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 37 of 204
Found at i:12959596 original size:5 final size:5
Alignment explanation
Indices: 12959586--12959620 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
12959576 TTTTTTAATT
12959586 GTATA GTATA GTATA GTATA GTATA GTATA GTATA
1 GTATA GTATA GTATA GTATA GTATA GTATA GTATA
12959621 CTCATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
GTATA
Found at i:12960799 original size:14 final size:14
Alignment explanation
Indices: 12960780--12960810 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12960770 TGAATAAATG
*
12960780 AATAAAAAATATTT
1 AATAAAAAATATAT
12960794 AATAAAAAATATAT
1 AATAAAAAATATAT
12960808 AAT
1 AAT
12960811 TCGAACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAAAAAATATAT
Found at i:12960886 original size:21 final size:19
Alignment explanation
Indices: 12960860--12960898 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
12960850 AACATTCTAC
12960860 AAAATTAATACACAAAAATAT
1 AAAATTAA-A-ACAAAAATAT
*
12960881 AAAATTCAAACAAAAATA
1 AAAATTAAAACAAAAATA
12960899 ATATGCACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAATTAAAACAAAAATAT
Found at i:12960912 original size:88 final size:87
Alignment explanation
Indices: 12960820--12961137 Score: 266
Period size: 89 Copynumber: 3.6 Consensus size: 87
12960810 TTCGAACAAA
*
12960820 AAATTAAATTTACAGATACAATAAAATACAAACATTCTACAAAATTAATACACAAAAATATAAAA
1 AAATTAAATTTACAGATACAA-AAAATACAAACATTCTA-AAAATTAATACACGAAAATATAAAA
* *
12960885 TTCAAAC-AAAAATAATA-TGCACT
64 TTCAAACTAAAAATAATACAG-AAT
* * * ** * ** * *
12960908 AAATTAAACTTAAACACCCAACAAACTACAAACAGATGGGT-AAAATTAATACACGAAAATTTTA
1 AAATTAAATTTACAGATACAA-AAAATACAAAC--AT-TCTAAAAATTAATACACGAAAATATAA
* *
12960972 AATTCAAACTACATATAATACAGAAT
62 AATTCAAACTAAAAATAATACAGAAT
* *
12960998 AAATTAAATTTACAGATACAAAAAATACAAATATTCTAAGAAATTAATACACGAAAATATAAAAA
1 AAATTAAATTTACAGATACAAAAAATACAAACATTCTAA-AAATTAATACACGAAAATATAAAAT
* * ** * *
12961063 TGAAACCT-TAAATCCTAAATAACT
65 TCAAA-CTAAAAATAATACAGAA-T
* * * *
12961087 ACATTAAATTTACAAATATAAAAAATACAAACATTCTAAAGAAATAATACA
1 AAATTAAATTTACAGATACAAAAAATACAAACATTCTAAA-AATTAATACA
12961138 ATTATTTTGA
Statistics
Matches: 180, Mismatches: 40, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
86 1 0.01
87 3 0.02
88 61 0.34
89 85 0.47
90 28 0.16
91 2 0.01
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.25
Consensus pattern (87 bp):
AAATTAAATTTACAGATACAAAAAATACAAACATTCTAAAAATTAATACACGAAAATATAAAATT
CAAACTAAAAATAATACAGAAT
Found at i:12961027 original size:89 final size:88
Alignment explanation
Indices: 12960820--12961061 Score: 220
Period size: 88 Copynumber: 2.7 Consensus size: 88
12960810 TTCGAACAAA
* * *
12960820 AAATTAAATTTACAGATACAATAAAATACAAACATTCTACAAAATTAATACACAAAAATATAAAA
1 AAATTAAATTTACAGATACAACAAAATACAAACAATCGACAAAATTAATACACAAAAATATAAAA
* *
12960885 TTCAAACAAAAATAATATGCACT
66 TTCAAACAAAAATAATAAGCAAT
* * * ** * * ** * * *
12960908 AAATTAAACTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATACACGAAAATTTTAA
1 AAATTAAATTTACAGATACAACAAAATACAAACA-ATCGACAAAATTAATACACAAAAATATAAA
* *
12960973 ATTCAAACTACATATAATACAG-AAT
65 ATTCAAAC-AAAAATAATA-AGCAAT
* * * *
12960998 AAATTAAATTTACAGATACAA-AAAATACAAATATTCTA-AGAAATTAATACACGAAAATATAAA
1 AAATTAAATTTACAGATACAACAAAATACAAACAATCGACA-AAATTAATACACAAAAATATAAA
12961061 A
65 A
12961062 ATGAAACCTT
Statistics
Matches: 118, Mismatches: 32, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
87 1 0.01
88 50 0.42
89 40 0.34
90 26 0.22
91 1 0.01
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (88 bp):
AAATTAAATTTACAGATACAACAAAATACAAACAATCGACAAAATTAATACACAAAAATATAAAA
TTCAAACAAAAATAATAAGCAAT
Found at i:12961861 original size:110 final size:109
Alignment explanation
Indices: 12961619--12961862 Score: 312
Period size: 109 Copynumber: 2.2 Consensus size: 109
12961609 ATGTGGTGCT
* * *
12961619 GGCCATCAATGTCCCAAAGT-AAAAAAAATGAATTGGGAGGAAAAAATGTACTTGGTGTCGGCCA
1 GGCCATCAATGTCCCAAAGTAAAAAAAAATGAATTGGGAGCAAAAAATGTACTTGATGTCAGCCA
* * * *
12961683 TTACATGGCCAGCACCCAAATTTTTTTTTAAATACACTCGTGTC
66 TTACATGGCCACCACCAAAATTTTTTTTTAAATAAACTAGTGTC
* * * ** * * *
12961727 AGCTATCAGTGTTTCAAAATAAAAAAAAATGCATTGGGAGCCAAAAATTGTACTTGATGTCAGCC
1 GGCCATCAATGTCCCAAAGTAAAAAAAAATGAATTGGGAG-CAAAAAATGTACTTGATGTCAGCC
*
12961792 ATTACATGGTCACCA-CAAAATTTTTTTTTAAATAAACTAGTGTC
65 ATTACATGGCCACCACCAAAATTTTTTTTTAAATAAACTAGTGTC
*
12961836 GGCCATCAATATCCCAAAGTAAAAAAA
1 GGCCATCAATGTCCCAAAGTAAAAAAA
12961863 TTGTGTATTG
Statistics
Matches: 111, Mismatches: 23, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
108 14 0.13
109 64 0.58
110 33 0.30
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (109 bp):
GGCCATCAATGTCCCAAAGTAAAAAAAAATGAATTGGGAGCAAAAAATGTACTTGATGTCAGCCA
TTACATGGCCACCACCAAAATTTTTTTTTAAATAAACTAGTGTC
Found at i:12961884 original size:110 final size:108
Alignment explanation
Indices: 12961619--12961922 Score: 290
Period size: 110 Copynumber: 2.8 Consensus size: 108
12961609 ATGTGGTGCT
* * * *
12961619 GGCCATCAATGTCCCAAAGTAAAAAAAATGAATTGGG-AGGAAAAAATGTACTTGGTGTCGGCCA
1 GGCCATCAATGTCCCAAAGTAAAAAAAATGAATTGGGAACG-AAAATTGTACTTGATGTCAGCCA
* * * *
12961683 TTACATGGCCAGCACCCAAATTTTTTTTTAAATACACTCGTGTC
65 TTACATGGCCACCACCAAAATTTTTTTTTAAATAAACTAGTGTC
* * * ** * * * *
12961727 AGCTATCAGTGTTTCAAAATAAAAAAAAATGCATTGGGAGCCAAAAATTGTACTTGATGTCAGCC
1 GGCCATCAATGTCCCAAAGT-AAAAAAAATGAATTGGGA-ACGAAAATTGTACTTGATGTCAGCC
*
12961792 ATTACATGGTCACCA-CAAAATTTTTTTTTAAATAAACTAGTGTC
64 ATTACATGGCCACCACCAAAATTTTTTTTTAAATAAACTAGTGTC
* * * * * * *
12961836 GGCCATCAATATCCCAAAGTAAAAAAATTGTGTATTGGGAATCGAAAATTGTACCTGGTGCCGGC
1 GGCCATCAATGTCCCAAAGTAAAAAAA--ATGAATTGGGAA-CGAAAATTGTACTTGATGTCAGC
*
12961901 CATCTAC-TGGCCAACACCAAAA
63 CAT-TACATGGCCACCACCAAAA
12961923 AAAAATTTTA
Statistics
Matches: 153, Mismatches: 35, Indels: 13
0.76 0.17 0.06
Matches are distributed among these distances:
108 21 0.14
109 55 0.36
110 69 0.45
111 8 0.05
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (108 bp):
GGCCATCAATGTCCCAAAGTAAAAAAAATGAATTGGGAACGAAAATTGTACTTGATGTCAGCCAT
TACATGGCCACCACCAAAATTTTTTTTTAAATAAACTAGTGTC
Found at i:12963920 original size:21 final size:20
Alignment explanation
Indices: 12963883--12963930 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
12963873 AACCCACATA
12963883 TTTTTTTTGAACTTTTTATATT
1 TTTTTTTTGAA--TTTTATATT
*
12963905 TTTTTTGTTGAATTTTAAATT
1 TTTTTT-TTGAATTTTATATT
12963926 TTTTT
1 TTTTT
12963931 ACTTTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 13 0.54
22 6 0.25
23 5 0.21
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (20 bp):
TTTTTTTTGAATTTTATATT
Found at i:12963938 original size:23 final size:21
Alignment explanation
Indices: 12963883--12963945 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 21
12963873 AACCCACATA
*
12963883 TTTTTTTTGAACTTTTTATATTT
1 TTTTTTTTGAA--TTTTAAATTT
*
12963906 TTTTTGTTGAATTTTAAATTT
1 TTTTTTTTGAATTTTAAATTT
12963927 TTTTACTTTTGAATATTTA
1 TTTT--TTTTGAAT-TTTA
12963946 TATAATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 13 0.38
23 17 0.50
24 4 0.12
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.68
Consensus pattern (21 bp):
TTTTTTTTGAATTTTAAATTT
Found at i:12972513 original size:15 final size:15
Alignment explanation
Indices: 12972493--12972521 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12972483 AAGAAAGGAT
12972493 GATTGAATTGGATTG
1 GATTGAATTGGATTG
12972508 GATTGAATTGGATT
1 GATTGAATTGGATT
12972522 TTCAATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (15 bp):
GATTGAATTGGATTG
Found at i:12972740 original size:22 final size:22
Alignment explanation
Indices: 12972700--12972745 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
12972690 TACAAGGAGC
12972700 TTTAAAGAATTTATATATATATT
1 TTTAAAGAATTTATATATAT-TT
* *
12972723 TTTAAATATTTTAT-TATATTT
1 TTTAAAGAATTTATATATATTT
12972744 TT
1 TT
12972746 ATAGGAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 5 0.24
23 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTAAAGAATTTATATATATTT
Found at i:12972956 original size:14 final size:15
Alignment explanation
Indices: 12972937--12972965 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12972927 GATTATGGTG
12972937 ATATATAA-TATAAT
1 ATATATAAGTATAAT
12972951 ATATATAAGTATAAT
1 ATATATAAGTATAAT
12972966 TTTATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
ATATATAAGTATAAT
Found at i:12984094 original size:23 final size:23
Alignment explanation
