Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold46
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: 2524624
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 119418 characters in sequence are not A, C, G, or T
File 14 of 15
Found at i:2207105 original size:20 final size:21
Alignment explanation
Indices: 2207026--2207104 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
2207016 AATGTCCAAA
*
2207026 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
2207046 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
2207071 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
2207091 TTGTATCGATACAT
1 ATGTATCGATACAT
2207105 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:2207109 original size:13 final size:13
Alignment explanation
Indices: 2207091--2207129 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2207081 ACATTTTTCT
2207091 TTGTATCGATACA
1 TTGTATCGATACA
2207104 TTGTATCGATACA
1 TTGTATCGATACA
*
2207117 CTGTATCGATACA
1 TTGTATCGATACA
2207130 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2208960 original size:34 final size:34
Alignment explanation
Indices: 2208917--2208986 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
2208907 GAAATAAATT
2208917 TTGATATGAATTACTTGATTAAGGGGGAGATTTA
1 TTGATATGAATTACTTGATTAAGGGGGAGATTTA
2208951 TTGATATGAATTACTTGATTAAGGGGGAGATTTA
1 TTGATATGAATTACTTGATTAAGGGGGAGATTTA
2208985 TT
1 TT
2208987 AATAAACGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.40
Consensus pattern (34 bp):
TTGATATGAATTACTTGATTAAGGGGGAGATTTA
Found at i:2209629 original size:20 final size:20
Alignment explanation
Indices: 2209606--2209678 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2209596 ACAATTCAAA
2209606 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2209626 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2209647 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2209667 GTATCGATACAT
1 GTATCGATACAT
2209679 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2209650 original size:21 final size:21
Alignment explanation
Indices: 2209624--2209699 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2209614 ACATGTTGCA
2209624 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2209645 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2209665 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2209686 ATGTATCGATACAT
1 ATGTATCGATACAT
2209700 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2209657 original size:41 final size:41
Alignment explanation
Indices: 2209606--2209699 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2209596 ACAATTCAAA
*
2209606 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2209647 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2209688 GTATCGATACAT
1 GTATCGATACAT
2209700 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2209756 original size:13 final size:13
Alignment explanation
Indices: 2209738--2209763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2209728 TACAGCAAGT
2209738 ATGTATCGATACA
1 ATGTATCGATACA
2209751 ATGTATCGATACA
1 ATGTATCGATACA
2209764 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2210617 original size:49 final size:50
Alignment explanation
Indices: 2210518--2210647 Score: 219
Period size: 49 Copynumber: 2.6 Consensus size: 50
2210508 TAAGCTTTCA
2210518 GAGACAAAAACATACAGAGGCATGCATGAGAAAGCATAAAAATTGCAATTG
1 GAGAC-AAAACATACAGAGGCATGCATGAGAAAGCATAAAAATTGCAATTG
2210569 GAGACAAAACATACAGAGGCATGCATG-GAAAGCATAAAAATTGCAATTG
1 GAGACAAAACATACAGAGGCATGCATGAGAAAGCATAAAAATTGCAATTG
* *
2210618 GAGACAAAA-ATGCAGAGGCATGCAAGAGAA
1 GAGACAAAACATACAGAGGCATGCATGAGAA
2210648 TGGAAAAAAG
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
48 15 0.20
49 34 0.45
50 22 0.29
51 5 0.07
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (50 bp):
GAGACAAAACATACAGAGGCATGCATGAGAAAGCATAAAAATTGCAATTG
Found at i:2211047 original size:44 final size:44
Alignment explanation
Indices: 2210992--2211078 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
2210982 AACAGTGAGC
*
2210992 AGCAACACCAGCAACGACTGCAGCTCCAGCACGCAACAACAGCA
1 AGCAACACCAGCAACGACTGCAACTCCAGCACGCAACAACAGCA
* * * *
2211036 AGCAACTCCAGCAGCGACTGCAACTCCAGCATGCAACAGCAGC
1 AGCAACACCAGCAACGACTGCAACTCCAGCACGCAACAACAGC
2211079 TCCAGCGAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.36, C:0.38, G:0.20, T:0.07
Consensus pattern (44 bp):
AGCAACACCAGCAACGACTGCAACTCCAGCACGCAACAACAGCA
Found at i:2212053 original size:50 final size:50
Alignment explanation
Indices: 2211999--2212117 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
2211989 CAATTGCTCA
**
2211999 TAATCAGGATACTCCAACCCCG-GTTTATTTTTCAAAACACCAA-TTTCC
1 TAATCAGGATACTCCAACCCCGAGTTTATTTCCCAAAACACCAATTTTCC
* * * *
2212047 TTTAATCGGGATACTCAAACTCCGATTTTATTTCCCAAAACACCAATTTTCC
1 --TAATCAGGATACTCCAACCCCGAGTTTATTTCCCAAAACACCAATTTTCC
2212099 -AATCGAGGATACTCCAACC
1 TAATC-AGGATACTCCAACC
2212118 TCGTTATCTC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
49 4 0.07
50 30 0.53
51 18 0.32
52 5 0.09
ACGTcount: A:0.32, C:0.29, G:0.09, T:0.30
Consensus pattern (50 bp):
TAATCAGGATACTCCAACCCCGAGTTTATTTCCCAAAACACCAATTTTCC
Found at i:2212092 original size:51 final size:50
Alignment explanation
Indices: 2211999--2212095 Score: 131
Period size: 51 Copynumber: 1.9 Consensus size: 50
2211989 CAATTGCTCA
* **
2211999 TAATCAGGATACTCCAACCCCGGTTTATTTTTCAAAACACCAATTTCCTT
1 TAATCAGGATACTCAAACCCCGGTTTATTTCCCAAAACACCAATTTCCTT
* * *
2212049 TAATCGGGATACTCAAACTCCGATTTTATTTCCCAAAACACCAATTT
1 TAATCAGGATACTCAAACCCCG-GTTTATTTCCCAAAACACCAATTT
2212096 TCCAATCGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 19 0.47
51 21 0.52
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (50 bp):
TAATCAGGATACTCAAACCCCGGTTTATTTCCCAAAACACCAATTTCCTT
Found at i:2212262 original size:49 final size:51
Alignment explanation
Indices: 2212131--2212400 Score: 270
Period size: 50 Copynumber: 5.4 Consensus size: 51
2212121 TTATCTCCGA
* * * * *
2212131 GGGGATACTCCAACCCCGGCTTT-ATTTCCAAAATA-TGA-TTTCTCTTAATG
1 GGGGATACTCCAACCCCGG-TTTCATTTTCAAAACACTAACTTT-TCATAATC
* *
2212181 GGGGATACTGCAACCCCGGTTTTCATTCT-AAAACACTAACTTTTCATAAT-
1 GGGGATACTCCAACCCCGG-TTTCATTTTCAAAACACTAACTTTTCATAATC
*
2212231 GGGGGTACTCCAACCCCGGTTTCATTTT-AAAACACTAACTTTTCATAATC
1 GGGGATACTCCAACCCCGGTTTCATTTTCAAAACACTAACTTTTCATAATC
* * * * * * *
2212281 GGGGATACTCTAAACCCGGTTTTATTTTTCAAAACACCAAATTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTCA-TTTTCAAAACACTAACTTTTC-ATAATC
2212334 GGGGATACTCCAACCCCGGTTT-ATTTTCAAAACA-TCAA-TTTTCATAATC
1 GGGGATACTCCAACCCCGGTTTCATTTTCAAAACACT-AACTTTTCATAATC
* *
2212383 AGGGATATTCCAACCCCG
1 GGGGATACTCCAACCCCG
2212401 TTATTTTCGA
Statistics
Matches: 187, Mismatches: 25, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
49 50 0.27
50 67 0.36
51 28 0.15
52 17 0.09
53 25 0.13
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTCATTTTCAAAACACTAACTTTTCATAATC
Found at i:2212588 original size:77 final size:78
Alignment explanation
Indices: 2212334--2212707 Score: 534
Period size: 78 Copynumber: 4.9 Consensus size: 78
2212324 TCCTTTAATC
* * *
2212334 GGGGATACTCCAACCCCGG-TTTATTTTCAAAACATCAA-TTTTCATAATCAGGGATATTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTCT-AAAACATCAATTTTTCATAATCGGGGATACTCCAAC
2212397 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* *
2212411 AGGGATACTCCAATCCCGGTTTTATCTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAA-
1 GGGGATACTCCAACCCCGGTTTTAT-TCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
2212475 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * *
2212489 GGGGATA-TCCAACCCCGGTTTTATTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACC
1 GGGGATACTCCAACCCCGGTTTTATTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACC
*
2212553 CC-TTATTTCCGA
66 CCGTTATTTTCGA
*
2212565 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTA-TTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
*
2212630 CCCGTTA-TTTCAA
65 CCCGTTATTTTCGA
*
2212643 GGGGATACTCCAA--CC-GTTTTATTTCTAAAACATCAATTTTTCATAA-CGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGGTTTTA-TTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
2212704 CCCG
65 CCCG
2212708 ATTTTAATTT
Statistics
Matches: 271, Mismatches: 19, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
74 18 0.07
75 30 0.11
76 53 0.20
77 52 0.19
78 91 0.34
79 27 0.10
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGGTTTTATTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACC
CCGTTATTTTCGA
Found at i:2212615 original size:154 final size:156
Alignment explanation
Indices: 2212334--2212707 Score: 541
Period size: 154 Copynumber: 2.4 Consensus size: 156
2212324 TCCTTTAATC
* * *
2212334 GGGGATACTCCAACCCCGG-TTTATTTTCAAAACATCAA-TTTTCATAATCAGGGATATTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTCT-AAAACATCAATTTTTCATAATCGGGGATACTCCAAC
* * *
2212397 CCCGTTATTTTCGAAGGGATACTCCAATCCCGGTTTTATCTCTAAAACATCAATTTTTCATAATC
65 CCCGTTATTTCCGAAGGGATACTCCAACCCCGGTTTTATCTCTAAAACACCAATTTTTCATAATC
*
2212462 GGGGATACTCCAA-CCCGTTATTTTCGA
130 GGGGATACTCCAACCCCGTTA-TTTCAA
* * *
2212489 GGGGATA-TCCAACCCCGGTTTTATTCTAAAATATTAATTTTTCACAATCGGGGATACTCCAACC
1 GGGGATACTCCAACCCCGGTTTTATTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACC
* *
2212553 CC-TTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCG
66 CCGTTATTTCCGAAGGGATACTCCAACCCCGGTTTTATCTCTAAAACACCAATTTTTCATAATCG
2212617 GGGATACTCCAACCCCGTTATTTCAA
131 GGGATACTCCAACCCCGTTATTTCAA
*
2212643 GGGGATACTCCAA--CC-GTTTTATTTCTAAAACATCAATTTTTCATAA-CGGGGATACTCTAAC
1 GGGGATACTCCAACCCCGGTTTTA-TTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
2212704 CCCG
65 CCCG
2212708 ATTTTAATTT
Statistics
Matches: 197, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
152 23 0.12
153 23 0.12
154 100 0.51
155 51 0.26
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (156 bp):
GGGGATACTCCAACCCCGGTTTTATTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACC
CCGTTATTTCCGAAGGGATACTCCAACCCCGGTTTTATCTCTAAAACACCAATTTTTCATAATCG
GGGATACTCCAACCCCGTTATTTCAA
Found at i:2218205 original size:1 final size:1
Alignment explanation
Indices: 2218201--2218855 Score: 176
Period size: 1 Copynumber: 655.0 Consensus size: 1
2218191 TAGACCCGCC
* ** * * *
2218201 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTGGTTGTGTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *** ** * * **
2218266 TGTGTTTGTTTTTTTTTTTTTTTTTTTTTGTTTGTTATTGGGTTTAATTTATTTTGTTTTGGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * * * * * * * *
2218331 TGTTTGGTTTTTTTTTTTTGTTTTTATTTGTTTGTTGTTTTTTTTGTTTTTGTTTCTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *** * * * * * * * ******
2218396 TTTTTTTTTTTTTTTTTTTGTTTATGGGTTGTTGTTTTGTTTTTTGTATTTTTGTGTTTCCCCCC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * ** * * * * *
2218461 ATTGTTTGTTTTTTTTTTTGTTGGTTTTTTTTTTTGTTGTTATTTTTTTTTTTTTTTGTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * ** ** * * * ** *
2218526 TTTTTTTGTTTTTTTTGTTGTTTGGTTGGTTTTTTTGTTGTTTTTTTTTTTGTTGGTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * * * *******
