Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 30 of 128
Found at i:9066894 original size:126 final size:127
Alignment explanation
Indices: 9066669--9066922 Score: 501
Period size: 126 Copynumber: 2.0 Consensus size: 127
9066659 TTTTTCTTTG
9066669 CCGACGCTTCCTAGGTAAACGTCATCCTTCCTATTATGAAAAAGTTTATTTATATTAATATTTTT
1 CCGACGCTTCCTAGGTAAACGTCATCCTTCCTATTATGAAAAAGTTTATTTATATTAATATTTTT
9066734 ATTTTTTATAATATTTTTAATATATTAAATCGTTTCAATTTGAGATACTAAA-TTATTAAAT
66 ATTTTTTATAATATTTTTAATATATTAAATCGTTTCAATTTGAGATACTAAATTTATTAAAT
9066795 CCGACGCTTCCTAGGTAAACGTCATCCTTCCTATTATGAAAAAGTTTATTTATATTAATATTTTT
1 CCGACGCTTCCTAGGTAAACGTCATCCTTCCTATTATGAAAAAGTTTATTTATATTAATATTTTT
9066860 ATTTTTTATAATATTTTTAATATATTAAATCGTTTCAATTTGAGATACTAAATTTATTAAAT
66 ATTTTTTATAATATTTTTAATATATTAAATCGTTTCAATTTGAGATACTAAATTTATTAAAT
9066922 C
1 C
9066923 TTTTAAAACT
Statistics
Matches: 127, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
126 117 0.92
127 10 0.08
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (127 bp):
CCGACGCTTCCTAGGTAAACGTCATCCTTCCTATTATGAAAAAGTTTATTTATATTAATATTTTT
ATTTTTTATAATATTTTTAATATATTAAATCGTTTCAATTTGAGATACTAAATTTATTAAAT
Found at i:9067999 original size:29 final size:29
Alignment explanation
Indices: 9067931--9068003 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
9067921 TATAGCAAAC
*
9067931 ATATTATTTTCATAATTAATTTATTCTTT
1 ATATTATTTTCATAATTAATTAATTCTTT
** ** *
9067960 ACCTTATTTTTGTAATTAATTAATTTTTT
1 ATATTATTTTCATAATTAATTAATTCTTT
9067989 AATATTATTTT-ATAA
1 -ATATTATTTTCATAA
9068004 AAAATACAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 26 0.76
30 8 0.24
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.60
Consensus pattern (29 bp):
ATATTATTTTCATAATTAATTAATTCTTT
Found at i:9069101 original size:22 final size:23
Alignment explanation
Indices: 9069073--9069123 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
9069063 TATTTTTTAA
9069073 TTTTAAAATA-ATTTTAAAATTT
1 TTTTAAAATACATTTTAAAATTT
*
9069095 TTTTAAAATACTTTTTAAAATTT
1 TTTTAAAATACATTTTAAAATTT
9069118 TTTTAA
1 TTTTAA
9069124 TTTTAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTAAAATACATTTTAAAATTT
Found at i:9069111 original size:12 final size:11
Alignment explanation
Indices: 9069073--9069149 Score: 67
Period size: 11 Copynumber: 7.4 Consensus size: 11
9069063 TATTTTTTAA
*
9069073 TTTTAAAATAA
1 TTTTAAAATAT
*
9069084 TTTTAAAATTT
1 TTTTAAAATAT
9069095 TTTTAAAATACT
1 TTTTAAAATA-T
9069107 TTTTAAAAT-T
1 TTTTAAAATAT
*
9069117 TTTT----TAA
1 TTTTAAAATAT
9069124 TTTTAAAATA-
1 TTTTAAAATAT
9069134 TTTTAAAATACT
1 TTTTAAAATA-T
9069146 TTTT
1 TTTT
9069150 TTAATTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
10 15 0.28
11 20 0.37
12 14 0.26
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:9069150 original size:40 final size:42
Alignment explanation
Indices: 9069081--9069173 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
9069071 AATTTTAAAA
*
9069081 TAATTTTAAAATTTTTTTAAAATAC-TTTTTAAAATTT-TTT
1 TAATTTTAAAATTATTTTAAAATACTTTTTTAAAATTTATTT
**
9069121 TAATTTTAAAA-TATTTTAAAATACTTTTTTTAATTTTTATTT
1 TAATTTTAAAATTATTTTAAAATAC-TTTTTTAAAATTTATTT
9069163 TAATTTTAAAA
1 TAATTTTAAAA
9069174 ATAAATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
39 12 0.26
40 11 0.23
41 10 0.21
42 14 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (42 bp):
TAATTTTAAAATTATTTTAAAATACTTTTTTAAAATTTATTT
Found at i:9071732 original size:24 final size:23
Alignment explanation
Indices: 9071684--9071732 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
9071674 CGGCCTCCCT
**
9071684 AAAATTAGAATTTTAAAATTTTA
1 AAAATTAGAATTTTAAAATGGTA
9071707 AAAATATA-AATTATTAAAATGGTA
1 AAAAT-TAGAATT-TTAAAATGGTA
9071731 AA
1 AA
9071733 TTACATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (23 bp):
AAAATTAGAATTTTAAAATGGTA
Found at i:9075067 original size:21 final size:21
Alignment explanation
Indices: 9075040--9075093 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
9075030 CCGCCATTTC
*
9075040 TAATCTCACTGTTACAGT-AT
1 TAATCTCACTGCTACAGTAAT
**
9075060 TCAATCTCACCACTACAGTAAT
1 T-AATCTCACTGCTACAGTAAT
9075082 TAATCTCACTGC
1 TAATCTCACTGC
9075094 CATCGTTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.85
22 3 0.11
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.33
Consensus pattern (21 bp):
TAATCTCACTGCTACAGTAAT
Found at i:9077926 original size:23 final size:24
Alignment explanation
Indices: 9077899--9077957 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 24
9077889 AGTTATATAC
*
9077899 AAAGGGAGCATTATATATC-ATTT
1 AAAGGGAGCATTATATATCAATTA
9077922 AAA-GGAGC-TGT-TATATCAATTA
1 AAAGGGAGCAT-TATATATCAATTA
9077944 AAAGGAGAGCATTA
1 AAAGG-GAGCATTA
9077958 CACCTCCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 4 0.14
24 5 0.17
25 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.29
Consensus pattern (24 bp):
AAAGGGAGCATTATATATCAATTA
Found at i:9079896 original size:18 final size:16
Alignment explanation
Indices: 9079860--9079903 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
9079850 AGAGAGAAGA
*
9079860 AAAATGAAAGAAAATG
1 AAAATGAAAGAAAAAG
9079876 AAAATGAAATCGAAAAAG
1 AAAATGAAA--GAAAAAG
9079894 AAAATGAAAG
1 AAAATGAAAG
9079904 TGAGAGTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 10 0.40
18 15 0.60
ACGTcount: A:0.68, C:0.02, G:0.18, T:0.11
Consensus pattern (16 bp):
AAAATGAAAGAAAAAG
Found at i:9084509 original size:59 final size:59
Alignment explanation
Indices: 9084446--9084624 Score: 250
Period size: 68 Copynumber: 2.9 Consensus size: 59
9084436 TCAAGTTTGT
*
9084446 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
9084505 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
9084570 AAA
57 AAA
* *
9084573 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAGTTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
9084625 AATAATTTGA
Statistics
Matches: 108, Mismatches: 3, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
59 46 0.43
60 1 0.01
62 2 0.02
65 2 0.02
67 1 0.01
68 56 0.52
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:9084547 original size:9 final size:9
Alignment explanation
Indices: 9084535--9084562 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
9084525 TTTTATTACA
9084535 ACAATTAAT
1 ACAATTAAT
9084544 ACAATTAAT
1 ACAATTAAT
9084553 ACAATTAAT
1 ACAATTAAT
9084562 A
1 A
9084563 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:9084553 original size:68 final size:68
Alignment explanation
Indices: 9084476--9084646 Score: 310
Period size: 68 Copynumber: 2.5 Consensus size: 68
9084466 TTTTGTTACA
9084476 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
9084541 AAT
66 AAT
9084544 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
9084609 AAT
66 AAT
* *
9084612 ACAGTT-A-ACAATTAATAATTTGATAATTTTACTAA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAA
9084647 CAATTAATTT
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
66 27 0.27
67 1 0.01
68 73 0.72
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
AAT
Found at i:9084656 original size:16 final size:16
Alignment explanation
Indices: 9084635--9084676 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
9084625 AATAATTTGA
*
9084635 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
9084651 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
9084667 TAGTTTTAAT
1 TAATTTTAAT
9084677 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:9084665 original size:59 final size:66
Alignment explanation
Indices: 9084476--9084668 Score: 274
Period size: 68 Copynumber: 3.0 Consensus size: 66
9084466 TTTTGTTACA
9084476 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAA-GTTAGATTTTA-TACAACAATT
9084541 AAT
64 AAT
9084544 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAA-GTTAGATTTTA-TACAACAATT
9084609 AAT
64 AAT
* * *
9084612 ACAGTT-A-ACAATTAATAATTTGATAATTTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAAGTTAGATTTTATACAACAATTA
9084669 GTTTTAATTT
Statistics
Matches: 122, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
59 9 0.07
61 6 0.05
62 3 0.02
64 2 0.02
65 1 0.01
66 27 0.22
67 1 0.01
68 73 0.60
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (66 bp):
ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAAGTTAGATTTTATACAACAATTAA
T
Found at i:9084675 original size:22 final size:23
Alignment explanation
Indices: 9084650--9084711 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
9084640 TTACTAACAA
* * *
9084650 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
9084672 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
*
9084695 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
9084712 CGGACCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:9090190 original size:23 final size:25
Alignment explanation
Indices: 9090164--9090212 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
9090154 TAAATATCAA
*
9090164 ATTAAAACAAA-A-AAATTTTAAAT
1 ATTAAAACAAATATAAATATTAAAT
9090187 ATTAAAACAAATATAAATATTAAAT
1 ATTAAAACAAATATAAATATTAAAT
9090212 A
1 A
9090213 ATATATTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 11 0.48
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
ATTAAAACAAATATAAATATTAAAT
Found at i:9090434 original size:22 final size:23
Alignment explanation
Indices: 9090404--9090448 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
9090394 TATTTGAATT
9090404 TTACATTTTTTTT-AATTTGGTA
1 TTACATTTTTTTTCAATTTGGTA
*
9090426 TTACCTTTTTTTTCAATTTGGTA
1 TTACATTTTTTTTCAATTTGGTA
9090449 CTTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (23 bp):
TTACATTTTTTTTCAATTTGGTA
Found at i:9090459 original size:24 final size:23
Alignment explanation
Indices: 9090408--9090459 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
9090398 TGAATTTTAC
* **
9090408 ATTTTTTTTAATTTGGTATTACC
1 ATTTTTTTCAATTTGGTATTAAA
*
9090431 TTTTTTTTCAATTTGGTACTTAAA
1 ATTTTTTTCAATTTGGTA-TTAAA
9090455 ATTTT
1 ATTTT
9090460 CAAATATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (23 bp):
ATTTTTTTCAATTTGGTATTAAA
Found at i:9091181 original size:19 final size:18
Alignment explanation
Indices: 9091159--9091197 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9091149 ATTACAAAAT
*
9091159 AATTCAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
*
9091178 AATTCCAAATATTTATAA
1 AATTCAAAATATTTATAA
9091196 AA
1 AA
9091198 ATATCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:9091198 original size:19 final size:19
Alignment explanation
Indices: 9091176--9091213 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
9091166 AATAATTTTT
9091176 AAAAT-TCCAAATATTTATA
1 AAAATATCCAAAT-TTTATA
9091195 AAAATATCCAAATTTTATA
1 AAAATATCCAAATTTTATA
9091214 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATATCCAAATTTTATA
Found at i:9111840 original size:44 final size:43
Alignment explanation
Indices: 9111792--9111976 Score: 133
Period size: 43 Copynumber: 4.3 Consensus size: 43
9111782 AGACTTTGCA
* *
9111792 TAAGACCATATCTAGGATA-TGACGTCGATATATGTGATTACGTG
1 TAAGACCATATCTAGGACATTGACATCG-T-TATGTGATTACGTG
* * * *
9111836 TAAGACCATGTCTGGGACATTGGCATCGTTATGTGATTTCGTG
1 TAAGACCATATCTAGGACATTGACATCGTTATGTGATTACGTG
* * * * * * *
9111879 GAAGACCATGTCTTGGACATTGGCATCGATATATGATT-CATG
1 TAAGACCATATCTAGGACATTGACATCGTTATGTGATTACGTG
* * * ** * * *
9111921 TAAGACCAAAGCT-GGGCTATTGGTATCGATATGTGATAACATG
1 TAAGACCATATCTAGGAC-ATTGACATCGTTATGTGATTACGTG
9111964 TAAGACCATATCT
1 TAAGACCATATCT
9111977 GGGATATGGC
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
41 3 0.03
42 29 0.25
43 62 0.53
44 17 0.15
45 6 0.05
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (43 bp):
TAAGACCATATCTAGGACATTGACATCGTTATGTGATTACGTG
Found at i:9111873 original size:43 final size:43
Alignment explanation
Indices: 9111821--9111998 Score: 186
Period size: 43 Copynumber: 4.2 Consensus size: 43
9111811 TGACGTCGAT
*
9111821 ATATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCG
1 ATATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG
* * * * *
9111864 TTATGTGATTTCGTGGAAGACCATGTCTTGGACATTGGCATCG
1 ATATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG
* * *
9111907 ATATATGATT-CATGTAAGACCAAAG-CTGGG-CTATTGGTATCG
1 ATATGTGATTACATGTAAGACC-ATGTCTGGGAC-ATTGGCATCG
* * * *
9111949 ATATGTGATAACATGTAAGACCATATCTGGGATA-TGGCAT-T
1 ATATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG
9111990 ATATGTGAT
1 ATATGTGAT
9111999 ATACGAGACT
Statistics
Matches: 112, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
41 10 0.09
42 36 0.32
43 66 0.59
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (43 bp):
ATATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG
Found at i:9111943 original size:42 final size:43
Alignment explanation
Indices: 9111897--9111988 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 43
9111887 TGTCTTGGAC
* *
9111897 ATTGGCATCGATATATGAT-TCATGTAAGACCAAAGCTGGGCT
1 ATTGGCATCGATATATGATAACATGTAAGACCAAAGCTGGGAT
* * * *
9111939 ATTGGTATCGATATGTGATAACATGTAAGACCATATCTGGGAT
1 ATTGGCATCGATATATGATAACATGTAAGACCAAAGCTGGGAT
9111982 A-TGGCAT
1 ATTGGCAT
9111989 TATATGTGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 22 0.52
43 20 0.48
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (43 bp):
ATTGGCATCGATATATGATAACATGTAAGACCAAAGCTGGGAT
Found at i:9137060 original size:81 final size:84
Alignment explanation
Indices: 9136957--9137108 Score: 186
Period size: 81 Copynumber: 1.8 Consensus size: 84
9136947 CACCTATCAT
* * ** ***
9136957 CCATCAATTCCTTTGAATCAGAATCATTCATACTTTCACCCTGA-T-CTTT-CAAACAAACCACA
1 CCATCAATTCCTTTCAACCAGAATCACCCATAAGGTCACCCTGATTACTTTCCAAACAAACCACA
*
9137019 GTATCATCATTCGCATTGC
66 CTATCATCATTCGCATTGC
*
9137038 CCATCAATTCC-TTCAAGCCAGAATCACCCATAAGGTCACCCTGATTATTTTCCAAACAAACCAC
1 CCATCAATTCCTTTCAA-CCAGAATCACCCATAAGGTCACCCTGATTACTTTCCAAACAAACCAC
9137102 ACTATCA
65 ACTATCA
9137109 CCGCACATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
80 4 0.07
81 32 0.55
82 1 0.02
83 3 0.05
84 18 0.31
ACGTcount: A:0.33, C:0.32, G:0.07, T:0.28
Consensus pattern (84 bp):
CCATCAATTCCTTTCAACCAGAATCACCCATAAGGTCACCCTGATTACTTTCCAAACAAACCACA
CTATCATCATTCGCATTGC
Found at i:9139180 original size:28 final size:28
Alignment explanation
Indices: 9139140--9139207 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
9139130 TATCTAAATA
*
9139140 GTCTCGAGACAAAGTGGTCTTTGTCTTT
1 GTCTCGAGACAAAGTGGTCTTTGCCTTT
*
9139168 GTCTCAAGACAAAGTGGTCTTTGCCTTT
1 GTCTCGAGACAAAGTGGTCTTTGCCTTT
*
9139196 ATCTCGAGACAA
1 GTCTCGAGACAA
9139208 GAAAACATCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (28 bp):
GTCTCGAGACAAAGTGGTCTTTGCCTTT
Found at i:9141480 original size:17 final size:18
Alignment explanation
Indices: 9141440--9141480 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
9141430 TTTATTTTAT
9141440 TATTTTTCCCAACATCTC
1 TATTTTTCCCAACATCTC
* *
9141458 TA-TTTTCCC-ACGTTTC
1 TATTTTTCCCAACATCTC
9141474 TATTTTT
1 TATTTTT
9141481 TCTCTTACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 7 0.35
17 11 0.55
18 2 0.10
ACGTcount: A:0.17, C:0.27, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTTTTCCCAACATCTC
Found at i:9153034 original size:24 final size:24
Alignment explanation
Indices: 9153005--9153054 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
9152995 AAAGCATAGG
*
9153005 TACTTTTTGGAAAAAATTTATTAC
1 TACTTTTTCGAAAAAATTTATTAC
**
9153029 TACTTTTTCGAAAAGGTTTATTAC
1 TACTTTTTCGAAAAAATTTATTAC
9153053 TA
1 TA
9153055 TAAATATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (24 bp):
TACTTTTTCGAAAAAATTTATTAC
Found at i:9155255 original size:3 final size:3
Alignment explanation
Indices: 9155247--9155300 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
9155237 AAAATGCAAG
9155247 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
9155295 GAA GAA
1 GAA GAA
9155301 AACCATCGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9155978 original size:15 final size:16
Alignment explanation
Indices: 9155958--9155987 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9155948 ATTGTATTAT
9155958 TTAATTGTT-TAATAG
1 TTAATTGTTGTAATAG
9155973 TTAATTGTTGTAATA
1 TTAATTGTTGTAATA
9155988 CAATAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (16 bp):
TTAATTGTTGTAATAG
Found at i:9156168 original size:37 final size:37
Alignment explanation
Indices: 9156098--9156168 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
9156088 TTTAACTTAC
* * *
9156098 AAGTATATGGTTATTTGATACATGAATGGAAATGAGT
