Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 23
Found at i:381530 original size:35 final size:35
Alignment explanation
Indices: 381437--381535 Score: 162
Period size: 35 Copynumber: 2.8 Consensus size: 35
381427 ATAACATCAC
*
381437 CAACTTCCATCACCATTGCACGCCAATATTATCTT
1 CAACTTCCATCACCATTGCACGCCTATATTATCTT
381472 CAACTTCCATCACCATTGCACGCCTATATTATCTT
1 CAACTTCCATCACCATTGCACGCCTATATTATCTT
* **
381507 CAACTTCTATCACCATTTTACGCCTATAT
1 CAACTTCCATCACCATTGCACGCCTATAT
381536 AACCACCAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.27, C:0.33, G:0.05, T:0.34
Consensus pattern (35 bp):
CAACTTCCATCACCATTGCACGCCTATATTATCTT
Found at i:383394 original size:16 final size:15
Alignment explanation
Indices: 383375--383432 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 15
383365 CATTTCTATC
383375 CATTTCCTTTTCTTAT
1 CATTT-CTTTTCTTAT
383391 CATTTCTTTTCTTATTT
1 CATTTCTTTTCTTA--T
*
383408 CATATTCTATTT-TAAT
1 CAT-TTCT-TTTCTTAT
383424 CATTTCTTT
1 CATTTCTTT
383433 CTTTAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 2 0.05
15 13 0.35
16 9 0.24
17 4 0.11
18 6 0.16
19 3 0.08
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (15 bp):
CATTTCTTTTCTTAT
Found at i:384303 original size:161 final size:161
Alignment explanation
Indices: 384038--384363 Score: 625
Period size: 161 Copynumber: 2.0 Consensus size: 161
384028 GGGATACAAC
*
384038 AAGGCTACCAACTTCTACATTATTGAAGAAGCCTGAATAGCCTTACATCACCTTCATTTTAGCTC
1 AAGGCTACCAACTTCTACATTATTGAAGAAGCCTGAATAGCCTTACATCACATTCATTTTAGCTC
384103 TTAGATTTAAACATTAGCTCACACATATTATATGATGATATATGTAGCTCATAACATGCAACCAT
66 TTAGATTTAAACATTAGCTCACACATATTATATGATGATATATGTAGCTCATAACATGCAACCAT
*
384168 AGCTCACAAGACCATGATCATGCATGGCAGT
131 AGCTCACAAGACCATGATCATGCATGACAGT
*
384199 AAGGCTACCAACTTCTCCATTATTGAAGAAGCCTGAATAGCCTTACATCACATTCATTTTAGCTC
1 AAGGCTACCAACTTCTACATTATTGAAGAAGCCTGAATAGCCTTACATCACATTCATTTTAGCTC
384264 TTAGATTTAAACATTAGCTCACACATATTATATGATGATATATGTAGCTCATAACATGCAACCAT
66 TTAGATTTAAACATTAGCTCACACATATTATATGATGATATATGTAGCTCATAACATGCAACCAT
384329 AGCTCACAAGACCATGATCATGCATGACAGT
131 AGCTCACAAGACCATGATCATGCATGACAGT
384360 AAGG
1 AAGG
384364 TATTTAGCTC
Statistics
Matches: 162, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 162 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (161 bp):
AAGGCTACCAACTTCTACATTATTGAAGAAGCCTGAATAGCCTTACATCACATTCATTTTAGCTC
TTAGATTTAAACATTAGCTCACACATATTATATGATGATATATGTAGCTCATAACATGCAACCAT
AGCTCACAAGACCATGATCATGCATGACAGT
Found at i:394273 original size:24 final size:21
Alignment explanation
Indices: 394239--394281 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
394229 TGCACAAGAT
*
394239 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
394261 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
394282 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:399009 original size:13 final size:12
Alignment explanation
Indices: 398984--399020 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
398974 TCCTCCCTCC
*
398984 TTTTTTCTGTTT
1 TTTTTTTTGTTT
398996 TTTTCTTTTGTTT
1 TTTT-TTTTGTTT
399009 TTTTTTTTGTTT
1 TTTTTTTTGTTT
399021 CGAATTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.86
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:399410 original size:25 final size:25
Alignment explanation
Indices: 399369--399492 Score: 205
Period size: 25 Copynumber: 5.0 Consensus size: 25
399359 AGTTAAGGGA
* *
399369 TTAGGG-TTAAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
399393 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
399418 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
399443 TTAGGGTTTGAAACCCTAAACTAAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
399468 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
399493 GGGTTGTTGG
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
24 6 0.06
25 88 0.94
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:399571 original size:3 final size:3
Alignment explanation
Indices: 399563--399626 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
399553 GCAAAAATTG
* **
399563 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
399607 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
399627 CGGAAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:399618 original size:32 final size:32
Alignment explanation
Indices: 399565--399628 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
399555 AAAAATTGTA
*
399565 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
399597 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
399629 GAAAAAAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:399988 original size:90 final size:89
Alignment explanation
Indices: 399873--400042 Score: 288
Period size: 90 Copynumber: 1.9 Consensus size: 89
399863 TTTTAGGAAG
* *
399873 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCTTAC
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATAC
399937 ATGATGAAGAGATCTGGCCATCTAAA
64 ATGATGAAGAGATCTGGCCATCTAAA
*
399963 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
400028 GATGAAGAGATCTGG
66 GATGAAGAGATCTGG
400043 TCTGGGGATG
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
88 2 0.03
89 34 0.45
90 40 0.53
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (89 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACAT
GATGAAGAGATCTGGCCATCTAAA
Found at i:400006 original size:46 final size:46
Alignment explanation
Indices: 399873--400006 Score: 132
Period size: 46 Copynumber: 3.0 Consensus size: 46
399863 TTTTAGGAAG
*
399873 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCT-AA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CTAAA
* * * * * * * **
399919 --TGTTGACACGGCTCTTACATGATGAAGA-GATCTGGCCATCTAAA
1 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAA
399963 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
400007 TGGTTGACAC
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
43 3 0.05
44 29 0.45
46 31 0.48
47 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (46 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAA
Found at i:400027 original size:43 final size:44
Alignment explanation
Indices: 399890--400032 Score: 139
Period size: 46 Copynumber: 3.2 Consensus size: 44
399880 ACTCGGTTCC
*
399890 TACGTGATGAGGACGGCTGGTTATCCTAAT-GTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTAT-CTAATGGTTGACACGGCTCA
* * * ** * * * *
399934 TACATGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATCTAATGGT--TGACACGGCTCA
399980 TACGTGATGAGGACGGCTGGTTATCT-ATGGTTGACACGGCTCA
1 TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
400023 TACGTGATGA
1 TACGTGATGA
400033 AGAGATCTGG
Statistics
Matches: 76, Mismatches: 18, Indels: 11
0.72 0.17 0.10
Matches are distributed among these distances:
43 24 0.32
44 19 0.25
45 4 0.05
46 28 0.37
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (44 bp):
TACGTGATGAGGACGGCTGGTTATCTAATGGTTGACACGGCTCA
Found at i:400043 original size:43 final size:44
Alignment explanation
Indices: 399906--400043 Score: 129
Period size: 43 Copynumber: 3.1 Consensus size: 44
399896 ATGAGGACGG
* *
399906 CTGGTTATCCTAAT-GTTGACACGGCTCTTACATGATGAAGAGAT
1 CTGGTTAT-CTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
** * * * * * *
399950 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-G
1 CTGGTTATCTAATGGT--TGACACGGCTCATACGTGATGAAGA-GAT
399996 CTGGTTATCT-ATGGTTGACACGGCTCATACGTGATGAAGAGAT
1 CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