2218591 TTTTTGTTTTTTTTTGGTTTTTTTGTTTTTTTGTTTTTTGTTTTTTTTTTTTGTTTTTCCCCCCA
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** * ** * * * ** * * * *
2218656 CCTTTTAGTGTTGATTTTTGTTGTTTTTTGTTTTTTTTTTTTTTGGTGTTTATTTGTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * ** * *** *
2218721 TGTTGTTTTTTTTTTGTTTTTTTTTGGTTTTTTTGTTTTGGGTTTTTTTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *** * * * *
2218786 TTTTTGTTTTTTTTTTTATTTTTTTTATTTGTGGGTTTTTTATGTTTTATTTTTTTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2218851 TTTTT
1 TTTTT
2218856 GTTGGTTGTG
Statistics
Matches: 467, Mismatches: 187, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 467 1.00
ACGTcount: A:0.03, C:0.02, G:0.14, T:0.81
Consensus pattern (1 bp):
T
Found at i:2218332 original size:65 final size:61
Alignment explanation
Indices: 2218212--2218414 Score: 202
Period size: 62 Copynumber: 3.3 Consensus size: 61
2218202 TTTTTTTTTT
* * * * *
2218212 TTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTGGTTGTGTTTTTTGTTTTTTTTTGTGTTTG
1 TTTTTTTTTTTTTTTTTTTTTGTTTGTTATTGGGTTGTGTTTTTTGTTTTGTTTTGT-TTGG
*
2218274 TTTTTTTTTTTTTTTTTTTTTGTTTGTTATTGGGTT-TAATTTATTTTGTTTTGGTTTTGTTTGG
1 TTTTTTTTTTTTTTTTTTTTTGTTTGTTATTGGGTTGT--GTT-TTTTGTTTT-GTTTTGTTTGG
* * ** *
2218338 TTTTTTTTTTTTGTTTTTATTTGTTTGTTGTT-TTTTTTG-TTTTTGTTTCT-TTTT-TTT-G
1 TTTTTTTTTTTT-TTTTTTTTTGTTTGTTATTGGGTTGTGTTTTTTGTTT-TGTTTTGTTTGG
2218396 TTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTT
2218415 GTTTATGGGT
Statistics
Matches: 122, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
57 6 0.05
58 13 0.11
59 3 0.02
60 4 0.03
61 9 0.07
62 35 0.29
63 2 0.02
64 26 0.21
65 24 0.20
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.84
Consensus pattern (61 bp):
TTTTTTTTTTTTTTTTTTTTTGTTTGTTATTGGGTTGTGTTTTTTGTTTTGTTTTGTTTGG
Found at i:2218481 original size:116 final size:112
Alignment explanation
Indices: 2218347--2218647 Score: 299
Period size: 116 Copynumber: 2.6 Consensus size: 112
2218337 GTTTTTTTTT
2218347 TTTGTTTTTATTTGTTTGTTGTTTTTTTTGTTTTTGTTTCTTTTTTTTGTTTTTTTTTTTTTTTT
1 TTTGTTTTT-TTT-TTTGTTGTTTTTTTTGTTTTTGTTT-TTTTTTTTGTTTTTTTTTTTTTTTT
* *
2218412 TTTGTTTATGGGTTGTTGTTTTGTT-TTTTGTATTTTTGTGTTTCCCCCCATTG
63 TTTGTTT-T-GGTTGTTGTTTGGTTGTTTT-T-TTGTTGTGTTTCCCCCCATTG
2218465 TTTGTTTTTTTTTTTGTTGGTTTTTTTT-TTTGTTGTTATTTTTTTTT-TTTTTTGTTATTTTTT
1 TTTGTTTTTTTTTTTGTT-GTTTTTTTTGTTT-TTGTT-TTTTTTTTTGTTTTTT-TT-TTTTTT
** * *******
2218528 TTTTTGTTTTTTTTGTTGTTTGGTTGGTTTTTTTGTTGTTTTTTTTTTTGTTG
61 TTTTTGTTTTGGTTGTTGTTTGGTT-GTTTTTTTGTTGTGTTTCCCCCCATTG
* * * *
2218581 GTTGTTTTTTTTTTTG-T-TTTTTTTTGGTTTT-TTTGTTTTTTTGTTTTTTGTTTTTTTTTTTT
1 TTTGTTTTTTTTTTTGTTGTTTTTTTTGTTTTTGTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTT
2218643 GTTTT
66 GTTTT
2218648 TCCCCCCACC
Statistics
Matches: 158, Mismatches: 16, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
110 16 0.10
111 9 0.06
112 8 0.05
113 10 0.06
114 2 0.01
115 1 0.01
116 54 0.34
117 29 0.18
118 29 0.18
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.81
Consensus pattern (112 bp):
TTTGTTTTTTTTTTTGTTGTTTTTTTTGTTTTTGTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTT
GTTTTGGTTGTTGTTTGGTTGTTTTTTTGTTGTGTTTCCCCCCATTG
Found at i:2218564 original size:136 final size:131
Alignment explanation
Indices: 2218330--2218578 Score: 318
Period size: 132 Copynumber: 1.9 Consensus size: 131
2218320 TGTTTTGGTT
2218330 TTGTTTGGTTTTTTTTTTTTGTTTTTATTTGTTTGTTGTTTTTTTTGTTTTTGTTTCTTTTTTTT
1 TTGTTTGGTTTTTTTTTTTTGTTTTTATTTGTTTGTTGTTTTTTTTGTTTTTGTTTCTTTTTTTT
2218395 GTTTTTTTTTTTTTTTTTTTGTTTATGGGTTGTTGTTTTGTTTTTTGTATTTTTGTGTTTCCCCC
66 GTTTTTTTTTTTTTTTTTTTGTTTAT-GGTTGTTGTTTTGTTTTTTGTATTTTTGTGTTTCCCCC
2218460 CA
130 CA
* *
2218462 TTGTTTGTTTTTTTTTTTGTTGGTTTTT-TTT-TTTGTTGTTATTTTTT-TTTTT-TTT-TGTTA
1 TTGTTTGGTTTTTTTTTT-TT-GTTTTTATTTGTTTGTTGTT-TTTTTTGTTTTTGTTTCT-TTT
* * * *
2218522 TTTT-TTTTTTTGTTTTTTTTGTTG-TT-TGGTTGGTTTTTTTGTTGTTTT-TTTTTTTGT
62 TTTTGTTTTTTTTTTTTTTTTTTTGTTTATGGTT-GTTGTTTTGTT-TTTTGTATTTTTGT
2218579 TGGTTGTTTT
Statistics
Matches: 105, Mismatches: 6, Indels: 16
0.83 0.05 0.13
Matches are distributed among these distances:
127 4 0.04
128 19 0.18
129 6 0.06
130 19 0.18
131 9 0.09
132 31 0.30
133 11 0.10
134 6 0.06
ACGTcount: A:0.02, C:0.03, G:0.15, T:0.80
Consensus pattern (131 bp):
TTGTTTGGTTTTTTTTTTTTGTTTTTATTTGTTTGTTGTTTTTTTTGTTTTTGTTTCTTTTTTTT
GTTTTTTTTTTTTTTTTTTTGTTTATGGTTGTTGTTTTGTTTTTTGTATTTTTGTGTTTCCCCCC
A
Found at i:2218674 original size:101 final size:97
Alignment explanation
Indices: 2218361--2218745 Score: 297
Period size: 97 Copynumber: 3.8 Consensus size: 97
2218351 TTTTTATTTG
* * *
2218361 TTTGTTGTTTTTTTTGTTT-TT-GTT-TCTTTTT-TTTGTTTTTTTTTTTTTTTTTTTGTTTATG
1 TTTG-TGTTTTTTTT-TTTGTTGGTTGTTTTTTTTTTTGTTGTTTTTTTGTTTTTTTTGTTT-T-
* *
2218422 GGTTGTTGTTTTGTTTTTTGTATTTTTGTGTTTCCCCCCAT
62 --TT-TTTTTTTGTTTTTT-T-TTTTTGTTTTTCCCCCCAT
*
2218463 TGTT-TGTTTTTTTTTTTGTTGGTT-TTTTTTTTTGTTGTTATTTTTTT-TTTTTTTTGTTATTT
1 T-TTGTGTTTTTTTTTTTGTTGGTTGTTTTTTTTT-TTGTTGTTTTTTTGTTTTTTTTGTT-TTT
* *****
2218525 TTTTTTTTG-TTTTTTTTGTTGTTTGGTT--GGTTTT
63 TTTTTTTTGTTTTTTTTTTTTGTTT--TTCCCCCCAT
*
2218559 TTTGTTGTTTTTTTTTTTGTTGGTTGTTTTTTTTTTTGTT-TTTTTTTGGTTTTTTTGTTTTTTT
1 TTTG-TGTTTTTTTTTTTGTTGGTTGTTTTTTTTTTTGTTGTTTTTTTGTTTTTTTTGTTTTTTT
2218623 GTTTTTTGTTTTTTTTTTTTGTTTTTCCCCCCACCT
65 -TTTTTTGTTTTTTTTTTTTGTTTTTCCCCCCA--T
* * * * *
2218659 TTTAGTGTTGATTTTTGTTGTTTTTTGTTTTTTTTTTTTTTGGTGTTTATTTGTTTGTTTTTTGT
1 TTT-GTGTT--TTTTT-TT-TTGTTGGTTGTTTTTTTTTTTGTTGTTTTTTTG-TT-TTTTTTGT
*
2218724 TGTTTTTTTTTTGTTTTTTTTT
59 TTTTTTTTTTTTGTTTTTTTTT
2218746 GGTTTTTTTG
Statistics
Matches: 233, Mismatches: 24, Indels: 48
0.76 0.08 0.16
Matches are distributed among these distances:
95 2 0.01
96 23 0.10
97 43 0.18
98 30 0.13
99 7 0.03
100 13 0.06
101 13 0.06
102 15 0.06
103 17 0.07
104 33 0.14
105 7 0.03
106 17 0.07
107 13 0.06
ACGTcount: A:0.02, C:0.04, G:0.15, T:0.79
Consensus pattern (97 bp):
TTTGTGTTTTTTTTTTTGTTGGTTGTTTTTTTTTTTGTTGTTTTTTTGTTTTTTTTGTTTTTTTT
TTTTTGTTTTTTTTTTTTGTTTTTCCCCCCAT
Found at i:2218781 original size:204 final size:206
Alignment explanation
Indices: 2218474--2218853 Score: 481
Period size: 205 Copynumber: 1.9 Consensus size: 206
2218464 GTTTGTTTTT
* * *
2218474 TTTTTTGTTGGTTTTTTTTTTTGTTGTTATTTTTTTTTTTTTTTGTTATTTTTTTTTTTGTTTTT
1 TTTTTTGTTGGTTTTTTTTTTTGGTGTTATTTTTTTTTTTTGTTGTTATTTTTTTTGTTGTTTTT
* *
2218539 TTTGTTGTTTGGTTGGTTTTTTTGTTGTTTTTTTTTTTGTTGGTTGTTT-TTTTTTTTGTT-TTT
66 TTGGTTGTTTGGTTGGTGTTTTTGTTGTTTTTTTTTTTGTT-GTTGTTTGTTTTTTTTGTTATTT
* * ** *
2218602 TTTTGGTTTTTTTGTTTTTT-TGTTTTTTGTTTTTTTTTTTTGTTTTTCCCCCCACCTTTTAGTG
130 TTTTGATTTGTGGGTTTTTTATGTTTTAT-TTTTTTTTTTTTGTTTTTCCCCCCACCTTTTAGTG
2218666 TTGATTTTTGTTG
194 TTGATTTTTGTTG
*
2218679 TTTTTTGTT-TTTTTTTTTTTTGGTGTTTATTTGTTTGTTTTTTGTTGTT-TTTTTTTTGTT-TT
1 TTTTTTGTTGGTTTTTTTTTTTGGTG-TTATTT-TTT-TTTTTTGTTGTTATTTTTTTTGTTGTT
* * * * *
2218741 TTTTTGGTTTTTTTGTTTTGG-GTTTTT-TT-TTTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTT
63 TTTTTGG-TTGTTTG-GTTGGTGTTTTTGTTGTTTTTTTTTTTGTTGTTGTTTGTTTTTTTTGTT
*
2218803 ATTTTTTTTATTTGTGGGTTTTTTATGTTTTATTTTTTTTTTTTTGTTTTT
126 ATTTTTTTGATTTGTGGGTTTTTTATGTTTTATTTTTTTTTTTTTGTTTTT
2218854 TTGTTGGTTG
Statistics
Matches: 150, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
203 5 0.03
204 38 0.25
205 61 0.41
206 31 0.21
207 15 0.10
ACGTcount: A:0.03, C:0.02, G:0.14, T:0.81
Consensus pattern (206 bp):
TTTTTTGTTGGTTTTTTTTTTTGGTGTTATTTTTTTTTTTTGTTGTTATTTTTTTTGTTGTTTTT
TTGGTTGTTTGGTTGGTGTTTTTGTTGTTTTTTTTTTTGTTGTTGTTTGTTTTTTTTGTTATTTT
TTTGATTTGTGGGTTTTTTATGTTTTATTTTTTTTTTTTTGTTTTTCCCCCCACCTTTTAGTGTT
GATTTTTGTTG
Found at i:2218793 original size:113 final size:107
Alignment explanation
Indices: 2218208--2218855 Score: 225
Period size: 110 Copynumber: 5.7 Consensus size: 107
2218198 GCCTTTTTTT
*
2218208 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTGGTTGTGTTTTTTGTTTTTTTTTGTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTT--TT-TGTTTTTTGTTTTTTTTT-TTTTT
* * * * ** *
2218273 -GTTTTTTTTTTTTTTTTTTTTTGTTTGTTATTGGGTTTAATTTATTTTG
62 GGTGTTTTTTTTTGTTTTTTGTTGTTT-TTTTTTTGTTT--TTT-TTTGG
** * ** * * * *
2218322 -TTTTGGTTTTGTTTGGTTTTTTTTTTTTGTTTTTATTTGTTTGTTGTTTTTTTTGTTTTT-GTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTGTTTTTTGTTTTTTTTTTTTTTGGTG
* *
2218385 TCTTTTTTTTGTTTTTT-TTTTTTTTTTTTTGTTTATGGGTTGTT-G
66 T-TTTTTTTTGTTTTTTGTTGTTTTTTTTTTGTTT-T---TTTTTGG
*** * * *
2218430 TTTTGTTTTTTGTATTTTTGTGTTTCCCCCCATTGTTTGTTTTTTTTT-TTGTTGGTTTTTTTTT
1 TTTT-TTTTTT-T-TTTTT-T-TTT----TTTTTTTTTGTTTTTTTTTGTTTTTTGTTTTTTTTT
* * * * *
2218494 TTGTTGTTATTTTTTTTT-TTTTTTGTTATTTTTTTTTTTGTTTTTTTTGTTG
57 TTTTTGGTGTTTTTTTTTGTTTTTTGTT-GTTTTTTTTTTGTTTTTTTT-TGG
* * * *
2218546 TTTGGTTGGTTTTTTTGTTGTTTTTTTTTTTGTTGGTTGTTTTT-TTTTTTGTTTTTTTTTGGTT
1 TTT--TT--TTTTTTT-TTTTTTTTTTTTTTTTTGTTTTTTTTTGTTTTTTGTTTTTTTTT--TT
*
2218610 TTT--T-TGTTTTTTTGTTTTTTGTT-TTTTTTTTTTGTTTTTCCCCCCACCTTTTAGTG
59 TTTGGTGTTTTTTTTTGTTTTTTGTTGTTTTTTTTTTGTTTTT---------TTTT-G-G
*
2218666 TTGATTTTTGTTGTTTTTTGTTTTTTTTTTTTTTGGTGTTTATTTGTTTGTTTTTTG-TTGTTTT
1 -T--TTTTT-TT-TTTTTT-TTTTTTTTTTTTTT--TGTTT-TTT-TTTGTTTTTTGTTTTTTTT
* *
2218730 TTTTTT-GT-TTTTTTTTGGTTTTTTTGTT-TTGGGTTTTTTTT-TTTTTTTTTTG
56 TTTTTTGGTGTTTTTTTTTG-TTTTTTGTTGTT---TTTTTTTTGTTTTTTTTTGG
* * *** * *
2218782 TTTTTTTTTGTTTTTTTTTTTATTTTTTTTATTTGTGGGTT-TTTTATGTTTTATTTTTTTTTTT
1 TTTTTTTTT-TTTTTTTTTTTTTTTTTTTTGTTT-TTTTTTGTTTTTTGTTTT-TTTTTTTTTTG
*
2218846 TTGTTTTTTT
63 GTGTTTTTTT
2218856 GTTGGTTGTG
Statistics
Matches: 412, Mismatches: 63, Indels: 121
0.69 0.11 0.20
Matches are distributed among these distances:
107 8 0.02
108 13 0.03
109 33 0.08
110 53 0.13
111 32 0.08
112 46 0.11
113 34 0.08
114 10 0.02
115 2 0.00
116 14 0.03
117 30 0.07
118 41 0.10
119 9 0.02
120 5 0.01
121 19 0.05
123 11 0.03
124 11 0.03
125 21 0.05
126 7 0.02
127 5 0.01
128 8 0.02
ACGTcount: A:0.03, C:0.02, G:0.14, T:0.81
Consensus pattern (107 bp):
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTGTTTTTTGTTTTTTTTTTTTTTGGTG
TTTTTTTTTGTTTTTTGTTGTTTTTTTTTTGTTTTTTTTTGG
Found at i:2224110 original size:1 final size:1
Alignment explanation
Indices: 2224106--2224133 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2224096 AAAAATGTCA
2224106 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2224134 GTGTTTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2226030 original size:16 final size:15
Alignment explanation
Indices: 2226009--2226044 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
2225999 ACAAAATAAA
2226009 GTTTTTTTTTTTTTT
1 GTTTTTTTTTTTTTT
2226024 GGTTTTTTTTTTTTTT
1 -GTTTTTTTTTTTTTT
2226040 GTTTT
1 GTTTT
2226045 CCGTCAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (15 bp):
GTTTTTTTTTTTTTT
Found at i:2226031 original size:15 final size:15
Alignment explanation
Indices: 2226011--2226044 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2226001 AAAATAAAGT
2226011 TTTTTTTTTTTTTGG
1 TTTTTTTTTTTTTGG
*
2226026 TTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTGG
2226041 TTTT
1 TTTT
2226045 CCGTCAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (15 bp):
