22 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (19 bp):
AATATAAAAATAGAAAAAA
Found at i:5949266 original size:28 final size:27
Alignment explanation
Indices: 5949235--5949340 Score: 88
Period size: 28 Copynumber: 3.8 Consensus size: 27
5949225 AAATTAGAAA
* *
5949235 AAAAATTATAAAAATCGTAAAAAAATAT
1 AAAAATTATAAAAAT-ATATAAAAATAT
* * *
5949263 AAAAAATTGTAAAATTTTATAAAAATCAT
1 -AAAAATTATAAAAATATATAAAAAT-AT
*
5949292 AAAAA-TATATAAAATATATAGAAATAT
1 AAAAATTATA-AAAATATATAAAAATAT
* * *
5949319 GAAAATTATAAAATTTTATAAA
1 AAAAATTATAAAAATATATAAA
5949341 TTCGTAAGAA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
27 18 0.29
28 29 0.47
29 15 0.24
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (27 bp):
AAAAATTATAAAAATATATAAAAATAT
Found at i:5949286 original size:19 final size:19
Alignment explanation
Indices: 5949234--5949401 Score: 91
Period size: 20 Copynumber: 8.8 Consensus size: 19
5949224 AAAATTAGAA
5949234 AAAAAATTATAAAAATCGT
1 AAAAAATTATAAAAATCGT
* *
5949253 AAAAAAATATAAAAAATTGT
1 AAAAAATTAT-AAAAATCGT
** *
5949273 AAAATTTTATAAAAATCAT
1 AAAAAATTATAAAAATCGT
*
5949292 -AAAAA-TATATAAAAT-AT
1 AAAAAATTATA-AAAATCGT
* *
5949309 ATAGAAA-TATGAAAAT--T
1 A-AAAAATTATAAAAATCGT
* * *
5949326 ATAAAATTTTATAAATTCGT
1 AAAAAATTATA-AAAATCGT
5949346 AAGAAAATTATACAAAAT-GT
1 AA-AAAATTATA-AAAATCGT
**
5949366 AAAGAAA-TATAAATTTCGT
1 AAA-AAATTATAAAAATCGT
5949385 AAAAAAATTATAAAAAT
1 -AAAAAATTATAAAAAT
5949402 TATTGTACCA
Statistics
Matches: 112, Mismatches: 24, Indels: 25
0.70 0.15 0.16
Matches are distributed among these distances:
16 3 0.03
17 10 0.09
18 20 0.18
19 33 0.29
20 34 0.30
21 12 0.11
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAAATTATAAAAATCGT
Found at i:5949620 original size:18 final size:18
Alignment explanation
Indices: 5949599--5949633 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5949589 AAAAGCTACA
*
5949599 TTTTAATAAATTTTAATT
1 TTTTAATAAAATTTAATT
5949617 TTTTAATAAAATTTAAT
1 TTTTAATAAAATTTAAT
5949634 AATTTTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATAAAATTTAATT
Found at i:5949840 original size:90 final size:87
Alignment explanation
Indices: 5949680--5949855 Score: 230
Period size: 90 Copynumber: 2.0 Consensus size: 87
5949670 AATAAGAGCT
* * *
5949680 GGGGCTTAATTGCTTTTTTGAAAATTTTTGAGGGTCTTTTTGATACATTTTGAAAGTTCAAGTAT
1 GGGGCTTAATTGCTTTTTTGAAAATGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAG-AT
* *
5949745 CCAATTGAGTGAGAAAAAAAAGTA
65 CCAATTAAGTG-CAAAAAAAAGTA
*
5949769 GGGGCTTAATTGCTTTTTTTGAAGAA-GTTTGAGGGCCTTTTTGATGCATTTTAAAAGTTCAA-A
1 GGGGCTTAATTGC-TTTTTTGAA-AATGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAGA
5949832 TGCTCAATTAAGTGCAAAAAAAAG
64 T-C-CAATTAAGTGCAAAAAAAAG
5949856 GGTTTAATTG
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
88 2 0.03
89 23 0.30
90 50 0.65
91 2 0.03
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (87 bp):
GGGGCTTAATTGCTTTTTTGAAAATGTTTGAGGGCCTTTTTGATACATTTTAAAAGTTCAAGATC
CAATTAAGTGCAAAAAAAAGTA
Found at i:5950613 original size:14 final size:15
Alignment explanation
Indices: 5950590--5950619 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5950580 TAAATTTAAT
5950590 TAAATCAATTAAAAA
1 TAAATCAATTAAAAA
5950605 TAAAT-AATTAAAAA
1 TAAATCAATTAAAAA
5950619 T
1 T
5950620 TTGAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATCAATTAAAAA
Found at i:5951111 original size:17 final size:16
Alignment explanation
Indices: 5951089--5951128 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
5951079 CCGATATAAT
5951089 AAATATATATAATTTTA
1 AAATAT-TATAATTTTA
*
5951106 AAATATTTTAATTTTA
1 AAATATTATAATTTTA
5951122 AAATATT
1 AAATATT
5951129 TTTAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATATTATAATTTTA
Found at i:5951117 original size:16 final size:16
Alignment explanation
Indices: 5951098--5951130 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5951088 TAAATATATA
5951098 TAATTTTAAAATATTT
1 TAATTTTAAAATATTT
5951114 TAATTTTAAAATATTT
1 TAATTTTAAAATATTT
5951130 T
1 T
5951131 TAAAATACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTTAAAATATTT
Found at i:5951185 original size:12 final size:11
Alignment explanation
Indices: 5951117--5951196 Score: 62
Period size: 11 Copynumber: 7.5 Consensus size: 11
5951107 AATATTTTAA
5951117 TTTTAAAATAT
1 TTTTAAAATAT
5951128 TTTTAAAATACT
1 TTTTAAAATA-T
** *
5951140 TTTTTTATTAT
1 TTTTAAAATAT
*
5951151 TTTT----TAA
1 TTTTAAAATAT
*
5951158 TTTTAAAATTT
1 TTTTAAAATAT
5951169 TTTTAAAATACT
1 TTTTAAAATA-T
5951181 TTTTAAAA-AT
1 TTTTAAAATAT
5951191 TTTTAA
1 TTTTAA
5951197 TTTTAAAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
7 6 0.11
10 7 0.12
11 26 0.46
12 17 0.30
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:5951185 original size:39 final size:40
Alignment explanation
