Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 30
Found at i:4025283 original size:149 final size:148
Alignment explanation
Indices: 4025016--4025461 Score: 522
Period size: 149 Copynumber: 3.0 Consensus size: 148
4025006 TCGAGTAGCA
* * * * *
4025016 TCAAGA-AGGAGTCTACCTACCAAGGAGAAGAGCCAGATATATGCCTGCTGAGGTAACAAGTTGG
1 TCAAGAGA-GAGTCTACCTACCAAGGAGACGATCCAAACATTTGCCT-CTGAGGTAACAAGTTGG
* * * * *
4025080 ACTCGAGACGATTCGACATCAAAGCCAACAGTTGAAGATAACAAACCA-ACTCGAAAGATTTCTG
64 ACTCGAGACGATTTGACGTCAAAGCCAATAGTTGAAGATCACGAACCAGA-TCGAAAGATTTCTG
4025144 GAAATAGGAGATGAAGTAGAG
128 GAAATAGGAGATGAAGTAGAG
*
4025165 TCAAGAGAGAGTCTACCTACCAAGGAGACGATCCATACATTTGCCTCATGAGGTAACAAGTTGGA
1 TCAAGAGAGAGTCTACCTACCAAGGAGACGATCCAAACATTTGCCTC-TGAGGTAACAAGTTGGA
* * ** *
4025230 CCCGAGACGATTTAACGTTGAAGCCAATAGTTGAAGATCACGAACCAGATCGAAAGATTTTTGGA
65 CTCGAGACGATTTGACGTCAAAGCCAATAGTTGAAGATCACGAACCAGATCGAAAGATTTCTGGA
*
4025295 AATAGGAGATTAAGTAGGAG
130 AATAGGAGATGAAGTA-GAG
* * * * * * * *
4025315 -CTAGAGGGAGTCTATCTACCAAAGAGACGATCCAAACATTTTCATGTTGAGGTAACAAGTTAGA
1 TCAAGAGAGAGTCTACCTACCAAGGAGACGATCCAAACATTTGCCT-CTGAGGTAACAAGTTGGA
* * * *
4025379 CTCGAGACGATTTGACGCCAAATCCAATAGTTGAAGATCACGAACCAGCTCGAAAGACTTCT-GA
65 CTCGAGACGATTTGACGTCAAAGCCAATAGTTGAAGATCACGAACCAGATCGAAAGATTTCTGGA
* *
4025443 AATTAGGAGACGATGTAGA
130 AA-TAGGAGATGAAGTAGA
4025462 AGCTTTAAAG
Statistics
Matches: 254, Mismatches: 37, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
148 7 0.03
149 242 0.95
150 5 0.02
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (148 bp):
TCAAGAGAGAGTCTACCTACCAAGGAGACGATCCAAACATTTGCCTCTGAGGTAACAAGTTGGAC
TCGAGACGATTTGACGTCAAAGCCAATAGTTGAAGATCACGAACCAGATCGAAAGATTTCTGGAA
ATAGGAGATGAAGTAGAG
Found at i:4025631 original size:14 final size:15
Alignment explanation
Indices: 4025612--4025648 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
4025602 CCTTGTTGCA
4025612 TTTGCATCTCACA-T
1 TTTGCATCTCACATT
*
4025626 TTTGCA-CTCCCATT
1 TTTGCATCTCACATT
4025640 TTTGCATCT
1 TTTGCATCT
4025649 TTGCATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.16, C:0.30, G:0.08, T:0.46
Consensus pattern (15 bp):
TTTGCATCTCACATT
Found at i:4025682 original size:20 final size:20
Alignment explanation
Indices: 4025642--4025682 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4025632 CTCCCATTTT
**
4025642 TGCATCTTTGCATTTGCATA
1 TGCATCTTTGCATAAGCATA
*
4025662 TGCATCTTTGCATAAGTATA
1 TGCATCTTTGCATAAGCATA
4025682 T
1 T
4025683 ACACATTGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (20 bp):
TGCATCTTTGCATAAGCATA
Found at i:4026955 original size:12 final size:13
Alignment explanation
Indices: 4026940--4026970 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
4026930 AATGAGAAAG
4026940 AAAAAAAGAG-GA
1 AAAAAAAGAGAGA
4026952 AAAAAAAGAGAGA
1 AAAAAAAGAGAGA
4026965 AAAAAA
1 AAAAAA
4026971 GGAAAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAGA
Found at i:4026985 original size:18 final size:19
Alignment explanation
Indices: 4026938--4027016 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 19
4026928 AAAATGAGAA
4026938 AGAAAAAAAGAGGAAAAAAAAG
1 AGAAAAAAA-A-G-AAAAAAAG
* *
4026960 AGAGAAAAAAAGGAAAAATG
1 AGA-AAAAAAAGAAAAAAAG
4026980 A-AAAAAAAAGAAAAAAAG
1 AGAAAAAAAAGAAAAAAAG
*
4026998 AGAAAAAAGAGAAAGAAAA
1 AGAAAAAAAAGAAA-AAAA
4027017 AATCGATCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 15 0.31
19 12 0.24
20 11 0.22
21 1 0.02
22 4 0.08
23 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.01
Consensus pattern (19 bp):
AGAAAAAAAAGAAAAAAAG
Found at i:4027006 original size:9 final size:9
Alignment explanation
Indices: 4026953--4027011 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 9
4026943 AAAAGAGGAA
4026953 AAAAAAGAG
1 AAAAAAGAG
*
4026962 AGAAAAAAAGG
1 A-AAAAAGA-G
*
4026973 AAAAATGA-
1 AAAAAAGAG
*
4026981 AAAAAAAAG
1 AAAAAAGAG
4026990 AAAAAAAGAG
1 -AAAAAAGAG
4027000 AAAAAAGAG
1 AAAAAAGAG
4027009 AAA
1 AAA
4027012 GAAAAAATCG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 6 0.15
9 13 0.32
10 19 0.47
11 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:4027016 original size:11 final size:9
Alignment explanation
Indices: 4026913--4027017 Score: 59
Period size: 9 Copynumber: 10.6 Consensus size: 9
4026903 AAGATATAGC
4026913 AAAAAGAAA
1 AAAAAGAAA
**
4026922 AATGAGAAA
1 AAAAAGAAA
4026931 ATGAGAAAGAAA
1 A--A-AAAGAAA
4026943 AAAAGAGGAAA
1 AAAA-A-GAAA
4026954 AAAAAGAGAGA
1 AAAAAGA-A-A
*
4026965 AAAAA-AGGA
1 AAAAAGA-AA
*
4026974 AAAATGAAAA
1 AAAAAG-AAA
4026984 AAAAAGAAA
1 AAAAAGAAA
4026993 AAAAGAGAAA
1 AAAA-AGAAA
*
4027003 AAAGAGAAA
1 AAAAAGAAA
4027012 GAAAAA
1 -AAAAA
4027018 ATCGATCAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
9 29 0.39
10 24 0.32
11 16 0.21
12 6 0.08
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:4028596 original size:65 final size:65
Alignment explanation
Indices: 4028482--4028922 Score: 477
Period size: 66 Copynumber: 6.8 Consensus size: 65
4028472 TTTGAGATTG
* ** *
4028482 TTTCTCTTGAAACAAA-TTT-TATCTCTTGAGACAGTTTCTCTCAAAACAAAAGC-TTGAGTCTA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAGTCTA
* * * * *
4028544 TTTCTCTTGAAACAGAATTTTGTCTCTCTTGAGACAATTTATCTCGAAACAAAAGC-CTGAGTCT
1 TTTCTCTTGAAACA-AATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAGTCT
4028608 A
65 A
* * ** * *
4028609 TTTCTCTTGAAACAGAATTTTGTCTCTCTTAAGATAGTTTCTCTTGAAACATTATCTTTGAATAT
1 TTTCTCTTGAAACA-AATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAGTCT
*
4028674 G
65 A
*
4028675 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATC
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAATCTTTGAG-TC
4028740 -A
64 TA
* ** * * *
4028741 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCAATCTTTGAAAT-
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAATCTTTG-AGTC
4028805 TA
64 TA
* * * *
4028807 TTTCCCTTGAAACTAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAAACATTGAGAT-
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AAATCTTTGAG-TC
*
4028871 TG
64 TA
* *
4028873 TTTCCCTTGAAACAAA--TTGTCTATCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
4028923 TTATCCTTAA
Statistics
Matches: 327, Mismatches: 43, Indels: 17
0.84 0.11 0.04
Matches are distributed among these distances:
62 14 0.04
63 4 0.01
64 34 0.10
65 120 0.37
66 153 0.47
67 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (65 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATCTTTGAGTCTA
Found at i:4029092 original size:37 final size:34
Alignment explanation
Indices: 4028999--4029092 Score: 89
Period size: 35 Copynumber: 2.6 Consensus size: 34
4028989 AAGCAAAGAT
* ** *
4028999 AAAAAATTTATCTGACTTGAGAGTGTTTTCCTTA
1 AAAAAATTTATCTCACTTGAGACAGTTTTCCTGA
* * *
4029033 AAACAATTTCGTCTCGCTTGAGACAGTTTTCCCTCGA
1 AAAAAATTT-ATCTCACTTGAGACAGTTTT-CCT-GA
4029070 AACAAAATTTATCTCACTTGAGA
1 AA-AAAATTTATCTCACTTGAGA
4029093 GAGCTTCTCT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
34 8 0.17
35 15 0.33
36 3 0.07
37 14 0.30
38 6 0.13
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (34 bp):
AAAAAATTTATCTCACTTGAGACAGTTTTCCTGA
Found at i:4029602 original size:91 final size:90
Alignment explanation
Indices: 4029383--4029904 Score: 576
Period size: 91 Copynumber: 5.8 Consensus size: 90
4029373 TTCCAATGGG
*
4029383 GAGTTCATAATGAGAAGAACTCATCCTATG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCC-AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * ** *
4029447 CGACCTTACATCAACATTTTCAACGG-
65 CGACCTTGCCTCAACA-TACCAGCGGA
* * *
4029473 GAGTTCATAATGAGAAGAACACATCCAACGAATG-AGAAGAAGTTCATAATGAGAATAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCCAA-GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
4029537 CGGCCTTGCCTCGAAGATACCAGTGGA
65 CGACCTTGCCTC-AACATACCAGCGGA
*
4029564 GAGTTCATAATGAGAAGAACTCATCCAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * ** * *
4029629 AACCTTGCATCAACTTTTTCACCGGG
66 GACCTTGCCTCAAC-ATACCAGCGGA
* *
4029655 GAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *
4029720 GACCTTGCCTCGACGTTACCAGTGGA
66 GACCTTGCCTCAAC-ATACCAGCGGA
* * * *
4029746 GAGTTCTTAATGAGAAGAACTTATCCAACGAATG-AGAAGAAGTTTATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCCAA-GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
4029810 CCACCTTGACTCAACATTGCCAGCAGA
65 CGACCTTGCCTCAACA-TACCAGCGGA
* *
4029837 GAG-TCATAATGAGAAGAACTCATCC--G-ACGAATG-AGAAGTTCATAATGAGAAGAACTTGTC
1 GAGTTCATAATGAGAAGAACTCATCCAAGAAGGAA-GAAGAAGTTCATAATGAGAAGAACTTGTT
*
4029897 CAACCTTG
65 CGACCTTG
4029905 GTAATTCCAT
Statistics
Matches: 366, Mismatches: 56, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
86 2 0.01
87 34 0.09
88 1 0.00
89 1 0.00
90 94 0.26
91 231 0.63
92 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (90 bp):
GAGTTCATAATGAGAAGAACTCATCCAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
GACCTTGCCTCAACATACCAGCGGA
Found at i:4029729 original size:182 final size:180
Alignment explanation
Indices: 4029383--4029904 Score: 689
Period size: 182 Copynumber: 2.9 Consensus size: 180
4029373 TTCCAATGGG
* **
4029383 GAGTTCATAATGAGAAGAACTCATCCTATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *
4029448 GACCTTACATCAACATTTTCAACGGGAGTTCATAATGAGAAGAACACATCCAACGAATG-AGAAG
66 AACCTTGCATCAACATTTTCAACGGGAGTTCATAATGAGAAGAACTCATCCAAC-AA-GAAGAAG
* *
4029512 AAGTTCATAATGAGAATAACTTGTTCGGCCTTGCCTCGAAGATACCAGTGGA
129 AAGTTCATAATGAGAAGAACTTGTTCGACCTTGCCTCGAAGATACCAGTGGA
4029564 GAGTTCATAATGAGAAGAACTCATCCAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCCAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
4029629 AACCTTGCATCAACTTTTTCACCGGGGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAG
66 AACCTTGCATCAACATTTTCAAC-GGGAGTTCATAATGAGAAGAACTCATCCAACAA-GAAGAAG
* * *
4029694 AAATTCATAATGAGAAGAACTTGTTCGACCTTGCCTCGACGTTACCAGTGGA
129 AAGTTCATAATGAGAAGAACTTGTTCGACCTTGCCTCGAAGATACCAGTGGA
* * * * *
4029746 GAGTTCTTAATGAGAAGAACTTATCCAACGAATG-AGAAGAAGTTTATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCCAA-AAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* ** * * *
4029810 CCACCTTG-ACTCAACATTGCCAGCAGAGAG-TCATAATGAGAAGAACTCATCCGAC--GAATG-
65 CAACCTTGCA-TCAACATTTTCAAC-GGGAGTTCATAATGAGAAGAACTCATCCAACAAGAA-GA
* *
4029870 AGAAGTTCATAATGAGAAGAACTTGTCCAACCTTG
127 AGAAGTTCATAATGAGAAGAACTTGTTCGACCTTG
4029905 GTAATTCCAT
Statistics
Matches: 306, Mismatches: 30, Indels: 13
0.88 0.09 0.04
Matches are distributed among these distances:
178 35 0.11
179 1 0.00
181 109 0.36
182 158 0.52
183 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (180 bp):
GAGTTCATAATGAGAAGAACTCATCCAAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTGCATCAACATTTTCAACGGGAGTTCATAATGAGAAGAACTCATCCAACAAGAAGAAGAA
GTTCATAATGAGAAGAACTTGTTCGACCTTGCCTCGAAGATACCAGTGGA
Found at i:4031571 original size:8 final size:8
Alignment explanation
Indices: 4031558--4031632 Score: 50
Period size: 8 Copynumber: 9.5 Consensus size: 8
4031548 CAACTTGTAT
4031558 TTATTTTA
1 TTATTTTA
4031566 TTATTTTA
1 TTATTTTA
* *
4031574 TTCTATTA
1 TTATTTTA
4031582 TGT-TTTTA
1 T-TATTTTA
* *
4031590 CTGTTTT-
1 TTATTTTA
4031597 TTATTTT-
1 TTATTTTA
*
4031604 TT-TTATTG
1 TTATT-TTA
4031612 TTATTTTA
1 TTATTTTA
4031620 TTATTTTAA
1 TTATTTT-A
4031629 TTAT
1 TTAT
4031633 GATTATTAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
6 2 0.04
7 10 0.19
8 34 0.63
9 8 0.15
ACGTcount: A:0.20, C:0.03, G:0.04, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:4031608 original size:19 final size:21