1 AAGTATATGGTTACTTGATACATGAACGAAAATGAGT
* * *
9156135 AAGTGTATGGTTACTTGATATATGTACGAAAATG
1 AAGTATATGGTTACTTGATACATGAACGAAAATG
9156169 TTCAAGAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (37 bp):
AAGTATATGGTTACTTGATACATGAACGAAAATGAGT
Found at i:9156974 original size:36 final size:36
Alignment explanation
Indices: 9156927--9157007 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 36
9156917 TGTTAAGTGA
9156927 TGTACTTGTGAATGTAACAGGATGCCAAATGATATT
1 TGTACTTGTGAATGTAACAGGATGCCAAATGATATT
*
9156963 TGTACTTGTGAATGTAACAGGATGCCAAATGTTATT
1 TGTACTTGTGAATGTAACAGGATGCCAAATGATATT
9156999 TGTACTTGT
1 TGTACTTGT
9157008 TACATTATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (36 bp):
TGTACTTGTGAATGTAACAGGATGCCAAATGATATT
Found at i:9158149 original size:23 final size:23
Alignment explanation
Indices: 9158123--9158167 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
9158113 TGAACAATAC
9158123 GACCATGTTCCATAGCTTCGCAT
1 GACCATGTTCCATAGCTTCGCAT
9158146 GACCATGTTCCATAGCTTCGCA
1 GACCATGTTCCATAGCTTCGCA
9158168 AGGCCTTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (23 bp):
GACCATGTTCCATAGCTTCGCAT
Found at i:9158856 original size:4 final size:4
Alignment explanation
Indices: 9158843--9158873 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
9158833 TGGTTTTTTA
9158843 AATT -ATT AATT AATT AATT AATT AATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT
9158874 GAAGTTCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
AATT
Found at i:9159454 original size:18 final size:17
Alignment explanation
Indices: 9159426--9159459 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9159416 AAAGTAGTGA
9159426 AAATTTATTTTAGGAAT
1 AAATTTATTTTAGGAAT
*
9159443 AAATTCTATTTTTGGAA
1 AAATT-TATTTTAGGAA
9159460 AATTGCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
AAATTTATTTTAGGAAT
Found at i:9163114 original size:42 final size:41
Alignment explanation
Indices: 9163010--9163172 Score: 166
Period size: 43 Copynumber: 3.8 Consensus size: 41
9163000 CAAAAATATC
* * *
9163010 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAA
1 ATACAATGCCAATGTCCCAGAC-CGGTCTTACACGTAATCAA
* * *
9163052 ATAACGATGCCACTGTCCCAGACCGAGTCTTACACGTAATCAT
1 AT-ACAATGCCAATGTCCCAGACCG-GTCTTACACGTAATCAA
* *
9163095 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCGCAA
1 ATACAATGCCAATGTCCCAGAC-CGGTCTTACACGT-AAT--CAA
* *
9163140 AT-CAATGCCAATGTCCTAGACAGGTCTTACACG
1 ATACAATGCCAATGTCCCAGACCGGTCTTACACG
9163173 ATATCACATA
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
42 33 0.32
43 49 0.48
44 17 0.17
45 4 0.04
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (41 bp):
ATACAATGCCAATGTCCCAGACCGGTCTTACACGTAATCAA
Found at i:9163167 original size:85 final size:84
Alignment explanation
Indices: 9163010--9163172 Score: 204
Period size: 85 Copynumber: 1.9 Consensus size: 84
9163000 CAAAAATATC
* * * *
9163010 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAACGATGCCACTGTCCCAGAC
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAAT-ACAATGCCAATGTCCCAGAC
*
9163075 CGAGTCTTACACGTAATCAT
65 AGAGTCTTACACGTAATCAT
* * *
9163095 ATACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCGCAAAT-CAATGCCAATGTCCTAG
1 ATACAATGCCAACGTCCCAGACATGGTCTTACACGT-AAT--CAAATACAATGCCAATGTCCCAG
9163159 ACAG-GTCTTACACG
63 ACAGAGTCTTACACG
9163173 ATATCACATA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
85 42 0.63
86 20 0.30
88 5 0.07
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (84 bp):
ATACAATGCCAACGTCCCAGACATGGTCTTACACGTAATCAAATACAATGCCAATGTCCCAGACA
GAGTCTTACACGTAATCAT
Found at i:9169735 original size:2 final size:2
Alignment explanation
Indices: 9169728--9169764 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
9169718 TTTAACTATA
*
9169728 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
9169765 AAGTATGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:9175657 original size:40 final size:40
Alignment explanation
Indices: 9175581--9175658 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
9175571 ATGCACACAC
* * *
9175581 GTGCCCCTATTTGTACTTCGATACCCCTGGATGCATATAT
1 GTGCCCCTATTAGTACTTCGATACCCCTGAAGGCATATAT
* * *
9175621 GTGCCCCTATTAGTACTTTGGTACTCCTGAAGGCATAT
1 GTGCCCCTATTAGTACTTCGATACCCCTGAAGGCATAT
9175659 TCATGCTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.35
Consensus pattern (40 bp):
GTGCCCCTATTAGTACTTCGATACCCCTGAAGGCATATAT
Found at i:9181932 original size:26 final size:27
Alignment explanation
Indices: 9181903--9181960 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
9181893 AACCTTAAAG
9181903 TAAAC-TTGTTTTCTCATTTTAATACC
1 TAAACTTTGTTTTCTCATTTTAATACC
* *
9181929 TAAACTTTTTTTTTCTCATTTTGATACC
1 TAAAC-TTTGTTTTCTCATTTTAATACC
9181957 TAAA
1 TAAA
9181961 GTACTATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.18
28 23 0.82
ACGTcount: A:0.28, C:0.17, G:0.03, T:0.52
Consensus pattern (27 bp):
TAAACTTTGTTTTCTCATTTTAATACC
Found at i:9182181 original size:89 final size:83
Alignment explanation
Indices: 9182034--9182208 Score: 242
Period size: 88 Copynumber: 2.0 Consensus size: 83
9182024 TGCAAAAAGT
* *
9182034 CCTCAAACTTAAAAAAAAAATTAAGCCCCTGATTTTTTTTTCACTCAATTGGGTACTTGAACTTT
1 CCTCAAACTTAAAAAAAAAATTAAGCCCATGATTTTTTTTTCACTCAATTGGGTACTTGAACTAT
*
9182099 CAAAATGCATAAAAAATGC
66 C-AAATGCATAAAAAAGGC
* *
9182118 CCTCAAACTTAAAAAAAAAGCAATTATGCCCATGTTTTTTTTTTTGCACTCAATTGGGTACTTGA
1 CCTCAAACTT-AAAAAAAA--AATTAAGCCCATG-ATTTTTTTTT-CACTCAATTGGGTACTTGA
*
9182183 ACTATCAAATGCATCAAAAAGGC
61 ACTATCAAATGCATAAAAAAGGC
9182206 CCT
1 CCT
9182209 TTGATCGTTA
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
84 10 0.12
85 8 0.10
87 11 0.14
88 27 0.34
89 24 0.30
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (83 bp):
CCTCAAACTTAAAAAAAAAATTAAGCCCATGATTTTTTTTTCACTCAATTGGGTACTTGAACTAT
CAAATGCATAAAAAAGGC
Found at i:9182348 original size:19 final size:19
Alignment explanation
Indices: 9182326--9182385 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
9182316 ATAAAAAATA
*
9182326 AAAATAAATAAAATTTATT
1 AAAATAATTAAAATTTATT
* *
9182345 AAAAT-ATTAAATTTTAATA
1 AAAATAATTAAAATTT-ATT
*
9182364 AAAATATTTAAAATTTATT
1 AAAATAATTAAAATTTATT
9182383 AAA
1 AAA
9182386 TATTAGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.24
19 17 0.52
20 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATAATTAAAATTTATT
Found at i:9182360 original size:18 final size:18
Alignment explanation
Indices: 9182334--9182390 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
9182324 TAAAAATAAA
9182334 TAAAATTTATTAAAATAT
1 TAAAATTTATTAAAATAT
* *
9182352 TAAATTTTAATAAAAATATT
1 TAAAATTT-ATTAAAATA-T
9182372 TAAAATTTATT-AAATAT
1 TAAAATTTATTAAAATAT
9182389 TA
1 TA
9182391 GAAAAAATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 3 0.09
18 12 0.36
19 10 0.30
20 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAAATTTATTAAAATAT
Found at i:9182632 original size:20 final size:19
Alignment explanation
Indices: 9182595--9182642 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
9182585 TTTTTATATG
9182595 AATTTTAT-ATTTCTTTAC
1 AATTTTATAATTTCTTTAC
9182613 ATATTTTATAATTT-TCTTAC
1 A-ATTTTATAATTTCT-TTAC
*
9182633 AACTTTATAA
1 AATTTTATAA
9182643 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (19 bp):
AATTTTATAATTTCTTTAC
Found at i:9182717 original size:20 final size:19
Alignment explanation
Indices: 9182674--9182735 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
9182664 TTTCTATATG
9182674 TTTTATAAAATTTTACGAT
1 TTTTATAAAATTTTACGAT
*
9182693 TTTTATAAAATTTTACAGTT
1 TTTTATAAAATTTTAC-GAT
**
9182713 TTTTATAATTTTTTTACGAT
1 TTTTATAA-AATTTTACGAT
9182733 TTT
1 TTT
9182736 GTAATTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 16 0.43
20 15 0.41
21 6 0.16
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (19 bp):
TTTTATAAAATTTTACGAT
Found at i:9182727 original size:21 final size:21
Alignment explanation
Indices: 9182703--9182779 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
9182693 TTTTATAAAA
9182703 TTTTACAGTTTTTTATAATTT
1 TTTTACAGTTTTTTATAATTT
* *
9182724 TTTTAC-G-ATTTTGTAATTGT
1 TTTTACAGTTTTTTATAATT-T
* * *
9182744 TTTT-CTAATTTTTAATATTTT
1 TTTTAC-AGTTTTTTATAATTT
