Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 210 of 210
Found at i:62452824 original size:26 final size:25
Alignment explanation
Indices: 62452795--62452854 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
62452785 AATAAATAAG
* *
62452795 TAATAAATAATAGAATAATAATAAAA
1 TAATAAATAAAAAAATAA-AATAAAA
*
62452821 TAATAAAGGAAAAAAATAAAATAAAA
1 TAATAAA-TAAAAAAATAAAATAAAA
*
62452847 TAAAAAAT
1 TAATAAAT
62452855 GCACAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (25 bp):
TAATAAATAAAAAAATAAAATAAAA
Found at i:62453690 original size:16 final size:16
Alignment explanation
Indices: 62453669--62453709 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
62453659 GGTTACTTTA
*
62453669 CAGCTTGTGTGAGTAG
1 CAGCTTGTATGAGTAG
62453685 CAGCTTGTATGAGTAG
1 CAGCTTGTATGAGTAG
*
62453701 CACCTTGTA
1 CAGCTTGTA
62453710 GCTATGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (16 bp):
CAGCTTGTATGAGTAG
Found at i:62459760 original size:19 final size:20
Alignment explanation
Indices: 62459738--62459775 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
62459728 TAATTTTAAA
62459738 AAATAGATTTAAAA-AAATT
1 AAATAGATTTAAAATAAATT
**
62459757 AAATCTATTTAAAATAAAT
1 AAATAGATTTAAAATAAAT
62459776 GTCGAACTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (20 bp):
AAATAGATTTAAAATAAATT
Found at i:62468230 original size:14 final size:14
Alignment explanation
Indices: 62468211--62468238 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
62468201 AGTTGTTGGC
62468211 TGCTTAAAAAGGTT
1 TGCTTAAAAAGGTT
62468225 TGCTTAAAAAGGTT
1 TGCTTAAAAAGGTT
62468239 AAGTTCTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
TGCTTAAAAAGGTT
Found at i:62468850 original size:20 final size:20
Alignment explanation
Indices: 62468825--62468865 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
62468815 CTGGTTAATG
62468825 ACTAAAAATTATAAAATTGA
1 ACTAAAAATTATAAAATTGA
62468845 ACTAAAAATTATAAAATTGA
1 ACTAAAAATTATAAAATTGA
62468865 A
1 A
62468866 TAATTAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (20 bp):
ACTAAAAATTATAAAATTGA
Found at i:62469481 original size:22 final size:21
Alignment explanation
Indices: 62469453--62469511 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
62469443 TTTATTAAAA
62469453 TTTAAAAATATTATTTTATTT
1 TTTAAAAATATTATTTTATTT
* * *
62469474 ATTAAAAATGTTTTTTTATTT
1 TTTAAAAATATTATTTTATTT
62469495 TTATAAAAATATTATTT
1 TT-TAAAAATATTATTT
62469512 AAAATTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTAAAAATATTATTTTATTT
Found at i:62469519 original size:22 final size:22
Alignment explanation
Indices: 62469447--62469519 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 22
62469437 ATTATTTTTA
62469447 TTAAAA-TT-TAAAAATATTAT
1 TTAAAATTTATAAAAATATTAT
* * *
62469467 TT--TATTTATTAAAAATGTTTT
1 TTAAAATTTA-TAAAAATATTAT
* **
62469488 TTTATTTTTATAAAAATATTAT
1 TTAAAATTTATAAAAATATTAT
62469510 TTAAAATTTA
1 TTAAAATTTA
62469520 AACATTTCAT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.03
19 2 0.05
20 2 0.05
21 12 0.31
22 17 0.44
23 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (22 bp):
TTAAAATTTATAAAAATATTAT
Found at i:62470699 original size:14 final size:14
Alignment explanation
Indices: 62470658--62470704 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 14
62470648 AAGTGGTATT
62470658 ATTTATAAAAAATAA
1 ATTTA-AAAAAATAA
62470673 TATTTTAATAAAAATAA
1 -A-TTTAA-AAAAATAA
62470690 ATTTAAAAAAATAA
1 ATTTAAAAAAATAA
62470704 A
1 A
62470705 AAAGTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.31
15 5 0.17
16 3 0.10
17 12 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTTAAAAAAATAA
Found at i:62478951 original size:20 final size:19
Alignment explanation
Indices: 62478912--62478964 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
62478902 TATCCTTAAA
* *
62478912 TTACACTTTCA-TTATCAT
1 TTACACTTTTATTTTTCAT
*
62478930 TTACATTATTTATTTTTCAT
1 TTACACT-TTTATTTTTCAT
62478950 TTACACTTTTATTTT
1 TTACACTTTTATTTT
62478965 ATTTCACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 6 0.21
19 11 0.38
20 12 0.41
ACGTcount: A:0.25, C:0.15, G:0.00, T:0.60
Consensus pattern (19 bp):
TTACACTTTTATTTTTCAT
Found at i:62479494 original size:22 final size:24
Alignment explanation
Indices: 62479466--62479509 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
62479456 GGTAACATTA
62479466 TAAAAAT-ATA-GTTTTAAATTTT
1 TAAAAATAATATGTTTTAAATTTT
*
62479488 TAAAAATAATATTTTTTAAATT
1 TAAAAATAATATGTTTTAAATT
62479510 CATTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TAAAAATAATATGTTTTAAATTTT
Found at i:62479569 original size:21 final size:23
Alignment explanation
Indices: 62479528--62479570 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
62479518 TTTGAAAAAT
*
62479528 AAAAATATAATATATATTTTTTG