TTTTTTTTTTTTTGG
Found at i:2229655 original size:22 final size:22
Alignment explanation
Indices: 2229630--2229677 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2229620 ACCCCATTTT
2229630 AAACA-AACTTACCTCCCAACCA
1 AAACACAACTTA-CTCCCAACCA
**
2229652 AAACACTCCTTACTCCCAACCA
1 AAACACAACTTACTCCCAACCA
2229674 AAAC
1 AAAC
2229678 TCCCCGCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.44, C:0.42, G:0.00, T:0.15
Consensus pattern (22 bp):
AAACACAACTTACTCCCAACCA
Found at i:2230087 original size:19 final size:19
Alignment explanation
Indices: 2230050--2230085 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2230040 CGGCCTTCCC
2230050 CCCTCTCTCCCTCTTTTTT
1 CCCTCTCTCCCTCTTTTTT
2230069 CCCTCTCT--CTCTTTTTT
1 CCCTCTCTCCCTCTTTTTT
2230086 TTTTTTCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (19 bp):
CCCTCTCTCCCTCTTTTTT
Found at i:2230096 original size:24 final size:24
Alignment explanation
Indices: 2230045--2230126 Score: 91
Period size: 24 Copynumber: 3.6 Consensus size: 24
2230035 CCCTCCGGCC
*
2230045 TTCCCC-C-CTCTCTCCCTCTTTT
1 TTCCCCTCTCTCTCTTCCTCTTTT
** *
2230067 TT-CCCTCTCTCTCTTTTTTTTTT
1 TTCCCCTCTCTCTCTTCCTCTTTT
*
2230090 TTCCCCTCTCTCTGTTCCTCTTTT
1 TTCCCCTCTCTCTCTTCCTCTTTT
2230114 TTCCCCT-TCTCTC
1 TTCCCCTCTCTCTC
2230127 CCACTCCTCC
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.06
22 3 0.06
23 18 0.38
24 24 0.50
ACGTcount: A:0.00, C:0.44, G:0.01, T:0.55
Consensus pattern (24 bp):
TTCCCCTCTCTCTCTTCCTCTTTT
Found at i:2230113 original size:22 final size:23
Alignment explanation
Indices: 2230065--2230113 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
2230055 TCTCCCTCTT
* ** *
2230065 TTTTCCCTCTCTCTCTTTTTTTT
1 TTTTCCCTCTCTCTCTGTTCCTC
2230088 TTTTCCC-CTCTCTCTGTTCCTC
1 TTTTCCCTCTCTCTCTGTTCCTC
2230110 TTTT
1 TTTT
2230114 TTCCCCTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.00, C:0.35, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTCCCTCTCTCTCTGTTCCTC
Found at i:2306205 original size:52 final size:51
Alignment explanation
Indices: 2306143--2306263 Score: 154
Period size: 52 Copynumber: 2.4 Consensus size: 51
2306133 GAGATAACAA
* *
2306143 CGGGGCTAGAGTATCCCCGATTATGGAAAAACAG-TGTTCTAAAAATTAAAAT
1 CGGGGTTAGAGTATCCCCGATTAT-GAAAAACAGATGTTCTAAAAA-TAAAAC
** * *
2306195 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGAAAAACAGATGTTCTAAAAATAAAAC
*
2306246 CGGGGTTGGAGTATCCCC
1 CGGGGTTAGAGTATCCCC
2306264 TTGGAAATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 29 0.48
52 32 0.52
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (51 bp):
CGGGGTTAGAGTATCCCCGATTATGAAAAACAGATGTTCTAAAAATAAAAC
Found at i:2306250 original size:51 final size:50
Alignment explanation
Indices: 2306128--2306263 Score: 157
Period size: 51 Copynumber: 2.6 Consensus size: 50
2306118 AAAATTAGTA
* *
2306128 TTTTAGAGATAACAACGGGGCTAGAGTATCCCCGATTATGGAAAAACAGTG
1 TTTTAGAAATAA-AACGGGGTTAGAGTATCCCCGATTATGGAAAAACAGTG
* * **
2306179 TTCTAAAAATTAAAATCGGGGTTAGAGTATCCCCGATTAT-GAAAAATTGATG
1 TTTTAGAAA-TAAAA-CGGGGTTAGAGTATCCCCGATTATGGAAAAACAG-TG
*
2306231 TTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
1 TTTTAGAAATAAAA-CGGGGTTAGAGTATCCCC
2306264 TTGGAAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
51 37 0.51
52 35 0.49
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (50 bp):
TTTTAGAAATAAAACGGGGTTAGAGTATCCCCGATTATGGAAAAACAGTG
Found at i:2306326 original size:79 final size:79
Alignment explanation
Indices: 2306195--2306579 Score: 637
Period size: 79 Copynumber: 4.9 Consensus size: 79
2306185 AAATTAAAAT
*
2306195 CGGGGTTAGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
* *
2306260 CCCCTTGGAAATAA
66 CCCCTCGAAAATAA
*
2306274 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
2306339 CCCCTCGGAAATAA
66 CCCCTCGAAAATAA
* * *
2306353 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
2306418 CCCCTCGAAAATAA
66 CCCCTCGAAAATAA
* *
2306432 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAGATAAAACCGGGATTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
*
2306497 CCCTTCGAAAATAA
66 CCCCTCGAAAATAA
* *
2306511 CGGGGTTGGAATATCCCTGATTATGAAAAATTGATGTTTT-GAAAATAAAACCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAG-AAATAAAACCGGGGTTGGAGTA
2306575 TCCCC
65 TCCCC
2306580 GATTAAAGGA
Statistics
Matches: 286, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
78 1 0.00
79 285 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
CCCCTCGAAAATAA
Found at i:2306652 original size:52 final size:51
Alignment explanation
Indices: 2306511--2306785 Score: 284
Period size: 51 Copynumber: 5.4 Consensus size: 51
2306501 TCGAAAATAA
* * * *
2306511 CGGGGTTGGAATATCCCTGATTATGAAAAATT-GATGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTATGAAAAGTTAG-TGTTTTAAAAATAAAAC
* * * *
2306562 CGGGGTTGGAGTATCCCCGATTAAAGGAAATTTGGTGTTTTGAAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-ATGAAAAGTTAGTGTTTT-AAAAATAAAAC
* * * *
2306615 CGGGTTTAGAGTATCCCCGATTATGAAAAGTTAGTGTTTTAGAAATGAAAC
1 CGGGGTTGGAGTATCCCCGATTATGAAAAGTTAGTGTTTTAAAAATAAAAC
* * *
2306666 CGGGGTTGGAGTACCCCCGATTATGAAAAGTTAGTGTTTTAGAAATGAAAC
1 CGGGGTTGGAGTATCCCCGATTATGAAAAGTTAGTGTTTTAAAAATAAAAC
* * * * * * ** *
2306717 CGGGGTTGCAGTATCCCCCATTAAGAGAAA-TCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTATGA-AAAGTTAGTGTTTTAAAAATAAAAC
2306768 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
2306786 TCGGAGATAA
Statistics
Matches: 192, Mismatches: 28, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
51 131 0.68
52 30 0.16
53 31 0.16
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAGTTAGTGTTTTAAAAATAAAAC
Found at i:2306929 original size:51 final size:51
Alignment explanation
Indices: 2306796--2306929 Score: 155
Period size: 51 Copynumber: 2.6 Consensus size: 51
2306786 TCGGAGATAA
* * *
2306796 CGAGGTTGGAGTATCCTCGATTGGA-AAATTGGTGTTTTGGGAAATAAAAT
1 CGAGGTTGGAGTATCCTCGATTAGAGAAATTGGTGTTTTGGAAAATAAAAC
* * * *
2306846 CGAAGTTAGAGTATCCCCGATTAAAGGAAATTGGTGTTTT-GAAAATAAAAC
1 CGAGGTTGGAGTATCCTCGATTAGA-GAAATTGGTGTTTTGGAAAATAAAAC
* *
2306897 CGGGGTTGGAGTATCCTCGATTATGAGCAATTG
1 CGAGGTTGGAGTATCCTCGATTA-GAGAAATTG
2306930 AGAAGCTTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
50 20 0.29
51 34 0.50
52 14 0.21
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCTCGATTAGAGAAATTGGTGTTTTGGAAAATAAAAC
Found at i:2307851 original size:18 final size:18
Alignment explanation
Indices: 2307828--2307897 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
2307818 ATTGCTACCT
2307828 GCTGGAGTTGCTGCTCTC
1 GCTGGAGTTGCTGCTCTC
* *
2307846 GCTGGAGCTGCTGTTGCAT-
1 GCTGGAGTTGCTGCT-C-TC
* *
2307865 GCTGGAGTTGCAG-TCGC
1 GCTGGAGTTGCTGCTCTC
2307882 TGCTGGAGTTGCTGCT
1 -GCTGGAGTTGCTGCT
2307898 GTTGTTGCGT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 1 0.02
18 26 0.63
19 13 0.32
20 1 0.02
ACGTcount: A:0.09, C:0.23, G:0.37, T:0.31
Consensus pattern (18 bp):
GCTGGAGTTGCTGCTCTC
Found at i:2307904 original size:43 final size:43
Alignment explanation
Indices: 2307852--2307947 Score: 138
Period size: 43 Copynumber: 2.2 Consensus size: 43
2307842 TCTCGCTGGA
*
2307852 GCTGCTGTTGCATGCTGGAGTTGCAGTCGCTGCTGGAGTTGCT
1 GCTGCTGTTGCATGCTGGAGCTGCAGTCGCTGCTGGAGTTGCT
* * * *
2307895 GCTGTTGTTGCGTGCTGGAGCTGCAGTCGTTGCTGGTGTTGCT
1 GCTGCTGTTGCATGCTGGAGCTGCAGTCGCTGCTGGAGTTGCT
*
2307938 GCTACTGTTG
1 GCTGCTGTTG
2307948 GAGCTGCTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.07, C:0.20, G:0.38, T:0.35
Consensus pattern (43 bp):
GCTGCTGTTGCATGCTGGAGCTGCAGTCGCTGCTGGAGTTGCT
Found at i:2307961 original size:55 final size:55
Alignment explanation
Indices: 2307902--2308024 Score: 129
Period size: 55 Copynumber: 2.2 Consensus size: 55
2307892 GCTGCTGTTG
* ** * * *
2307902 TTGCGTGCTGGAGCTGCAGTCGTTGCTGGTGTTGCTGCTACTGTTGGAGCTGCTT
1 TTGCGTGCTGGAGCTGCAGCCGCCGCTGGAGCTGCTGCTACTGCTGGAGCTGCTT
* * ** * *
2307957 TTGCGTGCTAGAACTGTTGCCGCCGCTGGAGCTGGTGCTGCTGCTGGAGCTGCTT
1 TTGCGTGCTGGAGCTGCAGCCGCCGCTGGAGCTGCTGCTACTGCTGGAGCTGCTT
*
2308012 TTGCGTGTTGGAG
1 TTGCGTGCTGGAG
2308025 TCGTTGGCTA
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.08, C:0.21, G:0.37, T:0.33
Consensus pattern (55 bp):
TTGCGTGCTGGAGCTGCAGCCGCCGCTGGAGCTGCTGCTACTGCTGGAGCTGCTT
Found at i:2308348 original size:50 final size:50
Alignment explanation
Indices: 2308294--2308418 Score: 232
Period size: 50 Copynumber: 2.5 Consensus size: 50
2308284 TCCATTCTCT
*
2308294 TGCATGCCTCTGCATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
1 TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
*
2308344 TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCTCA
1 TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
2308394 TGCATGCCTCTGTATGTTTTGTCTC
1 TGCATGCCTCTGTATGTTTTGTCTC
2308419 TGAAAGCTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.14, C:0.24, G:0.15, T:0.46
Consensus pattern (50 bp):
TGCATGCCTCTGTATGTTTTGTCTCCAATTGCAATTTTTATGCTTTCCCA
Found at i:2308392 original size:24 final size:24
Alignment explanation
Indices: 2308315--2308392 Score: 56
Period size: 24 Copynumber: 3.2 Consensus size: 24
2308305 GCATGTTTTG
2308315 TCTCCAATTGCAATTTTTATGCTT
1 TCTCCAATTGCAATTTTTATGCTT
* *
2308339 TC-CC-A-TGC-ATGCCTCTGTATGTTTT
1 TCTCCAATTGCAAT---T-TTTATG-CTT
2308364 GTCTCCAATTGCAATTTTTATGCTT
1 -TCTCCAATTGCAATTTTTATGCTT
2308389 TCTC
1 TCTC
2308393 ATGCATGCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 20
0.62 0.06 0.31
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 1 0.03
23 3 0.08
24 11 0.28
25 4 0.10
26 7 0.17
27 3 0.08
28 1 0.03
29 3 0.08
30 2 0.05
ACGTcount: A:0.17, C:0.24, G:0.12, T:0.47
Consensus pattern (24 bp):
TCTCCAATTGCAATTTTTATGCTT
Found at i:2308409 original size:24 final size:24
Alignment explanation
Indices: 2308332--2308409 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
2308322 TTGCAATTTT
*
2308332 TATGCTTTCCCATGCATGCCTCTG
1 TATGCTTTCTCATGCATGCCTCTG
* * * * * *
2308356 TATGTTTTGTC-TCCAATTGCAATTTT
1 TATGCTTTCTCATGC-A-TGC-CTCTG
2308382 TATGCTTTCTCATGCATGCCTCTG
1 TATGCTTTCTCATGCATGCCTCTG
2308406 TATG
1 TATG
2308410 TTTTGTCTCT
Statistics
Matches: 37, Mismatches: 13, Indels: 8
0.64 0.22 0.14
Matches are distributed among these distances:
23 2 0.05
24 15 0.41
25 6 0.16
26 12 0.32
27 2 0.05
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.45
Consensus pattern (24 bp):
TATGCTTTCTCATGCATGCCTCTG
Found at i:2309189 original size:13 final size:13
Alignment explanation
Indices: 2309171--2309196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2309161 CAATTTTTTG
2309171 TGTATCGATACAT
1 TGTATCGATACAT
2309184 TGTATCGATACAT
1 TGTATCGATACAT
2309197 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2309954 original size:61 final size:61
Alignment explanation
Indices: 2309854--2309969 Score: 223
Period size: 61 Copynumber: 1.9 Consensus size: 61
2309844 ATTTGTACAT
2309854 TCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAAA
1 TCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAAA
*
2309915 TCTCCCCCTTAATAAGGTAATTCACGCATTCTCTTCTTTATCTCCCCCGTTTATT
1 TCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATT
