Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_pilon, whole genome shotgun sequence
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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 17
Found at i:3442807 original size:136 final size:136
Alignment explanation
Indices: 3442559--3442913 Score: 568
Period size: 136 Copynumber: 2.6 Consensus size: 136
3442549 TGTTGATATG
* * * * * *
3442559 AGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCT-TGTTGGATGAATTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTTCCCTCTGTCGGATGAGTTCTTCTCATTAT
*
3442623 GAACTCTCCATTAGAAACATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCG
66 GAACTCTCAATTAGAAACATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCG
3442688 AGTGAT
131 AGTGAT
3442694 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTTCCCTCTGTCGGATGAGTTCTTCTCATTAT
** * *
3442759 GAACTCTCAATTAGAAATGTCAATCCCTCAAGGGAGGTGTCACTGATTCAAAATGTCGTGAATCG
66 GAACTCTCAATTAGAAACATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCG
3442824 AGTGAT
131 AGTGAT
* *
3442830 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTTCCCTCTTTCGTATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* *
3442895 GAACTCTCTATTGGAAACA
66 GAACTCTCAATTAGAAACA
3442914 CTGATGCGAG
Statistics
Matches: 202, Mismatches: 17, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
135 36 0.18
136 166 0.82
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (136 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTTTCCCTCTGTCGGATGAGTTCTTCTCATTAT
GAACTCTCAATTAGAAACATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCG
AGTGAT
Found at i:3442940 original size:92 final size:91
Alignment explanation
Indices: 3442830--3443002 Score: 267
Period size: 92 Copynumber: 1.9 Consensus size: 91
3442820 ATCGAGTGAT
* * *
3442830 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTT-TTCCCTCTTTCGTATGAGTTCTTCTCATTA
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CCTCGTTAG-ACGAGTTCTTCTCATTA
*
3442894 TGAACTCTCTATTGGAAACACTGATGCG
64 TGAACTCTCTACTGGAAACACTGATGCG
*
3442922 AGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTAGACGAGTTCTTCTCATTATG
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTAGACGAGTTCTTCTCATTATG
*
3442987 AACTCTGTACTGGAAA
66 AACTCTCTACTGGAAA
3443003 TATCGATATG
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
91 32 0.43
92 40 0.54
93 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.38
Consensus pattern (91 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTAGACGAGTTCTTCTCATTATG
AACTCTCTACTGGAAACACTGATGCG
Found at i:3442957 original size:20 final size:20
Alignment explanation
Indices: 3442934--3442990 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
3442924 GTCGAACAAG
*
3442934 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTAC
* * *
3442954 TTCTTCCTCGTTA-G-ACGAG
1 TTCTT-CTCATTATGAACTAC
3442973 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
3442991 CTGTACTGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
18 6 0.21
19 8 0.29
20 8 0.29
21 6 0.21
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.46
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTAC
Found at i:3443316 original size:61 final size:61
Alignment explanation
Indices: 3443264--3443489 Score: 389
Period size: 61 Copynumber: 3.7 Consensus size: 61
3443254 AGAGAAGCTC
* *
3443264 TCTCAAGTGAGATAAATTTTGCTTCGAAGGAAAATTGTCTCAAGGGTTTTAAGAAAAACCA
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGGGTTTTAAGAAAAACCA
* *
3443325 TCTCAAATGAGATAAATTTTGTTTCAAAGGAAAATCGTCTCAAGGGTTTTAAGAAAAACCA
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGGGTTTTAAGAAAAACCA
3443386 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGGGTTTTAAGAAAAACCA
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGGGTTTTAAGAAAAACCA
** *
3443447 TCTCAAGTGAGATAAATTTTGTTTTGAAGGAAAATTATCTCAA
1 TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAA
3443490 AAATTTGTTT
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 156 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (61 bp):
TCTCAAGTGAGATAAATTTTGTTTCAAAGGAAAATTGTCTCAAGGGTTTTAAGAAAAACCA
Found at i:3443508 original size:29 final size:29
Alignment explanation
Indices: 3443473--3443546 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
3443463 TTTTGTTTTG
* * *
3443473 AAGGAAAATTATCTCAAAAATTTGTTTC-
1 AAGGAAAATTGTCTCAAAAACTTATTTCA
*
3443501 AA-GAGAAACTGTCTCAAAAACTTATTTCA
1 AAGGA-AAATTGTCTCAAAAACTTATTTCA
3443530 AAGGAAAATTGTCTCAA
1 AAGGAAAATTGTCTCAA
3443547 GGATTTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 2 0.05
28 21 0.55
29 13 0.34
30 2 0.05
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.30
Consensus pattern (29 bp):
AAGGAAAATTGTCTCAAAAACTTATTTCA
Found at i:3443598 original size:36 final size:35
Alignment explanation
Indices: 3443551--3443653 Score: 107
Period size: 36 Copynumber: 2.9 Consensus size: 35
3443541 TCTCAAGGAT
* * *
3443551 TTTTAAGAAAAACCATCTCAAGCGAGACAAATTTGG
1 TTTTAAGAAAAACAATCTCAAGGGAGACAAACTT-G
* *
3443587 TTTTAAGAAAAATAATCTTAAGGGAGACAAAACTTG
1 TTTTAAGAAAAACAATCTCAAGGGAGAC-AAACTTG
* * **
3443623 TTTCAAGAGAAACTGTCTCAAGGGAGACAAA
1 TTTTAAGAAAAACAATCTCAAGGGAGACAAA
3443654 ATTCATTTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
35 3 0.05
36 47 0.85
37 5 0.09
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (35 bp):
TTTTAAGAAAAACAATCTCAAGGGAGACAAACTTG
Found at i:3443678 original size:36 final size:36
Alignment explanation
Indices: 3443565--3443679 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
3443555 AAGAAAAACC
* * * * *
3443565 ATCTCAAGCGAGAC-AAATTTGGTTTTAAGAAAAATA
1 ATCTCAAGGGAGACAAAACTT-ATTTCAAGAGAAATA
* *
3443601 ATCTTAAGGGAGACAAAACTTGTTTCAAGAGAAACT-
1 ATCTCAAGGGAGACAAAACTTATTTCAAGAGAAA-TA
* *
3443637 GTCTCAAGGGAGACAAAA-TTCATTTCAAGGGAAATA
1 ATCTCAAGGGAGACAAAACTT-ATTTCAAGAGAAATA
*
3443673 TTCTCAA
1 ATCTCAA
3443680 AATTTTCAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
35 3 0.05
36 56 0.86
37 6 0.09
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (36 bp):
ATCTCAAGGGAGACAAAACTTATTTCAAGAGAAATA
Found at i:3443690 original size:60 final size:60
Alignment explanation
Indices: 3443623--3443739 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
3443613 ACAAAACTTG
*
3443623 TTTCAAGAGAAACTGTCTCA-AGGGAGACAAAATTCATTTCAAGGGAAATAT-TCTCAAAAT
1 TTTCAAGAGAAACTATCTCAGA-GGAGACAAAATTCATTTCAAGGGAAA-ATGTCTCAAAAT
* * * **
3443683 TTTCAAGAGAAATTATTTCAGAGGAGAGAAAATTTGTTTCAAGGGAAAATGTCTCAA
1 TTTCAAGAGAAACTATCTCAGAGGAGACAAAATTCATTTCAAGGGAAAATGTCTCAA
3443740 GTGAAACAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 46 0.94
61 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (60 bp):
TTTCAAGAGAAACTATCTCAGAGGAGACAAAATTCATTTCAAGGGAAAATGTCTCAAAAT
Found at i:3443868 original size:40 final size:40
Alignment explanation
Indices: 3443775--3444108 Score: 512
Period size: 40 Copynumber: 8.4 Consensus size: 40
3443765 AACTATCTCA
* * * * * **
3443775 AGCGAGATAAAATCTTTTATTTCGAGG-GAAACTATCTCA
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
3443814 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
3443854 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
3443894 AGCGAGATAAAATCTTCTATTTCAAGGAAAAA-AATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
3443933 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAA-AATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
* *
3443972 AGTGAGATAAAATTTTCTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
3444012 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
**
3444052 AGTAAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
*
3444092 AGTGAGATAAAATCTTC
1 AGCGAGATAAAATCTTC
3444109 CGTATTAAAT
Statistics
Matches: 277, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 99 0.36
40 178 0.64
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (40 bp):
AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTG
Found at i:3443911 original size:80 final size:80
Alignment explanation
Indices: 3443775--3444108 Score: 512
Period size: 79 Copynumber: 4.2 Consensus size: 80
3443765 AACTATCTCA
* * * * * **
3443775 AGCGAGATAAAATCTTTTATTTCGAGG-GAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAA
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAA
3443839 GGAAAAACAATCTTG
66 GGAAAAACAATCTTG
* *
3443854 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCTATTTCAA
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAA
3443919 GGAAAAA-AATCTTG
66 GGAAAAACAATCTTG
* *
3443933 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAA-AATCTTGAGTGAGATAAAATTTTCTGTTTCAA
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAA
3443997 GGAAAAACAATCTTG
66 GGAAAAACAATCTTG
* **
3444012 AGTGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTAAGATAAAATCTTCTGTTTCAA
1 AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAA
3444077 GGAAAAACAATCTTG
66 GGAAAAACAATCTTG
*
3444092 AGTGAGATAAAATCTTC
1 AGCGAGATAAAATCTTC
3444109 CGTATTAAAT
Statistics
Matches: 238, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
78 36 0.15
79 101 0.42
80 101 0.42
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (80 bp):
AGCGAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCTGTTTCAA
GGAAAAACAATCTTG
Found at i:3444048 original size:23 final size:23
Alignment explanation
Indices: 3444022--3444090 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 23
3444012 AGTGAGATAA
3444022 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
** *
3444045 AATC-T-TGAGT-AA-G-ATAA-
1 AATCTTCTGTTTCAAGGAAAAAC
3444062 AATCTTCTGTTTCAAGGAAAAAC
1 AATCTTCTGTTTCAAGGAAAAAC
3444085 AATCTT
1 AATCTT
3444091 GAGTGAGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
17 4 0.12
18 4 0.12
19 4 0.12
20 4 0.12
21 4 0.12
22 4 0.12
23 10 0.29
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (23 bp):
AATCTTCTGTTTCAAGGAAAAAC
Found at i:3444607 original size:24 final size:22
Alignment explanation
Indices: 3444574--3444640 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 22
3444564 TCTTTTATTT
3444574 TCAAAAGTTTTGAAAATATCAA
1 TCAAAAGTTTTGAAAATATCAA
* *
3444596 TTAGAAGAGTTTTGAAAAATATTTAA
1 TCA-AA-AGTTTTG-AAAATA-TCAA
3444622 TCAAAAGTTTTGAAAATAT
1 TCAAAAGTTTTGAAAATAT
3444641 TGCCTCTCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
22 3 0.08
23 8 0.21
24 14 0.37
25 8 0.21
26 5 0.13
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (22 bp):
TCAAAAGTTTTGAAAATATCAA
Found at i:3446339 original size:18 final size:19
Alignment explanation
Indices: 3446316--3446355 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3446306 ACATCTGATC
3446316 TTTGCTTCTTC-TTCTTTT
1 TTTGCTTCTTCTTTCTTTT
*
3446334 TTTGCTTTTTCTTTCTTTT
1 TTTGCTTCTTCTTTCTTTT
3446353 TTT
1 TTT
3446356 TTTTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTGCTTCTTCTTTCTTTT
Found at i:3446370 original size:32 final size:33