Indices: 5951101--5951204 Score: 140
Period size: 41 Copynumber: 2.6 Consensus size: 40
5951091 ATATATATAA
5951101 TTTT-AAAATATTTTAATTTTAAAATATTTTTAAAATACTTT
1 TTTTAAAAAT-TTTTAATTTTAAAATATTTTTAAAATAC-TT
** * *
5951142 TTTTATTATTTTTTAATTTTAAAATTTTTTTAAAATAC-T
1 TTTTAAAAATTTTTAATTTTAAAATATTTTTAAAATACTT
5951181 TTTTAAAAATTTTTAATTTTAAAA
1 TTTTAAAAATTTTTAATTTTAAAA
5951205 ATAAAATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 22 0.40
41 31 0.56
42 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (40 bp):
TTTTAAAAATTTTTAATTTTAAAATATTTTTAAAATACTT
Found at i:5951885 original size:18 final size:18
Alignment explanation
Indices: 5951858--5951892 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5951848 TATGATTTAC
*
5951858 AATTTAAATTAGTTCTTA
1 AATTTAAATTAGATCTTA
*
5951876 AATTTTAATTAGATCTT
1 AATTTAAATTAGATCTT
5951893 TTCGTTATTA
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:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
AATTTAAATTAGATCTTA
Found at i:5952113 original size:16 final size:16
Alignment explanation
Indices: 5952060--5952118 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
5952050 ATATTTAAAG
5952060 ATTAAATATGTTGAATTAT
1 ATTAAATAT-TTG--TTAT
*
5952079 ATTAAA-ATTTGTTGTT
1 ATTAAATATTTGTT-AT
5952095 ATTAAATATTTGTTAT
1 ATTAAATATTTGTTAT
*
5952111 ATTTAATA
1 ATTAAATA
5952119 CTTATCTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 2 0.06
16 15 0.43
17 10 0.29
18 2 0.06
19 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (16 bp):
ATTAAATATTTGTTAT
Found at i:5952637 original size:20 final size:21
Alignment explanation
Indices: 5952597--5952653 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
5952587 GTAAAAAAAT
* * *
5952597 ATTTTTTAAAATTTTTA-TAA
1 ATTTTATAAAAGTATTATTAA
5952617 ATTTGTA-AAAA-TATTATTAA
1 ATTT-TATAAAAGTATTATTAA
5952637 ATTTTATAAAAGTATTA
1 ATTTTATAAAAGTATTA
5952654 AATAAATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 6 0.19
20 19 0.61
21 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
ATTTTATAAAAGTATTATTAA
Found at i:5966133 original size:33 final size:33
Alignment explanation
Indices: 5966069--5966133 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
5966059 ATGACTTGTT
* * *
5966069 TTTATTTTTTTATTTTTATCTTTTTCCATTTTG
1 TTTATTTTTTTATTATTATCTATTTACATTTTG
*
5966102 TTTATTTTTATTATTATT-TCTATTTATATTTT
1 TTTATTTTT-TTATTATTATCTATTTACATTTT
5966134 TTTTTAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (33 bp):
TTTATTTTTTTATTATTATCTATTTACATTTTG
Found at i:5970986 original size:23 final size:23
Alignment explanation
Indices: 5970960--5971006 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5970950 TTTCTTACTG
* *
5970960 TAGTAATTTTCGGGGTATTACAA
1 TAGTAATTTTCAGGATATTACAA
*
5970983 TAGTAATTTTTAGGATATTACAA
1 TAGTAATTTTCAGGATATTACAA
5971006 T
1 T
5971007 TTTGTAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (23 bp):
TAGTAATTTTCAGGATATTACAA
Found at i:6000305 original size:2 final size:2
Alignment explanation
Indices: 6000300--6000335 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6000290 CCTTTTTTTA
6000300 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
6000336 TGTAGTATCT
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:6007833 original size:59 final size:59
Alignment explanation
Indices: 6007753--6007960 Score: 251
Period size: 59 Copynumber: 3.5 Consensus size: 59
6007743 TATATTTGTG
* * *
6007753 CAAACTATTTTTATATTGTTTCATTGAATAAAATAGAAGTTGTTTTGAATATTTTTGAA
1 CAAATTATTTTTATATTGTTTCATTTAATAAAATATAAGTTGTTTTGAATATTTTTGAA
* *
6007812 CAAATTATTTTTATATTGTTTCATTTAATAAAACATAAGTTGTTTTGAATATTTTTGTA
1 CAAATTATTTTTATATTGTTTCATTTAATAAAATATAAGTTGTTTTGAATATTTTTGAA
* * *****
6007871 CAAATT-TTTTTATATTG-CTCTATTTAATAAAATATAAGTTCTTTTGAATA-AGGCAATA
1 CAAATTATTTTTATATTGTTTC-ATTTAATAAAATATAAGTTGTTTTGAATATTTTTGA-A
* *
6007929 CAAACTATTTTTTTATTGTTTCATTTAATAAA
1 CAAATTATTTTTATATTGTTTCATTTAATAAA
6007961 TTAGGAGTTA
Statistics
Matches: 128, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
57 2 0.02
58 44 0.34
59 80 0.62
60 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (59 bp):
CAAATTATTTTTATATTGTTTCATTTAATAAAATATAAGTTGTTTTGAATATTTTTGAA
Found at i:6010900 original size:41 final size:41
Alignment explanation
Indices: 6010855--6010973 Score: 193
Period size: 41 Copynumber: 2.9 Consensus size: 41
6010845 CCCGATACAT
* *
6010855 TTCACCGACACCAAGCCTGCTAGACATAAAGTCTGAAGTAA
1 TTCACCGACATCAAGTCTGCTAGACATAAAGTCTGAAGTAA
6010896 TTCACCGACATCAAGTCTGCTAGACATAAAGTCTGAAGTAA
1 TTCACCGACATCAAGTCTGCTAGACATAAAGTCTGAAGTAA
* * *
6010937 TTCACCGACATCAAGTCTGCTAGGCATTAAGCCTGAA
1 TTCACCGACATCAAGTCTGCTAGACATAAAGTCTGAA
6010974 AATCTCAGAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (41 bp):
TTCACCGACATCAAGTCTGCTAGACATAAAGTCTGAAGTAA