Alignment explanation
Indices: 4031558--4031626 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
4031548 CAACTTGTAT
* *
4031558 TTATTTTATTA-TTTTATTCTA
1 TTATTTT-TTACTGTTATTTTA
4031579 TTATGTTTTTACTGTT-TTTTA
1 TTAT-TTTTTACTGTTATTTTA
*
4031600 TT-TTTTTTATTGTTATTTTA
1 TTATTTTTTACTGTTATTTTA
4031620 TTATTTT
1 TTATTTT
4031627 AATTATGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 10 0.24
20 8 0.20
21 17 0.41
22 6 0.15
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.75
Consensus pattern (21 bp):
TTATTTTTTACTGTTATTTTA
Found at i:4036768 original size:3 final size:3
Alignment explanation
Indices: 4036760--4036788 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4036750 TATAGGATTA
4036760 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4036789 AACTTATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4038109 original size:3 final size:3
Alignment explanation
Indices: 4038101--4038178 Score: 126
Period size: 3 Copynumber: 27.0 Consensus size: 3
4038091 TTCGGTCCTG
*
4038101 TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4038149 TAA TAA TAA TAA TAA -AA TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4038179 AACTGGACAA
Statistics
Matches: 70, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
2 6 0.09
3 64 0.91
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4038718 original size:42 final size:42
Alignment explanation
Indices: 4038630--4038731 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
4038620 AAGGTTTTAT
* * * * *
4038630 TGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGGCTTTC
1 TGATGACCCGAAGGATTTAAGCATCTTGCTCGAAAGACTTAC
*
4038671 AGATGACCCGAAGGATTTAAGCATCATT-CTCGAAAGACTTAC
1 TGATGACCCGAAGGATTTAAGCATC-TTGCTCGAAAGACTTAC
4038713 TGATGACCCGAAGGATTTA
1 TGATGACCCGAAGGATTTA
4038732 CAAATCATGA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 15 0.29
42 35 0.67
43 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (42 bp):
TGATGACCCGAAGGATTTAAGCATCTTGCTCGAAAGACTTAC
Found at i:4039096 original size:271 final size:273
Alignment explanation
Indices: 4038603--4039301 Score: 1091
Period size: 271 Copynumber: 2.6 Consensus size: 273
4038593 ATGGAAATGT
* * * *
4038603 TGAAACCATTATGCCCGAAGGTTTTATTGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCT
1 TGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCT
*
4038668 T-TCAGATGACCCGAAGGATTTAAGCATCATTCTCGAAAGACTTACTGATGACCCGAAGGATTTA
66 TAT-AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTA
* *
4038732 CAAATCATGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTAAAATTAG
130 CAAATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTACTTGTCAAGGAACCCCTTAAAATTAG
* *
4038797 ACTTAGCTTCCTTTAACAACTCTTTTGAGATAAT-T-AAGAAACCCCTTAAAATTAGGCTTAGTT
195 ACTTAGCTTCCTTTAACAACTCTTTTGAGATAATATCAAGAAACCCCTAAAAATCAGGCTTAGTT
4038860 TCTAAAATCGCATA
260 TCTAAAATCGCATA
* * * * *
4038874 TGAAAACATCATGCCCGAAGGTCTTATGGATGGTCTGAAGGACTTTTCATCTTTCTTGAAAGGCT
1 TGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCT
*
4038939 TATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGGAGGATTTAC
66 TATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAC
* * *
4039004 AAATCAAGAAACCTTTAAAAATCAAGCTTA-TCTTCTTACTTGTTAAGGAACCCCTTAAAATTAG
131 AAATCAAGAAACCCTTGAAAATCAAGCTTAGT-TTCTTACTTGTCAAGGAACCCCTTAAAATTAG
* *
4039068 GCTTAGCTTCCTTTAACAACTCTTTTGAGATAATCATCAAGAAATCCCTAAAAATCAGGCTTAGT
195 ACTTAGCTTCCTTTAACAACTCTTTTGAGATAAT-ATCAAGAAACCCCTAAAAATCAGGCTTAGT
* *
4039133 TTCTAAAATCTCATT
259 TTCTAAAATCGCATA
* ** *
4039148 TGAAAACATCTTGGTCGAAGGTCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCT
1 TGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCT
* *
4039213 TATAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGATTTACTGATGACCCGAAGGATTTAC
66 TATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAC
4039278 AAATCAAGAAACCCTTGAAAATCA
131 AAATCAAGAAACCCTTGAAAATCA
4039302 GTGAAGCTCT
Statistics
Matches: 387, Mismatches: 36, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
270 1 0.00
271 207 0.53
272 1 0.00
273 1 0.00
274 177 0.46
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (273 bp):
TGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCT
TATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAC
AAATCAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTACTTGTCAAGGAACCCCTTAAAATTAGA
CTTAGCTTCCTTTAACAACTCTTTTGAGATAATATCAAGAAACCCCTAAAAATCAGGCTTAGTTT
CTAAAATCGCATA
Found at i:4039250 original size:42 final size:42
Alignment explanation
Indices: 4039181--4039276 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
4039171 TTACGGATGG
* * * *
4039181 CCCGAAGGACTT-ATCATCTTGCTCGAAAGGCTTA-TAGATAA
1 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT-GATAA
* *
4039222 CCCGAAGGATTTAAGCATCATGCTCGAAAGATTTACTGATGA
1 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAA
4039264 CCCGAAGGATTTA
1 CCCGAAGGATTTA
4039277 CAAATCAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 11 0.23
42 35 0.74
43 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAA
Found at i:4041185 original size:9 final size:8
Alignment explanation
Indices: 4041173--4041222 Score: 55
Period size: 9 Copynumber: 5.8 Consensus size: 8
4041163 TTTGTTCTTT
4041173 TTTTATTTC
1 TTTT-TTTC
*
4041182 TTTTTCATC
1 TTTTT-TTC
4041191 TCTTTTTTC
1 T-TTTTTTC
4041200 TTTTTTTTC
1 -TTTTTTTC
4041209 TTTTTTTC
1 TTTTTTTC
4041217 TTTTTT
1 TTTTTT
4041223 CTGATGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
8 15 0.42
9 16 0.44
10 5 0.14
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:4041201 original size:18 final size:17
Alignment explanation
Indices: 4041173--4041221 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
4041163 TTTGTTCTTT
4041173 TTTTATTTCTTTTTCATC
1 TTTT-TTTCTTTTTCATC
**
4041191 TCTTTTTTCTTTTTTTTC
1 T-TTTTTTCTTTTTCATC
4041209 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
4041222 TCTGATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 12 0.43
18 13 0.46
19 3 0.11
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTTTCATC
Found at i:4041701 original size:11 final size:11
Alignment explanation
Indices: 4041685--4041710 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4041675 TTTAAATCAA
4041685 TCTTTTTTTCT
1 TCTTTTTTTCT
4041696 TCTTTTTTTCT
1 TCTTTTTTTCT
4041707 TCTT
1 TCTT
4041711 CTTACTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TCTTTTTTTCT
Found at i:4046398 original size:22 final size:22
Alignment explanation
Indices: 4046345--4046398 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
4046335 AAGCTTAATG
* *
4046345 ACAAATATATTTCATTAATAAA
1 ACAAATTTTTTTCATTAATAAA
**
4046367 AC-TCTCTTTTTTCATTAATAAA
1 ACAAAT-TTTTTTCATTAATAAA
4046389 ACAAATTTTT
1 ACAAATTTTT
4046399 CAGAATAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
21 1 0.04
22 22 0.92
23 1 0.04
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.44
Consensus pattern (22 bp):
ACAAATTTTTTTCATTAATAAA
Found at i:4051529 original size:111 final size:111
Alignment explanation
Indices: 4051391--4051590 Score: 260
Period size: 111 Copynumber: 1.8 Consensus size: 111
4051381 AATAATGGTA
* * *
4051391 ATCGGTCGATTTTGTTAAATGTATAACGATGCATTATAGGCATAAAAGGT-TCCACCCATAGTAT
1 ATCGATCGATTTTGTTAAATGCATAACGATGCATTATAGACATAAAAGGTGT-CACCCATAGTAT
* * *
4051455 TAATAAGAGGTGATTTACCATTTCGGCATACTTCATGTATGAAAGCT
65 TAATAAAAGGTGAATAACCATTTCGGCATACTTCATGTATGAAAGCT
* * * * *
4051502 ATCGATCGATTTTGTTTAAA-GCATAACGGTGCATTATTGACGTAAAAGGTGTCACTCATGGTAT
1 ATCGATCGATTTTG-TTAAATGCATAACGATGCATTATAGACATAAAAGGTGTCACCCATAGTAT
*
4051566 TCATAAAAGGTGAATAACCATTTCG
65 TAATAAAAGGTGAATAACCATTTCG
4051591 TCACTTCGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
111 69 0.92
112 6 0.08
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (111 bp):
ATCGATCGATTTTGTTAAATGCATAACGATGCATTATAGACATAAAAGGTGTCACCCATAGTATT
AATAAAAGGTGAATAACCATTTCGGCATACTTCATGTATGAAAGCT
Found at i:4058220 original size:14 final size:14
Alignment explanation
Indices: 4058201--4058227 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4058191 TTTGGTCAAA
4058201 AATGGCAAATGGGG
1 AATGGCAAATGGGG
4058215 AATGGCAAATGGG
1 AATGGCAAATGGG
4058228 CGGCCAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15
Consensus pattern (14 bp):
AATGGCAAATGGGG
Found at i:4077341 original size:21 final size:19
Alignment explanation
Indices: 4077316--4077358 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
4077306 AAAAATACTA
4077316 TTTTACATCAATTTCGATATC
1 TTTTACATCAATTT-G-TATC
* *
4077337 TTTTATATTAATTTGTATC
1 TTTTACATCAATTTGTATC
4077356 TTT
1 TTT
4077359 AAAATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTACATCAATTTGTATC
Found at i:4091010 original size:2 final size:2
Alignment explanation
Indices: 4091005--4091109 Score: 171
Period size: 2 Copynumber: 54.0 Consensus size: 2
4090995 ATTTAGTGTG
4091005 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
4091045 TA CA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4091087 T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
4091110 ATACATAGTT
Statistics
Matches: 96, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
1 3 0.03
2 93 0.97
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4091262 original size:35 final size:36
Alignment explanation
Indices: 4091217--4091414 Score: 203
Period size: 35 Copynumber: 5.5 Consensus size: 36
4091207 ACGTTTTAAA
* * *
4091217 AAAACATATAT-TATATAGTTTTGAGAACAATTTT-G
1 AAAATATATATATATATAGTTTTGAAAAC-TTTTTCG
*
4091252 AAAATATATATAATAAATAGTTTTGAAAACATTTTTCG
1 AAAATATATAT-ATATATAGTTTTGAAAAC-TTTTTCG
* *
4091290 AAAATATATATAATATATAGTTTTAAAAACTTTTTCA
1 AAAATATATAT-ATATATAGTTTTGAAAACTTTTTCG
*
4091327 AAAATATATATAATATATAGTTTT-AAAACGTTTT-G
1 AAAATATATAT-ATATATAGTTTTGAAAACTTTTTCG
*
4091362 AAAATATATATAATATATAGTTTT-AAAACGTTTT-G
1 AAAATATATAT-ATATATAGTTTTGAAAACTTTTTCG
4091397 AAAACGTATA-ATATATAT
1 AAAA--TATATATATATAT
4091415 TTTTTTTTAA
Statistics
Matches: 149, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
35 55 0.37
36 11 0.07
37 54 0.36
38 29 0.19
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (36 bp):
AAAATATATATATATATAGTTTTGAAAACTTTTTCG
Found at i:4091272 original size:37 final size:37
Alignment explanation
Indices: 4091222--4091400 Score: 233
Period size: 37 Copynumber: 4.9 Consensus size: 37
4091212 TTAAAAAAAC
* * *
4091222 ATATATTATATAGTTTTGAGAACAATTTT-GAAAATAT
1 ATATAATATATAGTTTTGAAAAC-TTTTTCGAAAATAT
*
4091259 ATATAATAAATAGTTTTGAAAACATTTTTCGAAAATAT
1 ATATAATATATAGTTTTGAAAAC-TTTTTCGAAAATAT
* *
4091297 ATATAATATATAGTTTTAAAAACTTTTTCAAAAATAT
1 ATATAATATATAGTTTTGAAAACTTTTTCGAAAATAT
*
4091334 ATATAATATATAGTTTT-AAAACGTTTT-GAAAATAT
1 ATATAATATATAGTTTTGAAAACTTTTTCGAAAATAT
*
4091369 ATATAATATATAGTTTT-AAAACGTTTT-GAAAA
1 ATATAATATATAGTTTTGAAAACTTTTTCGAAAA
4091401 CGTATAATAT
Statistics
Matches: 132, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
35 39 0.30
36 9 0.07
37 55 0.42
38 29 0.22
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (37 bp):
ATATAATATATAGTTTTGAAAACTTTTTCGAAAATAT
Found at i:4091477 original size:4 final size:4
Alignment explanation
Indices: 4091464--4091503 Score: 64
Period size: 4 Copynumber: 10.0 Consensus size: 4
4091454 ATTATATAGT
4091464 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
4091504 GTTCATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 27 0.79
5 4 0.12
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:4091512 original size:17 final size:17
