Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 126 of 153
Found at i:39766111 original size:13 final size:13
Alignment explanation
Indices: 39766095--39766119 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39766085 TTTTATTTTT
39766095 CTTAGTTAATTTA
1 CTTAGTTAATTTA
39766108 CTTAGTTAATTT
1 CTTAGTTAATTT
39766120 TTAGTTTTTA
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:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (13 bp):
CTTAGTTAATTTA
Found at i:39768766 original size:22 final size:21
Alignment explanation
Indices: 39768704--39768768 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
39768694 GGAGGAAGTG
*
39768704 TATGGCTTGTAGCCGTTCTGT
1 TATGGCTTCTAGCCGTTCTGT
* *
39768725 TCAAGGCTTACTA-CCTTTCTGCT
1 T-ATGGCTT-CTAGCCGTTCTG-T
*
39768748 TATGGCTTTTAGCCGTTCTGT
1 TATGGCTTCTAGCCGTTCTGT
39768769 CTACGGTGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
21 4 0.12
22 26 0.76
23 4 0.12
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (21 bp):
TATGGCTTCTAGCCGTTCTGT
Found at i:39770959 original size:15 final size:15
Alignment explanation
Indices: 39770936--39770965 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39770926 TAAATTTCTG
*
39770936 ACTGTTTAAATCGTT
1 ACTGATTAAATCGTT
39770951 ACTGATTAAATCGTT
1 ACTGATTAAATCGTT
39770966 TAAGAGTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (15 bp):
ACTGATTAAATCGTT
Found at i:39795109 original size:95 final size:95
Alignment explanation
Indices: 39794946--39795133 Score: 376
Period size: 95 Copynumber: 2.0 Consensus size: 95
39794936 TCATTCTTGA
39794946 AATAATTTTTCAATATTTATTTTAAAAACAAGGCATGTTGCATGCTAGGGTTTAAAACAAAATTT
1 AATAATTTTTCAATATTTATTTTAAAAACAAGGCATGTTGCATGCTAGGGTTTAAAACAAAATTT
39795011 GCAAAATAATAAAAATGGTGAGAGAGAAGG
66 GCAAAATAATAAAAATGGTGAGAGAGAAGG
39795041 AATAATTTTTCAATATTTATTTTAAAAACAAGGCATGTTGCATGCTAGGGTTTAAAACAAAATTT
1 AATAATTTTTCAATATTTATTTTAAAAACAAGGCATGTTGCATGCTAGGGTTTAAAACAAAATTT
39795106 GCAAAATAATAAAAATGGTGAGAGAGAA
66 GCAAAATAATAAAAATGGTGAGAGAGAA
39795134 AGGATTTGAA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (95 bp):
AATAATTTTTCAATATTTATTTTAAAAACAAGGCATGTTGCATGCTAGGGTTTAAAACAAAATTT
GCAAAATAATAAAAATGGTGAGAGAGAAGG
Found at i:39796901 original size:20 final size:20
Alignment explanation
Indices: 39796876--39796918 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
39796866 AAAGTTACAA
39796876 GGCCTAGGGTGATTCCACAC
1 GGCCTAGGGTGATTCCACAC
39796896 GGCCTAGGGTGATTCCACAC
1 GGCCTAGGGTGATTCCACAC
39796916 GGC
1 GGC
39796919 GTGTGACCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.30, G:0.33, T:0.19
Consensus pattern (20 bp):
GGCCTAGGGTGATTCCACAC
Found at i:39799234 original size:24 final size:24
Alignment explanation
Indices: 39799203--39799248 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
39799193 GAATTTTAAT
39799203 ATTTTT-AATTGATTAAT-TTTTCA
1 ATTTTTAAATTG-TTAATCTTTTCA
39799226 ATTTATTAAATTGTTAATCTTTT
1 ATTT-TTAAATTGTTAATCTTTT
39799249 ATTTCTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 7 0.35
25 9 0.45
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (24 bp):
ATTTTTAAATTGTTAATCTTTTCA
Found at i:39804202 original size:41 final size:41
Alignment explanation
Indices: 39804063--39804202 Score: 153
Period size: 41 Copynumber: 3.5 Consensus size: 41
39804053 TGGCTCATGT
* * *
39804063 TTCGTTGATACATAGCTTAT-CACTAAGCTCAC---GGGAGC
1 TTCGCTGATACACAACTTATCCA-TAAGCTCACAAAGGGAGC
* * *
39804101 TTCGCTGATACACAACTTACCCGTAAGCTCACAAGGGGAGC
1 TTCGCTGATACACAACTTATCCATAAGCTCACAAAGGGAGC
* * * *
39804142 TTCGCTGATACACACCTTATCCATTAGTTCTCAAAGGGAGC
1 TTCGCTGATACACAACTTATCCATAAGCTCACAAAGGGAGC
39804183 TTCGCTGATACACAACTTAT
1 TTCGCTGATACACAACTTAT
39804203 AAAACCATTT
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
38 25 0.29
39 1 0.01
41 59 0.69
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (41 bp):
TTCGCTGATACACAACTTATCCATAAGCTCACAAAGGGAGC
Found at i:39812310 original size:54 final size:54
Alignment explanation
Indices: 39812252--39812383 Score: 221
Period size: 54 Copynumber: 2.4 Consensus size: 54
39812242 TGAGATACCC
* *
39812252 TGGACTGGTCCAAAATGGAGTGAT-CTTGATGCTTCAAATGATGCAAACAACTCA
1 TGGACTGGTTCAAAATGGAGTGATGC-TGAGGCTTCAAATGATGCAAACAACTCA
*
39812306 TGGACTGGTTCAAAATGGAGTGATGCTGAGGCTTCAAATGATGCGAACAACTCA
1 TGGACTGGTTCAAAATGGAGTGATGCTGAGGCTTCAAATGATGCAAACAACTCA
39812360 TGGACTGGTTCAAAATGGAGTGAT
1 TGGACTGGTTCAAAATGGAGTGAT
39812384 ACAGGTGCCT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
54 73 0.99
55 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.26
Consensus pattern (54 bp):
TGGACTGGTTCAAAATGGAGTGATGCTGAGGCTTCAAATGATGCAAACAACTCA
Found at i:39827311 original size:17 final size:17
Alignment explanation
Indices: 39827289--39827321 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39827279 GTTAGTGAAC
*
39827289 ATTGTCTTTGCATTTTT
1 ATTGTCATTGCATTTTT
39827306 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
39827322 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.61
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:39833104 original size:12 final size:12
Alignment explanation
Indices: 39833087--39833128 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
39833077 CCTCACACGC
*
39833087 CCGTGTGGTAAG
1 CCGTGTGGTAGG
39833099 CCGTGTGGTAGG
1 CCGTGTGGTAGG
39833111 CCGTGTGGTAGG
1 CCGTGTGGTAGG
39833123 CCGTGT
1 CCGTGT
39833129 AACTCTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.10, C:0.19, G:0.45, T:0.26
Consensus pattern (12 bp):
CCGTGTGGTAGG
Found at i:39838857 original size:41 final size:41
Alignment explanation
Indices: 39838780--39838876 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 41
39838770 ATAAGTGGGT
*** *
39838780 CTGCTCACAGAAGCTGTCGGTTGGAACATAGTTACATGGTG
1 CTGCTCACAGAAGCTGTCGGTCCAAACATAGCTACATGGTG
* * *
39838821 CTGCTCACAGAAGTTGTCGGTCCAAACGTAGCTACATTGTG
1 CTGCTCACAGAAGCTGTCGGTCCAAACATAGCTACATGGTG
* *
39838862 CTGCTAACACAAGCT
1 CTGCTCACAGAAGCT
39838877 ATCAAGAAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.26
Consensus pattern (41 bp):
CTGCTCACAGAAGCTGTCGGTCCAAACATAGCTACATGGTG
Found at i:39852839 original size:12 final size:12
Alignment explanation
Indices: 39852822--39852856 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
39852812 ACAAATCTGA
39852822 TTTCAATGTATT
1 TTTCAATGTATT
39852834 TTTCAATGTATT
1 TTTCAATGTATT
*
39852846 CTTCAAGTGTA
1 TTTCAA-TGTA
39852857 ATGTGTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (12 bp):
TTTCAATGTATT
Found at i:39854713 original size:18 final size:17
Alignment explanation
Indices: 39854690--39854728 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
39854680 CTCTTTTTGC
39854690 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
39854708 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
39854726 TCT
1 TCT
39854729 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:39863001 original size:65 final size:65
Alignment explanation
Indices: 39862917--39863088 Score: 218
Period size: 65 Copynumber: 2.6 Consensus size: 65
39862907 AGCTGCGATA
* * * * *
39862917 ACAATTCTGAACGCAATCTGGAATTAACCCATGCAGCGACATGTAGACATTTGTCAGGTGTGGCG
1 ACAATTCTGGATGCAATCTGGAATTAACCCATGCAGCGACATGCAGACATCTGTCAGGTGCGGCG
* *
39862982 ACAATTCTGGATGCAATCTGGAATTAACCCGTGCAGCGACATGCAGACATCTGTCAGGTGCGGTG
1 ACAATTCTGGATGCAATCTGGAATTAACCCATGCAGCGACATGCAGACATCTGTCAGGTGCGGCG
* * ** * * *
39863047 ACAATTTTAGATGCAATCTAAAATTAACTCATGTAACGACAT
1 ACAATTCTGGATGCAATCTGGAATTAACCCATGCAGCGACAT
39863089 TAATGCATTA
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
65 92 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (65 bp):
ACAATTCTGGATGCAATCTGGAATTAACCCATGCAGCGACATGCAGACATCTGTCAGGTGCGGCG
Found at i:39871412 original size:15 final size:15
Alignment explanation
Indices: 39871394--39871422 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39871384 TTTATTCTTT
39871394 CTTTTATTATTATTA
1 CTTTTATTATTATTA
39871409 CTTTTATTATTATT
1 CTTTTATTATTATT
39871423 TTAATCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
CTTTTATTATTATTA
Found at i:39876182 original size:28 final size:28
Alignment explanation
Indices: 39876151--39876211 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
39876141 GTGGAATCTA
* *
39876151 AAAAGAATAGCCTATATGGCAAACTTTG
1 AAAAGAATAACCTATATGGCAAACTCTG
* **
39876179 AAAAGAATAACCTATGTGGTGAACTCTG
1 AAAAGAATAACCTATATGGCAAACTCTG
39876207 AAAAG
1 AAAAG
39876212 GGAGGCCCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.20, T:0.23
Consensus pattern (28 bp):
AAAAGAATAACCTATATGGCAAACTCTG
Found at i:39881761 original size:104 final size:104
Alignment explanation
Indices: 39881581--39881788 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
39881571 TAGCACACTG
39881581 TGCAATCTAACAATCTCAGCAACATACAGGTTTACCAATCTTTTGAGTGAAAAATCTATATGGAC
1 TGCAATCTAACAATCTCAGCAACATACAGGTTTACCAATCTTTTGAGTGAAAAATCTATATGGAC
39881646 AGGAATGAAATGCGCGGACTTCATCGAACGATCTACAAT
66 AGGAATGAAATGCGCGGACTTCATCGAACGATCTACAAT
39881685 TGCAATCTAACAATCTCAGCAACATACAGGTTTACCAATCTTTTGAGTGAAAAATCTATATGGAC
1 TGCAATCTAACAATCTCAGCAACATACAGGTTTACCAATCTTTTGAGTGAAAAATCTATATGGAC
39881750 AGGAATGAAATGCGCGGACTTCATCGAACGATCTACAAT
66 AGGAATGAAATGCGCGGACTTCATCGAACGATCTACAAT
39881789 GACCCACACA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (104 bp):
TGCAATCTAACAATCTCAGCAACATACAGGTTTACCAATCTTTTGAGTGAAAAATCTATATGGAC
AGGAATGAAATGCGCGGACTTCATCGAACGATCTACAAT
Found at i:39896597 original size:5 final size:5
Alignment explanation
Indices: 39896556--39896639 Score: 107
Period size: 5 Copynumber: 16.4 Consensus size: 5
39896546 TATTTGTTTT
* * *
39896556 TATTA TATAA TATAA TATAA TA-TA TATTTA TATTTA TATTA TATTTA
1 TATTA TATTA TATTA TATTA TATTA TA-TTA TA-TTA TATTA TA-TTA
39896603 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA
39896640 AAAACAAACA
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
4 3 0.04
5 56 0.76
6 15 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:39897615 original size:25 final size:24
Alignment explanation
Indices: 39897574--39897653 Score: 83
Period size: 25 Copynumber: 3.3 Consensus size: 24
39897564 ACTTTAGCGC
* *
39897574 GCTCTCTAATTCTTAGCACGTTGGT
1 GCTCTCTGATTC-TAGCACGTTAGT
*
39897599 GCTCTCTGATTACTAGCACGATAGT
1 GCTCTCTGATT-CTAGCACGTTAGT
* *
39897624 GCTCTCCG-TT-TAGCACTTTAGT
1 GCTCTCTGATTCTAGCACGTTAGT
39897646 GCTCTCTG
1 GCTCTCTG
39897654 TTCATTAGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 17 0.36
24 2 0.04
25 27 0.57
26 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (24 bp):
GCTCTCTGATTCTAGCACGTTAGT
Found at i:39901324 original size:13 final size:13
Alignment explanation
Indices: 39901306--39901343 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
39901296 AATTTCCAAA
39901306 TTTTCAAATTAAG
1 TTTTCAAATTAAG
39901319 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
*
39901333 CTTTCAAATTA
1 TTTTCAAATTA
39901344 CAAATATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:39905679 original size:21 final size:22
Alignment explanation
Indices: 39905655--39905699 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
39905645 AGAAAAAGAG
39905655 AAATACAAAAAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
*
39905676 AAATCAAAAAGGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
39905698 AA
1 AA
