Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 130 of 210
Found at i:39477248 original size:51 final size:49
Alignment explanation
Indices: 39477126--39477472 Score: 206
Period size: 51 Copynumber: 7.2 Consensus size: 49
39477116 AGTCTCGTCG
* * * * *
39477126 CCCTGAAGTTGCAATGGAGCAGATTGAAG--ATAA-CA-AATCTTATTT
1 CCCTGAAGTTGCAATGGAACAGATTAAAGCTACAATTACAATCTTATCT
*
39477171 CCCTGAAGTTGCAATGGAACAAATTAAAGCTACAAATTACGAATCTTATCT
1 CCCTGAAGTTGCAATGGAACAGATTAAAGCTAC-AATTAC-AATCTTATCT
* * * *
39477222 CCCTGAAGTTTCAATTGAGCAGATTAAAGCTAC----A-AATCTTATTT
1 CCCTGAAGTTGCAATGGAACAGATTAAAGCTACAATTACAATCTTATCT
*
39477266 CCCTAAAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACAAATCTTATCT
1 CCCT-GAAGTTGCAATGGAACAGATTAAAGCTACAA-TTAC-AATCTTATCT
* * * * * *
39477318 CCCTGAAGTTACAGTGGAGCAGATTGAAGCAACAAGT-C---C-TATAC-
1 CCCTGAAGTTGCAATGGAACAGATTAAAGCTACAATTACAATCTTAT-CT
* **** * * * *
39477362 CTCTGAAGTTGCAATGGGTTGGATTAAATCTACCATAGTA-AGTCCTATCT
1 CCCTGAAGTTGCAATGGAACAGATTAAAGCTA-CA-ATTACAATCTTATCT
* * * *
39477412 CCCTGAAGTTGCAATGGAATAGACTAAAGCTACAAGCTGCAAATCTTATCT
1 CCCTGAAGTTGCAATGGAACAGATTAAAGCTACAA-TTAC-AATCTTATCT
39477463 -CCTCGAAGTT
1 CCCT-GAAGTT
39477473 ACAGCGGAGT
Statistics
Matches: 232, Mismatches: 43, Indels: 48
0.72 0.13 0.15
Matches are distributed among these distances:
44 38 0.16
45 55 0.24
46 4 0.02
47 1 0.00
48 3 0.01
49 7 0.03
50 34 0.15
51 77 0.33
52 13 0.06
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (49 bp):
CCCTGAAGTTGCAATGGAACAGATTAAAGCTACAATTACAATCTTATCT
Found at i:39477292 original size:45 final size:44
Alignment explanation
Indices: 39477212--39477301 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
39477202 ACAAATTACG
* * * *
39477212 AATCTTATCTCCCTGAAGTTTCAATTGAGCAGATTAAAGCTACA
1 AATCTTATCTCCCTAAAGTTGCAATGGAACAGATTAAAGCTACA
*
39477256 AATCTTATTTCCCTAAAAGTTGCAATGGAACAGATTAAAGCTACA
1 AATCTTATCTCCCT-AAAGTTGCAATGGAACAGATTAAAGCTACA
39477301 A
1 A
39477302 GTTACAAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 13 0.32
45 27 0.68
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTGCAATGGAACAGATTAAAGCTACA
Found at i:39479026 original size:4 final size:4
Alignment explanation
Indices: 39479017--39479049 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
39479007 TTTCATGAAA
*
39479017 TTAT TTAT TTAT TTAT TTAT GTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
39479050 CATTGATTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:39479131 original size:3 final size:3
Alignment explanation
Indices: 39479123--39479181 Score: 55
Period size: 3 Copynumber: 18.7 Consensus size: 3
39479113 CATTTTGTTC
* * * *
39479123 TTA TTA TTA TTA TTC TCA TTA TTA TTG TTA TTA TTTA TTT TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT-A TTA
39479170 TTA TTTA TTA TT
1 TTA -TTA TTA TT
39479182 TATTTTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
3 37 0.82
4 8 0.18
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39479172 original size:17 final size:18
Alignment explanation
Indices: 39479150--39479183 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
39479140 ATTATTATTG
39479150 TTATTATTTATT-TTTAA
1 TTATTATTTATTATTTAA
39479167 TTATTATTTATTATTTA
1 TTATTATTTATTATTTA
39479184 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTATTTATTATTTAA
Found at i:39479177 original size:24 final size:25
Alignment explanation
Indices: 39479123--39479220 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 25
39479113 CATTTTGTTC
*
39479123 TTATTA-TTATTATTCTCATTATTATT
1 TTATTATTTATTATT-TAATTATTA-T
39479149 GTTATTATTTATT-TTTAATTATTAT
1 -TTATTATTTATTATTTAATTATTAT
*
39479174 TTATTATTTA-T-TTTAA-AATT-T
1 TTATTATTTATTATTTAATTATTAT
*
39479195 TT-TTATATTATTATTTAATTAGTAT
1 TTATTAT-TTATTATTTAATTATTAT
39479220 T
1 T
39479221 AGAATTAGTA
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
20 4 0.07
21 6 0.10
22 4 0.07
23 11 0.18
24 12 0.20
25 3 0.05
26 8 0.13
27 8 0.13
28 5 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (25 bp):
TTATTATTTATTATTTAATTATTAT
Found at i:39480263 original size:16 final size:16
Alignment explanation
Indices: 39480238--39480271 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39480228 GCAAATAAAT
* *
39480238 TTAAACTTAAAAATAA
1 TTAAAATTAAAAAAAA
39480254 TTAAAATTAAAAAAAA
1 TTAAAATTAAAAAAAA
39480270 TT
1 TT
39480272 CAAACCTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAATTAAAAAAAA
Found at i:39482391 original size:83 final size:82
Alignment explanation
Indices: 39482273--39482476 Score: 320
Period size: 83 Copynumber: 2.5 Consensus size: 82
39482263 GGTATACATC
* *
39482273 TTTCAACAAATCATTTAAAAAAACAAACAAAATATGTTATACTAACAAAATGATCTTATAGC-AG
1 TTTCAACAAATCATTTAAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATA-CAAA
*
39482337 TAAGATGTTAACCAACCA
65 TAAGATGCTAACCAACCA
* * *
39482355 TTTTAACAAATCATTTAAAAAAAATAAACAAAATATGTTATGCTAACAAAATGATCCTATACAAA
1 TTTCAACAAATCATTT-AAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATACAAA
39482420 TAAGATGCTAACCAACCA
65 TAAGATGCTAACCAACCA
*
39482438 TTTCAACAAATCATTTCAAAAAACAAACAAAATATGTTA
1 TTTCAACAAATCATTTAAAAAAACAAACAAAATATGTTA
39482477 ACCATCTCAA
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
82 37 0.33
83 74 0.67
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (82 bp):
TTTCAACAAATCATTTAAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATACAAAT
AAGATGCTAACCAACCA
Found at i:39486537 original size:50 final size:50
Alignment explanation
Indices: 39486459--39486699 Score: 239
Period size: 50 Copynumber: 4.7 Consensus size: 50
39486449 TCCTTTACTT
* * * * * * *
39486459 CCAATGTCATATCTCAGATATGGTCTTACATGGGAGTTCTCATATCGGTA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGGTG
* * **
39486509 CCCATGCAATGTCCCAGACATGGTCTTACGGGGGACTTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGGTG
* * * * *
39486559 CCAACGCCATGTCTCAAACATGGTCTTACATGGGACCTCTCATCTCAGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGGTG
* * * *
39486609 CCAATGCCATGTCCCAGATATGGTCTTACATGAGACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CT-TC-TCATCTC---GGTG
*
39486665 CCAATGCCATGGCCCAGACATGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
39486700 TCTCTTTACC
Statistics
Matches: 153, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
50 110 0.72
51 1 0.01
52 2 0.01
53 6 0.04
56 34 0.22
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGGTG
Found at i:39488081 original size:18 final size:18
Alignment explanation
Indices: 39488058--39488095 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39488048 TCACGACCCT
*
39488058 CTCCCTCGCCCTCACCAC
1 CTCCCTCACCCTCACCAC
*
39488076 CTCCCTCACCCTTACCAC
1 CTCCCTCACCCTCACCAC
39488094 CT
1 CT
39488096 TTATTGCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.63, G:0.03, T:0.21
Consensus pattern (18 bp):
CTCCCTCACCCTCACCAC
Found at i:39488166 original size:24 final size:24
Alignment explanation
Indices: 39488122--39488167 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
39488112 CACCACCCTC
*
39488122 AACCTCACCAAATTTACTACCAAA
1 AACCTCACCAAATTCACTACCAAA
* *
39488146 AACCTCACCACATTCATTACCA
1 AACCTCACCAAATTCACTACCA
39488168 TCACCACCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (24 bp):
AACCTCACCAAATTCACTACCAAA
Found at i:39492808 original size:21 final size:22
Alignment explanation
Indices: 39492776--39492818 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
39492766 CTTTCTCTTC
*
39492776 TTCTTTTGTTTTTCTCC-CCTT
1 TTCTTTTGTTTTCCTCCTCCTT
39492797 TTCTTTCT-TTTTCCTCCTCCTT
1 TTCTTT-TGTTTTCCTCCTCCTT
39492819 CATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTGTTTTCCTCCTCCTT
Found at i:39494727 original size:25 final size:25
Alignment explanation
Indices: 39494672--39494724 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
39494662 GCCAATTTTG
*
39494672 AAATTTATTAAACATGACCAATATC
1 AAATTTATTAAACATGACCAAAATC
* *
39494697 AAATTTATTAAATATGATCAAGAATC
1 AAATTTATTAAACATGACCAA-AATC
39494723 AA
1 AA
39494725 TTTCATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (25 bp):
AAATTTATTAAACATGACCAAAATC
Found at i:39495806 original size:18 final size:18
Alignment explanation
Indices: 39495783--39495821 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
39495773 GGGTGAAAGT
39495783 TTGTTAAAATAGGATTGG
1 TTGTTAAAATAGGATTGG
39495801 TTGTTAAAATAGGATTGG
1 TTGTTAAAATAGGATTGG
39495819 TTG
1 TTG
39495822 ACCAATTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (18 bp):
TTGTTAAAATAGGATTGG
Found at i:39496701 original size:28 final size:28
Alignment explanation
Indices: 39496658--39496717 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
39496648 TTTTGTTATG
**
39496658 CACTTCGATGTTGTTCTAATATGATAAA
1 CACTTCGATGACGTTCTAATATGATAAA
* * *
39496686 CACTTCGATGACGTTCTGATATGTTAAG
1 CACTTCGATGACGTTCTAATATGATAAA
39496714 CACT
1 CACT
39496718 ATGGTGTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (28 bp):
CACTTCGATGACGTTCTAATATGATAAA
Found at i:39502455 original size:14 final size:15
Alignment explanation
Indices: 39502438--39502466 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
39502428 TCTTTCCATT
39502438 TCTTTCT-TCTTCCC
1 TCTTTCTCTCTTCCC
39502452 TCTTTCTCTCTTCCC
1 TCTTTCTCTCTTCCC
39502467 CTCTATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTCTCTCTTCCC
Found at i:39512925 original size:35 final size:35
Alignment explanation
Indices: 39512879--39512947 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
39512869 TAGACGTTAC
39512879 GGCCGAATCTGGAAGAGTTACATTAGTTTGTTTAT
1 GGCCGAATCTGGAAGAGTTACATTAGTTTGTTTAT
* *
39512914 GGCCGAATCTGGAATATTTACATTAGTTTGTTTA
1 GGCCGAATCTGGAAGAGTTACATTAGTTTGTTTA