Alignment explanation
Indices: 3446329--3446401 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
3446319 GCTTCTTCTT
3446329 CTTTTTTTGCTTTTT-CTTTCTTTTTTTTTTTA
1 CTTTTTTTGCTTTTTGCTTTCTTTTTTTTTTTA
* *
3446361 CTTTTTTTGCTTTTTGTTTTTTTTTTTTTTTTA
1 CTTTTTTTGCTTTTTGCTTTCTTTTTTTTTTTA
3446394 CTTTTTTT
1 CTTTTTTT
3446402 TACAAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 15 0.39
33 23 0.61
ACGTcount: A:0.03, C:0.10, G:0.04, T:0.84
Consensus pattern (33 bp):
CTTTTTTTGCTTTTTGCTTTCTTTTTTTTTTTA
Found at i:3446383 original size:18 final size:17
Alignment explanation
Indices: 3446316--3446401 Score: 69
Period size: 16 Copynumber: 5.2 Consensus size: 17
3446306 ACATCTGATC
*
3446316 TTTGCTTCTTCTTCTTTT
1 TTTGCTT-TTTTTCTTTT
3446334 TTTGC--TTTTTCTTTCT
1 TTTGCTTTTTTTCTTT-T
3446350 TTT--TTTTTTTACTTTT
1 TTTGCTTTTTTT-CTTTT
3446366 TTTGCTTTTTGTT-TTTT
1 TTTGCTTTTT-TTCTTTT
3446383 TTT--TTTTTTTACTTTT
1 TTTGCTTTTTTT-CTTTT
3446399 TTT
1 TTT
3446402 TACAAAATAT
Statistics
Matches: 58, Mismatches: 1, Indels: 20
0.73 0.01 0.25
Matches are distributed among these distances:
14 2 0.03
15 13 0.22
16 20 0.34
17 11 0.19
18 10 0.17
19 2 0.03
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTGCTTTTTTTCTTTT
Found at i:3448390 original size:15 final size:15
Alignment explanation
Indices: 3448370--3448399 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3448360 AATTAAAAGA
*
3448370 ATCCTTAATTTATTC
1 ATCCTTAATTCATTC
3448385 ATCCTTAATTCATTC
1 ATCCTTAATTCATTC
3448400 TATATTCGAA
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:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (15 bp):
ATCCTTAATTCATTC
Found at i:3450950 original size:24 final size:25
Alignment explanation
Indices: 3450918--3450971 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
3450908 TAAGAAAAAT
*
3450918 CGTTTTTAAAACAAAA-TTGGTTTG
1 CGTTTTTAAAACAAAAGCTGGTTTG
*
3450942 CGTTTTTAAGACAAAAGCTGGTTTG
1 CGTTTTTAAAACAAAAGCTGGTTTG
3450967 CGTTT
1 CGTTT
3450972 ACCAAAGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (25 bp):
CGTTTTTAAAACAAAAGCTGGTTTG
Found at i:3455788 original size:43 final size:43
Alignment explanation
Indices: 3455735--3456003 Score: 360
Period size: 43 Copynumber: 6.3 Consensus size: 43
3455725 TGGTAACAAA
*** * * *
3455735 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
* * *
3455778 AAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
* * *
3455821 AAACACCGCAATAGGTATTGATATTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
*
3455864 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
*
3455907 AAACGCCGCAATAGGTGTTGAGATTTAGCGACGTTTTTTCC-AC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCG-TTTTTCCAAC
* * *
3455950 AAACGTCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
*
3455993 AAACACCGCAA
1 AAACGCCGCAA
3456004 AAGGGCATAT
Statistics
Matches: 205, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
42 7 0.03
43 191 0.93
44 7 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
Found at i:3456182 original size:21 final size:21
Alignment explanation
Indices: 3456156--3456213 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3456146 ATTTTCCAAT
*
3456156 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
3456177 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
*
3456198 AAA-ATGAAATCCATAA
1 AAACTTGAAATCCATAA
3456214 TAATAAATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:3460111 original size:53 final size:52
Alignment explanation
Indices: 3460009--3460168 Score: 293
Period size: 52 Copynumber: 3.1 Consensus size: 52
3459999 TAACAACAAA
*
3460009 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAATCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
*
3460061 ATACATTATAATTTAGAAACATTAAAAGTACTTATGCATAAACAGTCTTCAAC
1 ATACATTATAATTTAGAAACATT-AAAGTACTTATGCATAAACAGTCTTCACC
3460114 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
1 ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
3460166 ATA
1 ATA
3460169 TTTTCAGTAC
Statistics
Matches: 104, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
52 54 0.52
53 50 0.48
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (52 bp):
ATACATTATAATTTAGAAACATTAAAGTACTTATGCATAAACAGTCTTCACC
Found at i:3461425 original size:42 final size:42
Alignment explanation
Indices: 3461209--3461401 Score: 223
Period size: 42 Copynumber: 4.6 Consensus size: 42
3461199 CCATGTTTTA
* * * * * *
3461209 CGGCGTTTATACAAAAAACGCCGCTA-ATTTACCACTCTATTG
1 CGGCGTTTTTACTATAAACGCCGCTACATGT-CTACTATATTG
** * * *
3461251 CGGCGTTTTTGGTATAAACGCCGCTAAATGT-TAAATATATTA
1 CGGCGTTTTTACTATAAACGCCGCTACATGTCT-ACTATATTG
*
3461293 CGGCG-TTTTAGCTA-AAACGCCACTACATGTCTACTATATTG
1 CGGCGTTTTTA-CTATAAACGCCGCTACATGTCTACTATATTG
3461334 CGGCGTTTTTACTATAAACGCCGCTACATGTCTACTATATTG
1 CGGCGTTTTTACTATAAACGCCGCTACATGTCTACTATATTG
3461376 CGGCGTTTTTACTATAAACGCCGCTA
1 CGGCGTTTTTACTATAAACGCCGCTA
3461402 TTGTTTAACC
Statistics
Matches: 128, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
41 33 0.26
42 92 0.72
43 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (42 bp):
CGGCGTTTTTACTATAAACGCCGCTACATGTCTACTATATTG
Found at i:3464749 original size:50 final size:50
Alignment explanation
Indices: 3464671--3464770 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
3464661 CAATTTCCTA
*
3464671 CTTGTTGATCTTCAAACGAAAATTCTATTTTGCGTACAACTTCATATTAT
1 CTTGTTGATCTTCAAACGAAAATACTATTTTGCGTACAACTTCATATTAT
* * *
3464721 CTTGTTGATCTTCAAACGAGAATACTATTTTGTGTACAACTTGATATTAT
1 CTTGTTGATCTTCAAACGAAAATACTATTTTGCGTACAACTTCATATTAT
3464771 TTTTTTTGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (50 bp):
CTTGTTGATCTTCAAACGAAAATACTATTTTGCGTACAACTTCATATTAT
Found at i:3466625 original size:4 final size:4
Alignment explanation
Indices: 3466605--3466639 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
3466595 CCTCTCTCAT
3466605 TTTC TTT- TTTC -TTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
3466640 CTCAAAAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:3469389 original size:81 final size:81
Alignment explanation
Indices: 3469250--3469408 Score: 228
Period size: 81 Copynumber: 2.0 Consensus size: 81
3469240 TGGATGACTC
* * * * *
3469250 CAGGCATCACAATGAATCAACTGCACAGACAGGTCTGGCAGGAAGAGATTTGGCTCAGAATACTA
1 CAGGCATCACAATAAATCAACTGCACAGACAAGCCTCGCAAGAAGAGATTTGGCTCAGAATACTA
3469315 CAGACGATATTGAGTA
66 CAGACGATATTGAGTA
* * *
3469331 CAGGCATCACGATAAATCAACTGCACAGACAAGCCTCGTAAGAAGAGATTTGGGTCAGAATACTA
1 CAGGCATCACAATAAATCAACTGCACAGACAAGCCTCGCAAGAAGAGATTTGGCTCAGAATACTA
**
3469396 CAGTGGATATTGA
66 CAGACGATATTGA
3469409 ACTCTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 68 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.20
Consensus pattern (81 bp):
CAGGCATCACAATAAATCAACTGCACAGACAAGCCTCGCAAGAAGAGATTTGGCTCAGAATACTA
CAGACGATATTGAGTA
Found at i:3471464 original size:14 final size:15
Alignment explanation
Indices: 3471441--3471469 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3471431 GTATGTATAT
3471441 TTTTATATTTATAAA
1 TTTTATATTTATAAA
3471456 TTTTA-ATTTATAAA
1 TTTTATATTTATAAA
3471470 CGTATTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTATATTTATAAA
Found at i:3471595 original size:17 final size:18
Alignment explanation
Indices: 3471575--3471614 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3471565 TATTAAGTTA
*
3471575 ATAAATT-TGATTTTTAT
1 ATAAATTATGATTATTAT
3471592 ATAAATTATGATTATTAT
1 ATAAATTATGATTATTAT
3471610 ATAAA
1 ATAAA
3471615 AAGTTAGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATAAATTATGATTATTAT
Found at i:3471997 original size:40 final size:41
Alignment explanation
Indices: 3471927--3472025 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 41
3471917 AAATGACCAA
3471927 CAAATTCGCAACGCGAA-CTCTAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGAATCTCT-ATTTCGCAACACAAGTTTC
* * * *
3471967 CAAATTCGCAACTCGAATTTCT-TTTCCGCAACGCAATTTTC
1 CAAATTCGCAACGCGAATCTCTATTT-CGCAACACAAGTTTC
*
3472008 CAAATTTGCAACGCGAAT
1 CAAATTCGCAACGCGAAT
3472026 ATATAAATCG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
39 3 0.06
40 23 0.46
41 24 0.48
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (41 bp):
CAAATTCGCAACGCGAATCTCTATTTCGCAACACAAGTTTC
Found at i:3472076 original size:19 final size:20
Alignment explanation
Indices: 3472052--3472114 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
3472042 AGAAGTCAAA
*
3472052 TTCGCAAAGCG-CGTTTATT
1 TTCGCAAAGCGAAGTTTATT
* *
3472071 TTCGCAACGCGAATTTTATT
1 TTCGCAAAGCGAAGTTTATT
* *
3472091 TTCGCAACGCGAATTTTATT
1 TTCGCAAAGCGAAGTTTATT
3472111 TTCG
1 TTCG
3472115 AATTCGAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TTCGCAAAGCGAAGTTTATT
Found at i:3472090 original size:20 final size:20
Alignment explanation
Indices: 3472065--3472114 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3472055 GCAAAGCGCG
3472065 TTTATTTTCGCAACGCGAAT
1 TTTATTTTCGCAACGCGAAT
3472085 TTTATTTTCGCAACGCGAAT
1 TTTATTTTCGCAACGCGAAT
3472105 TTTATTTTCG
1 TTTATTTTCG
3472115 AATTCGAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (20 bp):
TTTATTTTCGCAACGCGAAT
Found at i:3474846 original size:22 final size:22
Alignment explanation
Indices: 3474818--3474874 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
3474808 ACATCTACAT
3474818 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
3474840 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
3474862 TTTTCAAAGATGA
1 TCTTCAAAGATGA
3474875 AAACTTTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:3475619 original size:45 final size:45
Alignment explanation
Indices: 3475541--3476240 Score: 759
Period size: 45 Copynumber: 15.6 Consensus size: 45
3475531 ACATATGTAT
* * * **
3475541 GACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTTATCTGTAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* *
3475586 GATCTTCAGTACAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* * * **
3475631 GACCTACAGTGCATGATGTTTTCAAAACCTTCGAGTCATCTGTAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* ** * *
3475676 GACCTTCAGTACATAATGTTTTGAAAACTTTCGGGTCATCCATAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
** * * * **
3475721 GACCTAGAGTGCATGATGTTTTCAAAGCCTTCGGGTTATCTGTAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* *
3475766 GACCTAT-AGTGCAGGATGTTTTCAAAGCCTTTGGGTCAT-C-T--
1 GACCT-TCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* *
3475807 --CCTTTAGTGCAGGATGTTTTCAAAACATTCGGGTCATCCATAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* * ***
3475850 GTCCTACAGTGCAGGATGTTTTCAAAACCTTCGGGTCATATGTAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* ** **
3475895 GACCTTCAGTGCATGATGTTTTCAAAGTCTTCGGGTCATCTGTAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* * * *
3475940 GACCTACAGTGCATGATGTTTTCAAAGCCTTCGGGTCATCTATAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* *