1 AAAAATAGAATATATATTTTTTG
62479551 AAAAATAGAAT-TA-ATTTTTT
1 AAAAATAGAATATATATTTTTT
62479571 TGTTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
AAAAATAGAATATATATTTTTTG
Found at i:62486664 original size:18 final size:16
Alignment explanation
Indices: 62486631--62486669 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
62486621 TATATTTTTG
62486631 AATTTATATAACTATT
1 AATTTATATAACTATT
*
62486647 TATTTATATATACATATT
1 AATTTATATA-AC-TATT
62486665 AATTT
1 AATTT
62486670 TTAGGTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 9 0.47
17 2 0.11
18 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTTATATAACTATT
Found at i:62491991 original size:30 final size:30
Alignment explanation
Indices: 62491955--62492011 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
62491945 AGATTGATGT
* *
62491955 TTGAAAATAACATAGTGCATAATTAGCTGC
1 TTGAAAACAACATAGAGCATAATTAGCTGC
62491985 TTGAAAACAACATAGAGCATAATTAGC
1 TTGAAAACAACATAGAGCATAATTAGC
62492012 CTATGGTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (30 bp):
TTGAAAACAACATAGAGCATAATTAGCTGC
Found at i:62496935 original size:16 final size:16
Alignment explanation
Indices: 62496914--62496983 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
62496904 TTTGGTTCGC
* *
62496914 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
62496930 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
62496946 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
62496962 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
62496978 TGTAAT
1 TGTAAT
62496984 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:62497067 original size:39 final size:43
Alignment explanation
Indices: 62496962--62497071 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
62496952 GGAATAGAGG
62496962 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
62497007 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
62497047 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
62497072 TAATGAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:62497234 original size:16 final size:16
Alignment explanation
Indices: 62497197--62497238 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
62497187 TTAATCATAT
*
62497197 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
62497213 TT-AAATATATTATAA
1 TTAAAATATATTATAA
62497228 TTAAAATATAT
1 TTAAAATATAT
62497239 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:62497245 original size:14 final size:15
Alignment explanation
Indices: 62497206--62497247 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
62497196 TTTAAACATA
*
62497206 ATTATTATTAAATAT
1 ATTATAATTAAATAT
62497221 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
62497235 A-TATAATTTAATA
1 ATTATAATTAAATA
62497248 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:62497316 original size:39 final size:39
Alignment explanation
Indices: 62497272--62497436 Score: 97
Period size: 41 Copynumber: 4.2 Consensus size: 39
62497262 CAATATTCTT
*
62497272 ATATAAATTTACTCAAATCATAATATATGATACTATAAA
1 ATATAAATTTACTCAAATCATAATATATGATAATATAAA
* * * *
62497311 ATATAAATTAACAT-AATTATTATTATATATTATAAT-TAAA
1 ATATAAATTTAC-TCAA--ATCATAATATATGATAATATAAA
* * * ***
62497351 ATATATAATTTAATAAAATTCTTTTAATA-AT--TAATATTCTT
1 ATATA-AATTTACTCAAA-TC--ATAATATATGATAATA-TAAA
* *
62497392 ATATGAATTTACTCAAATCATAATATATGATACTATAAA
1 ATATAAATTTACTCAAATCATAATATATGATAATATAAA
*
62497431 AGATAA
1 ATATAA
62497437 TTTGAAATAA
Statistics
Matches: 90, Mismatches: 23, Indels: 26
0.65 0.17 0.19
Matches are distributed among these distances:
37 5 0.06
38 2 0.02
39 25 0.28
40 26 0.29
41 28 0.31
42 4 0.04
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (39 bp):
ATATAAATTTACTCAAATCATAATATATGATAATATAAA
Found at i:62497367 original size:57 final size:56
Alignment explanation
Indices: 62497200--62497369 Score: 148
Period size: 61 Copynumber: 2.9 Consensus size: 56
62497190 ATCATATTTA
* *
62497200 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATT--ATATATTATAATTAAAATATATAATTTAATAAAA-TATAAAT
* * * * * *
62497259 AATCA-ATATTCTTA-TATAAATTTACTCAAATCATAATATATGATACT-ATAAAATATAAATT
1 AA-CATA-ATTATTATTATATA-TTA-T--AATTAAAATATATAAT-TTAATAAAATATAAA-T
62497320 AACATAATTATTATTATATATTATAATTAAAATATATAATTTAATAAAAT
1 AACATAATTATTATTATATATTATAATTAAAATATATAATTTAATAAAAT
62497370 TCTTTTAATA
Statistics
Matches: 86, Mismatches: 14, Indels: 24
0.69 0.11 0.19
Matches are distributed among these distances:
56 1 0.01
57 24 0.28
58 3 0.03
59 6 0.07
60 23 0.27
61 28 0.33
62 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (56 bp):
AACATAATTATTATTATATATTATAATTAAAATATATAATTTAATAAAATATAAAT
Found at i:62497392 original size:120 final size:120
Alignment explanation