Alignment explanation
Indices: 4091463--4091519 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
4091453 TATTATATAG
*
4091463 TTTTA-TTATTTATTTA
1 TTTTATTTATTCATTTA
*
4091479 -TTTATTTATTTATTTA
1 TTTTATTTATTCATTTA
4091495 TTTTATTTAGTTCA-TTA
1 TTTTATTTA-TTCATTTA
4091512 TTATTATT
1 TT-TTATT
4091520 ATTATTATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 4 0.11
16 11 0.31
17 13 0.36
18 8 0.22
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTATTTATTCATTTA
Found at i:4093911 original size:18 final size:18
Alignment explanation
Indices: 4093888--4093941 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
4093878 TGGACCTAGA
4093888 TATTAATTGGACTTTATT
1 TATTAATTGGACTTTATT
* *
4093906 TATTAATTGTTATTATTATT
1 TATTAATTG-GACT-TTATT
*
4093926 T-TTATTTGGACTTTAT
1 TATTAATTGGACTTTAT
4093942 AATATTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
19 8 0.28
20 6 0.21
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (18 bp):
TATTAATTGGACTTTATT
Found at i:4093958 original size:13 final size:13
Alignment explanation
Indices: 4093940--4093969 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4093930 TTTGGACTTT
*
4093940 ATAATATTTAATA
1 ATAATAATTAATA
4093953 ATAATAATTAATA
1 ATAATAATTAATA
4093966 ATAA
1 ATAA
4093970 ATTGGTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATAATTAATA
Found at i:4095929 original size:5 final size:5
Alignment explanation
Indices: 4095921--4096045 Score: 67
Period size: 5 Copynumber: 24.4 Consensus size: 5
4095911 AGAAAAAAGT
* * * *
4095921 AATAA AAT-A AATAG AATAAA AATAAA AATAA AACAA AACAA AACAA AATAAA
1 AATAA AATAA AATAA AAT-AA AAT-AA AATAA AATAA AATAA AATAA AAT-AA
* * * *
4095973 ACAGTAA AAT-A AATAAA AATAA AACAA AATGA AATGA AATGA AA-AA
1 A-A-TAA AATAA AAT-AA AATAA AATAA AATAA AATAA AATAA AATAA
* * * *
4096019 AATTA AATTA AATTA AATAA AACAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
4096046 ATAAGAACAA
Statistics
Matches: 101, Mismatches: 11, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
4 11 0.11
5 67 0.66
6 18 0.18
7 4 0.04
8 1 0.01
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:4096296 original size:18 final size:18
Alignment explanation
Indices: 4096270--4096323 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
4096260 GAAACAATCA
*
4096270 AAAAGTAAAATAAA-AAT
1 AAAATTAAAATAAATAAT
*
4096287 AAAATATAAAAATAAATATT
1 AAAAT-T-AAAATAAATAAT
*
4096307 AACATTAAAATAAATAA
1 AAAATTAAAATAAATAA
4096324 AGTAAAGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 4 0.13
18 11 0.37
19 9 0.30
20 6 0.20
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAATTAAAATAAATAAT
Found at i:4098020 original size:28 final size:28
Alignment explanation
Indices: 4097941--4098025 Score: 80
Period size: 31 Copynumber: 2.9 Consensus size: 28
4097931 ACATCATTTC
** *
4097941 ATTTAATAATAATTAATAATATAATTGACT
1 ATTTAATAATTTTTAA-AATTTAA-TGACT
* *
4097971 ATTTTATAATATTTTGATAAATTTAATGATT
1 ATTTAATAAT-TTTT-A-AAATTTAATGACT
4098002 ATTTAATAATTTTTAAAATTTAAT
1 ATTTAATAATTTTTAAAATTTAAT
4098026 AAAAACATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
28 9 0.20
29 1 0.02
30 13 0.28
31 15 0.33
32 7 0.15
33 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (28 bp):
ATTTAATAATTTTTAAAATTTAATGACT
Found at i:4098832 original size:19 final size:19
Alignment explanation
Indices: 4098808--4098845 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4098798 ACTTTGTACC
4098808 TTAAAATAATACTAAAGAT
1 TTAAAATAATACTAAAGAT
4098827 TTAAAATAATACTAAAGAT
1 TTAAAATAATACTAAAGAT
4098846 ATATATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (19 bp):
TTAAAATAATACTAAAGAT
Found at i:4099213 original size:20 final size:20
Alignment explanation
Indices: 4099164--4099360 Score: 111
Period size: 20 Copynumber: 9.9 Consensus size: 20
4099154 TATACGATTT
4099164 TAACCA-AAATCGCAACGCG
1 TAACCATAAATCGCAACGCG
*
4099183 -AA-TATGAAAATCGCAACGCG
1 TAACCAT--AAATCGCAACGCG
*
4099203 -AACACATAAATCGCAATGCG
1 TAAC-CATAAATCGCAACGCG
* * *
4099223 TATCCGTAAATCGCAACGTG
1 TAACCATAAATCGCAACGCG
* *
4099243 TATCCGTAAATCGCAACGCG
1 TAACCATAAATCGCAACGCG
** * *
4099263 TTTCCGTATATCGCAACGCG
1 TAACCATAAATCGCAACGCG
* * *
4099283 TATCCGTAAATCGCAACG-A
1 TAACCATAAATCGCAACGCG
* *
4099302 TAATCCGTAAATCGCAACGAG
1 TAA-CCATAAATCGCAACGCG
** *
4099323 -AATCTGTAAATCGCAACG-A
1 TAA-CCATAAATCGCAACGCG
*
4099342 TAATCCGTAAATCGCAACG
1 TAA-CCATAAATCGCAACG
4099361 AGAATCTGTA
Statistics
Matches: 151, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
17 1 0.01
18 2 0.01
19 2 0.01
20 142 0.94
21 2 0.01
22 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
TAACCATAAATCGCAACGCG
Found at i:4099276 original size:60 final size:59
Alignment explanation
Indices: 4099170--4099379 Score: 210
Period size: 60 Copynumber: 3.5 Consensus size: 59
4099160 ATTTTAACCA
* ** * * *
4099170 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATC-CGTAAATCGCAA-GCGTATCCGT
* * ** *
4099230 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAA-GCGTATCCGT
*
4099290 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAAGCG-T-ATCCGT
* * *
4099350 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
4099380 ACTGAAATTT
Statistics
Matches: 126, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 121 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (59 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGCAAGCGTATCCGT
Found at i:4099361 original size:20 final size:20
Alignment explanation
Indices: 4099224--4099379 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
4099214 CGCAATGCGT
*
4099224 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
4099244 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
4099264 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
4099284 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
4099304 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
4099324 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
4099344 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
4099364 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
4099380 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:4099361 original size:40 final size:40
Alignment explanation
Indices: 4099190--4099379 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
4099180 GCGAATATGA
* *
4099190 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
4099230 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
4099270 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
4099310 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
4099350 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
4099380 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:4102048 original size:19 final size:19
Alignment explanation
Indices: 4102026--4102365 Score: 416
Period size: 19 Copynumber: 19.4 Consensus size: 19
4102016 CGGAAATTAC
*
4102026 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4102045 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
4102059 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
4102079 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
4102093 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4102112 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4102131 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
4102145 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4102164 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4102183 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
4102197 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4102216 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
4102235 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
4102249 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4102268 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4102287 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4102306 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
4102320 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4102339 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
4102358 AATCGCAA
1 AATCGCAA
4102366 CGAGAGAATC
Statistics
Matches: 282, Mismatches: 8, Indels: 62
0.80 0.02 0.18
Matches are distributed among these distances:
14 57 0.20
15 2 0.01
16 21 0.07
17 20 0.07
18 3 0.01
19 166 0.59
20 13 0.05
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:4102141 original size:52 final size:52
Alignment explanation
Indices: 4102054--4102346 Score: 461
Period size: 52 Copynumber: 5.6 Consensus size: 52
4102044 AAATCCCAAC
*
4102054 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
4102107 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
4102159 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
4102211 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
4102263 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
4102318 A-G--AATCGCAATGCGAAATGAAAATCGCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA
4102347 TGCGAAATGA
Statistics
Matches: 231, Mismatches: 4, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 197 0.85
53 16 0.07
54 3 0.01
55 5 0.02
56 1 0.00
57 9 0.04
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:4102347 original size:52 final size:52
Alignment explanation
Indices: 4102058--4102387 Score: 391
Period size: 52 Copynumber: 6.3 Consensus size: 52
4102048 CCCAACATGA
4102058 AAATCGCAATGCGGAAATGAAAATCGCAACG--AGAAAATCGCAATGCGAAATG
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAATG
*
4102110 AAAATCGCAATGCGAAATGAAAATCGCAACG--AGAGAATCGCAATGCGAAATG
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAATG
*
4102162 AAAATCGCAATGCGAAATGAAAATCGCAACGACAG--AATCGCAATGCGAAATG
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAATG
*
4102214 AAAATCGCAATGCGAAATGAAAATCGCAACGACAG--AATCGCAATGCGAAATG
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAA-GCGAAATG
4102266 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G
1 -AAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-GAAAATCGCAAGCGAAATG
*
4102320 -AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGA-G
1 AAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-GAAAATCGCAAGCGAAATG
4102372 -AATCGCAATGCGAAAT
1 AAATCGCAATGCGAAAT
4102388 TATAAACGCA
Statistics
Matches: 267, Mismatches: 3, Indels: 15
0.94 0.01 0.05
Matches are distributed among these distances:
52 234 0.88
53 12 0.04
54 7 0.03
55 6 0.02
57 8 0.03
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAAAGAAAATCGCAAGCGAAATG
Found at i:4102403 original size:71 final size:70
Alignment explanation
Indices: 4102026--4102387 Score: 342
Period size: 71 Copynumber: 5.2 Consensus size: 70
4102016 CGGAAATTAC
* *
4102026 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
4102086 ACGAGAA
65 ACGAG-A
* * *
4102093 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CG
* *
4102157 AAATGA-A
63 CAACGAGA
*
4102164 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
* *
4102224 TGCGA
66 CGAGA
* * *
4102229 AAT-GAAAAT-CGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
1 AATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
* *
4102292 CAATGCGA
63 CAACGAGA
* * *
4102300 AAT-GAAAAT-CGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
1 AATCG-CAATGCGAAATG-AA-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
4102363 CAACGAGA
63 CAACGAGA
4102371 GAATCGCAATGCGAAAT
1 -AATCGCAATGCGAAAT
4102388 TATAAACGCA
Statistics
Matches: 251, Mismatches: 22, Indels: 38