3475985 GACCTTCAGTGTAGGATGTTTTCAAAACCTTCAGGTCATCCATAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
* * **
3476030 GACCTACAATGCAGGATGTTTTCAAAACCTTCGGGTCATCTGTAA
1 GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
*
3476075 GACTTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGTCATCCATAA
1 GACCTTCAGTGCAGGATGTTTTC-AAAA-CCTTCGGGTCATCCATAA
* * *
3476122 GACCTACAGTGCAGAATATTTTCAAAAAGCCTTCGGGTCATCCATAA
1 GACCTTCAGTGCAGGATGTTTTC-AAAA-CCTTCGGGTCATCCATAA
* * * * *
3476169 GACCTTCACTGCAAGATGTTTTTAAAGTCCTTCAGG-CTATCCATAA
1 GACCTTCAGTGCAGGATGTTTTCAAA-ACCTTCGGGTC-ATCCATAA
*
3476215 GACCTTTAGTGCAGGATGTTTTCAAA
1 GACCTTCAGTGCAGGATGTTTTCAAA
3476241 GGAGATTTTA
Statistics
Matches: 555, Mismatches: 88, Indels: 23
0.83 0.13 0.03
Matches are distributed among these distances:
38 1 0.00
39 32 0.06
40 1 0.00
41 1 0.00
43 1 0.00
45 399 0.72
46 44 0.08
47 76 0.14
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (45 bp):
GACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGTCATCCATAA
Found at i:3481471 original size:6 final size:6
Alignment explanation
Indices: 3481454--3481496 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
3481444 ACCCTTGTGT
*
3481454 CATGAC CGTGAC CATGAC CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC CATGAC CATGAC C
3481497 TATGGTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:3482438 original size:463 final size:464
Alignment explanation
Indices: 3481574--3482501 Score: 1774
Period size: 463 Copynumber: 2.0 Consensus size: 464
3481564 TATTTCTTTT
3481574 TAAGGAAACTTGTATAACCTATCCAGATCCATAGAAATTATTCTTGAATACTTAAAACCTTTTCC
1 TAAGGAAACTTGTATAACCTATCCAGATCCATAGAAATTATTCTTGAATACTTAAAACCTTTTCC
3481639 ATCTCCAAGGAAAGTCTTAATGTTCACATCGTTCAATAAAAAACTTGATAAATTTGTAGCAATAA
66 ATCTCCAAGGAAAGTCTTAATGTTCACATCGTTCAATAAAAAACTTGATAAATTTGTAGCAATAA
3481704 CTGTCATAGCAGTTAATGCTAAAATCACACTAGTAACAAATTTACTCATTTTCTTATCATTACGA
131 CTGTCATAGCAGTTAATGCTAAAATCACACTAGTAACAAATTTACTCATTTTCTTATCATTACGA
3481769 ACTTGACCACTTTTAAAGTTCTTGAGAATCCATCTCAATCTAAACAATATTCATTGTAGCATGGA
196 ACTTGACCACTTTTAAAGTTCTTGAGAATCCATCTCAATCTAAACAATATTCATTGTAGCATGGA
*
3481834 AAAATGGACAATCCATTTTCACATATTTACCTTCACAAGGTAACTCTATCCAATCTTATGGACTT
261 AAAATGGACAATCCATTTTCACATATTTACCTTCACAAGGTAACTATATCCAATCTTATGGACTT
3481899 GATATCCATTTTCAAACCAACTCATAACCATTTGATTTACTAATAATTCAACTTTCTTTAAACGT
326 GATATCCATTTTCAAACCAACTCATAACCATTTGATTTACTAATAATTCAACTTTCTTTAAACGT
*
3481964 TTAGCGGAAATCATATTACTGCTTATGTATTTCCTCTTGCTCAAATCAACAATGC-TTT-CAATT
391 TTAGCGGAAATCATATTACCGCTTATGTATTTCCTCTTGCTCAAATCAACAATGCTTTTACAATT
3482027 TATTGCCTA
456 TATTGCCTA
3482036 TAAGGAAACTTGTATAACCTATCCAGATCCATAGAAATTATTCTTGAATACTTAAAACCTTTTCC
1 TAAGGAAACTTGTATAACCTATCCAGATCCATAGAAATTATTCTTGAATACTTAAAACCTTTTCC
3482101 ATCTCCAAGGAAAGTCTTAATGTTCACATCGTTCAATAAAAAAACTTGATAAATTTGTAGCAATA
66 ATCTCCAAGGAAAGTCTTAATGTTCACATCGTTCAAT-AAAAAACTTGATAAATTTGTAGCAATA
3482166 ACT-TCATAGCAGTTAATGCTAAAATCACACTAGTAAACAAATTTACTCATTTTCTTATCATTAC
130 ACTGTCATAGCAGTTAATGCTAAAATCACACTAGT-AACAAATTTACTCATTTTCTTATCATTAC
3482230 GAACTTGA-CACTTTTAAAGTTCTTGAGAATCCATCTCAATCTAAACAATAATTCATTGTAGCAT
194 GAACTTGACCACTTTTAAAGTTCTTGAGAATCCATCTCAATCTAAACAAT-ATTCATTGTAGCAT
3482294 GGAAAAATGGACAATCCATTTTCACATATTTACCTTCACAAGGTAACTATATCCAATCTTATGGA
258 GGAAAAATGGACAATCCATTTTCACATATTTACCTTCACAAGGTAACTATATCCAATCTTATGGA
3482359 CTTGATATCCATTTTCAAACCAACTCATAACCATTTGATTTACTAATAATTCAACTTTCTTTAAA
323 CTTGATATCCATTTTCAAACCAACTCATAACCATTTGATTTACTAATAATTCAACTTTCTTTAAA
3482424 CGTTTAGCGGAAATCATATTACCGCTTATGTATTTCCTCTTGCTCAAATCAACAATGCTTTTAAC
388 CGTTTAGCGGAAATCATATTACCGCTTATGTATTTCCTCTTGCTCAAATCAACAATGCTTTT-AC
3482489 AATTTATTGCCTA
452 AATTTATTGCCTA
3482502 GCTTAAATAT
Statistics
Matches: 458, Mismatches: 2, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
462 174 0.38
463 267 0.58
464 3 0.01
466 14 0.03
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (464 bp):
TAAGGAAACTTGTATAACCTATCCAGATCCATAGAAATTATTCTTGAATACTTAAAACCTTTTCC
ATCTCCAAGGAAAGTCTTAATGTTCACATCGTTCAATAAAAAACTTGATAAATTTGTAGCAATAA
CTGTCATAGCAGTTAATGCTAAAATCACACTAGTAACAAATTTACTCATTTTCTTATCATTACGA
ACTTGACCACTTTTAAAGTTCTTGAGAATCCATCTCAATCTAAACAATATTCATTGTAGCATGGA
AAAATGGACAATCCATTTTCACATATTTACCTTCACAAGGTAACTATATCCAATCTTATGGACTT
GATATCCATTTTCAAACCAACTCATAACCATTTGATTTACTAATAATTCAACTTTCTTTAAACGT
TTAGCGGAAATCATATTACCGCTTATGTATTTCCTCTTGCTCAAATCAACAATGCTTTTACAATT
TATTGCCTA
Found at i:3484943 original size:40 final size:40
Alignment explanation
Indices: 3484888--3485009 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
3484878 ACTGTAGTGC
3484888 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3484928 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3484968 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3485008 TA
1 TA
3485010 TAACCTGCAG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:3486233 original size:30 final size:30
Alignment explanation
Indices: 3486176--3486239 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
3486166 TTCTTCATCA
* * *
3486176 TTTTCCAAAATTTACGAATTTATCCCAAAC
1 TTTTCCAAAACTTACGAAATGATCCCAAAC
* *
3486206 TTTT-CAAAACTTACGAAATGATCCCCAAT
1 TTTTCCAAAACTTACGAAATGATCCCAAAC
3486235 TTTTC
1 TTTTC
3486240 TAAGGCTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCAAAC
Found at i:3495942 original size:39 final size:39
Alignment explanation
Indices: 3495887--3495984 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
3495877 TGCGGTACGA
*
3495887 ACTTACCTTGTGCACAAAGCAAAGGAGCATGC-GATAAGG
1 ACTTACCTTGAGCACAAAGCAAAGGAGCATGCAGA-AAGG
* ** *
3495926 GCTTACCTTGAGCACAAAGCCGAGGAGCCTGCAGAAAGG
1 ACTTACCTTGAGCACAAAGCAAAGGAGCATGCAGAAAGG
* *
3495965 ACTTACCCTGAGCATAAAGC
1 ACTTACCTTGAGCACAAAGC
3495985 TGAGGAGTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
39 48 0.96
40 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (39 bp):
ACTTACCTTGAGCACAAAGCAAAGGAGCATGCAGAAAGG
Found at i:3495990 original size:39 final size:39
Alignment explanation
Indices: 3495887--3496006 Score: 116
Period size: 39 Copynumber: 3.1 Consensus size: 39
3495877 TGCGGTACGA
* * **
3495887 ACTTACCTTGTGCACAAAGCAAAGGAGCATGCGATAAGG
1 ACTTACCCTGAGCACAAAGCCGAGGAGCATGCGATAAGG
* * *
3495926 GCTTACCTTGAGCACAAAGCCGAGGAGCCTGCAGA-AAGG
1 ACTTACCCTGAGCACAAAGCCGAGGAGCATGC-GATAAGG
* * * * *
3495965 ACTTACCCTGAGCATAAAGCTGAGGAGTATACTATAAGG
1 ACTTACCCTGAGCACAAAGCCGAGGAGCATGCGATAAGG
3496004 ACT
1 ACT
3496007 ACAAATCATA
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
38 1 0.02
39 63 0.95
40 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (39 bp):
ACTTACCCTGAGCACAAAGCCGAGGAGCATGCGATAAGG
Found at i:3508807 original size:2 final size:2
Alignment explanation
Indices: 3508802--3508845 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3508792 TATATATATA
3508802 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3508844 TG
1 TG
3508846 AACGTTAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3510084 original size:39 final size:39
Alignment explanation
Indices: 3510024--3510114 Score: 123
Period size: 39 Copynumber: 2.3 Consensus size: 39
3510014 AGGACATGCA
*
3510024 GTAAGGTCTTACCCTATGCACAAAG-CAGAGGAGCCTCAG
1 GTAAGGACTTACCCTATGCACAAAGACA-AGGAGCCTCAG
**
3510063 GTAAGGACTTACCCTGA-GCACAAAGACAAGGAGCCTGTG
1 GTAAGGACTTACCCT-ATGCACAAAGACAAGGAGCCTCAG
3510102 GTAAGGACTTACC
1 GTAAGGACTTACC
3510115 TGTAATACCC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
39 44 0.94
40 3 0.06
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (39 bp):
GTAAGGACTTACCCTATGCACAAAGACAAGGAGCCTCAG
Found at i:3510994 original size:55 final size:55
Alignment explanation
Indices: 3510929--3511269 Score: 416
Period size: 55 Copynumber: 6.2 Consensus size: 55
3510919 GTACTATCAG
*
3510929 CACTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGATCGTATCGA
1 CACTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGA
* * * *
3510984 CACTAAGTGTGCAAAACCACATAATTCATAATATGTTTATGAACGACTGTATCAA
1 CACTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGA
* ** *
3511039 CACTAAGTGTGCAAAACCACAAAATTTATAATATATTTATGAATTA--TTATCGA
1 CACTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGA
* ** *
3511092 CCCTAAGTGTGCAAAACCATGAAATTCATAATATGTTTATGAACGACCGTATCGA
1 CACTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGA
** * * * * * *
3511147 CACTAAGTGTGCAAAACCACGGAATTCATAATGTGTTTATGGATGACCATATCAA
1 CACTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGA
* * ** *
3511202 CTCTAAGTGTGTAAAACCATGAAATTCATAATATATTTATGAACGACCGTATCGG
1 CACTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGA
* *
3511257 CAGTACGTGTGCA
1 CACTAAGTGTGCA
3511270 TATCAAAGAA
Statistics
Matches: 241, Mismatches: 43, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
53 44 0.18
55 197 0.82
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (55 bp):
CACTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGA
Found at i:3511202 original size:163 final size:163
Alignment explanation
Indices: 3510931--3511244 Score: 484
Period size: 163 Copynumber: 1.9 Consensus size: 163
3510921 ACTATCAGCA
*
3510931 CTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGATCGTATCGACACTAAGTGTGC
1 CTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGACACTAAGTGTGC
* **
3510996 AAAACCACATAATTCATAATATGTTTATGAACGACTGTATCAACACTAAGTGTGCAAAACCACAA
66 AAAACCACAGAATTCATAATATGTTTATGAACGACCATATCAACACTAAGTGTGCAAAACCACAA
*
3511061 AATTTATAATATATTTATGAATTATTATCGACC
131 AATTCATAATATATTTATGAATTATTATCGACC
** *
3511094 CTAAGTGTGCAAAACCATGAAATTCATAATATGTTTATGAACGACCGTATCGACACTAAGTGTGC
1 CTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGACACTAAGTGTGC
* * * * * * **
3511159 AAAACCACGGAATTCATAATGTGTTTATGGATGACCATATCAACTCTAAGTGTGTAAAACCATGA
66 AAAACCACAGAATTCATAATATGTTTATGAACGACCATATCAACACTAAGTGTGCAAAACCACAA
3511224 AATTCATAATATATTTATGAA
131 AATTCATAATATATTTATGAA
3511245 CGACCGTATC
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
163 135 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.30
Consensus pattern (163 bp):
CTAAGTGTGCAAAACCACAAAATTCATAATATATTTATGAACGACCGTATCGACACTAAGTGTGC
AAAACCACAGAATTCATAATATGTTTATGAACGACCATATCAACACTAAGTGTGCAAAACCACAA
AATTCATAATATATTTATGAATTATTATCGACC
Found at i:3515754 original size:14 final size:14
Alignment explanation
Indices: 3515735--3515769 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
3515725 TTATTGTGTA
3515735 TACTTGCACAAAAT
1 TACTTGCACAAAAT
3515749 TACTTGCACAAAAT
1 TACTTGCACAAAAT
3515763 TACTTGC
1 TACTTGC
3515770 CTTATCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (14 bp):
TACTTGCACAAAAT
Found at i:3529680 original size:55 final size:55
Alignment explanation
Indices: 3529266--3529685 Score: 481
Period size: 55 Copynumber: 7.7 Consensus size: 55
3529256 CTAAGTGTAC
* *
3529266 TATCGACACTAAGTGTGCAAAACCATA-AAATTCATAATATGTTTATGAACGACTG
1 TATCGGCACTAAGTGTGCAAAACCA-AGAAATTCATAATATGTTTATGAACGACCG