39905700 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:39908587 original size:35 final size:33
Alignment explanation
Indices: 39908500--39908738 Score: 277
Period size: 35 Copynumber: 7.1 Consensus size: 33
39908490 GTCCAAAAAG
* *
39908500 AAATAATACATGAACAGGAGAGATTCCCTGCAAG
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAA
*
39908534 AAATGAT-GTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAA-A
*
39908567 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAG
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAA
* *
39908601 AAATGAT-GTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAA-A
*
39908634 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAG
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAA
* *
39908668 AAATGAT-GTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAA-A
* * *
39908701 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGA
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAA-A
39908736 AAA
1 AAA
39908739 GACAAGTGAA
Statistics
Matches: 177, Mismatches: 19, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
32 69 0.39
33 17 0.10
34 18 0.10
35 73 0.41
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (33 bp):
AAATAATCGTGAACAGGAGAGATTCCCTGCAAA
Found at i:39908608 original size:67 final size:67
Alignment explanation
Indices: 39908500--39908737 Score: 422
Period size: 67 Copynumber: 3.6 Consensus size: 67
39908490 GTCCAAAAAG
* * *
39908500 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
39908565 CA
66 CA
39908567 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
39908632 CA
66 CA
39908634 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
39908699 CA
66 CA
* * *
39908701 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAA
39908738 AGACAAGTGA
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 165 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (67 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
CA
Found at i:39916267 original size:35 final size:35
Alignment explanation
Indices: 39916227--39916393 Score: 252
Period size: 35 Copynumber: 4.9 Consensus size: 35
39916217 AAGAAATGAT
*
39916227 GTGAACAGGAGAGATTCCCTGCACCAAAATAATGC
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
* *
39916262 GTGAACAGGAGAGATTCCCTGCAA-GAAATGAT--
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
* *
39916294 GTGAACAGGAAAGATTCCCTGCAACAAAATAATGT
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
*
39916329 GTGAACAGGTGAGATTCCCTGCAACAAAATAATGC
1 GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
39916364 GTGAACAGGAGAGATTCCCTGCAA-AAAATA
1 GTGAACAGGAGAGATTCCCTGCAACAAAATA
39916394 TTCAATTTAT
Statistics
Matches: 119, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
32 23 0.19
33 6 0.05
34 12 0.10
35 78 0.66
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (35 bp):
GTGAACAGGAGAGATTCCCTGCAACAAAATAATGC
Found at i:39916325 original size:67 final size:67
Alignment explanation
Indices: 39916217--39916393 Score: 266
Period size: 67 Copynumber: 2.6 Consensus size: 67
39916207 CAGGTCCAAA
*
39916217 AAGAAATGATGTGAACAGGAGAGATTCCCTGCACCAAAATAATGCGTGAACAGGAGAGATTCCCT
1 AAGAAATGATGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCT
39916282 GC
66 GC
* * *
39916284 AAGAAATGATGTGAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGTGAGATTCCCT
1 AAGAAATGATGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCT
39916349 GC
66 GC
* *
39916351 AACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAA-AAAATA
1 AA-GAAATGAT--GTGAACAGGAGAGATTCCCTGCAACAAAATA
39916394 TTCAATTTAT
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
67 65 0.65
68 6 0.06
69 6 0.06
70 23 0.23
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (67 bp):
AAGAAATGATGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCT
GC
Found at i:39917407 original size:25 final size:25
Alignment explanation
Indices: 39917379--39917434 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
39917369 ACTTTAGCAC
* **
39917379 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTACTAGCACGGCGGT
39917404 GCTCTCTGATTACTAGCACGGCGGT
1 GCTCTCTGATTACTAGCACGGCGGT
39917429 GCTCTC
1 GCTCTC
39917435 CGTTTAGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.14, C:0.27, G:0.25, T:0.34
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGGCGGT
Found at i:39917474 original size:22 final size:22
Alignment explanation
Indices: 39917427--39917482 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
39917417 TAGCACGGCG
*
39917427 GTGCTCTCCGTTTAGCACATAT
1 GTGCTCTCTGTTTAGCACATAT
*
39917449 GTGCTCTCTGTTTAGCAC-TTT
1 GTGCTCTCTGTTTAGCACATAT
39917470 AGTGCTCTCTGTT
1 -GTGCTCTCTGTT
39917483 CATTAATGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (22 bp):
GTGCTCTCTGTTTAGCACATAT
Found at i:39919637 original size:18 final size:18
Alignment explanation
Indices: 39919604--39919643 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
39919594 TAGGCCTCGT
39919604 TGGGCCGAAATGGGCTGTG
1 TGGGCCGAAATGGGCT-TG
*
39919623 TGGGCC-AAGTGGGCTTG
1 TGGGCCGAAATGGGCTTG
39919640 TGGG
1 TGGG
39919644 TCACATAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 6 0.30
ACGTcount: A:0.12, C:0.15, G:0.50, T:0.23
Consensus pattern (18 bp):
TGGGCCGAAATGGGCTTG
Found at i:39920029 original size:27 final size:27
Alignment explanation
Indices: 39919999--39920519 Score: 297
Period size: 27 Copynumber: 19.3 Consensus size: 27
39919989 CCAATACTTA
* *
39919999 TAAAATGACTATAATGCCCCTGTAAGG
1 TAAAATGACCATAATGCCCCTGTAGGG
* * ** **
39920026 TAAAAAGATCGA-AAAACCCCTACAGGG
1 TAAAATGA-CCATAATGCCCCTGTAGGG
* *
39920053 TAAAATGACCGTAATGCCCCCGTAGGG
1 TAAAATGACCATAATGCCCCTGTAGGG
* * * *
39920080 TAAAATAATCGTAATGCCCCTGTAAGG
1 TAAAATGACCATAATGCCCCTGTAGGG
39920107 TAAAATGA-CAGTAAT-CCCCTTGTAGGG
1 TAAAATGACCA-TAATGCCCC-TGTAGGG
* ** ** *
39920134 TAAAATGACCAAAAAACCCCCATAGGA
1 TAAAATGACCATAATGCCCCTGTAGGG
* * *
39920161 TAAAATGATCGTAATGCCACTGTAGGG
1 TAAAATGACCATAATGCCCCTGTAGGG
* * * *
39920188 TAAAATTACCGTAATACCCCCAG-AGGG
1 TAAAATGACCATAAT-GCCCCTGTAGGG
* * * * *
39920215 TTAAATGATCGA-AATACCCCTATAAGG
1 TAAAATGA-CCATAATGCCCCTGTAGGG
*
39920242 TAAAATAACCATAATGCCCCTGTAGGG
1 TAAAATGACCATAATGCCCCTGTAGGG
* * ** * *
39920269 TAAAATGATCAAAAAACCCTTATAGGG
1 TAAAATGACCATAATGCCCCTGTAGGG
*
39920296 TAAAATGACCGTAATG-CCCTCGTAGGG
1 TAAAATGACCATAATGCCCCT-GTAGGG
* * *
39920323 TAAAATGACCGTAATGCCCTTGTAAGG
1 TAAAATGACCATAATGCCCCTGTAGGG
* ** ** *
39920350 TAAAATAACTGTAATATCCCTATAGGG
1 TAAAATGACCATAATGCCCCTGTAGGG
** **
39920377 TAAAATGACCGA-AAAACCCCCATAGGG
1 TAAAATGACC-ATAATGCCCCTGTAGGG
* *
39920404 TAAAATGATCGTAATGCCCCTGTAGGG
1 TAAAATGACCATAATGCCCCTGTAGGG
* * *
39920431 TAAAATGACCGAAAAATG-CTC-ATAGGG
1 TAAAATGACC--ATAATGCCCCTGTAGGG
*** *
39920458 TAAAATGATTGTAATACCCCTGTAGGG
1 TAAAATGACCATAATGCCCCTGTAGGG
* * * *
39920485 TAAAATGACCGTAATACCCGTGGAGGG
1 TAAAATGACCATAATGCCCCTGTAGGG
39920512 T-AAATGAC
1 TAAAATGAC
39920520 TATTTTGCCT
Statistics
Matches: 370, Mismatches: 106, Indels: 37
0.72 0.21 0.07
Matches are distributed among these distances:
25 3 0.01
26 24 0.06
27 321 0.87
28 18 0.05
29 4 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
TAAAATGACCATAATGCCCCTGTAGGG
Found at i:39920134 original size:81 final size:80
Alignment explanation
Indices: 39920010--39920499 Score: 435
Period size: 81 Copynumber: 6.0 Consensus size: 80
39920000 AAAATGACTA
* * * * * *
39920010 TAATGCCCCTGTAAGGTAAAAAGATC-GAAAAACCCCTACAGGGTAAAATGACCGTAATGCCCCC
1 TAATGCCCCTGTAAGGTAAAATGA-CAG-TAATCCCCTATAGGGTAAAATGACCGAAATACCCCC
* *
39920074 GTAGGGTAAAATAATCG
64 ATAGGGTAAAATGATCG
* * *
39920091 TAATGCCCCTGTAAGGTAAAATGACAGTAATCCCCTTGTAGGGTAAAATGACCAAAAAACCCCCA
1 TAATGCCCCTGTAAGGTAAAATGACAGTAATCCCC-TATAGGGTAAAATGACCGAAATACCCCCA
*
39920156 TAGGATAAAATGATCG
65 TAGGGTAAAATGATCG
* * * * * * * * *
39920172 TAATGCCACTGTAGGGTAAAATTACCGTAATACCCCCAGAGGGTTAAATGATCGAAATACCCCTA
1 TAATGCCCCTGTAAGGTAAAATGACAGTAAT-CCCCTATAGGGTAAAATGACCGAAATACCCCCA
* * * *
39920237 TAAGGTAAAATAACCA
65 TAGGGTAAAATGATCG
* ** * * * * * *
39920253 TAATGCCCCTGTAGGGTAAAATGATCAAAAAACCCTTATAGGGTAAAATGACCGTAATGCCCTCG
1 TAATGCCCCTGTAAGGTAAAATGA-CAGTAATCCCCTATAGGGTAAAATGACCGAAATACCCCCA
*
39920318 TAGGGTAAAATGACCG
65 TAGGGTAAAATGATCG
* * * * *
39920334 TAATGCCCTTGTAAGGTAAAATAACTGTAATATCCCTATAGGGTAAAATGACCGAAAAACCCCCA
1 TAATGCCCCTGTAAGGTAAAATGACAGTAAT-CCCCTATAGGGTAAAATGACCGAAATACCCCCA
39920399 TAGGGTAAAATGATCG
65 TAGGGTAAAATGATCG
* ** * * ** * *
39920415 TAATGCCCCTGTAGGGTAAAATGACCGAAAAATGCTC-ATAGGGTAAAATGATTGTAATACCCCT
1 TAATGCCCCTGTAAGGTAAAATGA-C-AGTAATCCCCTATAGGGTAAAATGACCGAAATACCCCC
* *
39920479 GTAGGGTAAAATGACCG
64 ATAGGGTAAAATGATCG
39920496 TAAT
1 TAAT
39920500 ACCCGTGGAG
Statistics
Matches: 324, Mismatches: 78, Indels: 14
0.78 0.19 0.03
Matches are distributed among these distances:
80 10 0.03
81 301 0.93
82 10 0.03
83 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (80 bp):
TAATGCCCCTGTAAGGTAAAATGACAGTAATCCCCTATAGGGTAAAATGACCGAAATACCCCCAT
AGGGTAAAATGATCG
Found at i:39920385 original size:54 final size:54
Alignment explanation
Indices: 39919999--39920515 Score: 332
Period size: 54 Copynumber: 9.6 Consensus size: 54
39919989 CCAATACTTA
** * * * **
39919999 TAAAATGACTATAATGCCCCTGTAAGGTAAAA-AGA-TCGAAAAACCCCTACAGGG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAATA-ACT-GTAATACCCCTGTAGGG
* * *
39920053 TAAAATGACCGTAATGCCCCCGTAGGGTAAAATAA-TCGTAATGCCCCTGTAAGG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACT-GTAATACCCCTGTAGGG
* * *** * ** *
39920107 TAAAATGACAGTAAT-CCCCTTGTAGGGTAAAATGACCAAAAAACCCCCATAGGA
1 TAAAATGACCGTAATGCCCC-TGTAGGGTAAAATAACTGTAATACCCCTGTAGGG
* * * * *
39920161 TAAAATGATCGTAATGCCACTGTAGGGTAAAATTACCGTAATACCCCCAG-AGGG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACTGTAATA-CCCCTGTAGGG
* * * * * * ** *
39920215 TTAAATGATCGAAATACCCCTATAAGGTAAAATAACCATAATGCCCCTGTAGGG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACTGTAATACCCCTGTAGGG
* ** ** * * * * *
39920269 TAAAATGATCAAAAAACCCTTATAGGGTAAAATGACCGTAAT-GCCCTCGTAGGG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACTGTAATACCCCT-GTAGGG
* * * *
39920323 TAAAATGACCGTAATGCCCTTGTAAGGTAAAATAACTGTAATATCCCTATAGGG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACTGTAATACCCCTGTAGGG
* ** ** * *
39920377 TAAAATGACCGAAAAACCCCCATAGGGTAAAATGA-TCGTAATGCCCCTGTAGGG
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACT-GTAATACCCCTGTAGGG
* * * * *
39920431 TAAAATGACCGAAAAATG-CTC-ATAGGGTAAAATGATTGTAATACCCCTGTAGGG
1 TAAAATGACCG--TAATGCCCCTGTAGGGTAAAATAACTGTAATACCCCTGTAGGG
* * *
39920485 TAAAATGACCGTAATACCCGTGGAGGGTAAA
1 TAAAATGACCGTAATGCCCCTGTAGGGTAAA
39920516 TGACTATTTT
Statistics
Matches: 367, Mismatches: 82, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
52 3 0.01
53 15 0.04
54 331 0.90
55 15 0.04
56 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (54 bp):
TAAAATGACCGTAATGCCCCTGTAGGGTAAAATAACTGTAATACCCCTGTAGGG
Found at i:39920568 original size:24 final size:24
Alignment explanation
Indices: 39920511--39920646 Score: 127
Period size: 24 Copynumber: 5.6 Consensus size: 24
39920501 CCCGTGGAGG
39920511 GTAAATGACT-ATTTTGCCTCT-TGAGT
1 GTAAATGACTGA-TTTG--TCTGTGA-T
* *
39920537 GTAAATGATTGATTTGTCCGTGAT
1 GTAAATGACTGATTTGTCTGTGAT
*
39920561 GTAAATGACTGATTTGTATGTGAT
1 GTAAATGACTGATTTGTCTGTGAT
*
39920585 TTAAATGACTGATTTGTCTGTGATT