2309970 TGCACATATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.22, C:0.32, G:0.07, T:0.40
Consensus pattern (61 bp):
TCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCGTTTATTAATAAA
Found at i:2311588 original size:21 final size:21
Alignment explanation
Indices: 2311564--2311610 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2311554 TTTAATGCTG
2311564 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
2311584 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
2311605 ATTTTG
1 ATTTTG
2311611 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:2311749 original size:13 final size:13
Alignment explanation
Indices: 2311731--2311769 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2311721 ATAATCACCC
*
2311731 TGTATCGATACAG
1 TGTATCGATACAA
2311744 TGTATCGATACAA
1 TGTATCGATACAA
2311757 TGTATCGATACAA
1 TGTATCGATACAA
2311770 GAAATGTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2311777 original size:17 final size:18
Alignment explanation
Indices: 2311755--2311790 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
2311745 GTATCGATAC
2311755 AATGTATCGATACA-AGA
1 AATGTATCGATACATAGA
2311772 AATGTATCGATACATAGA
1 AATGTATCGATACATAGA
2311790 A
1 A
2311791 TTTCCAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (18 bp):
AATGTATCGATACATAGA
Found at i:2313866 original size:15 final size:15
Alignment explanation
Indices: 2313846--2313876 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2313836 ATTTCGTTTG
*
2313846 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2313861 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2313876 G
1 G
2313877 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2315709 original size:21 final size:21
Alignment explanation
Indices: 2315680--2315724 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2315670 AAGTTTTCAT
*
2315680 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2315700 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2315722 TTT
1 TTT
2315725 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2318413 original size:50 final size:50
Alignment explanation
Indices: 2318338--2318470 Score: 248
Period size: 50 Copynumber: 2.7 Consensus size: 50
2318328 GATCCTAACA
*
2318338 GTCTCCAATTGCAATTTTTATGCTTTCCCATGCATGCCTCTGTATGTTTT
1 GTCTCCAATTGCAATTTTTATGCTTTCCCATGCATGCCTCTGCATGTTTT
*
2318388 GTCTCCAATTGAAATTTTTATGCTTTCCCATGCATGCCTCTGCATGTTTT
1 GTCTCCAATTGCAATTTTTATGCTTTCCCATGCATGCCTCTGCATGTTTT
2318438 GTCTCCAATTGCAATTTTTATGCTTTCCCATGC
1 GTCTCCAATTGCAATTTTTATGCTTTCCCATGC
2318471 TGCATTTTCT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 80 1.00
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (50 bp):
GTCTCCAATTGCAATTTTTATGCTTTCCCATGCATGCCTCTGCATGTTTT
Found at i:2318490 original size:26 final size:26
Alignment explanation
Indices: 2318460--2318550 Score: 155
Period size: 26 Copynumber: 3.5 Consensus size: 26
2318450 AATTTTTATG
2318460 CTTTCCCATGCTGCATTTTCTATTTC
1 CTTTCCCATGCTGCATTTTCTATTTC
2318486 CTTTCCCATGCTGCATTTTCTATTTC
1 CTTTCCCATGCTGCATTTTCTATTTC
**
2318512 CTTTCCCATGCTATATTTTCTATTTC
1 CTTTCCCATGCTGCATTTTCTATTTC
*
2318538 CTTTCCCACGCTG
1 CTTTCCCATGCTG
2318551 TTCGAATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.12, C:0.32, G:0.08, T:0.48
Consensus pattern (26 bp):
CTTTCCCATGCTGCATTTTCTATTTC
Found at i:2324278 original size:20 final size:21
Alignment explanation
Indices: 2324231--2324283 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2324221 GCCAATCACC
*
2324231 TGTATCGATACATTCTTTGTA
1 TGTATCGATACATTCTTGGTA
*
2324252 AGTATCGATACA-T-TTGGTCA
1 TGTATCGATACATTCTTGGT-A
2324272 TGTATCGATACA
1 TGTATCGATACA
2324284 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 11 0.39
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTTGGTA
Found at i:2324289 original size:13 final size:13
Alignment explanation
Indices: 2324271--2324295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2324261 ACATTTGGTC
2324271 ATGTATCGATACA
1 ATGTATCGATACA
2324284 ATGTATCGATAC
1 ATGTATCGATAC
2324296 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2324328 original size:20 final size:19
Alignment explanation
Indices: 2324305--2324343 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
2324295 CTGTGCATTA
*
2324305 TGTATCGATACATTTGAAGG
1 TGTATCAATACATTT-AAGG
2324325 TGTATCAATACATTTAAGG
1 TGTATCAATACATTTAAGG
2324344 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (19 bp):
TGTATCAATACATTTAAGG
Found at i:2327318 original size:13 final size:13
Alignment explanation
Indices: 2327277--2327325 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
2327267 TCGTTACAAG
2327277 CAATGTATCGATA
1 CAATGTATCGATA
2327290 CAAT-T-TC-AT-
1 CAATGTATCGATA
2327299 C-ATGTATCGATA
1 CAATGTATCGATA
2327311 CAATGTATCGATA
1 CAATGTATCGATA
2327324 CA
1 CA
2327326 TTGTCCCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 4 0.13
11 4 0.13
12 2 0.06
13 17 0.55
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2327341 original size:33 final size:34
Alignment explanation
Indices: 2327277--2327346 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
2327267 TCGTTACAAG
*
2327277 CAATGTATCGATACAATTTCATCATGTATCGATA
1 CAATGTATCGATACAATTTCACCATGTATCGATA
2327311 CAATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 CAATGTATCGATACAATT-TCACCATGTATCGATA
2327344 CAA
1 CAA
2327347 ATAATGATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 18 0.53
34 16 0.47
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (34 bp):
CAATGTATCGATACAATTTCACCATGTATCGATA
Found at i:2327414 original size:13 final size:13
Alignment explanation
Indices: 2327396--2327422 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2327386 ACAATTGTCC
2327396 ATGTATCGATACA
1 ATGTATCGATACA
2327409 ATGTATCGATACA
1 ATGTATCGATACA
2327422 A
1 A
2327423 AGCAGTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2334484 original size:3 final size:3
Alignment explanation
Indices: 2334476--2334502 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2334466 CTTCATCCGA
2334476 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
2334503 TTCCTCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:2336182 original size:13 final size:13
Alignment explanation
Indices: 2336164--2336189 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2336154 TACAATGAGC
2336164 ATGTATCGATACA
1 ATGTATCGATACA
2336177 ATGTATCGATACA
1 ATGTATCGATACA
2336190 TCTAGGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2336220 original size:20 final size:20
Alignment explanation
Indices: 2336180--2336220 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2336170 CGATACAATG
*
2336180 TATCGATACATCTAGGAGTT
1 TATCGATACATCAAGGAGTT
2336200 TATCGATACATTCAAGG-GTT
1 TATCGATACA-TCAAGGAGTT
2336220 T
1 T
2336221 TGACCTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (20 bp):
TATCGATACATCAAGGAGTT
Found at i:2340871 original size:12 final size:11
Alignment explanation
Indices: 2340854--2340919 Score: 64
Period size: 12 Copynumber: 5.7 Consensus size: 11
2340844 CCTTCGTACC
2340854 AAAAAAAACAA
1 AAAAAAAACAA
2340865 GAAAAAAAACAA
1 -AAAAAAAACAA
2340877 AAAAATAGAA-AA
1 AAAAA-A-AACAA
*
2340889 AACCAAAAAC-A
1 AA-AAAAAACAA
2340900 AAAAAAAACAA
1 AAAAAAAACAA
2340911 ACAAAAAAA
1 A-AAAAAAA
2340920 GGGTCTAGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
10 6 0.13
11 12 0.26
12 24 0.52
13 4 0.09
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.02
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:2342196 original size:28 final size:28
Alignment explanation
Indices: 2342165--2342604 Score: 440
Period size: 28 Copynumber: 15.1 Consensus size: 28
2342155 CGTTCATCTC
*
2342165 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
2342193 TTCAAAGCTCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
2342221 TTCAAAGCCCACAAGTCAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** * *
2342248 CTTCAAAATACCACAAGTCAATAGCATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
* *
2342278 TTCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
2342306 TTCAAAGCCCACTAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
2342336 TTCAAAGCCCACATAAATCAATGGCATCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCATCCT
2342366 TTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
2342396 TTCAAAGCCCACACAAATCAGTGGCA-CCC
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
* * *
2342425 TTCTAAAACCCACAAGTCAGTAGCACCCT
1 TTC-AAAGCCCACAAGTCAGTGGCATCCT
* *
2342454 TTCAAAGCCCACAAGTTAGTCGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
2342484 TTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
2342514 TTCAAAGCCCACAAGT-AGGGGGCACCCT
1 TTCAAAGCCCACAAGTCA-GTGGCATCCT
*
2342542 TTCAAAGCCCACACAAGTC-GATGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAG-TGGC-A-TCCT
*
2342574 TTCAAAGCCCACACAAGTTAGTGGCA-CCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
2342603 TT
1 TT
2342605 TTTTTAAAAA
Statistics
Matches: 349, Mismatches: 40, Indels: 45
0.80 0.09 0.10
Matches are distributed among these distances:
27 2 0.01
28 146 0.42
29 41 0.12
30 107 0.31
31 4 0.01
32 48 0.14
33 1 0.00
ACGTcount: A:0.31, C:0.32, G:0.15, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:2342368 original size:60 final size:58
Alignment explanation
Indices: 2342165--2342604 Score: 463
Period size: 60 Copynumber: 7.5 Consensus size: 58
2342155 CGTTCATCTC
* *
2342165 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCTCACAAGTCAGTGGCAT--CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCT
** * *
2342221 TTCAAAGCCCACAAGTCAGTGGCAT-CTCTTCAAAATACCACAAGTCAATAGCAT--CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT-TTC-AAAGCCCACAAGTCAGTGGCATACCCT
* * *
2342278 TTCAAAGCTCACAAGTCAGTGGCACCCTTTCAAAGCCCACTAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCT
* *
2342336 TTCAAAGCCCACATAAATCAATGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCT
* * * *
2342396 TTCAAAGCCCACACAAATCAGTGGCA-CCCTTCTAAAACCCACAAGTCAGTAGC--ACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCTTTC-AAAGCCCACAAGTCAGTGGCATACCCT
* *
2342454 TTCAAAGCCCACAAGTTAGTCGCATACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCTTTCAAAGCCCACAAGTCAGTGGCATACCCT
* * *
2342514 TTCAAAGCCCACAAGT-AGGGGGCACCCTTTCAAAGCCCACACAAGTC-GATGGCA-ACTCTT
1 TTCAAAGCCCACAAGTCA-GTGGCATCCTTTCAAAG-CC-CACAAGTCAG-TGGCATAC-CCT
*
2342574 TTCAAAGCCCACACAAGTTAGTGGCA-CCTTT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCTTT
2342605 TTTTTAAAAA
Statistics
Matches: 328, Mismatches: 33, Indels: 41
0.82 0.08 0.10
Matches are distributed among these distances:
55 2 0.01
56 56 0.17
57 48 0.15
58 56 0.17
59 16 0.05
60 125 0.38
61 9 0.03
62 15 0.05
63 1 0.00
ACGTcount: A:0.31, C:0.32, G:0.15, T:0.22
Consensus pattern (58 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCT
Found at i:2342527 original size:88 final size:87
Alignment explanation
Indices: 2342164--2342586 Score: 479
Period size: 88 Copynumber: 4.8 Consensus size: 87
2342154 ACGTTCATCT
* *
2342164 CTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCTCACAAGTCAGTGGCAT--CCTTTCAAA