Found at i:6012117 original size:41 final size:41
Alignment explanation
Indices: 6011973--6012119 Score: 215
Period size: 41 Copynumber: 3.6 Consensus size: 41
6011963 TTTAACATAT
*
6011973 TCACCGGCACTTAACCTGCTA-AGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGA-CTTATAGCCTGATTCAGA
** * *
6012014 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGAGTCAGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
* *
6012055 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGTTTTAGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
6012096 TCACCGGCACTTAGCCTGCTAGAC
1 TCACCGGCACTTAGCCTGCTAGAC
6012120 GTAAACTCCG
Statistics
Matches: 94, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
Found at i:6013537 original size:28 final size:28
Alignment explanation
Indices: 6013506--6013562 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
6013496 GTTTGTTTTT
6013506 TTTATTATAATAA-CTTTATAATATATTA
1 TTTATTATAATAACCTTTATAAT-TATTA
*
6013534 TTTATTATTATAACCTTTATAATTATTA
1 TTTATTATAATAACCTTTATAATTATTA
6013562 T
1 T
6013563 AAAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTATTATAATAACCTTTATAATTATTA
Found at i:6013773 original size:14 final size:15
Alignment explanation
Indices: 6013754--6013782 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6013744 TCACGAAACT
6013754 TTCACACAT-ATAAA
1 TTCACACATAATAAA
6013768 TTCACACATAATAAA
1 TTCACACATAATAAA
6013783 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:6014512 original size:9 final size:9
Alignment explanation
Indices: 6014500--6014527 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6014490 TTTTATTACA
6014500 ACAATTAAT
1 ACAATTAAT
6014509 ACAATTAAT
1 ACAATTAAT
6014518 ACAATTAAT
1 ACAATTAAT
6014527 A
1 A
6014528 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:6014542 original size:68 final size:68
Alignment explanation
Indices: 6014462--6014710 Score: 441
Period size: 68 Copynumber: 3.7 Consensus size: 68
6014452 AATATAATGG
6014462 TTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
1 TTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
6014527 AAT
66 AAT
6014530 TTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
1 TTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
6014595 AAT
66 AAT
*
6014598 TTGATAAATTTACTAATCAAAAGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAAT
1 TTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
6014661 AAT
66 AAT
* *
6014664 TTGATAATTTTACTAA-CAATTAGTTAGATTTTATTACAACAATTAAT
1 TTGATAAATTTACTAATCAAAT-GTTAGATTTTATTACAACAATTAAT
6014711 TTAATTTTAA
Statistics
Matches: 176, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
65 3 0.02
66 52 0.30
67 1 0.01
68 120 0.68
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
AAT
Found at i:6014580 original size:9 final size:9
Alignment explanation
Indices: 6014568--6014595 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6014558 TTTTATTACA
6014568 ACAATTAAT
1 ACAATTAAT
6014577 ACAATTAAT
1 ACAATTAAT
6014586 ACAATTAAT
1 ACAATTAAT
6014595 A
1 A
6014596 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:6014721 original size:136 final size:136
Alignment explanation
Indices: 6014462--6014710 Score: 441
Period size: 134 Copynumber: 1.8 Consensus size: 136
6014452 AATATAATGG
*
6014462 TTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
1 TTGATAAATTTACTAATCAAAAGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
6014527 AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATT
66 AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATT
6014592 AATAAT
131 AATAAT
6014598 TTGATAAATTTACTAATCAAAAGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAAT
1 TTGATAAATTTACTAATCAAAAGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
* *
6014661 AATTTGATAATTTTACTAA-CAATTAGTTAGATTTTATTACAACAATTAAT
66 AATTTGATAAATTTACTAATCAAAT-GTTAGATTTTATTACAACAATTAAT
6014711 TTAATTTTAA
Statistics
Matches: 109, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
133 4 0.04
134 52 0.48
135 1 0.01
136 52 0.48
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (136 bp):
TTGATAAATTTACTAATCAAAAGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAAT
AATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATT
AATAAT
Found at i:6015714 original size:40 final size:40
Alignment explanation
Indices: 6015670--6015797 Score: 107
Period size: 40 Copynumber: 3.1 Consensus size: 40
6015660 ACTGAAAAGA
6015670 GCATCCATCTGGGAGCTTTTTCAATACTTTTGCTGACAGT
1 GCATCCATCTGGGAGCTTTTTCAATACTTTTGCTGACAGT
* * * ** ** * * *
6015710 GCATCC-TGCTTGAAGCGTTTGTCACCAGC-ACTACTGAAAAGA
1 GCATCCAT-CTGGGAGC-TTTTTCAATA-CTTTTGCTG-ACAGT
*
6015752 GCATCCATCTGAGAGCTTTTTCAATACTTTTGCTGACAGT
1 GCATCCATCTGGGAGCTTTTTCAATACTTTTGCTGACAGT
6015792 GCATCC
1 GCATCC
6015798 TGCTTGAAGC
Statistics
Matches: 61, Mismatches: 21, Indels: 12