1 GTAAATGACTGATTTGTCTGTGA-T
39920610 GGT--ATGACTGATTTGTCTGTGAT
1 -GTAAATGACTGATTTGTCTGTGAT
* **
39920633 TTGTATGACTGATT
1 GTAAATGACTGATT
39920647 CTGAGCATGA
Statistics
Matches: 95, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 74 0.78
25 4 0.04
26 14 0.15
27 1 0.01
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.44
Consensus pattern (24 bp):
GTAAATGACTGATTTGTCTGTGAT
Found at i:39920586 original size:11 final size:11
Alignment explanation
Indices: 39920570--39920639 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
39920560 TGTAAATGAC
39920570 TGATTTGTATG
1 TGATTTGTATG
**
39920581 TGATTTAAATG
1 TGATTTGTATG
*
39920592 ACTGATTTGTCTG
1 --TGATTTGTATG
*
39920605 TGATTGGTATG
1 TGATTTGTATG
*
39920616 ACTGATTTGTCTG
1 --TGATTTGTATG
39920629 TGATTTGTATG
1 TGATTTGTATG
39920640 ACTGATTCTG
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
11 28 0.62
13 17 0.38
ACGTcount: A:0.20, C:0.06, G:0.26, T:0.49
Consensus pattern (11 bp):
TGATTTGTATG
Found at i:39920598 original size:48 final size:48
Alignment explanation
Indices: 39920538--39920646 Score: 141
Period size: 48 Copynumber: 2.3 Consensus size: 48
39920528 CTCTTGAGTG
*
39920538 TAAATGATTGATTTGTCCGTGA-T-GTAAATGACTGATTTGTATGTGATT
1 TAAATGACTGATTTGTCCGTGATTGGT--ATGACTGATTTGTATGTGATT
* *
39920586 TAAATGACTGATTTGTCTGTGATTGGTATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCCGTGATTGGTATGACTGATTTGTATGTGATT
**
39920634 TGTATGACTGATT
1 TAAATGACTGATT
39920647 CTGAGCATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 51 0.94
49 1 0.02
50 2 0.04
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (48 bp):
TAAATGACTGATTTGTCCGTGATTGGTATGACTGATTTGTATGTGATT
Found at i:39920885 original size:32 final size:31
Alignment explanation
Indices: 39920815--39920897 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 31
39920805 TTTTCTACGA
*
39920815 TGCTACTGATGGTTTGTGCGGATCATATTAC
1 TGCTACTGATGGTTTGTGCGGATCATATCAC
***
39920846 CATTACTGATGGTTGTGTGTC-GATCATATCAC
1 TGCTACTGATGGTT-TGTG-CGGATCATATCAC
39920878 TGCTACTGATGGCTTTGTGC
1 TGCTACTGATGG-TTTGTGC
39920898 CAACCATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
31 12 0.29
32 27 0.64
33 3 0.07
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (31 bp):
TGCTACTGATGGTTTGTGCGGATCATATCAC
Found at i:39922397 original size:42 final size:42
Alignment explanation
Indices: 39922351--39922435 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
39922341 TCAGGCCGTA
* *
39922351 TAACTCTCGAAATAACCCCACATGCCTGTGTGCCAAGCCATG
1 TAACTCTCGAAATAACCCCACACGCCCGTGTGCCAAGCCATG
* * *
39922393 TAACTCTCGAAATAGCCCTACACGCCCGTGTGCCAGGCCATG
1 TAACTCTCGAAATAACCCCACACGCCCGTGTGCCAAGCCATG
39922435 T
1 T
39922436 GCTAGGCTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (42 bp):
TAACTCTCGAAATAACCCCACACGCCCGTGTGCCAAGCCATG
Found at i:39930138 original size:19 final size:18
Alignment explanation
Indices: 39930105--39930140 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39930095 TAATATTTGT
*
39930105 TAAACATGTTTAATTAAA
1 TAAACATGATTAATTAAA
39930123 TAAACAATGATTAATTAA
1 TAAAC-ATGATTAATTAA
39930141 TTTTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (18 bp):
TAAACATGATTAATTAAA
Found at i:39936362 original size:40 final size:40
Alignment explanation
Indices: 39936318--39936581 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
39936308 GCTCCTCGTT
* *
39936318 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
39936358 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
39936398 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
39936438 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
39936478 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
39936517 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
39936558 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39936582 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:39944972 original size:40 final size:40
Alignment explanation
Indices: 39944928--39945189 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
39944918 GCTCCTCGTT
* *
39944928 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39944968 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39945008 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39945047 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39945086 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
39945125 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
39945166 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39945190 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39946855 original size:24 final size:24
Alignment explanation
Indices: 39946794--39946858 Score: 116
Period size: 23 Copynumber: 2.8 Consensus size: 24
39946784 ACAGAAATCA
39946794 TATGCGAATT-AAAAAAGAAAGTG
1 TATGCGAATTGAAAAAAGAAAGTG
39946817 TATGCGAATTG-AAAAAGAAAGTG
1 TATGCGAATTGAAAAAAGAAAGTG
39946840 TATGCGAATTGAAAAAAGA
1 TATGCGAATTGAAAAAAGA
39946859 TGTATCATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
23 33 0.82
24 7 0.17
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.22
Consensus pattern (24 bp):
TATGCGAATTGAAAAAAGAAAGTG
Found at i:39950594 original size:407 final size:407
Alignment explanation
Indices: 39949839--39950653 Score: 1630
Period size: 407 Copynumber: 2.0 Consensus size: 407
39949829 GGGAAACCAT
39949839 GGTTAGGGTTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTGTAATGTTCTT
1 GGTTAGGGTTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTGTAATGTTCTT
39949904 TACATTTTTGAAGTCCCGGTAGCTTAATTTAGCTTATTCTAGCAATAATTTAACCTACGGTTTAT
66 TACATTTTTGAAGTCCCGGTAGCTTAATTTAGCTTATTCTAGCAATAATTTAACCTACGGTTTAT
39949969 ATTTGAAAAAATACCCATAGGTGAAATGTGTTTATTTTTATTTTTTTATGGTAGAATATGAAGCT
131 ATTTGAAAAAATACCCATAGGTGAAATGTGTTTATTTTTATTTTTTTATGGTAGAATATGAAGCT
39950034 TGAAATTGTGTTAAACAATTTTTGCTAAGCGATTTTCAGTGAAAACAAGTGAAACGGCATAATCA
196 TGAAATTGTGTTAAACAATTTTTGCTAAGCGATTTTCAGTGAAAACAAGTGAAACGGCATAATCA
39950099 GTAAAAATTATTATGGTCCATAAGTGCATGTTAGAGCAAGAATTTGATGTTGCTATAGAAGGGAA
261 GTAAAAATTATTATGGTCCATAAGTGCATGTTAGAGCAAGAATTTGATGTTGCTATAGAAGGGAA
39950164 AAATTTTCAGCATGTTATAAAACATAAGAAAAATGAATAAAGTTTAATTTCCGAGCCTAGGAGTA
326 AAATTTTCAGCATGTTATAAAACATAAGAAAAATGAATAAAGTTTAATTTCCGAGCCTAGGAGTA
39950229 AAATCGTAATTTTGTGA
391 AAATCGTAATTTTGTGA
39950246 GGTTAGGGTTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTGTAATGTTCTT
1 GGTTAGGGTTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTGTAATGTTCTT
39950311 TACATTTTTGAAGTCCCGGTAGCTTAATTTAGCTTATTCTAGCAATAATTTAACCTACGGTTTAT
66 TACATTTTTGAAGTCCCGGTAGCTTAATTTAGCTTATTCTAGCAATAATTTAACCTACGGTTTAT
39950376 ATTTGAAAAAATACCCATAGGTGAAATGTGTTTATTTTTATTTTTTTATGGTAGAATATGAAGCT
131 ATTTGAAAAAATACCCATAGGTGAAATGTGTTTATTTTTATTTTTTTATGGTAGAATATGAAGCT
39950441 TGAAATTGTGTTAAACAATTTTTGCTAAGCGATTTTCAGTGAAAACAAGTGAAACGGCATAATCA
196 TGAAATTGTGTTAAACAATTTTTGCTAAGCGATTTTCAGTGAAAACAAGTGAAACGGCATAATCA
39950506 GTAAAAATTATTATGGTCCATAAGTGCATGTTAGAGCAAGAATTTGATGTTGCTATAGAAGGGAA
261 GTAAAAATTATTATGGTCCATAAGTGCATGTTAGAGCAAGAATTTGATGTTGCTATAGAAGGGAA
39950571 AAATTTTCAGCATGTTATAAAACATAAGAAAAATGAATAAAGTTTAATTTCCGAGCCTAGGAGTA
326 AAATTTTCAGCATGTTATAAAACATAAGAAAAATGAATAAAGTTTAATTTCCGAGCCTAGGAGTA
39950636 AAATCGTAATTTTGTGA
391 AAATCGTAATTTTGTGA
39950653 G
1 G
39950654 ACTTTAGGGG
Statistics
Matches: 408, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
407 408 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (407 bp):
GGTTAGGGTTTTCAAGCTTCCAAGCTCCATAGTAAGTGATTCCAAGCCCCGTTTGTAATGTTCTT
TACATTTTTGAAGTCCCGGTAGCTTAATTTAGCTTATTCTAGCAATAATTTAACCTACGGTTTAT
ATTTGAAAAAATACCCATAGGTGAAATGTGTTTATTTTTATTTTTTTATGGTAGAATATGAAGCT
TGAAATTGTGTTAAACAATTTTTGCTAAGCGATTTTCAGTGAAAACAAGTGAAACGGCATAATCA
GTAAAAATTATTATGGTCCATAAGTGCATGTTAGAGCAAGAATTTGATGTTGCTATAGAAGGGAA
AAATTTTCAGCATGTTATAAAACATAAGAAAAATGAATAAAGTTTAATTTCCGAGCCTAGGAGTA
AAATCGTAATTTTGTGA
Found at i:39951029 original size:51 final size:51
Alignment explanation
Indices: 39950842--39951030 Score: 231
Period size: 51 Copynumber: 3.7 Consensus size: 51
39950832 GAAGTTGCTA
* *
39950842 GGTCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATG-ATA-
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAG-ATGAATAT
* * * * *
39950892 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT-AGCTTT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATGA-ATAT
* * * *
39950943 GATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCAGATGAAAAT
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATGAATAT
*
39950994 GGTCACATGTGTAGTACTATGTGCAGGATACTATGTG
1 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
39951031 AACCGGGTAT
Statistics
Matches: 116, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
49 2 0.02
50 39 0.34
51 74 0.64
52 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (51 bp):
GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGATGAATAT
Found at i:39951036 original size:102 final size:101
Alignment explanation
Indices: 39950844--39951036 Score: 280
Period size: 101 Copynumber: 1.9 Consensus size: 101
39950834 AGTTGCTAGG
* *
39950844 TCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATGAAAGGTCACATGTGTAGTAC
* *
39950909 TATGTGCAGGCTACTATGCGTACCGGATAGCTTTGA
66 TATGTGCAGGATACTATGCGAACCGGATAGCTTTGA
* * * *
39950945 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCAG-ATGAAAATGGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATG-AAA-GGTCACATGTGTAGT
*
39951009 ACTATGTGCAGGATACTATGTGAACCGG
64 ACTATGTGCAGGATACTATGCGAACCGG
39951037 GTATCATTTA
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
100 3 0.04
101 39 0.48
102 39 0.48
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGAATGAAAGGTCACATGTGTAGTAC
TATGTGCAGGATACTATGCGAACCGGATAGCTTTGA
Found at i:39958993 original size:25 final size:23
Alignment explanation
Indices: 39958928--39958990 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
39958918 GTTGAGTGAA
39958928 AATTCTCTTTGAGTTTCTCCAAG
1 AATTCTCTTTGAGTTTCTCCAAG
39958951 AATTCTCTTTGAGTTTCTCCAAG
1 AATTCTCTTTGAGTTTCTCCAAG
39958974 AATTCTCTCTTGAGTTT
1 AATTCTCT-TTGAGTTT
39958991 TCTTTAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
23 31 0.79
24 8 0.21
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.46
Consensus pattern (23 bp):
AATTCTCTTTGAGTTTCTCCAAG
Found at i:39961915 original size:742 final size:742
Alignment explanation
Indices: 39960492--39961959 Score: 2927
Period size: 742 Copynumber: 2.0 Consensus size: 742
39960482 CAGGCTGCAG
39960492 CACTCAAACAAACAAATGCCATACTTCGAACATTGAGTGCTACTATCAATGAGATCTGATTGGAT
1 CACTCAAACAAACAAATGCCATACTTCGAACATTGAGTGCTACTATCAATGAGATCTGATTGGAT
39960557 CAGGAGCCTCAGTATCAGGGTCCAACTAAAGATGATGTGGATAACCAGCCTCGTTCTCATAGGCA
66 CAGGAGCCTCAGTATCAGGGTCCAACTAAAGATGATGTGGATAACCAGCCTCGTTCTCATAGGCA
39960622 CGCTCCTAGACATGTCCCTAGAACTGACTATGACTTTCATGATCGCGGACAATCCTTTTTGGCAA
131 CGCTCCTAGACATGTCCCTAGAACTGACTATGACTTTCATGATCGCGGACAATCCTTTTTGGCAA
39960687 AACCAAAATTCACAATTCCTCAATTTCGTGGTAAGAATTATCCAGAAGCTTATTGTGAATGGGAA
196 AACCAAAATTCACAATTCCTCAATTTCGTGGTAAGAATTATCCAGAAGCTTATTGTGAATGGGAA
*
39960752 TCTAAAATTGAACTTATGTTTCGCTATTATAAATGTTCGGATGATGAAAAAGTATCGTTAGCAAC
261 TCTAAAATTGAACTTATGTTTCGCTATTATAAATGTCCGGATGATGAAAAAGTATCGTTAGCAAC
39960817 ACTGGAATTTTTAGATTATGAATTAAGTTGGTGGACTCAACTTGGGGTAAATCGTCATAGGAATT