Indices: 62497200--62497492 Score: 466
Period size: 120 Copynumber: 2.4 Consensus size: 120
62497190 ATCATATTTA
62497200 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATT-AATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
62497265 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT-
65 TATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
*
62497320 AACATAATTATTATT-ATATATTATAATTAAAATATATAATTTAATAAAATTCTTTTAATAATTA
1 AACATAATTATTATTAATATATTATAATTAAAATATATAATTTAATAAAATTC--TTAATAATCA
* *
62497384 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
64 ATATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* * *
62497441 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATT-AATATATTATAATTAAAATATATAATTTAATAAAATT
62497493 TAAAATAATT
Statistics
Matches: 161, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
118 37 0.23
120 88 0.55
121 2 0.01
122 34 0.21
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAAT
ATTCTTATATAAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:62497394 original size:57 final size:55
Alignment explanation
Indices: 62497217--62497395 Score: 155
Period size: 57 Copynumber: 3.1 Consensus size: 55
62497207 TTATTATTAA
*
62497217 ATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCTT
1 ATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTT
* * * * * * * *
62497272 ATATAAATTTACTCAAATCATAATATATGATACT-ATAAAA-TATAAATTAACATAATTATTATT
1 ATAT--A-TTA-T--AATTAAAATATATAAT-TTAATAAAATTCTTAA-TAA-TTAA-TATTCTT
62497335 ATATATTATAATTAAAATATATAATTTAATAAAATTCTTTTAATAATTAATATTCTT
1 ATATATTATAATTAAAATATATAATTTAATAAAATTC--TTAATAATTAATATTCTT
62497392 ATAT
1 ATAT
62497396 GAATTTACTC
Statistics
Matches: 93, Mismatches: 17, Indels: 26
0.68 0.12 0.19
Matches are distributed among these distances:
55 4 0.04
56 1 0.01
57 30 0.32
58 7 0.08
59 5 0.05
60 10 0.11
61 23 0.25
62 3 0.03
63 10 0.11
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.45
Consensus pattern (55 bp):
ATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTT
Found at i:62497540 original size:47 final size:46
Alignment explanation
Indices: 62497474--62497640 Score: 146
Period size: 47 Copynumber: 3.6 Consensus size: 46
62497464 TTAATTAAAA
*
62497474 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTATCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTATCT
* * * * * *
62497521 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
* * * *
62497566 TA-AT-AATAATATATAATTTCATAA-AATTCTTAATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTATCT
*
62497612 TATATGAATTTATACAATTTAAAATAATT
1 TATATGAATTTATATAATTTAAAATAATT
62497641 CGGATCAATC
Statistics
Matches: 92, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
43 3 0.03
44 15 0.16
45 14 0.15
46 13 0.14
47 40 0.43
48 7 0.08
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTATCT
Found at i:62497562 original size:26 final size:28
Alignment explanation
Indices: 62497533--62497604 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
62497523 TATGAATTTG
*
62497533 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
62497559 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
62497587 TAAAATTCTTAATAATAA
1 TATAA-T-TTAATAATAA
62497605 ATTTTCTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 10 0.26
27 6 0.15
28 12 0.31
29 1 0.03
30 10 0.26
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:62497800 original size:22 final size:22
Alignment explanation
Indices: 62497772--62497816 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
62497762 ACTAAGCTTG
62497772 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
62497794 AATTTCATTAAATTACTTTCAA
1 AATTTCATTAAATTACTTTCAA
62497816 A
1 A
62497817 GTTAAGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTCATTAAATTACTTTCAA
Found at i:62500450 original size:5 final size:5
Alignment explanation
Indices: 62500440--62500470 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
62500430 TTGCTTGAAA
62500440 ATAAT ATAAT ATAAT ATAAT ATAAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT
62500471 TTGAGACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:62504759 original size:12 final size:12
Alignment explanation
Indices: 62504742--62504766 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62504732 AGAAAGTAAC
62504742 AAATATATAATT
1 AAATATATAATT
62504754 AAATATATAATT
1 AAATATATAATT
62504766 A
1 A
62504767 GTTAACTAAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATATAATT
Found at i:62511429 original size:3 final size:3
Alignment explanation
Indices: 62511421--62511480 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
62511411 ATACCTTATG
62511421 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62511469 AAT AAT AAT AAT
1 AAT AAT AAT AAT