*
9182765 TTTTATAGTTTTTTA
1 TTTTACAGTTTTTTA
9182780 ATTAAAATTT
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
19 10 0.24
20 6 0.15
21 18 0.44
22 7 0.17
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (21 bp):
TTTTACAGTTTTTTATAATTT
Found at i:9189124 original size:12 final size:12
Alignment explanation
Indices: 9189107--9189131 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9189097 GTAAAAGTGC
9189107 ATATTTTATTAA
1 ATATTTTATTAA
9189119 ATATTTTATTAA
1 ATATTTTATTAA
9189131 A
1 A
9189132 ATTAGTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTTTATTAA
Found at i:9190478 original size:27 final size:27
Alignment explanation
Indices: 9190437--9190490 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
9190427 TTGCACTCCA
*
9190437 AAATAGATAATGTTTATTAACTTTGTT
1 AAATAGATAAAGTTTATTAACTTTGTT
*
9190464 AAATATATAAAGTTTATTAACTTTGTT
1 AAATAGATAAAGTTTATTAACTTTGTT
9190491 GATGTGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (27 bp):
AAATAGATAAAGTTTATTAACTTTGTT
Found at i:9194151 original size:19 final size:19
Alignment explanation
Indices: 9194118--9194169 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
9194108 GCAATTTAGA
*
9194118 AACGA-AAATATTAATAAT
1 AACGATAAATAATAATAAT
*
9194136 GACGATAAATAATAATAAT
1 AACGATAAATAATAATAAT
* *
9194155 AACAATAAACAATAA
1 AACGATAAATAATAA
9194170 ACAATTTAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.23
Consensus pattern (19 bp):
AACGATAAATAATAATAAT
Found at i:9194357 original size:3 final size:3
Alignment explanation
Indices: 9194349--9194398 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
9194339 AAAAGGGGGA
9194349 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9194397 AA
1 AA
9194399 CAGAAAACAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9196040 original size:44 final size:44
Alignment explanation
Indices: 9195989--9196100 Score: 172
Period size: 44 Copynumber: 2.5 Consensus size: 44
9195979 ACAGTCTGCT
*
9195989 CCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAACCCGCT
1 CCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAACCCGCC
* *
9196033 TCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAACCTGCC
1 CCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAACCCGCC
*
9196077 CCATTACAACTTCAAGGG-GATAAG
1 CCACTACAACTTC-AGGGAGATAAG
9196101 GTTTATGGCT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 58 0.94
45 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (44 bp):
CCACTACAACTTCAGGGAGATAAGACTTGTTATTTCAACCCGCC
Found at i:9196247 original size:45 final size:45
Alignment explanation
Indices: 9196196--9196414 Score: 118
Period size: 44 Copynumber: 4.9 Consensus size: 45
9196186 GTCAGGCTGG
*
9196196 TATCTTCGATCTGCTTCGCTGCCAGTACAGAAAGACAAGATCTGC
1 TATCTTCGATCTGCTTCGCTGCCAGTACAGGAAGACAAGATCTGC
* * * * * * *
9196241 TATCTTC-AGTCTG-TTCCGCTACAAACT-CAAGGAGGTC-AG-GCTGG
1 TATCTTCGA-TCTGCTT-CGCTGC-CAGTAC-AGGAAGACAAGATCTGC
*
9196285 TGTCTTCGATCTGCTTCGCTGCC-GATACAGGAAGACAAGATCTGC
1 TATCTTCGATCTGCTTCGCTGCCAG-TACAGGAAGACAAGATCTGC
* * * * * *
9196330 TATCTTC-AGTCTG-TTCCGCTGCAAACT-CAGGGAGGTC-AG-GCTGG
1 TATCTTCGA-TCTGCTT-CGCTGC-CAGTACA-GGAAGACAAGATCTGC
* **
9196374 TGTCTTCGATCTGCTTCGCTGCTGGTACAGGAAGACAAGAT
1 TATCTTCGATCTGCTTCGCTGCCAGTACAGGAAGACAAGAT
9196415 ATGTTATTTT
Statistics
Matches: 124, Mismatches: 30, Indels: 40
0.64 0.15 0.21
Matches are distributed among these distances:
43 13 0.10
44 50 0.40
45 48 0.39
46 13 0.10
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (45 bp):
TATCTTCGATCTGCTTCGCTGCCAGTACAGGAAGACAAGATCTGC
Found at i:9196334 original size:89 final size:89
Alignment explanation
Indices: 9196178--9196414 Score: 395
Period size: 89 Copynumber: 2.7 Consensus size: 89
9196168 CACTGCAACT
* * *
9196178 TCAATGAGGTCAGGCTGGTATCTTCGATCTGCTTCGCTGCC-AGTACAGAAAGACAAGATCTGCT
1 TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGA-TACAGGAAGACAAGATCTGCT
9196242 ATCTTCAGTCTGTTCCGCTACAAAC
65 ATCTTCAGTCTGTTCCGCTACAAAC
9196267 TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGATACAGGAAGACAAGATCTGCTA
1 TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGATACAGGAAGACAAGATCTGCTA
*
9196332 TCTTCAGTCTGTTCCGCTGCAAAC
66 TCTTCAGTCTGTTCCGCTACAAAC
* * *
9196356 TCAGGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCTGGTACAGGAAGACAAGAT
1 TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGATACAGGAAGACAAGAT
9196415 ATGTTATTTT
Statistics
Matches: 140, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
89 139 0.99
90 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.27
Consensus pattern (89 bp):
TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGATACAGGAAGACAAGATCTGCTA
TCTTCAGTCTGTTCCGCTACAAAC
Found at i:9196394 original size:44 final size:43
Alignment explanation
Indices: 9196183--9196395 Score: 123
Period size: 45 Copynumber: 4.8 Consensus size: 43
9196173 CAACTTCAAT
* * *
9196183 GAGGTCAGGCTGGTATCTTCGATCTGCTTCGCTGC-CAGTACAG
1 GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCAAACT-CAG
* * * * * * *
9196226 AAAGACAAGATCTGCTATCTTC-AGTCTG-TTCCGCTACAAACTCAAG
1 GAGGTC-AG-GCTGGTGTCTTCGA-TCTGCTT-CGCTGCAAACTC-AG
**
9196272 GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGA-TACAG
1 GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCAAACT-CAG
* * * * *
9196315 GAAGACAAGATCTGCTATCTTC-AGTCTG-TTCCGCTGCAAACTCAGG
1 GAGGTC-AG-GCTGGTGTCTTCGA-TCTGCTT-CGCTGCAAACTCA-G
9196361 GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGC
1 GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGC
9196396 TGGTACAGGA
Statistics
Matches: 124, Mismatches: 29, Indels: 33
0.67 0.16 0.18
Matches are distributed among these distances:
43 10 0.08
44 49 0.40
45 52 0.42
46 13 0.10
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (43 bp):
GAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCAAACTCAG
Found at i:9196454 original size:89 final size:89
Alignment explanation
Indices: 9196162--9196439 Score: 387
Period size: 89 Copynumber: 3.1 Consensus size: 89
9196152 TATTTGTAAC
* * * *
9196162 CTGCTCCACTGC-AACTTCAATGAGGTCAGGCTGGTATCTTCGATCTGCTTCGCTGCCAGTACAG
1 CTGCTCCGCTGCAAAC-TCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAG
* *
9196226 AAAGACAAGATCTGCTATCTTCAGT
65 GAAGACAAGATCTGCTATCTTCAAT
* * *
9196251 CTGTTCCGCTACAAACTCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGATACAGG
1 CTGCTCCGCTGCAAACTCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAGG
*
9196316 AAGACAAGATCTGCTATCTTCAGT
66 AAGACAAGATCTGCTATCTTCAAT
* * *
9196340 CTGTTCCGCTGCAAACTCAGGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCTGGTACAGG
1 CTGCTCCGCTGCAAACTCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAGG
* * * *
9196405 AAGACAAGATATGTTATTTTTAAT
66 AAGACAAGATCTGCTATCTTCAAT
9196429 CTGCTCCGCTG
1 CTGCTCCGCTG
9196440 TAATTTCAGA
Statistics
Matches: 170, Mismatches: 18, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
89 167 0.98
90 3 0.02
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (89 bp):
CTGCTCCGCTGCAAACTCAAGGAGGTCAGGCTGGTGTCTTCGATCTGCTTCGCTGCCGGTACAGG
AAGACAAGATCTGCTATCTTCAAT
Found at i:9197455 original size:51 final size:51
Alignment explanation
Indices: 9197347--9197656 Score: 431
Period size: 51 Copynumber: 6.3 Consensus size: 51
9197337 CTTGCGTATG
** *
9197347 ATCACTTATCACTTGTCCCTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* **
9197397 ATCACTTGCCATTTACCACTGATCAGATAAGTGTAGCTGAAGCTACCAC-T
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
*
9197447 -T-A--T--CACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* *
9197492 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGTTGAAGCTATCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
*
9197543 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
* * *
9197594 ATCACTTGCCATTTGTCACTAATTAGATAAGTGTAGCTG-AGCTACCACTT
1 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
*
9197644 ATCACTTGTCACT
1 ATCACTTGCCACT
9197657 GATCAGAAGT
Statistics
Matches: 234, Mismatches: 18, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
44 36 0.15
45 1 0.00
46 2 0.01
47 1 0.00
48 1 0.00
49 2 0.01
50 54 0.23
51 137 0.59
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