326 ACTGGAATTTTTAGATTATGAATTAAGTTGGTGGACTCAACTTGGGGTAAATCGTCATAGGAATT
39960882 ATGAACGTGAGATTATGACATGGGATGAGTTGAAACAAGTCATGCGTAAAAGATTTATTCTGCCT
391 ATGAACGTGAGATTATGACATGGGATGAGTTGAAACAAGTCATGCGTAAAAGATTTATTCTGCCT
39960947 CATTACTATAGAGAGGTTAAAAAAAAACTTAGACGACTTGTTCAAGGTAGTAGGACGGTAGATGA
456 CATTACTATAGAGAGGTTAAAAAAAAACTTAGACGACTTGTTCAAGGTAGTAGGACGGTAGATGA
39961012 ATACTTTAAGGAGATGGAAATGCTCATTCAGAGAGCTAATGTAGAGGAGGAGGATGAAACAACTA
521 ATACTTTAAGGAGATGGAAATGCTCATTCAGAGAGCTAATGTAGAGGAGGAGGATGAAACAACTA
39961077 TGGTTCGATTTATTGATGGTTTAAATATGCCAATAGCTAATACATTAAGGCTACAAACATACATT
586 TGGTTCGATTTATTGATGGTTTAAATATGCCAATAGCTAATACATTAAGGCTACAAACATACATT
39961142 GATTTAGAAGAAGCAGTTCATAAAGCCATTGAGATCGAGCAACAATTAAAGGAACAAAGGTTTAG
651 GATTTAGAAGAAGCAGTTCATAAAGCCATTGAGATCGAGCAACAATTAAAGGAACAAAGGTTTAG
39961207 TTCCTTTTCTACTTCACAATATTATAA
716 TTCCTTTTCTACTTCACAATATTATAA
39961234 CACTCAAACAAACAAATGCCATACTTCGAACATTGAGTGCTACTATCAATGAGATCTGATTGGAT
1 CACTCAAACAAACAAATGCCATACTTCGAACATTGAGTGCTACTATCAATGAGATCTGATTGGAT
39961299 CAGGAGCCTCAGTATCAGGGTCCAACTAAAGATGATGTGGATAACCAGCCTCGTTCTCATAGGCA
66 CAGGAGCCTCAGTATCAGGGTCCAACTAAAGATGATGTGGATAACCAGCCTCGTTCTCATAGGCA
39961364 CGCTCCTAGACATGTCCCTAGAACTGACTATGACTTTCATGATCGCGGACAATCCTTTTTGGCAA
131 CGCTCCTAGACATGTCCCTAGAACTGACTATGACTTTCATGATCGCGGACAATCCTTTTTGGCAA
39961429 AACCAAAATTCACAATTCCTCAATTTCGTGGTAAGAATTATCCAGAAGCTTATTGTGAATGGGAA
196 AACCAAAATTCACAATTCCTCAATTTCGTGGTAAGAATTATCCAGAAGCTTATTGTGAATGGGAA
39961494 TCTAAAATTGAACTTATGTTTCGCTATTATAAATGTCCGGATGATGAAAAAGTATCGTTAGCAAC
261 TCTAAAATTGAACTTATGTTTCGCTATTATAAATGTCCGGATGATGAAAAAGTATCGTTAGCAAC
39961559 ACTGGAATTTTTAGATTATGAATTAAGTTGGTGGACTCAACTTGGGGTAAATCGTCATAGGAATT
326 ACTGGAATTTTTAGATTATGAATTAAGTTGGTGGACTCAACTTGGGGTAAATCGTCATAGGAATT
39961624 ATGAACGTGAGATTATGACATGGGATGAGTTGAAACAAGTCATGCGTAAAAGATTTATTCTGCCT
391 ATGAACGTGAGATTATGACATGGGATGAGTTGAAACAAGTCATGCGTAAAAGATTTATTCTGCCT
39961689 CATTACTATAGAGAGGTTAAAAAAAAACTTAGACGACTTGTTCAAGGTAGTAGGACGGTAGATGA
456 CATTACTATAGAGAGGTTAAAAAAAAACTTAGACGACTTGTTCAAGGTAGTAGGACGGTAGATGA
39961754 ATACTTTAAGGAGATGGAAATGCTCATTCAGAGAGCTAATGTAGAGGAGGAGGATGAAACAACTA
521 ATACTTTAAGGAGATGGAAATGCTCATTCAGAGAGCTAATGTAGAGGAGGAGGATGAAACAACTA
39961819 TGGTTCGATTTATTGATGGTTTAAATATGCCAATAGCTAATACATTAAGGCTACAAACATACATT
586 TGGTTCGATTTATTGATGGTTTAAATATGCCAATAGCTAATACATTAAGGCTACAAACATACATT
39961884 GATTTAGAAGAAGCAGTTCATAAAGCCATTGAGATCGAGCAACAATTAAAGGAACAAAGGTTTAG
651 GATTTAGAAGAAGCAGTTCATAAAGCCATTGAGATCGAGCAACAATTAAAGGAACAAAGGTTTAG
39961949 TTCCTTTTCTA
716 TTCCTTTTCTA
39961960 AAGCACCCTA
Statistics
Matches: 725, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
742 725 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (742 bp):
CACTCAAACAAACAAATGCCATACTTCGAACATTGAGTGCTACTATCAATGAGATCTGATTGGAT
CAGGAGCCTCAGTATCAGGGTCCAACTAAAGATGATGTGGATAACCAGCCTCGTTCTCATAGGCA
CGCTCCTAGACATGTCCCTAGAACTGACTATGACTTTCATGATCGCGGACAATCCTTTTTGGCAA
AACCAAAATTCACAATTCCTCAATTTCGTGGTAAGAATTATCCAGAAGCTTATTGTGAATGGGAA
TCTAAAATTGAACTTATGTTTCGCTATTATAAATGTCCGGATGATGAAAAAGTATCGTTAGCAAC
ACTGGAATTTTTAGATTATGAATTAAGTTGGTGGACTCAACTTGGGGTAAATCGTCATAGGAATT
ATGAACGTGAGATTATGACATGGGATGAGTTGAAACAAGTCATGCGTAAAAGATTTATTCTGCCT
CATTACTATAGAGAGGTTAAAAAAAAACTTAGACGACTTGTTCAAGGTAGTAGGACGGTAGATGA
ATACTTTAAGGAGATGGAAATGCTCATTCAGAGAGCTAATGTAGAGGAGGAGGATGAAACAACTA
TGGTTCGATTTATTGATGGTTTAAATATGCCAATAGCTAATACATTAAGGCTACAAACATACATT
GATTTAGAAGAAGCAGTTCATAAAGCCATTGAGATCGAGCAACAATTAAAGGAACAAAGGTTTAG
TTCCTTTTCTACTTCACAATATTATAA
Found at i:39970856 original size:40 final size:40
Alignment explanation
Indices: 39970812--39971073 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
39970802 GCTCCTCGTT
* *
39970812 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39970852 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39970892 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39970931 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39970970 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
39971009 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
39971050 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39971074 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39977613 original size:30 final size:30
Alignment explanation
Indices: 39977573--39977642 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
39977563 CCTACAAGGG
39977573 ACACAAGGCTGTGTCGCGTGGCCACGTGTC
1 ACACAAGGCTGTGTCGCGTGGCCACGTGTC
* * *
39977603 ACACACGGCTGTGTCGTGTGGCCATGTGTC
1 ACACAAGGCTGTGTCGCGTGGCCACGTGTC
*
39977633 ACACATGGCT
1 ACACAAGGCT
39977643 AAGACACATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.17, C:0.29, G:0.31, T:0.23
Consensus pattern (30 bp):
ACACAAGGCTGTGTCGCGTGGCCACGTGTC
Found at i:39979413 original size:25 final size:25
Alignment explanation
Indices: 39979384--39979440 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
39979374 ACCAGGCTCG
39979384 AAGCCTGATATAACACACCAGCACA
1 AAGCCTGATATAACACACCAGCACA
* * *
39979409 AAGCCTGATATAATACACCGGCACG
1 AAGCCTGATATAACACACCAGCACA
39979434 AAGCCTG
1 AAGCCTG
39979441 CTAGGCACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.30, G:0.18, T:0.14
Consensus pattern (25 bp):
AAGCCTGATATAACACACCAGCACA
Found at i:39979628 original size:114 final size:114
Alignment explanation
Indices: 39979420--39979667 Score: 345
Period size: 114 Copynumber: 2.2 Consensus size: 114
39979410 AGCCTGATAT
* *
39979420 AATA-CACCGGCACGAAGCCTGCTAGGCACAGAGCCCGAATATCAATGGCAAAAAGCCTACTAGG
1 AATATCACCGGCACGAAGCCTGCTAGGCACAGAGCCCGAATATCAACGACAAAAAGCCTACTAGG
* *
39979484 CACAGAGCTCGAAGATCACTAGCACGAAGCTTGCTAGACACAGAGCCCA
66 CACAGAGCCCGAAGATCACTAGCACAAAGCTTGCTAGACACAGAGCCCA
* * * * *
39979533 AATATCACCGGCATGAAGCCTGCTAGGCATAGAGCCCGAATATCACCGACACAAAGCCTGCTAGG
1 AATATCACCGGCACGAAGCCTGCTAGGCACAGAGCCCGAATATCAACGACAAAAAGCCTACTAGG
* * * * *
39979598 CATAGAGCCCGAATATCACTGGCACAAAGCTTGCTAGGCACAGAGCCCG
66 CACAGAGCCCGAAGATCACTAGCACAAAGCTTGCTAGACACAGAGCCCA
* *
39979647 AATATCACTGGCACAAAGCCT
1 AATATCACCGGCACGAAGCCT
39979668 ATTAAGAACA
Statistics
Matches: 117, Mismatches: 17, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
113 4 0.03
114 113 0.97
ACGTcount: A:0.34, C:0.29, G:0.23, T:0.14
Consensus pattern (114 bp):
AATATCACCGGCACGAAGCCTGCTAGGCACAGAGCCCGAATATCAACGACAAAAAGCCTACTAGG
CACAGAGCCCGAAGATCACTAGCACAAAGCTTGCTAGACACAGAGCCCA
Found at i:39979688 original size:38 final size:38
Alignment explanation
Indices: 39979420--39979667 Score: 309
Period size: 38 Copynumber: 6.6 Consensus size: 38
39979410 AGCCTGATAT
* *
39979420 AATA-CACCGGCACGAAGCCTGCTAGGCACAGAGCCCG
1 AATATCACTGGCACAAAGCCTGCTAGGCACAGAGCCCG
* * * *
39979457 AATATCAATGGCAAAAAGCCTACTAGGCACAGAGCTCG
1 AATATCACTGGCACAAAGCCTGCTAGGCACAGAGCCCG
* * * * * *
39979495 AAGATCACTAGCACGAAGCTTGCTAGACACAGAGCCCA
1 AATATCACTGGCACAAAGCCTGCTAGGCACAGAGCCCG
* ** *
39979533 AATATCACCGGCATGAAGCCTGCTAGGCATAGAGCCCG
1 AATATCACTGGCACAAAGCCTGCTAGGCACAGAGCCCG
* * *
39979571 AATATCACCGACACAAAGCCTGCTAGGCATAGAGCCCG
1 AATATCACTGGCACAAAGCCTGCTAGGCACAGAGCCCG
*
39979609 AATATCACTGGCACAAAGCTTGCTAGGCACAGAGCCCG
1 AATATCACTGGCACAAAGCCTGCTAGGCACAGAGCCCG
39979647 AATATCACTGGCACAAAGCCT
1 AATATCACTGGCACAAAGCCT
39979668 ATTAAGAACA
Statistics
Matches: 178, Mismatches: 32, Indels: 1
0.84 0.15 0.00
Matches are distributed among these distances:
37 4 0.02
38 174 0.98
ACGTcount: A:0.34, C:0.29, G:0.23, T:0.14
Consensus pattern (38 bp):
AATATCACTGGCACAAAGCCTGCTAGGCACAGAGCCCG
Found at i:39984057 original size:3 final size:3
Alignment explanation
Indices: 39984049--39984091 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
39984039 CTATTTAAAA
39984049 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
39984092 TCTTTTGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39997582 original size:9 final size:9
Alignment explanation
Indices: 39997568--39997594 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39997558 GAAATGTTTG
39997568 ATGATATAA
1 ATGATATAA
39997577 ATGATATAA
1 ATGATATAA
39997586 ATGATATAA
1 ATGATATAA
39997595 TTGTTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (9 bp):
ATGATATAA
Found at i:40001953 original size:23 final size:23
Alignment explanation
Indices: 40001923--40001968 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
40001913 GGTGCTATCA
40001923 CTTTGTTCTTAAGATTCCTTAAT
1 CTTTGTTCTTAAGATTCCTTAAT
40001946 CTTTGTTCTTAAGATTCCTTAAT
1 CTTTGTTCTTAAGATTCCTTAAT
40001969 ATTCAAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (23 bp):
CTTTGTTCTTAAGATTCCTTAAT
Found at i:40007961 original size:21 final size:21
Alignment explanation
Indices: 40007937--40007980 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40007927 TTAGTGAGTA
40007937 TGTTCAATAAGGGAGTTGGTG
1 TGTTCAATAAGGGAGTTGGTG
40007958 TGTTCAATAAGGGAGTTGGTG
1 TGTTCAATAAGGGAGTTGGTG
40007979 TG
1 TG
40007981 ATTCTTGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.05, G:0.39, T:0.34
Consensus pattern (21 bp):
TGTTCAATAAGGGAGTTGGTG
Found at i:40010350 original size:29 final size:28
Alignment explanation
Indices: 40010314--40010391 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
40010304 TCATGAGATT
40010314 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
40010344 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
40010371 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
40010392 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:40010609 original size:174 final size:174
Alignment explanation
Indices: 40010344--40010671 Score: 629
Period size: 174 Copynumber: 1.9 Consensus size: 174
40010334 AAATTGTACA
40010344 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
40010409 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCGA
40010474 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
40010518 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
40010583 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCGA
40010648 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
40010672 ACCTTGAGTT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 151 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCGA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:40014523 original size:48 final size:48
Alignment explanation
Indices: 40014426--40014523 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
40014416 GTTCATCTAC
* * **
40014426 TAATACAATTTTTATTTTAGTACTACGATCCGACCATATAATATTGCT
1 TAATACAAGTTTTATTTTAGTACTACGATCCGACCACATAATACCGCT
*
40014474 TAATACAAGTTTTATTTTAGTACTATGATCCGACCACATAATACCGCT
1 TAATACAAGTTTTATTTTAGTACTACGATCCGACCACATAATACCGCT
40014522 TA
1 TA
40014524 GTATTAGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (48 bp):
TAATACAAGTTTTATTTTAGTACTACGATCCGACCACATAATACCGCT
Found at i:40023579 original size:2 final size:2
Alignment explanation
Indices: 40023572--40023598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40023562 GTATACATAT
40023572 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
40023599 CAAACAAAAC
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40024867 original size:30 final size:29
Alignment explanation
Indices: 40024819--40024875 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
40024809 GTGCAAGGAC
* *
40024819 CAAAATGGACCTAGTTGCCAAGTTCAGTA
1 CAAAATGGACCCAATTGCCAAGTTCAGTA
*
40024848 CAAAAGTGGACCCAATTGCCAGGTTCAG
1 CAAAA-TGGACCCAATTGCCAAGTTCAG