62511481 GACAAACACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:62511857 original size:5 final size:5
Alignment explanation
Indices: 62511847--62511877 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
62511837 TTGCTTGAAA
62511847 ATAAT ATAAT ATAAT ATAAT ATAAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT
62511878 TTGAGCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:62512803 original size:21 final size:20
Alignment explanation
Indices: 62512765--62512804 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
62512755 ACTTTTATTT
62512765 AAATATAATATAAAAATATA
1 AAATATAATATAAAAATATA
* *
62512785 AAATATTATCATAATAATAT
1 AAATATAAT-ATAAAAATAT
62512805 TAATTATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATAATATAAAAATATA
Found at i:62525648 original size:30 final size:30
Alignment explanation
Indices: 62525612--62525668 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
62525602 AGATTGATGT
* *
62525612 TTGAAAATAACAGAGTGCATAATTAGCTGC
1 TTGAAAACAACAGAGAGCATAATTAGCTGC
*
62525642 TTGAAAACAACATAGAGCATAATTAGC
1 TTGAAAACAACAGAGAGCATAATTAGC
62525669 CTATGGTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.25
Consensus pattern (30 bp):
TTGAAAACAACAGAGAGCATAATTAGCTGC
Found at i:62530545 original size:1 final size:1
Alignment explanation
Indices: 62530539--62530564 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
62530529 AACTGACTTG
62530539 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
62530565 GTATCTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:62535362 original size:5 final size:5
Alignment explanation
Indices: 62535352--62535382 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
62535342 TTGCTTGAAA
62535352 ATAAT ATAAT ATAAT ATAAT ATAAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT
62535383 TTGAGACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:62535480 original size:29 final size:30
Alignment explanation
Indices: 62535411--62535482 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 30
62535401 TATTTGAAAA
62535411 GTTTTATTTGAGCACTTTCAAAAAAGTTTTG
1 GTTTTATTTGAGCACTTT-AAAAAAGTTTTG
**
62535442 GAACTTATTTGAGCACTTT-AAAAAG-TTTG
1 G-TTTTATTTGAGCACTTTAAAAAAGTTTTG
62535471 GTTTTCATTTGA
1 GTTTT-ATTTGA
62535483 ACATTTTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 2 0.06
29 11 0.31
30 6 0.17
31 1 0.03
32 15 0.43
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (30 bp):
GTTTTATTTGAGCACTTTAAAAAAGTTTTG
Found at i:62541599 original size:20 final size:19
Alignment explanation
Indices: 62541562--62541609 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
62541552 AGAAAGCTCG
*
62541562 ATACCCTTAAAAAGTATCA
1 ATACCCTTAAAAAATATCA
*
62541581 ATACCCTTCAAAAAATATCG
1 ATACCCTT-AAAAAATATCA
62541601 ATACCCTTA
1 ATACCCTTA
62541610 CTTGATATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.27
Consensus pattern (19 bp):
ATACCCTTAAAAAATATCA
Found at i:62542106 original size:35 final size:34
Alignment explanation
Indices: 62542029--62542106 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 34
62542019 ATAAACACAA
**
62542029 AAATATTTTAAAAATAAAAAAAATAAAAAAATTT
1 AAATATTTTAAAAATAAAAAAAATAAAAAAAAAT
*
62542063 AAAGTATTTTAAAATTAAAAAATAA-AAATAAAAAAT
1 AAA-TATTTTAAAAATAAAAAA-AATAAA-AAAAAAT
*
62542099 ATATATTT
1 AAATATTT
62542107 ATTATATTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 3 0.08
35 25 0.68
36 9 0.24
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (34 bp):
AAATATTTTAAAAATAAAAAAAATAAAAAAAAAT
Found at i:62546533 original size:118 final size:118
Alignment explanation
Indices: 62546391--62546604 Score: 419
Period size: 118 Copynumber: 1.8 Consensus size: 118
62546381 TTTTGTCAAA
*
62546391 TTACCAAAAACTTAAGTTTTAAAAGTCAAAACATAAGAAATCATCACAATCTGCACAGATTTTCT
1 TTACCAAAAACTTAAGTTTCAAAAGTCAAAACATAAGAAATCATCACAATCTGCACAGATTTTCT
62546456 GGGTTAACAGTTTTGACTAGCCTACTTTGGGAAACTTGTTTTGTCAAAATCAG
66 GGGTTAACAGTTTTGACTAGCCTACTTTGGGAAACTTGTTTTGTCAAAATCAG
62546509 TTACCAAAAACTTAAGTTTCAAAAGTCAAAACATAAGAAATCATCACAATCTGCACAGATTTTCT
1 TTACCAAAAACTTAAGTTTCAAAAGTCAAAACATAAGAAATCATCACAATCTGCACAGATTTTCT
62546574 GGGTTAACAGTTTTGACTAGCCTACTTTGGG
66 GGGTTAACAGTTTTGACTAGCCTACTTTGGG
62546605 GCCTCATATG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 95 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (118 bp):
TTACCAAAAACTTAAGTTTCAAAAGTCAAAACATAAGAAATCATCACAATCTGCACAGATTTTCT
GGGTTAACAGTTTTGACTAGCCTACTTTGGGAAACTTGTTTTGTCAAAATCAG
Found at i:62550904 original size:9 final size:9
Alignment explanation
Indices: 62550892--62551013 Score: 70
Period size: 9 Copynumber: 13.0 Consensus size: 9
62550882 TTTATGATTT
62550892 TTTTTATAA
1 TTTTTATAA
62550901 TTTTTATAA
1 TTTTTATAA
*
62550910 TTTATATAA
1 TTTTTATAA
* *
62550919 -GTATATAA