* * *
3529321 TATCGGCACTAAGTGTGCAAAACCGTAG-AATTCATAATATATTTATGAACAACCG
1 TATCGGCACTAAGTGTGCAAAACC-AAGAAATTCATAATATGTTTATGAACGACCG
* * * * *
3529376 TATCAGCACTAAGTGTGTAAAACCACGAAATTCATAATATGTTTATGAACAACTG
1 TATCGGCACTAAGTGTGCAAAACCAAGAAATTCATAATATGTTTATGAACGACCG
* * *
3529431 TATCGACAC-AAGTGTGCAAAACCATGGAATTCATAATATGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAAAACCAAGAAATTCATAATATGTTTATGAACGACCG
* * * *
3529485 TATCGACCCTAAGTGTGTAAAACCACA-AAATTCATAATATGTTTATGAATGACCG
1 TATCGGCACTAAGTGTGCAAAACCA-AGAAATTCATAATATGTTTATGAACGACCG
** * * * * **
3529540 TATCAACACTAAGTGTGCAAAACCACGAAATTCATAATGTGTTTATAAATGAATG
1 TATCGGCACTAAGTGTGCAAAACCAAGAAATTCATAATATGTTTATGAACGACCG
* * * *
3529595 TATTGGCACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATAAATGACCG
1 TATCGGCACTAAGTGTGCAAAACCAAGAAATTCATAATATGTTTATGAACGACCG
* * * *
3529650 TATCGGCAGTAAGTGTGCATATCAAAGAAATT-ATAA
1 TATCGGCACTAAGTGTGCAAAACCAAGAAATTCATAA
3529686 CGATTTGAAA
Statistics
Matches: 316, Mismatches: 43, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
54 53 0.17
55 263 0.83
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (55 bp):
TATCGGCACTAAGTGTGCAAAACCAAGAAATTCATAATATGTTTATGAACGACCG
Found at i:3545198 original size:18 final size:17
Alignment explanation
Indices: 3545175--3545216 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
3545165 TGCAAGTTTT
3545175 TTTTTTTGAAATTTTGAC
1 TTTTTTTG-AATTTTGAC
**
3545193 TTTTTTTGTTTTTTGAC
1 TTTTTTTGAATTTTGAC
3545210 TTTTTTT
1 TTTTTTT
3545217 TGTTTTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.12, C:0.05, G:0.10, T:0.74
Consensus pattern (17 bp):
TTTTTTTGAATTTTGAC
Found at i:3545206 original size:17 final size:18
Alignment explanation
Indices: 3545186--3545223 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3545176 TTTTTTGAAA
3545186 TTTTGAC-TTTTTTTGTT
1 TTTTGACTTTTTTTTGTT
3545203 TTTTGACTTTTTTTTGTT
1 TTTTGACTTTTTTTTGTT
3545221 TTT
1 TTT
3545224 GTTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.79
Consensus pattern (18 bp):
TTTTGACTTTTTTTTGTT
Found at i:3552115 original size:31 final size:31
Alignment explanation
Indices: 3552077--3552153 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 31
3552067 TAAGGCGACC
**
3552077 CTTGGGTAGGCTCTGCGGCCCCGAGATTTTT
1 CTTGGGTAGGCTCTGCGGCCCCGAGAACTTT
* * * *
3552108 CTTGGGTAAGCCTCCGTGGCCCTGAGAACTTT
1 CTTGGGT-AGGCTCTGCGGCCCCGAGAACTTT
3552140 CTTGGGTAGGCTCT
1 CTTGGGTAGGCTCT
3552154 TAGGCCCCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 12 0.32
32 25 0.68
ACGTcount: A:0.12, C:0.26, G:0.31, T:0.31
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGCGGCCCCGAGAACTTT
Found at i:3556277 original size:25 final size:26
Alignment explanation
Indices: 3556248--3556298 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
3556238 TAGAAAAATG
3556248 TATTTTTTAATTTTCAAAAAG-AATA
1 TATTTTTTAATTTTCAAAAAGTAATA
* *
3556273 TATTTTTTAGTTTTCGAAAAGTAATA
1 TATTTTTTAATTTTCAAAAAGTAATA
3556299 AACGACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (26 bp):
TATTTTTTAATTTTCAAAAAGTAATA
Found at i:3557550 original size:2 final size:2
Alignment explanation
Indices: 3557543--3557596 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3557533 AATTGCATGA
3557543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3557585 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3557597 TGTATAAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3558659 original size:31 final size:31
Alignment explanation
Indices: 3558584--3558688 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 31
3558574 GGGCCCTCAA
* * * *
3558584 AGCCTACCCAAGAATGATTCTC-AGGCCTCGG
1 AGCCTACCCAAGAA-AAATCTCGAGGCCGCAG
* ** * *
3558615 GGCCTACTTAAGAAAAATCTTGGGGCCGCAG
1 AGCCTACCCAAGAAAAATCTCGAGGCCGCAG
* * *
3558646 GGCTTACCCAAGAAAGATCTCGAGGCCGCAG
1 AGCCTACCCAAGAAAAATCTCGAGGCCGCAG
3558677 AGCCTACCCAAG
1 AGCCTACCCAAG
3558689 GGTCGCCTTA
Statistics
Matches: 56, Mismatches: 17, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
30 4 0.07
31 52 0.93
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (31 bp):
AGCCTACCCAAGAAAAATCTCGAGGCCGCAG
Found at i:3560562 original size:13 final size:15
Alignment explanation
Indices: 3560544--3560584 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
3560534 TTGACTTTTT
3560544 CGGTCAAAGTCA-A-
1 CGGTCAAAGTCAGAC
*
3560557 CGGTCAATGTCAGAC
1 CGGTCAAAGTCAGAC
*
3560572 CGATCAAAGTCAG
1 CGGTCAAAGTCAG
3560585 GAGGTTGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 1 0.04
15 11 0.48
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (15 bp):
CGGTCAAAGTCAGAC
Found at i:3564708 original size:20 final size:19
Alignment explanation
Indices: 3564683--3564756 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 19
3564673 AGTACAAAAG
3564683 AGAGAAAATAAAAAAAAATA
1 AGAGAAAA-AAAAAAAAATA
* *
3564703 AGAG-AAAGACAAAAAATA
1 AGAGAAAAAAAAAAAAATA
* * *
3564721 AAAGAAAAGAAAGAAAAAGA
1 AGAGAAAA-AAAAAAAAATA
3564741 AGAAGAAAGAAAAAAA
1 AG-AGAAA-AAAAAAA
3564757 GAAAAAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
18 12 0.29
19 6 0.15
20 12 0.29
21 10 0.24
22 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.04
Consensus pattern (19 bp):
AGAGAAAAAAAAAAAAATA
Found at i:3564710 original size:28 final size:28
Alignment explanation
Indices: 3564678--3564773 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 28
3564668 AATAAAGTAC
3564678 AAAAGAGAGAAAATAAAA-AAAA-ATAAGA
1 AAAAGA-AGAAAATAAAAGAAAAGA-AAGA
* *
3564706 GAAAGACAAAAAATAAAAGAAAAGAAAGA
1 AAAAGA-AGAAAATAAAAGAAAAGAAAGA
3564735 AAAAGAAGAAGAA-AGAAA-AAAAGAAA-A
1 AAAAGAAGAA-AATA-AAAGAAAAGAAAGA
3564762 AAAA-AAGGAAAA
1 AAAAGAA-GAAAA
3564774 AGCATAAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
26 4 0.07
27 8 0.14
28 27 0.47
29 18 0.31
30 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (28 bp):
AAAAGAAGAAAATAAAAGAAAAGAAAGA
Found at i:3564723 original size:23 final size:21
Alignment explanation
Indices: 3564678--3564773 Score: 77
Period size: 24 Copynumber: 4.2 Consensus size: 21
3564668 AATAAAGTAC
* *
3564678 AAAAGAGAGAAAATAAAAAAAA
1 AAAAGAAAGAAAA-AAAAAAAG
3564700 ATAAGAGAAAGACAAAAAATAAAAG
1 A-AA-AGAAAGA-AAAAAA-AAAAG
3564725 AAAAGAAAGAAAAAGAAGAAGAAAG
1 AAAAGAAAG-AAAA-AA-AA-AAAG
*
3564750 AAAA-AAAGAAAAAAAAAAGG
1 AAAAGAAAGAAAAAAAAAAAG
3564770 AAAA
1 AAAA
3564774 AGCATAAAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
20 7 0.11
21 2 0.03
22 3 0.05
23 15 0.24
24 19 0.30
25 17 0.27
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (21 bp):
AAAAGAAAGAAAAAAAAAAAG
Found at i:3564727 original size:38 final size:38
Alignment explanation
Indices: 3564685--3564766 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
3564675 TACAAAAGAG
* * *
3564685 AGAAAATAAAAAAAAATAAG-AGAAAGACAAAAAATAAA
1 AGAAAAGAAAAAAAAAGAAGAAGAAAGA-AAAAAAGAAA
*
3564723 AGAAAAGAAAGAAAAAGAAGAAGAAAGAAAAAAAGAAA
1 AGAAAAGAAAAAAAAAGAAGAAGAAAGAAAAAAAGAAA
*
3564761 AAAAAA
1 AGAAAA
3564767 AGGAAAAAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 31 0.82
39 7 0.18
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (38 bp):
AGAAAAGAAAAAAAAAGAAGAAGAAAGAAAAAAAGAAA
Found at i:3564738 original size:10 final size:10
Alignment explanation
Indices: 3564721--3564775 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 10
3564711 ACAAAAAATA
3564721 AAAG-AAAAG
1 AAAGAAAAAG
3564730 AAAGAAAAAG
1 AAAGAAAAAG
3564740 -AAGAAGAAAG
1 AAAGAA-AAAG
3564750 -AA-AAAAAG
1 AAAGAAAAAG
3564758 AAA-AAAAA-
1 AAAGAAAAAG
*
3564766 AAGGAAAAAG
1 AAAGAAAAAG
3564776 CATAAAAGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
8 6 0.15
9 23 0.57
10 11 0.28
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:3564746 original size:12 final size:11
Alignment explanation
Indices: 3564685--3564774 Score: 58
Period size: 12 Copynumber: 7.6 Consensus size: 11
3564675 TACAAAAGAG
3564685 AGAAAATAAAAA
1 AGAAAA-AAAAA
*
3564697 A-AAATAAGAGAA
1 AGAAA-AA-AAAA
3564709 AGACAAAAAATAA
1 AGA-AAAAAA-AA
* *
3564722 A-AGAAAAGAA
1 AGAAAAAAAAA
*
3564732 AGAAAAAGAAGA
1 AGAAAAA-AAAA
3564744 AGAAAGAAAAAA
1 AGAAA-AAAAAA
3564756 AGAAAAAAAAA
1 AGAAAAAAAAA
3564767 AGGAAAAA
1 A-GAAAAA
3564775 GCATAAAAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
10 3 0.05
11 19 0.31
12 29 0.48
13 8 0.13
14 2 0.03
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:3564757 original size:18 final size:18
Alignment explanation
Indices: 3564694--3564759 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
3564684 GAGAAAATAA
*
3564694 AAAAAAATAAG-AGAAAG
1 AAAAAAAGAAGAAGAAAG
*
3564711 ACAAAAAATAA-AAGAAAAG
1 A-AAAAAAGAAGAAG-AAAG
3564730 AAAGAAAAAGAAGAAGAAAG
1 -AA-AAAAAGAAGAAGAAAG
3564750 AAAAAAAGAA
1 AAAAAAAGAA
3564760 AAAAAAAAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
17 1 0.02
18 19 0.45
19 7 0.17
20 12 0.29
21 3 0.07
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.03
Consensus pattern (18 bp):
AAAAAAAGAAGAAGAAAG
Found at i:3568563 original size:32 final size:32
Alignment explanation
Indices: 3568499--3568565 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
3568489 GTGACCCTTA
* * **
3568499 GGTAGGCTCTGAGGCCCCGAGAAACTTTATTG
1 GGTAGGCTCTCAGGCCCCAAGAAACTCCATTG
**
3568531 GGTAGGCTCTCAGGCCCCAAGTCACTCCATTG
1 GGTAGGCTCTCAGGCCCCAAGAAACTCCATTG
3568563 GGT
1 GGT
3568566 TAATCATGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.24
Consensus pattern (32 bp):
GGTAGGCTCTCAGGCCCCAAGAAACTCCATTG
Found at i:3571036 original size:56 final size:56
Alignment explanation
Indices: 3570786--3571214 Score: 227
Period size: 55 Copynumber: 7.7 Consensus size: 56
3570776 CTAACGCAAT
* * * *
3570786 TTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGAT-A-T-TTTTAAATGAA
1 TTTTTAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATTTTAAATAAA
* * * ** * ** * * * *
3570839 TTTTGAAATAATCTAAGTATGGGTTTT-AGAAGTTTCTTGACGA-T-TTTCAAATGAG
1 TTTT-TAAGAAGCTAAGCCT-GATTTTCAGGGGTTTCTTGATGATTATTTTAAATAAA
* * ** * * **
3570894 TTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGACGA--CTTTTAAATGAGC
1 TTTTT-AAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATTTTAAAT-AAA
** * * *
3570950 TTTCAAAGAAGCTAAACCTAATTTTCAGGGGTTTCTTGATGATTATTTTCAATAAA
1 TTTTTAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATTTTAAATAAA
* * * *
3571006 TTTTTAAGAAGCTAAGCTTGATTTTTAGGGGTTTCCAT-ATGA-T-TTTTAAATGAA
1 TTTTTAAGAAGCTAAGCCTGATTTTCAGGGGTTT-CTTGATGATTATTTTAAATAAA
* * * * *
3571060 TTTTAAAGTATCTAAGCCTGATTTTCACGGGTTTCTTGATGATTATTTCCAAAT-AA
1 TTTTTAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATTT-TAAATAAA
* * * * *** *
3571116 TTTTTAAATAAGATAAGCCTAATATTT-AGGGGTTTCTTGATGATAACAGTAAACGAAA
1 TTTTT-AAGAAGCTAAGCCTGAT-TTTCAGGGGTTTCTTGATGATTATTTTAAA-TAAA
* * * *
3571174 GTTTTTAAGAAACTAAACTTGATTTTCAAGGGTTTCTTGAT
1 -TTTTTAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGAT
3571215 TAGTAAGTCC