0.81 0.07 0.12
Matches are distributed among these distances:
64 14 0.06
65 14 0.06
66 19 0.08
67 25 0.10
68 5 0.02
69 6 0.02
71 129 0.51
72 27 0.11
73 12 0.05
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (70 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
CGAGA
Found at i:4102503 original size:19 final size:19
Alignment explanation
Indices: 4102394--4102495 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
4102384 AAATTATAAA
4102394 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4102413 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
4102433 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
4102449 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4102466 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
4102485 CGCATTGCGAT
1 CGCATTGCGAT
4102496 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:4102621 original size:14 final size:14
Alignment explanation
Indices: 4102602--4102638 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4102592 CATCAATTAC
4102602 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4102616 ACAAATCATCTTTT
1 ACAAATCAACTTTT
4102630 ACAAATCAA
1 ACAAATCAA
4102639 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:4104486 original size:14 final size:14
Alignment explanation
Indices: 4104467--4104556 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
4104457 TTGAAATGAA
4104467 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4104481 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
4104500 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4104514 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4104533 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4104547 AATCGCAACG
1 AATCGCAACG
4104557 CGAAATAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4104498 original size:33 final size:33
Alignment explanation
Indices: 4104459--4104573 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
4104449 GTCTTTGGTT
4104459 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
4104492 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4104525 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
4104558 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
4104574 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:4104505 original size:19 final size:19
Alignment explanation
Indices: 4104481--4104578 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
4104471 GCAACGAGAG
*
4104481 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
4104500 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
4104514 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
4104533 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
4104547 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
4104566 AATCGCAATGCGA
1 AATCGCAACGCGA
4104579 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:4104609 original size:14 final size:14
Alignment explanation
Indices: 4104590--4104646 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4104580 TTTGGTTTCG
4104590 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4104604 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4104623 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4104637 CGTTGCGATT
1 CGTTGCGATT
4104647 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4104628 original size:19 final size:19
Alignment explanation
Indices: 4104604--4104692 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
4104594 GCGATTCTCT
4104604 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
4104623 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
4104637 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
4104656 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
4104676 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
4104693 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:4104684 original size:39 final size:33
Alignment explanation
Indices: 4104574--4104692 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
4104564 AAAATCGCAA
**
4104574 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
4104607 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
4104640 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
4104679 TGCGATTTTCATTT
1 TGCGATTTTCATTT
4104693 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 50 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.30
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:4104823 original size:33 final size:33
Alignment explanation
Indices: 4104781--4104851 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
4104771 AATACTAACT
4104781 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
4104814 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
4104847 TGAAA
1 TGAAA
4104852 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:4105085 original size:22 final size:22
Alignment explanation
Indices: 4105033--4105087 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
4105023 TGGTTGTGAG
**
4105033 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
4105055 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
4105077 GGATTTCTTCG
1 GGATTTCTTCG
4105088 CCGTAGAGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:4105254 original size:20 final size:20
Alignment explanation
Indices: 4105229--4105422 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
4105219 CTTTAAATAT
4105229 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4105249 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
4105271 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
4105290 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
4105310 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
4105330 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4105350 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
4105370 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
4105390 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
4105410 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4105423 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:4105394 original size:60 final size:60
Alignment explanation
Indices: 4105231--4105402 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
4105221 TTAAATATCG
* ** *
4105231 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACCGATACA
* *** * *
4105292 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
*
4105352 CGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTT
4105403 TCATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACCGATACA
Found at i:4105416 original size:60 final size:60
Alignment explanation
Indices: 4105228--4105543 Score: 232
Period size: 60 Copynumber: 5.2 Consensus size: 60
4105218 GCTTTAAATA
* ** * *
4105228 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTTCAGAT
* * *** * * *
4105289 ACGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * *
4105349 ACACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
* * * * * *
4105409 TCGCGTTGCGATTT-TGGAAAATCGCAATGCGAATT-TG-ACTATCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTACGG-ATA-CGCATTGCGATTTATGTA-T-TCGCGTTGCGATTTTC-AGAT
* * ** * * *
4105471 TCGCGTTGCGATTT-TGGAAACTG-ATTTGCGATTCTGGGGA-TCGCGTTGCGATTTTTA-TT
1 TCGCGTTGCGATTTACGGATAC-GCA-TTGCGATT-TATGTATTCGCGTTGCGATTTTCAGAT
4105530 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
4105544 TGTTGGTCAT
Statistics
Matches: 208, Mismatches: 37, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
59 16 0.08
60 92 0.44
61 78 0.38
62 20 0.10
63 1 0.00
64 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTTCAGAT
Found at i:4105439 original size:21 final size:20
Alignment explanation
Indices: 4105389--4105486 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
4105379 ATTTATGTGT
* * * *
4105389 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
4105409 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
4105430 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
4105450 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
4105471 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
4105487 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:4105462 original size:61 final size:60
Alignment explanation
Indices: 4105389--4105545 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
4105379 ATTTATGTGT
*
4105389 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
4105450 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
4105511 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
4105546 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:4105481 original size:41 final size:41
Alignment explanation
Indices: 4105389--4105545 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
4105379 ATTTATGTGT
* * *
4105389 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
4105430 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
4105471 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
4105511 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
4105546 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:4107062 original size:24 final size:24
Alignment explanation
Indices: 4107026--4107083 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
4107016 CGACCTACCC
* * *
4107026 CTCGGATGGCCTCGGTTGGATGCGT
1 CTCGGATGCCCTCGATCGGATG-GT
4107051 -TCGGATGCCCTCGATCGGATGGT
1 CTCGGATGCCCTCGATCGGATGGT
4107074 CTCGGATGCC
1 CTCGGATGCC
4107084 TAACGTGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.10, C:0.28, G:0.36, T:0.26
Consensus pattern (24 bp):
CTCGGATGCCCTCGATCGGATGGT
Found at i:4111543 original size:157 final size:157
Alignment explanation
Indices: 4111257--4111570 Score: 619
Period size: 157 Copynumber: 2.0 Consensus size: 157
4111247 TGAGGGTCCT
4111257 GCAAATGTTAACTCACAGTGGTTCTTCAAACAATGATCATCTAATGTGACAAAAGACGATAATCC
1 GCAAATGTTAACTCACAGTGGTTCTTCAAACAATGATCATCTAATGTGACAAAAGACGATAATCC
4111322 GGTCTCGAACCTGAATACAAGTGAACAGTAATCCTTCCATCTGAATTAGCAAGATTGATGAGACG
66 GGTCTCGAACCTGAATACAAGTGAACAGTAATCCTTCCATCTGAATTAGCAAGATTGATGAGACG
4111387 GAGTGTGCTTTGATCCTTCCGGCGGAA
131 GAGTGTGCTTTGATCCTTCCGGCGGAA
4111414 GCAAATGTTAACTCACAGTGGTTCTTCAAACAATGATCATCTAATGTGACAAAAGACGATAATCC
1 GCAAATGTTAACTCACAGTGGTTCTTCAAACAATGATCATCTAATGTGACAAAAGACGATAATCC
*
4111479 GGTCTCGAACCTGAATACAAGTGGACAGTAATCCTTCCATCTGAATTAGCAAGATTGATGAGACG
66 GGTCTCGAACCTGAATACAAGTGAACAGTAATCCTTCCATCTGAATTAGCAAGATTGATGAGACG
4111544 GAGTGTGCTTTGATCCTTCCGGCGGAA
131 GAGTGTGCTTTGATCCTTCCGGCGGAA
4111571 TCTTTGTCCA
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (157 bp):
GCAAATGTTAACTCACAGTGGTTCTTCAAACAATGATCATCTAATGTGACAAAAGACGATAATCC
GGTCTCGAACCTGAATACAAGTGAACAGTAATCCTTCCATCTGAATTAGCAAGATTGATGAGACG
GAGTGTGCTTTGATCCTTCCGGCGGAA
Found at i:4113546 original size:34 final size:35
Alignment explanation
Indices: 4113497--4113563 Score: 95
Period size: 34 Copynumber: 1.9 Consensus size: 35
4113487 TTTGGTCCTT
4113497 TATGTTTATGGTTATTTT-ATTT-TAGT-CCTAAA
1 TATGTTTATGGTTATTTTCATTTATAGTACCTAAA
4113529 TATGATTTATGGGTTATTTTCATTTATAGTACCTA
1 TATG-TTTAT-GGTTATTTTCATTTATAGTACCTA
4113564 TACTGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 4 0.13
33 5 0.17
34 9 0.30
35 4 0.13
36 4 0.13
37 4 0.13
ACGTcount: A:0.25, C:0.07, G:0.13, T:0.54
Consensus pattern (35 bp):
TATGTTTATGGTTATTTTCATTTATAGTACCTAAA
Found at i:4113654 original size:30 final size:30
Alignment explanation
Indices: 4113618--4113813 Score: 198