40024876 AACCTAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (29 bp):
CAAAATGGACCCAATTGCCAAGTTCAGTA
Found at i:40028100 original size:8 final size:8
Alignment explanation
Indices: 40028089--40028133 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
40028079 GCTAAATGTT
40028089 TGTTTATA
1 TGTTTATA
40028097 TGTTTATA
1 TGTTTATA
*
40028105 TATTTATA
1 TGTTTATA
40028113 TG--T-T-
1 TGTTTATA
40028117 TGTTTATA
1 TGTTTATA
40028125 TGTTTATA
1 TGTTTATA
40028133 T
1 T
40028134 CTGGAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
4 2 0.06
5 1 0.03
6 2 0.06
7 1 0.03
8 25 0.81
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.64
Consensus pattern (8 bp):
TGTTTATA
Found at i:40029063 original size:42 final size:42
Alignment explanation
Indices: 40029007--40029110 Score: 156
Period size: 42 Copynumber: 2.5 Consensus size: 42
40028997 ACAATTTTTA
***
40029007 TTATTTATAACAAATTAA-AGAGTTATTAATTTAAAATTCTAT
1 TTATTTATAACAAATTAATA-ACAAATTAATTTAAAATTCTAT
40029049 TTATTTATAACAAATTAATAACAAATTAATTTAAAATTCTAT
1 TTATTTATAACAAATTAATAACAAATTAATTTAAAATTCTAT
*
40029091 ATATTTATAACAAATTAATA
1 TTATTTATAACAAATTAATA
40029111 TAACAGTAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
42 56 0.98
43 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (42 bp):
TTATTTATAACAAATTAATAACAAATTAATTTAAAATTCTAT
Found at i:40029114 original size:13 final size:15
Alignment explanation
Indices: 40029096--40029141 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
40029086 TCTATATATT
40029096 TATAACA-AA-TTAA
1 TATAACAGAAGTTAA
40029109 TATAACAGTAAGTTAA
1 TATAACAG-AAGTTAA
40029125 TATAACAGCAAGTTAA
1 TATAACAG-AAGTTAA
40029141 T
1 T
40029142 TAAAGAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 7 0.24
15 2 0.07
16 20 0.69
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (15 bp):
TATAACAGAAGTTAA
Found at i:40029126 original size:16 final size:16
Alignment explanation
Indices: 40029105--40029141 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
40029095 TTATAACAAA
*
40029105 TTAATATAACAGTAAG
1 TTAATATAACAGCAAG
40029121 TTAATATAACAGCAAG
1 TTAATATAACAGCAAG
40029137 TTAAT
1 TTAAT
40029142 TAAAGAGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (16 bp):
TTAATATAACAGCAAG
Found at i:40031682 original size:22 final size:21
Alignment explanation
Indices: 40031657--40031721 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
40031647 CTTCTAAATA
40031657 TGTTGATGGACAACTTATATTT
1 TGTTGATGGACAA-TTATATTT
* *
40031679 TGTT-AT-GA-AATTA-AATA
1 TGTTGATGGACAATTATATTT
40031696 TGTTGATGGACAATTTATATTT
1 TGTTGATGGACAA-TTATATTT
40031718 TGTT
1 TGTT
40031722 ATGAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 4 0.12
20 4 0.12
21 5 0.15
22 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (21 bp):
TGTTGATGGACAATTATATTT
Found at i:40031694 original size:39 final size:39
Alignment explanation
Indices: 40031651--40031744 Score: 170
Period size: 39 Copynumber: 2.4 Consensus size: 39
40031641 GCTTTCCTTC
40031651 TAAATATGTTGATGGACAACTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAACTTATATTTTGTTATGAAAT
*
40031690 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAACTTATATTTTGTTATGAAAT
*
40031729 TAAATAGGTTGATGGA
1 TAAATATGTTGATGGA
40031745 TTAATGTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (39 bp):
TAAATATGTTGATGGACAACTTATATTTTGTTATGAAAT
Found at i:40031763 original size:39 final size:38
Alignment explanation
Indices: 40031651--40031763 Score: 95
Period size: 39 Copynumber: 2.9 Consensus size: 38
40031641 GCTTTCCTTC
* * *
40031651 TAAATATGTTGATGGACAACT-TATATTTTGTTATGAAAT
1 TAAATAGGTTGATGGACAA-TGTATA-TATATTATGAAAT
* * * *
40031690 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATAGGTTGATGGACAATGTATA-TATATTATGAAAT
*
40031729 TAAATAGGTTGATGGATTAATGTATGA-ATATTATG
1 TAAATAGGTTGATGGA-CAATGTAT-ATATATTATG
40031764 GTTTGTTGCT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 58 0.88
40 6 0.09
41 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.18, T:0.43
Consensus pattern (38 bp):
TAAATAGGTTGATGGACAATGTATATATATTATGAAAT
Found at i:40035936 original size:15 final size:15
Alignment explanation
Indices: 40035916--40035944 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40035906 GTGTATCAAC
40035916 TTTTAATTATTTTTA
1 TTTTAATTATTTTTA
40035931 TTTTAATTATTTTT
1 TTTTAATTATTTTT
40035945 GTTATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTAATTATTTTTA
Found at i:40035951 original size:18 final size:17
Alignment explanation
Indices: 40035916--40035960 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
40035906 GTGTATCAAC
40035916 TTTTAATTA--TTTTTA
1 TTTTAATTATTTTTTTA
40035931 TTTTAATTATTTTTGTTA
1 TTTTAATTATTTTT-TTA
*
40035949 TTTTATTTATTT
1 TTTTAATTATTT
40035961 AATTTTTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.35
17 3 0.12
18 14 0.54
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTAATTATTTTTTTA
Found at i:40043882 original size:29 final size:27
Alignment explanation
Indices: 40043820--40043907 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
40043810 TATTTCCATT
* *
40043820 TATATATATGTA-TTTTTTAATGTAAT-
1 TATATATATTTATTTTTTTAACG-AATG
*
40043846 TAT-TAT-TTAATTTTTTT-ACGTACATG
1 TATATATATTTATTTTTTTAACG-A-ATG
*
40043872 TATATATATTTATTTTTTTAACGAATT
1 TATATATATTTATTTTTTTAACGAATG
40043899 TATATATAT
1 TATATATAT
40043908 ATGGATATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
24 6 0.12
25 11 0.22
26 6 0.12
27 14 0.27
28 11 0.22
29 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (27 bp):
TATATATATTTATTTTTTTAACGAATG
Found at i:40044146 original size:30 final size:31
Alignment explanation
Indices: 40044106--40044175 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
40044096 ATATTATATA
* * *
40044106 TCTTCTTTTCTTTATTT-ATTTTGTTTGC-TT
1 TCTTCATTTC-TTATTTAATTGTGTTTACATT
40044136 TCTTCATTTCTTATTTAATTGTGTTTACATT
1 TCTTCATTTCTTATTTAATTGTGTTTACATT
*
40044167 TATTCATTT
1 TCTTCATTT
40044176 AATATTTTGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.18
30 18 0.53
31 10 0.29
ACGTcount: A:0.14, C:0.13, G:0.06, T:0.67
Consensus pattern (31 bp):
TCTTCATTTCTTATTTAATTGTGTTTACATT
Found at i:40044228 original size:12 final size:12
Alignment explanation
Indices: 40044199--40044236 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
40044189 TCATGGATTA
40044199 TTGTTT-TTTAT
1 TTGTTTATTTAT
40044210 TTCGTTTATTTAT
1 TT-GTTTATTTAT
40044223 TTGTTTATATTAT
1 TTGTTTAT-TTAT
40044236 T
1 T
40044237 CTATGCCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 10 0.42
13 12 0.50
ACGTcount: A:0.16, C:0.03, G:0.08, T:0.74
Consensus pattern (12 bp):
TTGTTTATTTAT
Found at i:40051373 original size:44 final size:44
Alignment explanation
Indices: 40051322--40051549 Score: 194
Period size: 44 Copynumber: 5.2 Consensus size: 44
40051312 AGATAGCAGA
* *
40051322 TCTTGCCTTCTTGTACCGACAGTGAAGCAGATCAAAGACACCAG
1 TCTTGCCTTCTTGTACTGACAGTGAAGCAGATCGAAGACACCAG
* * *** * * * * * * *
40051366 CCTTGCCTTCCTGGGTTG-CAGCGGAGCAGGTTGAAAATAGCAG
1 TCTTGCCTTCTTGTACTGACAGTGAAGCAGATCGAAGACACCAG
* *
40051409 ATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAG
1 -TCTTGCCTTCTTGTACTGACAGTGAAGCAGATCGAAGACACCAG
* * * * *
40051454 TCTTGCCTTCCTAGGT--TG-CAGTGGAGCAGATTGAAGATAGCAG
1 TCTTGCCTT-CT-TGTACTGACAGTGAAGCAGATCGAAGACACCAG
*
40051497 ATCTTGCCTTCTTGTACTGACAGTGAAGTAGATCGAAGACACCAG
1 -TCTTGCCTTCTTGTACTGACAGTGAAGCAGATCGAAGACACCAG
40051542 TCTTGCCT
1 TCTTGCCT
40051550 CCCTAGGTTA
Statistics
Matches: 139, Mismatches: 37, Indels: 16
0.72 0.19 0.08
Matches are distributed among these distances:
42 2 0.01
43 39 0.28
44 56 0.40
45 40 0.29
46 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (44 bp):
TCTTGCCTTCTTGTACTGACAGTGAAGCAGATCGAAGACACCAG
Found at i:40051767 original size:44 final size:44
Alignment explanation
Indices: 40051719--40051862 Score: 123
Period size: 44 Copynumber: 3.3 Consensus size: 44
40051709 AGGCACCAGC
*
40051719 CTTGCCTCCCTGGGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGAGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
* ** * * * * * * *
40051763 CTTGCCTTCCTGCA-CCGACAGCGAAGCAGATCT-AAGACACCA-AC
1 CTTGCCTCCCTG-AGTTG-TAGCGGAGCAGGT-TAAAAATAGCAGAT
*
40051807 CTTGCCTCCCTGAGTTGTTGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGAGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
*
40051851 CTTGCCTTCCTG
1 CTTGCCTCCCTG
40051863 TACCAGCAAC
Statistics
Matches: 71, Mismatches: 23, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
42 1 0.01
43 16 0.23
44 37 0.52
45 16 0.23
46 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (44 bp):
CTTGCCTCCCTGAGTTGTAGCGGAGCAGGTTAAAAATAGCAGAT
Found at i:40052212 original size:44 final size:44
Alignment explanation
Indices: 40051983--40052205 Score: 138
Period size: 44 Copynumber: 5.1 Consensus size: 44
40051973 AGACACTAGC
* * *
40051983 CTTGCCTCCCTCGGTGGCAGCGGAGCAGGTTAAAGATAGCAAAT
1 CTTGCCTTCCTCGGTGGCAGCAGAGCAGGTTAAAGATAGCAGAT
* * * * * * *
40052027 CTTGCCTT-CT-GGT-ACTAACAATGAAGCTGATTGAAGACA-CTAG-C
1 CTTGCCTTCCTCGGTGGC-AGC-A-G-AGCAGGTTAAAGATAGC-AGAT
* * *
40052071 CTTGACTCCCTCGGTGGCAGCGGAGCAGGTTAAAGATAGCAGAT
1 CTTGCCTTCCTCGGTGGCAGCAGAGCAGGTTAAAGATAGCAGAT
* * * * * * *
40052115 CTTGCCTTCCT-GTACTGGTAGCAAAGCAGATTGAAGACA-CTAG-C
1 CTTGCCTTCCTCG--GTGGCAGCAGAGCAGGTTAAAGATAGC-AGAT
40052159 CTTGCCTTCCTCGGTGGCAGCAGAGCAGGTTAAAGATAGCAGAT
1 CTTGCCTTCCTCGGTGGCAGCAGAGCAGGTTAAAGATAGCAGAT
40052203 CTT
1 CTT
40052206 ATCTTCCCAT
Statistics
Matches: 126, Mismatches: 37, Indels: 32
0.65 0.19 0.16
Matches are distributed among these distances:
41 1 0.01
42 5 0.04
43 37 0.29
44 42 0.33
45 35 0.28
46 5 0.04
47 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (44 bp):
CTTGCCTTCCTCGGTGGCAGCAGAGCAGGTTAAAGATAGCAGAT
Found at i:40052212 original size:88 final size:88
Alignment explanation
Indices: 40051311--40052205 Score: 974
Period size: 88 Copynumber: 10.2 Consensus size: 88
40051301 CAGATCATTG
* * * * *
40051311 AAGATAGCAGATCTTGCCTTCTTGTACCGACAGTGAAGCAGATCAAAGACACCAGCCTTGCCTTC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
40051376 CTGGGTTGCAGCGGAGCAGGTTGA
66 CTGGGTTGCAGCGGAGCAGGTT-A
* *
40051400 AA-ATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCTTC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * * *
40051464 CTAGGTTGCAGTGGAGCAGATTG
66 CTGGGTTGCAGCGGAGCAGGTTA
* * * *
40051487 AAGATAGCAGATCTTGCCTTCTTGTACTGACAGTGAAGTAGATCGAAGACACCAGTCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * * * *** *
40051552 CTAGGTTACAGTGAAGCAAACTG
66 CTGGGTTGCAGCGGAGCAGGTTA
* * * * *
40051575 AAGATA-CTAGATCTTGCCTTCCTATACCGACAGTGAAGTAGATC-AAGGAGACCAGCCTTGCCT
1 AAGATAGC-AGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA-GACACCAGCCTTGCCT
*
40051638 CCCTGGGTTGCAGCGGAGCAGATTA
64 CCCTGGGTTGCAGCGGAGCAGGTTA
* * * * * ** * *
40051663 AAAATTGTAGATCTTGCCTTCCTGCACCGACAGTAAAGCAGCTCGAAGGCACCAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
*
40051728 CTGGGTTGTAGCGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* * * * *
40051751 AAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCTAAGACACCAACCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* **
40051816 CTGAGTTGTTGCGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* * * *
40051839 AAAATAGCAGATCTTGCCTTCCTGTAC-CAGCAACGAAGCAGATCAAAGACACCAGCCTTGCCTC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTC
* *
40051903 CCTGGGATGCAGCGGAGTAGGTTGA
65 CCTGGGTTGCAGCGGAGCAGGTT-A
* * * ** *
40051928 AA-ATAGCAGATCTTGCCTTCCTGTACTGAAAGTGAAGTAGATTAAAGACACTAGCCTTGCCTCC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* *
40051992 CTCGGTGGCAGCGGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
* * ** * * * *
40052015 AAGATAGCAAATCTTGCCTT-CTGGTACTAACAATGAAGCTGATTGAAGACACTAGCCTTGACTC
1 AAGATAGCAGATCTTGCCTTCCT-GTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTC
* *
40052079 CCTCGGTGGCAGCGGAGCAGGTTA
65 CCTGGGTTGCAGCGGAGCAGGTTA
** * * * *
40052103 AAGATAGCAGATCTTGCCTTCCTGTACTGGTAGCAAAGCAGATTGAAGACACTAGCCTTGCCTTC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
* * *
40052168 CTCGGTGGCAGCAGAGCAGGTTA
66 CTGGGTTGCAGCGGAGCAGGTTA
40052191 AAGATAGCAGATCTT
1 AAGATAGCAGATCTT
40052206 ATCTTCCCAT
Statistics
Matches: 704, Mismatches: 91, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
87 11 0.02
88 683 0.97
89 10 0.01
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (88 bp):
AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCC
CTGGGTTGCAGCGGAGCAGGTTA
Found at i:40052394 original size:44 final size:44
Alignment explanation
Indices: 40052297--40052412 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 44
40052287 GAAGATGGCA
* * *
40052297 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCAGAAGTTGCAGTAGAGCAGATTAAAACCCAT
* * **
40052341 AATCCTATCTCCCAGAAGTTGCAGTGGAGTGGATTAAAACCACAT
1 AATCTTATCTCCCAGAAGTTGCAGTAGAGCAGATTAAAACC-CAT
** * *
40052386 -ATCTTATCTGTCTGAAGGTGCAGTAGA
1 AATCTTATCTCCCAGAAGTTGCAGTAGA
40052413 ATAGATCACA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 56 0.97
45 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCAGAAGTTGCAGTAGAGCAGATTAAAACCCAT
Found at i:40052478 original size:45 final size:44
Alignment explanation
Indices: 40052427--40052543 Score: 153
Period size: 45 Copynumber: 2.6 Consensus size: 44
40052417 ATCACATCGG
* *
40052427 GTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTCAATAAAGCAA
1 GTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAATAAA-AAA
* * *
40052472 GTCTTATCCCCCTAAAATTGTAGTGGGGCAGACTAAATAAAAAA
1 GTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAATAAAAAA
* * *
40052516 ATCCTGTCTCCCTAAAGTTGTAGTGGAG
1 GTCTTATCTCCCTAAAGTTGTAGTGGAG
40052544 TGGATTAGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
44 24 0.39
45 37 0.61
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
GTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTAAATAAAAAA
Found at i:40053630 original size:16 final size:16
Alignment explanation
Indices: 40053609--40053641 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
40053599 GTCGATGGCC
40053609 GGTGGCCGGCGCGGGG
1 GGTGGCCGGCGCGGGG
40053625 GGTGGCCGGCGCGGGG
1 GGTGGCCGGCGCGGGG
40053641 G
1 G
40053642 ACCGATGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.70, T:0.06
Consensus pattern (16 bp):
GGTGGCCGGCGCGGGG
Found at i:40069059 original size:37 final size:36
Alignment explanation
Indices: 40069017--40069152 Score: 118
Period size: 37 Copynumber: 3.7 Consensus size: 36
40069007 GCTTCACTCG
* *
40069017 GTATAACAGTAGAATTTGATCAATTAAACATCAGTCA
1 GTATAACAGTAGAATTTGCTCAATTAAAC-TCATTCA
*
40069054 GTATAACAGTA-AGATTTGCT-ATGTTAAACTCTATTCA
1 GTATAACAGTAGA-ATTTGCTCA-ATTAAACTC-ATTCA
* * *
40069091 GTATAACAGTATG-ATTTGCTCGATTGAGCTTCATTCA
1 GTATAACAGTA-GAATTTGCTCAATTAAAC-TCATTCA
40069128 GTATAACAGTA-AGATTTGGCTCAAT
1 GTATAACAGTAGA-ATTT-GCTCAAT
40069153 AGAGCATACT
Statistics
Matches: 81, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
36 4 0.05
37 69 0.85
38 8 0.10
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (36 bp):
GTATAACAGTAGAATTTGCTCAATTAAACTCATTCA
Found at i:40093081 original size:21 final size:22
Alignment explanation
Indices: 40093027--40093081 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
40093017 AAAAGGAGAA
*
40093027 GAGAAAAATAAAAGTGAAAAAG
1 GAGAAAAAGAAAAGTGAAAAAG
* *
40093049 AAGAAAATGAAAA-TGAAAAAG
1 GAGAAAAAGAAAAGTGAAAAAG
*
40093070 GAGAAAAGGAAA
1 GAGAAAAAGAAA
40093082 GCGAGAGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (22 bp):
GAGAAAAAGAAAAGTGAAAAAG
Found at i:40101273 original size:17 final size:16
Alignment explanation
Indices: 40101242--40101275 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
40101232 AAATATTATG
40101242 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
40101258 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
40101275 A
1 A
40101276 TGCCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:40107129 original size:25 final size:25
Alignment explanation
Indices: 40107100--40107159 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
40107090 TTTTTTCAAA
40107100 AATTTAATAAGTAT-AAAATATT-AAT
1 AATTTAATAA-TATGAAAA-ATTAAAT
*
40107125 AATTTAATAATTTGAAAAATTAAAT
1 AATTTAATAATATGAAAAATTAAAT
*
40107150 AATTAAATAA
1 AATTTAATAA
40107160 AATTGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (25 bp):
AATTTAATAATATGAAAAATTAAAT
Found at i:40107133 original size:8 final size:8
Alignment explanation
Indices: 40107100--40107159 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
40107090 TTTTTTCAAA
40107100 AATTTAAT
1 AATTTAAT
*
40107108 AAGTATAA-
1 AA-TTTAAT
40107116 AATATTAAT
1 AAT-TTAAT
40107125 AATTTAAT
1 AATTTAAT
*
40107133 AATTTGAAA
1 AATTT-AAT
*
40107142 AATTAAAT
1 AATTTAAT
*
40107150 AATTAAAT
1 AATTTAAT
40107158 AA
1 AA
40107160 AATTGAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
7 1 0.02
8 29 0.67
9 13 0.30
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
AATTTAAT
Found at i:40107799 original size:16 final size:15
Alignment explanation
Indices: 40107774--40107807 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40107764 AAAGTTGATA
*
40107774 ATAATTAATATATATT
1 ATAATAAATATA-ATT
40107790 ATAATAAATATAATT
1 ATAATAAATATAATT
40107805 ATA
1 ATA
40107808 TTATCATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:40107920 original size:30 final size:30
Alignment explanation
Indices: 40107865--40107921 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40107855 GTTTCGAAAG
* *
40107865 TATTTACAAAAAGAGACATCTAATTTTTAA
1 TATTTACAAAAAGAGACACCAAATTTTTAA
40107895 TATTTACAAAAAGAG-CAGCCAAATTTT
1 TATTTACAAAAAGAGACA-CCAAATTTT
40107922 GAAAATAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (30 bp):
TATTTACAAAAAGAGACACCAAATTTTTAA
Found at i:40111625 original size:179 final size:179
Alignment explanation
Indices: 40111325--40111689 Score: 658
Period size: 179 Copynumber: 2.0 Consensus size: 179
40111315 TAGGAAATGC
* * * *
40111325 CTTCCTAGGATGATTGATACTTATTTGTCTGCTTCAAAGTCTAGAATAACAAAGTCAATAAGAGA
1 CTTCCTAGGATGATTGACACTTATTTGTCTACTTCAAAGTCTAGAATAACAAAGTCAACAAGAAA
*
40111390 AATAAATTTGTCTACACGTACCAATACGTCCTCTAGTTTTTCTTCTAGATGTGCTAAGGATCGAT
66 AATAAATTTGTCTACACGTACCAATACGTCCTCTAGTTTTCCTTCTAGATGTGCTAAGGATCGAT
40111455 CTGCTAATTGAAGCGTAACTGTAGTAGGTCTAACTTCACCTATCCCTAA
131 CTGCTAATTGAAGCGTAACTGTAGTAGGTCTAACTTCACCTATCCCTAA
* * *
40111504 CTTCCTAGGATGATTGACAGTTATTTGTCTACTTTAAAGTCTAGAATAACAAAGTCAGCAAGAAA
1 CTTCCTAGGATGATTGACACTTATTTGTCTACTTCAAAGTCTAGAATAACAAAGTCAACAAGAAA
40111569 AATAAATTTGTCTACACGTACCAATACGTCCTCTAGTTTTCCTTCTAGATGTGCTAAGGATCGAT
66 AATAAATTTGTCTACACGTACCAATACGTCCTCTAGTTTTCCTTCTAGATGTGCTAAGGATCGAT
40111634 CTGCTAATTGAAGCGTAACTGTAGTAGGTCTAACTTCACCTATCCCTAA
131 CTGCTAATTGAAGCGTAACTGTAGTAGGTCTAACTTCACCTATCCCTAA
40111683 CTTCCTA
1 CTTCCTA
40111690 AATATTTACA
Statistics
Matches: 178, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
179 178 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (179 bp):
CTTCCTAGGATGATTGACACTTATTTGTCTACTTCAAAGTCTAGAATAACAAAGTCAACAAGAAA
AATAAATTTGTCTACACGTACCAATACGTCCTCTAGTTTTCCTTCTAGATGTGCTAAGGATCGAT
CTGCTAATTGAAGCGTAACTGTAGTAGGTCTAACTTCACCTATCCCTAA
Found at i:40126628 original size:76 final size:78
Alignment explanation
Indices: 40126379--40126632 Score: 377
Period size: 78 Copynumber: 3.3 Consensus size: 78
40126369 AAAGTATATA
40126379 AATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
40126444 GTATAAGTTCTTG
66 GTATAAGTTCTTG
40126457 AATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
1 AATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
*
40126522 GTATAAGTTTTTG
66 GTATAAGTTCTTG
* * * * * * *
40126535 AATTAAATTAAAGGTATGAATTTTACATATGTATGTGTGTGATTCG-A-ATAGATGTATATACAT
1 AATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
* * *
40126598 ATACAAGTACTTG
66 GTATAAGTTCTTG
* *
40126611 AGTTGAATTAAAAGTATGAATT
1 AATTGAATTAAAGGTATGAATT
40126633 GTAAATACTT
Statistics
Matches: 161, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
76 43 0.27
77 1 0.01
78 117 0.73
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (78 bp):
AATTGAATTAAAGGTATGAATTATATATATGTATATGTGAGGTTCGAATATATATGTATATACAT
GTATAAGTTCTTG
Found at i:40127027 original size:31 final size:30
Alignment explanation
Indices: 40126991--40127233 Score: 172
Period size: 31 Copynumber: 7.6 Consensus size: 30
40126981 AATAAGTATT
*
40126991 TATATGCATTCGGTTATATACCTTTGCA-GTG
1 TATATGCATTCGATTATATA-CTTTG-ATGTG
* * *
40127022 TATATGCTTTTGATTATAAGTA-TTTGATAGATATA
1 TATATGCATTCGATTAT-A-TACTTTGAT-G---TG
*
40127057 TATATGCATTCGGTTATATACCTTTGATGTG
1 TATATGCATTCGATTATATA-CTTTGATGTG
* * *
40127088 TATATGCATTTGATTTTAAGTA-TTTGATAGGTA
1 TATATGCATTCGATTAT-A-TACTTTGAT--GTG
* *
40127121 TATATGCATTCGGTTGTATACATTTGATGTG
1 TATATGCATTCGATTATATAC-TTTGATGTG
*
40127152 TATATGCATTCGATTATAAGTA-TTGGATAGGTG
1 TATATGCATTCGATTAT-A-TACTTTGAT--GTG
40127185 TATATGCATTCGAATGTATATA-TTTGATGTG
1 TATATGCATTCG-AT-TATATACTTTGATGTG
40127216 TATATGCATTCGATTATA
1 TATATGCATTCGATTATA
40127234 AGTAGTTGAT
Statistics
Matches: 171, Mismatches: 20, Indels: 44
0.73 0.09 0.19
Matches are distributed among these distances:
29 4 0.02
30 3 0.02
31 78 0.46
32 5 0.03
33 52 0.30
34 5 0.03
35 24 0.14
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.45
Consensus pattern (30 bp):
TATATGCATTCGATTATATACTTTGATGTG
Found at i:40127156 original size:64 final size:65
Alignment explanation
Indices: 40126976--40127286 Score: 369
Period size: 64 Copynumber: 4.8 Consensus size: 65
40126966 TATTATATCT
* * * * *
40126976 TATTTAATAAGTATTTATATGCATTCGGTTATATACCTTTGCA-GTGTATATGCTTTTGATTATA
1 TATTTGAT-AGTATATATATGCATTCGGTTATATACATTTG-ATGTGTATATGCATTCGATTATA
40127040 AG
64 AG
* * *
40127042 TATTTGATAGATATATATATGCATTCGGTTATATACCTTTGATGTGTATATGCATTTGATTTTAA
1 TATTTGATAG-TATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAA
40127107 G
65 G
* *
40127108 TATTTGATAG-GTATATATGCATTCGGTTGTATACATTTGATGTGTATATGCATTCGATTATAAG
1 TATTTGATAGTATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAAG
* * * ** * *
40127172 TATTGGATAG-GTGTATATGCATTCGAATGTATATATTTGATGTGTATATGCATTCGATTATAAG
1 TATTTGATAGTATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAAG
* * *
40127236 TAGTTGATTAGTATATATATGCATTCGGTTATA-ATTATTTGATGAGTATAT
1 TATTTGA-TAGTATATATATGCATTCGGTTATATA-CATTTGATGTGTATAT
40127287 ACATACATTT
Statistics
Matches: 218, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
64 113 0.52
65 7 0.03
66 98 0.45
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.45
Consensus pattern (65 bp):
TATTTGATAGTATATATATGCATTCGGTTATATACATTTGATGTGTATATGCATTCGATTATAAG
Found at i:40127204 original size:16 final size:17
