Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009587.1 Hibiscus syriacus cultivar Beakdansim tig00116965_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: 6483253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 29
Found at i:301494 original size:34 final size:32
Alignment explanation
Indices: 301447--301559 Score: 99
Period size: 34 Copynumber: 3.5 Consensus size: 32
301437 TTTTTTCCTT
*
301447 TTTTTCCTTTTTTTCTCATTTTTTCTCATTTTCC
1 TTTTT-CTCTTTTTCTC-TTTTTTCTCATTTTCC
** *
301481 TTTTTCATCTTTTTCATCTTTTTTCTTTTTTTCT
1 TTTTTC-TCTTTTTC-TCTTTTTTCTCATTTTCC
*
301515 TTTTTCTCATTTTTCT-TTTTTTCATC-TTTT-T
1 TTTTTCTC-TTTTTCTCTTTTTTC-TCATTTTCC
301546 TTTTTCT-TTTTTCT
1 TTTTTCTCTTTTTCT
301560 TTCTTTGCTG
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
29 7 0.10
31 8 0.11
32 11 0.16
33 5 0.07
34 37 0.53
35 2 0.03
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (32 bp):
TTTTTCTCTTTTTCTCTTTTTTCTCATTTTCC
Found at i:301527 original size:9 final size:8
Alignment explanation
Indices: 301456--301545 Score: 76
Period size: 9 Copynumber: 10.6 Consensus size: 8
301446 TTTTTTCCTT
301456 TTTTTCTC
1 TTTTTCTC
301464 ATTTTTTCTC
1 --TTTTTCTC
*
301474 ATTTTC-C
1 TTTTTCTC
301481 TTTTTCATC
1 TTTTTC-TC
301490 TTTTTCATC
1 TTTTTC-TC
301499 TTTTT-TC
1 TTTTTCTC
*
301506 TTTTTTTC
1 TTTTTCTC
301514 TTTTTTCTC
1 -TTTTTCTC
*
301523 ATTTTTCTT
1 -TTTTTCTC
301532 TTTTTCATC
1 TTTTTC-TC
301541 TTTTT
1 TTTTT
301546 TTTTTCTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
7 13 0.19
8 13 0.19
9 35 0.51
10 8 0.12
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCTC
Found at i:301536 original size:42 final size:41
Alignment explanation
Indices: 301438--301563 Score: 125
Period size: 42 Copynumber: 3.0 Consensus size: 41
301428 TTGGTTCAAT
* *
301438 TTTTTCCTTTTTTTCCT-TTTTTTCTCATTTTTTCTCATTTTC-C
1 TTTTT-CTTTTTTTCATCTTTTTTCT--TTTTTTCT-TTTTTCTC
*
301481 TTTTTCATCTTTTTCATCTTTTTTCTTTTTTTCTTTTTTCTC
1 TTTTTC-TTTTTTTCATCTTTTTTCTTTTTTTCTTTTTTCTC
301523 ATTTTTCTTTTTTTCATCTTTTTT-TTTTCTTT-TTTCTTTCT
1 -TTTTTCTTTTTTTCATCTTTTTTCTTTT-TTTCTTT-TTTCT
301564 TTGCTGGATG
Statistics
Matches: 73, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
41 12 0.16
42 34 0.47
43 19 0.26
44 8 0.11
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (41 bp):
TTTTTCTTTTTTTCATCTTTTTTCTTTTTTTCTTTTTTCTC
Found at i:301546 original size:27 final size:25
Alignment explanation
Indices: 301455--301546 Score: 100
Period size: 25 Copynumber: 3.6 Consensus size: 25
301445 TTTTTTTCCT
301455 TTTTTTCTCATTTTTTCTCA-TTTTC
1 TTTTTTCTC-TTTTTTCTCATTTTTC
* *
301480 CTTTTTCATC-TTTTTCATCTTTTTTC
1 TTTTTTC-TCTTTTTTC-TCATTTTTC
301506 TTTTTT-TCTTTTTTCTCATTTTTC
1 TTTTTTCTCTTTTTTCTCATTTTTC
301530 TTTTTTTCATCTTTTTT
1 -TTTTTTC-TCTTTTTT
301547 TTTTCTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
24 16 0.29
25 20 0.36
26 12 0.21
27 8 0.14
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTTTCTCTTTTTTCTCATTTTTC
Found at i:301548 original size:15 final size:14
Alignment explanation
Indices: 301490--301557 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 14
301480 CTTTTTCATC
301490 TTTTTCATCTTTTTT
1 TTTTTCAT-TTTTTT
* *
301505 CTTTT--TTTCTTT
1 TTTTTCATTTTTTT
*
301517 TTTCTCATTTTTCTT
1 TTTTTCATTTTT-TT
*
301532 TTTTTCATCTTTTT
1 TTTTTCATTTTTTT
301546 TTTTTC-TTTTTT
1 TTTTTCATTTTTT
301558 CTTTCTTTGC
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
12 8 0.19
13 6 0.14
14 12 0.29
15 16 0.38
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCATTTTTTT
Found at i:301550 original size:16 final size:17
Alignment explanation
Indices: 301446--301545 Score: 93
Period size: 17 Copynumber: 5.8 Consensus size: 17
301436 ATTTTTTCCT
*
301446 TTTTTTCCTTTTTTTCTC
1 TTTTTT-CTCTTTTTCTC
*
301464 ATTTTTTCTCATTTTC-C
1 -TTTTTTCTCTTTTTCTC
301481 -TTTTTCATCTTTTTCATC
1 TTTTTTC-TCTTTTTC-TC
301499 TTTTTTCT-TTTTT-TC
1 TTTTTTCTCTTTTTCTC
301514 TTTTTTCTCATTTTTCT-
1 TTTTTTCTC-TTTTTCTC
301531 TTTTTTCATCTTTTT
1 TTTTTTC-TCTTTTT
301546 TTTTTCTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
15 16 0.23
16 7 0.10
17 23 0.33
18 12 0.17
19 12 0.17
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTCTCTTTTTCTC
Found at i:301555 original size:9 final size:9
Alignment explanation
Indices: 301437--301561 Score: 64
Period size: 9 Copynumber: 14.1 Consensus size: 9
301427 CTTGGTTCAA
*
301437 TTTTTTCCT
1 TTTTTTCTT
*
301446 TTTTTTCCT
1 TTTTTTCTT
*
301455 TTTTTTCTCA
1 TTTTTTCT-T
*
301465 TTTTTTCTC
1 TTTTTTCTT
* *
301474 ATTTTCCTT
1 TTTTTTCTT
**
301483 TTTCATCTT
1 TTTTTTCTT
**
301492 TTTCATC--
1 TTTTTTCTT
301499 TTTTTTC-T
1 TTTTTTCTT
301507 TTTTTTC--
1 TTTTTTCTT
*
301514 TTTTTTCTC
1 TTTTTTCTT
*
301523 ATTTTTCTT
1 TTTTTTCTT
301532 TTTTTCATCTT
1 TTTTT--TCTT
301543 TTTTTT-TT
1 TTTTTTCTT
301551 CTTTTTTCTT
1 -TTTTTTCTT
301561 T
1 T
301562 CTTTGCTGGA
Statistics
Matches: 93, Mismatches: 15, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
7 12 0.13
8 9 0.10
9 53 0.57
10 10 0.11
11 9 0.10
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:305236 original size:14 final size:14
Alignment explanation
Indices: 305199--305226 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
305189 CAACAAATGC
305199 AAAATGAAAATACA
1 AAAATGAAAATACA
305213 AAAATGAAAATACA
1 AAAATGAAAATACA
305227 TGTATGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAATGAAAATACA
Found at i:306739 original size:19 final size:17
Alignment explanation
Indices: 306712--306755 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
306702 ATACCTGAAA
306712 AAAATATTAATAAAATAAT
1 AAAA-ATTAAT-AAATAAT
*
306731 ATAAAATTAATAAGTAAT
1 A-AAAATTAATAAATAAT
306749 AAAAATT
1 AAAAATT
306756 TGAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 6 0.26
18 7 0.30
19 7 0.30
20 3 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAAATTAATAAATAAT
Found at i:307549 original size:17 final size:17
Alignment explanation
Indices: 307529--307562 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
307519 TATATGTGAC
307529 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
307546 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
307563 CAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:307587 original size:16 final size:16
Alignment explanation
Indices: 307568--307600 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
307558 AATAACAAAT
307568 TAATA-TTATAAATAAA
1 TAATATTTA-AAATAAA
307584 TAATATTTAAAATAAA
1 TAATATTTAAAATAAA
307600 T
1 T
307601 TTAAAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATATTTAAAATAAA
Found at i:308884 original size:22 final size:22
Alignment explanation
Indices: 308856--308921 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
308846 ATTATTTATT
* * *
308856 TAATAATAATACTATAATATAA
1 TAATAATAATACTAAAACAAAA
* *
308878 TAATAATATTATTAAAACAAAA
1 TAATAATAATACTAAAACAAAA
*
308900 TAATAATAATAAATAAAACAAA
1 TAATAATAAT-ACTAAAACAAA
308922 TGAAATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 26 0.72
23 10 0.28
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAATAATACTAAAACAAAA
Found at i:308922 original size:22 final size:24
Alignment explanation
Indices: 308874--308921 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
308864 ATACTATAAT
*
308874 ATAATAATAATATTATTAAAACAAA
1 ATAATAATAATA-TAATAAAACAAA
308899 ATAATAATAATA-AATAAAACAAA
1 ATAATAATAATATAATAAAACAAA
308922 TGAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.45
25 12 0.55
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
ATAATAATAATATAATAAAACAAA
Found at i:310031 original size:32 final size:32
Alignment explanation
Indices: 309994--310082 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
309984 AGGAACAATG
* *
309994 GGGGCATCTTTGAAGATTCAACGTCAAATGTT
1 GGGGCATCTTTGAAGATTCAACATCAAATATT
* *
310026 GGGGCATTTTTGAAGATTCAACATCGAATATT
1 GGGGCATCTTTGAAGATTCAACATCAAATATT
* **
310058 GGGGTATCTTTGGGGATTCAACATC
1 GGGGCATCTTTGAAGATTCAACATC
310083 CTGATGTGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.33
Consensus pattern (32 bp):
GGGGCATCTTTGAAGATTCAACATCAAATATT
Found at i:310338 original size:40 final size:36
Alignment explanation
Indices: 310260--310334 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
310250 GCTTTAGGGT
310260 CAATTTCAACTTCACAAGGAAGGATATTGGACTCAA
1 CAATTTCAACTTCACAAGGAAGGATATTGGACTCAA
310296 CAATTTCAACTTCAC-AGCGAAGGATATTGGACTCAA
1 CAATTTCAACTTCACAAG-GAAGGATATTGGACTCAA
310332 CAA
1 CAA
310335 ACAACTTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 2 0.05
36 36 0.95
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (36 bp):
CAATTTCAACTTCACAAGGAAGGATATTGGACTCAA
Found at i:310375 original size:64 final size:65
Alignment explanation
Indices: 310296--310460 Score: 287
Period size: 64 Copynumber: 2.6 Consensus size: 65
310286 TTGGACTCAA
*
310296 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCC-AGTTTCATTTAGAGT
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAAGTTTCATTCAGAGT
* *
310360 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGACAAACAACTTTCCAAGTTTCGTTCAGAGT
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAAGTTTCATTCAGAGT
*
310425 CAATTTCAACTTCACAGCGAAGGATATTGAACTCAA
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
310461 AGCGAAACAA
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 48 0.51
65 47 0.49
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (65 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAAGTTTCATTCAGAGT
Found at i:310576 original size:65 final size:65
Alignment explanation
Indices: 310472--310596 Score: 180
Period size: 65 Copynumber: 1.9 Consensus size: 65
310462 GCGAAACAAT
* * *
310472 TTACTCGAGATTGGATTTTCACTTCACAACGAATGATATCCAACTCAAAGCCAATTTGGTGAAAC
1 TTACTCAAGATTGGATTTTCACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
** *
310537 TTACTCAAGATTGGA-TTTCAACTTCATGACGAAGGATATCCATCTCAAAACCAATTTGGT
1 TTACTCAAGATTGGATTTTC-ACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGT
310597 AAGACAATTC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 4 0.08
65 49 0.92
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (65 bp):
TTACTCAAGATTGGATTTTCACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
Found at i:310770 original size:121 final size:120
Alignment explanation
Indices: 310606--310949 Score: 445
Period size: 121 Copynumber: 2.8 Consensus size: 120
310596 TAAGACAATT
* * * * * * *
310606 CTTGGATTTCAACTTCACAACAAAGCATATCCGAGTCAAGGCTCAACTTCACAATGAAGGGGACA
1 CTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAG-CA
* *
310671 TCCACAATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCATCAATGAAACC
65 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGAAACC
* * *
310727 CTTGGATTTCAACTTCACGATGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAATGAGCTA
1 CTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGC-A
* * * * * *
310792 TCCATGATTTTAACTTCACGGCTAAGGATATCGTACCCACAAGCAGCAATGCAACC
65 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGAAACC
* * * *
310848 ATTGGATTTCAACTTCACAACGATGGATATCCAATTCAAAGCTCAACTTCATAACGAATGAGCCA
1 CTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAG-CA
* *
310913 TCCACGATTTCAAGTTCACGACGAAGGATATCATGCC
65 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCC
310950 TATCAGATTG
Statistics
Matches: 189, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
120 1 0.01
121 187 0.99
122 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (120 bp):
CTTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGAGCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGAAACC
Found at i:311247 original size:84 final size:84
Alignment explanation
Indices: 311003--311449 Score: 478
Period size: 84 Copynumber: 5.4 Consensus size: 84
310993 CCCTAGCCAA
* * * * * * * * *
311003 TGCAGCATAACTCGAGGTGAGAAGAGTTATCTGTCAACAAATGACCTTCGAGTTTGATTACACTT
1 TGCAGCATAGCTCAAGGCGATAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTC
311068 AGCTCAAAGGCACATCATT
66 AGCTCAAAGGCACATCATT
* * * * * * *
311087 TGCAGTATAGCTCAAGG-GAAAAAGGGCTATTTG---TC-AAATACCTTCTAGTTCGATTACACT
1 TGCAGCATAGCTCAAGGCG-ATAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACT
311147 CAGCTCAAAGGCACATCATT
65 CAGCTCAAAGGCACATCATT
* * *
311167 TTCAGCATAGCTCAAGACGATAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTC
1 TGCAGCATAGCTCAAGGCGATAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTC
*
311232 AGCT-AGATGGCACATCATT
66 AGCTCA-AAGGCACATCATT
* * **
311251 TGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACAA
1 TGCAGCATAGCTCAAGGCGATAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTC
311316 AGCTCAAAGGCACATCATT
66 AGCTCAAAGGCACATCATT
* * * * * *
311335 TGCAGCATAGCTAAAGGC-ATGAAAGGTTA-CTTCCAACAAAAGACCTTTGAGTTTGATTACATT
1 TGCAGCATAGCTCAAGGCGAT-AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACT
*
311398 CAGCTCAAAGGCATATCAAATT
65 CAGCTCAAAGGCACATC--ATT
* * * *
311420 TACAGCATAACTCAAGGCAAGAAGGGTTAT
1 TGCAGCATAGCTCAAGGCGATAAGGGTTAT
311450 TTGTCAATGA
Statistics
Matches: 302, Mismatches: 48, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
80 64 0.21
81 2 0.01
83 48 0.16
84 161 0.53
85 26 0.09
86 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (84 bp):
TGCAGCATAGCTCAAGGCGATAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTC
AGCTCAAAGGCACATCATT
Found at i:311471 original size:168 final size:165
Alignment explanation
Indices: 311028--311477 Score: 523
Period size: 164 Copynumber: 2.7 Consensus size: 165
311018 GGTGAGAAGA
** *
311028 GTTATCTGTCAACAAATGACCTTCGAGTTTGATTACACTT-AGCTCAAAGGCACATCATTTGCAG
1 GTTATCTACCAACAAAAGACCTTCGAGTTTGATTACA-TTCAGCTCAAAGGCACATCATTTGCAG
* * * * * **
311092 TATAGCTCAAGGGAAAAAGGGCTATTTGTC-AAATACCTTCTAGTTCGATTACACTCAGCTCAAA
65 CATAGCTCAAGGCAAGAAGGGCTATTTGTCAAAAAACCTTCGAGTTCGATTACACAAAGCTCAAA
* * *
311156 GGCACATCATTTTCAGCATAGCTCAAGACGATAAGG
130 GGCACATCATTTGCAGCATAGCTAAAGACGATAAAG
* * *
311192 GTTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAGCT-AGATGGCACATCATTTGCAG
1 GTTATCTACCAACAAAAGACCTTCGAGTTTGATTACATTCAGCTCA-AAGGCACATCATTTGCAG
* * *
311256 CATAGCTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACAAAGCTC
65 CATAGCTCAAGGCAAGAAGGGCTATTTGTC-A-AAAA-ACCTTCGAGTTCGATTACACAAAGCTC
*
311321 AAAGGCACATCATTTGCAGCATAGCTAAAGGC-ATGAAAG
127 AAAGGCACATCATTTGCAGCATAGCTAAAGACGAT-AAAG
* * * *
311360 GTTA-CTTCCAACAAAAGACCTTTGAGTTTGATTACATTCAGCTCAAAGGCATATCAAATTTACA
1 GTTATCTACCAACAAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCACATC--ATTTGCA
* * * *
311424 GCATAACTCAAGGCAAGAAGGGTTATTTGTCAATGAAAACTTTCGAGTACGATT
64 GCATAGCTCAAGGCAAGAAGGGCTATTTGTCAA--AAAACCTTCGAGTTCGATT
311478 CCATTCAACT
Statistics
Matches: 240, Mismatches: 34, Indels: 20
0.82 0.12 0.07
Matches are distributed among these distances:
163 2 0.01
164 78 0.32
167 49 0.20
168 76 0.32
169 35 0.15
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (165 bp):
GTTATCTACCAACAAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCACATCATTTGCAGC
ATAGCTCAAGGCAAGAAGGGCTATTTGTCAAAAAACCTTCGAGTTCGATTACACAAAGCTCAAAG
GCACATCATTTGCAGCATAGCTAAAGACGATAAAG
Found at i:312771 original size:32 final size:33
Alignment explanation
Indices: 312725--312805 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
312715 TAGGGGCATC
* *
312725 TTTGAAGATTCAACATCAAATGTTGCGGTAT-T
1 TTTGGAGATTCAACATCAAATATTGCGGTATCT
* *
312757 TTTGGAGATTCAACATCGAATATTGGGGTATCT
1 TTTGGAGATTCAACATCAAATATTGCGGTATCT
*
312790 TTAGG-GATTCAACATC
1 TTTGGAGATTCAACATC
312806 CAGATGTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 38 0.88
33 5 0.12
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (33 bp):
TTTGGAGATTCAACATCAAATATTGCGGTATCT
Found at i:313202 original size:65 final size:64
Alignment explanation
Indices: 312975--313204 Score: 345
Period size: 64 Copynumber: 3.6 Consensus size: 64
312965 TTTTTACAGT
* * * *
312975 TTTAGGGTCAATTTCAACTTCACAACGAATGATATTGGACTTAAGAAACAACTTTCCAGTTTCA
1 TTTAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCAACAAACAACTTTCCAGTTTCA
*
313039 TTTAGAGTCAATTTCAACTTCATAGCGAA-GAATATTGGACTCAACAAACAACTTTCCAGTTTCA
1 TTTAGAGTCAATTTCAACTTCACAGCGAATG-ATATTGGACTCAACAAACAACTTTCCAGTTTCA
* * *
313103 TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGACAAACAATTTTCCAAGTTTCA
1 TTTAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCAACAAACAACTTTCC-AGTTTCA
* *
313168 TTCAGAGTCAATTTCAACTTCACATCGAATGATATTG
1 TTTAGAGTCAATTTCAACTTCACAGCGAATGATATTG
313205 AACTAAAAGC
Statistics
Matches: 152, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
63 1 0.01
64 109 0.72
65 42 0.28
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (64 bp):
TTTAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCAACAAACAACTTTCCAGTTTCA
Found at i:313508 original size:121 final size:120
Alignment explanation
Indices: 313358--313700 Score: 461
Period size: 121 Copynumber: 2.8 Consensus size: 120
313348 AAGACAATTC
* * * * * * *
313358 TTGGATTTCAACTTCACAACAAAAGATATCCGAGTCAAGGATTAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGG-TTAACTTCACAACGAATGAGCCAT
* *
313423 CCACGATTTCAACTTCTCGATGAAGGATATCGTGCCCACAAGCAGCAATGCAACCC
65 CCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACAAGCAGCAATGCAACCA
* * * * * * *
313479 TTGGGTTTCAACTTCATGATGAAGGATATCTAATTCAAGGTTTAACTTCATAATGAATGAGCTAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGG-TTAACTTCACAACGAATGAGCCAT
**
313544 CCACGATTTCAACTTCACGGCGAAGGATATCGTGCCCACAAGCAGCAATGCAACCA
65 CCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACAAGCAGCAATGCAACCA
*
313600 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAATGTTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGTT-AACTTCACAACGAATGAGCCAT