0.65 0.22 0.13
Matches are distributed among these distances:
39 1 0.02
40 22 0.36
41 22 0.36
42 15 0.25
43 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (40 bp):
GCATCCATCTGGGAGCTTTTTCAATACTTTTGCTGACAGT
Found at i:6015784 original size:82 final size:82
Alignment explanation
Indices: 6015647--6015811 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
6015637 TGGGATACAC
*
6015647 TGTCACCAGCACTACTGAAAAGAGCATCCATCTGGGAGCTTTTTCAATACTTTTGCTGACAGTGC
1 TGTCACCAGCACTACTGAAAAGAGCATCCATCTGAGAGCTTTTTCAATACTTTTGCTGACAGTGC
6015712 ATCCTGCTTGAAGCGTT
66 ATCCTGCTTGAAGCGTT
6015729 TGTCACCAGCACTACTGAAAAGAGCATCCATCTGAGAGCTTTTTCAATACTTTTGCTGACAGTGC
1 TGTCACCAGCACTACTGAAAAGAGCATCCATCTGAGAGCTTTTTCAATACTTTTGCTGACAGTGC
6015794 ATCCTGCTTGAAGCGTT
66 ATCCTGCTTGAAGCGTT
6015811 T
1 T
6015812 TTCAATCCAA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (82 bp):
TGTCACCAGCACTACTGAAAAGAGCATCCATCTGAGAGCTTTTTCAATACTTTTGCTGACAGTGC
ATCCTGCTTGAAGCGTT
Found at i:6016149 original size:29 final size:29
Alignment explanation
Indices: 6016114--6016179 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
6016104 ATCAAAATAT
6016114 TTTTTTCAAAACACATCACGTCAAATTTA
1 TTTTTTCAAAACACATCACGTCAAATTTA
* * * **
6016143 TTTTTTCATATCCCATCTTGTCAAATTTA
1 TTTTTTCAAAACACATCACGTCAAATTTA
6016172 TTTCTTTC
1 TTT-TTTC
6016180 GGAACAATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.27, C:0.21, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTTTTCAAAACACATCACGTCAAATTTA
Found at i:6037994 original size:6 final size:7
Alignment explanation
Indices: 6037978--6038003 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6037968 ATTGTAAGGA
6037978 TTTTTCT
1 TTTTTCT
6037985 TTTTTCT
1 TTTTTCT
6037992 TTTTTCT
1 TTTTTCT
6037999 TTTTT
1 TTTTT
6038004 AGCTTAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:6046263 original size:20 final size:20
Alignment explanation
Indices: 6046219--6046263 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
6046209 TAATGGTTCT
*
6046219 ATTTTAATATTTAAATTATA
1 ATTTTAATAATTAAATTATA
6046239 A-TTTATATAATTAAATTA-A
1 ATTTTA-ATAATTAAATTATA
6046258 ATTTTA
1 ATTTTA
6046264 CAAATGATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTAATAATTAAATTATA
Found at i:6046592 original size:17 final size:17
Alignment explanation
Indices: 6046572--6046604 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6046562 TTTGCTGAAA
6046572 AATTTAATATTTTCAAT
1 AATTTAATATTTTCAAT
*
6046589 AATTTAATTTTTTCAA
1 AATTTAATATTTTCAA
6046605 GCATGTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTAATATTTTCAAT
Found at i:6054712 original size:29 final size:29
Alignment explanation
Indices: 6054680--6054773 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
6054670 ACATGGAACT
6054680 TAACATATCAACCCAATTCCTAAGCATGG
1 TAACATATCAACCCAATTCCTAAGCATGG
*** ** * *
6054709 TAACTGCATATTTTCGTAATATTCTAAACATGG
1 TAA---CATATCAACCCAAT-TCCTAAGCATGG
*
6054742 -AACATATCAACCCAATACCTAAGCATGG
1 TAACATATCAACCCAATTCCTAAGCATGG
6054770 TAAC
1 TAAC
6054774 TGCATATTTT
Statistics
Matches: 45, Mismatches: 15, Indels: 10
0.64 0.21 0.14
Matches are distributed among these distances:
28 9 0.20
29 15 0.33
32 11 0.24
33 10 0.22
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.28
Consensus pattern (29 bp):
TAACATATCAACCCAATTCCTAAGCATGG
Found at i:6054719 original size:32 final size:32
Alignment explanation
Indices: 6054683--6054780 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 32
6054673 TGGAACTTAA
6054683 CATATCAACCCAATTCCTAAGCATGGTAACTG
1 CATATCAACCCAATTCCTAAGCATGGTAACTG
*** ** * *
6054715 CATATTTTCGTAATATTCTAAACATGG-AA---
1 CATATCAACCCAAT-TCCTAAGCATGGTAACTG
*
6054744 CATATCAACCCAATACCTAAGCATGGTAACTG
1 CATATCAACCCAATTCCTAAGCATGGTAACTG
6054776 CATAT
1 CATAT
6054781 TTTTGTAATA
Statistics
Matches: 46, Mismatches: 15, Indels: 10
0.65 0.21 0.14
Matches are distributed among these distances:
28 9 0.20
29 11 0.24
32 16 0.35
33 10 0.22
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (32 bp):
CATATCAACCCAATTCCTAAGCATGGTAACTG
Found at i:6061428 original size:3 final size:3
Alignment explanation
Indices: 6061420--6061448 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6061410 TTGAGAAATA
6061420 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6061449 AATTAAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6061631 original size:13 final size:13
Alignment explanation
Indices: 6061615--6061691 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 13
6061605 AGTTCTTCAT
6061615 TGCTTTTAAAAAG
1 TGCTTTTAAAAAG
* *
6061628 TGCTTTTGAGAAG
1 TGCTTTTAAAAAG
* **
6061641 TGCTGTGGAAAAG
1 TGCTTTTAAAAAG
* *
6061654 TGCTTTTTAGAAG
1 TGCTTTTAAAAAG
* *
6061667 TGCTTTTAAGAGG
1 TGCTTTTAAAAAG
6061680 TGCTTTTGAAAA
1 TGCTTTT-AAAA
6061692 TTTTGAGTGT