39512948 AAAACTCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (35 bp):
GGCCGAATCTGGAAGAGTTACATTAGTTTGTTTAT
Found at i:39533847 original size:17 final size:17
Alignment explanation
Indices: 39533825--39533858 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39533815 CACTAACATG
* *
39533825 AAAATGTAATGACAATA
1 AAAATGCAATAACAATA
39533842 AAAATGCAATAACAATA
1 AAAATGCAATAACAATA
39533859 TATACTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAATGCAATAACAATA
Found at i:39542505 original size:27 final size:27
Alignment explanation
Indices: 39542475--39542740 Score: 372
Period size: 27 Copynumber: 9.9 Consensus size: 27
39542465 AATAATTGAT
*
39542475 ATACCCTTGAAGGGTAAAATGACCGAA
1 ATACCCTCGAAGGGTAAAATGACCGAA
**
39542502 ATACCCTCGAAGGGTAAAATGACTAAA
1 ATACCCTCGAAGGGTAAAATGACCGAA
* *
39542529 ATACCGTCGAAGGGTAAAATGACCAAA
1 ATACCCTCGAAGGGTAAAATGACCGAA
*
39542556 ATACCCTCGAAGGGTAAAATAACCGAA
1 ATACCCTCGAAGGGTAAAATGACCGAA
*
39542583 ATACCCTCGAAGGGTAAAATGATCGAA
1 ATACCCTCGAAGGGTAAAATGACCGAA
*
39542610 ATACCCTCGAAGGGTAAAATGATCGAA
1 ATACCCTCGAAGGGTAAAATGACCGAA
* *
39542637 CTACCCTCGAAGGGTAAAATGACTGAA
1 ATACCCTCGAAGGGTAAAATGACCGAA
* *
39542664 CTACCCTTGAAGGGTAAAATGACCGAA
1 ATACCCTCGAAGGGTAAAATGACCGAA
* *
39542691 ATACCCCCGAAGGGTAAAATGAGCGAA
1 ATACCCTCGAAGGGTAAAATGACCGAA
* *
39542718 ATACCC-CTATAAGGTAAAATGAC
1 ATACCCTCGA-AGGGTAAAATGAC
39542741 TATTATACCC
Statistics
Matches: 216, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
26 2 0.01
27 214 0.99
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.17
Consensus pattern (27 bp):
ATACCCTCGAAGGGTAAAATGACCGAA
Found at i:39543119 original size:28 final size:28
Alignment explanation
Indices: 39543087--39543167 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
39543077 TGTTTCTATA
*
39543087 TTGGGCTAAGGCCCACATTGTTACTGCT
1 TTGGGCTAAGGCCCAAATTGTTACTGCT
* * *
39543115 TTGGGCTAAGGCCTAGACTGTTACTGCT
1 TTGGGCTAAGGCCCAAATTGTTACTGCT
* * *
39543143 TAGGGCTCAGGCCCAAATTATTACT
1 TTGGGCTAAGGCCCAAATTGTTACT
39543168 ACATGTCGTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (28 bp):
TTGGGCTAAGGCCCAAATTGTTACTGCT
Found at i:39543622 original size:37 final size:31
Alignment explanation
Indices: 39543551--39543614 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
39543541 ATAACAAGAC
*
39543551 AAACATTTTTTATTTTAATAACAAAGAAGTT
1 AAACAATTTTTATTTTAATAACAAAGAAGTT
39543582 AAACAATTTTTATTTTAATAACAAAGAAGTT
1 AAACAATTTTTATTTTAATAACAAAGAAGTT
39543613 AA
1 AA
39543615 TGTTAAACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (31 bp):
AAACAATTTTTATTTTAATAACAAAGAAGTT
Found at i:39553022 original size:7 final size:7
Alignment explanation
Indices: 39553010--39553039 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
39553000 ATCACAAAAG
39553010 AATAAAT
1 AATAAAT
39553017 AATAAA-
1 AATAAAT
39553023 AATAAAT
1 AATAAAT
39553030 AATAAAT
1 AATAAAT
39553037 AAT
1 AAT
39553040 TAATTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AATAAAT
Found at i:39553028 original size:13 final size:13
Alignment explanation
Indices: 39553010--39553035 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39553000 ATCACAAAAG
39553010 AATAAATAATAAA
1 AATAAATAATAAA
39553023 AATAAATAATAAA
1 AATAAATAATAAA
39553036 TAATTAATTA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAATAATAAA
Found at i:39553072 original size:11 final size:11
Alignment explanation
Indices: 39553056--39553095 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
39553046 GTAAAGTTAG
39553056 AAATAAAATAA
1 AAATAAAATAA
39553067 AAATAAAATAA
1 AAATAAAATAA
* *
39553078 AAACTAAATTGA
1 AAA-TAAAATAA
39553090 AAATAA
1 AAATAA
39553096 TAATTTCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:39562611 original size:50 final size:50
Alignment explanation
Indices: 39562469--39562663 Score: 187
Period size: 50 Copynumber: 3.9 Consensus size: 50
39562459 GAATATAACA
* * * ** * * * *
39562469 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * **
39562518 TGCCAATGCCATATCCCAGATATGGTCTTACATTGGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
** * *
39562568 TGCGC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGC-CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* *
39562618 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
39562664 ATCTTAATGA
Statistics
Matches: 117, Mismatches: 26, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
49 38 0.32
50 78 0.67
51 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:39564087 original size:21 final size:21
Alignment explanation
Indices: 39564063--39564111 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
39564053 CAGCACAATC
*
39564063 AGATGTATCCACAACAAGA-CT
1 AGATGCATCCAC-ACAAGACCT
*
39564084 AGATGCATCCACACCAGACCT
1 AGATGCATCCACACAAGACCT
39564105 AGATGCA
1 AGATGCA
39564112 ATCAGAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.16
Consensus pattern (21 bp):
AGATGCATCCACACAAGACCT
Found at i:39566482 original size:47 final size:47
Alignment explanation
Indices: 39566426--39566519 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
39566416 AAATGTTTCT
39566426 GTATTTACTGATCACTCGGCATTGAAATATCTTTTTGCGAAGAAGGA
1 GTATTTACTGATCACTCGGCATTGAAATATCTTTTTGCGAAGAAGGA
39566473 GTATTTACTGATCACTCGGCATTGAAATATCTTTTTGCGAAGAAGGA
1 GTATTTACTGATCACTCGGCATTGAAATATCTTTTTGCGAAGAAGGA
39566520 TGCAAAACCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (47 bp):
GTATTTACTGATCACTCGGCATTGAAATATCTTTTTGCGAAGAAGGA
Found at i:39568039 original size:16 final size:17
Alignment explanation
Indices: 39568010--39568042 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39568000 TTCTTATGAA
39568010 ATTTATTATGTAATTTT
1 ATTTATTATGTAATTTT
*
39568027 ATTT-TTATTTAATTTT
1 ATTTATTATGTAATTTT
39568043 TTTGTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTATTATGTAATTTT
Found at i:39571299 original size:21 final size:21
Alignment explanation
Indices: 39571275--39571317 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
39571265 TTAGTTATCC
*
39571275 TTAGACC-ATATTTTAGTATTT
1 TTAGACCAATAATTTAG-ATTT
*
39571296 TTAGTCCAATAATTTAGATTT
1 TTAGACCAATAATTTAGATTT
39571317 T
1 T
39571318 ATGACTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (21 bp):
TTAGACCAATAATTTAGATTT
Found at i:39573620 original size:20 final size:20
Alignment explanation
Indices: 39573583--39573621 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39573573 TCAAACGAGC
* *
39573583 TAAATTAAACTCATGTGAGA
1 TAAATTAAAATCAGGTGAGA
*
39573603 TAAATTAAAATTAGGTGAG
1 TAAATTAAAATCAGGTGAG
39573622 CTGAACTAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (20 bp):
TAAATTAAAATCAGGTGAGA
Found at i:39575345 original size:33 final size:33
Alignment explanation
Indices: 39575308--39575379 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
39575298 GATTACTCTC
39575308 TTCACTCG-TTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CAGACTCTCTTTCTTT
* *
39575341 TTCACTCGATTTCTTTTCAGGCTCTTTTTCTTT
1 TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
*
39575374 TCCACT
1 TTCACT
39575380 TTCGTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.11, C:0.28, G:0.07, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
Found at i:39575492 original size:23 final size:24
Alignment explanation
Indices: 39575460--39575510 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
39575450 GAAATCTCAT
* *
39575460 TTTCATCTTTTTCTTTTCCAT-TTC
1 TTTCATCTTTCT-TTTTCAATGTTC
39575484 TTTCA-CTTTCTTTTTCAATGTTC
1 TTTCATCTTTCTTTTTCAATGTTC
39575507 TTTC
1 TTTC
39575511 CTCGCTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 12 0.50
24 5 0.21
ACGTcount: A:0.10, C:0.24, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTCATCTTTCTTTTTCAATGTTC
Found at i:39578541 original size:46 final size:43
Alignment explanation
Indices: 39578481--39578565 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 43
39578471 CATGGTGGAT
*
39578481 TCAGCACACAGCAACCACCCTTTGTAATCAATGATATCCGGTGGGA
1 TCAGCACACAGCAACCA-CC-TTATAATCAATGATA-CCGGTGGGA
* *
39578527 TCAGCACATAGCAACCACCTTATAATTAATGATACCGGT
1 TCAGCACACAGCAACCACCTTATAATCAATGATACCGGT
39578566 TCACATAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 5 0.14
44 13 0.36
45 2 0.06
46 16 0.44
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
TCAGCACACAGCAACCACCTTATAATCAATGATACCGGTGGGA
Found at i:39581530 original size:42 final size:42
Alignment explanation
Indices: 39581450--39581531 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
39581440 CGTTTTCTTT
* **
39581450 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGGCCAACTATGGTCTTACACATATGCACATATTG
*
39581492 ATGCCATAGGCCAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGGCCAACTATGGTCTTACACA-TATGCACATAT
39581532 CACACCGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATAGGCCAACTATGGTCTTACACATATGCACATATTG
Found at i:39584243 original size:16 final size:16
Alignment explanation
Indices: 39584222--39584253 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39584212 GTTTTGCTGC
*
39584222 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
39584238 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
39584254 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:39587031 original size:18 final size:18
Alignment explanation
Indices: 39587008--39587057 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
39586998 TACGATCGGG
39587008 CACATCAACGA-CTCGACT
1 CACATCAACGAGC-CGACT
* *
39587026 CACATCACCGAGCCGATT
1 CACATCAACGAGCCGACT
39587044 CACATCAACGAGCC
1 CACATCAACGAGCC
39587058 TTCGAGGCCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 27 0.96
19 1 0.04
ACGTcount: A:0.32, C:0.40, G:0.14, T:0.14
Consensus pattern (18 bp):
CACATCAACGAGCCGACT