1 TTTTTATAA
62550927 TATTTTCA-ATA
1 T-TTTT-ATA-A
*
62550938 TTTTTAGAA
1 TTTTTATAA
*
62550947 TTTTT-TGAG
1 TTTTTAT-AA
*
62550956 TTTTAATAA
1 TTTTTATAA
*
62550965 TATTTATAA
1 TTTTTATAA
62550974 GTTTTTTATGAA
1 --TTTTTAT-AA
62550986 TTATTTATAA
1 TT-TTTATAA
* *
62550996 GTTTTATAT
1 TTTTTATAA
62551005 TTTTTATAA
1 TTTTTATAA
62551014 GTTTCCTTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
8 7 0.08
9 50 0.57
10 14 0.16
11 14 0.16
12 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:62551011 original size:22 final size:22
Alignment explanation
Indices: 62550954--62551004 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
62550944 GAATTTTTTG
62550954 AGTTTTA-AT-AA-TATTTATA
1 AGTTTTATATGAATTATTTATA
*
62550973 AGTTTTTTATGAATTATTTATA
1 AGTTTTATATGAATTATTTATA
62550995 AGTTTTATAT
1 AGTTTTATAT
62551005 TTTTTATAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 6 0.22
20 2 0.07
21 2 0.07
22 17 0.63
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (22 bp):
AGTTTTATATGAATTATTTATA
Found at i:62551012 original size:18 final size:18
Alignment explanation
Indices: 62550876--62551017 Score: 63
Period size: 18 Copynumber: 7.4 Consensus size: 18
62550866 TTAATATTTA
62550876 ATAAGTTTTATGATTTTTTTT
1 ATAAGTTTTAT-A--TTTTTT
* * *
62550897 ATAATTTTTATAATTTAT
1 ATAAGTTTTATATTTTTT
* **
62550915 ATAAGTATATAATATTTTCA
1 ATAAGT-T-TTATATTTTTT
* * *
62550935 AT-ATTTTTAGAATTTTT
1 ATAAGTTTTATATTTTTT
* * *
62550952 -TGAGTTTTAATAATATTT
1 ATAAGTTTT-ATATTTTTT
*
62550970 ATAAGTTTTTTATGAATTATTT
1 ATAAG--TTTTAT--ATTTTTT
62550992 ATAAGTTTTATATTTTTT
1 ATAAGTTTTATATTTTTT
62551010 ATAAGTTT
1 ATAAGTTT
62551018 CCTTAAAAAT
Statistics
Matches: 92, Mismatches: 20, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
16 1 0.01
17 11 0.12
18 31 0.34
19 6 0.07
20 18 0.20
21 14 0.15
22 11 0.12
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (18 bp):
ATAAGTTTTATATTTTTT
Found at i:62551016 original size:40 final size:38
Alignment explanation
Indices: 62550938--62551017 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 38
62550928 ATTTTCAATA
*
62550938 TTTTTAGAATTTTTTGAGTTTTAATAATATTTATAAGT
1 TTTTTAGAATTTTTTAAGTTTTAATAATATTTATAAGT
* *
62550976 TTTTTATGAATTATTTATAAGTTTT-ATATTTTTTATAAGT
1 TTTTTA-GAATT-TTT-TAAGTTTTAATAATATTTATAAGT
62551016 TT
1 TT
62551018 CCTTAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 6 0.17
39 5 0.14
40 18 0.50
41 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (38 bp):
TTTTTAGAATTTTTTAAGTTTTAATAATATTTATAAGT
Found at i:62558328 original size:33 final size:33
Alignment explanation
Indices: 62558290--62558355 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
62558280 CTAATTATAA
*
62558290 AATTTA-ATGATTATATTTAAATATTTA-AAATAT
1 AATTTATAT-ATTATAATTAAAT-TTTATAAATAT
*
62558323 AATTTATATATTCTAATTAAATTTTATAAATAT
1 AATTTATATATTATAATTAAATTTTATAAATAT
62558356 TTATATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 4 0.14
33 23 0.79
34 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (33 bp):
AATTTATATATTATAATTAAATTTTATAAATAT
Found at i:62562544 original size:10 final size:10
Alignment explanation
Indices: 62562529--62562586 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
62562519 CTAAAGAAAC
62562529 TTTAAAAATA
1 TTTAAAAATA
62562539 TTTAAAAAT-
1 TTTAAAAATA
*
62562548 TATAAAAA-A
1 TTTAAAAATA
**
62562557 TACAAAAAATA
1 T-TTAAAAATA
*
62562568 TTTAAAATTA
1 TTTAAAAATA
62562578 -TTAAAAATA
1 TTTAAAAATA
62562587 GAAAAATTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
9 16 0.42
10 20 0.53
11 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:62562574 original size:28 final size:29
Alignment explanation
Indices: 62562532--62562592 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
62562522 AAGAAACTTT
62562532 AAAAATATTTAAAAATTATAAAAAATACA
1 AAAAATATTTAAAAATTATAAAAAATACA
* *
62562561 AAAAATATTT-AAAATTATTAAAAATAGA
1 AAAAATATTTAAAAATTATAAAAAATACA
62562589 AAAA
1 AAAA
62562593 TTATACAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (29 bp):
AAAAATATTTAAAAATTATAAAAAATACA
Found at i:62562975 original size:21 final size:22
Alignment explanation
Indices: 62562935--62562975 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
62562925 GTAATTTTAT
62562935 ATTTTTTTAGTTTTGTAATTTC
1 ATTTTTTTAGTTTTGTAATTTC
62562957 ATTTTTTCTA-TTTT-TAATT
1 ATTTTTT-TAGTTTTGTAATT
62562976 ATTTTTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 11 0.61
23 2 0.11
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (22 bp):
ATTTTTTTAGTTTTGTAATTTC
Found at i:62562982 original size:33 final size:33
Alignment explanation
Indices: 62562928--62563014 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 33
62562918 AATTTTAGTA
* *
62562928 ATTTTATATTTTT--TTAGTTTTGTAATTTCAT