1 CTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAA
*
2342227 GCCCACAAGTCAGTGGCAT-CT
66 GCCCACAAGTCAGTGGCATACC
** * * *
2342248 CTTCAAAATACCACAAGTCAATAGCATCCTTTCAAAGCTCACAAGTCAGTGGC--ACCCTTTCAA
1 CTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAA
*
2342311 AGCCCACTAGTCAGTGGCATACC
65 AGCCCACAAGTCAGTGGCATACC
* *
2342334 CTTTCAAAGCCCACATAAATCAATGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTC
1 C-TTCAAAGCCCAC--AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTC
*
2342399 AAAGCCCACACAAATCAGTGGC--ACC
63 AAAG-CC-CACAAGTCAGTGGCATACC
* * * * *
2342424 CTTCTAAAACCCACAAGTCAGTAGCACCCTTTCAAAGCCCACAAGTTAGTCGCATACCCTTTCAA
1 CTTC-AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAA
2342489 AGCCCACAAGTCAGTGGCATACC
65 AGCCCACAAGTCAGTGGCATACC
* * *
2342512 CTTTCAAAGCCCACAAGT-AGGGGGCACCCTTTCAAAGCCCACACAAGTC-GATGGCA-ACTCTT
1 C-TTCAAAGCCCACAAGTCA-GTGGCATCCTTTCAAAG-CC-CACAAGTCAG-TGGCATAC-CCT
2342574 TTCAAAGCCCACA
60 TTCAAAGCCCACA
2342587 CAAGTTAGTG
Statistics
Matches: 291, Mismatches: 28, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
84 4 0.01
85 70 0.24
86 22 0.08
87 6 0.02
88 114 0.39
89 11 0.04
90 50 0.17
91 2 0.01
92 12 0.04
ACGTcount: A:0.31, C:0.32, G:0.15, T:0.21
Consensus pattern (87 bp):
CTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAA
GCCCACAAGTCAGTGGCATACC
Found at i:2343622 original size:20 final size:20
Alignment explanation
Indices: 2343552--2343624 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
2343542 TACCCAGATA
2343552 TATCGATACATT-TTCAATG
1 TATCGATACATTCTTCAATG
* * * *
2343571 TATCGATCCATGCATGAATG
1 TATCGATACATTCTTCAATG
2343591 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
2343611 TATCGATACATTCT
1 TATCGATACATTCT
2343625 ATCTTTTTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 10 0.22
20 35 0.78
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:2345006 original size:128 final size:128
Alignment explanation
Indices: 2344776--2345028 Score: 398
Period size: 128 Copynumber: 2.0 Consensus size: 128
2344766 TAGGATAAAT
* * * *
2344776 TTAATTTTCAGGTCTGGAATCTTTATTAAATGAGGTTCAAATTTCTGATTTTGTAATCAAAATAG
1 TTAATTTTCAGGTCTGGAATATTGATTAAATGAGGTTCAAATTTCTAATTTTCTAATCAAAATAG
* *
2344841 CCATGCACATGCTCCTAAAATGTTTGTGCCTTACTTTGTGTCAAAACCTTGAGTGGTATGCTC
66 CCATGCACATGCTCCTAAAATGCTTATGCCTTACTTTGTGTCAAAACCTTGAGTGGTATGCTC
**
2344904 TTAATTTTCAGGTCTGGAATATTGATTAAATGAGGTTCAAATTTCTAATTTTCTTGTCAAAATAG
1 TTAATTTTCAGGTCTGGAATATTGATTAAATGAGGTTCAAATTTCTAATTTTCTAATCAAAATAG
* * * *
2344969 CCATGCGCATGCTCTTAAAATGCTTATGCCTTGCTTTGTGTCAAAATCTTGAGTGGTATG
66 CCATGCACATGCTCCTAAAATGCTTATGCCTTACTTTGTGTCAAAACCTTGAGTGGTATG
2345029 ATCAATGCGT
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
128 113 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (128 bp):
TTAATTTTCAGGTCTGGAATATTGATTAAATGAGGTTCAAATTTCTAATTTTCTAATCAAAATAG
CCATGCACATGCTCCTAAAATGCTTATGCCTTACTTTGTGTCAAAACCTTGAGTGGTATGCTC
Found at i:2357565 original size:8 final size:8
Alignment explanation
Indices: 2357563--2357617 Score: 67
Period size: 8 Copynumber: 6.9 Consensus size: 8
2357553 AAAAACCAAA
2357563 AAAAAAAC
1 AAAAAAAC
2357571 AAAAAAAC
1 AAAAAAAC
2357579 AGAAAAAAC
1 A-AAAAAAC
*
2357588 -CAAAAAC
1 AAAAAAAC
*
2357595 AAACAAAC
1 AAAAAAAC
*
2357603 AAACAAAC
1 AAAAAAAC
2357611 AAAAAAA
1 AAAAAAA
2357618 GGGTCCAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 6 0.15
8 28 0.68
9 7 0.17
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:2357567 original size:12 final size:11
Alignment explanation
Indices: 2357550--2357617 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 11
2357540 TCCTTTGTAC
*
2357550 AAAAAAAACCA
1 AAAAAAAAACA
2357561 AAAAAAAAACA
1 AAAAAAAAACA
2357572 AAAAAACAGAA-A
1 AAAAAA-A-AACA
*
2357584 AAACCAAAAACA
1 AAA-AAAAAACA
*
2357596 AACAAACAAACA
1 AA-AAAAAAACA
2357608 AACAAAAAAA
1 AA-AAAAAAA
2357618 GGGTCCAGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
11 18 0.38
12 24 0.51
13 5 0.11
ACGTcount: A:0.82, C:0.16, G:0.01, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:2357592 original size:24 final size:23
Alignment explanation
Indices: 2357560--2357616 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2357550 AAAAAAAACC
2357560 AAAA-AAAAAACAAAAAAACAGAA
1 AAAACAAAAAACAAAAAAACA-AA
* *
2357583 AAAACCAAAAACAAACAAACAAA
1 AAAACAAAAAACAAAAAAACAAA
*
2357606 CAAACAAAAAA
1 AAAACAAAAAA
2357617 AGGGTCCAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (23 bp):
AAAACAAAAAACAAAAAAACAAA
Found at i:2357593 original size:28 final size:29
Alignment explanation
Indices: 2357552--2357617 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 29
2357542 CTTTGTACAA
2357552 AAAAAACCAAAAAAAAAACAAAAAAACAG
1 AAAAAACCAAAAAAAAAACAAAAAAACAG
*
2357581 AAAAAACCAAAAACAAACAAACAAACAAACA-
1 AAAAAACC-AAAA-AAA-AAACAAAAAAACAG
2357612 AAAAAA
1 AAAAAA
2357618 GGGTCCAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 8 0.24
30 4 0.12
31 9 0.27
32 12 0.36
ACGTcount: A:0.82, C:0.17, G:0.02, T:0.00
Consensus pattern (29 bp):
AAAAAACCAAAAAAAAAACAAAAAAACAG
Found at i:2357600 original size:4 final size:4
Alignment explanation
Indices: 2357567--2357613 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
2357557 ACCAAAAAAA
* * *
2357567 AAAC AAAA AAAC AGAAA AAAC CAA- AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC A-AAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
2357614 AAAAGGGTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 2 0.06
4 30 0.86
5 3 0.09
ACGTcount: A:0.79, C:0.19, G:0.02, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:2358903 original size:28 final size:28
Alignment explanation
Indices: 2358866--2359327 Score: 462
Period size: 28 Copynumber: 15.9 Consensus size: 28
2358856 CGTTCATCTC
* * *
2358866 TTCAATGCCCACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
2358894 TTTAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** *
2358922 TTCAAAATCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
2358950 TTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
2358980 TTCAAAGCCCACACAAAT-AGTGGCACCCT
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
* *
2359009 TCCAAAGCCCACAAGTTAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
2359037 TTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* *
2359067 TTCAAAGCCCACACAAATCAGTGGCA-CCC
1 TTCAAAG-CC-CACAAGTCAGTGGCATCCT
* * * *
2359096 TTCTAAGTCCACAAGCCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
2359124 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * * *
2359152 TTCTATGCCCATAAGTCAGTGGTAACCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
2359180 TTCAAAGCCCACAAGTCAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
*
2359210 TTCAAAGCCCACAAGTCGGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
*
2359240 TTCAAAGCTCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
2359268 TTCAAAGCTCACGCAAGTCAGTGGTAACTCTT
1 TTCAAAGC-C-CACAAGTCAGTGG-CA-TCCT
*
2359300 TTCAAAGCCCACATAAGTTAGTGGCATC
1 TTCAAAGCCCAC--AAGTCAGTGGCATC
2359328 TTTTAAAAAA
Statistics
Matches: 365, Mismatches: 49, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
27 21 0.06
28 182 0.50
29 17 0.05
30 89 0.24
31 16 0.04
32 40 0.11
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:2359033 original size:87 final size:88
Alignment explanation
Indices: 2358866--2359326 Score: 505
Period size: 87 Copynumber: 5.3 Consensus size: 88
2358856 CGTTCATCTC
* * * * * *
2358866 TTCAATGCCCACAAGTTAGTGGCAT--CTTTTTAAAG-CC-CACAAGTCAGTGGCATCCTTTCAA
1 TTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACACAAATCAGTGGCACCCTTTCAA
**
2358927 AATCCACAAGTCAGTGGCACCCT
66 AGCCCACAAGTCAGTGGCACCCT
*
2358950 TTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACACAAAT-AGTGGCACCCTTCCAA
1 TTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACACAAATCAGTGGCACCCTTTCAA
* *
2359014 AGCCCACAAGTTAGTGGCACCTT
66 AGCCCACAAGTCAGTGGCACCCT
*
2359037 TTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACACAAATCAGTGGCACCC-TTCTA
1 TTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACACAAATCAGTGGCACCCTTTCAA
* *
2359101 AGTCCACAAGCCAGTGGCACCCT
66 AGCCCACAAGTCAGTGGCACCCT
* * * * * * *
2359124 TTCAAAGCCCACAAGTTAGTGGC--ACCCTTTCTATG-CC-CATAAGTCAGTGGTAACCTTTCAA
1 TTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACACAAATCAGTGGCACCCTTTCAA
2359185 AGCCCACAAGTCAGTGGCATACCCT
66 AGCCCACAAGTCAGTGGC--ACCCT
* * * *
2359210 TTCAAAGCCCACAAGTCGGTGGCATACCCTTTCAAAG--CTCACAAGTCAGTGGCATCCTTTCAA
1 TTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACACAAATCAGTGGCACCCTTTCAA
* * *
2359273 AGCTCACGCAAGTCAGTGGTAACTCTT
66 AGC-C-CACAAGTCAGTGG-CAC-CCT
*
2359300 TTCAAAGCCCACATAAGTTAGTGGCAT
1 TTCAAAGCCCAC--AAGTCAGTGGCAT
2359327 CTTTTAAAAA
Statistics
Matches: 321, Mismatches: 39, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
83 14 0.04
84 45 0.14
85 10 0.03
86 34 0.11
87 128 0.40
88 50 0.16
89 3 0.01
90 26 0.08
92 11 0.03
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (88 bp):
TTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACACAAATCAGTGGCACCCTTTCAA
AGCCCACAAGTCAGTGGCACCCT
Found at i:2359144 original size:143 final size:141
Alignment explanation
Indices: 2358866--2359331 Score: 544
Period size: 143 Copynumber: 3.2 Consensus size: 141
2358856 CGTTCATCTC
* * * *
2358866 TTCAATGCCCACAAGTTAGTGGCATCTTTTTAAAGCCCACAAGTCAGTGGCAT--CCTTTCAAAA
1 TTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAG
*
2358929 TCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACAC
66 CCCACAAGTCAGTGGCACCCTTTCAAAG-CCACAAGTCAGTGGC--ACCCTTTCAAAGCCCACA-
**
2358994 AAATAGTGGCACCCT
127 AGTTAGTGGCACCCT
*
2359009 TCCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAG
1 TTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAG
* * *
2359074 CCCACACAAATCAGTGGCACCC-TTCTAAGTCCACAAGCCAGTGGCACCCTTTCAAAGCCCACAA
66 -CC-CACAAGTCAGTGGCACCCTTTCAAAG-CCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA
2359138 GTTAGTGGCACCCT
128 GTTAGTGGCACCCT
* * * * *
2359152 TTCTATGCCCATAAGTCAGTGGTAACC-TTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAA
1 TTCAAAGCCCACAAGTTAGTGG-CACCTTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAA
* * *
2359216 GCCCACAAGTCGGTGGCATACCCTTTCAAAGCTCACAAGTCAGTGGCATCCTTTCAAAGCTCACG
65 GCCCACAAGTCAGTGGC--ACCCTTTCAAAGC-CACAAGTCAGTGGCACCCTTTCAAAGC-C-CA
* * *
2359281 CAAGTCAGTGGTAACTCTT
125 CAAGTTAGTGG-CAC-CCT
*
2359300 TTCAAAGCCCACATAAGTTAGTGGCATCTTTT
1 TTCAAAGCCCAC--AAGTTAGTGGCACCTTTT
2359332 AAAAAAAAAA
Statistics
Matches: 274, Mismatches: 33, Indels: 25
0.83 0.10 0.08
Matches are distributed among these distances:
141 12 0.04
142 2 0.01
143 122 0.45
144 52 0.19
145 10 0.04
146 32 0.12
147 19 0.07
148 11 0.04
149 2 0.01
150 12 0.04
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (141 bp):
TTCAAAGCCCACAAGTTAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAG
CCCACAAGTCAGTGGCACCCTTTCAAAGCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTT
AGTGGCACCCT
Found at i:2359511 original size:49 final size:45
Alignment explanation
Indices: 2359396--2359528 Score: 140
Period size: 49 Copynumber: 2.9 Consensus size: 45
2359386 ATCATCTTAA