Found at i:39604941 original size:18 final size:18
Alignment explanation
Indices: 39604918--39604952 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39604908 GCAAAACAAT
39604918 TTTATTTCTTTAGTTTTC
1 TTTATTTCTTTAGTTTTC
*
39604936 TTTATTTTTTTAGTTTT
1 TTTATTTCTTTAGTTTT
39604953 TTGTTTCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTATTTCTTTAGTTTTC
Found at i:39605913 original size:17 final size:18
Alignment explanation
Indices: 39605891--39605924 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39605881 TGTTTATGTA
*
39605891 ATTATT-TTTTTATTTTC
1 ATTATTGTTTTAATTTTC
39605908 ATTATTGTTTTAATTTT
1 ATTATTGTTTTAATTTT
39605925 ATTTTATTTA
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:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTATTGTTTTAATTTTC
Found at i:39610062 original size:27 final size:27
Alignment explanation
Indices: 39610040--39610188 Score: 160
Period size: 27 Copynumber: 5.5 Consensus size: 27
39610030 AAGGGTATAA
39610040 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
*
39610067 C-GATCATTTTACCCTATGGGGATATTT
1 CAG-TCATTTTACCCTATGGGGGTATTT
*
39610094 CCA-TCATTCTACCCTATGGGGGTATTT
1 -CAGTCATTTTACCCTATGGGGGTATTT
** *
39610121 TGGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTATTT
* * *
39610148 CGGTCATTCTACCCTA-GAGGGCTATTT
1 CAGTCATTTTACCCTATG-GGGGTATTT
* *
39610175 CGGTTATTTTACCC
1 CAGTCATTTTACCC
39610189 CAGGTTCGAT
Statistics
Matches: 104, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.01
27 102 0.98
28 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.40
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTATTT
Found at i:39610107 original size:54 final size:54
Alignment explanation
Indices: 39610043--39610188 Score: 197
Period size: 54 Copynumber: 2.7 Consensus size: 54
39610033 GGTATAACAG
* *
39610043 TCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTAT-GGGGATATTTCCA
1 TCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGG-TATTTCCA
* **
39610097 TCATTCTACCCTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTCGG
1 TCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCCA
* *
39610151 TCATTCTACCCTA-GAGGGCTATTTCGGTTATTTTACCC
1 TCATTCTACCCTATG-GGGGTATTTCGGTCATTTTACCC
39610189 CAGGTTCGAT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
53 1 0.01
54 77 0.94
55 4 0.05
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.40
Consensus pattern (54 bp):
TCATTCTACCCTATGGGGGTATTTCGGTCATTTTACCCTATAGGGGTATTTCCA
Found at i:39611575 original size:30 final size:30
Alignment explanation
Indices: 39611514--39611575 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
39611504 AGAATCAGTC
* * *
39611514 TGGGCCTTAGCCCTATACAATAGCAGTGTG
1 TGGGCCATAGCCCTATACAATAACAGAGTG
*
39611544 TGGGCCATAG-CCTAATACAATAATAGAGTG
1 TGGGCCATAGCCCT-ATACAATAACAGAGTG
39611574 TG
1 TG
39611576 AGCCTTATCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (30 bp):
TGGGCCATAGCCCTATACAATAACAGAGTG
Found at i:39611782 original size:26 final size:26
Alignment explanation
Indices: 39611680--39611771 Score: 123
Period size: 26 Copynumber: 3.5 Consensus size: 26
39611670 GCCAACACAC
39611680 CAGTATCGCAGCAAAGCTGCCAGTAT
1 CAGTATCGCAGCAAAGCTGCCAGTAT
* * *
39611706 CAGTAACACAACAAAGCTGCCAGTAAT
1 CAGTATCGCAGCAAAGCTGCCAGT-AT
* *
39611733 -AGTATCGCAGCAGAGCTGTCAGTAT
1 CAGTATCGCAGCAAAGCTGCCAGTAT
39611758 CAGTATCGCAGCAA
1 CAGTATCGCAGCAA
39611772 TGTTACCAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.04
26 51 0.93
27 2 0.04
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (26 bp):
CAGTATCGCAGCAAAGCTGCCAGTAT
Found at i:39612000 original size:27 final size:27
Alignment explanation
Indices: 39611970--39612418 Score: 247
Period size: 27 Copynumber: 16.7 Consensus size: 27
39611960 TCATCTCCTA
** *
39611970 GGGGTATAACGGTCATTTTACCCATTG
1 GGGGTATTTCGGTAATTTTACCCATTG
* *
39611997 GGGGTATTTCGATAATTTTACCCTTTG
1 GGGGTATTTCGGTAATTTTACCCATTG
*
39612024 GGGGCATTTCGGTAATTTTACCC-TTCG
1 GGGGTATTTCGGTAATTTTACCCATT-G
* * * * *
39612051 AGGGTATTTCGATAGTTTTATCC-TTCA
1 GGGGTATTTCGGTAATTTTACCCATT-G
* * * *
39612078 AGGGTATTTCAGTAATTTTACCAATCG
1 GGGGTATTTCGGTAATTTTACCCATTG
* **
39612105 AGGGTATTTTAGTAATTTTACCC-TTCG
1 GGGGTATTTCGGTAATTTTACCCATT-G
* * * *
39612132 AGAGTATTTCAGTAATTTTACCCTTTG
1 GGGGTATTTCGGTAATTTTACCCATTG
* * * *
39612159 AGGGTATTTCGATAA-TTTACACAATG
1 GGGGTATTTCGGTAATTTTACCCATTG
* ** **
39612185 AGGGTATTTTAGTAATTTTACCCAACG
1 GGGGTATTTCGGTAATTTTACCCATTG
** * * *
39612212 AAGGTATTTTGGTCATTTTACTC-TTCG
1 GGGGTATTTCGGTAATTTTACCCATT-G
*
39612239 AGGGTA-TTCTGGTAATTTTACCC-TTCG
1 GGGGTATTTC-GGTAATTTTACCCATT-G
* * * *
39612266 CGGGTATTTTGATAATTTTACCC-TTCA
1 GGGGTATTTCGGTAATTTTACCCATT-G
* *
39612293 AGGGTATTTCGGTAAATTTACCC-TTCG
1 GGGGTATTTCGGTAATTTTACCCATT-G
* *
39612320 GGGGTATTTTGGAAATTTTACCC-TTCG
1 GGGGTATTTCGGTAATTTTACCCATT-G
* *
39612347 AGGGTATTTCAGTAATTTTACCTC-TTG
1 GGGGTATTTCGGTAATTTTACC-CATTG
* * * *
39612374 AGGATATTTCGATCATTTTACCC-TTCG
1 GGGGTATTTCGGTAATTTTACCCATT-G
*
39612401 GGGGTATTTCGGTCATTT
1 GGGGTATTTCGGTAATTT
39612419 GCCCACAACT
Statistics
Matches: 342, Mismatches: 70, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
26 28 0.08
27 306 0.89
28 8 0.02
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCGGTAATTTTACCCATTG
Found at i:39612070 original size:54 final size:54
Alignment explanation
Indices: 39611979--39612418 Score: 444
Period size: 54 Copynumber: 8.2 Consensus size: 54
39611969 AGGGGTATAA
* * * * *
39611979 CGGTCATTTTACCCATT-GGGGGTATTTCGATAATTTTACCCTTTGGGGGCATTT
1 CGGTAATTTTACCC-TTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTT
* * *
39612033 CGGTAATTTTACCCTTCGAGGGTATTTCGATAGTTTTATCCTTCAAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTT
* ** * *
39612087 CAGTAATTTTACCAATCGAGGGTATTT-TAGTAATTTTACCCTTCGAGAGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTTCGA-TAATTTTACCCTTCGAGGGTATTT
* * **
39612141 CAGTAATTTTACCCTTTGAGGGTATTTCGATAA-TTTACACAAT-GAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTAC-CCTTCGAGGGTATTT
** ** * * * * *
39612194 TAGTAATTTTACCCAACGAAGGTATTTTGGTCATTTTACTCTTCGAGGGTA-TT
1 CGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTT
* * *
39612247 CTGGTAATTTTACCCTTCGCGGGTATTTTGATAATTTTACCCTTCAAGGGTATTT
1 C-GGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTT
* * *
39612302 CGGTAAATTTACCCTTCGGGGGTATTTTGGA-AATTTTACCCTTCGAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTA-TTTCGATAATTTTACCCTTCGAGGGTATTT
* * * *
39612356 CAGTAATTTTACCTCTT-GAGGATATTTCGATCATTTTACCCTTCGGGGGTATTT
1 CGGTAATTTTACC-CTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTT
*
39612410 CGGTCATTT
1 CGGTAATTT
39612419 GCCCACAACT
Statistics
Matches: 318, Mismatches: 57, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
53 50 0.16
54 256 0.81
55 12 0.04
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (54 bp):
CGGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTT
Found at i:39612120 original size:81 final size:80
Alignment explanation
Indices: 39611984--39612418 Score: 398
Period size: 81 Copynumber: 5.4 Consensus size: 80
39611974 TATAACGGTC
* * ** * * * **
39611984 ATTTTACCCATT-GGGGGTATTTCGATAATTTTACCCTTTGGGGGCATTTCGGTAATTTTACCCT
1 ATTTTACCC-TTCGAGGGTATTTCGGTAATTTTACCAATCGAGGGTATTTTAGTAATTTTACCCT
39612048 TCGAGGGTATTTCGAT
65 TCGAGGGTATTTCGAT
* * *
39612064 AGTTTTATCCTTCAAGGGTATTTCAGTAATTTTACCAATCGAGGGTATTTTAGTAATTTTACCCT
1 A-TTTTACCCTTCGAGGGTATTTCGGTAATTTTACCAATCGAGGGTATTTTAGTAATTTTACCCT
*
39612129 TCGAGAGTATTTC-AGT
65 TCGAGGGTATTTCGA-T
* *
39612145 AATTTTACCCTTTGAGGGTATTTCGATAA-TTTACACAAT-GAGGGTATTTTAGTAATTTTACCC
1 -ATTTTACCCTTCGAGGGTATTTCGGTAATTTTAC-CAATCGAGGGTATTTTAGTAATTTTACCC
** * * *
39612208 AACGAAGGTATTTTGGT
64 TTCGAGGGTATTTCGAT
* ** *
39612225 CATTTTACTCTTCGAGGGTA-TTCTGGTAATTTTACCCTTCGCGGGTATTTT-GATAATTTTACC
1 -ATTTTACCCTTCGAGGGTATTTC-GGTAATTTTACCAATCGAGGGTATTTTAG-TAATTTTACC
* *
39612288 CTTCAAGGGTATTTCGGT
63 CTTCGAGGGTATTTCGAT
* * * * ** *
39612306 AAATTTACCCTTCGGGGGTATTTTGGAAATTTTACCCTTCGAGGGTATTTCAGTAATTTTACCTC
1 -ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCAATCGAGGGTATTTTAGTAATTTTACC-C
*
39612371 TT-GAGGATATTTCGAT
64 TTCGAGGGTATTTCGAT
* *
39612387 CATTTTACCCTTCGGGGGTATTTCGGTCATTT
1 -ATTTTACCCTTCGAGGGTATTTCGGTAATTT
39612419 GCCCACAACT
Statistics
Matches: 290, Mismatches: 52, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
79 3 0.01
80 67 0.23
81 213 0.73
82 7 0.02
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (80 bp):
ATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCAATCGAGGGTATTTTAGTAATTTTACCCTT
CGAGGGTATTTCGAT
Found at i:39613537 original size:36 final size:36
Alignment explanation
Indices: 39613462--39613529 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
39613452 CTCCCACAAA
**
39613462 CTCCTTGATTTTCTCCTAAAATCCCTCCTCTTATCC
1 CTCCTTGATTTTCTCCTAAAATCCCTCCTCCAATCC
*
39613498 CTCCTTGATTTTCTCCATCAAAT-CCTCC-CCAA
1 CTCCTTGATTTTCTCC-TAAAATCCCTCCTCCAA
39613530 CTGCCTCCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 2 0.07
36 21 0.75
37 5 0.18
ACGTcount: A:0.19, C:0.40, G:0.03, T:0.38
Consensus pattern (36 bp):
CTCCTTGATTTTCTCCTAAAATCCCTCCTCCAATCC
Found at i:39617063 original size:15 final size:16
Alignment explanation
Indices: 39617038--39617067 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39617028 AATTTGTTCA
39617038 ATTATTTAAATTTTTT
1 ATTATTTAAATTTTTT
39617054 ATTA-TTAAATTTTT
1 ATTATTTAAATTTTT
39617068 ATAGATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTATTTAAATTTTTT
Found at i:39617842 original size:17 final size:17
Alignment explanation
Indices: 39617820--39617855 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39617810 AATTAATTTT