** *
313665 ATACGATTTCAAGTTCACGATGAAGGATATCGTGCC
65 CCACGATTTCAACTTCACGATGAAGGATATCGTGCC
313701 TATCGGATTG
Statistics
Matches: 189, Mismatches: 32, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
120 2 0.01
121 187 0.99
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (120 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGTTAACTTCACAACGAATGAGCCATC
CACGATTTCAACTTCACGATGAAGGATATCGTGCCCACAAGCAGCAATGCAACCA
Found at i:313990 original size:84 final size:84
Alignment explanation
Indices: 313755--314198 Score: 506
Period size: 84 Copynumber: 5.3 Consensus size: 84
313745 CCCAGCCCAG
* *
313755 TGCAGCATAACTCAAGGCGAGAAGGGTTATCTGT-CAACAAAAGACCTTCGAGTTCGATTACACT
1 TGCAGCATAGCTCAAGGCGAGAAGGGCTATCT-TCCAACAAAAGACCTTCGAGTTCGATTACACT
* *
313819 CAGCTCAAAAGCGCATCATT
65 CAGCTCAAAGGCACATCATT
* *
313839 TGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGT----C-AAAGACCTTCGAGATCGATTACACT
1 TGCAGCATAGCTCAAGGCGAGAAGGGCTATCT-TCCAACAAAAGACCTTCGAGTTCGATTACACT
**
313899 CAGCTCAAAGGTGCATCATT
65 CAGCTCAAAGGCACATCATT
* * *
313919 TGCAGCATAGCTCAAGACGAGAATGGCTATCTTCCAAGAAAAGACCTTCGAGTTCGATTACACTC
1 TGCAGCATAGCTCAAGGCGAGAAGGGCTATCTTCCAACAAAAGACCTTCGAGTTCGATTACACTC
313984 AGCTCAAAGGCACATCATT
66 AGCTCAAAGGCACATCATT
* * * * *
314003 TGCAGCATAGCTCAAGGCGAGAAGGGCTAACTGCCAATAAAAAACCTTCGAGTTCGATTACACAC
1 TGCAGCATAGCTCAAGGCGAGAAGGGCTATCTTCCAACAAAAGACCTTCGAGTTCGATTACACTC
* *
314068 ATCTCAAAGTCACATCATT
66 AGCTCAAAGGCACATCATT
* * * * * * *
314087 TACAGCATAGCTGAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTC-AATACATT
1 TGCAGCATAGCTCAAGGCGAGAAGGGCTATCTTCCAACAAAAGACCTTCGAG-TTCGATTACACT
* * *
314151 CATCTTAAAGGCATATCAAATT
65 CAGCTCAAAGGCACATC--ATT
** * *
314173 TATAGCATAACTCAAGACGAGAAGGG
1 TGCAGCATAGCTCAAGGCGAGAAGGG
314199 TTATTTGTCA
Statistics
Matches: 312, Mismatches: 40, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
79 1 0.00
80 71 0.23
81 1 0.00
84 212 0.68
85 3 0.01
86 24 0.08
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (84 bp):
TGCAGCATAGCTCAAGGCGAGAAGGGCTATCTTCCAACAAAAGACCTTCGAGTTCGATTACACTC
AGCTCAAAGGCACATCATT
Found at i:314028 original size:164 final size:164
Alignment explanation
Indices: 313755--314208 Score: 536
Period size: 164 Copynumber: 2.7 Consensus size: 164
313745 CCCAGCCCAG
*
313755 TGCAGCATAACTCAAGGCGAGAAGGGTTATCTGT-CAACAAAAGACCTTCGAGTTCGATTACACT
1 TGCAGCATAGCTCAAGGCGAGAAGGGTTATCT-TCCAACAAAAGACCTTCGAGTTCGATTACACT
* * * *
313819 CAGCTCAAAAGCGCATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAAAGACCTTC
65 CAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAAAACCTTC
* *
313884 GAGATCGATTACACTCAGCTCAAAGGT-GCATCATT
130 GAGATCGATTACACACAGCTCAAA-GTCACATCATT
* * * *
313919 TGCAGCATAGCTCAAGACGAGAATGGCTATCTTCCAAGAAAAGACCTTCGAGTTCGATTACACTC
1 TGCAGCATAGCTCAAGGCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGATTACACTC
* *
313984 AGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTAACTGCCAATAAAAAACC
66 AGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTG----TCAAAAACC
* *
314049 TTCGAGTTCGATTACACACATCTCAAAGTCACATCATT
127 TTCGAGATCGATTACACACAGCTCAAAGTCACATCATT
* * * * * *
314087 TACAGCATAGCTGAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTC-AATACATT
1 TGCAGCATAGCTCAAGGCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAG-TTCGATTACACT
* * * ** * * * *
314151 CATCTTAAAGGCATATCAAATTTATAGCATAACTCAAGACGAGAAGGGTTATTTGTCA
65 CAGCTCAAAGGCACATC--ATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCA
314209 TTGAAAACTT
Statistics