Statistics
Matches: 284, Mismatches: 72, Indels: 35
0.73 0.18 0.09
Matches are distributed among these distances:
53 6 0.02
54 66 0.23
55 85 0.30
56 48 0.17
57 45 0.16
58 29 0.10
59 5 0.02
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (56 bp):
TTTTTAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATTTTAAATAAA
Found at i:3571040 original size:111 final size:111
Alignment explanation
Indices: 3570870--3571155 Score: 280
Period size: 111 Copynumber: 2.6 Consensus size: 111
3570860 GGTTTTAGAA
* * * * **
3570870 GTTTCTTGACGA-T-TTT-CAAATGAGTTTTTAAAGAAACTAAG-TCTGATTTTCAGAAGTTTCT
1 GTTTCTTGATGATTATTTCCAAAT-AATTTTTAAAGAAGCTAAGCT-TGATTTTTAGGGGTTTCT
* *
3570931 TGACGACTTTTAAATGAGCTTTCAAAGAAGCTAAACCTAATTTTCAGGG
64 TGACGACTTTTAAATGA-ATTTCAAAGAAGCTAAACCTAATTTTCACGG
* *
3570980 GTTTCTTGATGATTATTTTC-AATAAATTTTT-AAGAAGCTAAGCTTGATTTTTAGGGGTTTCCA
1 GTTTCTTGATGATTATTTCCAAAT-AATTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTT-CT
* * * * * * *
3571043 T-ATGATTTTTAAATGAATTTTAAAGTATCTAAGCCTGATTTTCACGG
64 TGACGACTTTTAAATGAATTTCAAAGAAGCTAAACCTAATTTTCACGG
* * * * *
3571090 GTTTCTTGATGATTATTTCCAAATAATTTTTAAATAAGATAAGCCTAATATTTAGGGGTTTCTTG
1 GTTTCTTGATGATTATTTCCAAATAATTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTG
3571155 A
66 A
3571156 TGATAACAGT
Statistics
Matches: 144, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
110 63 0.44
111 65 0.45
112 15 0.10
113 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (111 bp):
GTTTCTTGATGATTATTTCCAAATAATTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTG
ACGACTTTTAAATGAATTTCAAAGAAGCTAAACCTAATTTTCACGG
Found at i:3571149 original size:57 final size:57
Alignment explanation
Indices: 3570797--3571159 Score: 229
Period size: 55 Copynumber: 6.6 Consensus size: 57
3570787 TTTTTAGAAA
* * *
3570797 CTAAGCCTAATTTTCAGGGGTTTCTTGAT-ATT-TTT-AAATGAATTTTGAAATAAT
1 CTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATTTCAAATAAATTTTTAAATAAG
** ** ** * * * * *
3570851 CTAAGTATGGGTTTT-AGAAGTTTCTTGACGA-T-TTTCAAATGAGTTTTTAAAGAAA
1 CTAAGCCT-AATTTTCAGGGGTTTCTTGATGATTATTTCAAATAAATTTTTAAATAAG
* * ** * * * ** * *
3570906 CTAAGTCTGATTTTCAGAAGTTTCTTGACGACT-TTT-AAATGAGCTTTCAAAGAAG
1 CTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATTTCAAATAAATTTTTAAATAAG
* *
3570961 CTAAACCTAATTTTCAGGGGTTTCTTGATGATTATTTTC-AATAAATTTTT-AAGAAG
1 CTAAGCCTAATTTTCAGGGGTTTCTTGATGATTA-TTTCAAATAAATTTTTAAATAAG
* * * * * *
3571017 CTAAGCTTGATTTTTAGGGGTTTCCAT-ATGATT-TTT-AAATGAA-TTTTAAAGT-AT
1 CTAAGCCTAATTTTCAGGGGTTT-CTTGATGATTATTTCAAATAAATTTTTAAA-TAAG
* *
3571071 CTAAGCCTGATTTTCACGGGTTTCTTGATGATTATTTCCAAAT-AATTTTTAAATAAG
1 CTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATTT-CAAATAAATTTTTAAATAAG
*
3571128 ATAAGCCTAATATTT-AGGGGTTTCTTGATGAT
1 CTAAGCCTAAT-TTTCAGGGGTTTCTTGATGAT
3571160 AACAGTAAAC
Statistics
Matches: 247, Mismatches: 43, Indels: 35
0.76 0.13 0.11
Matches are distributed among these distances:
53 6 0.02
54 63 0.26
55 88 0.36
56 38 0.15
57 49 0.20
58 3 0.01
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (57 bp):
CTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATTTCAAATAAATTTTTAAATAAG
Found at i:3571159 original size:111 final size:110
Alignment explanation
Indices: 3570798--3571159 Score: 314
Period size: 110 Copynumber: 3.3 Consensus size: 110
3570788 TTTTAGAAAC
**
3570798 TAAGCCTAATTTTCAGGGGTTTCTTGAT-ATTTTTAAATGAATTTTGAAA-TAATCTAAGTATGG
1 TAAGCCTAATTTTCAGGGGTTTCTTGATGATTTTTAAATGAATTTT-AAAGT-ATCTAAGCCT-G
* * * * *
3570861 GTTTT-AGAAGTTTCTTGACGA-T-TTTCAAATGAGTTTTTAAAGAA-A
63 ATTTTCAG-GGTTTCTTGATGATTATTTCAAATAAATTTTTAAAGAAGA
* * ** * * * * * * * *
3570906 CTAAGTCTGATTTTCAGAAGTTTCTTGACGACTTTTAAATGAGCTTTCAAAGAAGCTAAACCTAA
1 -TAAGCCTAATTTTCAGGGGTTTCTTGATGATTTTTAAATGA-ATTTTAAAGTATCTAAGCCTGA
*
3570971 TTTTCAGGGGTTTCTTGATGATTATTTTC-AATAAATTTTT-AAGAAGC
64 TTTTCA-GGGTTTCTTGATGATTA-TTTCAAATAAATTTTTAAAGAAGA
* * * *
3571018 TAAGCTTGATTTTTAGGGGTTTCCAT-ATGATTTTTAAATGAATTTTAAAGTATCTAAGCCTGAT
1 TAAGCCTAATTTTCAGGGGTTT-CTTGATGATTTTTAAATGAATTTTAAAGTATCTAAGCCTGAT
*
3571082 TTTCACGGGTTTCTTGATGATTATTTCCAAAT-AATTTTTAAATAAGA
65 TTTCA-GGGTTTCTTGATGATTATTT-CAAATAAATTTTTAAAGAAGA
3571129 TAAGCCTAATATTT-AGGGGTTTCTTGATGAT
1 TAAGCCTAAT-TTTCAGGGGTTTCTTGATGAT
3571160 AACAGTAAAC
Statistics
Matches: 198, Mismatches: 40, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
109 30 0.15
110 81 0.41
111 69 0.35
112 14 0.07
113 4 0.02
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (110 bp):
TAAGCCTAATTTTCAGGGGTTTCTTGATGATTTTTAAATGAATTTTAAAGTATCTAAGCCTGATT
TTCAGGGTTTCTTGATGATTATTTCAAATAAATTTTTAAAGAAGA
Found at i:3571474 original size:110 final size:110
Alignment explanation
Indices: 3571281--3571493 Score: 372
Period size: 110 Copynumber: 1.9 Consensus size: 110
3571271 GATCATTTAT
* *
3571281 AAGTCTTTTGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGGCATGATGTTTTC
1 AAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGGCAAGATGTTTTC
3571346 ACACGATTTTCGAAAAATGAGAAAGTGATTTCCAAAGTCATCTAA
66 ACACGATTTTCGAAAAATGAGAAAGTGATTTCCAAAGTCATCTAA
* **
3571391 AAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAAGATGTTTTC
1 AAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGGCAAGATGTTTTC
*
3571456 ACATGATTTTCGAAAAATGAGAAAGTGATTTCCAAAGT
66 ACACGATTTTCGAAAAATGAGAAAGTGATTTCCAAAGT
3571494 TTCTTACTTA
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 97 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (110 bp):
AAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCAGGCAAGATGTTTTC
ACACGATTTTCGAAAAATGAGAAAGTGATTTCCAAAGTCATCTAA
Found at i:3572613 original size:17 final size:17
Alignment explanation
Indices: 3572572--3572605 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3572562 CCTCAGGTCC
*
3572572 AACCAACCCAAAATAAA
1 AACCAAACCAAAATAAA
3572589 AACCAAACCAAAATAAA
1 AACCAAACCAAAATAAA
3572606 CCCCAAACTA
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:0.68, C:0.26, G:0.00, T:0.06
Consensus pattern (17 bp):
AACCAAACCAAAATAAA
Found at i:3573686 original size:108 final size:108
Alignment explanation
Indices: 3573496--3573698 Score: 300
Period size: 108 Copynumber: 1.9 Consensus size: 108
3573486 TGGTCACGTG
3573496 TAGGGACCAAAATTATTATTTTCCCTTTTCTATGCATGTTATATATTTTTGGTAAATTCACTGTT
1 TAGGGACCAAAATTATTATTTTCCCTTTTCTATGCATGTTATATATTTTTGGTAAATTCACTGTT
* * *
3573561 TAGTCCCTCTATCTTTAGCATGTTTTTACATTTCAGTCACTTA
66 TAGTCCCTATAACTTTAGCATGTTGTTACATTTCAGTCACTTA
* * ***
3573604 TAGGGACC-AAATCTATTATTTTCTCTTTTCTTTGCATGTTATATATTTTTGGTAAATTTTTTGT
1 TAGGGACCAAAAT-TATTATTTTCCCTTTTCTATGCATGTTATATATTTTTGGTAAATTCACTGT
* *
3573668 TTAGTCCCTATAAGTTTAGCGTGTTGTTACA
65 TTAGTCCCTATAACTTTAGCATGTTGTTACA
3573699 CTTTGGTCAT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 4 0.05
108 80 0.95
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (108 bp):
TAGGGACCAAAATTATTATTTTCCCTTTTCTATGCATGTTATATATTTTTGGTAAATTCACTGTT
TAGTCCCTATAACTTTAGCATGTTGTTACATTTCAGTCACTTA
Found at i:3574313 original size:2 final size:2
Alignment explanation
Indices: 3574306--3574335 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3574296 AATTGCATGA
3574306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3574336 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3577977 original size:18 final size:20
Alignment explanation
Indices: 3577931--3577977 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
3577921 TTAAAATATA
3577931 ATTTAATA-TAGTAATATTT
1 ATTTAATACTAGTAATATTT
3577950 ATTT-ATACTA-TAA-ATTT
1 ATTTAATACTAGTAATATTT
3577967 ATTTAATACTA
1 ATTTAATACTA
3577978 ACTATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.31
18 12 0.46
19 6 0.23
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTAATACTAGTAATATTT
Found at i:3578534 original size:59 final size:58
Alignment explanation
Indices: 3578455--3578625 Score: 234
Period size: 59 Copynumber: 2.9 Consensus size: 58
3578445 CTAACCCTAG
* * * *
3578455 TATGACACATAAGGTTGTGCCCACCATCTACACTAGTTATACTTTAGTGCAGTCCTGAA
1 TATGACACATAAGGTCGTGCCCACCATATA-ACTAGTTATAATTTAGTGCAATCCTGAA
* * *
3578514 TATGACACATAAGGTCGTGCCCACCATAGGAACTATTTATAATTTTGTGCAATCCTGAA
1 TATGACACATAAGGTCGTGCCCACCATA-TAACTAGTTATAATTTAGTGCAATCCTGAA
* *
3578573 TATGACACATAAGGTCATGCCCACCATATGAACTAGTTATATTTTAGTGCAAT
1 TATGACACATAAGGTCGTGCCCACCATAT-AACTAGTTATAATTTAGTGCAAT
3578626 GTCGAATATG
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
59 97 0.99
60 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (58 bp):
TATGACACATAAGGTCGTGCCCACCATATAACTAGTTATAATTTAGTGCAATCCTGAA
Found at i:3580747 original size:22 final size:21
Alignment explanation
Indices: 3580716--3580760 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
3580706 CTTTATGAAA
*
3580716 AATTTCCTTTCATTTCATGTT
1 AATTTCCTTTCATTTAATGTT
*
3580737 AATTTACCTTTTATTTAATGTT
1 AATTT-CCTTTCATTTAATGTT
3580759 AA
1 AA
3580761 ATGAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (21 bp):
AATTTCCTTTCATTTAATGTT
Found at i:3588459 original size:19 final size:19
Alignment explanation
Indices: 3588426--3588464 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3588416 ATTTTGCATC
*
3588426 TGCATTTTATTTTTCACAT
1 TGCATTTTATCTTTCACAT
* *
3588445 TGCATTTTGTCTTTCGCAT
1 TGCATTTTATCTTTCACAT
3588464 T
1 T
3588465 ACGTTATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.10, T:0.56
Consensus pattern (19 bp):
TGCATTTTATCTTTCACAT
Found at i:3591385 original size:3 final size:3
Alignment explanation
Indices: 3591370--3591431 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
3591360 TTCGTTCCTG
* * * *
3591370 TTA TTA ATA TTA TTA TTA GTA TTT TTA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3591418 -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
3591432 CACATAAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3592711 original size:138 final size:139
Alignment explanation
Indices: 3592461--3592746 Score: 502
Period size: 138 Copynumber: 2.1 Consensus size: 139
3592451 ATACGTCTAC
*
3592461 AGTCCCTATGAATTTGTAATCTTCTATTTTGGTCACAAAAACATGTTTTTACGCCTTTTAATTTG
1 AGTCCCTATAAATTTGTAATCTTCTATTTTGGTCACAAAAACATGTTTTTACGCCTTTTAATTTG
*
3592526 GTCTTTTAATTTTATTTATTTATATTTTAGTCCCTATCTATGTTTATATATATTTAGGGTAAAAT
66 GTCTTTTAATTTTATTTATTTATATTTTAGTCCCTATCTATGCTTATATATATTTAGGGTAAAAT
3592591 TACATATTT
131 TACATATTT
* *
3592600 AGTCCCTATAAATTTGTAATCTTCTATTTTGGTCATAAAAACATGTTTTTACGTCTTTT-ATTTG
1 AGTCCCTATAAATTTGTAATCTTCTATTTTGGTCACAAAAACATGTTTTTACGCCTTTTAATTTG
*
3592664 GTCTTTTAATTTTATTTATTTATATTTTAGTCCCTGTCTATGCTTATATATATTTAGGGTAAAAT
66 GTCTTTTAATTTTATTTATTTATATTTTAGTCCCTATCTATGCTTATATATATTTAGGGTAAAAT
*
3592729 TATATATTT
131 TACATATTT
*
3592738 AGTCTCTAT
1 AGTCCCTAT
3592747 TTTTTTTATA
Statistics
Matches: 140, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
138 84 0.60
139 56 0.40
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (139 bp):