Indices: 12984062--12984105 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12984052 ACTACCATTT
12984062 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
12984085 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
12984106 ATATTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:12984109 original size:11 final size:11
Alignment explanation
Indices: 12984066--12984111 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
12984056 CCATTTTCTA
*
12984066 AATAAAATAAT
1 AATAAAATATT
12984077 AAT-AAATATCT
1 AATAAAATAT-T
12984088 AAGTAAAATATT
1 AA-TAAAATATT
12984100 AATAAAATATT
1 AATAAAATATT
12984111 A
1 A
12984112 TTTAACTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 5 0.16
11 16 0.52
12 4 0.13
13 6 0.19
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:12988825 original size:2 final size:2
Alignment explanation
Indices: 12988818--12988842 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12988808 TATGTACAAC
12988818 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 T
12988843 GAAACATTGA
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:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12990260 original size:6 final size:6
Alignment explanation
Indices: 12990249--12990280 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12990239 TTCCTCACTT
*
12990249 CCTTTG CCTTTG CCTTTG CCTTTG CATTTG CC
1 CCTTTG CCTTTG CCTTTG CCTTTG CCTTTG CC
12990281 GCCGCTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.34, G:0.16, T:0.47
Consensus pattern (6 bp):
CCTTTG
Found at i:12996065 original size:39 final size:43
Alignment explanation
Indices: 12995960--12996069 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
12995950 TTTGGTTCGC
12995960 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
12996005 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
12996045 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
12996070 TAATGGAAAA
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:12996364 original size:14 final size:15
Alignment explanation
Indices: 12996325--12996366 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12996315 AATTAACATC
*
12996325 ATTATTATTAAATAT
1 ATTATAATTAAATAT
12996340 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
12996354 A-TATAATTTAATA
1 ATTATAATTAAATA
12996367 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:12996464 original size:120 final size:120
Alignment explanation
Indices: 12996198--12996595 Score: 742
Period size: 120 Copynumber: 3.3 Consensus size: 120
12996188 ATCATATTTA
* *
12996198 AACATAATTATTATTAAATATATTAAAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
12996263 TATTCTTATATGAATATTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAAT-TTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
12996319 AACATCATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
12996384 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
12996439 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
12996504 TATTCTTATATGAAATTATTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
12996559 AACATAATTATTATTAAATATATTATAATTAAAATAT
1 AACATAATTATTATTAAATATATTATAATTAAAATAT
12996596 CACAGAGCTT
Statistics
Matches: 271, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
120 194 0.72
121 77 0.28
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:12996484 original size:14 final size:15
Alignment explanation
Indices: 12996435--12996486 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
12996425 ATAAAATATA
12996435 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
12996450 TATTAAATATATTAT
1 AATTAAATATATTAT
12996465 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
12996478 AATTTAATA
1 AATTAAATA
12996487 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:12996583 original size:15 final size:15
Alignment explanation
Indices: 12996555--12996595 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
12996545 ATAAAATATA
12996555 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
12996570 TATTAAATATATTAT
1 AATTAAATATATTAT
12996585 AATTAAA-ATAT
1 AATTAAATATAT
12996596 CACAGAGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:12999531 original size:14 final size:14
Alignment explanation
Indices: 12999512--12999539 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12999502 AGCAGAAATC
12999512 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
12999526 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
12999540 GAAATGTGAG
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:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:12999537 original size:19 final size:18
Alignment explanation
Indices: 12999515--12999559 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
12999505 AGAAATCTGG
12999515 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
12999534 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
12999551 AGAAAAGAA
1 AGAAAAGAA
12999560 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:13000215 original size:29 final size:28
Alignment explanation
Indices: 13000143--13000209 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
13000133 TAAATCTCAA
* *
13000143 AATTATACATGAACTTTGATTTAATGTGC
1 AATTATACATGAACTTTAATTT-AGGTGC
*
13000172 AATTGTACATATGAACTTTAATTT-GGTGC
1 AATTATAC--ATGAACTTTAATTTAGGTGC
13000201 AATTATACA
1 AATTATACA
13000210 CGTGAAACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.03
29 18 0.56
31 13 0.41
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (28 bp):
AATTATACATGAACTTTAATTTAGGTGC
Found at i:13001280 original size:30 final size:30
Alignment explanation
Indices: 13001236--13001295 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
13001226 ACTTAACAAG
13001236 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
13001266 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
13001296 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:13005245 original size:39 final size:36
Alignment explanation
Indices: 13005186--13005262 Score: 86
Period size: 39 Copynumber: 2.1 Consensus size: 36
13005176 ATTAAATTAT
*
13005186 ATAATTTTTTGAGAATTAAAATTTACTTTTATTATTTTA
1 ATAATTTTTTGAGAATTAAAA-TTA-TTTT-TAATTTTA
13005225 ATAATTTTTT-A-AATAATAAAATTATTTTTAATTTTA
1 ATAATTTTTTGAGAAT--TAAAATTATTTTTAATTTTA
13005261 AT
1 AT
13005263 TTTAAAGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
36 9 0.26
37 7 0.20
38 4 0.11
39 15 0.43
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (36 bp):
ATAATTTTTTGAGAATTAAAATTATTTTTAATTTTA
Found at i:13012273 original size:20 final size:20
Alignment explanation
Indices: 13012248--13012285 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13012238 TTAGTCAATT
*
13012248 TTTAATTAAAAAATATTTAA
1 TTTAATCAAAAAATATTTAA
*
13012268 TTTAATCAAAAAGTATTT
1 TTTAATCAAAAAATATTT
13012286 TTAAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTAATCAAAAAATATTTAA
Found at i:13012828 original size:40 final size:40
Alignment explanation
Indices: 13012757--13012832 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
13012747 AATTTTAGTC
* * *
13012757 ATTATTTTACTCACCCTGCTTACCATATAAAATTATCACA
1 ATTATTTTACTCACCCTACTCACCAGATAAAATTATCACA
* * *
13012797 ATTATTTTATTCACCCTACTCATCAGGTAAAATTAT
1 ATTATTTTACTCACCCTACTCACCAGATAAAATTAT
13012833 ATATATATTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.39
Consensus pattern (40 bp):
ATTATTTTACTCACCCTACTCACCAGATAAAATTATCACA
Found at i:13018307 original size:26 final size:26
Alignment explanation
Indices: 13018255--13018307 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
13018245 CTATTTTAAC
*
13018255 ATTTAAACAATATTTTGTATAATTAA
1 ATTTAAACAATATTTTGTATAAATAA
13018281 ATTTATAA-AATATTTGTGT-TAAATAA
1 ATTTA-AACAATATTT-TGTATAAATAA
13018307 A
1 A
13018308 ATAGTTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (26 bp):
ATTTAAACAATATTTTGTATAAATAA
Found at i:13020176 original size:57 final size:58
Alignment explanation
Indices: 13020081--13020195 Score: 137
Period size: 57 Copynumber: 2.0 Consensus size: 58
13020071 CACCTGACCC
*
13020081 AAAATATTTTTTTAATCAGATAAAGGGGTGCCAGCCATCAACGTGCCAACACC-CAAA
1 AAAATATTTTTTTAATCAGATAAAGGGATGCCAGCCATCAACGTGCCAACACCTCAAA
* * ** *
13020138 AAAATTATTTTTTT-ATCTGATAAAGGGATG-CTGACCATCAGTGTGTCAACACCTCAAA
1 AAAA-TATTTTTTTAATCAGATAAAGGGATGCCAG-CCATCAACGTGCCAACACCTCAAA
13020196 TTTTTTTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
56 2 0.04
57 34 0.69
58 13 0.27
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (58 bp):
AAAATATTTTTTTAATCAGATAAAGGGATGCCAGCCATCAACGTGCCAACACCTCAAA