Period size: 30 Copynumber: 6.6 Consensus size: 30
4113608 TATGATTCAA
* * *
4113618 TCCTTTAAATTTTTATTTATCCTATTTTAG
1 TCCTTTAAGTTTCTATTTATGCTATTTTAG
* * * *
4113648 TCCTTTAAATTTCTATTTGTTCAATTTTAG
1 TCCTTTAAGTTTCTATTTATGCTATTTTAG
*
4113678 TCCTTTAAGTTTCTATTT-T-TTATTTTAG
1 TCCTTTAAGTTTCTATTTATGCTATTTTAG
* * * *
4113706 TCTTTTAAGTTTCTGTTTGTGCTATTCTAG
1 TCCTTTAAGTTTCTATTTATGCTATTTTAG
* * *
4113736 TCCTTTAAGTTTATTTTTTTGCTATTTTAG
1 TCCTTTAAGTTTCTATTTATGCTATTTTAG
* * **
4113766 TCCTTTAAGTTTCTGTTTATGTTATTTTTT
1 TCCTTTAAGTTTCTATTTATGCTATTTTAG
*
4113796 TCCTTTAATTTTCTATTT
1 TCCTTTAAGTTTCTATTT
4113814 TAGTCCTTTA
Statistics
Matches: 140, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
28 23 0.16
29 2 0.01
30 115 0.82
ACGTcount: A:0.18, C:0.12, G:0.08, T:0.62
Consensus pattern (30 bp):
TCCTTTAAGTTTCTATTTATGCTATTTTAG
Found at i:4113851 original size:25 final size:25
Alignment explanation
Indices: 4113804--4113853 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
4113794 TTTCCTTTAA
*
4113804 TTTTCTATTTTAGTCCTTTAAGTTT
1 TTTTCTATTTTAGTCCTTCAAGTTT
*
4113829 TTTTGCTATTTTGGTCC-TCAAGTTT
1 TTTT-CTATTTTAGTCCTTCAAGTTT
4113854 CTATTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (25 bp):
TTTTCTATTTTAGTCCTTCAAGTTT
Found at i:4115872 original size:202 final size:202
Alignment explanation
Indices: 4115472--4115884 Score: 763
Period size: 202 Copynumber: 2.0 Consensus size: 202
4115462 GCGGTTATGA
4115472 TTATTTTTTGTAAAACAATCATTTTGGGTAGAAAATATGTTCGAGTAGGAATGTTATTTAATTAA
1 TTATTTTTTGTAAAACAATCATTTTGGGTAGAAAATATGTTCGAGTAGGAATGTTATTTAATTAA
4115537 ATCATGTTCGGGTATATATCATGACAGGGTAGGTGTTATATTCATCTTTGAATAACATTTTATCT
66 ATCATGTTCGGGTATATATCATGACAGGGTAGGTGTTATATTCATCTTTGAATAACATTTTATCT
*
4115602 GTATCGATTGTCTCACCTGTACTAACTATTTCTTTTCTTTTGTTTGTGTACACAATATTTCTTTT
131 GTATCGATTGTCTCACCTGTACTAACTATTTCTTTTCTTTTGTTTGTGTACACAATATTTCATTT
4115667 CTTTTGT
196 CTTTTGT
4115674 TTATTTTTTGTAAAACAATCATTTTGGGTAGAAAATATGTTCGAGTAGGAATGTTATTTAATTAA
1 TTATTTTTTGTAAAACAATCATTTTGGGTAGAAAATATGTTCGAGTAGGAATGTTATTTAATTAA
4115739 ATCATGTTCGGGTATATATCATGACAGGGTAGGTGTTATATTCATCTTTGAATAACATTTTTATC
66 ATCATGTTCGGGTATATATCATGACAGGGTAGGTGTTATATTCATCTTTGAATAACA-TTTTATC
4115804 TGTATCGATTGTCTCACCTGTACTAACTAATTTCTTTTCTTTTGTTTGTGTACACTAATTTATTT
130 TGTATCGATTGTCTCACCTGTACTAACT-ATTTCTTTTCTTTTGTTTGTGTACAC-AA--TATTT
*
4115869 CTTTTCTTTTGT
191 CATTTCTTTTGT
4115881 TTAT
1 TTAT
4115885 ATCGTTTATC
Statistics
Matches: 206, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
202 122 0.59
203 35 0.17
204 26 0.13
205 2 0.01
207 21 0.10
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (202 bp):
TTATTTTTTGTAAAACAATCATTTTGGGTAGAAAATATGTTCGAGTAGGAATGTTATTTAATTAA
ATCATGTTCGGGTATATATCATGACAGGGTAGGTGTTATATTCATCTTTGAATAACATTTTATCT
GTATCGATTGTCTCACCTGTACTAACTATTTCTTTTCTTTTGTTTGTGTACACAATATTTCATTT
CTTTTGT
Found at i:4117679 original size:26 final size:24
Alignment explanation
Indices: 4117646--4117770 Score: 105
Period size: 20 Copynumber: 5.6 Consensus size: 24
4117636 AGATCCAATC
4117646 AAAACAAAGAGAAAAGAAGCAAAGAA
1 AAAACAAAGAGAAAAGAA--AAAGAA
* *
4117672 AAAACAAAGAGCAAAG-AGAA-AA
1 AAAACAAAGAGAAAAGAAAAAGAA
*
4117694 AAAGC-AA-AGAAAAGAAAAA-ACA
1 AAAACAAAGAGAAAAGAAAAAGA-A
4117716 AAAACAAAGA-AAAAGAAAAAG--
1 AAAACAAAGAGAAAAGAAAAAGAA
4117737 -AAACAAA-AGAAAAG-AAAAG-A
1 AAAACAAAGAGAAAAGAAAAAGAA
4117757 AAAACAAAGA-AAAA
1 AAAACAAAGAGAAAA
4117771 TGGATAAGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 23
0.74 0.05 0.20
Matches are distributed among these distances:
19 6 0.07
20 18 0.21
21 17 0.20
22 12 0.14
23 14 0.17
24 1 0.01
25 1 0.01
26 15 0.18
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAACAAAGAGAAAAGAAAAAGAA
Found at i:4117686 original size:18 final size:18
Alignment explanation
Indices: 4117658--4117729 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 18
4117648 AACAAAGAGA
4117658 AAAGAAGCAAAGAAAAAAC
1 AAAG-AGCAAAGAAAAAAC
4117677 AAAGAGCAAAGAGAAAAAAAGC
1 AAAGAGC-AA-AG-AAAAAA-C
4117699 AAAGA--AAAGAAAAAAC
1 AAAGAGCAAAGAAAAAAC
*
4117715 AAA-AACAAAGAAAAA
1 AAAGAGCAAAGAAAAA
4117730 GAAAAAGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 15 0.32
18 5 0.11
19 8 0.17
20 2 0.04
21 6 0.13
22 6 0.13
ACGTcount: A:0.76, C:0.08, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAGAGCAAAGAAAAAAC
Found at i:4117693 original size:19 final size:19
Alignment explanation
Indices: 4117658--4117749 Score: 84
Period size: 18 Copynumber: 4.8 Consensus size: 19
4117648 AACAAAGAGA
4117658 AAAGAAGCAAAGAAAAAAC
1 AAAGAAGCAAAGAAAAAAC
*
4117677 AAAG-AGCAAAGAGAAAA-
1 AAAGAAGCAAAGAAAAAAC
*
4117694 AAAGCAAAGAAAAGAAAAAAC
1 AAAG--AAGCAAAGAAAAAAC
*
4117715 AAA-AA-CAAAGAAAAAGAA
1 AAAGAAGCAAAGAAAAA-AC
*
4117733 AAAGAAACAAAAGAAAA
1 AAAGAAGC-AAAGAAAA
4117750 GAAAAGAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
17 13 0.22
18 18 0.30
19 6 0.10
20 12 0.20
21 11 0.18
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAGAAGCAAAGAAAAAAC
Found at i:4117707 original size:5 final size:5
Alignment explanation
Indices: 4117684--4117769 Score: 61
Period size: 5 Copynumber: 16.6 Consensus size: 5
4117674 AACAAAGAGC
* * *
4117684 AAAGA GAAA-A AAAGC AAAGA AAAGA AAAAA CAAAAA CAAAGAA AAAGA
1 AAAGA -AAAGA AAAGA AAAGA AAAGA AAAGA -AAAGA -AAAG-A AAAGA
*
4117732 AAA-A GAAACA AAAGA AAAGA AAAGA AAA-A CAAAGA AAA
1 AAAGA -AAAGA AAAGA AAAGA AAAGA AAAGA -AAAGA AAA
4117770 ATGGATAAGA
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
4 5 0.07
5 44 0.65
6 18 0.26
7 1 0.01
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:4117707 original size:20 final size:20
Alignment explanation
Indices: 4117670--4117769 Score: 105
Period size: 22 Copynumber: 4.8 Consensus size: 20
4117660 AGAAGCAAAG
4117670 AAAAAACAAAGAGCAAAGAGAA
1 AAAAAACAAAGA--AAAGAGAA
* *
4117692 AAAAAGCAAAGAAAAGAAAAA
1 AAAAAACAAAGAAAAG-AGAA
4117713 ACAAAAACAAAGAAAA-AGAA
1 A-AAAAACAAAGAAAAGAGAA
4117733 AAAGAAACAAAAGAAAAGA-AA
1 AAA-AAAC-AAAGAAAAGAGAA
4117754 AGAAAAACAAAGAAAA
1 A-AAAAACAAAGAAAA
4117770 ATGGATAAGA
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.03
20 20 0.29
21 19 0.28
22 27 0.40
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (20 bp):
AAAAAACAAAGAAAAGAGAA
Found at i:4117709 original size:38 final size:38
Alignment explanation
Indices: 4117651--4117770 Score: 120
Period size: 38 Copynumber: 3.1 Consensus size: 38
4117641 CAATCAAAAC
* *
4117651 AAAGAGAAAAGAAGC-AAAGAAAAAACAAAGAGCAAAG-A
1 AAAGA-AAAAGAAACAAAAGAAAAAACAAA-AACAAAGAA
* *
4117689 GAA-AAAAAGCAAAGAAAAGAAAAAACAAAAACAAAGAA
1 AAAGAAAAAG-AAACAAAAGAAAAAACAAAAACAAAGAA
*
4117727 AAAGAAAAAGAAACAAAAGAAAAGAAAAGAAAAACAAAGAA
1 AAAGAAAAAGAAACAAAAG--AA-AAAACAAAAACAAAGAA
4117768 AAA
1 AAA
4117771 TGGATAAGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
36 5 0.07
37 9 0.13
38 27 0.40
39 6 0.09
40 2 0.03
41 19 0.28
ACGTcount: A:0.78, C:0.07, G:0.16, T:0.00
Consensus pattern (38 bp):
AAAGAAAAAGAAACAAAAGAAAAAACAAAAACAAAGAA
Found at i:4117769 original size:15 final size:16
Alignment explanation
Indices: 4117646--4117766 Score: 74
Period size: 16 Copynumber: 7.6 Consensus size: 16
4117636 AGATCCAATC
4117646 AAAACAAAGAGAAA-A
1 AAAACAAAGAGAAAGA
* * *
4117661 GAAGCAAAGA-AAAAA
1 AAAACAAAGAGAAAGA
4117676 CAAAGAGCAAAGAGAAA-A
1 -AAA-A-CAAAGAGAAAGA
*
4117694 AAAGCAAAGA-AAAGAA
1 AAAACAAAGAGAAAG-A
* *
4117710 AAAACAAAAACAAAGA
1 AAAACAAAGAGAAAGA
* * *
4117726 AAAAGAAAAAGAAACA
1 AAAACAAAGAGAAAGA
4117742 AAAGA-AAAGA-AAAGA
1 AAA-ACAAAGAGAAAGA
4117757 AAAACAAAGA
1 AAAACAAAGA
4117767 AAAATGGATA
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
14 7 0.08
15 27 0.32
16 32 0.38
17 8 0.10
18 7 0.08
19 3 0.04
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAACAAAGAGAAAGA
Found at i:4117770 original size:10 final size:10
Alignment explanation
Indices: 4117665--4117770 Score: 65
Period size: 10 Copynumber: 10.0 Consensus size: 10
4117655 AGAAAAGAAG
4117665 CAAAGAAAAAA
1 CAAAG-AAAAA
4117676 CAAAGAGCAAAGA
1 CAAAGA--AAA-A
* *
4117689 GAAA-AAAAG
1 CAAAGAAAAA
4117698 CAAAGAAAAGAA
1 CAAAG-AAA-AA
* *
4117710 AAAACAAAAA
1 CAAAGAAAAA
4117720 CAAAGAAAAA
1 CAAAGAAAAA
*
4117730 GAAA-AAGAAA
1 CAAAGAA-AAA
4117740 CAAAAGAAAAGA
1 C-AAAGAAAA-A
4117752 -AAAGAAAAA
1 CAAAGAAAAA
4117761 CAAAGAAAAA
1 CAAAGAAAAA
4117771 TGGATAAGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
9 6 0.08
10 37 0.50
11 16 0.22
12 11 0.15
13 4 0.05
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (10 bp):
CAAAGAAAAA
Found at i:4118836 original size:32 final size:33
Alignment explanation
Indices: 4118800--4118865 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
4118790 TAATGAATAA
*
4118800 TGGGGCATCTTTGGAGATTCAACA-TCGAATGT
1 TGGGGCATATTTGGAGATTCAACATTCGAATGT
* *
4118832 TGGGGCATATTTGGGGATTCAACATTCTAATGT
1 TGGGGCATATTTGGAGATTCAACATTCGAATGT
4118865 T
1 T
4118866 AATGATCAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 22 0.73
33 8 0.27
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (33 bp):
TGGGGCATATTTGGAGATTCAACATTCGAATGT
Found at i:4119082 original size:35 final size:35
Alignment explanation
Indices: 4119029--4119191 Score: 111
Period size: 29 Copynumber: 5.0 Consensus size: 35
4119019 CTTTGAATCT
4119029 GTTTCTTTGGAAACAAAATTTTATCTCTTGAGACA
1 GTTTCTTTGGAAACAAAATTTTATCTCTTGAGACA
* * *
4119064 GTTTCTTTTG-AAGAAAA----ATCT-TTGAGTA-T
1 GTTTCTTTGGAAACAAAATTTTATCTCTTGAG-ACA
* *
4119093 GTTTCTTTGGAAACAAAATTTTGTCTCTTGAGACG
1 GTTTCTTTGGAAACAAAATTTTATCTCTTGAGACA
* * * * *
4119128 GTATCTTT-TAAAGAAAA----ATAT-TTGAGTA-T
1 GTTTCTTTGGAAACAAAATTTTATCTCTTGAG-ACA
*
4119157 GTTTCTTTGGAAACAAAGTTTTATCTCTTGAGACA
1 GTTTCTTTGGAAACAAAATTTTATCTCTTGAGACA
4119192 ATATCTTTTG
Statistics
Matches: 93, Mismatches: 19, Indels: 32
0.65 0.13 0.22
Matches are distributed among these distances:
29 26 0.28
30 20 0.22
34 21 0.23
35 26 0.28
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (35 bp):
GTTTCTTTGGAAACAAAATTTTATCTCTTGAGACA
Found at i:4119235 original size:64 final size:64
Alignment explanation
Indices: 4119017--4119225 Score: 319
Period size: 64 Copynumber: 3.3 Consensus size: 64
4119007 GACATAACCC
* * *
4119017 ATCTTTGAATCTGTTTCTTTGGAAACAAAATTTTATCTCTTGAGACAGTTTCTTTTGAAGAAAA
1 ATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTATCTCTTGAGACAGTATCTTTTGAAGAAAA
* * *
4119081 ATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTGAGACGGTATCTTTTAAAGAAAA
1 ATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTATCTCTTGAGACAGTATCTTTTGAAGAAAA
* * * *
4119145 ATATTTGAGTATGTTTCTTTGGAAACAAAGTTTTATCTCTTGAGACAATATCTTTTGAAGGAAA
1 ATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTATCTCTTGAGACAGTATCTTTTGAAGAAAA
*
4119209 ATCTTTGAGTCTGTTTC
1 ATCTTTGAGTATGTTTC
4119226 CCTTGAAACA
Statistics
Matches: 130, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 130 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.42
Consensus pattern (64 bp):
ATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTATCTCTTGAGACAGTATCTTTTGAAGAAAA
Found at i:4119244 original size:30 final size:30
Alignment explanation
Indices: 4119208--4119265 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
4119198 TTTGAAGGAA
4119208 AATCTTTGAG-TCTGTTTCCCTTGAAACATC
1 AATCTTTGAGAT-TGTTTCCCTTGAAACATC
4119238 AATCTTTGAGATTGTTTCCCTTGAAACA
1 AATCTTTGAGATTGTTTCCCTTGAAACA
4119266 AAGTTTTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (30 bp):
AATCTTTGAGATTGTTTCCCTTGAAACATC
Found at i:4119624 original size:130 final size:130
Alignment explanation