AGTCCCTATAAATTTGTAATCTTCTATTTTGGTCACAAAAACATGTTTTTACGCCTTTTAATTTG
GTCTTTTAATTTTATTTATTTATATTTTAGTCCCTATCTATGCTTATATATATTTAGGGTAAAAT
TACATATTT
Found at i:3598354 original size:31 final size:31
Alignment explanation
Indices: 3598290--3598360 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
3598280 GAATGTGTGA
* *
3598290 CATTTTGAAGGCTCATATTATCTATGTGAGG
1 CATTTTGAAGGCCCATATTATCTACGTGAGG
* *
3598321 CATTTTGAAGGCCCATGTTAT-TCACGTGGGG
1 CATTTTGAAGGCCCATATTATCT-ACGTGAGG
*
3598352 CATCTTGAA
1 CATTTTGAA
3598361 TTCCTATATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (31 bp):
CATTTTGAAGGCCCATATTATCTACGTGAGG
Found at i:3600447 original size:3 final size:3
Alignment explanation
Indices: 3600413--3600462 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
3600403 TCTGTTCTCG
* * * *
3600413 TTA TTA ATA TTA GTA TTA GTA TTA TTA CTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3600460 TTA
1 TTA
3600463 CACATAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:3600457 original size:11 final size:12
Alignment explanation
Indices: 3600432--3600463 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
3600422 TTAGTATTAG
3600432 TATTATTACTAT
1 TATTATTACTAT
3600444 TATTATTA-TAT
1 TATTATTACTAT
3600455 TATTATTAC
1 TATTATTAC
3600464 ACATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTACTAT
Found at i:3605882 original size:9 final size:9
Alignment explanation
Indices: 3605868--3605911 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
3605858 ACTTTGCCTG
3605868 AAAAAAATA
1 AAAAAAATA
3605877 AAAAAAATA
1 AAAAAAATA
3605886 AAAGAAAA-A
1 AAA-AAAATA
3605895 GAAAAAAATA
1 -AAAAAAATA
*
3605905 AATAAAA
1 AAAAAAA
3605912 GGGGGGCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (9 bp):
AAAAAAATA
Found at i:3605902 original size:23 final size:22
Alignment explanation
Indices: 3605867--3605912 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
3605857 TACTTTGCCT
*
3605867 GAAAAAAATAAAAAAAATAAAA
1 GAAAAAAAAAAAAAAAATAAAA
*
3605889 GAAAAAGAAAAAAATAAATAAAA
1 GAAAAA-AAAAAAAAAAATAAAA
3605912 G
1 G
3605913 GGGGGCTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (22 bp):
GAAAAAAAAAAAAAAAATAAAA
Found at i:3607571 original size:709 final size:701
Alignment explanation
Indices: 3606222--3607637 Score: 2706
Period size: 709 Copynumber: 2.0 Consensus size: 701
3606212 AATTTCACAC
3606222 CCTTATGCATTATCACAATTCTCAAGATCCCTTTAACAGAAGCTACACTTGAGTCACTATGTGGC
1 CCTTATGCATTATCACAATTCTCAAGATCCCTTTAACAGAAGCTACACTTGAGTCACTATGTGGC
3606287 ATGGCAATTCAAAATCATCCTTACTATTGATGTCTGAGGACGCCTACTTCTTTTCTTTTACTTCT
66 ATGGCAATTCAAAATCATCCTTACTATTGATGTCTGAGGACGCCTACTTCTTTTCTTTTACTTCT
3606352 CCAAAAAAGTTGCCATGTATTACCCAAAAATTCTTTACATTTATATAAATAAAAAGGGTCTTTAT
131 CCAAAAAAGTTGCCATGTATTACCCAAAAATTCTTTACATTTATATAAATAAAAAGGGTCTTTAT
3606417 TGTTAACACCCTTTTGCAAGCATCATACTTTGAAATAAAATACATGTAGTTTAACTTGAAAAAAT
196 TGTTAACACCCTTTTGCAAGCATCATACTTTGAAATAAAATACATGTAGTTTAACTTGAAAAAAT
3606482 GAAATCACCGTGTATTATTGTGCAAGATGTTTTGGAAAAGTGCAGACGTTTTGAAGCTGAAAATG
261 GAAATCACCGTGTATTATTGTGCAAGATGTTTTGGAAAAGTGCAGACGTTTTGAAGCTGAAAATG
3606547 GTTTTAGCATGACGCTTGCATGATGATGGGCTACATGAAACTGAAACATTGGGTACATAAAAAGT
326 GTTTTAGCATGACGCTTGCATGATGATGGGCTACATGAAACTGAAACATTGGGTACATAAAAAGT
3606612 TTTAGACAGTTAGGGTTAATAAAAGACGTTTGTCACTCATCAACCAGCTAGTCATGAATACTATC
391 TTTAGACAGTTAGGGTTAATAAAAGACGTTTGTCACTCATCAACCAGCTAGTCATGAATACTATC
3606677 GAGTTTCAAGAAGAAAGAAAACCAAGATCATTTCCAACCAAAGAATATCGAATCAATATTGTCAG
456 GAGTTTCAAGAAGAAAGAAAACCAAGATCATTTCCAACCAAAGAATATCGAATCAATATTGTCAG
3606742 CTGGAGTGAACCGGTCGTGATTTTTATACCCAAGATTGAACTGAATCATATAGTAATCAACAAGA
521 CTGGAGTGAACCGGTCGTGATTTTTATACCCAAGATTGAACTGAATCATATAGTAATCAACAAGA
3606807 GAGGGTTCTCTTTTGAAGATGAAAATATACCAAAATTTGCATCATTGCATACATGTTAGGCATTA
586 GAGGGTTCTCTTTTGAAGATGAAAATATACCAAAATTTGCATCATTGCATACATGTTAGGCATTA
3606872 ATAGGATTATGACATTCATAAAATACATGATGATGATAAATGCAATTGAGT
651 ATAGGATTATGACATTCATAAAATACATGATGATGATAAATGCAATTGAGT
3606923 CCTTATGCATTATCACAATTCTCAAGATCCCTTTAACAGAAGCTACACTTGAGTCACTATGTGGC
1 CCTTATGCATTATCACAATTCTCAAGATCCCTTTAACAGAAGCTACACTTGAGTCACTATGTGGC
3606988 ATGGCAATTCAAAATCATCCTTACTATTGATGTCTGAGGACGCCTACTTCATTTTCTTTTACTTC
66 ATGGCAATTCAAAATCATCCTTACTATTGATGTCTGAGGACGCCTACTTC-TTTTCTTTTACTTC
*
3607053 TCCCAATTAAAAGTTTGCCATGTATTTACCCAAAACTTCTTTACATTTATATAAATAAAAAGAGG
130 T-CCAA--AAAAG-TTGCCATGTA-TTACCCAAAAATTCTTTACATTTATATAAATAAAAAG-GG
3607118 TCTTTTATTGTTAACACCCTTTTGCAAGCATCATACTTTGAAATAAAATACATGTAGTTTAACTT
189 TC-TTTATTGTTAACACCCTTTTGCAAGCATCATACTTTGAAATAAAATACATGTAGTTTAACTT
3607183 GAAAAAATGAAATCACCGTGTATTATTGTGCAAGATGTTTTGGAAAAGTGCAGACGTTTTGAAGC
253 GAAAAAATGAAATCACCGTGTATTATTGTGCAAGATGTTTTGGAAAAGTGCAGACGTTTTGAAGC
3607248 TGAAAATGGTTTTAGCATGACGCTTGCATGATGATGGGCTACATGAAACTGAAACATTGGGTACA
318 TGAAAATGGTTTTAGCATGACGCTTGCATGATGATGGGCTACATGAAACTGAAACATTGGGTACA
*
3607313 TAAAAAGTTTTAGACAGTTAGGGTTAATAAAAGACGTTTGTCACTGATCAACCAGCTAGTCATGA
383 TAAAAAGTTTTAGACAGTTAGGGTTAATAAAAGACGTTTGTCACTCATCAACCAGCTAGTCATGA
* *
3607378 ATACTATCGGGTTTCAAGAAGAAAGAAAACCAAGATCATTTCCAACTAAAGAATATCGAATCAAT
448 ATACTATCGAGTTTCAAGAAGAAAGAAAACCAAGATCATTTCCAACCAAAGAATATCGAATCAAT
3607443 ATTGTCAGCTGGAGTGAACCGGTCGTGATTTTTATACCCAAGATTGAACTGAATCATATAGTAAT
513 ATTGTCAGCTGGAGTGAACCGGTCGTGATTTTTATACCCAAGATTGAACTGAATCATATAGTAAT
*
3607508 CAACAAGAGAGGGTTCTCTTTTGAAGATGAAAATATACCAAAATTTTCATCATTGCATACATGTT
578 CAACAAGAGAGGGTTCTCTTTTGAAGATGAAAATATACCAAAATTTGCATCATTGCATACATGTT
3607573 AGGCATTAATAGGATTATGACATTCATAAAATACATGATGATGATAAATGCAATTGAGT
643 AGGCATTAATAGGATTATGACATTCATAAAATACATGATGATGATAAATGCAATTGAGT
*
3607632 ACTTAT
1 CCTTAT
3607638 AGGTGTTCTA
Statistics
Matches: 701, Mismatches: 6, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
701 115 0.16
702 15 0.02
703 4 0.01
705 5 0.01
706 10 0.01
707 36 0.05
708 4 0.01
709 512 0.73
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (701 bp):
CCTTATGCATTATCACAATTCTCAAGATCCCTTTAACAGAAGCTACACTTGAGTCACTATGTGGC
ATGGCAATTCAAAATCATCCTTACTATTGATGTCTGAGGACGCCTACTTCTTTTCTTTTACTTCT
CCAAAAAAGTTGCCATGTATTACCCAAAAATTCTTTACATTTATATAAATAAAAAGGGTCTTTAT
TGTTAACACCCTTTTGCAAGCATCATACTTTGAAATAAAATACATGTAGTTTAACTTGAAAAAAT
GAAATCACCGTGTATTATTGTGCAAGATGTTTTGGAAAAGTGCAGACGTTTTGAAGCTGAAAATG
GTTTTAGCATGACGCTTGCATGATGATGGGCTACATGAAACTGAAACATTGGGTACATAAAAAGT
TTTAGACAGTTAGGGTTAATAAAAGACGTTTGTCACTCATCAACCAGCTAGTCATGAATACTATC
GAGTTTCAAGAAGAAAGAAAACCAAGATCATTTCCAACCAAAGAATATCGAATCAATATTGTCAG
CTGGAGTGAACCGGTCGTGATTTTTATACCCAAGATTGAACTGAATCATATAGTAATCAACAAGA
GAGGGTTCTCTTTTGAAGATGAAAATATACCAAAATTTGCATCATTGCATACATGTTAGGCATTA
ATAGGATTATGACATTCATAAAATACATGATGATGATAAATGCAATTGAGT
Found at i:3610192 original size:237 final size:239
Alignment explanation
Indices: 3609753--3610215 Score: 660
Period size: 237 Copynumber: 1.9 Consensus size: 239
3609743 TAAGTGCAAA
* * * ** *
3609753 TTGCTTATAAACGATTTTTTACATATATAGTTGCTCCAATTTCTCCCACAAAGAAACAATCATTT
1 TTGCTGATAAACGAATTTTTACATACATAGTTGCTCCAATTTCGACCACAAAGAAACAATCACTT
* *
3609818 TTTCTTTCAACACATCCTACAAAATTTTGATTTGATAATTATAAACAAATTTGAGAAAGAGCTTT
66 TTTCTTTCAACACATACTACAAAATTTTGATTTAATAATTATAAACAAATTTGAGAAAGAGCTTT
** * * * *
3609883 ACGATCCTTACGCTTTTCCTTATTTATCCACTGTGTTGTTGGCTTCTCATCAAATCTTTCTATTG
131 ACGATCCTTACAATTTTCCTCATTTATCAACTGTGTTGTTGGCTTCTCATCAAATCCTTATATTG
*
3609948 CATCGTCGAGATCTAATTGTGCAAGAACATCTTGAATCTTCACC
196 CATCGTCGAGATCTAACTGTGCAAGAACATCTTGAATCTTCACC
** *
3609992 TTGCTGATAAAC-AATTTTTACATACATAGTTGCTCCAATTTCGACCACAAAGAAGTAGTCACTT
1 TTGCTGATAAACGAATTTTTACATACATAGTTGCTCCAATTTCGACCACAAAGAAACAATCACTT
** * * *
3610056 TTTCTTTCAGTACATACTACAAAATTTT-ATTTAATAATTGTAAACGAATTTGAGAAAGAGTTTT
66 TTTCTTTCAACACATACTACAAAATTTTGATTTAATAATTATAAACAAATTTGAGAAAGAGCTTT
* * * * *
3610120 ACGATCCTTACAATTTTTCTCATTTGTCAATTGTGTTGTTGGCTTGTCATCAAATCCTTATATTT
131 ACGATCCTTACAATTTTCCTCATTTATCAACTGTGTTGTTGGCTTCTCATCAAATCCTTATATTG
3610185 CATCGTCGAGATCTAACTGTGCAAGAACATC
196 CATCGTCGAGATCTAACTGTGCAAGAACATC
3610216 CCAGATCTTC
Statistics
Matches: 196, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
237 116 0.59
238 69 0.35
239 11 0.06
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (239 bp):
TTGCTGATAAACGAATTTTTACATACATAGTTGCTCCAATTTCGACCACAAAGAAACAATCACTT
TTTCTTTCAACACATACTACAAAATTTTGATTTAATAATTATAAACAAATTTGAGAAAGAGCTTT
ACGATCCTTACAATTTTCCTCATTTATCAACTGTGTTGTTGGCTTCTCATCAAATCCTTATATTG
CATCGTCGAGATCTAACTGTGCAAGAACATCTTGAATCTTCACC
Found at i:3612668 original size:19 final size:19
Alignment explanation
Indices: 3612646--3612701 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
3612636 TCCTATGTTA
3612646 TGTTGAGTTACTAAAGATT
1 TGTTGAGTTACTAAAGATT
*
3612665 TGTTTA-TTA-T---G-TT
1 TGTTGAGTTACTAAAGATT
3612678 ATGTTGAGTTACTAAAGATT
1 -TGTTGAGTTACTAAAGATT
3612698 TGTT
1 TGTT
3612702 TATGTGCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
13 2 0.07
14 6 0.21
15 3 0.11
16 1 0.04
17 1 0.04
18 3 0.11
19 10 0.36
20 2 0.07
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.50
Consensus pattern (19 bp):
TGTTGAGTTACTAAAGATT
Found at i:3612681 original size:33 final size:33
Alignment explanation
Indices: 3612639--3612704 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3612629 TTTAAAATCC
3612639 TATGTTATGTTGAGTTACTAAAGATTTGTTTAT
1 TATGTTATGTTGAGTTACTAAAGATTTGTTTAT
3612672 TATGTTATGTTGAGTTACTAAAGATTTGTTTAT
1 TATGTTATGTTGAGTTACTAAAGATTTGTTTAT
3612705 GTGCAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (33 bp):
TATGTTATGTTGAGTTACTAAAGATTTGTTTAT
Found at i:3622576 original size:21 final size:20
Alignment explanation
Indices: 3622547--3622592 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3622537 TCATCCAAAG
*
3622547 AAGAAGAAAACGAAAAATAAA
1 AAGAAGAAAA-GAAAAAGAAA
* *
3622568 AAGAGGAAAATAAAAAGAAA
1 AAGAAGAAAAGAAAAAGAAA
3622588 AAGAA
1 AAGAA
3622593 AAAGTAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.04
Consensus pattern (20 bp):
AAGAAGAAAAGAAAAAGAAA
Found at i:3622588 original size:5 final size:6
Alignment explanation
Indices: 3622543--3622596 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
3622533 ATATTCATCC
* * * *
3622543 AAAGAA GAAGAA AACGAA AAATAA AAAGAGGA AAATAA AAAGAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGA--A AAAGAA AAAGAA AAAGAA
3622593 AAAG
1 AAAG
3622597 TAAATCAAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
6 33 0.87
8 5 0.13
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:3624861 original size:42 final size:41
Alignment explanation
Indices: 3624809--3624906 Score: 124
Period size: 42 Copynumber: 2.4 Consensus size: 41
3624799 CCAAAATTTG
* * *
3624809 TAAATACTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGA
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGA
* *
3624850 TTAAATCCTTCGGGTTATCTGTAAGTCTTTCAAGCAAGATGA
1 -TAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGA
* *
3624892 TAAGTCCTTTGGGTC
1 TAAATCCTTCGGGTC