1 ATTTTTTATTTTTAATTATTTTTGTAATTTCAT
*
62562959 -TTTTTCTATTTTTAATTATTTTTGTAATTTTAT
1 ATTTTT-TATTTTTAATTATTTTTGTAATTTCAT
62562992 ATTTTTTCATTTTTTAA-TATTTT
1 ATTTTTT-A-TTTTTAATTATTTT
62563015 AAAAGTTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
30 4 0.09
31 7 0.15
33 17 0.36
34 12 0.26
35 7 0.15
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.71
Consensus pattern (33 bp):
ATTTTTTATTTTTAATTATTTTTGTAATTTCAT
Found at i:62562996 original size:16 final size:16
Alignment explanation
Indices: 62562945--62562997 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
62562935 ATTTTTTTAG
*
62562945 TTTTGTAATTTCAT-T
1 TTTTGTAATTTTATAT
* *
62562960 TTTTCTATTTTTAATTAT
1 TTTTGTAATTTT-A-TAT
62562978 TTTTGTAATTTTATAT
1 TTTTGTAATTTTATAT
62562994 TTTT
1 TTTT
62562998 TCATTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 9 0.30
16 8 0.27
17 2 0.07
18 11 0.37
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (16 bp):
TTTTGTAATTTTATAT
Found at i:62563011 original size:18 final size:18
Alignment explanation
Indices: 62562957--62563014 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
62562947 TTGTAATTTC
62562957 ATTTTTTC-TATTTTTAATT
1 ATTTTTTCAT-TTTTTAA-T
*
62562976 ATTTTTGT-A-ATTTT-AT
1 ATTTTT-TCATTTTTTAAT
62562992 ATTTTTTCATTTTTTAAT
1 ATTTTTTCATTTTTTAAT
62563010 ATTTT
1 ATTTT
62563015 AAAAGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
15 1 0.03
16 8 0.25
17 5 0.16
18 11 0.34
19 6 0.19
20 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTTCATTTTTTAAT
Found at i:62566015 original size:42 final size:42
Alignment explanation
Indices: 62565963--62566060 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
62565953 GCATAATAAT
*
62565963 AACAAGATAACACTGTTGTGCAAGTGTAACCAGTAAATTAAC
1 AACAAAATAACACTGTTGTGCAAGTGTAACCAGTAAATTAAC
* *
62566005 AACAAAATAACACTGTTGTGTAAGTGTAACCAGTAAATTAAT
1 AACAAAATAACACTGTTGTGCAAGTGTAACCAGTAAATTAAC
62566047 AACAAAATAACACT
1 AACAAAATAACACT
62566061 TCTATTGGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.24
Consensus pattern (42 bp):
AACAAAATAACACTGTTGTGCAAGTGTAACCAGTAAATTAAC
Found at i:62568513 original size:128 final size:128
Alignment explanation
Indices: 62568283--62568539 Score: 487
Period size: 128 Copynumber: 2.0 Consensus size: 128
62568273 TTAGTTTAAT
62568283 TGACATTGTTGTAATATATAGCATAACCGAAATTTTAATGGGGTTAAATGACAATCCCAACTTAT
1 TGACATTGTTGTAATATATAGCATAACCGAAATTTTAATGGGGTTAAATGACAATCCCAACTTAT
*
62568348 GGTGCCTTTAAACTTAATACTAATGGATGATCGCTTGGTTATCCCAACATCAAAGATGTTGAG
66 GGTGCCTTTAAACTTAATACTAATGGATGATCACTTGGTTATCCCAACATCAAAGATGTTGAG
* *
62568411 TGACATTGTTGTAATATATAGCATAACCGAAATTTTAATGGGGTTAAATGGCAATCCCAATTTAT
1 TGACATTGTTGTAATATATAGCATAACCGAAATTTTAATGGGGTTAAATGACAATCCCAACTTAT
62568476 GGTGCCTTTAAACTTAATACTAATGGATGATCACTTGGTTATCCCAACATCAAAGATGTTGAG
66 GGTGCCTTTAAACTTAATACTAATGGATGATCACTTGGTTATCCCAACATCAAAGATGTTGAG
62568539 T
1 T
62568540 CTAGCATTAA
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 126 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (128 bp):
TGACATTGTTGTAATATATAGCATAACCGAAATTTTAATGGGGTTAAATGACAATCCCAACTTAT
GGTGCCTTTAAACTTAATACTAATGGATGATCACTTGGTTATCCCAACATCAAAGATGTTGAG
Found at i:62571103 original size:6 final size:6
Alignment explanation
Indices: 62571092--62571126 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
62571082 AGAGTTAAAC
62571092 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
62571127 GTTGAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:62576967 original size:50 final size:51
Alignment explanation
Indices: 62576913--62577017 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 51
62576903 GAAACAAGTA
*
62576913 TTTTAGCGTCTGTGTTGAGTTATTTGGGCTAATGGCAAATGCATTTGGA-T
1 TTTTAGCGTCTGTGTTGAGTTATTTGAGCTAATGGCAAATGCATTTGGAGT
62576963 TTTTAGCGTCTGTGTTGAGTTATTTGAGCTAATGGCAAATGCATTTGGAGT
1 TTTTAGCGTCTGTGTTGAGTTATTTGAGCTAATGGCAAATGCATTTGGAGT
62577014 TTTT
1 TTTT
62577018 TGATAGGGAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 48 0.91
51 5 0.09
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.44
Consensus pattern (51 bp):
TTTTAGCGTCTGTGTTGAGTTATTTGAGCTAATGGCAAATGCATTTGGAGT
Found at i:62584413 original size:5 final size:5
Alignment explanation
Indices: 62584403--62584427 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62584393 TATTAGAAAT
62584403 AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA
62584428 GAATAGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:62585781 original size:14 final size:15
Alignment explanation
Indices: 62585756--62585784 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
62585746 AACAATCGAC
62585756 AGAACAAAAAGAAAA
1 AGAACAAAAAGAAAA
62585771 AGAAC-AAAAGAAAA
1 AGAACAAAAAGAAAA
62585785 GAGCTAAATA