Found at i:13021867 original size:16 final size:16
Alignment explanation
Indices: 13021828--13021867 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
13021818 AATATCATAA
13021828 ATTAAAATATTATTTT
1 ATTAAAATATTATTTT
13021844 ATTCAAAAT-TTATTTTT
1 ATT-AAAATATTA-TTTT
13021861 ATTAAAA
1 ATTAAAA
13021868 AAAAGCCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAAAATATTATTTT
Found at i:13023957 original size:15 final size:15
Alignment explanation
Indices: 13023937--13023973 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
13023927 TAATTTTTTT
13023937 TGTAAAATTCTAAAA
1 TGTAAAATTCTAAAA
13023952 TGTAAAATTCTAAAA
1 TGTAAAATTCTAAAA
*
13023967 TTTAAAA
1 TGTAAAA
13023974 AGTCAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (15 bp):
TGTAAAATTCTAAAA
Found at i:13023974 original size:23 final size:23
Alignment explanation
Indices: 13023939--13023982 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
13023929 ATTTTTTTTG
13023939 TAAAATTCTAAAATGT-AAAATTC
1 TAAAATTCTAAAA-GTCAAAATTC
13023962 TAAAATT-TAAAAAGTCAAAAT
1 TAAAATTCT-AAAAGTCAAAAT
13023983 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.32
Consensus pattern (23 bp):
TAAAATTCTAAAAGTCAAAATTC
Found at i:13026129 original size:19 final size:19
Alignment explanation
Indices: 13026102--13026158 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
13026092 GTACACCAAT
*
13026102 AGAAACTCGAAAGCTGAAC
1 AGAAGCTCGAAAGCTGAAC
* * *
13026121 AGAAGCTCGTAAGCTAAAT
1 AGAAGCTCGAAAGCTGAAC
13026140 AGAAGCTCGTAAGAGCTGA
1 AGAAGCTCG-AA-AGCTGA
13026159 TCCAACCTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 24 0.80
20 1 0.03
21 5 0.17
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.16
Consensus pattern (19 bp):
AGAAGCTCGAAAGCTGAAC
Found at i:13026673 original size:17 final size:16
Alignment explanation
Indices: 13026653--13026700 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
13026643 CTTAATTAGT
13026653 TAATCTATCAAATTAA
1 TAATCTATCAAATTAA
* *
13026669 CTAATTTTCTCAAATTAA
1 -TAA-TCTATCAAATTAA
13026687 TAATCTATCCAAAT
1 TAATCTAT-CAAAT
13026701 ATTCTAGGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 11 0.44
18 11 0.44
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATCTATCAAATTAA
Found at i:13044061 original size:19 final size:19
Alignment explanation
Indices: 13044018--13044060 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
13044008 TTTTTTTCGA
13044018 TTTTTTTCTATTTCAACTG
1 TTTTTTTCTATTTCAACTG
*
13044037 TTTTTTTCTGTTTC-ACT-
1 TTTTTTTCTATTTCAACTG
13044054 TTTTTTT
1 TTTTTTT
13044061 TAAATTCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 3 0.13
19 13 0.57
ACGTcount: A:0.09, C:0.14, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTTTTCTATTTCAACTG
Found at i:13048304 original size:2 final size:2
Alignment explanation
Indices: 13048297--13048323 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13048287 ACTAATATCA
13048297 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 A
13048324 ACGTTTGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13049520 original size:11 final size:11
Alignment explanation
Indices: 13049506--13049619 Score: 69
Period size: 11 Copynumber: 10.4 Consensus size: 11
13049496 ATTTTTTTAA
13049506 TTTTAAAATAT
1 TTTTAAAATAT
13049517 TTTTAAAATATT
1 TTTTAAAATA-T
*** *
13049529 TTTTATTTTTTAA
1 TTTTA--AAATAT
13049542 TTTTAAAATAT
1 TTTTAAAATAT
13049553 TTTTAAAATACT
1 TTTTAAAATA-T
13049565 TTTT---A-A-
1 TTTTAAAATAT
13049571 TTTTAAAATAT
1 TTTTAAAATAT
13049582 TTTTAAAATACT
1 TTTTAAAATA-T
***
13049594 TTTTTTTA-AT
1 TTTTAAAATAT
13049604 TTTTAAAATAAT
1 TTTTAAAAT-AT
13049616 TTTT
1 TTTT
13049620 TAGTATTTAT
Statistics
Matches: 77, Mismatches: 14, Indels: 23
0.68 0.12 0.20
Matches are distributed among these distances:
6 4 0.05
8 1 0.01
9 2 0.03
10 7 0.09
11 33 0.43
12 23 0.30
13 5 0.06
14 2 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:13049543 original size:36 final size:36
Alignment explanation
Indices: 13049498--13049597 Score: 142
Period size: 29 Copynumber: 3.0 Consensus size: 36
13049488 TTTTTTAAAT
*
13049498 TTTTTTAATTTTAAAATATTTTTAAAATATTTTTTA
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTA
13049534 TTTTTTAATTTTAAAATATTTTTAAAATAC------
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTA
13049564 -TTTTTAATTTTAAAATATTTTTAAAATACTTTTT
1 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTT
13049598 TTTAATTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 12
0.82 0.01 0.17
Matches are distributed among these distances:
29 29 0.50
36 29 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (36 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTA
Found at i:13049574 original size:18 final size:17
Alignment explanation
Indices: 13049477--13049587 Score: 74
Period size: 17 Copynumber: 6.7 Consensus size: 17
13049467 CCGATATAAT
* * *
13049477 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
13049494 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
*
13049511 AAATATTTTTAAAATATTTT
1 AAATATTTTT--AAT-TTTA
**
13049531 TTAT-TTTTTAATTTTA
1 AAATATTTTTAATTTTA
13049547 AAATA----T--TTTTA
1 AAATATTTTTAATTTTA
13049558 AAATACTTTTTAATTTTA
1 AAATA-TTTTTAATTTTA
13049576 AAATATTTTTAA
1 AAATATTTTTAA
13049588 AATACTTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
11 10 0.14
13 1 0.01
16 6 0.08
17 32 0.44
18 10 0.14
19 8 0.11
20 5 0.07
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:13049632 original size:23 final size:21
Alignment explanation
Indices: 13049579--13049634 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
13049569 AATTTTAAAA
* *
13049579 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATAATTTTTTG
13049600 TAATTTTTAAAATAATTTTTTAG
1 T-ATTTTTAAAATAATTTTTT-G
13049623 TATTTATTAAAA
1 TATTT-TTAAAA
13049635 AATGGGCCGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.03
22 22 0.73
23 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TATTTTTAAAATAATTTTTTG
Found at i:13050823 original size:180 final size:180
Alignment explanation
Indices: 13050521--13050873 Score: 616
Period size: 180 Copynumber: 2.0 Consensus size: 180
13050511 AATAAAATTT
* *
13050521 ACTATGTCGAATTCGAATAATTACAAGAGGAGTAGATTATGTCTATTTGTAGGCTTGTAAAACCA
1 ACTATGTCGAATTCGAATAATTACAAAAGGAGTAGATTATGTCTATTTATAGGCTTGTAAAACCA
13050586 TATTCTAATAGGAATGTAGTAAGATTAAAACACCTTATTCTAATCAATATCAAATAGATAGAGTT
66 TATTCTAATAGGAATGTAGTAAGATTAAAACACCTTATTCTAATCAATATCAAATAGATAGAGTT
* *
13050651 TAATAAGGTTTTAAAAACCTTATTTTAAAATAAAATAAAAGAAAAAAATC
131 TAATAAGGTTTAAAAAACCTTATTCTAAAATAAAATAAAAGAAAAAAATC
*
13050701 ACTATGTCGAATTCGAATAATTACAAAAGGAGTAGGTTATGTCTATTTATAGGCTTGTAAAACCA
1 ACTATGTCGAATTCGAATAATTACAAAAGGAGTAGATTATGTCTATTTATAGGCTTGTAAAACCA
* * * *
13050766 TATTCTAATAGGAGTGTAGTAAGATTGAAACACTTTATTCTAATTAATATCAAATAGATAGAGTT
66 TATTCTAATAGGAATGTAGTAAGATTAAAACACCTTATTCTAATCAATATCAAATAGATAGAGTT
*
13050831 TAATAAGGTTTAAAAAATCTTATTCTAAAATAAAATAAAAGAA
131 TAATAAGGTTTAAAAAACCTTATTCTAAAATAAAATAAAAGAA
13050874 GTGTAGTTCT
Statistics
Matches: 163, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
180 163 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (180 bp):
ACTATGTCGAATTCGAATAATTACAAAAGGAGTAGATTATGTCTATTTATAGGCTTGTAAAACCA
TATTCTAATAGGAATGTAGTAAGATTAAAACACCTTATTCTAATCAATATCAAATAGATAGAGTT
TAATAAGGTTTAAAAAACCTTATTCTAAAATAAAATAAAAGAAAAAAATC
Found at i:13064574 original size:21 final size:21
Alignment explanation
Indices: 13064541--13064589 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
13064531 GAAGTATACT
* *
13064541 ATTAT-TTTATTATATTGTAA
1 ATTATATTAATTATATTATAA
*
13064561 ATTATATTAATTATATTATAT
1 ATTATATTAATTATATTATAA
13064582 ATTATATT
1 ATTATATT
13064590 CCAAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTATATTAATTATATTATAA
Found at i:13064823 original size:26 final size:27
Alignment explanation
Indices: 13064785--13064836 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
13064775 ATAGGCAAAC
13064785 GAAAACAGGGAA-GAAAGGAAAGAAAAA
1 GAAAACAGGGAAGGAAA-GAAAGAAAAA
13064812 GAAAA-AGGGAAGGAAAGAAAGAAAA
1 GAAAACAGGGAAGGAAAGAAAGAAAA
13064837 TTTGGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (27 bp):
GAAAACAGGGAAGGAAAGAAAGAAAAA
Found at i:13066051 original size:22 final size:22
Alignment explanation
Indices: 13066013--13066055 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13066003 ATTTATTTCA
*
13066013 GGTGTGTTTTGGTTGGATATTCT
1 GGTGTGTTTTGGGTGGA-ATTCT
13066036 GGTGTG-TTTGGGTGGAATTC
1 GGTGTGTTTTGGGTGGAATTC