400039 CTGGT
1 CTGGT
400044 CTGGGGATGA
Statistics
Matches: 72, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
42 1 0.01
43 30 0.42
44 8 0.11
45 4 0.06
46 28 0.39
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
CTGGTTATCTAATGGTTGACACGGCTCATACGTGATGAAGAGAT
Found at i:401162 original size:1 final size:1
Alignment explanation
Indices: 401158--401182 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
401148 TTTCATTTCC
401158 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
401183 AGGTGTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:414090 original size:13 final size:12
Alignment explanation
Indices: 414065--414101 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
414055 TCCTCCCTCC
*
414065 TTTTTTCTGTTT
1 TTTTTTTTGTTT
414077 TTTTCTTTTGTTT
1 TTTT-TTTTGTTT
414090 TTTTTTTTGTTT
1 TTTTTTTTGTTT
414102 CGAATTTCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.86
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:414491 original size:25 final size:25
Alignment explanation
Indices: 414450--414567 Score: 193
Period size: 25 Copynumber: 4.8 Consensus size: 25
414440 AGTTAAGGGA
* * *
414450 TTAGGG-TTAAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTAAT
*
414474 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTAAT
414499 TTAGGGTTTGAAACCCTAAACTAAT
1 TTAGGGTTTGAAACCCTAAACTAAT
414524 TTAGGGTTTGAAACCCTAAACTAAT
1 TTAGGGTTTGAAACCCTAAACTAAT
414549 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
414568 TCTGATGGGT
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
24 6 0.07
25 84 0.93
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTAAT
Found at i:414652 original size:3 final size:3
Alignment explanation
Indices: 414644--414707 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
414634 GCAAAAATTG
* **
414644 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
414688 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
414708 CGGAAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:414699 original size:32 final size:32
Alignment explanation
Indices: 414646--414709 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
414636 AAAAATTGTA
*
414646 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
414678 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
414710 GAAAAAAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:416400 original size:19 final size:21
Alignment explanation
Indices: 416357--416408 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
416347 GAAATCCCTT
416357 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
416378 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
416397 TGAAGATACATG
1 TGAAAATACATG
416409 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:420928 original size:14 final size:14
Alignment explanation
Indices: 420911--420948 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
420901 TTGGCTAGCT
*
420911 TTCTCTTTTTGAAC
1 TTCTCTTTTTAAAC
420925 TTCTCTTTTTAAAC
1 TTCTCTTTTTAAAC
420939 TTCTCTTTTT
1 TTCTCTTTTT
420949 CTTTTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.63
Consensus pattern (14 bp):
TTCTCTTTTTAAAC
Found at i:420992 original size:16 final size:16
Alignment explanation
Indices: 420955--421002 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
420945 TTTTCTTTTC
420955 TTTTCTTCTTTTCTGAA
1 TTTTCTTCTTTT-TGAA
*
420972 TTTTCTTCTTTTTGTA
1 TTTTCTTCTTTTTGAA
420988 TTTTCTTTCTTTTTG
1 TTTTC-TTCTTTTTG
421003 CACTCCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (16 bp):
TTTTCTTCTTTTTGAA
Found at i:425745 original size:16 final size:16
Alignment explanation
Indices: 425726--425789 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
425716 TTTTTTTAAT
425726 TTTTCTTTTTCTTTTC
1 TTTTCTTTTTCTTTTC
425742 TTTTC---TTCTTTTC
1 TTTTCTTTTTCTTTTC
*
425755 --TTCTTTTTCTCTTTT
1 TTTTCTTTTTCT-TTTC
425770 TTTGTCTTTTTC-TTTC
1 TTT-TCTTTTTCTTTTC
425786 TTTT
1 TTTT
425790 TGCACTCCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 15
0.70 0.04 0.27
Matches are distributed among these distances:
11 3 0.08
13 8 0.21
14 4 0.10
15 4 0.10
16 11 0.28
17 1 0.03
18 8 0.21
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:425758 original size:27 final size:28
Alignment explanation
Indices: 425727--425790 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
425717 TTTTTTAATT
*
425727 TTTCTTTTTCT-TTTCTTT-TCTTCTTT-
1 TTTCTTTTTCTCTTTTTTTGTCTT-TTTC
425753 TCTTCTTTTTCTCTTTTTTTGTCTTTTTC
1 T-TTCTTTTTCTCTTTTTTTGTCTTTTTC
425782 TTTCTTTTT
1 TTTCTTTTT
425791 GCACTCCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 1 0.03
27 10 0.30
28 17 0.52
29 5 0.15
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (28 bp):
TTTCTTTTTCTCTTTTTTTGTCTTTTTC
Found at i:425767 original size:8 final size:9
Alignment explanation
Indices: 425728--425790 Score: 67
Period size: 10 Copynumber: 6.9 Consensus size: 9
425718 TTTTTAATTT
425728 TTCTTTTTC
1 TTCTTTTTC
*
425737 TTTTCTTTTC
1 TTCT-TTTTC
425747 TTC-TTTTC
1 TTCTTTTTC
425755 TTCTTTTTC
1 TTCTTTTTC
*
425764 -TCTTTTTT
1 TTCTTTTTC
425772 TGTCTTTTTC
1 T-TCTTTTTC
425782 TTTCTTTTT
1 -TTCTTTTT
425791 GCACTCCAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
8 15 0.33
9 8 0.18
10 21 0.47
11 1 0.02
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:425779 original size:7 final size:6
Alignment explanation
Indices: 425725--425784 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
425715 TTTTTTTTAA
* *
425725 TTTTTC TTTTTC -TTTTC -TTTTC TTCTT- TTCTTC TTTTTC TCTTTT-
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC
*
425770 TTTGTC TTTTTC TTT
1 TTTTTC TTTTTC TTT
425785 CTTTTTGCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 18 0.39
6 24 0.52
7 4 0.09
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:425854 original size:10 final size:11
Alignment explanation
Indices: 425816--425851 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
425806 TGAAGGAGTC
425816 TTTTCTTCTAT
1 TTTTCTTCTAT
425827 TTTTCTTCTAT
1 TTTTCTTCTAT
425838 TTTTCTTCTAT
1 TTTTCTTCTAT
425849 TTT
1 TTT
425852 CTTTTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTCTTCTAT
Found at i:426073 original size:22 final size:21
Alignment explanation
Indices: 426039--426082 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
426029 GGCTGCGGAA
*
426039 TTGATGGTCTTGATGGATGAAG
1 TTGATGATCTTGAT-GATGAAG
*
426061 TTGATGATGTTGATGATGAAG
1 TTGATGATCTTGATGATGAAG
426082 T
1 T
426083 AGAGATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.25, C:0.02, G:0.34, T:0.39
Consensus pattern (21 bp):
TTGATGATCTTGATGATGAAG
Found at i:426477 original size:19 final size:21
Alignment explanation
Indices: 426434--426485 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
426424 GAAATCCCTT
426434 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
426455 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
426474 TGAAGATACATG
1 TGAAAATACATG
426486 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:434386 original size:22 final size:22
Alignment explanation
Indices: 434361--434409 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
434351 CACCATCTTC
434361 CATTACCATTGCACACCTATAT
1 CATTACCATTGCACACCTATAT
*
434383 CATTACCATTGCACGCCTATAT
1 CATTACCATTGCACACCTATAT
434405 CATTA
1 CATTA
434410 TCATCTTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.33
Consensus pattern (22 bp):
CATTACCATTGCACACCTATAT
Found at i:438825 original size:28 final size:28