*
39617820 AATTAATTAATTTTCTC
1 AATTAAATAATTTTCTC
*
39617837 AATTAAATGATTTTCTC
1 AATTAAATAATTTTCTC
39617854 AA
1 AA
39617856 CCTGATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:39620331 original size:50 final size:50
Alignment explanation
Indices: 39620263--39620438 Score: 217
Period size: 50 Copynumber: 3.5 Consensus size: 50
39620253 GATTATGAAC
*
39620263 GGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATGAGA
1 GGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGA
* * *
39620313 GGTCCCACGTAAGGCCATGTCTGGGACATGGCGTTGGCACCAAGATGAGA
1 GGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGA
* * * * * *
39620363 GGTCCCCCATTAGACCATGTCTGGGACATGGGATGGGCACCGATATGAGA
1 GGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGA
** * * *
39620413 ACTCTCAAGTAAGACCATATCTGGGA
1 GGTCCCACGTAAGACCATGTCTGGGA
39620439 TATAACATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 105 1.00
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
GGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGA
Found at i:39620727 original size:20 final size:20
Alignment explanation
Indices: 39620702--39620750 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
39620692 TGAGTTATTT
39620702 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
39620722 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
39620742 AAG-AAGCAA
1 AAGTAAGCAA
39620751 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:39620999 original size:24 final size:24
Alignment explanation
Indices: 39620967--39621012 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
39620957 ACATTTTTAC
39620967 TTCTGGCATGTATAGGGACTTAAG
1 TTCTGGCATGTATAGGGACTTAAG
39620991 TTCTGGCATGTATAGGGACTTA
1 TTCTGGCATGTATAGGGACTTA
39621013 GTCATTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (24 bp):
TTCTGGCATGTATAGGGACTTAAG
Found at i:39628085 original size:50 final size:50
Alignment explanation
Indices: 39627989--39628167 Score: 205
Period size: 50 Copynumber: 3.5 Consensus size: 50
39627979 AGATCCCATG
* * *
39627989 TAAGACCATGTCTCGGACATGGCATTGGTATTATTGAGGTTATGAGAGGTCCCACA
1 TAAGACCATGTCTGGGACATGGCGTTGG---CATTGA-G--ATGAGAGGTCCCACA
*
39628045 TAAGACCATGTCTGGGACATGGCGTTGGCATTGAGATGAGAGGTCTCACA
1 TAAGACCATGTCTGGGACATGGCGTTGGCATTGAGATGAGAGGTCCCACA
** ***
39628095 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCTTG
1 TAAGACCATGTCTGGGACATGGCGTTGGCATTGAGATGAGAGGTCCCACA
* *
39628145 TAAGACTATGTCTAGGACATGGC
1 TAAGACCATGTCTGGGACATGGC
39628168 ATGGGTACCA
Statistics
Matches: 111, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
50 79 0.71
52 1 0.01
53 5 0.05
56 26 0.23
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCGTTGGCATTGAGATGAGAGGTCCCACA
Found at i:39628500 original size:20 final size:20
Alignment explanation
Indices: 39628475--39628523 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
39628465 TGAGTTATTT
39628475 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
* *
39628495 AAGTAAG-AGAGTAAGTGAAG
1 AAGTAAGCA-AGTAAGTAAAC
39628515 AAG-AAGCAA
1 AAGTAAGCAA
39628524 AGACCATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.55, C:0.06, G:0.27, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:39631156 original size:21 final size:21
Alignment explanation
Indices: 39631131--39631170 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39631121 TATTCTTCAT
* *
39631131 AATAATTAATAATATTGATTA
1 AATAATAAATAATAGTGATTA
39631152 AATAATAAATAATAGTGAT
1 AATAATAAATAATAGTGAT
39631171 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
AATAATAAATAATAGTGATTA
Found at i:39635491 original size:22 final size:21
Alignment explanation
Indices: 39635466--39635509 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
39635456 CCGGATAATG
39635466 TTATTTTTAAATTTTTCTATTT
1 TTATTTTTAAATTTTTC-ATTT
**
39635488 TTATTTTTCTATTTTTCATTT
1 TTATTTTTAAATTTTTCATTT
39635509 T
1 T
39635510 CTTCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTTTAAATTTTTCATTT
Found at i:39635495 original size:14 final size:15
Alignment explanation
Indices: 39635476--39635509 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
39635466 TTATTTTTAA
39635476 ATTTTTCTATTTTT-
1 ATTTTTCTATTTTTC
39635490 ATTTTTCTATTTTTC
1 ATTTTTCTATTTTTC
39635505 ATTTT
1 ATTTT
39635510 CTTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTCTATTTTTC
Found at i:39637032 original size:9 final size:8
Alignment explanation
Indices: 39637011--39637045 Score: 52
Period size: 9 Copynumber: 4.1 Consensus size: 8
39637001 ACACATTCTC
39637011 AACAGAAT
1 AACAGAAT
39637019 AACAGAAGT
1 AACAGAA-T
39637028 AACAGAAAT
1 AACAG-AAT
39637037 AACAGAAT
1 AACAGAAT
39637045 A
1 A
39637046 CTAAGTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 11 0.44
9 12 0.48
10 2 0.08
ACGTcount: A:0.63, C:0.11, G:0.14, T:0.11
Consensus pattern (8 bp):
AACAGAAT
Found at i:39640030 original size:22 final size:23
Alignment explanation
Indices: 39640005--39640053 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
39639995 AATATATTTT
* *
39640005 AAATATTATATA-ATTATATTAA
1 AAATATTATAAACATTAAATTAA
*
39640027 AAAT-TTATAAACATTAAATTAT
1 AAATATTATAAACATTAAATTAA
39640049 AAATA
1 AAATA
39640054 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATATTATAAACATTAAATTAA
Found at i:39640084 original size:32 final size:33
Alignment explanation
Indices: 39640026--39640090 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
39640016 AATTATATTA
39640026 AAAATTTATAAACATTAAATTATAAATAAAAAT
1 AAAATTTATAAACATTAAATTATAAATAAAAAT
*
39640059 AAAATTTCA-AAACATT-AATTATAAATATAAAT
1 AAAATTT-ATAAACATTAAATTATAAATAAAAAT
39640091 TGTTTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.50
33 14 0.47
34 1 0.03
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.34
Consensus pattern (33 bp):
AAAATTTATAAACATTAAATTATAAATAAAAAT
Found at i:39652489 original size:11 final size:11
Alignment explanation
Indices: 39652473--39652497 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39652463 TCATTAACTC
39652473 AATTATCATCA
1 AATTATCATCA
39652484 AATTATCATCA
1 AATTATCATCA
39652495 AAT
1 AAT
39652498 GTAAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTATCATCA
Found at i:39655024 original size:2 final size:2
Alignment explanation
Indices: 39655017--39655042 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39655007 CGCTTGGGTA
39655017 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
39655043 CATGTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:39660423 original size:37 final size:37
Alignment explanation
Indices: 39660377--39660450 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
39660367 GAACACTTTC
*
39660377 AATCAAAATCCGAAAGGCTATTGAATTGAAATAGAGT
1 AATCAAAATCCAAAAGGCTATTGAATTGAAATAGAGT
*
39660414 AATCCAAATCCAAAAGGCTATTGAATTGAAATAGAGT
1 AATCAAAATCCAAAAGGCTATTGAATTGAAATAGAGT
39660451 TTACTTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (37 bp):
AATCAAAATCCAAAAGGCTATTGAATTGAAATAGAGT
Found at i:39674703 original size:27 final size:26
Alignment explanation
Indices: 39674665--39674933 Score: 186
Period size: 27 Copynumber: 10.0 Consensus size: 26
39674655 ATGGGCCACC
39674665 AATTATCAAAATACCCCCATAAGGTAA
1 AATTATCAAAATACCCCCA-AAGGTAA
* * *
39674692 AATTATCGAAATAACCTCGAAAGGTAA
1 AATTATCAAAAT-ACCCCCAAAGGTAA
** * ** *
39674719 AATTATTGAAATTCCCTTTAACGGTAA
1 AATTATCAAAATACCC-CCAAAGGTAA
* *
39674746 AATTA-CTGAAATACCCCCATAGGCTAA
1 AATTATC-AAAATACCCCCAAAGG-TAA
* * *
39674773 AATTACCAAAATACCCTCGAAGGGTAA
1 AATTATCAAAATACCC-CCAAAGGTAA
*
39674800 AATTATCAAAATA-CCTCAAAGGGTAA
1 AATTATCAAAATACCCCCAAA-GGTAA
* * *
39674826 AATTACCGAAATACCCTCATAAGGTAA
1 AATTATCAAAATACCCCCA-AAGGTAA
* *
39674853 AATTACCAAAATACCCTC-AAGAGTAA
1 AATTATCAAAATACCCCCAAAG-GTAA
* *
39674879 AATTATCAAAATACCCTCGAAATGTAA
1 AATTATCAAAATACCC-CCAAAGGTAA
* *
39674906 AATGA-CTAAAATACTCCCAAAGGGTAA
1 AATTATC-AAAATACCCCCAAA-GGTAA
39674933 A
1 A
39674934 GTGACAGTTA
Statistics
Matches: 194, Mismatches: 34, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
25 5 0.03
26 47 0.24
27 128 0.66
28 14 0.07
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (26 bp):
AATTATCAAAATACCCCCAAAGGTAA
Found at i:39674840 original size:53 final size:52
Alignment explanation
Indices: 39674665--39674933 Score: 213
Period size: 53 Copynumber: 5.0 Consensus size: 52
39674655 ATGGGCCACC
* * *
39674665 AATTATCAAAATACCC-CCATAAGGTAAAATTATCGAAATAACCTCGAAA-GGTAA
1 AATTACCAAAATACCCTCGA-AAGGTAAAATTA-CAAAAT-ACCTC-AAAGGGTAA
*** * ** * * * * *
39674719 AATTATTGAAATTCCCTTTAACGGTAAAATTACTGAAATACCCCCATAGGCTAA
1 AATTACCAAAATACCCTCGAAAGGTAAAATTAC-AAAATA-CCTCAAAGGGTAA
*
39674773 AATTACCAAAATACCCTCGAAGGGTAAAATTATCAAAATACCTCAAAGGGTAA
1 AATTACCAAAATACCCTCGAAAGGTAAAATTA-CAAAATACCTCAAAGGGTAA
* *
39674826 AATTACCGAAATACCCTC-ATAAGGTAAAATTACCAAAATACCCTC-AAGAGTAA
1 AATTACCAAAATACCCTCGA-AAGGTAAAATTA-CAAAATA-CCTCAAAGGGTAA
* * * *
39674879 AATTATCAAAATACCCTCGAAATGTAAAATGACTAAAATACTCCCAAAGGGTAA
1 AATTACCAAAATACCCTCGAAAGGTAAAATTAC-AAAATAC-CTCAAAGGGTAA
39674933 A
1 A
39674934 GTGACAGTTA
Statistics
Matches: 174, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
52 3 0.02
53 90 0.52
54 79 0.45
55 2 0.01
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (52 bp):
AATTACCAAAATACCCTCGAAAGGTAAAATTACAAAATACCTCAAAGGGTAA
Found at i:39674906 original size:80 final size:80
Alignment explanation
Indices: 39674673--39674908 Score: 291
Period size: 80 Copynumber: 2.9 Consensus size: 80
39674663 CCAATTATCA
* * * ** *
39674673 AAATACCCCCATAAGGTAAAATTATCGAAATAACCTCGAA-AGGTAAAATTATTGAAATTCCCTT
1 AAATACCCCCATAAGGTAAAATTACCAAAATACCCTCGAAGA-GTAAAATTATCAAAATACCC-T
* * *
39674737 TAACGGTAAAATTACTG
64 CAAAGGTAAAATTACCG