Matches: 245, Mismatches: 36, Indels: 16
0.82 0.12 0.05
Matches are distributed among these distances:
163 1 0.00
164 106 0.43
166 2 0.01
167 2 0.01
168 102 0.42
169 3 0.01
170 29 0.12
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (164 bp):
TGCAGCATAGCTCAAGGCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGATTACACTC
AGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAAAACCTTCG
AGATCGATTACACACAGCTCAAAGTCACATCATT
Found at i:314606 original size:3 final size:3
Alignment explanation
Indices: 314598--314678 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
314588 ATATTATAAA
314598 TAT TAT TAT TAT TAT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
314644 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
314679 AACTTATTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 72 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:316085 original size:22 final size:20
Alignment explanation
Indices: 316039--316079 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
316029 ATGTTTATAT
*
316039 AATTTTTTTTAATTTATTTC
1 AATTTTTTTTAATTGATTTC
316059 AATTTGTTTGTTAATTGATTT
1 AATTT-TTT-TTAATTGATTT
316080 AGATTTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (20 bp):
AATTTTTTTTAATTGATTTC
Found at i:329381 original size:23 final size:23
Alignment explanation
Indices: 329354--329431 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
329344 ATTACAAGTA
329354 TTATGTTTTGAGTTTGTTTGATG
1 TTATGTTTTGAGTTTGTTTGATG
*
329377 TTATGATTTT-AGTTTGTTTGATC
1 TTATG-TTTTGAGTTTGTTTGATG
* * * *
329400 CTATGATTTGAGTTTATTTGGTG
1 TTATGTTTTGAGTTTGTTTGATG
*
329423 TAATGTTTT
1 TTATGTTTT
329432 AAAATGTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
22 3 0.07
23 37 0.84
24 4 0.09
ACGTcount: A:0.17, C:0.03, G:0.22, T:0.59
Consensus pattern (23 bp):
TTATGTTTTGAGTTTGTTTGATG
Found at i:329746 original size:20 final size:21
Alignment explanation
Indices: 329702--329747 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
329692 ATACTTTTCA
**
329702 TAATTCATTTTCCAAAAATTG
1 TAATTCATTTTCCAAAAATAC
329723 TAATTCATTTTCCAAAAA-AC
1 TAATTCATTTTCCAAAAATAC
329743 TAATT
1 TAATT
329748 ATAGTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (21 bp):
TAATTCATTTTCCAAAAATAC
Found at i:332538 original size:14 final size:13
Alignment explanation
Indices: 332521--332595 Score: 84
Period size: 13 Copynumber: 5.8 Consensus size: 13
332511 TTATAAAAAG
*
332521 AAAAGAAAATACAA
1 AAAAGAAAAGA-AA
332535 AAAAG--AAGAAA
1 AAAAGAAAAGAAA
332546 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
332559 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
*
332572 AAGAAGAAAAGTCAA
1 AA-AAGAAAAG-AAA
332587 AAAA-AAAAG
1 AAAAGAAAAG
332596 CAAGCCAACG
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
11 7 0.13
12 3 0.05
13 26 0.47
14 15 0.27
15 4 0.07
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:332548 original size:24 final size:25
Alignment explanation
Indices: 332516--332576 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
332506 TTGGATTATA
*
332516 AAAAG-AAAAGAAAATACAAAAAAGA
1 AAAAGAAAAAGAAAAGA-AAAAAAGA
*
332541 AGAA-AAAAAGAAAAGAAAAAAAG-
1 AAAAGAAAAAGAAAAGAAAAAAAGA
332564 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
332577 GAAAAGTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 3 0.10
24 15 0.48
25 13 0.42
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAAGAAAAGAAAAAAAGA
Found at i:337885 original size:14 final size:14
Alignment explanation
Indices: 337866--337895 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