13066056 GCGTATCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.09, C:0.05, G:0.40, T:0.47
Consensus pattern (22 bp):
GGTGTGTTTTGGGTGGAATTCT
Found at i:13081600 original size:3 final size:3
Alignment explanation
Indices: 13081592--13081626 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
13081582 AGGGGTTTTC
*
13081592 CTT CTT CTT GTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
13081627 CACTGCTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:13085297 original size:17 final size:17
Alignment explanation
Indices: 13085275--13085308 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13085265 TTACATAAAA
13085275 ACATATATTCTTTTATT
1 ACATATATTCTTTTATT
13085292 ACATATATTCTTTTATT
1 ACATATATTCTTTTATT
13085309 GGGAGTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (17 bp):
ACATATATTCTTTTATT
Found at i:13087063 original size:18 final size:19
Alignment explanation
Indices: 13087042--13087086 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
13087032 ATTAACTTTA
*
13087042 AAAATATGATTTT-TTAAT
1 AAAATATGATTTTATAAAT
13087060 AAAAGT-T-ATTTTATAAAT
1 AAAA-TATGATTTTATAAAT
13087078 AAAATATGA
1 AAAATATGA
13087087 AATTGATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
17 6 0.27
18 14 0.64
19 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
AAAATATGATTTTATAAAT
Found at i:13087190 original size:17 final size:17
Alignment explanation
Indices: 13087148--13087194 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
13087138 AATTCAATTT
13087148 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
13087164 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
13087182 TAATATAAATAAT
1 TAATATAAATAAT
13087195 ATAAAATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 13 0.48
18 8 0.30
19 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:13087676 original size:30 final size:29
Alignment explanation
Indices: 13087622--13087681 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
13087612 AGAGGGGAGG
*
13087622 GGAGTAAAAGTTTTGAACAAAAGTAGAAA
1 GGAGTAAAAGTTTTGAACAAAAGTAAAAA
*
13087651 GGAGTAAAAGTTTT-AAGGGAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAA--CAAAAGTAAAAA
13087681 G
1 G
13087682 ATTTGGGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 14 0.52
30 11 0.41
ACGTcount: A:0.52, C:0.02, G:0.27, T:0.20
Consensus pattern (29 bp):
GGAGTAAAAGTTTTGAACAAAAGTAAAAA
Found at i:13087741 original size:9 final size:9
Alignment explanation
Indices: 13087724--13087760 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
13087714 TATAATTTAA
13087724 TATTCGAAT
1 TATTCGAAT
*
13087733 TATTTGAAT
1 TATTCGAAT
*
13087742 TATTTGAAT
1 TATTCGAAT
13087751 TATTCGAAT
1 TATTCGAAT
13087760 T
1 T
13087761 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (9 bp):
TATTCGAAT
Found at i:13093613 original size:3 final size:3
Alignment explanation
Indices: 13093605--13093642 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
13093595 TTTGATTTGC
13093605 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
13093643 ACTTCGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:13095878 original size:17 final size:19
Alignment explanation
Indices: 13095856--13095894 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
13095846 ACAAGAGCTT
*
13095856 AAATA-TCATTATAAAC-C
1 AAATATTCATTACAAACAC
13095873 AAATATTCATTACAAACAC
1 AAATATTCATTACAAACAC
13095892 AAA
1 AAA
13095895 CAAGTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATATTCATTACAAACAC
Found at i:13098749 original size:32 final size:32
Alignment explanation
Indices: 13098699--13098761 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
13098689 TGCAATTTTA
*
13098699 GTACCGATTTAAGACTGGAACAGTATGTATTT
1 GTACCGATATAAGACTGGAACAGTATGTATTT
*
13098731 GTACTGATATAAGACTGGAACAGTATGTATT
1 GTACCGATATAAGACTGGAACAGTATGTATT
13098762 AATTTAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (32 bp):
GTACCGATATAAGACTGGAACAGTATGTATTT
Found at i:13100382 original size:22 final size:22
Alignment explanation
Indices: 13100354--13100397 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13100344 GAGATTTCAG
*
13100354 GTTTTCAATGTATAAGTCAACC
1 GTTTTCAATGTATAAGCCAACC
13100376 GTTTTCAATGTATAAGCCAACC
1 GTTTTCAATGTATAAGCCAACC
13100398 TTAAAGGGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (22 bp):
GTTTTCAATGTATAAGCCAACC
Found at i:13114432 original size:13 final size:13
Alignment explanation
Indices: 13114414--13114448 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
13114404 TCAATTTAAG
*
13114414 AAATAGAAAATGA
1 AAATAGAAAATAA
13114427 AAATAGAAAATAA
1 AAATAGAAAATAA
*
13114440 AAACAGAAA
1 AAATAGAAA
13114449 CTATTTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.11
Consensus pattern (13 bp):
AAATAGAAAATAA
Found at i:13123853 original size:3 final size:3
Alignment explanation
Indices: 13123845--13123874 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
13123835 ATCAGTGAGA
13123845 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
13123875 CTTTTCTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:13130812 original size:12 final size:12
Alignment explanation
Indices: 13130795--13130819 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13130785 ATTTCATTCC
13130795 ACATATATATAT
1 ACATATATATAT
13130807 ACATATATATAT
1 ACATATATATAT
13130819 A
1 A
13130820 TATAAACACA
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATATATATAT
Found at i:13131173 original size:21 final size:22
Alignment explanation
Indices: 13131141--13131185 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
13131131 ATTTTCACAC
13131141 CAAAATTTGGACAGCATATATA
1 CAAAATTTGGACAGCATATATA
* *
13131163 CAAAA-TTGGACTGCATTTATA
1 CAAAATTTGGACAGCATATATA
13131184 CA
1 CA
13131186 TCAAAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (22 bp):
CAAAATTTGGACAGCATATATA
Found at i:13131217 original size:47 final size:47
Alignment explanation
Indices: 13131141--13131444 Score: 461
Period size: 47 Copynumber: 6.5 Consensus size: 47
13131131 ATTTTCACAC
* * *
13131141 CAAAATTTGGACAGCATAT--ATACAAAATTGGACTGCATTTATACAT
1 CAAAAATT-GACAGCATATACATATATAATTGGACTGCATTTATACAT
13131187 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* *
13131234 CAAAAATTGACAGCATATACATATATATTTGGACTGCATTTGTACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
* * *
13131281 CAAAATTTGACAGCATATATATATATATAATTGGACTGCATTTATACGT
1 CAAAAATTGACAGC--ATATACATATATAATTGGACTGCATTTATACAT
*
13131330 CAAAAATTGACAGCATATACATATATAATTGGACTGC-CTTATACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
13131376 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTGTACAT
1 CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
*
13131423 CAAAATTTGACAGCATATACAT
1 CAAAAATTGACAGCATATACAT
13131445 TCATTTACTC
Statistics
Matches: 236, Mismatches: 17, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
45 10 0.04
46 51 0.22
47 133 0.56
49 42 0.18
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (47 bp):
CAAAAATTGACAGCATATACATATATAATTGGACTGCATTTATACAT
Found at i:13131432 original size:142 final size:141
Alignment explanation
Indices: 13131141--13131441 Score: 518
Period size: 142 Copynumber: 2.1 Consensus size: 141
13131131 ATTTTCACAC
13131141 CAAAATTTGGACAGC--ATATATACAAAATTGGACTGCATTTATACATCAAAAATTGACAGCATA
1 CAAAATTT-GACAGCATATATATACAAAATTGGACTGCATTTATACATCAAAAATTGACAGCATA
* *
13131204 TACATATATAATTGGACTGCATTTATACATCAAAAATTGACAGCATATACATATATATTTGGACT
65 TACATATATAATTGGACTGCACTTATACATCAAAAATTGACAGCATATACATATATAATTGGACT
13131269 GCATTTGTACAT
130 GCATTTGTACAT
* *
13131281 CAAAATTTGACAGCATATATATATATATAATTGGACTGCATTTATACGTCAAAAATTGACAGCAT
1 CAAAATTTGACAGCATATATATACA-A-AATTGGACTGCATTTATACATCAAAAATTGACAGCAT
13131346 ATACATATATAATTGGACTGC-CTTATACATCAAAAATTGACAGCATATACATATATAATTGGAC
64 ATACATATATAATTGGACTGCACTTATACATCAAAAATTGACAGCATATACATATATAATTGGAC
13131410 TGCATTTGTACAT
129 TGCATTTGTACAT
13131423 CAAAATTTGACAGCATATA
1 CAAAATTTGACAGCATATA
13131442 CATTCATTTA
Statistics
Matches: 153, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
139 6 0.04
140 8 0.05
141 8 0.05
142 74 0.48
143 57 0.37
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (141 bp):
CAAAATTTGACAGCATATATATACAAAATTGGACTGCATTTATACATCAAAAATTGACAGCATAT
ACATATATAATTGGACTGCACTTATACATCAAAAATTGACAGCATATACATATATAATTGGACTG
CATTTGTACAT
Found at i:13131821 original size:14 final size:15
Alignment explanation
Indices: 13131797--13131831 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
13131787 TATATACATT
13131797 ACCATATAAATACTA
1 ACCATATAAATACTA