*
39674754 AAATACCCCCAT-AGGCTAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCAAAATA-CCTC
1 AAATACCCCCATAAGG-TAAAATTACCAAAATACCCTCGAAGAGTAAAATTATCAAAATACCCTC
39674817 AAAGGGTAAAATTACCG
65 AAA-GGTAAAATTACCG
*
39674834 AAATACCCTCATAAGGTAAAATTACCAAAATACCCTC-AAGAGTAAAATTATCAAAATACCCTCG
1 AAATACCCCCATAAGGTAAAATTACCAAAATACCCTCGAAGAGTAAAATTATCAAAATACCCTC-
*
39674898 AAATGTAAAAT
65 AAAGGTAAAAT
39674909 GACTAAAATA
Statistics
Matches: 136, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
79 23 0.17
80 60 0.44
81 53 0.39
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (80 bp):
AAATACCCCCATAAGGTAAAATTACCAAAATACCCTCGAAGAGTAAAATTATCAAAATACCCTCA
AAGGTAAAATTACCG
Found at i:39675200 original size:26 final size:26
Alignment explanation
Indices: 39675129--39675203 Score: 105
Period size: 26 Copynumber: 2.9 Consensus size: 26
39675119 ATGCCATATA
* * *
39675129 TACTGTTACTGGTAGCTTTCCTACGT
1 TACTGTTACTGGTAGCTTTGCTGCAT
*
39675155 TACTGTTATTGGTAGCTTTGCTGCAT
1 TACTGTTACTGGTAGCTTTGCTGCAT
*
39675181 TACTGTTACTGGCAGCTTTGCTG
1 TACTGTTACTGGTAGCTTTGCTG
39675204 TAATATTGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.43
Consensus pattern (26 bp):
TACTGTTACTGGTAGCTTTGCTGCAT
Found at i:39675361 original size:28 final size:28
Alignment explanation
Indices: 39675316--39675448 Score: 142
Period size: 28 Copynumber: 4.8 Consensus size: 28
39675306 ATTGTAATGT
*
39675316 TTACTGTAATGGGATAAGGCCCACACTA
1 TTACTGTAATGGGCTAAGGCCCACACTA
* * * *
39675344 TTTCTGTATTGGGCTAAGGCCCACAGTG
1 TTACTGTAATGGGCTAAGGCCCACACTA
* *
39675372 TTACTGTAATGGCCTAAGGCCCACAATA
1 TTACTGTAATGGGCTAAGGCCCACACTA
* * * * *
39675400 CTT-CTGTATTAGGCTAAGGCCTATACTG
1 -TTACTGTAATGGGCTAAGGCCCACACTA
39675428 TTACTGTAATGGGCTAAGGCC
1 TTACTGTAATGGGCTAAGGCC
39675449 ATACTGTACT
Statistics
Matches: 84, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
27 2 0.02
28 80 0.95
29 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (28 bp):
TTACTGTAATGGGCTAAGGCCCACACTA
Found at i:39675405 original size:56 final size:56
Alignment explanation
Indices: 39675316--39675448 Score: 194
Period size: 56 Copynumber: 2.4 Consensus size: 56
39675306 ATTGTAATGT
* * * * *
39675316 TTACTGTAATGGGATAAGGCCCACACTATTTCTGTATTGGGCTAAGGCCCACAGTG
1 TTACTGTAATGGGCTAAGGCCCACAATACTTCTGTATTAGGCTAAGGCCCACACTG
* * *
39675372 TTACTGTAATGGCCTAAGGCCCACAATACTTCTGTATTAGGCTAAGGCCTATACTG
1 TTACTGTAATGGGCTAAGGCCCACAATACTTCTGTATTAGGCTAAGGCCCACACTG
39675428 TTACTGTAATGGGCTAAGGCC
1 TTACTGTAATGGGCTAAGGCC
39675449 ATACTGTACT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (56 bp):
TTACTGTAATGGGCTAAGGCCCACAATACTTCTGTATTAGGCTAAGGCCCACACTG
Found at i:39675575 original size:22 final size:22
Alignment explanation
Indices: 39675549--39675618 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
39675539 CATAAACTCA
39675549 CATGGCTAACGTACTAAGCTCT
1 CATGGCTAACGTACTAAGCTCT
39675571 CATGGCTAACGTACTAAGCTCT
1 CATGGCTAACGTACTAAGCTCT
** *
39675593 CATGTTTCACGTACTAAGCTCT
1 CATGGCTAACGTACTAAGCTCT
39675615 CATG
1 CATG
39675619 TTTGAACAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (22 bp):
CATGGCTAACGTACTAAGCTCT
Found at i:39681956 original size:27 final size:26
Alignment explanation
Indices: 39681939--39682323 Score: 339
Period size: 27 Copynumber: 14.3 Consensus size: 26
39681929 ACTCCCGTAA
* *
39681939 GGTAAAATTACTAAAATACCCTGAAAG
1 GGTAAAATTACTGAAATACCC-CAAAG
*
39681966 GGTAAAATTACCGAAATACCCTCAAAG
1 GGTAAAATTACTGAAATACCC-CAAAG
*
39681993 GGTAAAATTACTGAAATACCCCATAG
1 GGTAAAATTACTGAAATACCCCAAAG
39682019 GGTAAAATTA-TAGAAATACCCTCAAAG
1 GGTAAAATTACT-GAAATACCC-CAAAG
*
39682046 GGTAAAATTATTGAAATACCCTCAAAG
1 GGTAAAATTACTGAAATACCC-CAAAG
* *
39682073 GGTAAAATTA-TCGAAATACCCCCGATG
1 GGTAAAATTACT-GAAATA-CCCCAAAG
* * * **
39682100 GATAAAATTAC-CAAAGCACCCTTGAAG
1 GGTAAAATTACTGAAA-TACCC-CAAAG
*
39682127 GGTAAAATTATTGAAATACCCTCGAAA-
1 GGTAAAATTACTGAAATACCC-C-AAAG
*
39682154 GGTAAAATTACTGAAATACCCCTATAG
1 GGTAAAATTACTGAAATACCCC-AAAG
**
39682181 GGTAAAATTTTTGAAATACCCTCAAAG
1 GGTAAAATTACTGAAATACCC-CAAAG
**
39682208 GGTAAAATTACCAAAATACCCCTAAAG
1 GGTAAAATTACTGAAATACCCC-AAAG
*
39682235 GGTAAAATTACTAAAATACCCTCAAAG
1 GGTAAAATTACTGAAATACCC-CAAAG
**
39682262 GGTAAAATTACCAAAATACCCCCGAAA-
1 GGTAAAATTACTGAAATA-CCCC-AAAG
** ** *
39682289 GGTAAAAAGACCAAAATACCCCCGAAG
1 GGTAAAATTACTGAAATA-CCCCAAAG
39682316 GGTAAAAT
1 GGTAAAAT
39682324 GATCGTTATA
Statistics
Matches: 306, Mismatches: 35, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.00
26 36 0.12
27 252 0.82
28 17 0.06
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (26 bp):
GGTAAAATTACTGAAATACCCCAAAG
Found at i:39681997 original size:54 final size:54
Alignment explanation
Indices: 39681918--39682323 Score: 398
Period size: 54 Copynumber: 7.5 Consensus size: 54
39681908 TGGGCCACAG
*
39681918 ATTATCGAAATACTCC-CGTAA-GGTAAAATTACTAAAATACCCTGAAAGGGTAAA
1 ATTATCGAAATAC-CCTC-AAAGGGTAAAATTACTAAAATACCCTGAAAGGGTAAA
* * * *
39681972 ATTACCGAAATACCCTCAAAGGGTAAAATTACTGAAATACCC-CATAGGGTAAA
1 ATTATCGAAATACCCTCAAAGGGTAAAATTACTAAAATACCCTGAAAGGGTAAA
* * * *
39682025 ATTATAGAAATACCCTCAAAGGGTAAAATTATTGAAATACCCTCAAAGGGTAAA
1 ATTATCGAAATACCCTCAAAGGGTAAAATTACTAAAATACCCTGAAAGGGTAAA
* * * * * **
39682079 ATTATCGAAATACCCCCGATGGATAAAATTACCAAAGCACCCTTG-AAGGGTAAA
1 ATTATCGAAATACCCTCAAAGGGTAAAATTACTAAAATACCC-TGAAAGGGTAAA
* * *
39682133 ATTATTGAAATACCCTCGAAA-GGTAAAATTACTGAAATACCCCT-ATAGGGTAAA
1 ATTATCGAAATACCCTC-AAAGGGTAAAATTACTAAAATA-CCCTGAAAGGGTAAA
* * *
39682187 ATTTTTGAAATACCCTCAAAGGGTAAAATTACCAAAATACCCCT-AAAGGGTAAA
1 ATTATCGAAATACCCTCAAAGGGTAAAATTACTAAAATA-CCCTGAAAGGGTAAA
* * *
39682241 ATTA-CTAAAATACCCTCAAAGGGTAAAATTACCAAAATACCCCCGAAA-GGTAAA
1 ATTATC-GAAATACCCTCAAAGGGTAAAATTACTAAAATA-CCCTGAAAGGGTAAA
** * * * *
39682295 AAGACCAAAATACCCCCGAAGGGTAAAAT
1 ATTATCGAAATACCCTCAAAGGGTAAAAT
39682324 GATCGTTATA
Statistics
Matches: 299, Mismatches: 42, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
53 55 0.18
54 235 0.79
55 9 0.03
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.22
Consensus pattern (54 bp):
ATTATCGAAATACCCTCAAAGGGTAAAATTACTAAAATACCCTGAAAGGGTAAA
Found at i:39682293 original size:81 final size:81
Alignment explanation
Indices: 39681939--39682323 Score: 394
Period size: 81 Copynumber: 4.8 Consensus size: 81
39681929 ACTCCCGTAA
39681939 GGTAAAATTACTAAAATACCCT-GAAAGGGTAAAATTACCGAAATA-CCCTCAAAGGGTAAAATT
1 GGTAAAATTACTAAAATACCCTCGAAAGGGTAAAATTACCGAAATACCCCT-AAAGGGTAAAATT
*
39682002 ACTGAAATACCCCATAG
65 ACTGAAATACCCCAAAG
**
39682019 GGTAAAATTA-TAGAAATACCCTC-AAAGGGTAAAATTATTGAAATA-CCCTCAAAGGGTAAAAT
1 GGTAAAATTACTA-AAATACCCTCGAAAGGGTAAAATTACCGAAATACCCCT-AAAGGGTAAAAT
* *
39682081 TA-TCGAAATACCCCCGATG
64 TACT-GAAATA-CCCCAAAG
* * ** * ** *
39682100 GATAAAATTACCAAAGCACCCTTG-AAGGGTAAAATTATTGAAATACCCTCGAAA-GGTAAAATT
1 GGTAAAATTACTAAAATACCCTCGAAAGGGTAAAATTACCGAAATACCC-CTAAAGGGTAAAATT
*
39682163 ACTGAAATACCCCTATAG
65 ACTGAAATACCCC-AAAG
** * *
39682181 GGTAAAATTTTTGAAATACCCTC-AAAGGGTAAAATTACCAAAATACCCCTAAAGGGTAAAATTA
1 GGTAAAATTACTAAAATACCCTCGAAAGGGTAAAATTACCGAAATACCCCTAAAGGGTAAAATTA
*
39682245 CTAAAATACCCTCAAAG
66 CTGAAATACCC-CAAAG
* * ** * **
39682262 GGTAAAATTACCAAAATACCCCCGAAA-GGTAAAAAGACCAAAATACCCCCGAAGGGTAAAAT
1 GGTAAAATTACTAAAATACCCTCGAAAGGGTAAAATTACCGAAATACCCCTAAAGGGTAAAAT
39682324 GATCGTTATA
Statistics
Matches: 254, Mismatches: 37, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
79 3 0.01
80 72 0.28
81 167 0.66
82 11 0.04
83 1 0.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (81 bp):
GGTAAAATTACTAAAATACCCTCGAAAGGGTAAAATTACCGAAATACCCCTAAAGGGTAAAATTA
CTGAAATACCCCAAAG
Found at i:39682545 original size:26 final size:26
Alignment explanation
Indices: 39682516--39682639 Score: 151
Period size: 26 Copynumber: 4.8 Consensus size: 26
39682506 ATACCACTTA
39682516 TACTGTTACTGGCAGCTTTGTTGCGT
1 TACTGTTACTGGCAGCTTTGTTGCGT
*
39682542 TACTGTTACTGGTAGCTTTGTTGCGT
1 TACTGTTACTGGCAGCTTTGTTGCGT
* * * *
39682568 TACTATTACTGGAAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTGTTGCGT
* *
39682594 TACTGTTACTGGCAGATTTGCTT-TGT
1 TACTGTTACTGGCAGCTTTG-TTGCGT
* *
39682620 TACTATTACTGGCAACTTTG
1 TACTGTTACTGGCAGCTTTG
39682640 CTACAATATT
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
26 82 0.99
27 1 0.01
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.43
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGTTGCGT
Found at i:39682800 original size:28 final size:28
Alignment explanation
Indices: 39682751--39682861 Score: 147
Period size: 28 Copynumber: 4.0 Consensus size: 28
39682741 TGCATTGTAT
*
39682751 TGTTTACTGTAATGGGCT-AGGCCCATAC
1 TGTTT-CTGTAATGGGCTAAGGCCCACAC
*
39682779 TGTTTCTGTATTGGGCTAAGGCCCACAC
1 TGTTTCTGTAATGGGCTAAGGCCCACAC
39682807 TGTTAT-TGTAATGGGCTAAGGCCCACAC
1 TGTT-TCTGTAATGGGCTAAGGCCCACAC
* *
39682835 TATTTCTATAATGGGCTAAGG-CCACAC
1 TGTTTCTGTAATGGGCTAAGGCCCACAC
39682862 CGTATGATAC
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
27 18 0.24
28 56 0.75
29 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (28 bp):
TGTTTCTGTAATGGGCTAAGGCCCACAC
Found at i:39686145 original size:14 final size:14
Alignment explanation
Indices: 39686126--39686154 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39686116 AATCACTTAG
39686126 TCTGTATGTATAGT
1 TCTGTATGTATAGT
39686140 TCTGTATGTATAGT
1 TCTGTATGTATAGT
39686154 T
1 T
39686155 TCCTGCGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (14 bp):
TCTGTATGTATAGT
Found at i:39692297 original size:45 final size:45
Alignment explanation
Indices: 39692199--39692314 Score: 184
Period size: 46 Copynumber: 2.6 Consensus size: 45
39692189 TTTGAGTAGT