Alignment explanation
Indices: 438763--438827 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
438753 AAAGAAAATC
* * *
438763 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAAATCAAGCACTCAAAAAGA
*
438791 A-AGAAAGAAAATCCAGCACTCAAAAAGA
1 AGA-AAAGAAAATCAAGCACTCAAAAAGA
438819 AGAAAAGAA
1 AGAAAAGAA
438828 TAGAAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 29 0.94
29 1 0.03
ACGTcount: A:0.62, C:0.14, G:0.17, T:0.08
Consensus pattern (28 bp):
AGAAAAGAAAATCAAGCACTCAAAAAGA
Found at i:442125 original size:19 final size:20
Alignment explanation
Indices: 442084--442134 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
442074 GAAACCCCTT
*
442084 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
442104 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
442123 TGAAGATACATG
1 TGAAAATACATG
442135 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:444120 original size:22 final size:20
Alignment explanation
Indices: 444095--444134 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
444085 ATGTTTGTTT
444095 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
444117 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
444135 CATCATTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:445491 original size:13 final size:13
Alignment explanation
Indices: 445469--445498 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
445459 ACTAAACACC
445469 TTTC-ACATACCT
1 TTTCAACATACCT
445481 TTTCAACATACCT
1 TTTCAACATACCT
445494 TTTCA
1 TTTCA
445499 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:450277 original size:30 final size:31
Alignment explanation
Indices: 450237--450296 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
450227 ACATGCTGCC
**
450237 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
450268 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
450297 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:452759 original size:11 final size:11
Alignment explanation
Indices: 452745--452802 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 11
452735 ATCTTTTGAA
452745 TTTCTTTTTCT
1 TTTCTTTTTCT
452756 TTTCTTTTT-T
1 TTTCTTTTTCT
452766 TTTCTGATTCTTCTTT
1 TTTCT--TT-TTC--T
452782 TTGTCTTTTTCT
1 TT-TCTTTTTCT
452794 TTTCTTTTT
1 TTTCTTTTT
452803 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
10 6 0.15
11 16 0.40
12 5 0.12
13 2 0.05
14 3 0.08
15 2 0.05
16 3 0.08
17 3 0.08
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:453583 original size:19 final size:20
Alignment explanation
Indices: 453541--453592 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
453531 TGAAACCCCT
*
453541 ATGAAAATACATGATTTTTG
1 ATGAAAATACATGATTTTTA
453561 ATGAAAATACATGA-TTTTA
1 ATGAAAATACATGATTTTTA
*
453580 ATGAAGATACATG
1 ATGAAAATACATG
453593 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGAAAATACATGATTTTTA
Found at i:454531 original size:30 final size:32
Alignment explanation
Indices: 454490--454554 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
454480 ACATGCTGCC
454490 ATGATATCTAAATA-AAATGCAAACATAATA-A
1 ATGATATCTAAA-ACAAATGCAAACATAATATA
* *
454521 ATGA-ATCTAAAACATATGTAAACATAATATA
1 ATGATATCTAAAACAAATGCAAACATAATATA
454552 ATG
1 ATG
454555 CTAAGTAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 21 0.70
31 8 0.27
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (32 bp):
ATGATATCTAAAACAAATGCAAACATAATATA
Found at i:461299 original size:19 final size:20
Alignment explanation
Indices: 461272--461311 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
461262 GAATAATAAT
461272 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
461292 ATAA-TAATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
461311 A
1 A
461312 CGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:462584 original size:15 final size:16
Alignment explanation
Indices: 462564--462606 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
462554 AGTTATCATC
462564 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
462579 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
462595 AAAATAACTATA
1 ATAATAACTATA
462607 TTAAAGCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:466668 original size:20 final size:20
Alignment explanation
Indices: 466643--466681 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
466633 TACCATTCGG
466643 TAAAAAGCATGTATTTTCAT
1 TAAAAAGCATGTATTTTCAT
*
466663 TAAAAATCATGTATTTTCA
1 TAAAAAGCATGTATTTTCA
466682 AAGGGGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (20 bp):
TAAAAAGCATGTATTTTCAT
Found at i:471368 original size:21 final size:20
Alignment explanation
Indices: 471321--471378 Score: 84
Period size: 18 Copynumber: 3.0 Consensus size: 20
471311 TACCATTCGG
*
471321 TAAAAAGCATGTATTTTCAT
1 TAAAAATCATGTATTTTCAT
471341 T--AAATCATGTATTTTCAT
1 TAAAAATCATGTATTTTCAT
471359 TAAAAAATCATGTATTTTCA
1 T-AAAAATCATGTATTTTCA
471379 AAGGGGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 17 0.50
20 1 0.03
21 16 0.47
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (20 bp):
TAAAAATCATGTATTTTCAT
Found at i:472730 original size:13 final size:13
Alignment explanation
Indices: 472712--472737 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
472702 TATATTTTCA
472712 TTAAAAAAAACAT
1 TTAAAAAAAACAT
472725 TTAAAAAAAACAT
1 TTAAAAAAAACAT
472738 GTTTTTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
TTAAAAAAAACAT
Found at i:473559 original size:23 final size:23
Alignment explanation
Indices: 473533--473577 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
473523 TTTGGAGTGC
473533 AAAAGAAA-GAAAAGAAAAAGAAG
1 AAAA-AAATGAAAAGAAAAAGAAG
**
473556 AAAAAAATTCAAAGAAAAAGAA
1 AAAAAAATGAAAAGAAAAAGAA
473578 AAGTGAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (23 bp):
AAAAAAATGAAAAGAAAAAGAAG
Found at i:475380 original size:17 final size:16
Alignment explanation
Indices: 475311--475383 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 16
475301 ATTCATGCAT
475311 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
* *
475328 GTTGGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
* *
475346 GTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
475363 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
475380 CTAG
1 CTAG
475384 ATCCACAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.02
17 28 0.62
18 16 0.36
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:475585 original size:24 final size:24
Alignment explanation
Indices: 475533--475599 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 24
475523 AAACAAAGTG
*
475533 AAGCACTCAAAAGAAAGAAAAATC
1 AAGCACTCAAAAGAAAGAAAAAGC
*
475557 CAGCACTCAAAA-AGAAG-AAAAGC
1 AAGCACTCAAAAGA-AAGAAAAAGC
***
475580 AAAGCAAAGAAAAGAAAGAA
1 -AAGCACTCAAAAGAAAGAA
475600 GTTGAAGCAG
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
23 6 0.18
24 25 0.76
25 2 0.06
ACGTcount: A:0.64, C:0.15, G:0.16, T:0.04
Consensus pattern (24 bp):
AAGCACTCAAAAGAAAGAAAAAGC
Found at i:481110 original size:18 final size:17
Alignment explanation
Indices: 481087--481136 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
481077 GCCATCTCTA
481087 TCATTTCTTTATTTTATT
1 TCATTTCTTTATTTTA-T
481105 TCATTTC-TTATCTTTAT
1 TCATTTCTTTAT-TTTAT
481122 T-ATTTCATTTATTTT
1 TCATTTC-TTTATTTT
481137 CCTTTACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.17
17 9 0.31
18 15 0.52
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (17 bp):
TCATTTCTTTATTTTAT