* * *
2359396 AGTCCGATATCGCTGGCATTGAATCAGCATATTGGCACTTTTATT
1 AGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTTATT
* * * *
2359441 AGCCCAATGTAGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTT
1 AGTCCAATATCGCTGGCCTTGAATCAGCACATTGG--CACTTTT--ATT
* **
2359490 AGTCCAATTTCGCTGGCCTTGAATTGGCACATTGGCACT
1 AGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACT
2359529 CCTCTCATCT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
45 29 0.40
47 11 0.15
49 32 0.44
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (45 bp):
AGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTTATT
Found at i:2360272 original size:20 final size:20
Alignment explanation
Indices: 2360222--2360295 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
2360212 GAAAACCCAG
* **
2360222 ATGTATGGATACATTTTTCA
1 ATGTATCGATACATTCATCA
* *
2360242 ACGTA-CGATACATGT-ATGA
1 ATGTATCGATACAT-TCATCA
*
2360261 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCATCA
2360281 ATGTATCGATACATT
1 ATGTATCGATACATT
2360296 TTGTCTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 14 0.32
20 30 0.68
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCATCA
Found at i:2361662 original size:128 final size:128
Alignment explanation
Indices: 2361428--2361678 Score: 423
Period size: 128 Copynumber: 2.0 Consensus size: 128
2361418 AGGGTAAATT
*
2361428 TAATTTTCAGGTCTAGAATCTTGATTAAATGAGGTTCAAATTTCTAATTTAGTAATCAAAATAGC
1 TAATTTTCAGGTCTAGAATCTTGATTAAATGAGGTTCAAATTTCTAATTTACTAATCAAAATAGC
* *
2361493 TATGCACATGCTCCTAAAATGTTTGTGTCTTGCTTTATGTCAAAACCTTGAGTGGTATTCTCC
66 TATGCACATGCTCCTAAAATGTTTGTGCCTTGCTTGATGTCAAAACCTTGAGTGGTATTCTCC
* * *
2361556 TAATTTTCATGTCTAGAATCTTGATTAAATGAGGTTCAAATTTCTGATTTTCTAATCAAAATAG-
1 TAATTTTCAGGTCTAGAATCTTGATTAAATGAGGTTCAAATTTCTAATTTACTAATCAAAATAGC
*
2361620 TCATGCACATGCTCCTAAAATGTTTGTGCCTTGCTTGGTGTCAAAACCTTGAGTGGTAT
66 T-ATGCACATGCTCCTAAAATGTTTGTGCCTTGCTTGATGTCAAAACCTTGAGTGGTAT
2361679 GATCAATGGG
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
127 1 0.01
128 114 0.99
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (128 bp):
TAATTTTCAGGTCTAGAATCTTGATTAAATGAGGTTCAAATTTCTAATTTACTAATCAAAATAGC
TATGCACATGCTCCTAAAATGTTTGTGCCTTGCTTGATGTCAAAACCTTGAGTGGTATTCTCC
Found at i:2364922 original size:20 final size:19
Alignment explanation
Indices: 2364889--2364926 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2364879 ATACTAATCT
*
2364889 AAAACAACTTTTACAACAA
1 AAAAAAACTTTTACAACAA
2364908 AAAAAAACTTATTACAACA
1 AAAAAAACTT-TTACAACA
2364927 TAATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAAACTTTTACAACAA
Found at i:2365087 original size:19 final size:19
Alignment explanation
Indices: 2365063--2365107 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
2365053 TTACAATGAA
2365063 AGTAAATTTAATTATGATT
1 AGTAAATTTAATTATGATT
2365082 AGTAAATTTAATTATGATT
1 AGTAAATTTAATTATGATT
2365101 A-TAAATT
1 AGTAAATT
2365108 GTAAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (19 bp):
AGTAAATTTAATTATGATT
Found at i:2365534 original size:20 final size:20
Alignment explanation
Indices: 2365509--2365548 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2365499 CAAAAAAATC
2365509 AAAAAAAAATTATATGTTGA
1 AAAAAAAAATTATATGTTGA
2365529 AAAAAAAAATTATATGTTGA
1 AAAAAAAAATTATATGTTGA
2365549 GTTCCCAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (20 bp):
AAAAAAAAATTATATGTTGA
Found at i:2367130 original size:2 final size:2
Alignment explanation
Indices: 2367123--2367152 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2367113 TAAAAAGTTT
2367123 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2367153 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2367157 original size:2 final size:2
Alignment explanation
Indices: 2367152--2367181 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2367142 TATATATATA
2367152 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2367182 GCTTTAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2368339 original size:79 final size:79
Alignment explanation
Indices: 2368182--2368404 Score: 211
Period size: 79 Copynumber: 2.8 Consensus size: 79
2368172 TGAGAAATTT
* * * *
2368182 AATATTTTGGAGATAATAA-CGGGGTTGGAGTA-TCCCTTTGAAAATAACGCGGTTGGAGTATCC
1 AATATTTAGGAAATAA-AACCGGGGTTGGAGTATTCCC-TTGGAAATAACGGGGTTGGAGTATCC
*
2368245 CCAGTTTCAAAAAATC
64 CCAATTTCAAAAAATC
* * *
2368261 GATGA-TTAGGAAATAAAATCGGGATTGGAGTATTCCCTTGGAAATAACGGGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCGGGGTTGGAGTATTCCCTTGGAAATAACGGGGTTGGAGTATCCC
* *
2368325 CAATTAT-GAGAAATC
65 CAATT-TCAAAAAATC
* * * * * * ***
2368340 AATATTTTGGACATAAAGCCGGGGTAGGAGTATCCCCTCGGAGGCAACGGGGTTGGAGTATCCCC
1 AATATTTAGGAAATAAAACCGGGGTTGGAGTATTCCCTTGGAAATAACGGGGTTGGAGTATCCCC
2368405 GATGAAATAA
Statistics
Matches: 118, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
78 3 0.03
79 109 0.92
80 6 0.05
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (79 bp):
AATATTTAGGAAATAAAACCGGGGTTGGAGTATTCCCTTGGAAATAACGGGGTTGGAGTATCCCC
AATTTCAAAAAATC
Found at i:2368568 original size:51 final size:51
Alignment explanation
Indices: 2368418--2368792 Score: 391
Period size: 51 Copynumber: 7.3 Consensus size: 51
2368408 GAAATAACGA
* * * * * * *
2368418 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATTGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGT-GTTTTGAAAATAAAACTGG
* * * *
2368470 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACTGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAATTAGTGTTTTGAAAATAAAACTGG
* *
2368522 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTT-ATAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGA-AAATAAAACTGG
* * * * * *
2368573 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGAAAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAACTGG
* *
2368624 GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACTGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAATTAGTGTTTTGAAAATAAAACTGG
* *
2368676 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTT-AGAAATAAATC-GG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGA-AAATAAAACTGG
* * * * *
2368726 GGTTGGAGTATCCCCGATTAT-GAGAAATCAATAATTTTGGAAAT-AAAGTCGG
1 GGTTGGAGTATCCCCGATTATGGA-AAATTAGT-GTTTTGAAAATAAAACT-GG
2368778 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2368793 TCGAAGATAA
Statistics
Matches: 273, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
49 2 0.01
50 32 0.12
51 118 0.43
52 111 0.41
53 10 0.04
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTGAAAATAAAACTGG
Found at i:2368652 original size:154 final size:153
Alignment explanation
Indices: 2368418--2368792 Score: 597
Period size: 154 Copynumber: 2.4 Consensus size: 153
2368408 GAAATAACGA
* * *** * * *
2368418 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATTGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCAATA-TTTTGGAAATAAAGTCGGGGTTGGAGTATCC
*
2368483 CCGATTAAAGGAAAATTGGTGTTTTGAAGATAAAACTGGGGTTGGAGTATCCCCGATTGTGGAAA
65 CCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATCCCCGATTGTGGAAA
*
2368548 ATTAGTGTTTTATAAATAAAACCGG
130 ATTAGTGTTTTAGAAAT-AAACCGG
* *
2368573 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGAAAATAAAGCCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
2368638 CGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATCCCCGATTGTGGAAAA
66 CGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATCCCCGATTGTGGAAAA
*
2368703 TTAGTGTTTTAGAAATAAATCGG
131 TTAGTGTTTTAGAAATAAACCGG
*
2368726 GGTTGGAGTATCCCCGATTATGAGAAATCAATAATTTTGGAAATAAAGTCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTATGAAAAATCAAT-ATTTTGGAAATAAAGTCGGGGTTGGAGTATCC
2368791 CC
65 CC
2368793 TCGAAGATAA
Statistics
Matches: 203, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
153 37 0.18
154 138 0.68
155 28 0.14
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (153 bp):
GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCC
CGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACTGGGGTTGGAGTATCCCCGATTGTGGAAAA
TTAGTGTTTTAGAAATAAACCGG
Found at i:2368815 original size:28 final size:27
Alignment explanation
Indices: 2368775--2368846 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
2368765 GAAATAAAGT
2368775 CGGGGTTGGAGTATCCCC-TCGAAGATAA
1 CGGGGTTGGAGTATCCCCAT-GAA-ATAA
2368803 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCC-ATGAAATAA
*
2368831 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
2368847 TCGATTGTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 37 0.90
29 3 0.07
30 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATGAAATAA
Found at i:2368924 original size:52 final size:53
Alignment explanation
Indices: 2368857--2368957 Score: 143
Period size: 52 Copynumber: 1.9 Consensus size: 53
2368847 TCGATTGTGA
*
2368857 AAAATTGATGTTTTTGGAAATAAAATCG-GAGTCGGAGTATCCCCAATTAAAGG
1 AAAATTGATGTTTTTGAAAATAAAATCGAG-GTCGGAGTATCCCCAATTAAAGG
* * *
2368910 AAAATTGGTG-TTTTGAAAATAAAATCGAGGTTGGAGTATTCCCAATTA
1 AAAATTGATGTTTTTGAAAATAAAATCGAGGTCGGAGTATCCCCAATTA
2368958 TGAACAATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
52 33 0.77
53 10 0.23
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.31
Consensus pattern (53 bp):
AAAATTGATGTTTTTGAAAATAAAATCGAGGTCGGAGTATCCCCAATTAAAGG
Found at i:2371354 original size:21 final size:20
Alignment explanation
Indices: 2371330--2371368 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
2371320 GTATCCATAC
2371330 AATGTATCGATACACTTTCTT
1 AATGTATCGATACA-TTTCTT
2371351 AATGTATCGATACATTTC
1 AATGTATCGATACATTTC
2371369 CTTGGCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTCTT
Found at i:2371429 original size:19 final size:20
Alignment explanation
Indices: 2371405--2371458 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
2371395 TTGTATCGAT
*
2371405 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGAA
**
2371424 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACTGAA
2371445 TGTATCGATACAAA
1 TGTATCGATACAAA
2371459 TTATTGAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAAAACTGAA
Found at i:2374377 original size:20 final size:20
Alignment explanation
Indices: 2374287--2374378 Score: 61
Period size: 20 Copynumber: 4.6 Consensus size: 20
2374277 ATTATATGAT
2374287 ATAAATATATAAATATTTTAAA
1 ATAAATATAT-AATATTTT-AA
**
2374309 ATTTATATAATACATATTATT-A
1 ATAAATAT-ATA-ATATT-TTAA
*
2374331 AT--ATAT-TAA-ATTTTAT
1 ATAAATATATAATATTTTAA
2374347 ATAAATATATAATATTTTAA
1 ATAAATATATAATATTTTAA
2374367 ATATAAT-TATAA
1 ATA-AATATATAA
2374379 AATAATAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
15 2 0.04
16 5 0.09
17 1 0.02
18 6 0.11
19 3 0.05
20 18 0.32
21 3 0.05
22 10 0.18
23 7 0.12
24 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAATATATAATATTTTAA
Found at i:2374390 original size:13 final size:12
Alignment explanation
Indices: 2374345--2374409 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 12
2374335 ATTAAATTTT
2374345 ATATAAATATATA
1 ATATAAA-ATATA
*
2374358 ATATTTTAAATATA
1 ATA--TAAAATATA
2374372 ATTATAAAATAATA
1 A-TATAAAAT-ATA
*
2374386 ATATATAATAT-
1 ATATAAAATATA
2374397 ATATAAAA-ATA
1 ATATAAAATATA