Found at i:9205023 original size:16 final size:16
Alignment explanation
Indices: 9204998--9205048 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
9204988 AATAAAGAGC
9204998 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
*
9205014 AAATATGCTAGTAAAT
1 AAATACGCTAGTAAAT
* *
9205030 AAACACGCGAGTAAAT
1 AAATACGCTAGTAAAT
9205046 AAA
1 AAA
9205049 ATACTAGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.22
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:9205964 original size:19 final size:19
Alignment explanation
Indices: 9205931--9205982 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
9205921 GCAATTTAGA
*
9205931 AACGA-AAATATTAATAAT
1 AACGATAAATAATAATAAT
*
9205949 GACGATAAATAATAATAAT
1 AACGATAAATAATAATAAT
* *
9205968 AACAATAAACAATAA
1 AACGATAAATAATAA
9205983 ACAATTTAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.63, C:0.08, G:0.06, T:0.23
Consensus pattern (19 bp):
AACGATAAATAATAATAAT
Found at i:9206200 original size:3 final size:3
Alignment explanation
Indices: 9206192--9206243 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
9206182 AAAAGGGAAC
* *
9206192 ATA ATA ATA ATA ATA ATA ATA ATA AGA ATA ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9206240 ATA A
1 ATA A
9206244 CAGCAAACAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:9207870 original size:22 final size:22
Alignment explanation
Indices: 9207822--9207874 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
9207812 AGGTAGTGTT
* * *
9207822 GCGACACCGATCTTGTGATGTT
1 GCGACATCGATCCTGTGATGTC
*
9207844 ACGACATCGATCCTGTGATGTC
1 GCGACATCGATCCTGTGATGTC
9207866 GCGACATCG
1 GCGACATCG
9207875 GGCAATGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCGACATCGATCCTGTGATGTC
Found at i:9213297 original size:18 final size:18
Alignment explanation
Indices: 9213274--9213308 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9213264 TTATTGATTG
9213274 AATTGAA-TACTTGAATTT
1 AATTGAAGTACTT-AATTT
9213292 AATTGAAGTACTTAATT
1 AATTGAAGTACTTAATT
9213309 GAATGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (18 bp):
AATTGAAGTACTTAATTT
Found at i:9214293 original size:28 final size:28
Alignment explanation
Indices: 9214261--9214339 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
9214251 GAATCATTGC
* ** *
9214261 AATATAGCACACATTAAGTGTTGAGTCA
1 AATATAACACACATTAACCGTTGAATCA
9214289 AATATAACACACATTAACCGTTGAATCA
1 AATATAACACACATTAACCGTTGAATCA
** *
9214317 AATATAACATGCATTAAGCGTTG
1 AATATAACACACATTAACCGTTG
9214340 GATCTCCCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (28 bp):
AATATAACACACATTAACCGTTGAATCA
Found at i:9215727 original size:4 final size:4
Alignment explanation
Indices: 9215718--9215748 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
9215708 TCTTCCTCAA
9215718 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
9215749 GCATGACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:9216202 original size:21 final size:21
Alignment explanation
Indices: 9216157--9216232 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
9216147 ATCTTCAAGG
*
9216157 ATATGTAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
9216176 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
9216197 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
9216218 TTATGCAATCTTAGA
1 ATATGCAATCTTAGA
9216233 ATATATGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.34
21 35 0.66
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:9216254 original size:23 final size:24
Alignment explanation
Indices: 9216177--9216255 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 24
9216167 TTAGATATGA
*
9216177 TATGCAATCTTAG---ATATGATA
1 TATGCAATCTTAGAATATATGATT
9216198 TATGCAATCTTAG---ATATGATT
1 TATGCAATCTTAGAATATATGATT
9216219 TATGCAATCTTAGAATATATGATT
1 TATGCAATCTTAGAATATATGATT
*
9216243 T-TGTAATCTTAGA
1 TATGCAATCTTAGA
9216256 GATTTAATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 33 0.62
23 11 0.21
24 9 0.17
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (24 bp):
TATGCAATCTTAGAATATATGATT
Found at i:9220520 original size:19 final size:18
Alignment explanation
Indices: 9220496--9220537 Score: 75
Period size: 19 Copynumber: 2.3 Consensus size: 18
9220486 CATATTGCCT
9220496 AAAAAGATGGCGCAAACAA
1 AAAAAGATGGCGCAAA-AA
9220515 AAAAAGATGGCGCAAAAA
1 AAAAAGATGGCGCAAAAA
9220533 AAAAA
1 AAAAA
9220538 CTCTATCGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.64, C:0.12, G:0.19, T:0.05
Consensus pattern (18 bp):
AAAAAGATGGCGCAAAAA
Found at i:9235771 original size:13 final size:13
Alignment explanation
Indices: 9235753--9235778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9235743 CAATCAAATG
9235753 CACACAAAATAAT
1 CACACAAAATAAT
9235766 CACACAAAATAAT
1 CACACAAAATAAT
9235779 ATTAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (13 bp):
CACACAAAATAAT
Found at i:9245854 original size:24 final size:23
Alignment explanation
Indices: 9245823--9245870 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
9245813 GTTGTTGCTG
9245823 ATATTATTAAAAAT-TTATTCATT
1 ATATTATTAAAAATATTATT-ATT
9245846 ATATATATTAAAAATATTATTATT
1 ATAT-TATTAAAAATATTATTATT
9245870 A
1 A
9245871 AAGTGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTATTAAAAATATTATTATT
Found at i:9245921 original size:56 final size:56
Alignment explanation
Indices: 9245855--9245965 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
9245845 TATATATATT
*
9245855 AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTATAATTATTTTGACATA
1 AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTACAATTATTTTGACATA
9245911 AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTACAATTATTTTGACAT
1 AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTACAATTATTTTGACAT
9245966 GTTATAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (56 bp):
AAAAATATTATTATTAAAGTGTTTATGTTTTTATATTTTACAATTATTTTGACATA
Found at i:9255757 original size:26 final size:25
Alignment explanation
Indices: 9255701--9255778 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 25
9255691 AATAATTTTC
* *
9255701 TCAAAATTTTATCGAGGGTAAAATCG
1 TCAAAATTTTATCG-GGGTAAATTTG
*
9255727 CCAAAATTTTATCAGGGGTAAATTTG
1 TCAAAATTTTATC-GGGGTAAATTTG
9255753 TCAAAAATTTTA-CTGGGGTAAATTTG
1 TC-AAAATTTTATC-GGGGTAAATTTG
9255779 CGATAAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 35 0.78
27 10 0.22
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (25 bp):
TCAAAATTTTATCGGGGTAAATTTG
Found at i:9286567 original size:24 final size:24
Alignment explanation
Indices: 9286519--9286567 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
9286509 TAAATGAAAA
* *
9286519 AAATAAATTTTTAGCTTATATTTT
1 AAATAAATTTTGAGATTATATTTT
9286543 AAATAAA-TTTGAGATTATATATTT
1 AAATAAATTTTGAGATTATAT-TTT
9286567 A
1 A
9286568 TAAATTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
AAATAAATTTTGAGATTATATTTT
Found at i:9289709 original size:51 final size:50
Alignment explanation
Indices: 9289630--9289764 Score: 153
Period size: 50 Copynumber: 2.7 Consensus size: 50
9289620 GATAATAACA
* * ***
9289630 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGAGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGA-CCCCTCATATCGG
* * * * ** *
9289681 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCCCTTGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCCCTCATATCGG
9289731 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATG
9289765 GGATCTCTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
50 38 0.54
51 32 0.46
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCCCTCATATCGG
Found at i:9290145 original size:30 final size:30
Alignment explanation
Indices: 9290111--9290168 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
9290101 CCTCGAATCT
9290111 AACTTTGGA-AAAATTACAATTTTGCCCCTA
1 AACTTT-GACAAAATTACAATTTTGCCCCTA
* * *
9290141 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
9290169 AAGGCTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:9309505 original size:46 final size:44
Alignment explanation
Indices: 9309453--9309552 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 44
9309443 AACAGAAAAA
9309453 GAGAAATGAGAAACATTG-AGAAATGATTAT-GGTTTTCTCCAAAATG