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
13 48 0.94
14 3 0.06
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.38
Consensus pattern (13 bp):
TGCTTTTAAAAAG
Found at i:6061682 original size:26 final size:25
Alignment explanation
Indices: 6061615--6061688 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 25
6061605 AGTTCTTCAT
6061615 TGCTTTTAAAAAGTGCTTTTGAGAAG
1 TGCTTTT-AAAAGTGCTTTTGAGAAG
** *
6061641 TGCTGTGGAAAAGTGCTTTTTAGAAG
1 TGCT-TTTAAAAGTGCTTTTGAGAAG
*
6061667 TGCTTTTAAGAGGTGCTTTTGA
1 TGCTTTTAA-AAGTGCTTTTGA
6061689 AAATTTTGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.08
26 35 0.90
27 1 0.03
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.39
Consensus pattern (25 bp):
TGCTTTTAAAAGTGCTTTTGAGAAG
Found at i:6062176 original size:15 final size:15
Alignment explanation
Indices: 6062156--6062251 Score: 128
Period size: 15 Copynumber: 6.5 Consensus size: 15
6062146 TTGTTAATTC
6062156 TATTTATGTAATTAA
1 TATTTATGTAATTAA
6062171 TATTTATGTAATT-A
1 TATTTATGTAATTAA
*
6062185 TAAGTT-TGTAATTAA
1 T-ATTTATGTAATTAA
6062200 TATTTATGTAATT-A
1 TATTTATGTAATTAA
*
6062214 TAAGTT-TGTAATTAA
1 T-ATTTATGTAATTAA
6062229 TATTTATGTAATTAA
1 TATTTATGTAATTAA
6062244 TATTTATG
1 TATTTATG
6062252 ATTTTAGTCC
Statistics
Matches: 71, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
14 24 0.34
15 47 0.66
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (15 bp):
TATTTATGTAATTAA
Found at i:6062194 original size:29 final size:29
Alignment explanation
Indices: 6062162--6062242 Score: 162
Period size: 29 Copynumber: 2.8 Consensus size: 29
6062152 ATTCTATTTA
6062162 TGTAATTAATATTTATGTAATTATAAGTT
1 TGTAATTAATATTTATGTAATTATAAGTT
6062191 TGTAATTAATATTTATGTAATTATAAGTT
1 TGTAATTAATATTTATGTAATTATAAGTT
6062220 TGTAATTAATATTTATGTAATTA
1 TGTAATTAATATTTATGTAATTA
6062243 ATATTTATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (29 bp):
TGTAATTAATATTTATGTAATTATAAGTT
Found at i:6062196 original size:14 final size:14
Alignment explanation
Indices: 6062177--6062227 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
6062167 TTAATATTTA
6062177 TGTAATTATAAGTT
1 TGTAATTATAAGTT
*
6062191 TGTAATTA-ATATTT
1 TGTAATTATA-AGTT
6062205 ATGTAATTATAAGTT
1 -TGTAATTATAAGTT
6062220 TGTAATTA
1 TGTAATTA
6062228 ATATTTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 1 0.03
14 19 0.59
15 11 0.34
16 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (14 bp):
TGTAATTATAAGTT
Found at i:6062212 original size:44 final size:44
Alignment explanation
Indices: 6062156--6062251 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
6062146 TTGTTAATTC
*
6062156 TATTTATGTAATTA-ATATTTATGTAATT-ATAAGTT-TGTAATTAA
1 TATTTATGTAATTATA-AGTT-TGTAATTAAT-AGTTATGTAATTAA
*
6062200 TATTTATGTAATTATAAGTTTGTAATTAATATTTATGTAATTAA
1 TATTTATGTAATTATAAGTTTGTAATTAATAGTTATGTAATTAA
6062244 TATTTATG
1 TATTTATG
6062252 ATTTTAGTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
43 10 0.21
44 36 0.77
45 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (44 bp):
TATTTATGTAATTATAAGTTTGTAATTAATAGTTATGTAATTAA
Found at i:6063909 original size:211 final size:211
Alignment explanation
Indices: 6063539--6063960 Score: 826
Period size: 211 Copynumber: 2.0 Consensus size: 211
6063529 TGAAGAGGAA
*
6063539 ATCATTTTGTAAAATGACTACTTTTTTCCCCACTTTGTTTCACCTGGAAAGGATATTATTTGTTG
1 ATCATGTTGTAAAATGACTACTTTTTTCCCCACTTTGTTTCACCTGGAAAGGATATTATTTGTTG
6063604 TAAATCATGAATTATTCAAAAACAAAATACAATGCAATTTGTAATTCATATGACTCTTTGACGGT
66 TAAATCATGAATTATTCAAAAACAAAATACAATGCAATTTGTAATTCATATGACTCTTTGACGGT
6063669 ATCTTTTGATTATTCCATATTTTTCAAAGATGGTGAGTTTATGCACGCTGCAGCGCCGAGAGATA
131 ATCTTTTGATTATTCCATATTTTTCAAAGATGGTGAGTTTATGCACGCTGCAGCGCCGAGAGATA
6063734 ACATGAGCCGGACATG
196 ACATGAGCCGGACATG
6063750 ATCATGTTGTAAAATGACTACTTTTTTCCCCACTTTGTTTCACCTGGAAAGGATATTATTTGTTG
1 ATCATGTTGTAAAATGACTACTTTTTTCCCCACTTTGTTTCACCTGGAAAGGATATTATTTGTTG
6063815 TAAATCATGAATTATTCAAAAACAAAATACAATGCAATTTGTAATTCATATGACTCTTTGACGGT
66 TAAATCATGAATTATTCAAAAACAAAATACAATGCAATTTGTAATTCATATGACTCTTTGACGGT
6063880 ATCTTTTGATTATTCCATATTTTTCAAAGATGGTGAGTTTATGCACGCTGCAGCGCCGAGAGATA
131 ATCTTTTGATTATTCCATATTTTTCAAAGATGGTGAGTTTATGCACGCTGCAGCGCCGAGAGATA
*
6063945 ACATGAGCCGGCCATG
196 ACATGAGCCGGACATG
6063961 TCCGTAGGGT
Statistics
Matches: 209, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
211 209 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (211 bp):
ATCATGTTGTAAAATGACTACTTTTTTCCCCACTTTGTTTCACCTGGAAAGGATATTATTTGTTG
TAAATCATGAATTATTCAAAAACAAAATACAATGCAATTTGTAATTCATATGACTCTTTGACGGT
ATCTTTTGATTATTCCATATTTTTCAAAGATGGTGAGTTTATGCACGCTGCAGCGCCGAGAGATA
ACATGAGCCGGACATG
Found at i:6068419 original size:16 final size:16
Alignment explanation
Indices: 6068398--6068451 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