39692199 TCTGATCAAGTGACAAAGTGATAAGTGGTACCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTACC-TTAGCTACACTTA
39692245 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTA-CCTTAGCTACACTTA
*
39692290 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
39692315 ATCATACGTA
Statistics
Matches: 68, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
43 12 0.18
44 5 0.07
45 19 0.28
46 30 0.44
47 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTACCTTAGCTACACTTA
Found at i:39699636 original size:29 final size:29
Alignment explanation
Indices: 39699593--39699750 Score: 196
Period size: 29 Copynumber: 5.4 Consensus size: 29
39699583 ATCATCGACC
*
39699593 AATGAAAAGGGATAGCTTCAGCTATTGAAT
1 AATGAAAAGGGATAGCTTCGGCTA-TGAAT
*
39699623 -ATGAAAAGGGATAGCTTCGGCTAAAGAAT
1 AATGAAAAGGGATAGCTTCGGCT-ATGAAT
* *
39699652 -ATGAAAAAGGATAGCTTCGGCTATCAAT
1 AATGAAAAGGGATAGCTTCGGCTATGAAT
* *
39699680 AATGAAAAGGGATAGATTCAGCTATCG-AT
1 AATGAAAAGGGATAGCTTCGGCTAT-GAAT
* *
39699709 AATGAAAAGGGATAGCTTTGGCTATCAAT
1 AATGAAAAGGGATAGCTTCGGCTATGAAT
39699738 AATGAAAAGGGAT
1 AATGAAAAGGGAT
39699751 GTTGACGACC
Statistics
Matches: 111, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.04
29 106 0.95
30 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (29 bp):
AATGAAAAGGGATAGCTTCGGCTATGAAT
Found at i:39699764 original size:29 final size:28
Alignment explanation
Indices: 39699674--39699780 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 28
39699664 AGCTTCGGCT
* *
39699674 ATCAATAATGAAAAGGGATAGATTCAGCT
1 ATCAATAATGAAAAGGGAT-GATTGAGCC
* * *
39699703 ATCGATAATGAAAAGGGATAGCTTTG-GCT
1 ATCAATAATGAAAAGGGAT-G-ATTGAGCC
39699732 ATCAATAATGAAAAGGGATG-TTGACGACC
1 ATCAATAATGAAAAGGGATGATTGA-G-CC
39699761 ATCAACT-ATGAAAAGGGATG
1 ATCAA-TAATGAAAAGGGATG
39699781 GTGACAACCA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.04
28 2 0.03
29 60 0.88
30 3 0.04
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.23
Consensus pattern (28 bp):
ATCAATAATGAAAAGGGATGATTGAGCC
Found at i:39699765 original size:87 final size:88
Alignment explanation
Indices: 39699593--39699779 Score: 224
Period size: 87 Copynumber: 2.1 Consensus size: 88
39699583 ATCATCGACC
* * *
39699593 AATGAAAAGGGATAGCTTCAGCTATTGAATATGAAAAGGGATAGCTTCGGCTAAAGAATATGAAA
1 AATGAAAAGGGATAGATTCAGCTATCGAATATGAAAAGGGATAGCTTCGGCTAAACAATATGAAA
* *
39699658 AAGGATAGCTTCGGCTATCAA-T
66 AAGGATAGCTTCGACCATCAACT
* *
39699680 AATGAAAAGGGATAGATTCAGCTATCG-ATAATGAAAAGGGATAGCTTTGGCT-ATCAATAATGA
1 AATGAAAAGGGATAGATTCAGCTATCGAAT-ATGAAAAGGGATAGCTTCGGCTAAACAAT-ATGA
*
39699743 AAAGGGAT-G-TTGACGACCATCAACT
64 AAAAGGATAGCTT--CGACCATCAACT
39699768 -ATGAAAAGGGAT
1 AATGAAAAGGGAT
39699780 GGTGACAACC
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
85 2 0.02
86 7 0.08
87 77 0.89
88 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.24
Consensus pattern (88 bp):
AATGAAAAGGGATAGATTCAGCTATCGAATATGAAAAGGGATAGCTTCGGCTAAACAATATGAAA
AAGGATAGCTTCGACCATCAACT
Found at i:39699772 original size:58 final size:57
Alignment explanation
Indices: 39699594--39699779 Score: 189
Period size: 58 Copynumber: 3.2 Consensus size: 57
39699584 TCATCGACCA
* * * * * **
39699594 ATGAAAAGGGATAGCTTCAGCTATTGAAT-ATGAAAAGGGATAGCTTCGGCTAAAGAAT
1 ATGAAAAGGGATAGCTTCGGCTA-TCAATAATGAAAAGGGATAGATTCAGC-CATCAAT
* * *
39699652 ATGAAAAAGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTCAGCTATCGAT
1 ATGAAAAGGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTCAGCCATCAAT
* *
39699709 AATGAAAAGGGATAGCTTTGGCTATCAATAATGAAAAGGGAT-G-TTGACGACCATCAACT
1 -ATGAAAAGGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTCA-G-CCATCAA-T
39699768 ATGAAAAGGGAT
1 ATGAAAAGGGAT
39699780 GGTGACAACC
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
56 3 0.03
57 9 0.08
58 96 0.88
59 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (57 bp):
ATGAAAAGGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTCAGCCATCAAT
Found at i:39699871 original size:29 final size:29
Alignment explanation
Indices: 39699739--39699871 Score: 135
Period size: 29 Copynumber: 4.6 Consensus size: 29
39699729 GCTATCAATA
* *
39699739 ATGAAAAGGGAT-GTTGACGACCATC-AACT
1 ATGAAAAGGGATGGTT-TCAACCATCGAA-T
** *
39699768 ATGAAAAGGGATGGTGACAACCATCGATT
1 ATGAAAAGGGATGGTTTCAACCATCGAAT
*
39699797 AATGAAAAGGGATGGTTTCAAGCATCGAAT
1 -ATGAAAAGGGATGGTTTCAACCATCGAAT
* **
39699827 ATGAAAACGGATGGTTTTGACCATCGAAT
1 ATGAAAAGGGATGGTTTCAACCATCGAAT
*
39699856 ATGAAAAGGGACGGTT
1 ATGAAAAGGGATGGTT
39699872 ATGGAAAGGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
29 60 0.68
30 28 0.32
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.23
Consensus pattern (29 bp):
ATGAAAAGGGATGGTTTCAACCATCGAAT
Found at i:39705760 original size:29 final size:29
Alignment explanation
Indices: 39705725--39705790 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
39705715 TCATCGAACA
39705725 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* *
39705754 ATGAAAAAGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
39705783 ATGAAAAG
1 ATGAAAAG
39705791 AGATGACGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAAT
Found at i:39705846 original size:29 final size:29
Alignment explanation
Indices: 39705776--39706011 Score: 156
Period size: 29 Copynumber: 8.1 Consensus size: 29
39705766 AGCTTCGGCT
* * ** *
39705776 ATCGATTATGAAAAGAGATGACGACAACC
1 ATCGAATATGAAAAGGGATGGTGACGACC
* *
39705805 ATC-AACTACGAAAAGGGATGGTGACAACC
1 ATCGAA-TATGAAAAGGGATGGTGACGACC
* ** *
39705834 ATCGAATATGAAAAGGGATAGCTTTCG-CT
1 ATCGAATATGAAAAGGGAT-GGTGACGACC
* *
39705863 ATCG-ATAATGTAAAGGAATGGTGACGACC
1 ATCGAAT-ATGAAAAGGGATGGTGACGACC
* * * *
39705892 AT-TAATTATGAAAAGGGGTGTTGACAACC
1 ATCGAA-TATGAAAAGGGATGGTGACGACC
* **
39705921 ATCGATTAATGAAAAGGGATGGTTTCGACC
1 ATCGAAT-ATGAAAAGGGATGGTGACGACC
* * ** *
39705951 ATCAAATATGAAAACGGATGGTTCCGATC
1 ATCGAATATGAAAAGGGATGGTGACGACC
* *
39705980 ATCGAATATGAAAAGGGACGGTTACGACC
1 ATCGAATATGAAAAGGGATGGTGACGACC
39706009 ATC
1 ATC
39706012 ATTTAGCACA
Statistics
Matches: 158, Mismatches: 40, Indels: 18
0.73 0.19 0.08
Matches are distributed among these distances:
28 7 0.04
29 122 0.77
30 29 0.18
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (29 bp):
ATCGAATATGAAAAGGGATGGTGACGACC
Found at i:39705893 original size:87 final size:87
Alignment explanation
Indices: 39705747--39705940 Score: 239
Period size: 87 Copynumber: 2.2 Consensus size: 87
39705737 AGCTTCGGCT
* *
39705747 ATCGAATATGAAAAAGGATAGCTTCGGCTATCGATTATGAAAAGAGATGACGACAACCATCAACT
1 ATCGAATATGAAAAGGGATAGCTTCGGCTATCGATAATGAAAAGAGATGACGACAACCATCAACT
39705812 ACGAAAAGGGATGGTGACAACC
66 ACGAAAAGGGATGGTGACAACC
* ** * *
39705834 ATCGAATATGAAAAGGGATAGCTTTC-GCTATCGATAATGTAAAG-GAATGGTGACGACCATTAA
1 ATCGAATATGAAAAGGGATAGC-TTCGGCTATCGATAATGAAAAGAG-ATGACGACAACCATCAA
* * * *
39705897 TTATGAAAAGGGGTGTTGACAACC
64 CTACGAAAAGGGATGGTGACAACC
*
39705921 ATCGATTAATGAAAAGGGAT
1 ATCGAAT-ATGAAAAGGGAT
39705941 GGTTTCGACC
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
86 1 0.01
87 76 0.83
88 15 0.16
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (87 bp):
ATCGAATATGAAAAGGGATAGCTTCGGCTATCGATAATGAAAAGAGATGACGACAACCATCAACT
ACGAAAAGGGATGGTGACAACC
Found at i:39714886 original size:29 final size:29
Alignment explanation
Indices: 39714812--39714934 Score: 99
Period size: 28 Copynumber: 4.3 Consensus size: 29
39714802 CATATAACTT
* * * *
39714812 AGCCTTTATGGCTATATTTATTAAATGGA
1 AGCCTTTGTGGCTATCTTTGTTAAAAGGA
* *
39714841 AGCCTCTGTAG-TGATCTTTGTTAAAAGGA
1 AGCCTTTGTGGCT-ATCTTTGTTAAAAGGA
* * *
39714870 ATCCTTTGTGGCTATCTCTGTT-AACGGA
1 AGCCTTTGTGGCTATCTTTGTTAAAAGGA
* * *
39714898 AGCCTTTGTGACTATCTCTCTT-AAAGGA
1 AGCCTTTGTGGCTATCTTTGTTAAAAGGA
*
39714926 AGCATTTGT
1 AGCCTTTGT
39714935 TAAAAGGGAG
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
28 38 0.50
29 37 0.49
30 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (29 bp):
AGCCTTTGTGGCTATCTTTGTTAAAAGGA
Found at i:39718152 original size:20 final size:20
Alignment explanation
Indices: 39718124--39718203 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
39718114 CGTGCCTCTG
* *
39718124 TTTGGACTTCAGTACCCCTA
1 TTTGTACTTTAGTACCCCTA
*
39718144 TTTGTACTTTTGTACCCCTAA
1 TTTGTACTTTAGTACCCCT-A
* * * * *
39718165 ATTGCAC-ATACGTGCCCCTT
1 TTTGTACTTTA-GTACCCCTA
39718185 TTTGTACTTTAGTACCCCT
1 TTTGTACTTTAGTACCCCT
39718204 GAATTACACA
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.40
Consensus pattern (20 bp):
TTTGTACTTTAGTACCCCTA
Found at i:39718276 original size:41 final size:41
Alignment explanation
Indices: 39718138--39718283 Score: 193
Period size: 41 Copynumber: 3.6 Consensus size: 41
39718128 GACTTCAGTA
** *
39718138 CCCCTATTTGTACTTTTGTACCCCTAAATTGCACATACGTG
1 CCCCTATTTGTACTTCGGTACCCCTAAATTACACATACGTG
* ** *
39718179 CCCCTTTTTGTACTTTAGTACCCCTGAATTACACATACGTG
1 CCCCTATTTGTACTTCGGTACCCCTAAATTACACATACGTG
* * * *
39718220 CCCCTGTTTCTACTTCGGTACCCCTAAATTATAGATACGTG
1 CCCCTATTTGTACTTCGGTACCCCTAAATTACACATACGTG
39718261 CCCCTATTTGTACTTCGGTACCC
1 CCCCTATTTGTACTTCGGTACCC
39718284 TTGGATGTAC
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.36
Consensus pattern (41 bp):
CCCCTATTTGTACTTCGGTACCCCTAAATTACACATACGTG
Found at i:39722439 original size:31 final size:32
Alignment explanation
Indices: 39722403--39722467 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
39722393 CTTAGATAAT
39722403 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
39722434 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
39722466 TT
1 TT
39722468 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:39722814 original size:30 final size:27
Alignment explanation
Indices: 39722763--39722822 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