Alignment explanation
Indices: 40127121--40127229 Score: 65
Period size: 14 Copynumber: 6.8 Consensus size: 17
40127111 TTGATAGGTA
*
40127121 TATATGCATTCGGT-TG
1 TATATGCATTCGATATG
* *
40127137 TATA--CATTTGATGTG
1 TATATGCATTCGATATG
40127152 TATATGCATTCG--AT-
1 TATATGCATTCGATATG
* * *
40127166 TATAAGTATTGGATAGGTG
1 TATATGCATTCGATA--TG
40127185 TATATGCATTCGA-ATG
1 TATATGCATTCGATATG
* *
40127201 TATAT--ATTTGATGTG
1 TATATGCATTCGATATG
40127216 TATATGCATTCGAT
1 TATATGCATTCGAT
40127230 TATAAGTAGT
Statistics
Matches: 69, Mismatches: 13, Indels: 21
0.67 0.13 0.20
Matches are distributed among these distances:
14 20 0.29
15 14 0.20
16 12 0.17
17 11 0.16
18 2 0.03
19 10 0.14
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (17 bp):
TATATGCATTCGATATG
Found at i:40127243 original size:31 final size:32
Alignment explanation
Indices: 40127018--40127287 Score: 214
Period size: 31 Copynumber: 8.2 Consensus size: 32
40127008 ATACCTTTGC
* *
40127018 AGTGTATATGCTTTTGATTATAAGTATTTGAT
1 AGTGTATATGCATTCGATTATAAGTATTTGAT
* *
40127050 AGATATATATATGCATTCGGTTAT-A-TACCTTTGAT
1 AG---TGTATATGCATTCGATTATAAGTA--TTTGAT
* *
40127085 -GTGTATATGCATTTGATTTTAAGTATTTGAT
1 AGTGTATATGCATTCGATTATAAGTATTTGAT
* * * *
40127116 AGGTATATATGCATTCGGTTGTATA-CATTTGAT
1 A-GTGTATATGCATTCGATTATA-AGTATTTGAT
*
40127149 -GTGTATATGCATTCGATTATAAGTATTGGAT
1 AGTGTATATGCATTCGATTATAAGTATTTGAT
40127180 AGGTGTATATGCATTCGAATGTAT-A-TATTTGAT
1 A-GTGTATATGCATTCG-AT-TATAAGTATTTGAT
*
40127213 -GTGTATATGCATTCGATTATAAGTAGTTGATT
1 AGTGTATATGCATTCGATTATAAGTATTTGA-T
* * *
40127245 AGTATATATATGCATTCGGTTATAATTATTTGAT
1 AG--TGTATATGCATTCGATTATAAGTATTTGAT
*
40127279 GAGTATATA
1 -AGTGTATA
40127288 CATACATTTG
Statistics
Matches: 192, Mismatches: 24, Indels: 43
0.74 0.09 0.17
Matches are distributed among these distances:
29 3 0.02
30 4 0.02
31 66 0.34
32 4 0.02
33 57 0.30
34 7 0.04
35 51 0.27
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (32 bp):
AGTGTATATGCATTCGATTATAAGTATTTGAT
Found at i:40132265 original size:132 final size:132
Alignment explanation
Indices: 40132037--40132280 Score: 337
Period size: 132 Copynumber: 1.8 Consensus size: 132
40132027 CTATGCTCTC
* * *
40132037 AGCTGAGGTTTAAAGGTGAGATGAGTTGTACTCACAACCTTCATTTATTTGAGTAAGCTAAGTTA
1 AGCTGAGGTTTAAAGGTGAGATGAATTATACTCACAACCTTCATTTATTTCAGTAAGCTAAGTTA
* *
40132102 AGCTCACTACTTCAGAACAACTCATGGACCTAAGCTCCCAACTGACAACTTGAGGACCTACGCTC
66 AGCTCACTACTTCAGAACAACTCACGAACCTAAGCTCCCAACTGACAACTTGAGGACCTACGCTC
40132167 CA
131 CA
* * * * *
40132169 AGCTGATGTTTAAAGGTTAGATGAATTATACTTACAACCTTCATTTATTTCAGTAAGTTGAGTTA
1 AGCTGAGGTTTAAAGGTGAGATGAATTATACTCACAACCTTCATTTATTTCAGTAAGCTAAGTTA
* * * * *
40132234 AGCTCACTAC-TCTGGGACAACTCGCGAACCTACGCTCTCAACTGACA
66 AGCTCACTACTTC-AGAACAACTCACGAACCTAAGCTCCCAACTGACA
40132281 GCTCATGGAC
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
131 2 0.02
132 94 0.98
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (132 bp):
AGCTGAGGTTTAAAGGTGAGATGAATTATACTCACAACCTTCATTTATTTCAGTAAGCTAAGTTA
AGCTCACTACTTCAGAACAACTCACGAACCTAAGCTCCCAACTGACAACTTGAGGACCTACGCTC
CA
Found at i:40132476 original size:28 final size:28
Alignment explanation
Indices: 40132422--40132476 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
40132412 ACTCCGAAAT
* * * *
40132422 AGCTCGCGGACCTATGCTCTCAGCTGAC
1 AGCTCACGAACCTACGCTCTCAACTGAC
*
40132450 AGCTCACGAACCTACGCTCTTAACTGA
1 AGCTCACGAACCTACGCTCTCAACTGA
40132477 TAAACTTCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.22
Consensus pattern (28 bp):
AGCTCACGAACCTACGCTCTCAACTGAC
Found at i:40132480 original size:171 final size:171
Alignment explanation
Indices: 40132156--40132486 Score: 425
Period size: 170 Copynumber: 1.9 Consensus size: 171
40132146 ACAACTTGAG
*
40132156 GACCTACGCTCCAAGCTGATGTTTAAAGGTTAGATGAATTATACTTACAACCTTCATTTATTTCA
1 GACCTACGCTCCAAGCTGATGTTTAAAGGTTAGATGAATTATACTCACAACCTTCATTTATTTCA
* * **
40132221 GTAAGTTGAGTTAAGCTCACTACTCTGGGACAACTCGCGAACCTACGCTCTCAACTGACAGCTCA
66 GTAAGCTGAGTTAAGCTCACTACTCCGAAACAACTCGCGAACCTACGCTCTCAACTGACAGCTCA
* * * *
40132286 TGGACCTACATTTCTATTGATAAACTTCAACACAGCCCACC
131 CGAACCTACATTTCAACTGATAAACTTCAACACAGCCCACC
* * * *
40132327 GACCTACGCTCCCAGCTGATGTTTAATGGTTAGATGAGTTATACTCACAACCTT-ATTTATTTGA
1 GACCTACGCTCCAAGCTGATGTTTAAAGGTTAGATGAATTATACTCACAACCTTCATTTATTTCA
* * * * * * *
40132391 GTAAGCTGTGTTAAGC-CTGCTACTCCGAAATAGCTCGCGGACCTATGCTCTCAGCTGACAGCTC
66 GTAAGCTGAGTTAAGCTC-ACTACTCCGAAACAACTCGCGAACCTACGCTCTCAACTGACAGCTC
*
40132455 ACGAACCTACGCTCTT-AACTGATAAACTTCAA
130 ACGAACCTAC-AT-TTCAACTGATAAACTTCAA
40132487 TGCAGCTCGT
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
169 1 0.01
170 68 0.50
171 65 0.48
172 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (171 bp):
GACCTACGCTCCAAGCTGATGTTTAAAGGTTAGATGAATTATACTCACAACCTTCATTTATTTCA
GTAAGCTGAGTTAAGCTCACTACTCCGAAACAACTCGCGAACCTACGCTCTCAACTGACAGCTCA
CGAACCTACATTTCAACTGATAAACTTCAACACAGCCCACC
Found at i:40137181 original size:34 final size:34
Alignment explanation
Indices: 40137138--40137202 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
40137128 ACACTTTATA
*
40137138 ATTTAACTCAACTAAACTTAACCCAACCCAAATT
1 ATTTAACTCAACTAAACTCAACCCAACCCAAATT
*
40137172 ATTTAACTCAACTAAACTCAACTCAACCCAA
1 ATTTAACTCAACTAAACTCAACCCAACCCAA
40137203 CCCAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.25
Consensus pattern (34 bp):
ATTTAACTCAACTAAACTCAACCCAACCCAAATT
Found at i:40146611 original size:59 final size:59
Alignment explanation
Indices: 40146542--40146846 Score: 287
Period size: 59 Copynumber: 5.3 Consensus size: 59
40146532 TATTGTCGGG
*
40146542 ATTACCAGTCCATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
1 ATTACCAGTCCAGGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
* * * * * * ***
40146601 ATTACCAGTCCAGGCTAAATCCCCTGTAA-TATAA--AC-C-CATAGAG-TATTG-TCGGG
1 ATTACCAGTCCAGGCTAAATCTCCTGCAACGAAAATTACTCTAAT-GAGCT-TGGATCTAA
*
40146655 ATTACCAGTCCATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
1 ATTACCAGTCCAGGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
* * * * * * ***
40146714 ATTACCAGTCCAGGCTAAATCCCCTGTAA-TATAA--AC-C-CATAGAG-TATTG-TCGGG
1 ATTACCAGTCCAGGCTAAATCTCCTGCAACGAAAATTACTCTAAT-GAGCT-TGGATCTAA
*
40146768 ATTACCAGTCCATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
1 ATTACCAGTCCAGGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
40146827 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
40146847 TCAGACCCTA
Statistics
Matches: 187, Mismatches: 41, Indels: 36
0.71 0.16 0.14
Matches are distributed among these distances:
54 62 0.33
55 18 0.10
56 4 0.02
57 4 0.02
58 18 0.10
59 81 0.43
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (59 bp):
ATTACCAGTCCAGGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
Found at i:40146672 original size:54 final size:54
Alignment explanation
Indices: 40146484--40146793 Score: 268
Period size: 54 Copynumber: 5.6 Consensus size: 54
40146474 ATCCTTACAG
40146484 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGT
* * * * * * *
40146538 CGGGATTACCAGTCCATGCTAAATCTCCTGCAACGAAAATTACTC-TAATGAGCT-TGGAT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAA-TATAA--ACCCAT-A-GAG-TATTG-T
***
40146597 CTAAATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGT
* * * * * * *
40146651 CGGGATTACCAGTCCATGCTAAATCTCCTGCAACGAAAATTACTC-TAATGAGCT-TGGAT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAA-TATAA--ACCCAT-A-GAG-TATTG-T
***
40146710 CTAAATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGT
* *
40146764 CGGGATTACCAGTCCATGCTAAATCTCCTG
1 CGGGATTACCAGTCCAGGCTAAATCCCCTG
40146794 CAACGAAAAT
Statistics
Matches: 196, Mismatches: 42, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
54 86 0.44
55 16 0.08
56 10 0.05
57 10 0.05
58 16 0.08
59 58 0.30
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.27
Consensus pattern (54 bp):
CGGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGT
Found at i:40146686 original size:113 final size:113
Alignment explanation
Indices: 40146488--40146846 Score: 718
Period size: 113 Copynumber: 3.2 Consensus size: 113
40146478 TTACAGCGGG
40146488 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGTCGGGATTACCAGTCC
1 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGTCGGGATTACCAGTCC
40146553 ATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
66 ATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
40146601 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGTCGGGATTACCAGTCC
1 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGTCGGGATTACCAGTCC
40146666 ATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
66 ATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
40146714 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGTCGGGATTACCAGTCC
1 ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGTCGGGATTACCAGTCC
40146779 ATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
66 ATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
40146827 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
40146847 TCAGACCCTA
Statistics
Matches: 246, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 246 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (113 bp):
ATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACCCATAGAGTATTGTCGGGATTACCAGTCC
ATGCTAAATCTCCTGCAACGAAAATTACTCTAATGAGCTTGGATCTAA
Found at i:40149598 original size:27 final size:27
Alignment explanation
Indices: 40149557--40149608 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40149547 GATTTTATTT
* *
40149557 AGTCTCAATTTCTAGAAGGTCGTGGGC
1 AGTCCCAATTCCTAGAAGGTCGTGGGC
* *
40149584 AGTCCCAATTCCTAGAGGGTTGTGG
1 AGTCCCAATTCCTAGAAGGTCGTGG
40149609 ATATATACTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (27 bp):
AGTCCCAATTCCTAGAAGGTCGTGGGC
Found at i:40159516 original size:30 final size:28
Alignment explanation
Indices: 40159482--40159537 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
40159472 GTGATTAAAT
40159482 AAAATCGACA-CAAGCAGAATTTAAAAGAAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAAA
*
40159512 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
40159538 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 10 0.42
31 4 0.17
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (28 bp):
AAAATCGACAGCAAGAAATTAAAAGAAA
Found at i:40165370 original size:20 final size:19
Alignment explanation
Indices: 40165326--40165380 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
40165316 ATTGTGGAAT
*
40165326 CAAAGGCACCAAAGTGCAA
1 CAAAGGCACCGAAGTGCAA
*
40165345 -ATAAGGACACCGAAGTGTAA
1 CA-AAGG-CACCGAAGTGCAA
*
40165365 CAAAGGCACTGAAGTG
1 CAAAGGCACCGAAGTG
40165381 AAAACCCGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.03
19 13 0.43
20 15 0.50
21 1 0.03
ACGTcount: A:0.44, C:0.20, G:0.25, T:0.11
Consensus pattern (19 bp):
CAAAGGCACCGAAGTGCAA
Found at i:40175339 original size:240 final size:241
Alignment explanation
Indices: 40174916--40175401 Score: 857
Period size: 240 Copynumber: 2.0 Consensus size: 241
40174906 ATGAATTAAT
40174916 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAACTGACATTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAACTGACATTCTCTCCAACCTT
*
40174981 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACAGGTTGCCTTATATCGAG
* *
40175046 TTGTAAGATATAATGGATCCTTCCTAGGTGTAACAACGCCACGCATGATGAATCTT-AAAAATTC