1 GAGAAATGA-AAACATTGCA-AAATGATTATAGG-TTTC-CCAAAATG
*
9309499 GAGAAATGAAATCATTGCAAAATGATTATAGGTTTCCCAAAAT-
1 GAGAAATGAAAACATTGCAAAATGATTATAGGTTTCCCAAAATG
9309542 G-GAAATGAAAA
1 GAGAAATGAAAA
9309553 TAGAAATGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
42 9 0.18
43 1 0.02
44 7 0.14
45 21 0.42
46 12 0.24
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.26
Consensus pattern (44 bp):
GAGAAATGAAAACATTGCAAAATGATTATAGGTTTCCCAAAATG
Found at i:9309553 original size:6 final size:6
Alignment explanation
Indices: 9309538--9309613 Score: 125
Period size: 6 Copynumber: 12.7 Consensus size: 6
9309528 AGGTTTCCCA
* *
9309538 AAATGG AAATGA AAATAG AAATGG AAATGG AAATGG AAATGG AAATGG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
*
9309586 AAATGG AAATGG AAATGA AAATGG AAAT
1 AAATGG AAATGG AAATGG AAATGG AAAT
9309614 AAAAAAGAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:9309561 original size:18 final size:18
Alignment explanation
Indices: 9309538--9309630 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
9309528 AGGTTTCCCA
*
9309538 AAATGGAAATGAAAATAG
1 AAATGGAAATGAAAATGG
*
9309556 AAATGGAAATGGAAATGG
1 AAATGGAAATGAAAATGG
*
9309574 AAATGGAAATGGAAATGG
1 AAATGGAAATGAAAATGG
9309592 AAATGGAAATGAAAATGG
1 AAATGGAAATGAAAATGG
** *
9309610 AAATAAAAAAGAAAATGG
1 AAATGGAAATGAAAATGG
9309628 AAA
1 AAA
9309631 CTTGCAATCT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (18 bp):
AAATGGAAATGAAAATGG
Found at i:9309804 original size:26 final size:26
Alignment explanation
Indices: 9309775--9309834 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
9309765 TTTTTTCAAA
9309775 ATTTTATTAAGGGTAAAATCGTAAAT
1 ATTTTATTAAGGGTAAAATCGTAAAT
* * * *
9309801 ATTTTACTAGGGGTAAAATTGTCAAT
1 ATTTTATTAAGGGTAAAATCGTAAAT
9309827 ATTTTATT
1 ATTTTATT
9309835 GGGATAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (26 bp):
ATTTTATTAAGGGTAAAATCGTAAAT
Found at i:9312224 original size:7 final size:7
Alignment explanation
Indices: 9312212--9312243 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
9312202 AGTGTCGATT
*
9312212 ATATGTG
1 ATATGTA
9312219 ATATGTA
1 ATATGTA
9312226 ATATGTA
1 ATATGTA
9312233 ATATGTA
1 ATATGTA
9312240 ATAT
1 ATAT
9312244 ATGAGAAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (7 bp):
ATATGTA
Found at i:9313606 original size:80 final size:80
Alignment explanation
Indices: 9313473--9313634 Score: 297
Period size: 80 Copynumber: 2.0 Consensus size: 80
9313463 CATAAACGGA
* *
9313473 TCTAGGATCTATTCTACTTAGTTCATGTTTGATGTAGTGTCAGTTTTTTCAGTCATATCTATGTC
1 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
9313538 TTTATCTTTTAAGAT
66 TTTATCTTTTAAGAT
9313553 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
1 TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
*
9313618 TTTATCTTTTAGGAT
66 TTTATCTTTTAAGAT
9313633 TC
1 TC
9313635 ATTTGCTTCG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (80 bp):
TCTAGGATCTATTCTACTTAGTTCATGTTCGATGTAGTGTCAGTTTTGTCAGTCATATCTATGTC
TTTATCTTTTAAGAT
Found at i:9317882 original size:51 final size:50
Alignment explanation
Indices: 9317821--9317990 Score: 162
Period size: 58 Copynumber: 3.2 Consensus size: 50
9317811 CATTTCCGAG
*
9317821 TCATTTTCATTTAGGAGAAAACCACATTCATTTCCAAATGATTCCACTTCT
1 TCATTTTCATTTAGGAGAAAACCA-ATTCATTTCCAAATGTTTCCACTTCT
* *
9317872 CCATTTTCATTTTA-GAGAAAACCATTATCATTTCCAAATGTTTCCCATTTCTTCATTT
1 TCATTTTCA-TTTAGGAGAAAACCAAT-TCATTTCCAAATGTTT-CCA---CTTC---T
* * * *
9317930 TTATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTCATTTCT
1 TCATTTTCATTTAGGAGAAAACCA-ATTCATTTCCAAATGTTTC-CACTTCT
9317982 TCATTTTCA
1 TCATTTTCA
9317991 CCATTTCTAT
Statistics
Matches: 97, Mismatches: 10, Indels: 23
0.75 0.08 0.18
Matches are distributed among these distances:
50 1 0.01
51 33 0.34
52 16 0.16
55 7 0.07
57 4 0.04
58 36 0.37
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (50 bp):
TCATTTTCATTTAGGAGAAAACCAATTCATTTCCAAATGTTTCCACTTCT
Found at i:9317938 original size:58 final size:58
Alignment explanation
Indices: 9317874--9317988 Score: 203
Period size: 58 Copynumber: 2.0 Consensus size: 58
9317864 CCACTTCTCC
*
9317874 ATTTTCATTTTAGAGAAAACCATTATCATTTCCAAATGTTTCCCATTTCTTCATTTTT
1 ATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCTTCATTTTT
* *
9317932 ATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCTCATTTCTTCATTTT
1 ATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCTTCATTTT
9317989 CACCATTTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (58 bp):
ATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCTTCATTTTT
Found at i:9328274 original size:25 final size:25
Alignment explanation
Indices: 9328220--9328312 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 25
9328210 GGATACTTCG
* *
9328220 CAGCTCGTGA-GAGCATACCAATTTA
1 CAGCTCATGATGAGCATACCGA-TTA
*
9328245 TAGCTCATGA-GAGCATACCGATCTA
1 CAGCTCATGATGAGCATACCGAT-TA
*
9328270 CAGCTCA-AATGAGCATACCGATTCA
1 CAGCTCATGATGAGCATACCGATT-A
9328295 CAGCTCAT-ATGAGCATAC
1 CAGCTCATGATGAGCATAC
9328313 TTGTACATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.05
25 56 0.95
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (25 bp):
CAGCTCATGATGAGCATACCGATTA
Found at i:9338882 original size:2 final size:2
Alignment explanation
Indices: 9338875--9338899 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9338865 CAATAATAAA
9338875 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
9338900 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9339326 original size:16 final size:16
Alignment explanation
Indices: 9339305--9339340 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
9339295 TTTGGTTCGC
9339305 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
9339321 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
9339337 TGTA
1 TGTA
9339341 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:9339405 original size:44 final size:45
Alignment explanation
Indices: 9339321--9339411 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
9339311 GGATTAGAGG
* * *
9339321 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
9339366 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
9339410 TG
1 TG
9339412 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:9339734 original size:18 final size:17
Alignment explanation
Indices: 9339713--9339747 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9339703 ATATTATTAA
*
9339713 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
9339731 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
9339748 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:9339755 original size:120 final size:120
Alignment explanation
Indices: 9339541--9339800 Score: 443
Period size: 120 Copynumber: 2.2 Consensus size: 120
9339531 TCANNNNNNN
9339541 AAATCATAATATATGATACTGTAAAATATAAATTAACATAATATATGATTAAATATATTTTAATT
1 AAATCATAATATATGATACTGTAAAATATAAATTAACATAATATATGATTAAATATATTTTAATT
*
9339606 GAACAATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATTAATTTACTC
66 GAAAAATATAATTTAATAAAATTCTTAATAATTAATATTCTTATA-TAATTTACTC
* *
9339662 AAATCATAATATTTGATACTGTAAAATATAAATTAACATAA-ATATTATTAAATATATTTTAATT
1 AAATCATAATATATGATACTGTAAAATATAAATTAACATAATATATGATTAAATATATTTTAATT
* *
9339726 -AAAATATATAATTTAATAAAATTCTTAATAATTCATATTCTTATATAATTTATTC
66 GAAAA-ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATAATTTACTC
9339781 AAATCATAATATATGATACT
1 AAATCATAATATATGATACT
9339801 ATAATTAATA
Statistics
Matches: 132, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
119 31 0.23
120 61 0.46
121 40 0.30
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.43
Consensus pattern (120 bp):
AAATCATAATATATGATACTGTAAAATATAAATTAACATAATATATGATTAAATATATTTTAATT
GAAAAATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATAATTTACTC
Found at i:9339876 original size:26 final size:27
Alignment explanation
Indices: 9339801--9339882 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 27
9339791 ATATGATACT
* *
9339801 ATAATTAATATTAAATATATTTTAATTA
1 ATAATTATTATTAAATATAATTTAA-TA
* *
9339829 A-AATATATGATTAAATACAATTTAA-A
1 ATAAT-TATTATTAAATATAATTTAATA
*
9339855 ATAATTATTATTAAATATAATTTCATA
1 ATAATTATTATTAAATATAATTTAATA
9339882 A
1 A