39722753 AAATCTATCC
*
39722763 TTTTATTATTATTGTTATTATTTAACTAA
1 TTTTATTATTATCGTTATTATTT--CTAA
* *
39722792 TTTTATTTATTCTCGTTTTTATTTCTAA
1 TTTTA-TTATTATCGTTATTATTTCTAA
39722820 TTT
1 TTT
39722823 GTGTTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 5 0.19
30 15 0.56
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (27 bp):
TTTTATTATTATCGTTATTATTTCTAA
Found at i:39728664 original size:31 final size:32
Alignment explanation
Indices: 39728629--39728693 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
39728619 CTTAGATAAT
*
39728629 TTTAAAGAG-TTATATTAGGATTCAGTTACTC
1 TTTAAAGAGTTTATATTAGGATTCAATTACTC
*
39728660 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTATATTAGGATTCAATTACTC
39728692 TT
1 TT
39728694 GTAATTTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (32 bp):
TTTAAAGAGTTTATATTAGGATTCAATTACTC
Found at i:39733507 original size:27 final size:27
Alignment explanation
Indices: 39733477--39733538 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
39733467 AAAATTATCA
39733477 AAATACCCTCGAAGGGTAAAATGACCG
1 AAATACCCTCGAAGGGTAAAATGACCG
*
39733504 AAATACCCTCGAAGGGTAAAATGACTG
1 AAATACCCTCGAAGGGTAAAATGACCG
39733531 AAATACCC
1 AAATACCC
39733539 CTATAAGGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATGACCG
Found at i:39733548 original size:27 final size:26
Alignment explanation
Indices: 39733477--39733568 Score: 85
Period size: 27 Copynumber: 3.4 Consensus size: 26
39733467 AAAATTATCA
* * *
39733477 AAATACCCTCGAAGGGTAAAATGACCG
1 AAATACCC-CTAAAGGTAAAATGACTG
* *
39733504 AAATACCCTCGAAGGGTAAAATGACTG
1 AAATACCC-CTAAAGGTAAAATGACTG
*
39733531 AAATACCCCTATAAGGTAAAATGATTG
1 AAATACCCCTA-AAGGTAAAATGACTG
**
39733558 TTATACCCCTA
1 AAATACCCCTA
39733569 GGAGATGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
26 2 0.03
27 56 0.97
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (26 bp):
AAATACCCCTAAAGGTAAAATGACTG
Found at i:39736384 original size:41 final size:41
Alignment explanation
Indices: 39736306--39736386 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
39736296 TATTTTGTTG
*
39736306 AATTGCACATACGTGCCCCTATTTGTACTTTGATACCCCTA
1 AATTGCACATACGTGCCCCTATTTGTACTTAGATACCCCTA
* * *
39736347 AATTGTACATGCGTGCCCCTGTTTGTACTTCAG-TACCCCT
1 AATTGCACATACGTGCCCCTATTTGTACTT-AGATACCCCT
39736387 GGATGTAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 34 0.97
42 1 0.03
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.35
Consensus pattern (41 bp):
AATTGCACATACGTGCCCCTATTTGTACTTAGATACCCCTA
Found at i:39754077 original size:15 final size:15
Alignment explanation
Indices: 39754057--39754102 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 15
39754047 TCACTCGCTT
39754057 TTTCTTTTTCATCTC
1 TTTCTTTTTCATCTC
*
39754072 TTTC-TTTTC-TCAC
1 TTTCTTTTTCATCTC
39754085 TTT-TTTTTCACTCTC
1 TTTCTTTTTCA-TCTC
39754100 TTT
1 TTT
39754103 TTTCAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.42
14 5 0.19
15 10 0.38
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTCTTTTTCATCTC
Found at i:39754122 original size:19 final size:20
Alignment explanation
Indices: 39754098--39754142 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
39754088 TTTTTCACTC
39754098 TCTTTTT-TCAAGTTTTC-TT
1 TCTTTTTCTC-AGTTTTCTTT
*
39754117 TCTTTTTCTCATTTTTCTTT
1 TCTTTTTCTCAGTTTTCTTT
39754137 TCTTTT
1 TCTTTT
39754143 GTATTTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (20 bp):
TCTTTTTCTCAGTTTTCTTT
Found at i:39754163 original size:14 final size:13
Alignment explanation
Indices: 39754115--39754166 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
39754105 TCAAGTTTTC
39754115 TTTCTTTTTCTCATT
1 TTTCTTTTTCT--TT
39754130 TTTC-TTTTCTTT
1 TTTCTTTTTCTTT
* *
39754142 TGTATTTTTGCTTT
1 TTTCTTTTT-CTTT
39754156 TTTCTTTTTCT
1 TTTCTTTTTCT
39754167 CTCACTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 4 0.13
13 6 0.19
14 17 0.55
15 4 0.13
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTCTTTTTCTTT
Found at i:39757952 original size:11 final size:11
Alignment explanation
Indices: 39757936--39757985 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
39757926 TCGTAAGTGT
39757936 TTGAGCTGAAA
1 TTGAGCTGAAA
39757947 TTGAGCTG--A
1 TTGAGCTGAAA
*
39757956 TTCGAGCT--CA
1 TT-GAGCTGAAA
39757966 TTGAGCTGAAA
1 TTGAGCTGAAA
39757977 TTGAGCTGA
1 TTGAGCTGA
39757986 TTCGAGCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 8 0.24
10 8 0.24
11 18 0.53
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (11 bp):
TTGAGCTGAAA
Found at i:39757970 original size:19 final size:19
Alignment explanation
Indices: 39757946--39758004 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
39757936 TTGAGCTGAA
39757946 ATTGAGCTGATTCGAGCTC
1 ATTGAGCTGATTCGAGCTC
39757965 ATTGAGCTGA----A----
1 ATTGAGCTGATTCGAGCTC
39757976 ATTGAGCTGATTCGAGCTC
1 ATTGAGCTGATTCGAGCTC
39757995 ATTGAGCTGA
1 ATTGAGCTGA
39758005 AATGGAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 16
0.67 0.00 0.33
Matches are distributed among these distances:
11 10 0.31
15 2 0.06
19 20 0.62
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (19 bp):
ATTGAGCTGATTCGAGCTC
Found at i:39757972 original size:30 final size:30
Alignment explanation
Indices: 39757936--39758007 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
39757926 TCGTAAGTGT
39757936 TTGAGCTGAAATTGAGCTGATTCGAGCTCA
1 TTGAGCTGAAATTGAGCTGATTCGAGCTCA
39757966 TTGAGCTGAAATTGAGCTGATTCGAGCTCA
1 TTGAGCTGAAATTGAGCTGATTCGAGCTCA
39757996 TTGAGCTGAAAT
1 TTGAGCTGAAAT
39758008 GGAATTTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATTGAGCTGATTCGAGCTCA
Found at i:39760037 original size:28 final size:28
Alignment explanation
Indices: 39759982--39760130 Score: 167
Period size: 28 Copynumber: 5.4 Consensus size: 28
39759972 TATACCGTAT
*
39759982 CAGT-ACAGTGT-GGCCTTAACCCATTA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
* *
39760008 CAGTAACAGTGTGGGGCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
* * *
39760036 CAGAAATAGTGTGGGCCTTAGCCTATTA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
* * *
39760064 TAGTAACAATGTGGGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
* * *
39760092 TAGAAATAGTGTGGGCCTTAGCCCATTA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
39760120 CAGTAAACAGT
1 CAGT-AACAGT
39760131 ACAATGCAGT
Statistics
Matches: 99, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
26 4 0.04
27 7 0.07
28 83 0.84
29 5 0.05
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCATTA
Found at i:39760069 original size:56 final size:56
Alignment explanation
Indices: 39759988--39760130 Score: 216
Period size: 56 Copynumber: 2.6 Consensus size: 56
39759978 GTATCAGTAC
* *
39759988 AGTGT-GGCCTTAACCCATTACAGTAACAGTGTGGGGCTTAGCCCAATACAGAAAT
1 AGTGTGGGCCTTAGCCCATTACAGTAACAGTGTGGGCCTTAGCCCAATACAGAAAT
* * * *
39760043 AGTGTGGGCCTTAGCCTATTATAGTAACAATGTGGGCCTTAGCCCAATATAGAAAT
1 AGTGTGGGCCTTAGCCCATTACAGTAACAGTGTGGGCCTTAGCCCAATACAGAAAT
39760099 AGTGTGGGCCTTAGCCCATTACAGTAAACAGT
1 AGTGTGGGCCTTAGCCCATTACAGT-AACAGT
39760131 ACAATGCAGT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
55 5 0.06
56 67 0.87
57 5 0.06
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (56 bp):
AGTGTGGGCCTTAGCCCATTACAGTAACAGTGTGGGCCTTAGCCCAATACAGAAAT
Found at i:39760265 original size:26 final size:26
Alignment explanation
Indices: 39760236--39760338 Score: 161
Period size: 26 Copynumber: 4.0 Consensus size: 26
39760226 ACACCAATAT
*
39760236 CGCAACAAAGCTGCCAGTAATAGTAA
1 CGCAACAAAGCTGCCAGTAACAGTAA
* *
39760262 CGCAGCAAAGTTGCCAGTAACAGTAA
1 CGCAACAAAGCTGCCAGTAACAGTAA
*
39760288 CGTAACAAAGCTGCCAGTAACAGTAA
1 CGCAACAAAGCTGCCAGTAACAGTAA
*
39760314 CGCAACAAAGCTGCCAGTAAGAGTA
1 CGCAACAAAGCTGCCAGTAACAGTA
39760339 TATGTGGCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (26 bp):
CGCAACAAAGCTGCCAGTAACAGTAA
Found at i:39760362 original size:52 final size:52
Alignment explanation
Indices: 39760239--39760364 Score: 137
Period size: 52 Copynumber: 2.4 Consensus size: 52
39760229 CCAATATCGC
** * * *
39760239 AACAAAGCTGCCAGTAATAGTAACGCAGCAAAGTTGCCAGTAACAGTAACGT
1 AACAAAGCCACCAGTAACAGTAACGCAACAAAGCTGCCAGTAACAGTAACGT
** * *
39760291 AACAAAGCTGCCAGTAACAGTAACGCAACAAAGCTGCCAGTAAGAGTATATGT
1 AACAAAGCCACCAGTAACAGTAACGCAACAAAGCTGCCAGTAACAGTA-ACGT
**
39760344 GGCAAAGCCACCAG-AACAGTA
1 AACAAAGCCACCAGTAACAGTA
39760365 TACTTCCCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 51 0.80
53 13 0.20
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.15
Consensus pattern (52 bp):
AACAAAGCCACCAGTAACAGTAACGCAACAAAGCTGCCAGTAACAGTAACGT
Found at i:39760547 original size:27 final size:27
Alignment explanation
Indices: 39760517--39760966 Score: 423
Period size: 27 Copynumber: 16.7 Consensus size: 27
39760507 TCCATTTCCT
**
39760517 AGGGGTATAACGGTAATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
* *
39760544 AGGGGTATTTCGATCATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
* * **
39760571 GGGGGTATTTTGGTCCTTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
* * *
39760598 AGAGGTATTTCAGTAATTTTACCCTTT
1 AGGGGTATTTCGGTAATTTTACCCTTC
* *
39760625 ATGGGTATTTCGATAATTTTACCCTT-
1 AGGGGTATTTCGGTAATTTTACCCTTC
* * *
39760651 TGAGGGTATTTTGGTAATTTTACTCTAT-
1 AG-GGGTATTTCGGTAATTTTACCCT-TC
* *
39760679 GGGGGTATTTTGGTAATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
* *
39760706 AAGGGTATTTCGGTAACTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
* *
39760733 -GAGGGTATTTCGGTAATTTTACCATTT
1 AG-GGGTATTTCGGTAATTTTACCCTTC
* * * *
39760760 GGGGGTGTTTCAGTAATTTTACCCATC
1 AGGGGTATTTCGGTAATTTTACCCTTC
** ** *
39760787 AATGGTATTTCAATAAATTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
39760814 -GAGGGTATTTCGGTAATTTTACCCTT-