Found at i:481401 original size:18 final size:18
Alignment explanation
Indices: 481378--481428 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
481368 AATTGGAGTG
481378 CAAAAAGAAAGAAAAAAA
1 CAAAAAGAAAGAAAAAAA
*
481396 CAAAAAG-AAGAAAAGAA
1 CAAAAAGAAAGAAAAAAA
*
481413 -GAAAAGAAAAGAAAAA
1 CAAAAAG-AAAGAAAAA
481429 GAATTCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 14 0.50
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAAAA
Found at i:481408 original size:21 final size:20
Alignment explanation
Indices: 481382--481431 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
481372 GGAGTGCAAA
481382 AAGAAAGAAAAAAACAAAAAG
1 AAGAAAGAAAAAAA-AAAAAG
* *
481403 AAGAAAAGAAGAAAAGAAAAG
1 AAG-AAAGAAAAAAAAAAAAG
481424 AA-AAAGAA
1 AAGAAAGAA
481432 TTCAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 6 0.23
21 10 0.38
22 10 0.38
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAAAAAAAAAAAG
Found at i:486556 original size:18 final size:17
Alignment explanation
Indices: 486533--486582 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
486523 ACCATCTCTA
486533 TCATTTCTTTATTTTATT
1 TCATTTCTTTATTTTA-T
486551 TCATTTC-TTATCTTTAT
1 TCATTTCTTTAT-TTTAT
486568 T-ATTTCATTTATTTT
1 TCATTTC-TTTATTTT
486583 CCTTTACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.17
17 9 0.31
18 15 0.52
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (17 bp):
TCATTTCTTTATTTTAT
Found at i:486789 original size:13 final size:14
Alignment explanation
Indices: 486753--486793 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
486743 AAGATATATT
*
486753 ATCTTTCCATCACT
1 ATCTTTCCATCACC
486767 ATCTTTCCATCACC
1 ATCTTTCCATCACC
486781 ATC-TTCCATCACC
1 ATCTTTCCATCACC
486794 TTCCATGCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (14 bp):
ATCTTTCCATCACC
Found at i:492268 original size:18 final size:18
Alignment explanation
Indices: 492226--492271 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
492216 TAGTTTGATT
*
492226 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
492244 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
492262 AATGAACTAA
1 AATGAACTAA
492272 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:492347 original size:17 final size:17
Alignment explanation
Indices: 492327--492361 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
492317 ACTACTTCCC
492327 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
492344 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
492361 T
1 T
492362 TAATATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:498229 original size:13 final size:13
Alignment explanation
Indices: 498207--498236 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
498197 ACTAGACACC
498207 TTTC-ACATACCT
1 TTTCAACATACCT
498219 TTTCAACATACCT
1 TTTCAACATACCT
498232 TTTCA
1 TTTCA
498237 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:502121 original size:19 final size:20
Alignment explanation
Indices: 502078--502123 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
502068 AACTTTTTTT
502078 TTTTTTAATTTTCGGAATTC
1 TTTTTTAATTTTCGGAATTC
*
502098 TTTTTTAATTTTTGGAATTC
1 TTTTTTAATTTTCGGAATTC
502118 TTTTTT
1 TTTTTT
502124 TTTTCAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.07, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTTTTAATTTTCGGAATTC
Found at i:503940 original size:30 final size:30
Alignment explanation
Indices: 503904--503979 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
503894 TCCTTAGTGC
503904 CCAAATGCTCCACCAAACTGTACATGTCTT
1 CCAAATGCTCCACCAAACTGTACATGTCTT
* * *
503934 CCAAATGCTCCACTAAGCTGTATATGTCTT
1 CCAAATGCTCCACCAAACTGTACATGTCTT
503964 CCAAATGCTCCACCAA
1 CCAAATGCTCCACCAA
503980 GTTGTCCCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.30, C:0.33, G:0.11, T:0.26
Consensus pattern (30 bp):
CCAAATGCTCCACCAAACTGTACATGTCTT
Found at i:505297 original size:30 final size:30
Alignment explanation
Indices: 505261--505333 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
505251 GGACATCTTG
* *
505261 GTGGAGCATTTGTAATAAATATACAGTTTA
1 GTGGAGCATTTGGAATAAATATACAGCTTA
* *
505291 GTGGAGCATTTGGAATATATATACAGCTTG
1 GTGGAGCATTTGGAATAAATATACAGCTTA
505321 GTGGAGCATTTGG
1 GTGGAGCATTTGG
505334 GAAACATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.34
Consensus pattern (30 bp):
GTGGAGCATTTGGAATAAATATACAGCTTA
Found at i:509906 original size:19 final size:20
Alignment explanation
Indices: 509863--509913 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
509853 GAAACCCCTT
**
509863 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
*
509883 TGAAAATACATTA-TTTAAA
1 TGAAAATACATGATTTTAAA
509902 TGAAAATACATG
1 TGAAAATACATG
509914 CTCTTGGCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:511393 original size:17 final size:17
Alignment explanation
Indices: 511371--511409 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
511361 TGTCTTGTAC
*
511371 TTCAAAGGTTGTATCCT
1 TTCAAACGTTGTATCCT
*
511388 TTCAAAACGTTGTATCTT
1 TTC-AAACGTTGTATCCT
511406 TTCA
1 TTCA
511410 CTCTTACTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (17 bp):
TTCAAACGTTGTATCCT
Found at i:511887 original size:24 final size:22
Alignment explanation
Indices: 511843--511894 Score: 52
Period size: 24 Copynumber: 2.3 Consensus size: 22
511833 ACTTCAATTT
* *
511843 GTACATTCTTTTGAATTTCAAGAG
1 GTACA-TCCTTTGAATGTCAA-AG
511867 GTACATCCTTTGAAATGTCAAAG
1 GTACATCCTTTG-AATGTCAAAG
511890 G-ACAT
1 GTACAT
511895 GTCTTGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 4 0.16
23 9 0.36
24 12 0.48
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (22 bp):
GTACATCCTTTGAATGTCAAAG
Found at i:513180 original size:23 final size:24
Alignment explanation
Indices: 513132--513184 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
513122 TTTCTTTGCT
*
513132 TTTCTTCTTTTTGAGTGCTGTAAA
1 TTTCTTCTTTTGGAGTGCTGTAAA
*
513156 TTTCTTCTTTTGGAGTGCT-TTAA
1 TTTCTTCTTTTGGAGTGCTGTAAA
513179 TTTCTT
1 TTTCTT
513185 TTCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.58
Consensus pattern (24 bp):
TTTCTTCTTTTGGAGTGCTGTAAA
Found at i:513199 original size:11 final size:13
Alignment explanation
Indices: 513178--513209 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
513168 GAGTGCTTTA
513178 ATTTCTTTTC-TG
1 ATTTCTTTTCTTG
513190 ATTT-TTTTCTTG
1 ATTTCTTTTCTTG
513202 ATTTCTTT
1 ATTTCTTT
513210 GACTTTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 10 0.56
13 3 0.17
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.72
Consensus pattern (13 bp):
ATTTCTTTTCTTG
Found at i:513886 original size:19 final size:20
Alignment explanation
Indices: 513839--513887 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
513829 GAAACCCCTT
**
513839 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
*
513859 TGAATATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
513878 TGAAGATACA
1 TGAAAATACA
513888 AGCTCTTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:516137 original size:11 final size:11
Alignment explanation
Indices: 516121--516161 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
516111 GCTATTTTTT
516121 ACAAAAAAAAA
1 ACAAAAAAAAA
516132 ACAAAAAAAAA
1 ACAAAAAAAAA
516143 AC-AAAAAAAA
1 ACAAAAAAAAA
516153 ACAAAAAAA
1 ACAAAAAAA
516162 CAAAAAAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:516168 original size:10 final size:10
Alignment explanation
Indices: 516124--516161 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