Indices: 4119306--4119703 Score: 379
Period size: 130 Copynumber: 3.0 Consensus size: 130
4119296 TGAAATAAAT
* * * * ** *
4119306 CCCTAAAGAAGGC-TAGCCATCCTCATCGCGTAGGAATCGTGTCATCCTTCGACCATACCTCCTC
1 CCCTAAAGATGGCAT-GTCATCCTCATCACGTAGAAATCGTGTCATCCACCGACCAGACCTCCTC
* ** * * * * * * * *
4119370 ATCAACTAGGAGCCGTGTCACCCTTAGATAACCAGTCGTCCTCATCGCGTAGAAACCATGTCATC
65 AACATGTAGGAACCATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACAATGTTATC
4119435 A
130 A
* * * * * *
4119436 CCTTTCCTAAAGATGGCATGTCGTCCTCATCACGTAGGAATCGTGTTATCCCCCGACCAGGCCTT
1 -C---CCTAAAGATGGCATGTCATCCTCATCACGTAGAAATCGTGTCATCCACCGACCAGACCTC
* ** * * * **
4119501 CTCATCATGTAGGAGTCGTGTCACCCCT-GATAACCAGCTGTCCTCATCATGTAGGAACTGTGTT
62 CTCAACATGTAGGAACCATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACAATGTT
4119565 ATCA
127 ATCA
* * *
4119569 TCCCTAAATATGGTATGTCATCCTCATCACGTATGAAAT-GTGTCATCCACTGACCAGACCTCCT
1 -CCCTAAAGATGGCATGTCATCCTCATCACGTA-GAAATCGTGTCATCCACCGACCAGACCTCCT
* *
4119633 CAACATGTGGGAACCATGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACAATGTTAT
64 CAACATGTAGGAACCATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACAATGTTAT
4119698 CA
129 CA
4119700 CCCT
1 CCCT
4119704 TCCTAAAGAT
Statistics
Matches: 219, Mismatches: 42, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
130 73 0.33
131 40 0.18
133 33 0.15
134 72 0.33
135 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (130 bp):
CCCTAAAGATGGCATGTCATCCTCATCACGTAGAAATCGTGTCATCCACCGACCAGACCTCCTCA
ACATGTAGGAACCATGTCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACAATGTTATCA
Found at i:4119780 original size:134 final size:132
Alignment explanation
Indices: 4119323--4119792 Score: 439
Period size: 134 Copynumber: 3.5 Consensus size: 132
4119313 GAAGGCTAGC
* * * * * * *
4119323 CATCCTCATCGCGTAGGAATCGTGTCATCC-TTCGACCATACCTCCTCATCAACTAGGAGCCGTG
1 CATCCTCATCACGTATGAAACGTGTCATCCACT-GACCAGACCTCCTCATC-AGTAGGAACCGTG
* * * * *
4119387 TCACCCTTAGATAACCAGTCGTCCTCATCGCGTAGAAACCATGTCATCACCTTTCCTAAAGATGG
64 TCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACAATGTTATCACC-TTCCTAAAGATGG
4119452 CATGT
128 CATGT
* * * * * * * * **
4119457 CGTCCTCATCACGTAGGAATCGTGTTATCCCCCGACCAGGCCTTCTCATCATGTAGGAGTCGTGT
1 CATCCTCATCACGTATGAAACGTGTCATCCACTGACCAGACCTCCTCATCA-GTAGGAACCGTGT
* ** ** * * *
4119522 CACCCCT-GATAACCAGCTGTCCTCATCATGTAGGAACTGTGTTATCA--TCCCTAAATATGGTA
65 CACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACAATGTTATCACCTTCCTAAAGATGGCA
4119584 TGT
130 TGT
* * * *
4119587 CATCCTCATCACGTATGAAATGTGTCATCCACTGACCAGACCTCCTCAACATGTGGGAACCATGT
1 CATCCTCATCACGTATGAAACGTGTCATCCACTGACCAGACCTCCTCATCA-GTAGGAACCGTGT
*
4119652 CACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACAATGTTATCACCCTTCCTAAAGATGAC
65 CACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACAATGTTATCA-CCTTCCTAAAGATG-G
**
4119717 CATAA
128 CATGT
* ** *
4119722 C-TCTTCATCACGTATGAGCCGTGTCATCCACTGACCAGATCTCCTCATTGCA-TAGGAACCGTG
1 CATCCTCATCACGTATGAAACGTGTCATCCACTGACCAGACCTCCTCA-T-CAGTAGGAACCGTG
*
4119785 TCATCCCT
64 TCACCCCT
4119793 TTAGATGACC
Statistics
Matches: 271, Mismatches: 56, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
130 73 0.27
131 35 0.13
133 33 0.12
134 125 0.46
135 3 0.01
136 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (132 bp):
CATCCTCATCACGTATGAAACGTGTCATCCACTGACCAGACCTCCTCATCAGTAGGAACCGTGTC
ACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACAATGTTATCACCTTCCTAAAGATGGCAT
GT
Found at i:4119996 original size:3 final size:3
Alignment explanation
Indices: 4119988--4120075 Score: 117
Period size: 3 Copynumber: 29.0 Consensus size: 3
4119978 ACAAAAAATT
* *
4119988 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA CTTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
4120034 TTA TTA TTA TTA TTA TTA CTT- TTA TTA TTAA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA TTA TTA TTA
4120076 ATAACAAAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
2 4 0.05
3 65 0.86
4 7 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4121635 original size:30 final size:30
Alignment explanation
Indices: 4121599--4121795 Score: 218
Period size: 30 Copynumber: 6.6 Consensus size: 30
4121589 TATGATTCAA
* *
4121599 TCCTTTAAATTTATGTTTGTGCTATTTTAG
1 TCCTTTAAGTTTTTGTTTGTGCTATTTTAG
* * *
4121629 TCCTTTAAATTTTTATTTGTGATATTTTAG
1 TCCTTTAAGTTTTTGTTTGTGCTATTTTAG
* *
4121659 TCCTTTAAGTTTTTGTTTATGCTATTTTAT
1 TCCTTTAAGTTTTTGTTTGTGCTATTTTAG
* * *
4121689 TCCTTTAAGTTTTTATTTTTTCTATTTTAG
1 TCCTTTAAGTTTTTGTTTGTGCTATTTTAG
* *
4121719 TCCTTTAAGTTTTGGTTTGTGTTATTTTAG
1 TCCTTTAAGTTTTTGTTTGTGCTATTTTAG
* * *
4121749 TCCTTTAAGTTTCTAT-TTTTTACTATTTTGG
1 TCCTTTAAGTTT-T-TGTTTGTGCTATTTTAG
*
4121780 TCC-TCAAGTTTTTGTT
1 TCCTTTAAGTTTTTGTT
4121796 AATTATTTTT
Statistics
Matches: 141, Mismatches: 23, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
28 1 0.01
29 3 0.02
30 122 0.87
31 15 0.11
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.61
Consensus pattern (30 bp):
TCCTTTAAGTTTTTGTTTGTGCTATTTTAG
Found at i:4121676 original size:60 final size:60
Alignment explanation
Indices: 4121599--4121795 Score: 261
Period size: 60 Copynumber: 3.3 Consensus size: 60
4121589 TATGATTCAA
* * * * *
4121599 TCCTTTAAATTTATGTTTGTGCTATTTTAGTCCTTTAAATTTTTATTTGTGATATTTTAG
1 TCCTTTAAGTTTTTGTTTGTGCTATTTTAGTCCTTTAAGTTTTTATTTTTTATATTTTAG
* * *
4121659 TCCTTTAAGTTTTTGTTTATGCTATTTTATTCCTTTAAGTTTTTATTTTTTCTATTTTAG
1 TCCTTTAAGTTTTTGTTTGTGCTATTTTAGTCCTTTAAGTTTTTATTTTTTATATTTTAG
* * * *
4121719 TCCTTTAAGTTTTGGTTTGTGTTATTTTAGTCCTTTAAGTTTCTATTTTTTACTATTTTGG
1 TCCTTTAAGTTTTTGTTTGTGCTATTTTAGTCCTTTAAGTTTTTATTTTTTA-TATTTTAG
*
4121780 TCC-TCAAGTTTTTGTT
1 TCCTTTAAGTTTTTGTT
4121796 AATTATTTTT
Statistics
Matches: 119, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
60 109 0.92
61 10 0.08
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.61
Consensus pattern (60 bp):
TCCTTTAAGTTTTTGTTTGTGCTATTTTAGTCCTTTAAGTTTTTATTTTTTATATTTTAG
Found at i:4121807 original size:60 final size:60
Alignment explanation
Indices: 4121623--4121826 Score: 218
Period size: 60 Copynumber: 3.4 Consensus size: 60
4121613 GTTTGTGCTA
* * * ** *
4121623 TTTTAGTCCTTTAAATTTTTATTTGTGA-TATTTTAGTCCTTTAAGTTTTTGTTTATGCTA
1 TTTTAGTCCTTTAAGTTTTTATTTTTTACTATTTTAGTCCTTTAAGTTTTTG-TTATTATT
* * *
4121683 TTTTATTCCTTTAAGTTTTTATTTTTT-CTATTTTAGTCCTTTAAGTTTTGGTT-TGTGTT
1 TTTTAGTCCTTTAAGTTTTTATTTTTTACTATTTTAGTCCTTTAAGTTTTTGTTAT-TATT
* * *
4121742 ATTTTAGTCCTTTAAGTTTCTATTTTTTACTATTTTGGTCC-TCAAGTTTTTGTTAATTATT
1 -TTTTAGTCCTTTAAGTTTTTATTTTTTACTATTTTAGTCCTTTAAGTTTTTGTT-ATTATT
*
4121803 TTTTAGTTCTTTAAAGTTTTTATT
1 TTTTAGTCCTTT-AAGTTTTTATT
4121827 GTTATGTTTT
Statistics
Matches: 121, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
58 1 0.01
59 3 0.02
60 92 0.76
61 24 0.20
62 1 0.01
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.62
Consensus pattern (60 bp):
TTTTAGTCCTTTAAGTTTTTATTTTTTACTATTTTAGTCCTTTAAGTTTTTGTTATTATT
Found at i:4121807 original size:90 final size:90
Alignment explanation
Indices: 4121621--4121822 Score: 228
Period size: 90 Copynumber: 2.2 Consensus size: 90
4121611 ATGTTTGTGC
* * *
4121621 TATTTTAGTCCTTTAAATTTTTATTTGTGATATTTTAGTCCTTTAAGTTTTTGTTTATGCTATTT
1 TATTTTAGTCCTTTAAGTTTTGATTTGTGATATTTTAGTCCTTTAAGTTTTTGTTTATACTATTT
* * ** *
4121686 TATTCCTTTAAGTTTTTATTTTTTC
66 TAGTCCTTCAAGTTTTTATTAATTA
* * *
4121711 TATTTTAGTCCTTTAAGTTTTGGTTTGTGTTATTTTAGTCCTTTAAGTTTCTAT-TTTTTACTAT
1 TATTTTAGTCCTTTAAGTTTTGATTTGTGATATTTTAGTCCTTTAAGTTT-T-TGTTTATACTAT
* *
4121775 TTTGGTCC-TCAAGTTTTTGTTAATTA
64 TTTAGTCCTTCAAGTTTTTATTAATTA
* *
4121801 TTTTTTAGTTCTTTAAAGTTTT
1 TATTTTAGTCCTTT-AAGTTTT
4121823 TATTGTTATG
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
90 71 0.76
91 22 0.23
92 1 0.01
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.62
Consensus pattern (90 bp):
TATTTTAGTCCTTTAAGTTTTGATTTGTGATATTTTAGTCCTTTAAGTTTTTGTTTATACTATTT
TAGTCCTTCAAGTTTTTATTAATTA
Found at i:4123710 original size:6 final size:6
Alignment explanation
Indices: 4123699--4124914 Score: 1998
Period size: 6 Copynumber: 207.0 Consensus size: 6
4123689 AAAGAAGTCT
4123699 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4123747 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4123795 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4123843 TACATA TAC--A TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
4123889 TACATA TAC--A TACATA TACATA TACATC TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4123935 TACATA TACATA T--ATA TACATA TACATA TACATA TACATA TAC--A
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4123979 TACATA -ACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4124026 TACATA T-CATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4124073 TAC-TA TACATA TACATA TACATA TACATA TACATA TAC--A TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
4124118 TACATA TACATA TACATA TACATA TACATA TACATA TAC-CA TACA-A
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
4124164 TACATA TACCTA TAC--A TACATA TACATATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TAC--ATA TACATA TACATA TACATA
4124212 TAC--A TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
4124258 TAC--A TACATA TACATA TACATA TACATA TACATA -CCATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
4124303 TACATA TACATA TACATA TACATA TACATA CA-ATA CTACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA -TACATA TACATA
4124351 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4124399 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4124447 TACATA TAC--A TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4124493 TACATA TACATACA TACAATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACAT--A TAC-ATA TACATA TACATA TACATA TACATA TACATA
4124544 TACATA TACATA TACATA TACATA TACATA T-CATA TA-ATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4124590 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4124638 TACATA TAC--A TACATA TACATA TACATA TACATATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TAC--ATA TACATA TACATA
4124686 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4124734 TACATA TACATA TAC--A TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* *
4124780 TACATA TACATA TACATA TACATA TACATA TAC--A TACATG TACATG
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* * * * *
4124826 TACATG TACATG TACATG TACATG TAC--A TACATG TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
4124872 TACATA TACATA TACATA TACATA TACATA TAACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA T-ACATA TACATA
4124915 ATGTGACACA
Statistics
Matches: 1154, Mismatches: 12, Indels: 88
0.92 0.01 0.07
Matches are distributed among these distances:
4 51 0.04
5 41 0.04
6 1031 0.89
7 13 0.01
8 16 0.01
9 2 0.00
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (6 bp):
TACATA
Found at i:4125596 original size:20 final size:20
Alignment explanation
Indices: 4125568--4125606 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4125558 CCAAATCATT
* *
4125568 TTTCCAAATCTTATTTTGTC
1 TTTCAAAATCTAATTTTGTC
4125588 TTTCAAAATCTAATTTTGT
1 TTTCAAAATCTAATTTTGT
4125607 TTTTAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTCAAAATCTAATTTTGTC
Found at i:4130890 original size:18 final size:18
Alignment explanation
Indices: 4130867--4130909 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4130857 TCTTTGAAAG
4130867 AAAAAAAATCCAAAAATT
1 AAAAAAAATCCAAAAATT