2374408 AT
1 AT
2374410 TTTAATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 2 0.05
11 9 0.21
12 2 0.05
13 15 0.35
14 10 0.23
15 5 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATAAAATATA
Found at i:2374398 original size:28 final size:30
Alignment explanation
Indices: 2374285--2374399 Score: 75
Period size: 28 Copynumber: 3.9 Consensus size: 30
2374275 TAATTATATG
*
2374285 ATATAAATATATAAATATTTTAAA-AT--TT
1 ATATAAATATAT-AATATTATAAATATAATT
* * *
2374313 ATAT-AATACATATTATTA-ATATATTAAATTTT
1 ATATAAATATATAATATTATAAATA-T-AA--TT
*
2374345 ATATAAATATATAATATTTTAAATATAATT
1 ATATAAATATATAATATTATAAATATAATT
2374375 ATA-AAATA-ATAATA-TATAATATATA
1 ATATAAATATATAATATTATAA-ATATA
2374400 TAAAAATAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
25 2 0.03
26 6 0.09
27 11 0.16
28 15 0.22
29 5 0.07
30 5 0.07
32 8 0.12
33 12 0.18
34 4 0.06
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATAAATATATAATATTATAAATATAATT
Found at i:2374399 original size:22 final size:22
Alignment explanation
Indices: 2374344--2374409 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
2374334 TATTAAATTT
* **
2374344 TATATAAATATATAATATTTTAA
1 TATAT-AATATATAAAATAATAA
2374367 -ATATAAT-TATAAAATAATAA
1 TATATAATATATAAAATAATAA
2374387 TATATAATATATATAAA-AATAA
1 TATATAATATATA-AAATAATAA
2374409 T
1 T
2374410 TTTAATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.27
21 10 0.27
22 14 0.38
23 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TATATAATATATAAAATAATAA
Found at i:2374417 original size:24 final size:24
Alignment explanation
Indices: 2374366--2374437 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
2374356 TAATATTTTA
* **
2374366 AATATAATTATAAAATAATAATATAT
1 AATATAA-TAAAAAATAATTTTA-AT
2374392 AATAT-ATATAAAAATAATTTTAAT
1 AATATAATA-AAAAATAATTTTAAT
* *
2374416 AATTTAATAAAAAATTATTTTA
1 AATATAATAAAAAATAATTTTA
2374438 TTTTCACGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 20 0.51
25 14 0.36
26 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AATATAATAAAAAATAATTTTAAT
Found at i:2374499 original size:2 final size:2
Alignment explanation
Indices: 2374488--2374531 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2374478 AAGCAAATCT
2374488 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2374529 TA T
1 TA T
2374532 TGACGCTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2374768 original size:29 final size:29
Alignment explanation
Indices: 2374713--2374773 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
2374703 ATAAGATAAA
* * *
2374713 AAATAACTAAATATGATATATATATATAT
1 AAATAAATAAATATGATATAAAAATATAT
*
2374742 AAATAAAT-AATATGAATATAAAAATATTT
1 AAATAAATAAATATG-ATATAAAAATATAT
2374771 AAA
1 AAA
2374774 AATTTATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (29 bp):
AAATAAATAAATATGATATAAAAATATAT
Found at i:2374792 original size:27 final size:31
Alignment explanation
Indices: 2374762--2374830 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 31
2374752 TATGAATATA
2374762 AAAATATTTAAAAAT-TTA-TATAA-A-AAT
1 AAAATATTTAAAAATATTATTATAATATAAT
*
2374789 AAAATATTT-TAAATATTATTATAATATAAT
1 AAAATATTTAAAAATATTATTATAATATAAT
2374819 AAAATATATTAA
1 AAAATAT-TTAA
2374831 TATGATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 4 0.12
27 12 0.35
28 5 0.15
29 1 0.03
30 10 0.29
31 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAAATATTTAAAAATATTATTATAATATAAT
Found at i:2374846 original size:8 final size:8
Alignment explanation
Indices: 2374720--2374858 Score: 55
Period size: 8 Copynumber: 15.6 Consensus size: 8
2374710 AAAAAATAAC
2374720 TAAATATGA
1 TAAATAT-A
*
2374729 TATATATA
1 TAAATATA
* *
2374737 TATATAAA
1 TAAATATA
2374745 TAAATAATA
1 TAAAT-ATA
*
2374754 TGAATATA
1 TAAATATA
*
2374762 AAAATATTTA
1 TAAATA--TA
*
2374772 AAAATTTATA
1 TAAA--TATA
*
2374782 TAAAAATA
1 TAAATATA
*
2374790 -AAATATTT
1 TAAATA-TA
2374798 TAAATATTA
1 TAAATA-TA
2374807 TTATAATATAA
1 -TA-AATAT-A
2374818 TAAAATATA
1 T-AAATATA
2374827 TTAATATGATA
1 -TAA-AT-ATA
2374838 TAAATATA
1 TAAATATA
*
2374846 TAAATAGA
1 TAAATATA
2374854 TAAAT
1 TAAAT
2374859 TTTTATATAT
Statistics
Matches: 103, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
7 4 0.04
8 38 0.37
9 24 0.23
10 26 0.25
11 9 0.09
12 2 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
TAAATATA
Found at i:2375282 original size:44 final size:42
Alignment explanation
Indices: 2375214--2375298 Score: 152
Period size: 44 Copynumber: 2.0 Consensus size: 42
2375204 ACGGGATAAC
2375214 GTAATGAAAATAAAAAATGGTAAATAAAGAGAAAAGTAAAAT
1 GTAATGAAAATAAAAAATGGTAAATAAAGAGAAAAGTAAAAT
2375256 GTAATGAAAGATAAAAAAATGGTAAATAAAGAGAAAAGTAAAA
1 GTAATGAAA-AT-AAAAAATGGTAAATAAAGAGAAAAGTAAAA
2375299 AATAATTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 9 0.22
43 2 0.05
44 30 0.73
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (42 bp):
GTAATGAAAATAAAAAATGGTAAATAAAGAGAAAAGTAAAAT
Found at i:2375286 original size:21 final size:21
Alignment explanation
Indices: 2375225--2375292 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
2375215 TAATGAAAAT
2375225 AAAAAATGGTAAATAAAGAGAA
1 AAAAAATGGTAAATAAAGA-AA
*
2375247 AAGTAAAAT-GT-AATGAAAGATA
1 AA--AAAATGGTAAAT-AAAGAAA
*
2375269 AAAAAATGGTAAATAAAGAGA
1 AAAAAATGGTAAATAAAGAAA
2375290 AAA
1 AAA
2375293 GTAAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
20 5 0.13
21 11 0.28
22 11 0.28
23 7 0.18
24 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (21 bp):
AAAAAATGGTAAATAAAGAAA
Found at i:2377013 original size:17 final size:18
Alignment explanation
Indices: 2376982--2377015 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2376972 TAAATTATAT
*
2376982 AAAAAGTTATCTTATTTA
1 AAAAAATTATCTTATTTA
2377000 AAAAAATTAT-TTATTT
1 AAAAAATTATCTTATTT
2377016 TTTTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAAAATTATCTTATTTA
Found at i:2377547 original size:13 final size:13
Alignment explanation
Indices: 2377529--2377571 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
2377519 AAGGATCACT
2377529 TTTTTTTTGAAAG-
1 TTTTTTTT-AAAGA
2377542 TTTTTTTTAAAGAA
1 TTTTTTTTAAAG-A
2377556 TTTTTTTTAAA-A
1 TTTTTTTTAAAGA
2377568 TTTT
1 TTTT
2377572 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.32
13 8 0.29
14 11 0.39
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (13 bp):
TTTTTTTTAAAGA
Found at i:2377569 original size:12 final size:13
Alignment explanation
Indices: 2377529--2377571 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2377519 AAGGATCACT
* *
2377529 TTTTTTTTGAAAG
1 TTTTTTTTAAAAA
2377542 TTTTTTTTAAAGAA
1 TTTTTTTTAAA-AA
2377556 TTTTTTTT-AAAA
1 TTTTTTTTAAAAA
2377568 TTTT
1 TTTT
2377572 ATATTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 6 0.22
13 12 0.44
14 9 0.33
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (13 bp):
TTTTTTTTAAAAA
Found at i:2377992 original size:2 final size:2
Alignment explanation
Indices: 2377985--2378011 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2377975 GATCTTCCCT
2377985 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2378012 TTTCCCCTGC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2379236 original size:17 final size:17
Alignment explanation
Indices: 2379214--2379248 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2379204 AAAAAATTAA
2379214 ATATATCCATATTAAAT
1 ATATATCCATATTAAAT
* *
2379231 ATATATCTATATTCAAT
1 ATATATCCATATTAAAT
2379248 A
1 A
2379249 CTTATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATCCATATTAAAT
Found at i:2383705 original size:57 final size:57
Alignment explanation
Indices: 2383617--2383731 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
2383607 TTTTTTTTCC
2383617 AAGAGAGTTTGGTTATGTGTTGCTATATATGTCATTTTAATTATTTGATTATTTTAA
1 AAGAGAGTTTGGTTATGTGTTGCTATATATGTCATTTTAATTATTTGATTATTTTAA
2383674 AAGAGAGTTTGGTTATGTGTTGCTATATATGTCATTTTAATTATTTGATTATTTTAA
1 AAGAGAGTTTGGTTATGTGTTGCTATATATGTCATTTTAATTATTTGATTATTTTAA
2383731 A
1 A
2383732 TTCAAATACC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.50
Consensus pattern (57 bp):
AAGAGAGTTTGGTTATGTGTTGCTATATATGTCATTTTAATTATTTGATTATTTTAA
Found at i:2389641 original size:15 final size:15
Alignment explanation
Indices: 2389621--2389693 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 15
2389611 TATAGTTAAA
2389621 TATATTTAATATATT
1 TATATTTAATATATT
*
2389636 TATATTTAAAATTATAAT
1 TATATTT--AA-TATATT
*
2389654 T-TATTTAATAATTTT
1 TATATTTAAT-ATATT
2389669 TATATTT-ATAT-TT
1 TATATTTAATATATT
*
2389682 TAATAATTAATA
1 T-ATATTTAATA
2389694 AAAAAATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
13 3 0.06
14 8 0.17
15 18 0.38
16 5 0.11
17 7 0.15
18 6 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTTAATATATT
Found at i:2389963 original size:8 final size:8
Alignment explanation
Indices: 2389950--2390059 Score: 61
Period size: 7 Copynumber: 13.6 Consensus size: 8
2389940 ATTGTATTTA
2389950 TATATATT
1 TATATATT
2389958 TATATATTAT
1 TATATA-T-T
2389968 TATTATATT
1 TA-TATATT
*
2389977 TAAATA-T
1 TATATATT
2389984 TATATATT
1 TATATATT
2389992 TATATAAATAT
1 TATAT--AT-T
2390003 TAATATATT
1 T-ATATATT
*
2390012 AATA-ATT
1 TATATATT
*
2390019 TATAT-TA
1 TATATATT
*
2390026 TATAAATT
1 TATATATT
*
2390034 T-TA-ATA
1 TATATATT
*
2390040 TATTTATT
1 TATATATT
2390048 T-TATATT
1 TATATATT
2390055 TATAT
1 TATAT
2390060 TATATACCTT
Statistics
Matches: 78, Mismatches: 11, Indels: 26
0.68 0.10 0.23
Matches are distributed among these distances:
6 3 0.04
7 26 0.33
8 26 0.33
9 5 0.06
10 8 0.10
11 6 0.08
12 4 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:2389971 original size:6 final size:7
Alignment explanation
Indices: 2389950--2390065 Score: 78
Period size: 6 Copynumber: 17.9 Consensus size: 7
2389940 ATTGTATTTA
2389950 TATATATT
1 TATATA-T
2389958 TATATAT
1 TATATAT
2389965 TAT-TAT
1 TATATAT
2389971 TATAT-T
1 TATATAT
*
2389977 TAAATAT
1 TATATAT
2389984 TATATAT
1 TATATAT
2389991 T-TATA-
1 TATATAT
*
2389996 TAAATAT
1 TATATAT
2390003 TAATATAT
1 T-ATATAT
2390011 TA-ATAAT
1 TATAT-AT
2390018 T-TATAT
1 TATATAT
2390024 TATATA-
1 TATATAT
*
2390030 -A-ATTT
1 TATATAT
2390035 TAATATAT
1 T-ATATAT
2390043 T-TAT-T
1 TATATAT
2390048 T-TATAT
1 TATATAT
2390054 T-TATAT
1 TATATAT
2390060 TATATA
1 TATATA
2390066 CCTTATTTAA
Statistics
Matches: 88, Mismatches: 6, Indels: 29
0.72 0.05 0.24
Matches are distributed among these distances:
4 2 0.02
5 7 0.08
6 34 0.39
7 29 0.33
8 16 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATAT
Found at i:2389987 original size:36 final size:34
Alignment explanation
Indices: 2389939--2390065 Score: 107
Period size: 36 Copynumber: 3.4 Consensus size: 34
2389929 ATTAATAATT
2389939 TATTGTAT-TTATATATATTTATATATTATTATTA
1 TATT-TATATTATATATATTTATATATTATTATTA
2389973 TATTTAAATATTATATAT-TTATATAAATATTAATATATTAA
1 TATTT--ATATTATATATATT-TAT--ATATT-AT-TATT-A
*
2390014 TAATTTATATTATATAAATTTTAATATATTTATT-TTA
1 T-ATTTATATTATATATA-TTT-ATATA-TTATTATTA
2390051 TATTTATATTATATA
1 TATTTATATTATATA
2390066 CCTTATTTAA
Statistics
Matches: 78, Mismatches: 1, Indels: 26
0.74 0.01 0.25
Matches are distributed among these distances:
33 1 0.01
34 4 0.05
35 4 0.05
36 25 0.32