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:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (15 bp):
AGAACAAAAAGAAAA
Found at i:62587228 original size:2 final size:2
Alignment explanation
Indices: 62587221--62587249 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
62587211 TCAAGATTAG
62587221 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 A
62587250 AGTANNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62597019 original size:5 final size:5
Alignment explanation
Indices: 62597009--62597046 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
62596999 ACCAGAACCA
62597009 GACAT GACAT GACAT GACAT GACAT GACAT GACAT GAC
1 GACAT GACAT GACAT GACAT GACAT GACAT GACAT GAC
62597047 TCGGATCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (5 bp):
GACAT
Found at i:62607093 original size:30 final size:30
Alignment explanation
Indices: 62607057--62607117 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
62607047 ATTTACATCG
62607057 AATAAATTATCCGTTTAATATGATATATGA
1 AATAAATTATCCGTTTAATATGATATATGA
62607087 AATAAATTATCCGTTTAATATGATATATGA
1 AATAAATTATCCGTTTAATATGATATATGA
62607117 A
1 A
62607118 TGGTGATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (30 bp):
AATAAATTATCCGTTTAATATGATATATGA
Found at i:62613652 original size:2 final size:2
Alignment explanation
Indices: 62613645--62613669 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62613635 TACATGCACG
62613645 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
62613670 TCTTTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:62619049 original size:50 final size:51
Alignment explanation
Indices: 62618995--62619096 Score: 161
Period size: 50 Copynumber: 2.0 Consensus size: 51
62618985 TAAATTTCGC
* * *
62618995 TGCATGCATCTGTAAGTGAAATGTG-TATGTATATATTCTTTTGGTATATT
1 TGCATGCATCTGTAAGTGAAATGTGATATATATATATTATTTTGATATATT
62619045 TGCATGCATCTGTAAGTGAAATGTGCATATATATATATTATTTTGATATATT
1 TGCATGCATCTGTAAGTGAAATGTG-ATATATATATATTATTTTGATATATT
62619097 CTTTCTTTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 25 0.53
52 22 0.47
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (51 bp):
TGCATGCATCTGTAAGTGAAATGTGATATATATATATTATTTTGATATATT
Found at i:62628192 original size:2 final size:2
Alignment explanation
Indices: 62628185--62628217 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
62628175 AGTCTTGTAT
62628185 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 T
62628218 CACNNNNNNN
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:62647302 original size:78 final size:78
Alignment explanation
Indices: 62647173--62647321 Score: 244
Period size: 78 Copynumber: 1.9 Consensus size: 78
62647163 CTCATATTCT
* * *
62647173 ACCATTAAACCATGATCCCTTGATCTTACCAGCTGGGAGAGTCGGTGATCATGTTGATAATGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
62647238 ACCATGCAGTTCG
66 ACCATGCAGTTCG
* * *
62647251 ACCATTAAACCATGATCCCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
62647316 ACCATG
66 ACCATG
62647322 GACTTTGTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (78 bp):
ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
ACCATGCAGTTCG
Found at i:62650840 original size:21 final size:21
Alignment explanation
Indices: 62650814--62650863 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
62650804 ATATCCCGTC
62650814 CCGGTTCAGCAGTTTTGGTGG
1 CCGGTTCAGCAGTTTTGGTGG
62650835 CCGGTTCAGCAGTTTTGGTGG
1 CCGGTTCAGCAGTTTTGGTGG
62650856 CCGGTTCA
1 CCGGTTCA
62650864 ATTTTTAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.10, C:0.22, G:0.36, T:0.32
Consensus pattern (21 bp):
CCGGTTCAGCAGTTTTGGTGG
Found at i:62650950 original size:31 final size:31
Alignment explanation
Indices: 62650912--62650976 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
62650902 ATTCCAGTCA
* *
62650912 GGGATATCCTATTCTAGGGATATCCCGCCTT
1 GGGATATCCCATTATAGGGATATCCCGCCTT
*
62650943 GGGATATCCCATTATAGGGATATCCCGGCTT
1 GGGATATCCCATTATAGGGATATCCCGCCTT
62650974 GGG
1 GGG
62650977 GTCTAGGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (31 bp):
GGGATATCCCATTATAGGGATATCCCGCCTT
Found at i:62650968 original size:16 final size:15
Alignment explanation
Indices: 62650911--62650968 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
62650901 TATTCCAGTC
*
62650911 AGGGATATCCTATTCT
1 AGGGATATCCCATT-T
**
62650927 AGGGATATCCCGCCTT
1 AGGGATATCCC-ATTT
62650943 -GGGATATCCCATTAT
1 AGGGATATCCCATT-T
62650958 AGGGATATCCC
1 AGGGATATCCC
62650969 GGCTTGGGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 1 0.03
15 11 0.32
16 21 0.62
17 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (15 bp):
AGGGATATCCCATTT
Found at i:62654084 original size:20 final size:19
Alignment explanation
Indices: 62654059--62654103 Score: 81