516114 ATTTTTTACA
516124 AAAAAAAAAC
1 AAAAAAAAAC
516134 AAAAAAAAAAC
1 -AAAAAAAAAC
516145 AAAAAAAAAC
1 AAAAAAAAAC
516155 AAAAAAA
1 AAAAAAA
516162 CAAAAAAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:516185 original size:1 final size:1
Alignment explanation
Indices: 516123--516168 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
516113 TATTTTTTAC
* * * *
516123 AAAAAAAAAACAAAAAAAAAACAAAAAAAAACAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
516169 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:516721 original size:12 final size:13
Alignment explanation
Indices: 516704--516736 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
516694 AGTGCTTTAG
516704 GTTCTTTTGT-TT
1 GTTCTTTTGTATT
516716 GTTCTTTT-TATT
1 GTTCTTTTGTATT
516728 GTTCTTTTG
1 GTTCTTTTG
516737 CATTATCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 18 0.95
ACGTcount: A:0.03, C:0.09, G:0.15, T:0.73
Consensus pattern (13 bp):
GTTCTTTTGTATT
Found at i:522207 original size:18 final size:18
Alignment explanation
Indices: 522186--522224 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
522176 GCATTGTTTC
522186 AGGTTCTTCATCAAAAAT
1 AGGTTCTTCATCAAAAAT
522204 AGGTTCTTCATCAAAAAT
1 AGGTTCTTCATCAAAAAT
522222 AGG
1 AGG
522225 CTCGTCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (18 bp):
AGGTTCTTCATCAAAAAT
Found at i:523730 original size:5 final size:5
Alignment explanation
Indices: 523720--523745 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
523710 CTTCAACTTC
523720 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
523746 CTTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:538734 original size:21 final size:21
Alignment explanation
Indices: 538703--538759 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
538693 TCGAACTTCT
*
538703 TTTTCTTTTCTTTTTTTCTGAA
1 TTTTATTTTCTTTTTTT-TGAA
* **
538725 TTTT-TTTTCTTCTTTTTGTC
1 TTTTATTTTCTTTTTTTTGAA
538745 TTTTATTTTCTTTTT
1 TTTTATTTTCTTTTT
538760 GCACTCCAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.20
21 20 0.67
22 4 0.13
ACGTcount: A:0.05, C:0.12, G:0.04, T:0.79
Consensus pattern (21 bp):
TTTTATTTTCTTTTTTTTGAA
Found at i:539099 original size:22 final size:21
Alignment explanation
Indices: 539073--539116 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
539063 GGCTACGGAA
*
539073 TTGATGGTCTTGATGGATGAAG
1 TTGATGATCTTGAT-GATGAAG
*
539095 TTGATGATGTTGATGATGAAG
1 TTGATGATCTTGATGATGAAG
539116 T
1 T
539117 GGAGATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.25, C:0.02, G:0.34, T:0.39
Consensus pattern (21 bp):
TTGATGATCTTGATGATGAAG
Found at i:539517 original size:19 final size:21
Alignment explanation
Indices: 539469--539520 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
539459 GAAACCCCTT
539469 TGAAAATACATGATTTTTAAG
1 TGAAAATACATGATTTTTAAG
539490 TGAAAATACATGA-TTTTAA-
1 TGAAAATACATGATTTTTAAG
*
539509 TGAAGATACATG
1 TGAAAATACATG
539521 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAG
Found at i:540467 original size:30 final size:31
Alignment explanation
Indices: 540427--540486 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
540417 ACATACTGTC
***
540427 ATGATATCTAAATGGTATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
540458 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
540487 TAAAACTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:542777 original size:19 final size:20
Alignment explanation
Indices: 542753--542801 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
542743 TATCCTTTCT
542753 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
542772 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
542792 -TATTATTATT
1 TTATT-TTATT
542802 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:546689 original size:19 final size:20
Alignment explanation
Indices: 546665--546713 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
546655 TATCCTTTCT
546665 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
546684 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
546704 -TATTATTATT
1 TTATT-TTATT
546714 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:554481 original size:140 final size:141
Alignment explanation
Indices: 554229--554509 Score: 555
Period size: 140 Copynumber: 2.0 Consensus size: 141
554219 ACAAGTATAG
554229 TTCTATACTTGTGGCGTCATTCCTTCCATTTTGATTCCAAAATTCCTAGATTGATATCTAGTGGG
1 TTCTATACTTGTGGCGTCATTCCTTCCATTTTGATTCCAAAATTCCTAGATTGATATCTAGTGGG
554294 TTGAAGACACTATCACCACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGC-TTCATAGCATA
66 TTGAAGACACTATCACCACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGCTTTCATAGCATA
554358 ATTTCCTCTTT
131 ATTTCCTCTTT
554369 TTCTATACTTGTGGCGTCATTCCTTCCATTTTGATTCCAAAATTCCTAGATTGATATCTAGTGGG
1 TTCTATACTTGTGGCGTCATTCCTTCCATTTTGATTCCAAAATTCCTAGATTGATATCTAGTGGG
554434 TTGAAGACACTATCACCACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGCTTTCATAGCATA
66 TTGAAGACACTATCACCACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGCTTTCATAGCATA
554499 ATTTCCTCTTT
131 ATTTCCTCTTT
554510 GGCGTGTTTG
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
140 118 0.84
141 22 0.16
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (141 bp):
TTCTATACTTGTGGCGTCATTCCTTCCATTTTGATTCCAAAATTCCTAGATTGATATCTAGTGGG
TTGAAGACACTATCACCACCCCTCAAGCAAGTTTGTGAAGACCGGGATTGTGCTTTCATAGCATA
ATTTCCTCTTT
Found at i:558548 original size:19 final size:19
Alignment explanation
Indices: 558518--558554 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
558508 CTTTTCTTTA
558518 TTTTATTTCATT-CTTATT
1 TTTTATTTCATTACTTATT
558536 TTTTATATTCATTACTTAT
1 TTTTAT-TTCATTACTTAT
558555 ATTATTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 6 0.35
20 5 0.29
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATTTCATTACTTATT
Found at i:560793 original size:22 final size:21
Alignment explanation
Indices: 560767--560810 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
560757 GGCTGCGGAA
*
560767 TTGATGGTCTTGATGGATGAAG
1 TTGATGATCTTGAT-GATGAAG
*
560789 TTGATGATGTTGATGATGAAG
1 TTGATGATCTTGATGATGAAG
560810 T
1 T
560811 GGAGATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.25, C:0.02, G:0.34, T:0.39
Consensus pattern (21 bp):
TTGATGATCTTGATGATGAAG
Found at i:561211 original size:19 final size:21
Alignment explanation
Indices: 561163--561214 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
561153 GAAACCCCTT
561163 TGAAAATACATGATTTTTAAG
1 TGAAAATACATGATTTTTAAG
561184 TGAAAATACATGA-TTTTAA-
1 TGAAAATACATGATTTTTAAG
*
561203 TGAAGATACATG
1 TGAAAATACATG
561215 CTCTTGGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAG
Found at i:564440 original size:22 final size:21
Alignment explanation
Indices: 564410--564450 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
564400 CATCTCCATT
564410 TCATCATCAACACAATCAACA
1 TCATCATCAACACAATCAACA
* *
564431 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACAATCAA
564451 TTTCGCAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.44, C:0.34, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACAATCAACA
Found at i:566328 original size:123 final size:124
Alignment explanation
Indices: 566103--566347 Score: 474
Period size: 123 Copynumber: 2.0 Consensus size: 124
566093 TGACGTATAG
566103 AAAGGATTCAAGAAATTCTACCCACTTGGCATGTCGTTTGTTAAGTTTGTGTTGGCCTTTAATAT
1 AAAGGATTCAAGAAATTCTACCCACTTGGCATGTCGTTTGTTAAGTTTGTGTTGGCCTTTAATAT
566168 GCTTTAATGCCTCATGATCAGTATGGATGACAAACTCCTTGGGCCATAGATAATGTTGC