131 GTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGCATGATGAATCTTAAAAAATTC
*
40175110 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTATATCGAGCTCATTTACTATTGAATA
* * *
40175156 TTTATTACCATGTAGCTTGCTTGTTCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAACTGACATTCTCTCCAACCTT
* *
40175221 ATTTTAAATATTTTAAAGATTCGAAGTATATAGGCTGGAAATCTGACAGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACAGGTTGCCTTATATCGAG
*
40175286 GTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 GTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGCATGATGAATCTTAAAAAATTC
* *
40175351 AAAAAGACTTGGAAAAAGTTATATCGATCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTATATCGAGCTCATTTACTATTGAATA
40175397 TTTAT
1 TTTAT
40175402 ATAACCTTAA
Statistics
Matches: 233, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
240 177 0.76
241 56 0.24
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAACTGACATTCTCTCCAACCTT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACAGGTTGCCTTATATCGAG
GTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGCATGATGAATCTTAAAAAATTC
AAAAAGACTTGAAAAAAGTTATATCGAGCTCATTTACTATTGAATA
Found at i:40175626 original size:9 final size:9
Alignment explanation
Indices: 40175581--40175747 Score: 127
Period size: 9 Copynumber: 17.6 Consensus size: 9
40175571 ATTGATCATT
*
40175581 ACTTAAATA
1 ACTTACATA
*
40175590 AATTACATA
1 ACTTACATA
* *
40175599 ACTTAAAAA
1 ACTTACATA
* *
40175608 ACTCATATA
1 ACTTACATA
*
40175617 ACCTACATA
1 ACTTACATA
*
40175626 ATTTACATA
1 ACTTACATA
40175635 ACAATTTACATA
1 AC---TTACATA
*
40175647 ACTCACATA
1 ACTTACATA
40175656 ACTTACATA
1 ACTTACATA
*
40175665 ATTTACATAACA
1 ACTTACAT---A
40175677 ACTTACATA
1 ACTTACATA
*
40175686 ACTCACATA
1 ACTTACATA
40175695 ACTTACATA
1 ACTTACATA
*
40175704 ATTTACATA
1 ACTTACATA
*
40175713 ACTCACATA
1 ACTTACATA
*
40175722 ACGTACATAACA
1 ACTTACAT---A
40175734 ACTTACATA
1 ACTTACATA
40175743 ACTTA
1 ACTTA
40175748 ACTAATACAT
Statistics
Matches: 123, Mismatches: 26, Indels: 18
0.74 0.16 0.11
Matches are distributed among these distances:
9 98 0.80
12 25 0.20
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:40175657 original size:39 final size:39
Alignment explanation
Indices: 40175598--40175714 Score: 189
Period size: 39 Copynumber: 3.0 Consensus size: 39
40175588 TAAATTACAT
* * * *
40175598 AACTTAAAAAACTCATATAACCTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
*
40175637 AATTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
40175676 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
40175715 TCACATAACG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:40175743 original size:39 final size:37
Alignment explanation
Indices: 40175581--40175732 Score: 148
Period size: 39 Copynumber: 4.1 Consensus size: 37
40175571 ATTGATCATT
* * * * * *
40175581 ACTTAAATAAATTACAT-AACTTAAAAAACTCATATA
1 ACTTACATAATTTACATAAACTCACATAACTCACATA
* * *
40175617 ACCTACATAATTTACATAACAATTTACATAACTCACATA
1 ACTTACATAATTTACAT-A-AACTCACATAACTCACATA
*
40175656 ACTTACATAATTTACATAACAACTTACATAACTCACATA
1 ACTTACATAATTTACAT-A-AACTCACATAACTCACATA
40175695 ACTTACATAATTTACAT-AACTCACATAACGT-ACATA
1 ACTTACATAATTTACATAAACTCACATAAC-TCACATA
40175731 AC
1 AC
40175733 AACTTACATA
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
36 32 0.31
37 1 0.01
39 69 0.68
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.30
Consensus pattern (37 bp):
ACTTACATAATTTACATAAACTCACATAACTCACATA
Found at i:40181320 original size:21 final size:21
Alignment explanation
Indices: 40181296--40181336 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40181286 ACTTAGAGCG
40181296 GAGGCAGCAACGAGGGAGGCA
1 GAGGCAGCAACGAGGGAGGCA
**
40181317 GAGGCAGCAGTGAGGGAGGC
1 GAGGCAGCAACGAGGGAGGC
40181337 GGAGCAGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.51, T:0.02
Consensus pattern (21 bp):
GAGGCAGCAACGAGGGAGGCA
Found at i:40181727 original size:43 final size:43
Alignment explanation
Indices: 40181634--40181740 Score: 160
Period size: 43 Copynumber: 2.5 Consensus size: 43
40181624 ACTGGGCAAA
* * *
40181634 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGATCCTGGTCT
1 TTAGCGGTGTTTTTTGAAGAAGCGCCGCTAAAGATCCTGGTCT
* *
40181677 ATAGCGGTGTTTTTTGAAGAAGCGCCGCTAAAGGTCCTGGTCT
1 TTAGCGGTGTTTTTTGAAGAAGCGCCGCTAAAGATCCTGGTCT
*
40181720 TTAGCGGTATTTTTTGAAGAA
1 TTAGCGGTGTTTTTTGAAGAA
40181741 ACATGATGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
TTAGCGGTGTTTTTTGAAGAAGCGCCGCTAAAGATCCTGGTCT
Found at i:40183296 original size:28 final size:28
Alignment explanation
Indices: 40183258--40183325 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
40183248 CCGTGTGCAA
40183258 TTTTGAAGAAGCAGTCTTTAGCGGCGTT
1 TTTTGAAGAAGCAGTCTTTAGCGGCGTT
40183286 TTTTGAAGAAGCAGTCTTTAGCGGCGTT
1 TTTTGAAGAAGCAGTCTTTAGCGGCGTT
*
40183314 TTTTGTAGAAGC
1 TTTTGAAGAAGC
40183326 GCCGCTAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (28 bp):
TTTTGAAGAAGCAGTCTTTAGCGGCGTT
Found at i:40183364 original size:43 final size:43
Alignment explanation
Indices: 40183299--40183661 Score: 627
Period size: 43 Copynumber: 8.4 Consensus size: 43
40183289 TGAAGAAGCA
40183299 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
* * *
40183342 GTCTTTAGCGGCATTTTATGTAGAAGCGCCGCTAAAGGTCATG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
40183385 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
* * *
40183428 GTCTTTAGCGGCATTTTATGTAGAAGCGCCGCTAAAGGTCATG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
40183471 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
* * *
40183514 GTCTTTAGCGGCATTTTATGTAGAAGCGCCGCTAAAGGTCATG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
40183557 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
* *
40183600 GTCTTTAGCGGCGTTTTTTATAGAAGCACCGCTAAAGGTCCTG
1 GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
40183643 GTCTTTAGCGGCGTTTTTT
1 GTCTTTAGCGGCGTTTTTT
40183662 CTGAAAAACG
Statistics
Matches: 300, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 300 1.00
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.33
Consensus pattern (43 bp):
GTCTTTAGCGGCGTTTTTTGTAGAAGCGCCGCTAAAGGTCCTG
Found at i:40189988 original size:20 final size:19
Alignment explanation
Indices: 40189958--40190041 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
40189948 GATGTTAGAA
40189958 TATTAATTCTATTATATATT
1 TATT-ATTCTATTATATATT
40189978 TATCTATTCTATTATATA--
1 TAT-TATTCTATTATATATT
*
40189996 TA-TATTCTAATATATATT
1 TATTATTCTATTATATATT
40190014 AGTATTATT-T-TTATATTATT
1 --TATTATTCTATTATA-TATT
40190034 TATCTATT
1 TAT-TATT
40190042 TCTTATCTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 13 0.24
18 5 0.09
19 8 0.15
20 23 0.43
21 5 0.09
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (19 bp):
TATTATTCTATTATATATT
Found at i:40190003 original size:16 final size:17
Alignment explanation
Indices: 40189963--40190012 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 17
40189953 TAGAATATTA
40189963 ATTCTATTATATATTTATCT
1 ATTCTATTATATA--TA-CT
40189983 ATTCTATTATATATA-T
1 ATTCTATTATATATACT
*
40189999 ATTCTAATATATAT
1 ATTCTATTATATAT
40190013 TAGTATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.48
18 2 0.07
20 13 0.45
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTCTATTATATATACT
Found at i:40191767 original size:18 final size:18
Alignment explanation
Indices: 40191746--40191782 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40191736 AATTCGACGC
* *
40191746 AGTGGATAAATTAGATAA
1 AGTGGAAAAATGAGATAA
40191764 AGTGGAAAAATGAGATAA
1 AGTGGAAAAATGAGATAA
40191782 A
1 A
40191783 CCAGCTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (18 bp):
AGTGGAAAAATGAGATAA
Found at i:40194646 original size:17 final size:17
Alignment explanation
Indices: 40194624--40194657 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40194614 ATAGACTCGC
*
40194624 TTAGATATACTTAGTAT
1 TTAGATATAATTAGTAT
40194641 TTAGATATAATTAGTAT
1 TTAGATATAATTAGTAT
40194658 AATATACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGATATAATTAGTAT
Found at i:40195045 original size:81 final size:81
Alignment explanation
Indices: 40194906--40195067 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
40194896 TATTTTTTTT
40194906 TCAAGACTTAGATGTCATGGATACCTATTTAGTAAAATATTGTAGAACATCCGACTTACCCGAAC
1 TCAAGACTTAGATGTCATGGATACCTATTTAGTAAAATATTGTAGAACATCCGACTTACCCGAAC
40194971 CGAACATAAATGAAAA
66 CGAACATAAATGAAAA
*
40194987 TCAAGACTTAGATGTCATGGATACCTATTTAGTAAAATATTGTAGAACATCCGGCTTACCCGAAC
1 TCAAGACTTAGATGTCATGGATACCTATTTAGTAAAATATTGTAGAACATCCGACTTACCCGAAC
40195052 CGAACATAAATGAAAA
66 CGAACATAAATGAAAA
40195068 AGCCCCTCTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAAGACTTAGATGTCATGGATACCTATTTAGTAAAATATTGTAGAACATCCGACTTACCCGAAC
CGAACATAAATGAAAA
Found at i:40199733 original size:17 final size:17
Alignment explanation
Indices: 40199713--40199746 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40199703 TTCGTATATT
*
40199713 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
40199730 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
40199747 GCGAGTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:40220865 original size:12 final size:13
Alignment explanation
Indices: 40220843--40220872 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
40220833 ATAAATTTAC
40220843 AAAAAACAAAAAT
1 AAAAAACAAAAAT
40220856 AAAAAA-AAAAAT
1 AAAAAACAAAAAT
40220868 AAAAA
1 AAAAA
40220873 GGGTAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAAACAAAAAT
Found at i:40222003 original size:3 final size:3
Alignment explanation
Indices: 40221990--40222019 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
40221980 GTTGGGGGAT
*
40221990 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
40222020 GGGTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:40222752 original size:16 final size:13
Alignment explanation
Indices: 40222721--40222758 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
40222711 ATATTAAGAA
40222721 TATTATTTTTAAT
1 TATTATTTTTAAT
40222734 TATTATTTTTGAAT
1 TATTATTTTT-AAT
*
40222748 T-TTATTATTAA
1 TATTATTTTTAA
40222759 AATAAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 2 0.09
13 17 0.74
14 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
TATTATTTTTAAT
Found at i:40233233 original size:33 final size:33
Alignment explanation
Indices: 40233173--40233246 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
40233163 AACTTAAGTT
* * * *
40233173 GGGAGGAGTGGAGTACTGCGATTGATACGGGTC
1 GGGAGGAGTAGAGTACGGCGATGGATACGGGCC
* *
40233206 GGGAGGAGTAGAGTACGGTGGTGGATACGGGCC
1 GGGAGGAGTAGAGTACGGCGATGGATACGGGCC
*
40233239 GGAAGGAG
1 GGGAGGAG
40233247 CGGAGCACTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.23, C:0.11, G:0.50, T:0.16
Consensus pattern (33 bp):
GGGAGGAGTAGAGTACGGCGATGGATACGGGCC
Found at i:40235954 original size:21 final size:21
Alignment explanation
Indices: 40235928--40235973 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
40235918 CTTGGGGGAG
40235928 GGGCAGCTGGGTTTACTGTTC
1 GGGCAGCTGGGTTTACTGTTC
40235949 GGGCAGCTGGGTTTACTGTTC
1 GGGCAGCTGGGTTTACTGTTC
40235970 GGGC
1 GGGC
40235974 TGCCCATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.09, C:0.20, G:0.41, T:0.30
Consensus pattern (21 bp):
GGGCAGCTGGGTTTACTGTTC
Done.