* * *
4130885 AAAAAAATTTCGAAAATT
1 AAAAAAAATCCAAAAATT
4130903 AAAAAAA
1 AAAAAAA
4130910 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAAAATCCAAAAATT
Found at i:4138075 original size:3 final size:3
Alignment explanation
Indices: 4138061--4138095 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
4138051 TTTAAAAATG
4138061 TAT TACT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4138096 TTTCTTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4138888 original size:18 final size:15
Alignment explanation
Indices: 4138836--4138885 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
4138826 GAATATATTA
* *
4138836 ATATTTTAAAATAAC
1 ATATTTTATAATAAT
4138851 ATATTTTATAATAAT
1 ATATTTTATAATAAT
4138866 ATATTTTATAATAAT
1 ATATTTTATAATAAT
4138881 -TATTT
1 ATATTT
4138886 ATTATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
14 5 0.15
15 28 0.85
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTTTATAATAAT
Found at i:4138924 original size:23 final size:23
Alignment explanation
Indices: 4138855--4138924 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
4138845 AATAACATAT
*
4138855 TTTATAATAATATATTTTATAATA
1 TTTA-AATAATATATTTTATATTA
* ** * *
4138879 ATTATTTATTATATTTTAAATTA
1 TTTAAATAATATATTTTATATTA
*
4138902 TTTAAATAATATATTATATATTA
1 TTTAAATAATATATTTTATATTA
4138925 ATTTTTATAT
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
23 31 0.91
24 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTAAATAATATATTTTATATTA
Found at i:4138931 original size:35 final size:33
Alignment explanation
Indices: 4138873--4138939 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 33
4138863 AATATATTTT
*
4138873 ATAATAATTATTTATTATATTTTAAATTATTTAA
1 ATAATAATTATATATTATATTTTAAATT-TTTAA
*
4138907 ATAATATATTATATATTA-ATTTTTATATTTTTA
1 ATAATA-ATTATATATTATA-TTTTAAATTTTTA
4138940 GTAATTATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
ATAATAATTATATATTATATTTTAAATTTTTAA
Found at i:4142351 original size:17 final size:17
Alignment explanation
Indices: 4142329--4142370 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
4142319 TTATTAAGTT
*
4142329 GAATTTGGTCTAACCTA
1 GAATTTGGCCTAACCTA
4142346 GAATTTGGCCTAACCTA
1 GAATTTGGCCTAACCTA
*
4142363 GGATTTGG
1 GAATTTGG
4142371 AGGAAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (17 bp):
GAATTTGGCCTAACCTA
Found at i:4143075 original size:19 final size:20
Alignment explanation
Indices: 4143048--4143085 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4143038 TTCGAACGTA
*
4143048 AATCTATGCAAGT-ATACAC
1 AATCGATGCAAGTAATACAC
4143067 AATCGATGCAAGTAATACA
1 AATCGATGCAAGTAATACA
4143086 GTAGTAAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (20 bp):
AATCGATGCAAGTAATACAC
Found at i:4146868 original size:12 final size:12
Alignment explanation
Indices: 4146851--4146876 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4146841 TGTCCAAATC
4146851 GACCCATGACTT
1 GACCCATGACTT
4146863 GACCCATGACTT
1 GACCCATGACTT
4146875 GA
1 GA
4146877 TTTGTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (12 bp):
GACCCATGACTT
Found at i:4151151 original size:173 final size:174
Alignment explanation
Indices: 4150862--4151209 Score: 680
Period size: 173 Copynumber: 2.0 Consensus size: 174
4150852 AATATATTGA
4150862 ATCAAGTGAAAGCATTAACCATAGAGAAAAAAATTCAATTTCTTTTAAAAGAACATAATGAATTA
1 ATCAAGTGAAAGCATTAACCATAGAGAAAAAAATTCAATTTCTTTTAAAAGAACATAATGAATTA
4150927 TAAATTAAATAAATTTGAATTCAAAGCTTCCAAATTCCAAATATAGGGTAATCGACTCGTGGCTC
66 TAAATTAAATAAATTTGAATTCAAAGCTTCCAAATTCCAAATATAGGGTAATCGACTCGTGGCTC
4150992 GACTCTCAGTTTTTGTTTT-AAAATAGAAGTCCCCAGCGGAGTC
131 GACTCTCAGTTTTTGTTTTAAAAATAGAAGTCCCCAGCGGAGTC
4151035 ATCAAGTGAAAGCATTAACCATAGAGAAAAAAATTCAATTTCTTTTAAAAGAACATAATGAATTA
1 ATCAAGTGAAAGCATTAACCATAGAGAAAAAAATTCAATTTCTTTTAAAAGAACATAATGAATTA
4151100 TAAATTAAATAAATTTGAATTCAAAGCTTCCAAATTCCAAATATAGGGTAATCGACTCGTGGCTC
66 TAAATTAAATAAATTTGAATTCAAAGCTTCCAAATTCCAAATATAGGGTAATCGACTCGTGGCTC
4151165 GACTCTCAGTTTTTGTTTTAGAAAATAGAAGTCCCCAGCGGAGTC
131 GACTCTCAGTTTTTGTTTTA-AAAATAGAAGTCCCCAGCGGAGTC
4151210 GCCAAGCTAT
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
173 149 0.86
175 24 0.14
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (174 bp):
ATCAAGTGAAAGCATTAACCATAGAGAAAAAAATTCAATTTCTTTTAAAAGAACATAATGAATTA
TAAATTAAATAAATTTGAATTCAAAGCTTCCAAATTCCAAATATAGGGTAATCGACTCGTGGCTC
GACTCTCAGTTTTTGTTTTAAAAATAGAAGTCCCCAGCGGAGTC
Found at i:4153728 original size:17 final size:17
Alignment explanation
Indices: 4153670--4153733 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
4153660 TTCCTTTACC
*
4153670 ACTATTTCTTTTATTGT
1 ACTATATCTTTTATTGT
* * **
4153687 ACTGTTTAATTTATTGT
1 ACTATATCTTTTATTGT
** *
4153704 GTTGTATCTTTTATTGT
1 ACTATATCTTTTATTGT
4153721 ACTATATCTTTTA
1 ACTATATCTTTTA
4153734 CTAATTGCAG
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (17 bp):
ACTATATCTTTTATTGT
Found at i:4153940 original size:24 final size:24
Alignment explanation
Indices: 4153866--4153978 Score: 102
Period size: 24 Copynumber: 4.7 Consensus size: 24
4153856 ACCCATTGGT
* * *
4153866 ACTAATACGGGAGTGCACAAT-GAT
1 ACTAATACAGGAGTGCATAATCG-C
* * * * *
4153890 ACTAATATAGGAATGCGTATTCAC
1 ACTAATACAGGAGTGCATAATCGC
4153914 ACTAATACAGGAGTGCATAATCGC
1 ACTAATACAGGAGTGCATAATCGC
* *
4153938 ACTGATTCAGGAGTGCATAATCGC
1 ACTAATACAGGAGTGCATAATCGC
* *
4153962 ACTGATTCAGGAGTGCA
1 ACTAATACAGGAGTGCA
4153979 CGAAGGCAGA
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (24 bp):
ACTAATACAGGAGTGCATAATCGC
Found at i:4155600 original size:23 final size:23
Alignment explanation
Indices: 4155569--4155621 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
4155559 ACCTTGTATA
4155569 ATTTT-CCACTATTTTTCTTTAT
1 ATTTTCCCACTATTTTTCTTTAT
4155591 ATTTTCCCACTATTTTTCTTTAT
1 ATTTTCCCACTATTTTTCTTTAT
4155614 ATTTTCCC
1 ATTTTCCC
4155622 TTAGGTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTCCCACTATTTTTCTTTAT
Found at i:4157562 original size:16 final size:16
Alignment explanation
Indices: 4157543--4157601 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
4157533 TCGAACTCTG
*
4157543 CTAACCGCTAACTTTT
1 CTAACAGCTAACTTTT
4157559 CTAACTAG-TAACTTTT
1 CTAAC-AGCTAACTTTT
* *
4157575 CTAATAGCTAACATTT
1 CTAACAGCTAACTTTT
*
4157591 CTAACCGCTAA
1 CTAACAGCTAA
4157602 TACTAACTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 2 0.06
16 33 0.92
17 1 0.03
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (16 bp):
CTAACAGCTAACTTTT
Found at i:4157672 original size:16 final size:17
Alignment explanation
Indices: 4157647--4157681 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4157637 ATTTCTGCTA
4157647 TTTAACTTTATGCA-CT
1 TTTAACTTTATGCATCT
*
4157663 TTTAATTTTATGCATCT
1 TTTAACTTTATGCATCT
4157680 TT
1 TT
4157682 ATTTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTAACTTTATGCATCT
Found at i:4157894 original size:12 final size:12
Alignment explanation
Indices: 4157877--4157919 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 12
4157867 TGTATGGATA
4157877 TTGTATATTTAT
1 TTGTATATTTAT
4157889 TTGTATTATTTAT
1 TTGTA-TATTTAT
4157902 GTATGTATATATTAT
1 -T-TGTATAT-TTAT
4157917 TTG
1 TTG
4157920 CTCTTGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.19
13 9 0.33
14 5 0.19
15 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (12 bp):
TTGTATATTTAT
Found at i:4161433 original size:15 final size:14
Alignment explanation
Indices: 4161394--4161462 Score: 76
Period size: 15 Copynumber: 5.1 Consensus size: 14
4161384 AGATCAAATC
4161394 AAAGCAAAGA-AAA
1 AAAGCAAAGAGAAA
*
4161407 AAA-CAAAAAGAAA
1 AAAGCAAAGAGAAA
4161420 ATAAGCAAAGAGAAA
1 A-AAGCAAAGAGAAA
4161435 AGAAGCAAAGAG-AA
1 A-AAGCAAAGAGAAA
4161449 AAAG-AAAGA-AAA
1 AAAGCAAAGAGAAA
4161461 AA
1 AA
4161463 TAAAAAAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
12 14 0.29
13 10 0.20
14 5 0.10
15 20 0.41
ACGTcount: A:0.75, C:0.06, G:0.17, T:0.01
Consensus pattern (14 bp):
AAAGCAAAGAGAAA
Found at i:4161452 original size:8 final size:7
Alignment explanation
Indices: 4161399--4161487 Score: 56
Period size: 7 Copynumber: 11.7 Consensus size: 7
4161389 AAATCAAAGC
4161399 AAAGAAA
1 AAAGAAA
4161406 AAA-ACAA
1 AAAGA-AA
4161413 AAAGAAA
1 AAAGAAA
*
4161420 ATAAGCAA
1 A-AAGAAA
*
4161428 AGAGAAA
1 AAAGAAA
4161435 AGAAGCAAA
1 A-AAG-AAA
4161444 GAGAA-AAA
1 -A-AAGAAA
4161452 GAAAGAAA
1 -AAAGAAA
*
4161460 AAATAAA
1 AAAGAAA
4161467 AAAGAAA
1 AAAGAAA
4161474 GAAAGAAA
1 -AAAGAAA
4161482 AGAAGA
1 A-AAGA
4161488 CAAGAAGCAC
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
6 1 0.01
7 31 0.46
8 28 0.42
9 3 0.04
10 4 0.06
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:4161492 original size:8 final size:8
Alignment explanation
Indices: 4161414--4161494 Score: 55
Period size: 8 Copynumber: 10.4 Consensus size: 8
4161404 AAAAAACAAA
*
4161414 AAGAAAAT
1 AAGAAAAG
*
4161422 AAGCAAAG
1 AAGAAAAG
4161430 -AGAAAAG
1 AAGAAAAG
*
4161437 AAGCAAAG
1 AAGAAAAG
4161445 -AGAAAAAG
1 AAG-AAAAG
4161453 AAAGAAAA-
1 -AAGAAAAG
*
4161461 AATAAAA-
1 AAGAAAAG
4161468 AAG-AAAG
1 AAGAAAAG
4161475 AAAGAAAAG
1 -AAGAAAAG
*
4161484 AAGACAAG
1 AAGAAAAG
4161492 AAG
1 AAG
4161495 CACATTCAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
6 3 0.05
7 16 0.28
8 29 0.50
9 8 0.14
10 2 0.03
ACGTcount: A:0.73, C:0.04, G:0.21, T:0.02
Consensus pattern (8 bp):
AAGAAAAG
Found at i:4164018 original size:36 final size:36
Alignment explanation
Indices: 4163920--4164020 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 36
4163910 AAAAGTTTCG
* * *
4163920 TCTCACTAGAGACAGTTTTTCATGAAACAAAATTGA
1 TCTCACTTGAGACAGTTTTTCATTAAACAAAATTCA
* *
4163956 TCTCGCTTGAGACAGTTTTTCTTTAAA-AAAATTCCA
1 TCTCACTTGAGACAGTTTTTCATTAAACAAAATT-CA
* *
4163992 TCTCACTTGAGACAGTCTTCCATTAAACA
1 TCTCACTTGAGACAGTTTTTCATTAAACA
4164021 CAAACATTTG
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
35 6 0.11
36 47 0.87
37 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (36 bp):
TCTCACTTGAGACAGTTTTTCATTAAACAAAATTCA
Found at i:4164097 original size:66 final size:66
Alignment explanation
Indices: 4163971--4164135 Score: 169
Period size: 66 Copynumber: 2.5 Consensus size: 66
4163961 CTTGAGACAG
* * *
4163971 TTTTTCTTTAAAA-AAATTCCATCTCACTTGAGACAGTCTTCCATTAAACACAAACATTTGATAT
1 TTTTTC-TTAAAACAAATTTCATCTCACTTGAGACAGTCTTCCATGAAACACAAACATTTGAAAT
4164035 T-
65 TC
* * *
4164036 TTTTTCTTAAAAACAAATTTCATCTCACTTGAGACAGT-TTCCCCTAGAAATACAAA-TTTTGAA
1 TTTTTCTT-AAAACAAATTTCATCTCACTTGAGACAGTCTT-CCAT-GAAACACAAACATTTGAA
4164099 ATTC
63 ATTC
** *
4164103 TTTCACTTGAAACAATATTT-ATCTCACTTGAGA
1 TTTTTCTTAAAACAA-ATTTCATCTCACTTGAGA
4164136 TTGTTCTCAA
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
64 2 0.02
65 12 0.14
66 53 0.62
67 18 0.21
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.38
Consensus pattern (66 bp):
TTTTTCTTAAAACAAATTTCATCTCACTTGAGACAGTCTTCCATGAAACACAAACATTTGAAATT
C
Found at i:4164322 original size:103 final size:100
Alignment explanation
Indices: 4164023--4164426 Score: 361
Period size: 103 Copynumber: 4.0 Consensus size: 100
4164013 ATTAAACACA
* * * * * *
4164023 AACATTTGATATTTTTTTCTTAAAAACAAATTTCATCTCACTTGAGACAGTTTCCCCT-AGAAAT
1 AACATTTGAGATTGTTTCCTT-AAAACAAATTTCGTCTCACTTGAGACAGTTTTCCCTCA-AAAC
* * *
4164087 ACAAATTTTGAAATTCTTTCACTTGAAACAATATTTAT
64 ACAAA-TTTGAAATTGTTTCACTTGAAACAAAATTGAT
** * * * * * *
4164125 CTCACTTGAGATTG-TT-CTCAAAACAAATTTTGTCTCACTTGAGACAATTTGT-CTTCGAAACA
1 AACATTTGAGATTGTTTCCTTAAAACAAATTTCGTCTCACTTGAGACAGTTT-TCCCTCAAAACA
*