13131812 ACCATA-AAATACTA
1 ACCATATAAATACTA
13131826 ATCCAT
1 A-CCAT
13131832 GATTAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (15 bp):
ACCATATAAATACTA
Found at i:13132577 original size:43 final size:43
Alignment explanation
Indices: 13132489--13132612 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 43
13132479 AGCTAGTACA
* *** * *
13132489 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-CCG
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA-AGTCG
13132532 ATGCC-ACCGTCCCAGACAG-GGTCTTACACAAAAACACAAGTCG
1 ATGCCGA-CGTCCCAGAC-GTGGTCTTACACAAAAACACAAGTCG
*
13132575 ATGCCGACGTCCCAGACGTGGTCTTACACGAAAACACA
1 ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACA
13132613 TATCGGAGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 3 0.04
43 65 0.93
44 2 0.03
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.18
Consensus pattern (43 bp):
ATGCCGACGTCCCAGACGTGGTCTTACACAAAAACACAAGTCG
Found at i:13137523 original size:10 final size:9
Alignment explanation
Indices: 13137367--13137542 Score: 51
Period size: 9 Copynumber: 19.0 Consensus size: 9
13137357 TTTATAGTCT
13137367 TTTTTATAA
1 TTTTTATAA
*
13137376 TTTTATGTTAA
1 TTTT-T-ATAA
*
13137387 TTTTAATACA
1 TTTTTATA-A
13137397 -TTTTATAA
1 TTTTTATAA
**
13137405 TATTTTATGG
1 T-TTTTATAA
13137415 TTTTTAT-A
1 TTTTTATAA
13137423 TTTTTATTAAA
1 TTTTTA-T-AA
** *
13137434 AATTTAAATA
1 TTTTTATA-A
*
13137444 TGTTTTGTTAA
1 T-TTTT-ATAA
*
13137455 TTTTATATAT
1 TTTT-TATAA
13137465 TTTTTATAA
1 TTTTTATAA
** *
13137474 CTGATTAGAA
1 -TTTTTATAA
13137484 TTTTTA-AA
1 TTTTTATAA
*
13137492 TTTTAAT-A
1 TTTTTATAA
13137500 -TTTTATAA
1 TTTTTATAA
*
13137508 TATTTATAA
1 TTTTTATAA
*
13137517 GTTTT-T-A
1 TTTTTATAA
13137524 TTTTTATAA
1 TTTTTATAA
*
13137533 GTTTATATAA
1 -TTTTTATAA
13137543 CTTAAAATTT
Statistics
Matches: 119, Mismatches: 29, Indels: 37
0.64 0.16 0.20
Matches are distributed among these distances:
7 10 0.08
8 18 0.15
9 39 0.33
10 33 0.28
11 18 0.15
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:13158071 original size:22 final size:24
Alignment explanation
Indices: 13158045--13158089 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
13158035 ATAAAAATGT
*
13158045 ATGAACATATAAAT-TT-TAAAAC
1 ATGAAAATATAAATATTATAAAAC
13158067 ATGAAAATATAAATATTATAAAA
1 ATGAAAATATAAATATTATAAAA
13158090 AATATGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 2 0.10
24 5 0.25
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
ATGAAAATATAAATATTATAAAAC
Found at i:13158096 original size:26 final size:25
Alignment explanation
Indices: 13158032--13158097 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 25
13158022 ATATGTACAT
* *
13158032 TTTATAAAAATGTATGAACATATAAA
1 TTTATAAAAA-ATATGAAAATATAAA
*
13158058 TTT-T--AAAACATGAAAATATAAA
1 TTTATAAAAAATATGAAAATATAAA
13158080 TATTATAAAAAATATGAA
1 T-TTATAAAAAATATGAA
13158098 TGTATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 13 0.41
23 5 0.16
24 1 0.03
25 1 0.03
26 12 0.38
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (25 bp):
TTTATAAAAAATATGAAAATATAAA
Found at i:13158107 original size:19 final size:18
Alignment explanation
Indices: 13158070--13158114 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
13158060 TTAAAACATG
13158070 AAAATATAAATATTATAA
1 AAAATATAAATATTATAA
* *
13158088 AAAATATGAATGTATATAA
1 AAAATATAAATAT-TATAA
*
13158107 AATATATA
1 AAAATATA
13158115 TAAACTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAATATAAATATTATAA
Found at i:13158847 original size:15 final size:15
Alignment explanation
Indices: 13158827--13158862 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
13158817 AATCTGTTTA
13158827 TTCTTTTCTT-GTATT
1 TTCTTTT-TTCGTATT
13158842 TTCTTTTTTCGTATT
1 TTCTTTTTTCGTATT
13158857 TTCTTT
1 TTCTTT
13158863 AACTTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.75
Consensus pattern (15 bp):
TTCTTTTTTCGTATT
Found at i:13160750 original size:25 final size:25
Alignment explanation
Indices: 13160709--13160845 Score: 127
Period size: 25 Copynumber: 5.5 Consensus size: 25
13160699 AGCTGTAAAC
* *
13160709 GGGAAGCTCCT-CTGAGCTGAATAAT
1 GGGAAGCTCATGC-GAGCTAAATAAT
* * *
13160734 GGGAAGCTTATGCGAGCTATATAAC
1 GGGAAGCTCATGCGAGCTAAATAAT
13160759 GGGAAGCTCATGCGAGCTAAAT-AT
1 GGGAAGCTCATGCGAGCTAAATAAT
* * * *
13160783 CCGGAAGTTCATGAGAGCTAAATATT
1 -GGGAAGCTCATGCGAGCTAAATAAT
* *
13160809 GTGAAGCTCATGCAAGCTAAAT-AT
1 GGGAAGCTCATGCGAGCTAAATAAT
13160833 CGGGAAGCTCATG
1 -GGGAAGCTCATG
13160846 AGAATGGTGG
Statistics
Matches: 89, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
24 2 0.02
25 85 0.96
26 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (25 bp):
GGGAAGCTCATGCGAGCTAAATAAT
Found at i:13160776 original size:50 final size:51
Alignment explanation
Indices: 13160692--13160845 Score: 149
Period size: 50 Copynumber: 3.1 Consensus size: 51
13160682 TCATGTATGC
* * * *
13160692 TCATACGAGCTGTA-AACGGGAAGCTCCT-CTGAGCTGAATAAT-GGGAAGCT
1 TCATGCGAGCTATATAACGGGAAGCTCATGC-GAGCTAAAT-ATCGGGAAGCT
*
13160742 T-ATGCGAGCTATATAACGGGAAGCTCATGCGAGCTAAATATCCGGAAG-T
1 TCATGCGAGCTATATAACGGGAAGCTCATGCGAGCTAAATATCGGGAAGCT
* * ** * *
13160791 TCATGAGAGCTAAATATTGTGAAGCTCATGCAAGCTAAATATCGGGAAGC-
1 TCATGCGAGCTATATAACGGGAAGCTCATGCGAGCTAAATATCGGGAAGCT
13160841 TCATG
1 TCATG
13160846 AGAATGGTGG
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
49 14 0.16
50 72 0.83
51 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (51 bp):
TCATGCGAGCTATATAACGGGAAGCTCATGCGAGCTAAATATCGGGAAGCT
Found at i:13161373 original size:25 final size:25
Alignment explanation
Indices: 13161346--13161474 Score: 150
Period size: 25 Copynumber: 5.2 Consensus size: 25
13161336 AAGCTCCTCT
* * *
13161346 GAGCTGAATAACGAGAAGTTCATGT
1 GAGCTGAATAACGGGAAGCTCATGC
*
13161371 GAGCTGAATAACGGGAAACTCATGC
1 GAGCTGAATAACGGGAAGCTCATGC
* * * *
13161396 GAGCTGTATAATGGAAATCTCATGC
1 GAGCTGAATAACGGGAAGCTCATGC
*
13161421 GAGCTGTATAACGGGAAGCTCATGC
1 GAGCTGAATAACGGGAAGCTCATGC
* * *
13161446 GAGCTAAATATCGGGAAGCTCATGA
1 GAGCTGAATAACGGGAAGCTCATGC
13161471 GAGC
1 GAGC
13161475 GGTGGTGTGT
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 89 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (25 bp):
GAGCTGAATAACGGGAAGCTCATGC
Found at i:13161468 original size:50 final size:50
Alignment explanation
Indices: 13161314--13161474 Score: 150
Period size: 50 Copynumber: 3.2 Consensus size: 50
13161304 ATTCATGTAT
* * * *
13161314 GCTCAT-ATGAGCTGTA-AACGAGAAGCTCCT-CTGAGCTGAATAACGAGAA
1 GCTCATGA-GAGCTGTATAACGGGAAGCTCATGC-GAGCTGAATATCGGGAA
* * * * * *
13161363 GTTCATGTGAGCTGAATAACGGGAAACTCATGCGAGCTGTATAAT-GGAAA
1 GCTCATGAGAGCTGTATAACGGGAAGCTCATGCGAGCTGAAT-ATCGGGAA
* * *
13161413 TCTCATGCGAGCTGTATAACGGGAAGCTCATGCGAGCTAAATATCGGGAA
1 GCTCATGAGAGCTGTATAACGGGAAGCTCATGCGAGCTGAATATCGGGAA
13161463 GCTCATGAGAGC
1 GCTCATGAGAGC
13161475 GGTGGTGTGT
Statistics
Matches: 87, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
49 14 0.16
50 71 0.82
51 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (50 bp):
GCTCATGAGAGCTGTATAACGGGAAGCTCATGCGAGCTGAATATCGGGAA
Found at i:13167054 original size:11 final size:10
Alignment explanation
Indices: 13166996--13167061 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 10
13166986 ATTTTCACAA
13166996 TTTATAATTAT
1 TTTATAATT-T
*
13167007 CTTT-TAAGTT
1 -TTTATAATTT
*
13167017 TTTGTAATTT
1 TTTATAATTT
13167027 GTTTATAA--T
1 -TTTATAATTT
13167036 TTTA-AATTCT
1 TTTATAATT-T
13167046 TTTATAATTT
1 TTTATAATTT
13167056 TTTATA
1 TTTATA
13167062 CAACTATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
7 2 0.04
8 4 0.09
9 4 0.09
10 18 0.40
11 14 0.31
12 3 0.07
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.64
Consensus pattern (10 bp):
TTTATAATTT
Found at i:13168546 original size:4 final size:4
Alignment explanation
Indices: 13168537--13168565 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
13168527 TGGTGTTTTG
13168537 CCAC CCAC CCAC CCAC CCAC CCAC CCAC C
1 CCAC CCAC CCAC CCAC CCAC CCAC CCAC C
13168566 AAATCTCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.76, G:0.00, T:0.00
Consensus pattern (4 bp):
CCAC
Found at i:13174473 original size:48 final size:48
Alignment explanation
Indices: 13174417--13174514 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
13174407 AACTTGAATC
13174417 TAAGCTGTGAAAGTTCCTGGAAAACAAGAAGAAGAATAGAACAATAAT
1 TAAGCTGTGAAAGTTCCTGGAAAACAAGAAGAAGAATAGAACAATAAT
13174465 TAAGCTGTGAAAGTTCCTGGAAAACAAGAAGAAGAATAGAACAATAAT
1 TAAGCTGTGAAAGTTCCTGGAAAACAAGAAGAAGAATAGAACAATAAT