3624907 GTCCTTAAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 12 0.25
42 36 0.75
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGA
Found at i:3625166 original size:41 final size:42
Alignment explanation
Indices: 3625061--3625156 Score: 133
Period size: 41 Copynumber: 2.3 Consensus size: 42
3625051 CCAAAATTTG
* *
3625061 TAAATCCTTCGGGTCATCAGT-AGTCTTTCGAGCATGATGAT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGAT
* *
3625102 TAAATCCTTCAGGTCATCTGTAAGTCTTTCAAGCAAGATGA-
1 TAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGAT
*
3625143 TAAGTCCTTCGGGT
1 TAAATCCTTCGGGT
3625157 TGTCCGTAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 31 0.65
42 17 0.35
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGAT
Found at i:3626440 original size:41 final size:41
Alignment explanation
Indices: 3626381--3626489 Score: 163
Period size: 38 Copynumber: 2.7 Consensus size: 41
3626371 ATGTTTTCAC
*
3626381 TATTTGTTATTATTGACTTCCTCGTAAAGAAAAGAAGTCAA
1 TATTTGTTATTCTTGACTTCCTCGTAAAGAAAAGAAGTCAA
3626422 -ATTTTGTTATTCTTGACTTCCTCGT---GAAAAGAAGTCAA
1 TA-TTTGTTATTCTTGACTTCCTCGTAAAGAAAAGAAGTCAA
*
3626460 TATTTGTTATCCTTGACTTCCTCGTAAAGA
1 TATTTGTTATTCTTGACTTCCTCGTAAAGA
3626490 GAAGTCAACC
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
38 35 0.57
39 1 0.02
40 1 0.02
41 24 0.39
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (41 bp):
TATTTGTTATTCTTGACTTCCTCGTAAAGAAAAGAAGTCAA
Found at i:3626451 original size:38 final size:38
Alignment explanation
Indices: 3626383--3626507 Score: 155
Period size: 38 Copynumber: 3.2 Consensus size: 38
3626373 GTTTTCACTA
*
3626383 TTTGTTATTATTGACTTCCTCGTAAAGAAAAGAAGTCAAAT
1 TTTGTTATTCTTGACTTCCTCGT---GAAAAGAAGTCAAAT
3626424 TTTGTTATTCTTGACTTCCTCGTGAAAAGAAGTC-AAT
1 TTTGTTATTCTTGACTTCCTCGTGAAAAGAAGTCAAAT
* **
3626461 ATTTGTTATCCTTGACTTCCTCGT-AAAGAGAAGTCAACC
1 -TTTGTTATTCTTGACTTCCTCGTGAAA-AGAAGTCAAAT
3626500 TTTGTTAT
1 TTTGTTAT
3626508 CCCTTACTCC
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
37 6 0.08
38 48 0.62
39 1 0.01
41 22 0.29
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (38 bp):
TTTGTTATTCTTGACTTCCTCGTGAAAAGAAGTCAAAT
Found at i:3626569 original size:62 final size:62
Alignment explanation
Indices: 3626471--3626622 Score: 198
Period size: 62 Copynumber: 2.5 Consensus size: 62
3626461 ATTTGTTATC
* * *
3626471 CTTGACTTCCTCGTAAAGAGAAGTCAACCTTTGTTATCCCTT-ACTCCCCAGTAGAGTCAATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTAT-CCTTGACTCCCCAATAGAGTCAATT
* ** * *
3626533 TTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTTTTGACTCTCCAATAGAGTCTATT
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATCCTTGACTCCCCAATAGAGTCAATT
* *
3626595 CTTGACTTCCTCGGGAAGAGAAATCAAT
1 CTTGACTTCCTCGTGAAGAGAAGTCAAT
3626623 ATTGCAGATT
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
61 2 0.03
62 76 0.97
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (62 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATCCTTGACTCCCCAATAGAGTCAATT
Found at i:3627163 original size:12 final size:12
Alignment explanation
Indices: 3627146--3627187 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
3627136 ATATATTTAT
*
3627146 TTATTCTTATTC
1 TTATTCTTATTA
3627158 TTATTCTTATTTA
1 TTATTCTTA-TTA
*
3627171 TTATTATTATTA
1 TTATTCTTATTA
3627183 TTATT
1 TTATT
3627188 AAATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTCTTATTA
Found at i:3627167 original size:22 final size:22
Alignment explanation
Indices: 3627142--3627184 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3627132 TTCCATATAT
* *
3627142 TTATTTATTCTTATTCTTATTC
1 TTATTTATTATTATTATTATTC
3627164 TTATTTATTATTATTATTATT
1 TTATTTATTATTATTATTATT
3627185 ATTAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTATTATTATTATTATTC
Found at i:3627176 original size:3 final size:3
Alignment explanation
Indices: 3627146--3627188 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
3627136 ATATATTTAT
* * *
3627146 TTA TTC TTA TTC TTA TTC TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
3627189 AATAATAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3628923 original size:17 final size:16
Alignment explanation
Indices: 3628894--3628935 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
3628884 ATCGCAGATC
3628894 AATT-TTTTATCTTTTAA
1 AATTATTTTATC--TTAA
3628911 AATTATTTT-TCTTAA
1 AATTATTTTATCTTAA
3628926 AATTATTTTA
1 AATTATTTTA
3628936 AAAGGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTATTTTATCTTAA
Found at i:3629157 original size:21 final size:21
Alignment explanation
Indices: 3629131--3629170 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3629121 ATTATAAACC
3629131 ATTGTGCACTG-CTATGTCAAT
1 ATTGTGCACTGTC-ATGTCAAT
*
3629152 ATTGTGGACTGTCATGTCA
1 ATTGTGCACTGTCATGTCA
3629171 GCACCATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (21 bp):
ATTGTGCACTGTCATGTCAAT
Found at i:3629189 original size:21 final size:21
Alignment explanation
Indices: 3629165--3629205 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3629155 GTGGACTGTC
3629165 ATGTCAGCACCATGAACTACT
1 ATGTCAGCACCATGAACTACT
*
3629186 ATGTCAGCACCATTAACTAC
1 ATGTCAGCACCATGAACTAC
3629206 CACGTCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (21 bp):
ATGTCAGCACCATGAACTACT
Found at i:3629212 original size:21 final size:21
Alignment explanation
Indices: 3629167--3629212 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3629157 GGACTGTCAT
* *
3629167 GTCAGCACCATGAACTACTAT
1 GTCAGCACCATGAACTACCAC
*
3629188 GTCAGCACCATTAACTACCAC
1 GTCAGCACCATGAACTACCAC
3629209 GTCA
1 GTCA
3629213 ACACTATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.22
Consensus pattern (21 bp):
GTCAGCACCATGAACTACCAC
Found at i:3631381 original size:16 final size:15
Alignment explanation
Indices: 3631362--3631412 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
3631352 AAAAGTAACT
*
3631362 CGAACTGAAAGCAATC
1 CGAA-TGAAAGCAACC
*
3631378 CGAATCGAAAACAACC
1 CGAAT-GAAAGCAACC
3631394 CGAATTGAAAGCAACC
1 CGAA-TGAAAGCAACC
3631410 CGA
1 CGA
3631413 GCCAATAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.10
Consensus pattern (15 bp):
CGAATGAAAGCAACC
Found at i:3631909 original size:20 final size:20
Alignment explanation
Indices: 3631886--3631936 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3631876 CAATTGACTC
*
3631886 GAAAATATAAAGATTGACCT
1 GAAAATCTAAAGATTGACCT
* *
3631906 GAAACTCTAAAGGTTGACCT
1 GAAAATCTAAAGATTGACCT
3631926 GAAAATCTAAA
1 GAAAATCTAAA
3631937 TGTTGACCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (20 bp):
GAAAATCTAAAGATTGACCT
Found at i:3631941 original size:20 final size:19
Alignment explanation
Indices: 3631886--3631944 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
3631876 CAATTGACTC
*
3631886 GAAAATATAAAGATTGACCT
1 GAAAATCTAAAG-TTGACCT
*
3631906 GAAACTCTAAAGGTTGACCT
1 GAAAATCTAAA-GTTGACCT
3631926 GAAAATCTAAATGTTGACC
1 GAAAATCTAAA-GTTGACC
3631945 CGAATTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (19 bp):
GAAAATCTAAAGTTGACCT
Found at i:3636491 original size:24 final size:24
Alignment explanation
Indices: 3636461--3636575 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
3636451 AAACATAATT
*
3636461 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
3636485 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* * *
3636509 CAAGTCAAGTATCAGATTAGAATC
1 CATGTCAAGTATCATATCAGAATC
3636533 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
3636557 CATGTCAAGTATCAGATCA
1 CATGTCAAGTATCATATCA
3636576 AAATTCAAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:3636595 original size:72 final size:72
Alignment explanation
Indices: 3636461--3636597 Score: 179
Period size: 72 Copynumber: 1.9 Consensus size: 72
3636451 AAACATAATT
* * * *
3636461 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGAT
1 CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAAAATCCAAATCAAGAATCAGAT
3636526 TAGAATC
66 TAGAATC
* * *
3636533 CATGTC-AGATATCATATCAGAATCCATGTCAAGTATCAGATCAAAATTCAAATCGAA-AATCAG
1 CATGTCAAG-TATCATATCAAAATCCAGGTCAAGTATCAGATCAAAATCCAAATC-AAGAATCAG
3636596 AT
64 AT
3636598 AAAATATTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
71 2 0.04
72 52 0.93
73 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (72 bp):
CATGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAAAATCCAAATCAAGAATCAGAT
TAGAATC
Found at i:3642559 original size:3 final size:3
Alignment explanation
Indices: 3642528--3642604 Score: 59
Period size: 3 Copynumber: 25.3 Consensus size: 3
3642518 ATGATAAAAC
* * * * * *
3642528 AAT AAT ATT AAT ATT AAT ATT ATT AAAT AAT AAT AAT ATT AAA ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A-AT
3642575 AA- AAT AAT AAT AAT AAT AAT ATAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A
3642605 TATACTAGGC
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.07
3 48 0.81
4 7 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:3647867 original size:46 final size:47
Alignment explanation
Indices: 3647799--3647888 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 47
3647789 ATGAATATTA
3647799 CCGATATTAACATTTCTAGTAG-AAAAAATAACATTTTAGGTAGAGC
1 CCGATATTAACATTTCTAGTAGAAAAAAATAACATTTTAGGTAGAGC
* *
3647845 CCGATATT-ACTATTTCTGGTAGAAAAAAATAACATTTTTGGTAG
1 CCGATATTAAC-ATTTCTAGTAGAAAAAAATAACATTTTAGGTAG
3647889 CGATTTACCG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
45 2 0.05
46 18 0.45
47 20 0.50
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (47 bp):
CCGATATTAACATTTCTAGTAGAAAAAAATAACATTTTAGGTAGAGC
Found at i:3649483 original size:20 final size:21
Alignment explanation
Indices: 3649450--3649601 Score: 141
Period size: 20 Copynumber: 7.0 Consensus size: 21
3649440 TAAATGAAAT
**
3649450 GCATGAAACAATG-CATAAAG
1 GCATGAAAGGATGCCATAAAG
3649470 GCATGAAAGGATGCCATAAATG
1 GCATGAAAGGATGCCATAAA-G
*
3649492 AAATGCATGAAAGGATG-CATTAAG
1 ----GCATGAAAGGATGCCATAAAG
3649516 GCATGAAAGGATGCCATAAATG
1 GCATGAAAGGATGCCATAAA-G
3649538 AAATGCATGAAAGGATGCCAT-AAG
1 ----GCATGAAAGGATGCCATAAAG
*
3649562 GCATGAAAGGATG-CATTAAG
1 GCATGAAAGGATGCCATAAAG
*
3649582 GCATGAAATGATGCCATAAA
1 GCATGAAAGGATGCCATAAA
3649602 TGCAATTAAC
Statistics
Matches: 112, Mismatches: 6, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.03
20 52 0.46
21 16 0.14
22 2 0.02
24 2 0.02
25 7 0.06
26 30 0.27
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.18
Consensus pattern (21 bp):
GCATGAAAGGATGCCATAAAG
Found at i:3649490 original size:46 final size:45
Alignment explanation
Indices: 3649437--3649575 Score: 233
Period size: 46 Copynumber: 3.0 Consensus size: 45
3649427 TAAAACGAAT
**
3649437 CCATAAATGAAATGCATGAAACAATGCATAAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCAT-AAGGCATGAAAGGATG
3649483 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCA-TAAGGCATGAAAGGATG
3649529 CCATAAATGAAATGCATGAAAGGATGCCATAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG-CATAAGGCATGAAAGGATG