6068388 TTTGGTTCAC
6068398 TGTAATGGAATAAAGA
1 TGTAATGGAATAAAGA
* * *
6068414 TGTAATTGAATAGAGC
1 TGTAATGGAATAAAGA
*
6068430 TGTAATGGAATAAAGT
1 TGTAATGGAATAAAGA
6068446 TGTAAT
1 TGTAAT
6068452 TAGTAATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAAAGA
Found at i:6071653 original size:25 final size:24
Alignment explanation
Indices: 6071588--6071722 Score: 113
Period size: 25 Copynumber: 5.6 Consensus size: 24
6071578 ACCTTAGCGC
* * * *
6071588 GCTCTCTGATTATTACCAAATCAAT
1 GCTCTCTG-TTATTAGCACATTAGT
6071613 GCTCTCTGATTATTAGCACATTAGT
1 GCTCTCTG-TTATTAGCACATTAGT
*
6071638 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTG-TTATTAGCACATTAGT
6071663 GCTCT-TCG--ATTAGCACATCTA-T
1 GCTCTCT-GTTATTAGCACAT-TAGT
6071685 GCTCTCTG-TA-TAGCAC-TTAAGT
1 GCTCTCTGTTATTAGCACATT-AGT
6071707 GCTCTCTGTTCATTAG
1 GCTCTCTGTT-ATTAG
6071723 TGCATAATAA
Statistics
Matches: 95, Mismatches: 6, Indels: 18
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 31 0.33
23 5 0.05
24 2 0.02
25 54 0.57
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTCTCTGTTATTAGCACATTAGT
Found at i:6071722 original size:47 final size:49
Alignment explanation
Indices: 6071612--6071722 Score: 114
Period size: 47 Copynumber: 2.3 Consensus size: 49
6071602 ACCAAATCAA
6071612 TGCTCTCTGATT-ATTAGCACATTAGTGCTCTCTGATTATTAGCACGTTAG
1 TGCTCTCTG-TTCATTAGCACATTAGTGCTCTCTGA-TATTAGCACGTTAG
6071662 TG--CTC--TTCGATTAGCACATCTA-TGCTCTCTG-TA-TAGCAC-TTAAG
1 TGCTCTCTGTTC-ATTAGCACAT-TAGTGCTCTCTGATATTAGCACGTT-AG
6071706 TGCTCTCTGTTCATTAG
1 TGCTCTCTGTTCATTAG
6071723 TGCATAATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 19
0.74 0.00 0.26
Matches are distributed among these distances:
43 2 0.04
44 10 0.19
45 4 0.08
46 3 0.06
47 24 0.45
48 8 0.15
50 2 0.04
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.40
Consensus pattern (49 bp):
TGCTCTCTGTTCATTAGCACATTAGTGCTCTCTGATATTAGCACGTTAG
Found at i:6076283 original size:30 final size:31
Alignment explanation
Indices: 6076239--6076315 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
6076229 ATCATATTTT
* * * *
6076239 TATAAATAATATATTAATTACACTATTAG-A
1 TATAATTAAAATATTAACTAAACTATTAGAA
* *
6076269 TATATTTAAAATATT-ACTAAATTATTAGAA
1 TATAATTAAAATATTAACTAAACTATTAGAA
*
6076299 TTTAATTAAAATATTAA
1 TATAATTAAAATATTAA
6076316 AAATTTATAG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 10 0.27
30 26 0.70
31 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.43
Consensus pattern (31 bp):
TATAATTAAAATATTAACTAAACTATTAGAA
Found at i:6076319 original size:29 final size:31
Alignment explanation
Indices: 6076274--6076338 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
6076264 TTAGATATAT
* *
6076274 TTAAAATATTACTAAA-TTATTAGA-ATTTAA
1 TTAAAATATTACAAAATTTA-TAGATATTAAA
6076304 TTAAAATATTA-AAAATTTATAGATATTAAA
1 TTAAAATATTACAAAATTTATAGATATTAAA
6076334 TTAAA
1 TTAAA
6076339 TTTATATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (31 bp):
TTAAAATATTACAAAATTTATAGATATTAAA
Found at i:6076407 original size:16 final size:16
Alignment explanation
Indices: 6076388--6076441 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
6076378 AATATTATTA
6076388 AATTATATTTAATAAT
1 AATTATATTTAATAAT
*
6076404 AATTATATTAAAATATGATT
1 AATTATATT-TAATA--A-T
6076424 AAATTATATTTAATAAT
1 -AATTATATTTAATAAT
6076441 A
1 A
6076442 GCACTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 10 0.32
17 5 0.16
18 1 0.03
19 1 0.03
20 5 0.16
21 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AATTATATTTAATAAT
Found at i:6076450 original size:37 final size:37
Alignment explanation
Indices: 6076378--6076454 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
6076368 AATAAAAATT
* **
6076378 AATATTATTAAATTATATTTAATAATAATTATATTAA
1 AATATGATTAAATTATATTTAATAATAAGCATATTAA
6076415 AATATGATTAAATTATATTTAATAAT-AGCACTATTAA
1 AATATGATTAAATTATATTTAATAATAAGCA-TATTAA
6076452 AAT
1 AAT
6076455 TTAATAACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 2 0.06
37 34 0.94
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (37 bp):
AATATGATTAAATTATATTTAATAATAAGCATATTAA
Found at i:6077075 original size:42 final size:43
Alignment explanation
Indices: 6076999--6077085 Score: 140
Period size: 42 Copynumber: 2.0 Consensus size: 43
6076989 CATTATGAGC
*
6076999 ATGGTAAATTCTAATATTATAAAATAAAATAATTATTTTAAAT
1 ATGGTAAAATCTAATATTATAAAATAAAATAATTATTTTAAAT
* *
6077042 ATGGTAAAATCTAATA-TATAAAATCAATTAATTATTTTAAAT
1 ATGGTAAAATCTAATATTATAAAATAAAATAATTATTTTAAAT
6077084 AT
1 AT
6077086 AATTATTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 26 0.63
43 15 0.37
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (43 bp):
ATGGTAAAATCTAATATTATAAAATAAAATAATTATTTTAAAT
Found at i:6090075 original size:21 final size:21
Alignment explanation