9339883 AATGTTCTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 19 0.43
27 8 0.18
28 17 0.39
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
ATAATTATTATTAAATATAATTTAATA
Found at i:9347525 original size:26 final size:24
Alignment explanation
Indices: 9347482--9347533 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
9347472 TATATACTAC
*
9347482 ATAAATTAATAATAAAATAATAAAAT
1 ATAAATTAAAAATAAAAT--TAAAAT
* *
9347508 ATAATTTAAAAATCAAATTAAAAT
1 ATAAATTAAAAATAAAATTAAAAT
9347532 AT
1 AT
9347534 TAATAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
26 15 0.65
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATTAAAAATAAAATTAAAAT
Found at i:9349319 original size:2 final size:2
Alignment explanation
Indices: 9349312--9349336 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9349302 ATCAACATCA
9349312 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
9349337 TATAATCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9352148 original size:47 final size:47
Alignment explanation
Indices: 9352079--9352173 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
9352069 TTTTTCAAAC
9352079 AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
1 AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
9352126 AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
1 AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
9352173 A
1 A
9352174 TATTATCCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (47 bp):
AAGTTGGATTAATAGTAATGTCCATTAATTATAGTAATACCCTTCGT
Found at i:9358305 original size:24 final size:23
Alignment explanation
Indices: 9358234--9358296 Score: 63
Period size: 27 Copynumber: 2.5 Consensus size: 23
9358224 ATTAATAATA
* *
9358234 AGTTAGTGAAACGATTAGTTTTG
1 AGTTAATGAAACGATGAGTTTTG
9358257 ATTTAGTTAATGAAACGATGAGTTTTG
1 ----AGTTAATGAAACGATGAGTTTTG
9358284 AGTTAAATGAAAC
1 AGTT-AATGAAAC
9358297 ATGGCGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 4 0.12
24 8 0.24
27 21 0.64
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (23 bp):
AGTTAATGAAACGATGAGTTTTG
Found at i:9358926 original size:17 final size:17
Alignment explanation
Indices: 9358904--9358947 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
9358894 ATAGAAATAA
9358904 AGTCCAAAA-CCCAAAAC
1 AGTCCAAAAGCCC-AAAC
*
9358921 AGTCCAAAATGTCCAAAC
1 AGTCCAAAA-GCCCAAAC
9358939 AGTCCAAAA
1 AGTCCAAAA
9358948 TTTACAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 9 0.38
18 13 0.54
19 2 0.08
ACGTcount: A:0.50, C:0.30, G:0.09, T:0.11
Consensus pattern (17 bp):
AGTCCAAAAGCCCAAAC
Found at i:9358955 original size:18 final size:18
Alignment explanation
Indices: 9358917--9358955 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
9358907 CCAAAACCCA
*
9358917 AAACAGTCCAAAATGTCC
1 AAACAGTCCAAAATGTAC
*
9358935 AAACAGTCCAAAATTTAC
1 AAACAGTCCAAAATGTAC
9358953 AAA
1 AAA
9358956 ACTCTTAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.23, G:0.08, T:0.18
Consensus pattern (18 bp):
AAACAGTCCAAAATGTAC
Found at i:9359369 original size:20 final size:20
Alignment explanation
Indices: 9359346--9359384 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9359336 AATAAAACAA
9359346 ATTTAATTTAAT-TAAAAATT
1 ATTT-ATTTAATCTAAAAATT
*
9359366 ATTTATTTTATCTAAAAAT
1 ATTTATTTAATCTAAAAAT
9359385 ACAAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATTTAATCTAAAAATT
Found at i:9368563 original size:64 final size:64
Alignment explanation
Indices: 9368426--9368602 Score: 212
Period size: 64 Copynumber: 2.8 Consensus size: 64
9368416 GTGCAGGGTT
* * * *
9368426 CACACGGGTAAGACACACGGGCATGTGTCCAGGCCGTGTAACTCTCTGTGTTAGGATTTGGAGC
1 CACACGGGCAAGACACACGGGCATGTGTCCAGGCCGTGTAACTCTCTGAGTTAGGATTTAGAGA
* * * * * *
9368490 CATATGGGCAAAACACACGGGCATGTGTCCAGGCTGTGTAACTC-CTTGAGTTCGTATTTAGAGA
1 CACACGGGCAAGACACACGGGCATGTGTCCAGGCCGTGTAACTCTC-TGAGTTAGGATTTAGAGA
* * * *
9368554 CACACGGGCAAGAGACACGGGCATGTGTCCAAGCCATGTAACTCACTGA
1 CACACGGGCAAGACACACGGGCATGTGTCCAGGCCGTGTAACTCTCTGA
9368603 CTTCAGATTT
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
63 1 0.01
64 92 0.98
65 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (64 bp):
CACACGGGCAAGACACACGGGCATGTGTCCAGGCCGTGTAACTCTCTGAGTTAGGATTTAGAGA
Found at i:9369096 original size:20 final size:21
Alignment explanation
Indices: 9369063--9369102 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
9369053 ATATACCTAT
*
9369063 TGGTGTGTAGAGTGGGTGGAGA
1 TGGTGTGTA-AGTGGATGGAGA
9369085 TGGTGTGT-AGTGGATGGA
1 TGGTGTGTAAGTGGATGGA
9369103 ATAGGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.30
Consensus pattern (21 bp):
TGGTGTGTAAGTGGATGGAGA
Found at i:9369207 original size:60 final size:60
Alignment explanation
Indices: 9369126--9369252 Score: 184
Period size: 60 Copynumber: 2.1 Consensus size: 60
9369116 TCTGTATCTA
* * *
9369126 TACCGTATGACATATACATCTGATCGTATTTGTGTTATATGTGCATTTGTACTAATATGC
1 TACCATATGACATATACATCTGATCGTATTTGTGTTATACGTGCATCTGTACTAATATGC
* * * *
9369186 TACCATATGACATGTGCATCTGATCGTATTTGTGTTATACGTGCATCTGTATTAATCTGC
1 TACCATATGACATATACATCTGATCGTATTTGTGTTATACGTGCATCTGTACTAATATGC
9369246 TA-CATAT
1 TACCATAT
9369253 AAGGACTGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
59 5 0.08
60 55 0.92
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (60 bp):
TACCATATGACATATACATCTGATCGTATTTGTGTTATACGTGCATCTGTACTAATATGC
Found at i:9373295 original size:2 final size:2
Alignment explanation
Indices: 9373288--9373322 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9373278 AAGGAAATAA
9373288 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9373323 AGAAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9376885 original size:21 final size:21
Alignment explanation
Indices: 9376859--9376900 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9376849 CAATGAATTA
*
9376859 ACTTTTCTTGTTTTGATTTTG
1 ACTTTTCTTGTTTCGATTTTG
9376880 ACTTTTCTTGTTTCGATTTTG
1 ACTTTTCTTGTTTCGATTTTG
9376901 TTGATCACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (21 bp):
ACTTTTCTTGTTTCGATTTTG
Found at i:9378866 original size:16 final size:16
Alignment explanation
Indices: 9378845--9378907 Score: 90
Period size: 16 Copynumber: 3.9 Consensus size: 16
9378835 CGCTGTATTA
*
9378845 GAATAGAGGCATAATG
1 GAATAGAGGCGTAATG
9378861 GAATAGAGGCGTAATG
1 GAATAGAGGCGTAATG
*
9378877 GAATAGAGGTGTAATG
1 GAATAGAGGCGTAATG
* *
9378893 GATTAGAGGTGTAAT
1 GAATAGAGGCGTAAT
9378908 AGCAAATCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.24
Consensus pattern (16 bp):
GAATAGAGGCGTAATG
Found at i:9378936 original size:45 final size:44
Alignment explanation
Indices: 9378886--9378980 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 44
9378876 GGAATAGAGG
* *
9378886 TGTAATGGATTAGAGGTGTAATAGCAAATCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAA
* * *
9378931 TGTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
9378975 TGTAAT
1 TGTAAT
9378981 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 22 0.50
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAA
Found at i:9379162 original size:18 final size:17
Alignment explanation
Indices: 9379141--9379175 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9379131 TTATTATTAA
*
9379141 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
9379159 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
9379176 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:9379722 original size:13 final size:13
Alignment explanation
Indices: 9379704--9379728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9379694 GCCTTAACAA
9379704 GAGCAGCACTCAT
1 GAGCAGCACTCAT
9379717 GAGCAGCACTCA
1 GAGCAGCACTCA
9379729 AAACAGATTT
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:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (13 bp):
GAGCAGCACTCAT
Found at i:9383287 original size:44 final size:44
Alignment explanation
Indices: 9383224--9383313 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
9383214 TAAAATCATA
*
9383224 AGATATGCTTGTTATATGTGATGAATTTCAGTATAATAGCAAAG
1 AGATATGCTCGTTATATGTGATGAATTTCAGTATAATAGCAAAG
* *
9383268 AGATATGCTCGTTCTATGTGATGAATTTCAGTGTAATAGCAAAG
1 AGATATGCTCGTTATATGTGATGAATTTCAGTATAATAGCAAAG
9383312 AG
1 AG
9383314 CATACTTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (44 bp):