66 GCTTTAATGCCTCATGATCAGTATGGATGACAAACTCCTTGGGCCATAGATAATGTTGC
*
566227 AAAGTATTCAAGAAATTCTACCCACTTGGCATGTCGTTTGTTAAGTTTGTG-TGGCCTTTAATAT
1 AAAGGATTCAAGAAATTCTACCCACTTGGCATGTCGTTTGTTAAGTTTGTGTTGGCCTTTAATAT
566291 GCTTTAATGCCTCATGATCAGTATGGATGACAAACTCCTTGGGCCATAGATAATGTT
66 GCTTTAATGCCTCATGATCAGTATGGATGACAAACTCCTTGGGCCATAGATAATGTT
566348 AATTTAGTGA
Statistics
Matches: 120, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
123 70 0.58
124 50 0.42
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (124 bp):
AAAGGATTCAAGAAATTCTACCCACTTGGCATGTCGTTTGTTAAGTTTGTGTTGGCCTTTAATAT
GCTTTAATGCCTCATGATCAGTATGGATGACAAACTCCTTGGGCCATAGATAATGTTGC
Found at i:571502 original size:13 final size:13
Alignment explanation
Indices: 571484--571509 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
571474 TGGCCAAAGA
571484 TGAAAAGGTATGT
1 TGAAAAGGTATGT
571497 TGAAAAGGTATGT
1 TGAAAAGGTATGT
571510 GAGAGGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:576799 original size:19 final size:20
Alignment explanation
Indices: 576761--576803 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
576751 GAAACCCCTT
*
576761 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
576781 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
576800 TGAA
1 TGAA
576804 GATTAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:580256 original size:19 final size:20
Alignment explanation
Indices: 580232--580282 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
580222 CGGCCAAGAG
* *
580232 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
580251 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
580271 CATGTATTTTCA
1 CATGTATTTTCA
580283 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:581541 original size:11 final size:12
Alignment explanation
Indices: 581514--581540 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
581504 GCTGGTAAGG
581514 TTTTAATTTTTT
1 TTTTAATTTTTT
581526 TTTTAATTTTTT
1 TTTTAATTTTTT
581538 TTT
1 TTT
581541 ACTAACAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTAATTTTTT
Found at i:584486 original size:19 final size:20
Alignment explanation
Indices: 584462--584512 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
584452 CGGCCAAGAG
*
584462 CATGTATCTTCATC-AAAAT
1 CATGTATTTTCATCAAAAAT
584481 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
584501 CATGTATTTTCA
1 CATGTATTTTCA
584513 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:585549 original size:10 final size:10
Alignment explanation
Indices: 585534--585559 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
585524 TTTCATAAAC
585534 AAAACATACA
1 AAAACATACA
585544 AAAACATACA
1 AAAACATACA
585554 AAAACA
1 AAAACA
585560 ACCATTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.19, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAACATACA
Found at i:600695 original size:39 final size:38
Alignment explanation
Indices: 600613--600713 Score: 114
Period size: 39 Copynumber: 2.6 Consensus size: 38
600603 AATATAACAT
* *
600613 AAGGACCTGCGGTAAGGACTTACCCTATGCACAAATCA
1 AAGGAGCTGCGGTAAGGACTTACCCTATGCACAAAGCA
*
600651 AAGGAGTCTGCGGTAAGGACTTACCCTGA-GCACAAAGCC
1 AAGGAG-CTGCGGTAAGGACTTACCCT-ATGCACAAAGCA
* * *
600690 TAGGAGCTTGCGATAAGGTCTTAC
1 AAGGAGC-TGCGGTAAGGACTTAC
600714 AAGTAATAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
38 6 0.11
39 47 0.87
40 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.20
Consensus pattern (38 bp):
AAGGAGCTGCGGTAAGGACTTACCCTATGCACAAAGCA
Found at i:604416 original size:16 final size:16
Alignment explanation
Indices: 604389--604432 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
604379 TAGTTAAGAA
604389 TATTTTTCATATTTAAT
1 TATTTTT-ATATTTAAT
604406 TATTTTTATATTTAAT
1 TATTTTTATATTTAAT
*
604422 TATTTTAATAT
1 TATTTTTATAT
604433 AGATTGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTTTATATTTAAT
Found at i:604835 original size:13 final size:14
Alignment explanation
Indices: 604809--604840 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
604799 AGTTAACTAA
604809 ATTATTTAATTTAT
1 ATTATTTAATTTAT
604823 ATTATTTAA-TTAT
1 ATTATTTAATTTAT
604836 ATTAT
1 ATTAT
604841 ACATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTAATTTAT
Found at i:610597 original size:44 final size:46
Alignment explanation
Indices: 610477--610603 Score: 152
Period size: 47 Copynumber: 2.8 Consensus size: 46
610467 TATAAAATCT
*
610477 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
610522 CTTATCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
610569 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTT
610604 CATGGTTACC
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
44 24 0.34
45 9 0.13
46 2 0.03
47 36 0.51
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:616598 original size:133 final size:130
Alignment explanation
Indices: 616374--616616 Score: 305
Period size: 133 Copynumber: 1.8 Consensus size: 130
616364 GGTCAATTCA
* * *
616374 GAGGCTTTCGGGTTTGAATTTGGCAAAACGGTCTTCCGAATCAGACTCAGAACGTCAAAAGACAT
1 GAGGCTTTCGGGTTCGAATTTGGCAAAACGGACTTCAGAATCAGACTCAGAACGTCAAAAGACAT
* * *
616439 CAAATATGACTTTTCAAAAATTTTAACTTTTTTGTCAGTCAAAGTCAATGGGTTTGACTAACAAT
66 AAAATATGAATTTTCAAAAATCTTAACTTTTTTG---GTCAAAGTCAATGGGTTTGACTAACAAT
616504 TTG
128 TTG
* **
616507 GAGGCTTTCGGGTTCGAATTTGG-AAAATCGGACTTTAGAATTGGACTCATG-ACGTCAAAA-AT
1 GAGGCTTTCGGGTTCGAATTTGGCAAAA-CGGACTTCAGAATCAGACTCA-GAACGTCAAAAGA-
*
616569 CATAAAATAT-AATTTTCCAGAAATCTTAACTTTTTTGGTCAAAGTCAA
63 CATAAAATATGAATTTT-CAAAAATCTTAACTTTTTTGGTCAAAGTCAA
616617 CGGTCAACGG
Statistics
Matches: 96, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
130 11 0.11
132 10 0.10
133 74 0.77
134 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (130 bp):
GAGGCTTTCGGGTTCGAATTTGGCAAAACGGACTTCAGAATCAGACTCAGAACGTCAAAAGACAT
AAAATATGAATTTTCAAAAATCTTAACTTTTTTGGTCAAAGTCAATGGGTTTGACTAACAATTTG
Found at i:620887 original size:19 final size:18
Alignment explanation
Indices: 620846--620894 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
620836 ATTGTAATTC
*
620846 AATAATTTTATATTTTAA
1 AATAATTTTATATTATAA
620864 AATAATATTTGATATTAT-A
1 AATAAT-TTT-ATATTATAA
620883 AATAATTATTAT
1 AATAATT-TTAT
620895 TAATAGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 9 0.33
19 12 0.44
20 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATAATTTTATATTATAA
Found at i:621386 original size:21 final size:19
Alignment explanation
Indices: 621334--621409 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 19
621324 CCCAGGTTCC
**
621334 AAATTCGCAACGCGATTTT
1 AAATTCGCAACGCGATTCG
*
621353 AAGATTTGCAACGCGATAGTCG
1 AA-ATTCGCAACGCGAT--TCG
*
621375 AAATTCGCAACGCGATT-T
1 AAATTCGCAACGCGATTCG
*
621393 AATATTCGCAACTCGAT
1 AA-ATTCGCAACGCGAT
621410 ACTCCAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.04
19 16 0.34
20 13 0.28
21 13 0.28
22 3 0.06
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (19 bp):
AAATTCGCAACGCGATTCG
Found at i:621410 original size:40 final size:41
Alignment explanation
Indices: 621334--621410 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
621324 CCCAGGTTCC
*
621334 AAATTCGCAACGCGATTTTAAGATTTGCAACGCGATAGTCG
1 AAATTCGCAACGCGATTTTAAGATTCGCAACGCGATAGTCG
* *
621375 AAATTCGCAACGCGA-TTTAATATTCGCAACTCGATA
1 AAATTCGCAACGCGATTTTAAGATTCGCAACGCGATA
621411 CTCCAAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 18 0.55
41 15 0.45
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (41 bp):