13174513 TA
1 TA
13174515 TAAATTATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.19
Consensus pattern (48 bp):
TAAGCTGTGAAAGTTCCTGGAAAACAAGAAGAAGAATAGAACAATAAT
Found at i:13175512 original size:16 final size:16
Alignment explanation
Indices: 13175475--13175514 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
13175465 TTAATGAAAT
* *
13175475 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
13175491 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
13175507 TAAAATTA
1 TAAAATTA
13175515 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:13175599 original size:9 final size:9
Alignment explanation
Indices: 13175587--13175629 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
13175577 TTTATCAAAT
13175587 TATTAATTG
1 TATTAATTG
13175596 TATTAATTG
1 TATTAATTG
13175605 --TTAATTG
1 TATTAATTG
13175612 TATTAATTG
1 TATTAATTG
13175621 TATTAATTG
1 TATTAATTG
13175630 CTGTAACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.22
9 25 0.78
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (9 bp):
TATTAATTG
Found at i:13175603 original size:16 final size:16
Alignment explanation
Indices: 13175584--13175629 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
13175574 AAATTTATCA
13175584 AATTATTAATTGTATT
1 AATTATTAATTGTATT
*
13175600 AATTGTTAATTGTATT
1 AATTATTAATTGTATT
13175616 AATTGTATTAATTG
1 AA-T-TATTAATTG
13175630 CTGTAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 1 0.04
18 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (16 bp):
AATTATTAATTGTATT
Found at i:13177216 original size:23 final size:23
Alignment explanation
Indices: 13177168--13177217 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
13177158 TAAATCAAAC
*
13177168 TTAAAATAAAAACTATTATATTT
1 TTAAAATAAAAACTATTATATAT
*
13177191 TTAAAATAAAAA-TATATGTATAT
1 TTAAAATAAAAACTAT-TATATAT
13177214 TTAA
1 TTAA
13177218 TATATTCTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TTAAAATAAAAACTATTATATAT
Found at i:13179728 original size:18 final size:18
Alignment explanation
Indices: 13179705--13179742 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
13179695 CGACTCGATT
13179705 AAGCAACAAACAAGTAAA
1 AAGCAACAAACAAGTAAA
*
13179723 AAGCAACGAACAAGTAAA
1 AAGCAACAAACAAGTAAA
13179741 AA
1 AA
13179743 TAGCGGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.66, C:0.16, G:0.13, T:0.05
Consensus pattern (18 bp):
AAGCAACAAACAAGTAAA
Found at i:13183687 original size:15 final size:14
Alignment explanation
Indices: 13183667--13183697 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
13183657 ATTTAATTAA
13183667 TTTTTTAAAAATAAT
1 TTTTTTAAAAA-AAT
13183682 TTTTTTAAAAAAAT
1 TTTTTTAAAAAAAT
13183696 TT
1 TT
13183698 AAATTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTTTTAAAAAAAT
Found at i:13183707 original size:16 final size:16
Alignment explanation
Indices: 13183688--13183739 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
13183678 TAATTTTTTT
13183688 AAAAAAATTTAAATTA
1 AAAAAAATTTAAATTA
** *
13183704 AAAATCATTAAAATTA
1 AAAAAAATTTAAATTA
*
13183720 TAAAAAAATATAAATATA
1 -AAAAAAATTTAAAT-TA
13183738 AA
1 AA
13183740 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
16 13 0.48
17 12 0.44
18 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAAATTTAAATTA
Found at i:13186456 original size:21 final size:22
Alignment explanation
Indices: 13186432--13186473 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13186422 TTTTTTTACT
*
13186432 AATTTTATGT-TTTTTAATTTA
1 AATTTTATATGTTTTTAATTTA
13186453 AATTTTATATGTTTTTAATTT
1 AATTTTATATGTTTTTAATTT
13186474 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
AATTTTATATGTTTTTAATTTA
Found at i:13186479 original size:23 final size:21
Alignment explanation
Indices: 13186431--13186480 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
13186421 TTTTTTTTAC
*
13186431 TAATTTTATGTTTTTTAATTT
1 TAATTTTATATTTTTTAATTT
*
13186452 AAATTTTATATGTTTTTAATTTT
1 TAATTTTATAT-TTTTTAA-TTT
13186475 TAATTT
1 TAATTT
13186481 AAACTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.38
22 7 0.29
23 8 0.33
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
TAATTTTATATTTTTTAATTT
Found at i:13186502 original size:29 final size:29
Alignment explanation
Indices: 13186442--13186503 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
13186432 AATTTTATGT
* * **
13186442 TTTTTAATTTAAATTTTATATGTTTTTAA
1 TTTTTAATTTAAACTTTATACGGATTTAA
*
13186471 TTTTTAATTTAAACTTTATACGGATTTCA
1 TTTTTAATTTAAACTTTATACGGATTTAA
13186500 TTTT
1 TTTT
13186504 ATTTTTTGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (29 bp):
TTTTTAATTTAAACTTTATACGGATTTAA
Found at i:13188304 original size:21 final size:22
Alignment explanation
Indices: 13188263--13188314 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
13188253 TAAAATATAT
13188263 AAATTATTAAAAATTAGAAAAC
1 AAATTATTAAAAATTAGAAAAC
* *
13188285 AAATTA-TAAAAA-TCGTAAA-
1 AAATTATTAAAAATTAGAAAAC
13188304 AAATTATTAAA
1 AAATTATTAAA
13188315 TATATAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 6 0.22
20 9 0.33
21 6 0.22
22 6 0.22
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (22 bp):
AAATTATTAAAAATTAGAAAAC
Found at i:13188465 original size:10 final size:10
Alignment explanation
Indices: 13188450--13188549 Score: 57
Period size: 10 Copynumber: 10.2 Consensus size: 10
13188440 TTCTTATAAC
13188450 TTTATAAATT
1 TTTATAAATT
13188460 TTTAT-AATT
1 TTTATAAATT
* *
13188469 TTTTTCAATT
1 TTTATAAATT
13188479 TTTATAAATT
1 TTTATAAATT
*
13188489 TATTCT-AATT
1 T-TTATAAATT
*
13188499 TTTA-ATTATT
1 TTTATA-AATT
* *
13188509 TTAATATATT
1 TTTATAAATT
*
13188519 TTTATTAAAAT
1 TTTA-TAAATT
*
13188530 TTAAT-AA-T
1 TTTATAAATT
*
13188538 TTTATAACTT
1 TTTATAAATT
13188548 TT
1 TT
13188550 ATTTATTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
8 5 0.07
9 13 0.19
10 40 0.58
11 11 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTATAAATT
Found at i:13188480 original size:19 final size:20
Alignment explanation
Indices: 13188456--13188502 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
13188446 TAACTTTATA
* *
13188456 AATTTTTATAATTTTTTTC-
1 AATTTTTATAAATTTATTCT
13188475 AATTTTTATAAATTTATTCT
1 AATTTTTATAAATTTATTCT
13188495 AATTTTTA
1 AATTTTTA
13188503 ATTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTTTTATAAATTTATTCT
Found at i:13188559 original size:19 final size:18
Alignment explanation
Indices: 13188430--13188561 Score: 63
Period size: 19 Copynumber: 6.9 Consensus size: 18
13188420 TTATTTACAT
13188430 TTTTATATT-TTTCTTATAA
1 TTTTAT-TTATTT-TTATAA
* **
13188449 CTTTATAAATTTTTATAA
1 TTTTATTTATTTTTATAA
13188467 TTTT-TTTCAATTTTTATAA
1 TTTTATTT--ATTTTTATAA
* *
13188486 ATTTATTCTAATTTTTAATTA
1 TTTTATT-T-ATTTTT-ATAA
*
13188507 TTTTAATATATTTTTATTAAA
1 TTTT-ATTTATTTTTA-T-AA
* * *
13188528 ATTTA-ATAATTTTATAA
1 TTTTATTTATTTTTATAA
13188545 CTTTTATTTATTTTTAT
1 -TTTTATTTATTTTTAT
13188562 TTATTATATT
Statistics
Matches: 86, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
17 3 0.03
18 14 0.16
19 38 0.44
20 17 0.20
21 12 0.14
22 2 0.02
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATTTATTTTTATAA
Found at i:13194514 original size:23 final size:23
Alignment explanation
Indices: 13194471--13194514 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
13194461 TTAAAAGTCT
* *
13194471 ATATGTTAAAAAGATCTTTAAGA
1 ATATGTGAAAAAGATCATTAAGA
13194494 ATATGTGAAAAA-ATCAATTAA
1 ATATGTGAAAAAGATC-ATTAA
13194515 ATGTCTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.32
Consensus pattern (23 bp):
ATATGTGAAAAAGATCATTAAGA
Found at i:13194828 original size:31 final size:31
Alignment explanation
Indices: 13194780--13194839 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
13194770 TATTTAAAAT
* * *
13194780 TTTATAAAAATGTATAAACATTCTTAAAACA
1 TTTATAAAAATGCATAAAAATTATTAAAACA
13194811 TTTATAAAAAAT-CATAAAAATTATTAAAA
1 TTTAT-AAAAATGCATAAAAATTATTAAAA
13194840 ATATTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (31 bp):
TTTATAAAAATGCATAAAAATTATTAAAACA
Found at i:13194844 original size:9 final size:10
Alignment explanation
Indices: 13194738--13194847 Score: 54
Period size: 10 Copynumber: 11.1 Consensus size: 10
13194728 AAAATCTAAT
13194738 AAATT-TTAA
1 AAATTATTAA
13194747 TAAATTA-T-A
1 -AAATTATTAA
*
13194756 AAATTAATAA
1 AAATTATTAA
*
13194766 TAAA-TATTTA
1 -AAATTATTAA
*
13194776 AAATTTTATAA
1 AAATTAT-TAA
13194787 AAATGTA-TAA
1 AAAT-TATTAA
* *
13194797 ACATTCTTAA
1 AAATTATTAA
*
13194807 AACATTTATAAA
1 AA-A-TTATTAA
*
13194819 AAATCA-TAA