37 2 0.03
38 7 0.09
39 3 0.04
40 19 0.24
41 5 0.06
42 8 0.10
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (34 bp):
TATTTATATTATATATATTTATATATTATTATTA
Found at i:2389996 original size:32 final size:31
Alignment explanation
Indices: 2389938--2390062 Score: 93
Period size: 33 Copynumber: 4.0 Consensus size: 31
2389928 AATTAATAAT
* *
2389938 TTATTGTATTT-ATATATAT-TTATATATTA
1 TTATTATATTTAATATTTATATTATATATTA
*
2389967 TTATTATATTTAAATATTATATATT-TATATAA
1 TTATTATATTT-AATATT-TATATTATATATTA
*
2389999 ATATTAATATATTAATAATTTATATTATATAAATT-
1 TTATT-ATAT-TTAAT-ATTTATATTATAT--ATTA
*
2390034 TTAATATATTT-AT-TTTATATT-TATATTA
1 TTATTATATTTAATATTTATATTATATATTA
2390062 T
1 T
2390063 ATACCTTATT
Statistics
Matches: 78, Mismatches: 7, Indels: 23
0.72 0.06 0.21
Matches are distributed among these distances:
27 3 0.04
28 1 0.01
29 13 0.17
30 8 0.10
31 4 0.05
32 15 0.19
33 17 0.22
34 12 0.15
35 3 0.04
36 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (31 bp):
TTATTATATTTAATATTTATATTATATATTA
Found at i:2390075 original size:38 final size:37
Alignment explanation
Indices: 2389980--2390075 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 37
2389970 TTATATTTAA
* *
2389980 ATATTATATATTTATATAAATA-TTAATATA-TTA--AT
1 ATATT-TATA-TTATATAATTATTTAATATATTTATTTT
*
2390015 A-ATTTATATTATATAAAT-TTTAATATATTTATTTT
1 ATATTTATATTATATAATTATTTAATATATTTATTTT
*
2390050 ATATTTATATTATATACCTTATTTAA
1 ATATTTATATTATATA-ATTATTTAA
2390076 AATTATTAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
32 18 0.35
33 7 0.14
34 3 0.06
35 3 0.06
36 14 0.27
37 1 0.02
38 5 0.10
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (37 bp):
ATATTTATATTATATAATTATTTAATATATTTATTTT
Found at i:2393788 original size:65 final size:66
Alignment explanation
Indices: 2393667--2393806 Score: 219
Period size: 65 Copynumber: 2.1 Consensus size: 66
2393657 CTACTTGGGC
* *
2393667 AGAGTGGATCATCACTGACGTGCTATGGCAGAGGCCAAAGGGTGGGTTGTGAATTGTGTTAGAGG
1 AGAGTGGATCATCACTGACGTGC-ATGGCAGACGCCAAAGGGTGGGTTGTGAATTGTGATAGAGG
2393732 CG
65 CG
* * *
2393734 AGAGTGGATCATCACTGACGTGC-TGGCAGACGCCGAATGGTGGGTTGTGAATTGTGATAGAGGG
1 AGAGTGGATCATCACTGACGTGCATGGCAGACGCCAAAGGGTGGGTTGTGAATTGTGATAGAGGC
2393798 G
66 G
2393799 AGAGTGGA
1 AGAGTGGA
2393807 ACGTGCCTGA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
65 45 0.66
67 23 0.34
ACGTcount: A:0.24, C:0.13, G:0.40, T:0.23
Consensus pattern (66 bp):
AGAGTGGATCATCACTGACGTGCATGGCAGACGCCAAAGGGTGGGTTGTGAATTGTGATAGAGGC
G
Found at i:2394043 original size:7 final size:6
Alignment explanation
Indices: 2394016--2394040 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2394006 ACTTGACTTA
2394016 TGATTT TGATTT TGATTT TGATTT T
1 TGATTT TGATTT TGATTT TGATTT T
2394041 TGAGAACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TGATTT
Found at i:2394816 original size:495 final size:494
Alignment explanation
Indices: 2394226--2395125 Score: 1241
Period size: 495 Copynumber: 1.8 Consensus size: 494
2394216 TTTTTTTAAA
* *
2394226 AAAAATTTTAGAAATCAACTTTTCTTAATGTTCAAATCAAAATTGTGTAATGTAGTATAAAAACG
1 AAAAATTCTAGAAATCAACTTTTCTTAATGTCCAAATCAAAATTGTGTAATGTAGTATAAAAACG
* **
2394291 AAAAATCTATTTTCTTATTCTTTCCTAAATAAATGATTTTAGA-TATTGTTGAATGTTTACTCTT
66 AAAAATCTATTCTCTTATTCTTTCCTAAATAAAT-ATTGAAGATTA-TG-T-AATGTTTACTCTT
*
2394355 AAACTCTTTATTTATGTGATAGTGATATTCTTTATATCATAGTGATATTTTTTA-TTTT-TTTA-
127 AAACTCTTTATTTATATGATAGTGATATTCTTTATATCATAGTGATATTTTTTATTTTTATTTAT
* * *
2394417 TTTTTGAATTTTTATCTAATAATCAATCATA-AACCTGATCTTTGTTATCTTTATTTATACAAAC
192 TTTTTAAATTTTTAT-T--TAAT-AATCA-AGAACCTAATCTTTGCTATCTTTATTTATACAAAC
* *
2394481 ACCACTGT-AAAAGAGAG-GAGACAACTCTATGTAATGACAAGTCAATATAAATTGAATAAA-AA
252 ACCACTATAAAAAGAGAGAG-GACAACTCTATGCAATGACAAGTCAATATAAATTGAA-AAAGAA
*
2394543 -C-TTTTTTT-AAAATCAAAATATTTAAAAAATCTTGAATTATTTTA-TTTTTAAGTAATTTTTT
315 TCTTTTTTTTGAAAATCAAAATATTTAAAAAATCATGAATTATTTTATTTTTTAAGTAA-TTTTT
**
2394604 GATATGGATATGTATTTTTTATTATTGTAAATTGAATAAGAATCTCATTGTAAAATATTTTTTTA
379 -ATATAAATATGTATTTTTTATTATTGTAAATTGAATAAGAATCTCATTGTAAAATATTTTTTTA
2394669 TAATAAAAAACTCTTATTACAAGTGAATTTTTGAAAATCCTTTTTGATTTCT
443 TAATAAAAAACTCTTATTACAAGTGAATTTTTGAAAATCCTTTTTGATTTCT
** *
2394721 AAAAATTCTAGAAATCAACTTTTCTTGGTGTCCAAATCAAAATTGTGTAATGTGGTATAAAAATC
1 AAAAATTCTAGAAATCAACTTTTCTTAATGTCCAAATCAAAATTGTGTAATGTAGTATAAAAA-C
* * *
2394786 -AAGAATCTATTCTCTTATTCTTTCCTAAATAAATCTTGAAGATTATGTAATGTTTACTTTTAAA
65 GAAAAATCTATTCTCTTATTCTTTCCTAAATAAATATTGAAGATTATGTAATGTTTACTCTTAAA
* * * *
2394850 CTTTTTATTTATATGTTAGTGATATTTTTTATATCGTAGTGATATTTTTTATTTTTATTTATTTT
130 CTCTTTATTTATATGATAGTGATATTCTTTATATCATAGTGATATTTTTTATTTTTATTTA--TT
* * * * *
2394915 TTTTAAATTTTTATTTAATGATCAAGGACGTAATCTTTGCTATCTTTATTTATACAAACACTATT
193 TTTTAAATTTTTATTTAATAATCAAGAACCTAATCTTTGCTATCTTTATTTATACAAACACCACT
* * *
2394980 ATAAAAAGAGAGAGGGCAACTCTATGCAATGACAGGTTAATATAAATTGAAAAAGAATCTTTTTT
258 ATAAAAAGAGAGAGGACAACTCTATGCAATGACAAGTCAATATAAATTGAAAAAGAATC--TTTT
* *
2395045 TTTTGTAAATTAAAATATTTAAAAAATCATGAATTATTTTATTTTTTAAGTAATTTTTATATAAA
321 TTTTGAAAATCAAAATATTTAAAAAATCATGAATTATTTTATTTTTTAAGTAATTTTTATATAAA
2395110 TATGTATTTTTTATTA
386 TATGTATTTTTTATTA
2395126 CCATATTTTG
Statistics
Matches: 354, Mismatches: 34, Indels: 31
0.84 0.08 0.07
Matches are distributed among these distances:
492 62 0.18
493 46 0.13
494 59 0.17
495 94 0.27
496 2 0.01
497 14 0.04
498 28 0.08
499 38 0.11
500 11 0.03
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (494 bp):
AAAAATTCTAGAAATCAACTTTTCTTAATGTCCAAATCAAAATTGTGTAATGTAGTATAAAAACG
AAAAATCTATTCTCTTATTCTTTCCTAAATAAATATTGAAGATTATGTAATGTTTACTCTTAAAC
TCTTTATTTATATGATAGTGATATTCTTTATATCATAGTGATATTTTTTATTTTTATTTATTTTT
TAAATTTTTATTTAATAATCAAGAACCTAATCTTTGCTATCTTTATTTATACAAACACCACTATA
AAAAGAGAGAGGACAACTCTATGCAATGACAAGTCAATATAAATTGAAAAAGAATCTTTTTTTTG
AAAATCAAAATATTTAAAAAATCATGAATTATTTTATTTTTTAAGTAATTTTTATATAAATATGT
ATTTTTTATTATTGTAAATTGAATAAGAATCTCATTGTAAAATATTTTTTTATAATAAAAAACTC
TTATTACAAGTGAATTTTTGAAAATCCTTTTTGATTTCT
Found at i:2394882 original size:20 final size:20
Alignment explanation
Indices: 2394857--2394901 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
2394847 AAACTTTTTA
2394857 TTTATAT-GTTAGTGATATTT
1 TTTATATCG-TAGTGATATTT
2394877 TTTATATCGTAGTGATATTT
1 TTTATATCGTAGTGATATTT
2394897 TTTAT
1 TTTAT
2394902 TTTTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.60
Consensus pattern (20 bp):
TTTATATCGTAGTGATATTT
Found at i:2395437 original size:19 final size:22
Alignment explanation
Indices: 2395413--2395458 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 22
2395403 AATTGAAAAA
2395413 TTATAAAA-AAATAA-AT-ATT
1 TTATAAAATAAATAATATCATT
*
2395432 TTATAAAATGAATAATATCATT
1 TTATAAAATAAATAATATCATT
2395454 TTATA
1 TTATA
2395459 TATTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 5 0.22
21 2 0.09
22 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TTATAAAATAAATAATATCATT
Found at i:2396191 original size:232 final size:232
Alignment explanation
Indices: 2395933--2396398 Score: 790
Period size: 232 Copynumber: 2.0 Consensus size: 232
2395923 TAATAAGAAC
* **
2395933 TATATATGTATCAAATTGATATAAATACAAACTATTTTATACATGATTATGATGTAATAAAATTT
1 TATATATGTATCAAATTGATATAAATACAAACTATTTTACACATGATTATGACATAATAAAATTT
** *
2395998 ATAAATATAACAATAATATATGTATTATGAAATTTACTTTTAAGTCAAACAACACAGTTTCTCTT
66 ATAAATATAACAATAATATACATATTATGAAATTTACTTTTAAGTCAAACAACACAATTTCTCTT
2396063 TTGCTTTATCAAATTTGTATTATTTAATAGAGG-GCGACTTGAAAAGTTTTAACATTATTTAATT
131 TTGCTTTATCAAATTTGTATTATTTAATAG-GGAGCGACTTGAAAAGTTTTAACATTATTTAATT
*
2396127 AATTCTTAATTTAATATCTAATTCTAATAATATATATA
195 AATTCTTAATTTAATATCTAATACTAATAATATATATA
* *
2396165 TATATATGTATCAAATTGATATAAATATAAACTATTTTACATATGATTATGACATAATAAAATTT
1 TATATATGTATCAAATTGATATAAATACAAACTATTTTACACATGATTATGACATAATAAAATTT
*
2396230 ATAAATATAACAATTATATACATATTATGAAATTTACTTTTAAGTCAAACAACACAATTTCTCTT
66 ATAAATATAACAATAATATACATATTATGAAATTTACTTTTAAGTCAAACAACACAATTTCTCTT
*
2396295 TTGCTTTATTAAATTTGTATTATTTAATAGGGAGCGACTTGAAAAGTTTTAACATTATTTAATTA
131 TTGCTTTATCAAATTTGTATTATTTAATAGGGAGCGACTTGAAAAGTTTTAACATTATTTAATTA
* * *
2396360 ATTTTTAATTTAATATCTAATAGTACTAATATATATA
196 ATTCTTAATTTAATATCTAATACTAATAATATATATA
2396397 TA
1 TA
2396399 GTATTGCAAT
Statistics
Matches: 219, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
231 2 0.01
232 217 0.99
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (232 bp):
TATATATGTATCAAATTGATATAAATACAAACTATTTTACACATGATTATGACATAATAAAATTT
ATAAATATAACAATAATATACATATTATGAAATTTACTTTTAAGTCAAACAACACAATTTCTCTT
TTGCTTTATCAAATTTGTATTATTTAATAGGGAGCGACTTGAAAAGTTTTAACATTATTTAATTA
ATTCTTAATTTAATATCTAATACTAATAATATATATA
Found at i:2397901 original size:17 final size:17
Alignment explanation
Indices: 2397870--2397915 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
2397860 AAAATAAGAT
*
2397870 GCAT-AATGCACGAATG
1 GCATGAATGCATGAATG
*
2397886 GCATGTATGCATGAATG
1 GCATGAATGCATGAATG
*
2397903 TCATGAATGCATG
1 GCATGAATGCATG
2397916 CATGCTATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (17 bp):
GCATGAATGCATGAATG
Found at i:2397909 original size:9 final size:8
Alignment explanation
Indices: 2397868--2397931 Score: 60
Period size: 8 Copynumber: 7.9 Consensus size: 8
2397858 ATAAAATAAG
2397868 ATGCAT-A
1 ATGCATGA
*
2397875 ATGCACGA
1 ATGCATGA
*
2397883 ATGGCATGT
1 AT-GCATGA
2397892 ATGCATGA
1 ATGCATGA
2397900 ATGTCATGA
1 ATG-CATGA
*
2397909 ATGCATGC
1 ATGCATGA
2397917 ATGCTATGA
1 ATGC-ATGA
2397926 A-GCATG
1 ATGCATG
2397932 TTCTGAGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
7 8 0.17
8 21 0.45
9 18 0.38
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.27
Consensus pattern (8 bp):
ATGCATGA
Found at i:2399168 original size:25 final size:23
Alignment explanation
Indices: 2399132--2399177 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
2399122 ATCAATAATA
*
2399132 AATAATTTAATTTTAATAAATTTTT
1 AATAATTAAATTTT--TAAATTTTT
2399157 AATAATTAAATTTTTAAATTT
1 AATAATTAAATTTTTAAATTT
2399178 AAAAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
25 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATAATTAAATTTTTAAATTTTT
Found at i:2399938 original size:20 final size:20
Alignment explanation
Indices: 2399910--2399984 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
2399900 TTTTACCCAG
2399910 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
2399930 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
2399950 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
2399970 ATGTATCGATACATT
1 ATGTATCGATACATT
2399985 CTGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:2402970 original size:19 final size:18
Alignment explanation
Indices: 2402942--2403009 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
2402932 AATTTAACGA
2402942 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
2402960 TGTTGTGTCGATAC--AA-
1 T-TTGTATCGATACATAAG
2402976 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2402992 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
2403010 TTAGCTACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
18 1 0.02
19 26 0.63
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Done.