AAATTCGCAACGCGATTTTAAGATTCGCAACGCGATAGTCG
Found at i:622369 original size:21 final size:21
Alignment explanation
Indices: 622343--622396 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
622333 AACAAATGCA
*
622343 TTGCGATTTTGGAGTATCGCG
1 TTGCGATTTTGGACTATCGCG
* *
622364 TTGCGAATTTCGACTATCGCG
1 TTGCGATTTTGGACTATCGCG
622385 TTGCGAATTTTG
1 TTGCG-ATTTTG
622397 CGAATTTGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTGGACTATCGCG
Found at i:622414 original size:29 final size:30
Alignment explanation
Indices: 622364--622423 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
622354 GAGTATCGCG
622364 TTGCGAATTTCGACTATCGCGTTGCGAATT
1 TTGCGAATTTCGACTATCGCGTTGCGAATT
*
622394 TTGCGAATTT-GACTTTCGCGTTGCGAATT
1 TTGCGAATTTCGACTATCGCGTTGCGAATT
622423 T
1 T
622424 GGAACCTGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (30 bp):
TTGCGAATTTCGACTATCGCGTTGCGAATT
Found at i:622436 original size:20 final size:20
Alignment explanation
Indices: 622413--622463 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
622403 TGACTTTCGC
622413 GTTGCGAATTTGGA-ACCTGG
1 GTTGCGAATTTGGAGACC-GG
*
622433 GTTGCGAATTT-GAGATCGG
1 GTTGCGAATTTGGAGACCGG
622452 GTTGCGAATTTG
1 GTTGCGAATTTG
622464 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.20, C:0.12, G:0.35, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGGAGACCGG
Found at i:622455 original size:19 final size:19
Alignment explanation
Indices: 622394--622463 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
622384 GTTGCGAATT
** *
622394 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGA-GATCGGG
*
622414 TTGCGAATTTG-GAACCTGGG
1 TTGCGAATTTGAG-ATC-GGG
622434 TTGCGAATTTGAGATCGGG
1 TTGCGAATTTGAGATCGGG
622453 TTGCGAATTTG
1 TTGCGAATTTG
622464 TTGGTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 15 0.36
20 26 0.62
21 1 0.02
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.36
Consensus pattern (19 bp):
TTGCGAATTTGAGATCGGG
Found at i:622552 original size:2 final size:2
Alignment explanation
Indices: 622545--622577 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
622535 TTATTTTCTC
622545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
622578 GTGACAAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:626427 original size:3 final size:3
Alignment explanation
Indices: 626410--626451 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
626400 AAAGTAACAT
*
626410 TTA TTA ATA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
626452 AAAAGAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:628541 original size:54 final size:54
Alignment explanation
Indices: 628483--628639 Score: 226
Period size: 54 Copynumber: 2.9 Consensus size: 54
628473 CGAATTGGAA
* * * **
628483 ATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGCCAAAAAGATT
1 ATTCATAAACACATTATGAATACCATGGATTGCACATTTAGTGCCAAAAAGATT
* * * *
628537 ATTCATAAACACATTACGAATACCATGGGTTGCACATTTAGTGCCGAAATGATT
1 ATTCATAAACACATTATGAATACCATGGATTGCACATTTAGTGCCAAAAAGATT
628591 ATTCATAAACACATTATGAATACCAT-GATTGCACATTTAGTGCCAAAAA
1 ATTCATAAACACATTATGAATACCATGGATTGCACATTTAGTGCCAAAAA
628640 TGCACCGTTA
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 20 0.22
54 70 0.78
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (54 bp):
ATTCATAAACACATTATGAATACCATGGATTGCACATTTAGTGCCAAAAAGATT
Found at i:632341 original size:19 final size:20
Alignment explanation
Indices: 632300--632350 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
632290 GAAACCCCTT
*
632300 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
632320 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
632339 TGAAGATACATG
1 TGAAAATACATG
632351 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:633288 original size:30 final size:31
Alignment explanation
Indices: 633248--633307 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
633238 ACATGCTGCC
**
633248 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
633279 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
633308 TAAATTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:636169 original size:23 final size:24
Alignment explanation
Indices: 636143--636188 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
636133 GAACCGTTGG
*
636143 AAATCTAAAAGATA-GATGACCAT
1 AAATCCAAAAGATATGATGACCAT
* *
636166 AAATCCAGAAGATATGTTGACCA
1 AAATCCAAAAGATATGATGACCA
636189 AATAACATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (24 bp):
AAATCCAAAAGATATGATGACCAT
Found at i:638184 original size:21 final size:21
Alignment explanation
Indices: 638155--638200 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
638145 GATGAAGTGG
* *
638155 AAGTTGATGAAGTACCTTGGT
1 AAGTAGATGAAGTACATTGGT
638176 AAGTAGATGAAGTACATTGGT
1 AAGTAGATGAAGTACATTGGT
638197 AAGT
1 AAGT
638201 TTATTGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (21 bp):
AAGTAGATGAAGTACATTGGT
Found at i:643194 original size:21 final size:21
Alignment explanation
Indices: 643160--643215 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
643150 TGAAGTGGAA
643160 GTAGATGAAAGTACCTT-GTTAT
1 GTAGATG-AAGTACCTTAG-TAT
643182 GTAGATGAAGTACCTTAGTAT
1 GTAGATGAAGTACCTTAGTAT
* *
643203 GTAGCTGCAGTAC
1 GTAGATGAAGTAC
643216 ATTGGTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 23 0.74
22 8 0.26
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.32
Consensus pattern (21 bp):
GTAGATGAAGTACCTTAGTAT
Found at i:645083 original size:238 final size:238
Alignment explanation
Indices: 644665--645140 Score: 936
Period size: 238 Copynumber: 2.0 Consensus size: 238
644655 TCCAAGATTA
644665 TGGAGTGAAGGAGAGACAAAAATGTTCCAGCTCAACTCCGAAGCCATCTATATCACATTTTGTGC
1 TGGAGTGAAGGAGAGACAAAAATGTTCCAGCTCAACTCCGAAGCCATCTATATCACATTTTGTGC
644730 TCTTGGACCAGATGAATACGGAAGAGTTTCATCTTGTACAACCGCCAAATAAGGATAAACTTCAA
66 TCTTGGACCAGATGAATACGGAAGAGTTTCATCTTGTACAACCGCCAAATAAGGATAAACTTCAA
644795 GTCACTCATGAAGGTACCGAAGAGGTAAAGAAATCTAAAATTAGTATTCTAAACGCATAGCTATG
131 GTCACTCATGAAGGTACCGAAGAGGTAAAGAAATCTAAAATTAGTATTCT-AACGCATAGCTATG
644860 AAAATTTCAGGAT-AAACCAAATGAAGATATCAAAGCTATGACG
195 AAAATTTCAGGATGAAACCAAATGAAGATATCAAAGCTATGACG
644903 TGGAGTGAAGGAGAGACAAAAATGTTCCAGCTCAACTCCGAAGCCATCTATATCACATTTTGTGC
1 TGGAGTGAAGGAGAGACAAAAATGTTCCAGCTCAACTCCGAAGCCATCTATATCACATTTTGTGC
644968 TCTTGGACCAGATGAATACGGAAGAGTTTCATCTTGTACAACCGCCAAATAAGGATAAACTTCAA
66 TCTTGGACCAGATGAATACGGAAGAGTTTCATCTTGTACAACCGCCAAATAAGGATAAACTTCAA
645033 GTCACTCATGAAGGTACCGAAGAGGTAAAGAAATCTAAAATTAGTATTCTAACGCATAGCTATGA
131 GTCACTCATGAAGGTACCGAAGAGGTAAAGAAATCTAAAATTAGTATTCTAACGCATAGCTATGA
645098 AAATTTCAGGATGAAACCAAATGAAGATATCAAAGCTATGACG
196 AAATTTCAGGATGAAACCAAATGAAGATATCAAAGCTATGACG
645141 GATAGATTCT
Statistics
Matches: 237, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
237 27 0.11
238 210 0.89
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (238 bp):
TGGAGTGAAGGAGAGACAAAAATGTTCCAGCTCAACTCCGAAGCCATCTATATCACATTTTGTGC
TCTTGGACCAGATGAATACGGAAGAGTTTCATCTTGTACAACCGCCAAATAAGGATAAACTTCAA
GTCACTCATGAAGGTACCGAAGAGGTAAAGAAATCTAAAATTAGTATTCTAACGCATAGCTATGA
AAATTTCAGGATGAAACCAAATGAAGATATCAAAGCTATGACG
Found at i:649614 original size:20 final size:20
Alignment explanation
Indices: 649561--649615 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
649551 GGTGCATAGA
649561 GAATCGATACCCCCATGAGG
1 GAATCGATACCCCCATGAGG
* * *
649581 GAACCGACT-CCCCCCTTAGGG
1 GAATCGA-TACCCCCATGA-GG
649602 GAATCGATACCCCC
1 GAATCGATACCCCC