1 AAATTATTAA
13194828 AAATTATTAA
1 AAATTATTAA
13194838 AAA-TATTAA
1 AAATTATTAA
13194847 A
1 A
13194848 TTGATATAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 23
0.68 0.12 0.21
Matches are distributed among these distances:
8 6 0.08
9 20 0.26
10 31 0.41
11 11 0.14
12 8 0.11
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (10 bp):
AAATTATTAA
Found at i:13195534 original size:21 final size:19
Alignment explanation
Indices: 13195501--13195556 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
13195491 AATTTCATAA
13195501 TTTATTAAAATTTTTTAGATT
1 TTTATT-AAATTTTTTAG-TT
* * *
13195522 TTTAATAATATTTATAAGTT
1 TTTATTAA-ATTTTTTAGTT
13195542 TTTATTAAATTTTTT
1 TTTATTAAATTTTTT
13195557 TATAATTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 5 0.18
20 11 0.39
21 12 0.43
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTATTAAATTTTTTAGTT
Found at i:13195567 original size:9 final size:9
Alignment explanation
Indices: 13195484--13195634 Score: 67
Period size: 9 Copynumber: 15.4 Consensus size: 9
13195474 TTTAAATATG
13195484 TTTTATTAA-
1 TTTTA-TAAT
*
13195493 TTTCATAAT
1 TTTTATAAT
*
13195502 TTATTAAAAT
1 TT-TTATAAT
13195512 TTTT-TAGAT
1 TTTTATA-AT
13195521 TTTTAATAAT
1 TTTT-ATAAT
*
13195531 ATTTATAAGT
1 TTTTATAA-T
13195541 TTTTATTAAATTT
1 TTTTA-T-AA--T
13195554 TTTTATAAT
1 TTTTATAAT
*
13195563 TTTTACAAGT
1 TTTTATAA-T
*
13195573 TTATATCAAT
1 TTTTAT-AAT
* *
13195583 TTTAATTAT
1 TTTTATAAT
13195592 TTTT-TAAAT
1 TTTTAT-AAT
13195601 ATTTTA-AAT
1 -TTTTATAAT
13195610 TTTTATAATGAT
1 TTTTAT-A--AT
13195622 TTTTATAAT
1 TTTTATAAT
13195631 TTTT
1 TTTT
13195635 TTTTGATTTT
Statistics
Matches: 109, Mismatches: 15, Indels: 36
0.68 0.09 0.22
Matches are distributed among these distances:
8 10 0.09
9 42 0.39
10 32 0.29
11 8 0.07
12 11 0.10
13 6 0.06
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:13223453 original size:42 final size:42
Alignment explanation
Indices: 13223402--13223491 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
13223392 CATCAAGTGT
*
13223402 TTTC-TTCTTGCCTAAAATTGATTGAAGGAGATGACAATCTC
1 TTTCTTTCTTGCCTAAAATTGATTGAAAGAGATGACAATCTC
13223443 TTTCTTTCTTGCCTAAAATTGATTGAAAGAGATGACAATCTC
1 TTTCTTTCTTGCCTAAAATTGATTGAAAGAGATGACAATCTC
13223485 TTTCTTT
1 TTTCTTT
13223492 TCACTAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (42 bp):
TTTCTTTCTTGCCTAAAATTGATTGAAAGAGATGACAATCTC
Found at i:13252709 original size:6 final size:7
Alignment explanation
Indices: 13252690--13252718 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
13252680 ATCACTCAAG
13252690 ATAAAAA
1 ATAAAAA
13252697 ATAAAAA
1 ATAAAAA
13252704 ATAAAAA
1 ATAAAAA
13252711 ATAAAAA
1 ATAAAAA
13252718 A
1 A
13252719 AGAAGCATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
ATAAAAA
Found at i:13254440 original size:24 final size:25
Alignment explanation
Indices: 13254379--13254502 Score: 71
Period size: 24 Copynumber: 5.0 Consensus size: 25
13254369 AAAATTCATT
*
13254379 AATATTATGATATATGAAATATATA
1 AATATTATAATATATGAAATATATA
* *
13254404 AAT-TTA-AATTATATTAAGTA-ATA
1 AATATTATAA-TATATGAAATATATA
* * *
13254427 AATATTATAATATAAGTAATACATGA
1 AATATTATAATATATGAAATATAT-A
* * *
13254453 AATATATATAA-AT-TTAAACT-TTTT
1 AATAT-TATAATATATGAAA-TATATA
* *
13254477 AATATTGTGATATATGAAATATATA
1 AATATTATAATATATGAAATATATA
13254502 A
1 A
13254503 CCTTAAATAA
Statistics
Matches: 71, Mismatches: 18, Indels: 20
0.65 0.17 0.18
Matches are distributed among these distances:
23 10 0.14
24 30 0.42
25 17 0.24
26 9 0.13
27 5 0.07
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (25 bp):
AATATTATAATATATGAAATATATA
Found at i:13255453 original size:18 final size:18
Alignment explanation
Indices: 13255430--13255479 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
13255420 TTATAGTCCA
13255430 CCTCCACCACCTTCTTGG
1 CCTCCACCACCTTCTTGG
13255448 CCTCCACCACCTTCTTGG
1 CCTCCACCACCTTCTTGG
*
13255466 CATCCACCACCTTC
1 CCTCCACCACCTTC
13255480 GCCTCCACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.14, C:0.52, G:0.08, T:0.26
Consensus pattern (18 bp):
CCTCCACCACCTTCTTGG
Found at i:13255486 original size:15 final size:16
Alignment explanation
Indices: 13255430--13255488 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 16
13255420 TTATAGTCCA
13255430 CCTCCACCACCTTCTTGG
1 CCTCCACCACCTTC-T-G
13255448 CCTCCACCACCTTCTTGG
1 CCTCCACCACCTTC-T-G
*
13255466 CATCCACCACCTTC-G
1 CCTCCACCACCTTCTG
13255481 CCTCCACC
1 CCTCCACC
13255489 TGTTAGACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
15 8 0.21
18 31 0.79
ACGTcount: A:0.14, C:0.54, G:0.08, T:0.24
Consensus pattern (16 bp):
CCTCCACCACCTTCTG
Found at i:13256010 original size:135 final size:135
Alignment explanation
Indices: 13255768--13256040 Score: 528
Period size: 135 Copynumber: 2.0 Consensus size: 135
13255758 CACGTCCAAG
13255768 ACCGCTAAGGCAGCCAAGTCCAGCTTTAGCAGCACGACCTTTCTTAACATGTACATCACAATCTC
1 ACCGCTAAGGCAGCCAAGTCCAGCTTTAGCAGCACGACCTTTCTTAACATGTACATCACAATCTC
13255833 AAGGGATGGCTGAATCATCAGTGGCACTGGAACTAAACCCTTCTGGTTCTGCGACGCCTTCACAT
66 AAGGGATGGCTGAATCATCAGTGGCACTGGAACTAAACCCTTCTGGTTCTGCGACGCCTTCACAT
13255898 GCAAA
131 GCAAA
* *
13255903 ACCGCTAAGGCAGCCAAGTCCAGCTTTAGCAGCACGCCCTTTCTTAACATGTATATCACAATCTC
1 ACCGCTAAGGCAGCCAAGTCCAGCTTTAGCAGCACGACCTTTCTTAACATGTACATCACAATCTC
13255968 AAGGGATGGCTGAATCATCAGTGGCACTGGAACTAAACCCTTCTGGTTCTGCGACGCCTTCACAT
66 AAGGGATGGCTGAATCATCAGTGGCACTGGAACTAAACCCTTCTGGTTCTGCGACGCCTTCACAT
13256033 GCAAA
131 GCAAA
13256038 ACC
1 ACC
13256041 TGGTTTGACT
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 136 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (135 bp):
ACCGCTAAGGCAGCCAAGTCCAGCTTTAGCAGCACGACCTTTCTTAACATGTACATCACAATCTC
AAGGGATGGCTGAATCATCAGTGGCACTGGAACTAAACCCTTCTGGTTCTGCGACGCCTTCACAT
GCAAA
Found at i:13257328 original size:20 final size:21
Alignment explanation
Indices: 13257293--13257332 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
13257283 GTGTTTTATT
13257293 TAATTTATAAAAATAAAAATC
1 TAATTTATAAAAATAAAAATC
*
13257314 TAATTT-TATAAATAAAAAT
1 TAATTTATAAAAATAAAAAT
13257333 TCATTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATTTATAAAAATAAAAATC
Found at i:13259730 original size:2 final size:2
Alignment explanation
Indices: 13259723--13259754 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13259713 AATTCAAATC
13259723 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
13259755 TATTCATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:13259883 original size:48 final size:48
Alignment explanation
Indices: 13259823--13259991 Score: 221
Period size: 48 Copynumber: 3.5 Consensus size: 48
13259813 AGATTTCTCA
* * * * ** * *
13259823 GTGGCCTACACACAGTCCGTACCACCTTTGTGTAATAACAGACTCTCG
1 GTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATCG
* *
13259871 GTGGCCTGCACACAGTCTGTGCCACCCTTGTATCTTAACAGAATATTG
1 GTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATCG
*
13259919 GTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATTG
1 GTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATCG
* *
13259967 GCGGCCTGCATACAGTCCGTGCCAC
1 GTGGCCTGCACACAGTCCGTGCCAC
13259992 ATATACGACC
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 108 1.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.25
Consensus pattern (48 bp):
GTGGCCTGCACACAGTCCGTGCCACCCTTGTATCTTAACAGAATATCG
Found at i:13265332 original size:24 final size:24
Alignment explanation
Indices: 13265305--13265356 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13265295 TTAGTAAGTC
*
13265305 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
13265329 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
13265353 AAAT
1 AAAT
13265357 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:13267287 original size:24 final size:24
Alignment explanation
Indices: 13267260--13267311 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13267250 TTAGTAAGTC
*
13267260 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
13267284 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
13267308 AAAT
1 AAAT
13267312 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:13271198 original size:87 final size:87
Alignment explanation
Indices: 13271047--13271323 Score: 509
Period size: 87 Copynumber: 3.2 Consensus size: 87
13271037 ATACTCGATC
* *
13271047 ACCTTCTCGGTCTCCACCACAAAGTCGTCCACCTATTAGACGTACTCCTTCATATCCACCGCCTC
1 ACCTCCTCGGCCTCCACCACAAAGTCGTCCACCTATTAGACGTACTCCTTCATATCCACCGCCTC
13271112 GTACATTTCCTCCCTCATGTCA
66 GTACATTTCCTCCCTCATGTCA
*