Period size: 19 Copynumber: 2.3 Consensus size: 19
62654049 AAATTTCAGT
62654059 TTTTTTTTTTGCTGTTTCTA
1 TTTTTTTTTT-CTGTTTCTA
62654079 TTTTTTTTTTCTGTTTCTA
1 TTTTTTTTTTCTGTTTCTA
62654098 TTTTTT
1 TTTTTT
62654104 GTAATTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.04, C:0.09, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTTTTTTCTGTTTCTA
Found at i:62660185 original size:55 final size:56
Alignment explanation
Indices: 62660090--62660195 Score: 205
Period size: 55 Copynumber: 1.9 Consensus size: 56
62660080 AGAGAAAATG
62660090 ACACTTTCTTTTATTGGTTTTTTTCATAAAGATTACAAATGAAAACATTTTCAGGT
1 ACACTTTCTTTTATTGGTTTTTTTCATAAAGATTACAAATGAAAACATTTTCAGGT
62660146 ACACTTTCTTTTATTGG-TTTTTTCATAAAGATTACAAATGAAAACATTTT
1 ACACTTTCTTTTATTGGTTTTTTTCATAAAGATTACAAATGAAAACATTTT
62660196 AATAAATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 33 0.66
56 17 0.34
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (56 bp):
ACACTTTCTTTTATTGGTTTTTTTCATAAAGATTACAAATGAAAACATTTTCAGGT
Found at i:62667856 original size:21 final size:22
Alignment explanation
Indices: 62667830--62667877 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
62667820 TTTCTCTTTA
*
62667830 GGTTTTAGGTTTCCGG-TTAGG
1 GGTTTTAGGTTCCCGGATTAGG
*
62667851 GGTTTTAGGTTCCCGGATTGGG
1 GGTTTTAGGTTCCCGGATTAGG
62667873 GGTTT
1 GGTTT
62667878 GGGGGTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.08, C:0.10, G:0.40, T:0.42
Consensus pattern (22 bp):
GGTTTTAGGTTCCCGGATTAGG
Found at i:62667902 original size:16 final size:16
Alignment explanation
Indices: 62667868--62667920 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
62667858 GGTTCCCGGA
* *
62667868 TTGGGGGTTT-GGGGG
1 TTGGGGTTTTAGGGGC
62667883 TTGGGGTTTTAGGGGC
1 TTGGGGTTTTAGGGGC
62667899 TTGGGGTTTTAGGGGC
1 TTGGGGTTTTAGGGGC
62667915 TTGGGG
1 TTGGGG
62667921 CTTGGTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 9 0.26
16 26 0.74
ACGTcount: A:0.04, C:0.04, G:0.57, T:0.36
Consensus pattern (16 bp):
TTGGGGTTTTAGGGGC
Found at i:62668104 original size:25 final size:25
Alignment explanation
Indices: 62668076--62668123 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
62668066 TTCTTCTTTG
*
62668076 TTTAAATTTTGTTTATTTTTCTTGC
1 TTTAAATTTTGTTTATTTATCTTGC
* *
62668101 TTTAATTTTTGTTTCTTTATCTT
1 TTTAAATTTTGTTTATTTATCTT
62668124 TGATCTAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.15, C:0.08, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTAAATTTTGTTTATTTATCTTGC
Found at i:62670782 original size:80 final size:80
Alignment explanation
Indices: 62670649--62670808 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
62670639 TGAAGCTTTC
62670649 AAGTTAATAATCCGTTAAACTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTT
1 AAGTTAATAATCCGTTAAACTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTT
62670714 TACCCATTTATTATA
66 TACCCATTTATTATA
62670729 AAGTTAATAATCCGTTAAACTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTT
1 AAGTTAATAATCCGTTAAACTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTT
*
62670794 TACCTATTTATTATA
66 TACCCATTTATTATA
62670809 CAGCTGATTT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (80 bp):
AAGTTAATAATCCGTTAAACTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTT
TACCCATTTATTATA
Found at i:62671080 original size:21 final size:21
Alignment explanation
Indices: 62671056--62671095 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
62671046 GAATTTTAGC
62671056 TGACCGGTTCTGCTGTTTTGG
1 TGACCGGTTCTGCTGTTTTGG
*
62671077 TGACCGGTTCTGTTGTTTT
1 TGACCGGTTCTGCTGTTTT
62671096 ATGAGCCCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.17, G:0.30, T:0.47
Consensus pattern (21 bp):
TGACCGGTTCTGCTGTTTTGG
Found at i:62671146 original size:15 final size:15
Alignment explanation
Indices: 62671126--62671177 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
62671116 CTCTCGCGCT
62671126 TATCCCGCATGGGGA
1 TATCCCGCATGGGGA
** * **
62671141 TATCCCATTATGCGCT
1 TATCCC-GCATGGGGA
62671157 TATCCCGCATGGGGA
1 TATCCCGCATGGGGA
62671172 TATCCC
1 TATCCC
62671178 ACACCAAGGG
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.19, C:0.31, G:0.23, T:0.27
Consensus pattern (15 bp):
TATCCCGCATGGGGA
Found at i:62680890 original size:31 final size:31
Alignment explanation
Indices: 62680816--62680891 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
62680806 GAGGGCTGTT
62680816 TCGGGGATATCCCAAGCTGAATTAAGCTATA
1 TCGGGGATATCCCAAGCTGAATTAAGCTATA
* * * *
62680847 TCGCGGAAATCCCAA-CTTGATTTAAGGTAT-
1 TCGGGGATATCCCAAGC-TGAATTAAGCTATA
62680877 TCTGGGGATATCCCA
1 TC-GGGGATATCCCA
62680892 TCCAAATCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 3 0.08
31 34 0.92
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (31 bp):
TCGGGGATATCCCAAGCTGAATTAAGCTATA
Done.