3649575 C
1 C
3649576 ATTAAGGCAT
Statistics
Matches: 89, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
46 86 0.97
47 3 0.03
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (45 bp):
CCATAAATGAAATGCATGAAAGGATGCATAAGGCATGAAAGGATG
Found at i:3649505 original size:26 final size:26
Alignment explanation
Indices: 3649437--3649560 Score: 137
Period size: 26 Copynumber: 5.2 Consensus size: 26
3649427 TAAAACGAAT
**
3649437 CCATAAATGAAATGCATGAAACAATG
1 CCATAAATGAAATGCATGAAAGGATG
3649463 -CATAAA-G----GCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
3649483 CCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
*
3649509 -CAT---T--AAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
3649529 CCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
3649555 CCATAA
1 CCATAA
3649561 GGCATGAAAG
Statistics
Matches: 82, Mismatches: 4, Indels: 24
0.75 0.04 0.22
Matches are distributed among these distances:
20 26 0.32
21 9 0.11
22 2 0.02
24 2 0.02
25 9 0.11
26 34 0.41
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.19
Consensus pattern (26 bp):
CCATAAATGAAATGCATGAAAGGATG
Found at i:3650815 original size:118 final size:118
Alignment explanation
Indices: 3650668--3650906 Score: 478
Period size: 118 Copynumber: 2.0 Consensus size: 118
3650658 ATAAATTTCT
3650668 GTTTCTTTATAATATTATGCCTCACTAAGTAAATATTTAACGTGTATTGATTTCACGCCTAGGTA
1 GTTTCTTTATAATATTATGCCTCACTAAGTAAATATTTAACGTGTATTGATTTCACGCCTAGGTA
3650733 AAAGAAAAGACTAGTTGGATAAGGGGTGCAGTAGCAACTATCATAAATTTAAG
66 AAAGAAAAGACTAGTTGGATAAGGGGTGCAGTAGCAACTATCATAAATTTAAG
3650786 GTTTCTTTATAATATTATGCCTCACTAAGTAAATATTTAACGTGTATTGATTTCACGCCTAGGTA
1 GTTTCTTTATAATATTATGCCTCACTAAGTAAATATTTAACGTGTATTGATTTCACGCCTAGGTA
3650851 AAAGAAAAGACTAGTTGGATAAGGGGTGCAGTAGCAACTATCATAAATTTAAG
66 AAAGAAAAGACTAGTTGGATAAGGGGTGCAGTAGCAACTATCATAAATTTAAG
3650904 GTT
1 GTT
3650907 GACTCTCATC
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 121 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (118 bp):
GTTTCTTTATAATATTATGCCTCACTAAGTAAATATTTAACGTGTATTGATTTCACGCCTAGGTA
AAAGAAAAGACTAGTTGGATAAGGGGTGCAGTAGCAACTATCATAAATTTAAG
Found at i:3652933 original size:38 final size:37
Alignment explanation
Indices: 3652881--3652961 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
3652871 AAATGATATC
*
3652881 AAATTTGTATTTCAAGAAAAAGTAAACTTAGGTGAGATG
1 AAATTTGTATTTCAAGAAAAA-TAAACTCA-GTGAGATG
* **
3652920 AAATTT-TGTTTCAAGGGAAATAAACTCAGTGAGATG
1 AAATTTGTATTTCAAGAAAAATAAACTCAGTGAGATG
3652956 -AATTTG
1 AAATTTG
3652962 GGTTTAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 5 0.14
36 8 0.22
37 7 0.19
38 11 0.30
39 6 0.16
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (37 bp):
AAATTTGTATTTCAAGAAAAATAAACTCAGTGAGATG
Found at i:3653147 original size:35 final size:36
Alignment explanation
Indices: 3653081--3653150 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
3653071 AAGTAAGACA
3653081 AAATTTGTTTCAAGAAAAAGAATCTCAAGTGAGATG
1 AAATTTGTTTCAAGAAAAAGAATCTCAAGTGAGATG
*
3653117 AAATTTGTTTTAAGAAAAA-AATCTCAAGTGAGAT
1 AAATTTGTTTCAAGAAAAAGAATCTCAAGTGAGAT
3653151 AAGATATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 15 0.45
36 18 0.55
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (36 bp):
AAATTTGTTTCAAGAAAAAGAATCTCAAGTGAGATG
Found at i:3653165 original size:36 final size:36
Alignment explanation
Indices: 3653081--3653162 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 36
3653071 AAGTAAGACA
* *
3653081 AAATTTGTTTCAAGAAAAAGAATCTCAAGTGAGATG
1 AAATATGTTTTAAGAAAAAGAATCTCAAGTGAGATG
*
3653117 AAATTTGTTTTAAGAAAAA-AATCTCAAGTGAGAT-
1 AAATATGTTTTAAGAAAAAGAATCTCAAGTGAGATG
3653151 AAGATATGTTTT
1 AA-ATATGTTTT
3653163 TAATTAAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 2 0.05
35 23 0.53
36 18 0.42
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (36 bp):
AAATATGTTTTAAGAAAAAGAATCTCAAGTGAGATG
Found at i:3654899 original size:2 final size:2
Alignment explanation
Indices: 3654892--3654930 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3654882 AGATGTAAAC
3654892 TA TA TA TA TA 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 TA TA TA TA TA T
3654931 TAGATGTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3656433 original size:17 final size:19
Alignment explanation
Indices: 3656411--3656447 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
3656401 AGCATTAAAG
*
3656411 GAAAAATAAA-AA-GGAAT
1 GAAAAAGAAATAATGGAAT
3656428 GAAAAAGAAATAATGGAAT
1 GAAAAAGAAATAATGGAAT
3656447 G
1 G
3656448 GTACAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAAAGAAATAATGGAAT
Found at i:3664517 original size:265 final size:265
Alignment explanation
Indices: 3664111--3664648 Score: 1031
Period size: 265 Copynumber: 2.0 Consensus size: 265
3664101 TTCTTTAAAC
3664111 ACTCTATAGTTCACACATATAGTGCCAATACATTCATTTCCCAACCATTCCTATAATTTACATGG
1 ACTCTATAGTTCACACATATAGTGCCAATACATTCATTTCCCAACCATTCCTATAATTTACATGG
3664176 GTTGCACACACAATACCAATACAAAAATTCATATAATTTCTTAGTTTTTTCACATAAAGTGCCCA
66 GTTGCACACACAATACCAATACAAAAATTCATATAATTTCTTAGTTTTTTCACATAAAGTGCCCA
3664241 TAAACTAATTATGAATTTCTTAACTTTTTGCACACGAAGTGCCCATACAAAAATTCATAAACTAA
131 TAAACTAATTATGAATTTCTTAACTTTTTGCACACGAAGTGCCCATACAAAAATTCATAAACTAA
*
3664306 TTACAAAATTCTTAACTTTTTGCACACTCAGTGCCTTTTGGTAATCACCATACATATATCAATCA
196 TTACAAAATTCTTAACTTTTTGCACACTAAGTGCCTTTTGGTAATCACCATACATATATCAATCA
3664371 ATCAT
261 ATCAT
*
3664376 ACTCTATAGTTCACACATATAGTGCCAATACATTCATTTCCCAACCTTTCCTATAATTTACATGG
1 ACTCTATAGTTCACACATATAGTGCCAATACATTCATTTCCCAACCATTCCTATAATTTACATGG
*
3664441 GTTGCACACACAATACCAATACAAAAATTCATATAATTTCTTAGTTTTTTCACATAAAGTTCCCA
66 GTTGCACACACAATACCAATACAAAAATTCATATAATTTCTTAGTTTTTTCACATAAAGTGCCCA
3664506 TAAACTAATTATGAATTTCTTAACTTTTTGCACACGAAGTGCCCATACAAAAATTCATAAACTAA
131 TAAACTAATTATGAATTTCTTAACTTTTTGCACACGAAGTGCCCATACAAAAATTCATAAACTAA
*
3664571 TTACAAAATTCTTAACTTTTTGCACACTAAGTGCCTTTTGGTAATCACCATACATATATTAATCA
196 TTACAAAATTCTTAACTTTTTGCACACTAAGTGCCTTTTGGTAATCACCATACATATATCAATCA
3664636 ATCAT
261 ATCAT
3664641 ACATCTAT
1 AC-TCTAT
3664649 GACTACAGTA
Statistics
Matches: 268, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
265 263 0.98
266 5 0.02
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (265 bp):
ACTCTATAGTTCACACATATAGTGCCAATACATTCATTTCCCAACCATTCCTATAATTTACATGG
GTTGCACACACAATACCAATACAAAAATTCATATAATTTCTTAGTTTTTTCACATAAAGTGCCCA
TAAACTAATTATGAATTTCTTAACTTTTTGCACACGAAGTGCCCATACAAAAATTCATAAACTAA
TTACAAAATTCTTAACTTTTTGCACACTAAGTGCCTTTTGGTAATCACCATACATATATCAATCA
ATCAT
Found at i:3690360 original size:21 final size:21
Alignment explanation
Indices: 3690334--3690381 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3690324 TTTGCTAAGT
3690334 AGTATCAATATTGATTCAATC
1 AGTATCAATATTGATTCAATC
*
3690355 AGTATCAATATTGATTGAATC
1 AGTATCAATATTGATTCAATC
*
3690376 AATATC
1 AGTATC
3690382 GATACTAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
AGTATCAATATTGATTCAATC
Found at i:3690556 original size:95 final size:95
Alignment explanation
Indices: 3690393--3690581 Score: 252
Period size: 95 Copynumber: 2.0 Consensus size: 95
3690383 ATACTAATGA
* * *
3690393 GGTAGTATTGATACCATGGTAAGGGTATCGATACCAAGAAACATTAAATCTAATTTTGGTACCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAATTTTGGTACCGA
* * *
3690458 TACCGGTAGGGGGTATTAATACCATAGTAG
66 TACCCGAAGGGGGTATCAATACCATAGTAG
** * * * **
3690488 GGTAGTATCGATACTGTGGTAAGGGTATCGATACCAGGAAGCATCAAACCTATTTTTGGTATTGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAATTTTGGTACCGA
*
3690553 TACCCGAAGGGGGTATCAGTACCATAGTA
66 TACCCGAAGGGGGTATCAATACCATAGTA
3690582 TAGAAGTATC
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 80 1.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAACCTAATTTTGGTACCGA
TACCCGAAGGGGGTATCAATACCATAGTAG
Found at i:3690611 original size:95 final size:95
Alignment explanation
Indices: 3690409--3690616 Score: 231
Period size: 95 Copynumber: 2.2 Consensus size: 95
3690399 ATTGATACCA
* * * * *
3690409 TGGTAAGGGTATCGATACCAAGAAACATTAAATCTAATTTTGGTACCGATACCGGTAGGGGGTAT
1 TGGTAAGAGTATCGATACCAAGAAACATCAAACCTAATTTTGGTACCGATACCCGAAGGGGGTAT
* * *
3690474 TAATACCATAGTAGGGTAGTATCGATACTG
66 CAATACCATAGTAGAGAAGTATCGATACTG
* * * * **
3690504 TGGTAAGGGTATCGATACCAGGAAGCATCAAACCTATTTTTGGTATTGATACCCGAAGGGGGTAT
1 TGGTAAGAGTATCGATACCAAGAAACATCAAACCTAATTTTGGTACCGATACCCGAAGGGGGTAT
* * *
3690569 CAGTACCATAGTATAGAAGTATCGGTACTAG
66 CAATACCATAGTAGAGAAGTATCGATACT-G
3690600 -GGT-AGTAGTATCGATAC
1 TGGTAAG-AGTATCGATAC
3690617 TATGGAGCCA
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
94 2 0.02
95 92 0.97
96 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (95 bp):
TGGTAAGAGTATCGATACCAAGAAACATCAAACCTAATTTTGGTACCGATACCCGAAGGGGGTAT
CAATACCATAGTAGAGAAGTATCGATACTG
Found at i:3698223 original size:31 final size:32
Alignment explanation
Indices: 3698163--3698224 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3698153 AAGGATAAAA
*
3698163 GAAATGGTTTAAGGAAAGAAAGTGAAAAGAAT
1 GAAATGGTTTAAGAAAAGAAAGTGAAAAGAAT
3698195 GAAATGGTTTAAGAAAATG-AA-TGAAAAGAA
1 GAAATGGTTTAAGAAAA-GAAAGTGAAAAGAA
3698225 AGAAGGAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.32
32 18 0.64
33 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (32 bp):
GAAATGGTTTAAGAAAAGAAAGTGAAAAGAAT
Found at i:3703427 original size:30 final size:31
Alignment explanation
Indices: 3703391--3703450 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
3703381 CTTAGCTTTA
**
3703391 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
3703421 TATTATGTTTACATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
3703451 GGCAGCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:3704384 original size:19 final size:20
Alignment explanation
Indices: 3704360--3704410 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
3704350 CGGCCAAGAG
* *
3704360 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
3704379 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
3704399 CATGTATTTTCA
1 CATGTATTTTCA
3704411 AAAGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:3704848 original size:19 final size:19
Alignment explanation
Indices: 3704824--3704865 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
3704814 ATCCTTTCTT
3704824 TATTTCATTTCATT-CTTAA
1 TATTTCATTTCATTACTT-A
3704843 TATTTCATTTCATTACTTA
1 TATTTCATTTCATTACTTA
3704862 TATT
1 TATT
3704866 ATTATCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTCATTTCATTACTTA
Found at i:3706592 original size:21 final size:21
Alignment explanation
Indices: 3706557--3706597 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3706547 TTGCCAGATC
*
3706557 ACACCAATCCCTTTGATGTTT
1 ACACCAATCCATTTGATGTTT
* *
3706578 ACACCAATGCATTTGTTGTT
1 ACACCAATCCATTTGATGTT
3706598 GCCATTTGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (21 bp):
ACACCAATCCATTTGATGTTT
Done.