AGATATGCTCGTTATATGTGATGAATTTCAGTATAATAGCAAAG
Found at i:9389484 original size:21 final size:21
Alignment explanation
Indices: 9389459--9389506 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
9389449 AGAGTTGAAG
9389459 AAGCTACCTGGAAACAAGAAA
1 AAGCTACCTGGAAACAAGAAA
* * *
9389480 AAGCTACCTGGGAACCAGAAG
1 AAGCTACCTGGAAACAAGAAA
9389501 AAGCTA
1 AAGCTA
9389507 TGAAAGTGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (21 bp):
AAGCTACCTGGAAACAAGAAA
Found at i:9395297 original size:2 final size:2
Alignment explanation
Indices: 9395290--9395318 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9395280 TTGGTATGTT
9395290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9395319 TAAAATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9400308 original size:20 final size:21
Alignment explanation
Indices: 9400283--9400324 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
9400273 TTGTAAATTA
9400283 ATTTAATT-TTT-TGATTTATT
1 ATTTAATTGTTTATGA-TTATT
9400303 ATTTAATTGTTTATGATTATT
1 ATTTAATTGTTTATGATTATT
9400324 A
1 A
9400325 ATTGAGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 9 0.45
22 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATTTAATTGTTTATGATTATT
Found at i:9408471 original size:13 final size:13
Alignment explanation
Indices: 9408453--9408491 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
9408443 AGATAAATTG
9408453 AACATCTTTTTGT
1 AACATCTTTTTGT
*
9408466 AACATC-TTTAGTT
1 AACATCTTTTTG-T
9408479 AACATCTTTTTGT
1 AACATCTTTTTGT
9408492 TGATATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.18
13 14 0.64
14 4 0.18
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (13 bp):
AACATCTTTTTGT
Found at i:9415966 original size:11 final size:12
Alignment explanation
Indices: 9415933--9415966 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
9415923 TTTACTCTAC
9415933 ATTTATTTTGAT
1 ATTTATTTTGAT
*
9415945 ATTTGTTTTGAT
1 ATTTATTTTGAT
9415957 -TTTATTTTGA
1 ATTTATTTTGA
9415967 AACTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (12 bp):
ATTTATTTTGAT
Found at i:9423679 original size:23 final size:23
Alignment explanation
Indices: 9423649--9423702 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
9423639 GAAGTCCTAA
9423649 TTGGTGTGATAGGTTGGTTGGAG
1 TTGGTGTGATAGGTTGGTTGGAG
9423672 TTGGTGTGATAGGTTGGTTGGAG
1 TTGGTGTGATAGGTTGGTTGGAG
9423695 TTGGTGTG
1 TTGGTGTG
9423703 TAGCGAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.11, C:0.00, G:0.48, T:0.41
Consensus pattern (23 bp):
TTGGTGTGATAGGTTGGTTGGAG
Found at i:9423689 original size:13 final size:13
Alignment explanation
Indices: 9423649--9423689 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
9423639 GAAGTCCTAA
9423649 TTGGTGTGATAGG
1 TTGGTGTGATAGG
*
9423662 TTGGT-TG-GA-G
1 TTGGTGTGATAGG
9423672 TTGGTGTGATAGG
1 TTGGTGTGATAGG
9423685 TTGGT
1 TTGGT
9423690 TGGAGTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
10 6 0.26
11 3 0.13
12 3 0.13
13 11 0.48
ACGTcount: A:0.12, C:0.00, G:0.46, T:0.41
Consensus pattern (13 bp):
TTGGTGTGATAGG
Found at i:9429257 original size:4 final size:4
Alignment explanation
Indices: 9429248--9429274 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9429238 TGATTTTAGT
9429248 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
9429275 TCTTTTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:9429916 original size:3 final size:3
Alignment explanation
Indices: 9429908--9429959 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
9429898 TTGTTTTTAC
* * *
9429908 TAT TAT TAT TAT T-T AATT TAT TAT TAT TGT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
9429953 TAT TAT T
1 TAT TAT T
9429960 GNNNNNNNNN
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 38 0.93
4 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:9429932 original size:21 final size:20
Alignment explanation
Indices: 9429903--9429959 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
9429893 TGTCCTTGTT
*
9429903 TTTACTATTATTATTATTTAA
1 TTTATTATTATTATTA-TTAA
* *
9429924 TTTATTATTATTGTTATTAC
1 TTTATTATTATTATTATTAA
9429944 TATTATTATTATTATT
1 T-TTATTATTATTATT
9429960 GNNNNNNNNN
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTATTATTATTATTATTAA
Found at i:9432942 original size:38 final size:38
Alignment explanation
Indices: 9432891--9432968 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
9432881 ATTTGTTGGC
9432891 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
1 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
9432929 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
1 ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
9432967 AT
1 AT
9432969 GATCTCAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (38 bp):
ATTTGTGACTTATTTTTATCTTGGATTCATTTTACCAA
Found at i:9436376 original size:148 final size:146
Alignment explanation
Indices: 9436082--9436432 Score: 348
Period size: 148 Copynumber: 2.3 Consensus size: 146
9436072 AAATAGGCAT
* * * * *
9436082 TAAATATGGAATTTAACCATTCTTTATAATCTCAAAAAATTAGAGGGATTAGAATTGATATTTGG
1 TAAATATGAAATTTAACCATTCTTTATAATCTCAAAAAAGTAGAGGGACTAAAATTGATATTTGA
* ** * * * * *
9436147 CCATTAGCTTCTCATATTAAAGAAAGCAATTAACATTGGACAAGTATCATGTAAAAAGTAGAGGG
66 ACATTAGCTTCTCATAAAAAAAAAAACAACTAACATTGGACAAGTATCATGTAAAAAGCAGAGAG
*
9436212 GTTAAAAAAGTAGAAAA
131 ATT-AAAAAGTAGAAAA
*
9436229 TAAATATGAAATTTAACCATTTTTATATAATCTCAAAAAAGTAGAGGGACTAAAATTGATATTTG
1 TAAATATGAAATTTAACCATTCTT-TATAATCTCAAAAAAGTAGAGGGACTAAAATTGATATTTG
*** *
9436294 AACATTAGCTTCTCATGTAAGAAAAAAAAAACAACTAACATTGGATTGGTGTCATGTAAAAA-CA
65 AACATTAGCTTCTCA--T-A-AAAAAAAAAACAACTAACATTGGACAAGTATCATGTAAAAAGCA
* * *
9436358 GAGAGATTAGAATTGAAAAATAGGAAT
126 GAGAGATT---A---AAAAGTAGAAAA
*
9436385 TAAATATTG-AATTTAACTATTCTTATATAATCTC-AAAAAGTAGAGGGA
1 TAAATA-TGAAATTTAACCATTCTT-TATAATCTCAAAAAAGTAGAGGGA
9436433 TTGAACCCCA
Statistics
Matches: 169, Mismatches: 24, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
147 22 0.13
148 50 0.30
150 1 0.01
151 8 0.05
152 32 0.19
153 2 0.01
155 14 0.08
156 38 0.22
157 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (146 bp):
TAAATATGAAATTTAACCATTCTTTATAATCTCAAAAAAGTAGAGGGACTAAAATTGATATTTGA
ACATTAGCTTCTCATAAAAAAAAAAACAACTAACATTGGACAAGTATCATGTAAAAAGCAGAGAG
ATTAAAAAGTAGAAAA
Found at i:9441961 original size:17 final size:18
Alignment explanation
Indices: 9441930--9441964 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
9441920 AAAAGCCTCA
*
9441930 TTTTATTTATTTATTTAC
1 TTTTATTTATATATTTAC
9441948 TTTT-TTTATATATTTAC
1 TTTTATTTATATATTTAC
9441965 ATCGCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTATATATTTAC
Found at i:9442382 original size:30 final size:30
Alignment explanation
Indices: 9442343--9442435 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
9442333 TCAGGCATTA
* *
9442343 ACATTAGCATCGACTACTGCATGGGCATCT
1 ACATCAGCATCGACTACTACATGGGCATCT
9442373 ACATCAGCATCGACTACTACATGGGCATCT
1 ACATCAGCATCGACTACTACATGGGCATCT
* * *
9442403 ACATC-GACATCGATTGCTATATGGGCATCT
1 ACATCAG-CATCGACTACTACATGGGCATCT
9442433 ACA
1 ACA
9442436 CCTATATCGT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 1 0.02
30 56 0.98
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (30 bp):
ACATCAGCATCGACTACTACATGGGCATCT
Found at i:9445896 original size:19 final size:18
Alignment explanation
Indices: 9445869--9445907 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
9445859 ATTTTTTATA
*
9445869 TATTCTTTATATTGTTTTT
1 TATTCTTTATAAT-TTTTT
*
9445888 TATTTTTTATAATTTTTT
1 TATTCTTTATAATTTTTT
9445906 TA
1 TA
9445908 AAAATATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TATTCTTTATAATTTTTT
Found at i:9445967 original size:19 final size:19
Alignment explanation
Indices: 9445912--9445967 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 19
9445902 TTTTTAAAAA
**
9445912 TATAAATT-TTTAAATTTT
1 TATAAATTATTTTGATTTT
*
9445930 TATAAA-TATTTTGAATTT
1 TATAAATTATTTTGATTTT
9445948 TATAAATTATTTTGATTTT
1 TATAAATTATTTTGATTTT
9445967 T
1 T
9445968 TTGTATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 1 0.03
18 19 0.59
19 12 0.38
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (19 bp):
TATAAATTATTTTGATTTT
Done.