649616 CTGGGGTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.25, C:0.38, G:0.22, T:0.15
Consensus pattern (20 bp):
GAATCGATACCCCCATGAGG
Found at i:651620 original size:17 final size:17
Alignment explanation
Indices: 651587--651620 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
651577 TTGAATATTT
* *
651587 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
651604 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
651621 AATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:654425 original size:14 final size:13
Alignment explanation
Indices: 654403--654459 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
654393 ATTTTTTTAA
654403 TTTTT-TTTTATT
1 TTTTTCTTTTATT
* * *
654415 TTTTTGGTTTTCTC
1 TTTTT-CTTTTATT
*
654429 TTTTTCTTTTTATG
1 TTTTTC-TTTTATT
654443 TTTTTCTTTTATT
1 TTTTTCTTTTATT
654456 TTTT
1 TTTT
654460 ATAAAAATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
12 5 0.14
13 10 0.28
14 21 0.58
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.82
Consensus pattern (13 bp):
TTTTTCTTTTATT
Found at i:654432 original size:22 final size:20
Alignment explanation
Indices: 654393--654459 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
654383 TGATCTCTGG
**
654393 ATTTTTTTAATTTT-TTTTT
1 ATTTTTTTGTTTTTCTTTTT
654412 ATTTTTTTGGTTTTCTCTTTTT
1 ATTTTTTT-GTTTT-TCTTTTT
* *
654434 CTTTTTATGTTTTTC-TTTT
1 ATTTTTTTGTTTTTCTTTTT
654453 ATTTTTT
1 ATTTTTT
654460 ATAAAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 17 0.44
20 5 0.13
21 6 0.15
22 11 0.28
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (20 bp):
ATTTTTTTGTTTTTCTTTTT
Found at i:654438 original size:20 final size:20
Alignment explanation
Indices: 654414--654452 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
654404 TTTTTTTTAT
*
654414 TTTTTTGGTTTTCTCTTTTTC
1 TTTTTAGGTTTT-TCTTTTTC
*
654435 TTTTTATGTTTTTCTTTT
1 TTTTTAGGTTTTTCTTTT
654453 ATTTTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.03, C:0.10, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTTAGGTTTTTCTTTTTC
Found at i:654458 original size:20 final size:21
Alignment explanation
Indices: 654403--654461 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
654393 ATTTTTTTAA
654403 TTTTT-TTTTATTTTTT-TGG
1 TTTTTCTTTTATTTTTTATGG
654422 TTTTCTCTTTT-TCTTTTTAT-G
1 TTTT-TCTTTTAT-TTTTTATGG
654443 TTTTTCTTTTATTTTTTAT
1 TTTTTCTTTTATTTTTTAT
654462 AAAAATGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
19 4 0.11
20 15 0.43
21 15 0.43
22 1 0.03
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.81
Consensus pattern (21 bp):
TTTTTCTTTTATTTTTTATGG
Found at i:656057 original size:31 final size:31
Alignment explanation
Indices: 655990--656057 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
655980 TAGTCCTAGA
*
655990 TATTATTGAATTATATTTTTAATATAGAAAT
1 TATTTTTGAATTATATTTTTAATATAGAAAT
* * * *
656021 GATTTTTGAACTTGTATTTTTATTA-ATAAAT
1 TATTTTTGAA-TTATATTTTTAATATAGAAAT
656052 TATTTT
1 TATTTT
656058 ATGATTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.35, C:0.01, G:0.07, T:0.56
Consensus pattern (31 bp):
TATTTTTGAATTATATTTTTAATATAGAAAT
Found at i:657795 original size:20 final size:20
Alignment explanation
Indices: 657751--657962 Score: 212
Period size: 20 Copynumber: 10.4 Consensus size: 20
657741 GATTCTGACT
* *
657751 ATCGCAACGAGTATTCGTAAA
1 ATCGCAACGCGTATACGT-AA
*
657772 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
*
657792 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATACGT-AA
* *
657813 ATCGCAACGCATATCCGTAA
1 ATCGCAACGCGTATACGTAA
* *
657833 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATACGTAA
657853 ATCGCAACGCGTAT-CTGTAA
1 ATCGCAACGCGTATAC-GTAA
* * *
657873 ATCGCAATGAGAATACGTAA
1 ATCGCAACGCGTATACGTAA
* *
657893 ATCGCAATGCGTATTCGTAA
1 ATCGCAACGCGTATACGTAA
* *
657913 ATCGCAATGCGAATACGTAAA
1 ATCGCAACGCGTATACGT-AA
* *
657934 ATCACAACGCGTATCCGTAA
1 ATCGCAACGCGTATACGTAA
657954 ATCGCAACG
1 ATCGCAACG
657963 TGATTTTTAA
Statistics
Matches: 160, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
19 1 0.01
20 109 0.68
21 50 0.31
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATACGTAA
Found at i:657873 original size:40 final size:41
Alignment explanation
Indices: 657751--657962 Score: 311
Period size: 41 Copynumber: 5.2 Consensus size: 41
657741 GATTCTGACT
* *
657751 ATCGCAACGAGTATTCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
657792 ATCGCAACGACAATACGTAAAATCGCAACGCATATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
657833 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
657873 ATCGCAATGAGAATACGT-AAATCGCAATGCGTATTCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
657913 ATCGCAATGCGAATACGTAAAATCACAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
657954 ATCGCAACG
1 ATCGCAACG
657963 TGATTTTTAA
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 73 0.47
41 81 0.53
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:658551 original size:20 final size:20
Alignment explanation
Indices: 658526--658617 Score: 123
Period size: 20 Copynumber: 4.5 Consensus size: 20
658516 TTCTAAACTT
658526 AAAATCGCAACATGAAAATG
1 AAAATCGCAACATGAAAATG
658546 AAAATCGCAACATGAAAATG
1 AAAATCGCAACATGAAAATG
* *
658566 AAAATCGCAACACGAAATTG
1 AAAATCGCAACATGAAAATG
**
658586 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ATGA-AAATG
658607 AAAATCGCAAC
1 AAAATCGCAAC
658618 GAGATAATCG
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
20 49 0.78
21 14 0.22
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACATGAAAATG
Found at i:658685 original size:19 final size:19
Alignment explanation
Indices: 658663--658727 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
658653 GAAACCAAAA
*
658663 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
658682 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
658696 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
658715 TCGCGTTGCGATT
1 TCGCGTTGCGATT
658728 CTCTCATTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:658710 original size:33 final size:33
Alignment explanation
Indices: 658666--658758 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
658656 ACCAAAATCG
658666 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
658699 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
**
658732 CATTGCGATAGTCATTTCCGCGTTGCG
1 CATTGCGATTTTCATTT-CGCGTTGCG
658759 TTTTTCATTC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 46 0.84
34 9 0.16
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.42
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:658766 original size:20 final size:20
Alignment explanation
Indices: 658743--658789 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
658733 ATTGCGATAG
* *
658743 TCATTTCCGCGTTGCGTTTT
1 TCATTTCCGCGTTACGATTT
* *
658763 TCATTCCCTCGTTACGATTT
1 TCATTTCCGCGTTACGATTT
658783 TCATTTC
1 TCATTTC
658790 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.28, G:0.13, T:0.49
Consensus pattern (20 bp):
TCATTTCCGCGTTACGATTT
Found at i:660828 original size:21 final size:21
Alignment explanation
Indices: 660804--660870 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
660794 TCATTCCTTG
660804 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
660825 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
660846 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
660867 AGAG
1 AGAG
660871 CCGATTCACA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Done.