4164187 CAAATTCTAAAATTGTTTCACTTGAAACAAAATTGAT
65 CAAATT-TGAAATTGTTTCACTTGAAACAAAATTGAT
*
4164224 AACATTTGAGATTGTTAATCCTTAAAACAAATTTCGTCTCCCTTGAGACAGTTTTCCCTCAAAAC
1 AACATTTGAGATTGTT--TCCTTAAAACAAATTTCGTCTCACTTGAGACAGTTTTCCCTCAAAAC
*
4164289 CCGAAATTTGGAAATTGTTTCACTTGAAA-AAAATTGAT
64 AC-AAATTT-GAAATTGTTTCACTTGAAACAAAATTGAT
* * * * * * **
4164327 AAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCATGAGACAG-TTTCTCTTGAAAC
1 -AACATTTGAGATTGTTTC-CTTAAAACAAATTTCGTCTCACTTGAGACAGTTTTCCCTCAAAAC
* * * *
4164391 ATTAACCTTTGAGATTGTTTCTCTTGAAACAAAATT
64 A-CAA-ATTTGAAATTGTTTCACTTGAAACAAAATT
4164427 TGTCTCGCTT
Statistics
Matches: 246, Mismatches: 41, Indels: 29
0.78 0.13 0.09
Matches are distributed among these distances:
98 2 0.01
99 75 0.30
100 3 0.01
101 2 0.01
102 42 0.17
103 84 0.34
104 38 0.15
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (100 bp):
AACATTTGAGATTGTTTCCTTAAAACAAATTTCGTCTCACTTGAGACAGTTTTCCCTCAAAACAC
AAATTTGAAATTGTTTCACTTGAAACAAAATTGAT
Found at i:4164403 original size:66 final size:66
Alignment explanation
Indices: 4164325--4164786 Score: 773
Period size: 66 Copynumber: 7.0 Consensus size: 66
4164315 AAAAAAATTG
*
4164325 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCATGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
4164390 C
66 C
* * *
4164391 ATTAACCTTTGAGATTGTTTCTCTTGAAACAAAATTTGTCTCGCTTGAGACAGTTTCTCTTTAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
4164456 C
66 C
* * * *
4164457 ATAAACCTTCGAGATTGTTTCTCTTGAACCAAATTTTGTCTCGTTTGAGATAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
4164522 C
66 C
* *
4164523 AT-AACCTTTGAGATTGTTTCCCTTGTAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
4164587 C
66 C
* * *
4164588 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCACTTAAGACAATTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
4164653 C
66 C
* *
4164654 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
4164719 C
66 C
*
4164720 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
4164785 C
66 C
4164786 A
1 A
4164787 AAATTAACCT
Statistics
Matches: 369, Mismatches: 26, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
65 59 0.16
66 310 0.84
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (66 bp):
ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
C
Found at i:4164573 original size:197 final size:198
Alignment explanation
Indices: 4164325--4164786 Score: 782
Period size: 197 Copynumber: 2.3 Consensus size: 198
4164315 AAAAAAATTG
* *
4164325 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCATGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
* * * * *
4164390 CATTAACCTTTGAGATTGTTTCTCTTGAAACAAAATTTGTCTCGCTTGAGACAGTTTCTCTTTAA
66 CATAAACCTTTGAGATTGTTTCTCTTGAAACAAAATTTGTCTCACTTAAGACAATTTCTCTTGAA
* * * * *
4164455 ACATAAACCTTCGAGATTGTTTCTCTTGAACCAAATTTTGTCTCGTTTGAGATAGTTTCTCTTGA
131 ACATAAACCTTCGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGA
4164520 AAC
196 AAC
*
4164523 AT-AACCTTTGAGATTGTTTCCCTTGTAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
*
4164587 CATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCACTTAAGACAATTTCTCTTGAA
66 CATAAACCTTTGAGATTGTTTCTCTTGAAACAAAATTTGTCTCACTTAAGACAATTTCTCTTGAA
*
4164652 ACATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGA
131 ACATAAACCTTCGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGA
4164717 AAC
196 AAC
4164720 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
4164785 CA
66 CA
4164787 AAATTAACCT
Statistics
Matches: 247, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
197 182 0.74
198 65 0.26
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (198 bp):
ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAA
CATAAACCTTTGAGATTGTTTCTCTTGAAACAAAATTTGTCTCACTTAAGACAATTTCTCTTGAA
ACATAAACCTTCGAGATTGTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTTGA
AAC
Found at i:4164803 original size:36 final size:35
Alignment explanation
Indices: 4164341--4164805 Score: 137
Period size: 36 Copynumber: 13.9 Consensus size: 35
4164331 CTTTGAGATT
* *** *
4164341 GTTTCTCTTGAAACAAATTTTGTCTCGCATGAGACA
1 GTTTCTCTTGAAACAAAATTAACCTC-CTTGAGACA
**
4164377 GTTTCTCTTGAAAC---ATTAACCT--TTGAGATT
1 GTTTCTCTTGAAACAAAATTAACCTCCTTGAGACA
***
4164407 GTTTCTCTTGAAACAAAATTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAAATTAACCTC-CTTGAGACA
* * * **
4164443 GTTTCTCTTTAAAC---ATAAACCT--TCGAGATT
1 GTTTCTCTTGAAACAAAATTAACCTCCTTGAGACA
* * *** * *
4164473 GTTTCTCTTGAACCAAATTTTGTCTCGTTTGAGATA
1 GTTTCTCTTGAAACAAAATTAACCTC-CTTGAGACA
**
4164509 GTTTCTCTTGAAAC---A-TAACCT--TTGAGATT
1 GTTTCTCTTGAAACAAAATTAACCTCCTTGAGACA
* * * ***
4164538 GTTTCCCTTGTAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAAATTAACCTC-CTTGAGACA
* **
4164574 GTTTCTCTTGAAAC---ATAAACCT--TTGAGATT
1 GTTTCTCTTGAAACAAAATTAACCTCCTTGAGACA
* *** *
4164604 GTTTCTCTTGAAACAAATTTTGTCTCACTTAAGACA
1 GTTTCTCTTGAAACAAAATTAACCTC-CTTGAGACA
* * **
4164640 ATTTCTCTTGAAAC---ATAAACCT--TTGAGATT
1 GTTTCTCTTGAAACAAAATTAACCTCCTTGAGACA
* * ***
4164670 GTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAAATTAACCTC-CTTGAGACA
* * **
4164706 ATTTCTCTTGAAAC---ATAAACCT--TTGAGATT
1 GTTTCTCTTGAAACAAAATTAACCTCCTTGAGACA
* * ***
4164736 GTTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACA
1 GTTTCTCTTGAAACAAAATTAACCTC-CTTGAGACA
4164772 GTTTCTCTTGAAACAAAATTAACCTCACTTGAGA
1 GTTTCTCTTGAAACAAAATTAACCTC-CTTGAGA
4164806 TTGTTATCTC
Statistics
Matches: 290, Mismatches: 102, Indels: 74
0.62 0.22 0.16
Matches are distributed among these distances:
29 19 0.07
30 91 0.31
32 3 0.01
33 37 0.13
36 140 0.48
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (35 bp):
GTTTCTCTTGAAACAAAATTAACCTCCTTGAGACA
Found at i:4165096 original size:139 final size:139
Alignment explanation
Indices: 4164835--4165228 Score: 484
Period size: 139 Copynumber: 2.8 Consensus size: 139
4164825 CCTAAAGACG
* * * *
4164835 ATCACATAGGAACAATGTTGTCCACCGACCAGATCTTCTCAATGCGTAGGAGCAGCGTCATCCTC
1 ATCACGTAGGAACAATGTCGTCCACCGACCAGATCTCCTCAAAGCGTAGGAGCAGCGTCATCCTC
* * * * *
4164900 AGATAACCATACTTCCCCATGACGTAGGAACAGTGTTGTTTCCAAATTATCCCTAAAGAC-GACT
66 AGATAACCAAACTTCCTCATCACGTAGGAACAGTGTTGTCTCCAAATTATCCATAAAGACAG-CT
4164964 AGACATCCTC
130 AGACATCCTC
* * * * * * *
4164974 ATCCCGTAGGAACAATGTCGTCCACCTAACAGATCTCCTCAACGCGTAGGAGCACCATCATCCTT
1 ATCACGTAGGAACAATGTCGTCCACCGACCAGATCTCCTCAAAGCGTAGGAGCAGCGTCATCCTC
*
4165039 AGATAACCAAACTTCCTCATCACGTAGGAACTGTGTTGTCTCCAAATTATCCATAAAGACAGCTA
66 AGATAACCAAACTTCCTCATCACGTAGGAACAGTGTTGTCTCCAAATTATCCATAAAGACAGCTA
* *
4165104 GACGTCCTT
131 GACATCCTC
* * * * * *
4165113 ATCACGTAGGAATAATGTCATCCACCGACCAGATCTCCTCAAAACGTAAGAGCAGTGTCATCATC
1 ATCACGTAGGAACAATGTCGTCCACCGACCAGATCTCCTCAAAGCGTAGGAGCAGCGTCATCCTC
* * * * * * *
4165178 AGACAATCAGACTTCCTCATCACTTAGAAACCGTGTTGTCACCAAATTATC
66 AGATAACCAAACTTCCTCATCACGTAGGAACAGTGTTGTCTCCAAATTATC
4165229 TTCAAATTGA
Statistics
Matches: 216, Mismatches: 38, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
139 215 1.00
140 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (139 bp):
ATCACGTAGGAACAATGTCGTCCACCGACCAGATCTCCTCAAAGCGTAGGAGCAGCGTCATCCTC
AGATAACCAAACTTCCTCATCACGTAGGAACAGTGTTGTCTCCAAATTATCCATAAAGACAGCTA
GACATCCTC
Found at i:4166612 original size:131 final size:132
Alignment explanation
Indices: 4166381--4166634 Score: 359
Period size: 131 Copynumber: 1.9 Consensus size: 132
4166371 AACTACTAAC
* * *
4166381 TTTTATTTTATTGCACTCTAGCCATTGTTTTATTTATTTATTTATTTATTGTTTCAAATATTCAG
1 TTTTATTTTATTGCACTCTAACCATTG---T-TTTATTTATTTATTTATTGTTTCAAATATTAAA
* * * *
4166446 TTCGACCTTGTGGTGACCTGGTCCGAGGTATGATCCACATTACTATGGTTCGGACTCTGCTAGCT
62 TTCGACATTGTGGTGACCCGATCCGAGGTATGATCCACATTACTATGGTTCAGACTCTGCTAGCT
4166511 ACTGAT
127 ACTGAT
*
4166517 TTTTATTTTATTGCACTCTAACCATTG-TTTATTTATTTATTTATTGTTTCTAATATTTAAATT-
1 TTTTATTTTATTGCACTCTAACCATTGTTTTATTTATTTATTTATTGTTTCAAATA-TTAAATTC
* *
4166580 GACATTGTGGTGACCCGATCCGGGGTATGATCCACATTATTATGGTTCAGACTCT
65 GACATTGTGGTGACCCGATCCGAGGTATGATCCACATTACTATGGTTCAGACTCT
4166635 ACTAACCACT
Statistics
Matches: 107, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
131 76 0.71
132 5 0.05
136 26 0.24
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.46
Consensus pattern (132 bp):
TTTTATTTTATTGCACTCTAACCATTGTTTTATTTATTTATTTATTGTTTCAAATATTAAATTCG
ACATTGTGGTGACCCGATCCGAGGTATGATCCACATTACTATGGTTCAGACTCTGCTAGCTACTG
AT
Found at i:4166655 original size:2 final size:2
Alignment explanation
Indices: 4166648--4166680 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4166638 AACCACTAAC
4166648 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 T
4166681 TGTTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4166781 original size:16 final size:16
Alignment explanation
Indices: 4166760--4166825 Score: 80
Period size: 16 Copynumber: 4.1 Consensus size: 16
4166750 TTATGGTTCG
*
4166760 AACTTTGCTAA-TCGCT
1 AACTTTTCTAACT-GCT
4166776 AACTTTTCTAACTGCT
1 AACTTTTCTAACTGCT
**
4166792 AACTTTTCTAACAACT
1 AACTTTTCTAACTGCT
*
4166808 AACATTTCTAACTGCT
1 AACTTTTCTAACTGCT
4166824 AA
1 AA
4166826 TTACTAACTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
16 42 0.98
17 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (16 bp):
AACTTTTCTAACTGCT
Found at i:4166897 original size:16 final size:17
Alignment explanation
Indices: 4166872--4166906 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4166862 ATTTCTTCTA
*
4166872 TTTAACTTTATGCA-CT
1 TTTAAATTTATGCATCT
4166888 TTTAAATTTATGCATCT
1 TTTAAATTTATGCATCT
4166905 TT
1 TT
4166907 ATTTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATGCATCT
Found at i:4168319 original size:29 final size:30
Alignment explanation
Indices: 4168259--4168319 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
4168249 GTGTAGTTCT
* * ** *
4168259 TAAACTTTCTAAACTTTATATTTTTTTTAC
1 TAAACTTTCTAAAATTTAAATTTTGGTCAC
4168289 TAAACTTT-TAAAATTTAAATTTTGGTCAC
1 TAAACTTTCTAAAATTTAAATTTTGGTCAC
4168318 TA
1 TA
4168320 GCCAAAATTC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.51
Consensus pattern (30 bp):
TAAACTTTCTAAAATTTAAATTTTGGTCAC
Found at i:4171580 original size:21 final size:21
Alignment explanation
Indices: 4171556--4171595 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4171546 TCTTTCGCAA
*
4171556 AAAGGGATCGATCCTTTTTGC
1 AAAGAGATCGATCCTTTTTGC
4171577 AAAGAGATCGATCCTTTTT
1 AAAGAGATCGATCCTTTTT
4171596 TCTGGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
AAAGAGATCGATCCTTTTTGC
Found at i:4175801 original size:23 final size:23
Alignment explanation
Indices: 4175713--4175805 Score: 96
Period size: 23 Copynumber: 4.0 Consensus size: 23
4175703 GAGTCGAGGG
* *
4175713 TTCTACACGGTCCTTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAT
* * * *
4175736 TTCTACGTGATCATTCAGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
** *
4175759 TTCTACGCGGTATTTTGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
*
4175782 TTCTACGCAGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
4175805 T
1 T
4175806 CTATGTGGCA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:4175841 original size:24 final size:24
Alignment explanation
Indices: 4175804--4175851 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4175794 CTTCGGGACA
* * *
4175804 TTCTATGTGGCACTTCGGTGCAAT
1 TTCTATGCGACACTTCAGTGCAAT
*
4175828 TTCTATGCGACACTTTAGTGCAAT
1 TTCTATGCGACACTTCAGTGCAAT
4175852 ATATACGAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (24 bp):
TTCTATGCGACACTTCAGTGCAAT
Done.