1 AG-GGGTATTTCGGTAATTTTACCCTTC
* *
39760840 AGGGGTATTTTGTTAATTTTACCCTT-
1 AGGGGTATTTCGGTAATTTTACCCTTC
* *
39760866 TGTGGGTATTTTGGTAATTTTACCCTAT-
1 AG-GGGTATTTCGGTAATTTTACCCT-TC
**
39760894 AGGGGTATTTCTATAATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
39760921 -GAGGGTATTTCGGTAATTTTACCCTAT-
1 AG-GGGTATTTCGGTAATTTTACCCT-TC
*
39760948 AGAGGTATTTCGGTAATTT
1 AGGGGTATTTCGGTAATTT
39760967 GTGGCCCATT
Statistics
Matches: 348, Mismatches: 62, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
26 26 0.07
27 315 0.91
28 7 0.02
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (27 bp):
AGGGGTATTTCGGTAATTTTACCCTTC
Found at i:39760965 original size:54 final size:54
Alignment explanation
Indices: 39760516--39760966 Score: 473
Period size: 54 Copynumber: 8.4 Consensus size: 54
39760506 TTCCATTTCC
** * *
39760516 TAGGGGTATAACGGTAATTTTACCCTTC-AGGGGTATTTCGATCATTTTACCCT-
1 TAGGGGTATTTCGGTAATTTTACCCTTCGA-GGGTATTTCGGTAATTTTACCCTA
* * ** * *
39760569 TCGGGGGTATTTTGGTCCTTTTACCCTTC-AGAGGTATTTCAGTAATTTTACCCTT
1 T-AGGGGTATTTCGGTAATTTTACCCTTCGAG-GGTATTTCGGTAATTTTACCCTA
* * * * *
39760624 TATGGGTATTTCGATAATTTTACCCTTTGAGGGTATTTTGGTAATTTTACTCTA
1 TAGGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTA
* * * *
39760678 TGGGGGTATTTTGGTAATTTTACCCTTCAAGGGTATTTCGGTAACTTTACCCT-
1 TAGGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTA
* * * * * *
39760731 TCGAGGGTATTTCGGTAATTTTACCATTTGGGGGTGTTTCAGTAATTTTACCC-A
1 TAG-GGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTA
** ** *
39760785 TCAATGGTATTTCAATAAATTTACCCTTCGAGGGTATTTCGGTAATTTTACCCT-
1 T-AGGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTA
* * * * *
39760839 TAGGGGTATTTTGTTAATTTTACCCTTTGTGGGTATTTTGGTAATTTTACCCTA
1 TAGGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTA
**
39760893 TAGGGGTATTTCTATAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTA
1 TAGGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTA
*
39760947 TAGAGGTATTTCGGTAATTT
1 TAGGGGTATTTCGGTAATTT
39760967 GTGGCCCATT
Statistics
Matches: 322, Mismatches: 67, Indels: 17
0.79 0.17 0.04
Matches are distributed among these distances:
53 47 0.15
54 272 0.84
55 3 0.01
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (54 bp):
TAGGGGTATTTCGGTAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTA
Found at i:39761160 original size:42 final size:42
Alignment explanation
Indices: 39761097--39761181 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
39761087 TCTTTTTCGG
*
39761097 CTTTTCGGCTTTTACCGATTTGCAGATGAGAGGGTGTGATCA
1 CTTTTCGGCTTTTACCAATTTGCAGATGAGAGGGTGTGATCA
* *
39761139 CTTTTCGGCTTTTGCTAATTTGCAGATGAGAGGGTGTGATCA
1 CTTTTCGGCTTTTACCAATTTGCAGATGAGAGGGTGTGATCA
39761181 C
1 C
39761182 ACACCTGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.36
Consensus pattern (42 bp):
CTTTTCGGCTTTTACCAATTTGCAGATGAGAGGGTGTGATCA
Found at i:39764661 original size:5 final size:5
Alignment explanation
Indices: 39764651--39764675 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
39764641 TCACTCAACC
39764651 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
39764676 ATTAATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:39767726 original size:29 final size:30
Alignment explanation
Indices: 39767677--39767766 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 30
39767667 TTTATTTAAT
39767677 GTGCAATTTGATACACA--AACTTTAATT-TG
1 GTGCAA-TT-ATACACATGAACTTTAATTGTG
*
39767706 GTGCAATTATACACATGAACTTTGATTGTG
1 GTGCAATTATACACATGAACTTTAATTGTG
* * * *
39767736 GTTCAAATGTATACATGAAACTTTAATTGTG
1 GTGCAATTATACACATG-AACTTTAATTGTG
39767767 ATTTAATCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
27 7 0.14
28 2 0.04
29 15 0.29
30 15 0.29
31 12 0.24
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (30 bp):
GTGCAATTATACACATGAACTTTAATTGTG
Found at i:39767765 original size:31 final size:31
Alignment explanation
Indices: 39767693--39767766 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 31
39767683 TTTGATACAC
*
39767693 AAACTTTAATT-TGGTGCAATTATACACATG
1 AAACTTTAATTGTGGTGCAAATATACACATG
* * * *
39767723 -AACTTTGATTGTGGTTCAAATGTATACATG
1 AAACTTTAATTGTGGTGCAAATATACACATG
39767753 AAACTTTAATTGTG
1 AAACTTTAATTGTG
39767767 ATTTAATCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 9 0.25
30 15 0.42
31 12 0.33
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (31 bp):
AAACTTTAATTGTGGTGCAAATATACACATG
Found at i:39768014 original size:3 final size:3
Alignment explanation
Indices: 39768006--39768062 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
39767996 TCTTCAAATA
39768006 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39768054 TAT TAT TAT
1 TAT TAT TAT
39768063 CTAAAAACGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39768667 original size:21 final size:22
Alignment explanation
Indices: 39768629--39768669 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39768619 TTCAAAATTA
39768629 AAATTCTATTCATCTAAAATGT
1 AAATTCTATTCATCTAAAATGT
* *
39768651 AAATT-TATTTATTTAAAAT
1 AAATTCTATTCATCTAAAAT
39768670 TATTTGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATTCTATTCATCTAAAATGT
Found at i:39788827 original size:28 final size:30
Alignment explanation
Indices: 39788766--39788830 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
39788756 ATAAAAATAA
*
39788766 ATAAAATTAATTTTTTTTCATAAATCAAGT
1 ATAAAATTAATTTTTTTTCATAAATAAAGT
39788796 -TAAAATTAA-TTTTTTT-AT-AATAAAAGT
1 ATAAAATTAATTTTTTTTCATAAAT-AAAGT
39788823 ATAAAATT
1 ATAAAATT
39788831 CGACAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
27 6 0.19
28 14 0.44
29 9 0.28
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
ATAAAATTAATTTTTTTTCATAAATAAAGT
Found at i:39797624 original size:40 final size:40
Alignment explanation
Indices: 39797567--39797651 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
39797557 AGTGTCATTA
39797567 GAGGCCCTAACACATGGTTGAGTGATGTAGATACATGTTG
1 GAGGCCCTAACACATGGTTGAGTGATGTAGATACATGTTG
*
39797607 GAGGCCCTAACATATGGTTGAGTGATGTAGATACATGTTG
1 GAGGCCCTAACACATGGTTGAGTGATGTAGATACATGTTG
39797647 GAGGC
1 GAGGC
39797652 TAAAATCGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.27, C:0.14, G:0.32, T:0.27
Consensus pattern (40 bp):
GAGGCCCTAACACATGGTTGAGTGATGTAGATACATGTTG
Found at i:39799738 original size:14 final size:14
Alignment explanation
Indices: 39799719--39799749 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
39799709 TTCTGAGATG
39799719 TTTTCAAGTTATGT
1 TTTTCAAGTTATGT
39799733 TTTTCAAGTTATGT
1 TTTTCAAGTTATGT
39799747 TTT
1 TTT
39799750 ATGCGTGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTTTCAAGTTATGT
Found at i:39818996 original size:11 final size:11
Alignment explanation
Indices: 39818982--39819031 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
39818972 GGTGCTAGGA
39818982 TGGTTGAATGG
1 TGGTTGAATGG
*
39818993 TGG-TGATTAGG
1 TGGTTGAAT-GG
*
39819004 TGGTTGTATGG
1 TGGTTGAATGG
39819015 TGG-TGATATGG
1 TGGTTGA-ATGG
39819026 TGGTTG
1 TGGTTG
39819032 TTCAGTGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
10 6 0.19
11 20 0.65
12 5 0.16
ACGTcount: A:0.14, C:0.00, G:0.46, T:0.40
Consensus pattern (11 bp):
TGGTTGAATGG
Found at i:39819032 original size:22 final size:22
Alignment explanation
Indices: 39818952--39819032 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
39818942 GATACGATTT
* * *
39818952 TGATGTGGTGGTGGTGTGGTGG
1 TGATATGGTGGTTGTATGGTGG
* *
39818974 TGCTA-GGATGGTTGAATGGTGG
1 TGATATGG-TGGTTGTATGGTGG
39818996 TGAT-TAGGTGGTTGTATGGTGG
1 TGATAT-GGTGGTTGTATGGTGG
39819018 TGATATGGTGGTTGT
1 TGATATGGTGGTTGT
39819033 TCAGTGGTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.04
22 43 0.90
23 3 0.06
ACGTcount: A:0.12, C:0.01, G:0.48, T:0.38
Consensus pattern (22 bp):
TGATATGGTGGTTGTATGGTGG
Found at i:39819039 original size:22 final size:22
Alignment explanation
Indices: 39818977--39819041 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
39818967 GTGGTGGTGC
* *
39818977 TAGGATGGTTGAATGGTGGTGAT
1 TAGG-TGGTTGTATAGTGGTGAT
*
39819000 TAGGTGGTTGTATGGTGGTGA-
1 TAGGTGGTTGTATAGTGGTGAT
39819021 TATGGTGGTTGT-TCAGTGGTG
1 TA-GGTGGTTGTAT-AGTGGTG
39819042 TTTCAGTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 3 0.08
22 31 0.82
23 4 0.11
ACGTcount: A:0.15, C:0.02, G:0.45, T:0.38
Consensus pattern (22 bp):
TAGGTGGTTGTATAGTGGTGAT
Found at i:39830930 original size:16 final size:17
Alignment explanation
Indices: 39830909--39830940 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
39830899 AAAAACAACA
39830909 TAATAAACATT-TAATT
1 TAATAAACATTATAATT
39830925 TAATAAACATTATAAT
1 TAATAAACATTATAAT
39830941 GATTACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAAACATTATAATT
Found at i:39833121 original size:21 final size:19
Alignment explanation
Indices: 39833086--39833140 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
39833076 GCACACATGA
* * *
39833086 TTCCACTACTCACACACGG
1 TTCCACTAATCAAACACAG
*
39833105 TTCCACTAATCAGACACAG
1 TTCCACTAATCAAACACAG
39833124 TTCCACTAATCAAACAC
1 TTCCACTAATCAAACAC
39833141 CATTAACGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.35, C:0.36, G:0.07, T:0.22
Consensus pattern (19 bp):
TTCCACTAATCAAACACAG
Found at i:39840054 original size:35 final size:35
Alignment explanation
Indices: 39840008--39840079 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
39839998 GTGGCACTAC
39840008 GTCACTTCTTTCAATTATGAGGTTAAAAAAAATTG
1 GTCACTTCTTTCAATTATGAGGTTAAAAAAAATTG
39840043 GTCACTTCTTTCAATTATGAGGTTAAAAAAAATTG
1 GTCACTTCTTTCAATTATGAGGTTAAAAAAAATTG
39840078 GT
1 GT
39840080 GTCGGTCACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (35 bp):
GTCACTTCTTTCAATTATGAGGTTAAAAAAAATTG
Done.