13271134 ACCTCCTCGGCCTCCACCACAAAGTCGTCCACCTATTAGACATACTCCTTCATATCCACCGCCTC
1 ACCTCCTCGGCCTCCACCACAAAGTCGTCCACCTATTAGACGTACTCCTTCATATCCACCGCCTC
*
13271199 GTACATTTCCTCCCTCAAGTCA
66 GTACATTTCCTCCCTCATGTCA
*
13271221 ACCTCCTCGGCCTCCACCGCAAAGTCGTCCACCTATTAGACGTACTCCTTCATATCCACCGCCTC
1 ACCTCCTCGGCCTCCACCACAAAGTCGTCCACCTATTAGACGTACTCCTTCATATCCACCGCCTC
13271286 GTACATTTCCTCCCTCATGTCA
66 GTACATTTCCTCCCTCATGTCA
13271308 ACCTCCTCGGCCTCCA
1 ACCTCCTCGGCCTCCA
13271324 ACTCCAACGG
Statistics
Matches: 183, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 183 1.00
ACGTcount: A:0.21, C:0.43, G:0.10, T:0.26
Consensus pattern (87 bp):
ACCTCCTCGGCCTCCACCACAAAGTCGTCCACCTATTAGACGTACTCCTTCATATCCACCGCCTC
GTACATTTCCTCCCTCATGTCA
Found at i:13276517 original size:23 final size:23
Alignment explanation
Indices: 13276487--13276546 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
13276477 CCCCAAAACT
13276487 GACGGACAAGATTAAGTTACATC
1 GACGGACAAGATTAAGTTACATC
13276510 GACGGACAAGATTAAGTTACATC
1 GACGGACAAGATTAAGTTACATC
*
13276533 GACGGACGAGATTA
1 GACGGACAAGATTA
13276547 GCCATATCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (23 bp):
GACGGACAAGATTAAGTTACATC
Found at i:13283795 original size:2 final size:2
Alignment explanation
Indices: 13283788--13283831 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
13283778 CTCTGCAAGA
*
13283788 AG AG AG AG AG AG AG AG AG -G AG -G AG AG AG AG GG AG AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13283827 -G AG AG
1 AG AG AG
13283832 GNNNNNNNNN
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13283814 original size:18 final size:18
Alignment explanation
Indices: 13283791--13283831 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
13283781 TGCAAGAAGA
13283791 GAGAGAGAGAGAGAGGAG
1 GAGAGAGAGAGAGAGGAG
*
13283809 GAGAGAGAGGGAGAGGAG
1 GAGAGAGAGAGAGAGGAG
13283827 GAGAG
1 GAGAG
13283832 GNNNNNNNNN
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (18 bp):
GAGAGAGAGAGAGAGGAG
Found at i:13288069 original size:10 final size:10
Alignment explanation
Indices: 13288054--13288263 Score: 147
Period size: 10 Copynumber: 20.8 Consensus size: 10
13288044 NNNNNNNNNN
*
13288054 GAGGGAGAGG
1 GAGGGAGAGA
* *
13288064 GAGGGACAGC
1 GAGGGAGAGA
*
13288074 GAGCGG-GAGG
1 GAG-GGAGAGA
*
13288084 GAGAGAGA--
1 GAGGGAGAGA
13288092 GAGGGAGAGA
1 GAGGGAGAGA
*
13288102 GAAGGAGAGAGG
1 G-AGG-GAGAGA
*
13288114 GAGGGAGGGA
1 GAGGGAGAGA
*
13288124 GAGCGAGAGA
1 GAGGGAGAGA
* *
13288134 GAGGGGGAAA
1 GAGGGAGAGA
* * *
13288144 GAGGAAGGGG
1 GAGGGAGAGA
*
13288154 GAGGGAGAGT
1 GAGGGAGAGA
* *
13288164 GAGGAAGAGG
1 GAGGGAGAGA
*
13288174 GAGGGAGAGT
1 GAGGGAGAGA
13288184 GAGGAAGAGAGA
1 GAGG--GAGAGA
*
13288196 GAGAGAGAGA
1 GAGGGAGAGA
13288206 GAGGGAGAGA
1 GAGGGAGAGA
*
13288216 GAGAGAGAGA
1 GAGGGAGAGA
*
13288226 GAGAGAGAGA
1 GAGGGAGAGA
*
13288236 GAGAGAGAGA
1 GAGGGAGAGA
*
13288246 GAGAGAGAGA
1 GAGGGAGAGA
*
13288256 GAGAGAGA
1 GAGGGAGA
13288264 AATTACATGT
Statistics
Matches: 162, Mismatches: 30, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
8 7 0.04
9 1 0.01
10 132 0.81
11 8 0.05
12 14 0.09
ACGTcount: A:0.40, C:0.02, G:0.57, T:0.01
Consensus pattern (10 bp):
GAGGGAGAGA
Found at i:13288135 original size:4 final size:4
Alignment explanation
Indices: 13288084--13288263 Score: 160
Period size: 4 Copynumber: 47.0 Consensus size: 4
13288074 GAGCGGGAGG
* * * * *
13288084 GAGA GAGA GAGG GAGA GAGA -AG- GAGA GAGG GAGG GAGG GAGA GCGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * * * * * * *
13288130 GAGA GAGG GGGA AAGA G-GA -AGG GGGA GGGA GAGT GAG- GA-A GAGG
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * *
13288174 GAGG GAGA GTGA G-GA -AGA GAGA GAGA GAGA GAGA GGGA GAGA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
13288220 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
13288264 AATTACATGT
Statistics
Matches: 146, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
3 15 0.10
4 131 0.90
ACGTcount: A:0.42, C:0.01, G:0.56, T:0.01
Consensus pattern (4 bp):
GAGA
Found at i:13289609 original size:24 final size:24
Alignment explanation
Indices: 13289594--13289645 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13289584 AATCAATGTC
* *
13289594 AAATATATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATGCT
*
13289618 AAATAAATTATACTAATAAATGAT
1 AAATAAATTATACTAATAAATGCT
13289642 AAAT
1 AAAT
13289646 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATGCT
Found at i:13290688 original size:36 final size:35
Alignment explanation
Indices: 13290608--13290700 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 35
13290598 ACTCTCTGTT
* **
13290608 TTGGTGTGTTTTGGTTGGACTAGCTCTTTGGAGCCA
1 TTGGTGTGTTTTGGTTGGATTAGCTCTTT-GAAACA
* *
13290644 TTGATGTGTTTTGGATGGATTAGCTCTTAT-AAACA
1 TTGGTGTGTTTTGGTTGGATTAGCTCTT-TGAAACA
13290679 TCTGGTGTGTTTTGGTTGGATT
1 T-TGGTGTGTTTTGGTTGGATT
13290701 TTCGATGTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
35 4 0.08
36 43 0.90
37 1 0.02
ACGTcount: A:0.15, C:0.10, G:0.30, T:0.45
Consensus pattern (35 bp):
TTGGTGTGTTTTGGTTGGATTAGCTCTTTGAAACA
Found at i:13291606 original size:12 final size:12
Alignment explanation
Indices: 13291589--13291618 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13291579 TCAGTGAGTT
13291589 ACACAGCCTGGC
1 ACACAGCCTGGC
*
13291601 ACACAGCTTGGC
1 ACACAGCCTGGC
13291613 ACACAG
1 ACACAG
13291619 ACATGTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.37, G:0.23, T:0.10
Consensus pattern (12 bp):
ACACAGCCTGGC
Found at i:13293444 original size:24 final size:24
Alignment explanation
Indices: 13293411--13293468 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
13293401 AATTCTAGTG
* *
13293411 AATGTCAAATATATTATGCTAATA
1 AATGTTAAATATATTATACTAATA
*
13293435 AATGTTAAATATGTTATACTAATA
1 AATGTTAAATATATTATACTAATA
*
13293459 AATATTAAAT
1 AATGTTAAAT
13293469 CTTCTAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (24 bp):
AATGTTAAATATATTATACTAATA
Found at i:13294720 original size:23 final size:22
Alignment explanation
Indices: 13294692--13294736 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
13294682 TTTTTTTTTA
13294692 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTGCATCAAG-TCTTT
*
13294715 TTAAGTTTTTCATCAAGTCTTT
1 TTAAGTTTTGCATCAAGTCTTT
13294737 GCATAAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.53
Consensus pattern (22 bp):
TTAAGTTTTGCATCAAGTCTTT
Found at i:13294761 original size:13 final size:12
Alignment explanation
Indices: 13294642--13294766 Score: 65
Period size: 12 Copynumber: 9.8 Consensus size: 12
13294632 TCTTCAAGTA
13294642 TTTTTCATCAAG
1 TTTTTCATCAAG
*
13294654 TTCTTTTATCAAG
1 TT-TTTCATCAAG
*
13294667 TTTTTAATTACCAAG
1 TTTTTCA-T--CAAG
* *
13294682 TTTTTTTTTATTAAG
1 ---TTTTTCATCAAG
*
13294697 TTTTGCATCAAG
1 TTTTTCATCAAG
*
13294709 TTCTTT--TTAAG
1 TT-TTTCATCAAG
13294720 TTTTTCATCAAG
1 TTTTTCATCAAG
* *
13294732 TCTTTGCATAAAG
1 T-TTTTCATCAAG
*
13294745 TTTTCCATCAAG
1 TTTTTCATCAAG
*
13294757 TTTTTAATCA
1 TTTTTCATCA
13294767 TTATGTTTTT
Statistics
Matches: 86, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
10 3 0.03
11 6 0.07
12 39 0.45
13 24 0.28
15 7 0.08
17 1 0.01
18 6 0.07
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.52
Consensus pattern (12 bp):
TTTTTCATCAAG
Found at i:13295984 original size:20 final size:20
Alignment explanation
Indices: 13295951--13295989 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13295941 TTATCGGGGT
*
13295951 AAATTATAATTAAGATTATG
1 AAATTATAAGTAAGATTATG
* *
13295971 AAATTATTAGTAAGTTTAT
1 AAATTATAAGTAAGATTAT
13295990 TTTTAGTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (20 bp):
AAATTATAAGTAAGATTATG
Found at i:13297640 original size:24 final size:24
Alignment explanation
Indices: 13297612--13297663 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
13297602 TTAGTAAGTC
* *
13297612 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
13297636 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
13297660 AAAT
1 AAAT
13297664 TTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:13304561 original size:30 final size:30
Alignment explanation
Indices: 13304526--13304586 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
13304516 AAGATAACCA
13304526 ATGAGAGAGACAACATCTAGGAAAGAATCC
1 ATGAGAGAGACAACATCTAGGAAAGAATCC
13304556 ATGAGAGAGACAACATCTAGGAAAGAATCC
1 ATGAGAGAGACAACATCTAGGAAAGAATCC
13304586 A
1 A
13304587 CCTAGACTTC
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (30 bp):
ATGAGAGAGACAACATCTAGGAAAGAATCC
Done.