Indices: 6090049--6090089 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
6090039 CCAAGAGGTG
6090049 GTTGGCTACAAAACAGTTTTA
1 GTTGGCTACAAAACAGTTTTA
6090070 GTTGGCTACAAAACAGTTTT
1 GTTGGCTACAAAACAGTTTT
6090090 TCTTTTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (21 bp):
GTTGGCTACAAAACAGTTTTA
Found at i:6096451 original size:96 final size:95
Alignment explanation
Indices: 6096283--6096569 Score: 495
Period size: 96 Copynumber: 3.0 Consensus size: 95
6096273 ACTCTTGGGT
* *
6096283 GTTTTGTGGCAATAAACAAGATTGTGGGTCTCGA-TTTGGTGAGGTAAGCCAACATCTCTTTCTC
1 GTTTCGTGGCAATAAACAAGATTGTGGGTCTCGATTTTGGTGAGGTAAGCCAACATCTCTTGCTC
*
6096347 TCCTCTTTAACCGTCATTTATTCAATTCTAC
66 TCCTCTTTAACC-CCATTTATTCAATTCTAC
6096378 GTTTCGTGGCAATAAACAAGATTGTGGGTCTCGATTTTGGTGAGGTAAGCCAACATCTCTTGCTC
1 GTTTCGTGGCAATAAACAAGATTGTGGGTCTCGATTTTGGTGAGGTAAGCCAACATCTCTTGCTC
6096443 TCCTCTTTAACACCCATTTATTCAATTCTAC
66 TCCTCTTTAAC-CCCATTTATTCAATTCTAC
6096474 GTTTCGTGGCAATAAACAAGATTGTGGGTCTCGATTTTGGTGAGGTAAGCCAACATCTCTTGCTC
1 GTTTCGTGGCAATAAACAAGATTGTGGGTCTCGATTTTGGTGAGGTAAGCCAACATCTCTTGCTC
* *
6096539 TCCTCTTTAACCCCCATTTGTTTAATTCTAC
66 TCCTCTTTAA-CCCCATTTATTCAATTCTAC
6096570 TTTTTTTGAA
Statistics
Matches: 184, Mismatches: 5, Indels: 5
0.95 0.03 0.03
Matches are distributed among these distances:
95 33 0.18
96 149 0.81
97 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (95 bp):
GTTTCGTGGCAATAAACAAGATTGTGGGTCTCGATTTTGGTGAGGTAAGCCAACATCTCTTGCTC
TCCTCTTTAACCCCATTTATTCAATTCTAC
Found at i:6115657 original size:33 final size:33
Alignment explanation
Indices: 6115615--6115680 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
6115605 AAAAGATTGC
6115615 AACCAGATAATATCAATATCTGTTCCAATGATG
1 AACCAGATAATATCAATATCTGTTCCAATGATG
6115648 AACCAGATAATATCAATATCTGTTCCAATGATG
1 AACCAGATAATATCAATATCTGTTCCAATGATG
6115681 CATAAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (33 bp):
AACCAGATAATATCAATATCTGTTCCAATGATG
Found at i:6119033 original size:30 final size:31
Alignment explanation
Indices: 6118999--6119056 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
6118989 TTAACGATAA
* * *
6118999 TGATTAATTTAAATAATT-ATTTAATTAGAG
1 TGATTAAATTAAAAAATTAAATTAATTAGAG
6119029 TGATTAAATTAAAAAATTAAATTAATTA
1 TGATTAAATTAAAAAATTAAATTAATTA
6119057 AAATAAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (31 bp):
TGATTAAATTAAAAAATTAAATTAATTAGAG
Found at i:6121651 original size:3 final size:3
Alignment explanation
Indices: 6121643--6121668 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6121633 GAAAAACAAG
6121643 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6121669 AAGAGAGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6128710 original size:16 final size:16
Alignment explanation
Indices: 6128689--6128719 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6128679 ATGGTAATGT
6128689 TTTTTAATATAAATAC
1 TTTTTAATATAAATAC
6128705 TTTTTAATATAAATA
1 TTTTTAATATAAATA
6128720 ACATCAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTTAATATAAATAC
Found at i:6128911 original size:40 final size:39
Alignment explanation
Indices: 6128867--6128951 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 39
6128857 ATGTCAAGTC
* *
6128867 TTTTATTTTTAATTAATGT-TTTGATTATATTTTTAA-TTTT
1 TTTTATTTTTAAATAATGTATTT--TT-TATTTTTAACTCTT
6128907 TTTTATTTTTAAATAATGTATTTTTTATTTTTAACTCTT
1 TTTTATTTTTAAATAATGTATTTTTTATTTTTAACTCTT
6128946 TTTTAT
1 TTTTAT
6128952 AAAATCCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
38 9 0.22
39 11 0.27
40 18 0.44
41 3 0.07
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (39 bp):
TTTTATTTTTAAATAATGTATTTTTTATTTTTAACTCTT
Found at i:6132038 original size:51 final size:51
Alignment explanation
Indices: 6131961--6132149 Score: 213
Period size: 51 Copynumber: 3.7 Consensus size: 51
6131951 AATGTTATTC
* * * *
6131961 GGTACACATAGTAGGCTACACTTAGTACTACACATGTGACCAATACCATCT
1 GGTACATATAGTAGCCTACACATAGTACTACACATGTGACCAATACTATCT
* * *
6132012 GGTACATGTAGTAGCCTGCACATAGTACTACACATGTGACCAA-AGCTATCC
1 GGTACATATAGTAGCCTACACATAGTACTACACATGTGACCAATA-CTATCT
* * * *
6132063 GGTACACATAGTAGCCTGCACTTAGTACTACATATGTGACC-ATAACTATCT
1 GGTACATATAGTAGCCTACACATAGTACTACACATGTGACCAAT-ACTATCT
**
6132114 TATAC-TCATAGTAGCCTACACATAGTACTACACATG
1 GGTACAT-ATAGTAGCCTACACATAGTACTACACATG
6132150 AGTTCTCATG
Statistics
Matches: 116, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
50 2 0.02
51 113 0.97
52 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (51 bp):
GGTACATATAGTAGCCTACACATAGTACTACACATGTGACCAATACTATCT
Found at i:6132103 original size:102 final size:102
Alignment explanation
Indices: 6131960--6132149 Score: 276
Period size: 102 Copynumber: 1.9 Consensus size: 102
6131950 CAATGTTATT
* * *
6131960 CGGTACACATAGTAGGCTACACTTAGTACTACACATGTGACCA-ATACCATCTGGTACAT-GTAG
1 CGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCATA-ACCATCTGATAC-TCATAG
*
6132023 TAGCCTGCACATAGTACTACACATGTGACCAAAGCTATC
64 TAGCCTACACATAGTACTACACATGTGACCAAAGCTATC
* * * *
6132062 CGGTACACATAGTAGCCTGCACTTAGTACTACATATGTGACCATAACTATCTTATACTCATAGTA
1 CGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCATAACCATCTGATACTCATAGTA
6132127 GCCTACACATAGTACTACACATG
66 GCCTACACATAGTACTACACATG
6132150 AGTTCTCATG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 1 0.01
102 76 0.97
103 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (102 bp):
CGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCATAACCATCTGATACTCATAGTA
GCCTACACATAGTACTACACATGTGACCAAAGCTATC
Found at i:6134634 original size:50 final size:50
Alignment explanation
Indices: 6134559--6134660 Score: 141
Period size: 50 Copynumber: 2.0 Consensus size: 50
6134549 CATCATAACT
** * * **
6134559 TGTAAGTTACTGGTTAATCTGCATAGGGTAATGCTCATTATTTCTTATAA
1 TGTAAGTTACTGGTTAATCCACATAGGATAATACTCATTACATCTTATAA
*
6134609 TGTAAGTTACTGGTTAGTCCACATAGGATAATACTCATTACATCTTATAA
1 TGTAAGTTACTGGTTAATCCACATAGGATAATACTCATTACATCTTATAA
6134659 TG
1 TG
6134661 CACCATAACT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (50 bp):
TGTAAGTTACTGGTTAATCCACATAGGATAATACTCATTACATCTTATAA
Found at i:6135614 original size:20 final size:20
Alignment explanation
Indices: 6135589--6135656 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 20
6135579 CAAATTAAAG
**
6135589 GTATCGATAGTTATCAACTA
1 GTATCGATAGTTATCAAAAA
* *
6135609 GTATCGGTAGTTTATGAAAAA
1 GTATCGATAG-TTATCAAAAA
* *
6135630 GTATCGATACTTAT-ATAAA
1 GTATCGATAGTTATCAAAAA
6135649 -TATCGATA
1 GTATCGATA
6135657 TCATTTTGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 8 0.20
19 4 0.10
20 13 0.32
21 15 0.38
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (20 bp):
GTATCGATAGTTATCAAAAA
Found at i:6139583 original size:29 final size:30
Alignment explanation
Indices: 6139524--6139581 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6139514 TCCGAGCCTT
*
6139524 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
6139554 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
6139582 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:6139812 original size:13 final size:13
Alignment explanation
Indices: 6139794--6139824 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
6139784 TTCCAGCAAC
6139794 TATGAATTTATTT
1 TATGAATTTATTT
6139807 TATGAATTTATTT
1 TATGAATTTATTT
*
6139820 GATGA
1 TATGA
6139825 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:6139994 original size:50 final size:50
Alignment explanation
Indices: 6139919--6140161 Score: 387
Period size: 50 Copynumber: 4.8 Consensus size: 50
6139909 ATTTGGGTAA
6139919 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
6139969 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
6140019 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
6140069 AGAGGTCCCCCGTAAGACAATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
6140119 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
6140162 TGTTATTATC
Statistics
Matches: 176, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 143 0.81
51 33 0.19
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:6147582 original size:50 final size:50
Alignment explanation
Indices: 6147508--6147799 Score: 460
Period size: 50 Copynumber: 5.8 Consensus size: 50
6147498 ATTTGGGTAA
6147508 AGAGGTCCCAT-TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
6147557 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
6147607 AGAGGTCCCATGTAAGACCATGTCTGGAACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
6147657 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
6147707 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
6147757 AGAACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
6147800 TGTTATTATC
Statistics
Matches: 224, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
49 11 0.05
50 180 0.80
51 33 0.15
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:6150831 original size:21 final size:21
Alignment explanation
Indices: 6150796--6150867 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
6150786 GTTTAACTCA
* *
6150796 TATGAGTTTCAGTTCAACCCT
1 TATGGGTTTCCGTTCAACCCT
* * *
6150817 AATGGGTTTCCGTTCAGCTCT
1 TATGGGTTTCCGTTCAACCCT
* * *
6150838 TATGAGCTTCCGTTCAACCAT
1 TATGGGTTTCCGTTCAACCCT
6150859 TATGGGTTT
1 TATGGGTTT
6150868 TTATTTAGCA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (21 bp):
TATGGGTTTCCGTTCAACCCT
Found at i:6153319 original size:2 final size:2
Alignment explanation
Indices: 6153268--6153302 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6153258 TTTTATAAAC
6153268 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6153303 TCTTTAGCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.