337856 ATCAAAAATG
337866 ATATTCATTACCAA
1 ATATTCATTACCAA
*
337880 ATATTCGTTACCAA
1 ATATTCATTACCAA
337894 AT
1 AT
337896 CTTAAGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (14 bp):
ATATTCATTACCAA
Found at i:338290 original size:107 final size:105
Alignment explanation
Indices: 338165--338504 Score: 319
Period size: 107 Copynumber: 3.2 Consensus size: 105
338155 AAATGTAGTT
* * *
338165 TTTTTGAAAATATGTAATATATGGTTTTTAAAATATTTTTGAAAACATATAATATATAATTTTTA
1 TTTTTGAAAATGTATAATATATGGTTTTTAAAATATTTTTGAAAACGTATAATATATAATTTTTA
* *
338230 AAAAATATTTTTGAAAACGTATAATATATAATTTTT-TAAATA
66 AAAAATA---TTGAAAACATATAATATATAATTTTTAAAAATA
* * * * *
338272 TTTTTGAAAATGTATAATATATAGTTTTTTTAAATATTTTTGAAAACGCAAAATATATAGTTTTT
1 TTTTTGAAAATGTATAATATAT-GGTTTTTAAAATATTTTTGAAAACGTATAATATATA-ATTTT
* * *
338337 TTAAAAA-ATTGCAAACATATAATATATAGTTTTTGAAAAATA
64 TAAAAAATATTGAAAACATATAATATATAATTTTT-AAAAATA
* * * * * * *
338379 TTTTTGAAAACGTATTATATATTGTTTTTAAAAATACTTTTGAAAACGTATGATATATAGTTTTA
1 TTTTTGAAAATGTATAATATATGGTTTTT-AAAATATTTTTGAAAACGTATAATATATAATTTTT
* * *
338444 AAAAAATGACTTTGAAAACAAATACA-ATATAATGGGTTTGAAAATA
65 AAAAAAT-A--TTGAAAACATATA-ATATATAAT--TTTTAAAAATA
*
338490 -TTTTAAAAATGTATA
1 TTTTTGAAAATGTATA
338505 TAATATAGTT
Statistics
Matches: 188, Mismatches: 33, Indels: 21
0.78 0.14 0.09
Matches are distributed among these distances:
105 23 0.12
106 14 0.07
107 69 0.37
108 33 0.18
109 10 0.05
110 29 0.15
111 7 0.04
112 3 0.02
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (105 bp):
TTTTTGAAAATGTATAATATATGGTTTTTAAAATATTTTTGAAAACGTATAATATATAATTTTTA
AAAAATATTGAAAACATATAATATATAATTTTTAAAAATA
Found at i:338327 original size:36 final size:36
Alignment explanation
Indices: 338165--338442 Score: 305
Period size: 37 Copynumber: 7.8 Consensus size: 36
338155 AAATGTAGTT
** * *
338165 TTTTTGAAAATATGTAATATAT-GGTTTTTAAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTTTAAAATA
* * *
338200 TTTTTGAAAACATATAATATATAATTTTTAAAAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTT-TAAAATA
*
338237 TTTTTGAAAACGTATAATATATAATTTTTT-AAATA
1 TTTTTGAAAACGTATAATATATAGTTTTTTAAAATA
* *
338272 TTTTTGAAAATGTATAATATATAGTTTTTTTAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTTTAAAATA
* *
338308 TTTTTGAAAACGCAAAATATATAGTTTTTTTAAAA-A
1 TTTTTGAAAACGTATAATATATAG-TTTTTTAAAATA
* * * *
338344 --ATTGCAAACATATAATATATAGTTTTTGAAAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTT-TAAAATA
* * *
338379 TTTTTGAAAACGTATTATATATTGTTTTTAAAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTTTAAAATA
* *
338415 CTTTTGAAAACGTATGATATATAGTTTT
1 TTTTTGAAAACGTATAATATATAGTTTT
338443 AAAAAAATGA
Statistics
Matches: 208, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.02
34 21 0.10
35 54 0.26
36 63 0.30
37 65 0.31
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTTTGAAAACGTATAATATATAGTTTTTTAAAATA
Found at i:338448 original size:36 final size:36
Alignment explanation
Indices: 338165--338448 Score: 310
Period size: 36 Copynumber: 7.9 Consensus size: 36
338155 AAATGTAGTT
** * *
338165 TTTTTGAAAATATGTAATATATGGTTTTT-AAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTTAAAAATA
* *
338200 TTTTTGAAAACATATAATATATAATTTTTAAAAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTT-AAAAATA
* *
338237 TTTTTGAAAACGTATAATATATAATTTTT-TAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTTAAAAATA
* **
338272 TTTTTGAAAATGTATAATATATAGTTTTTTTAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTTAAAAATA
* *
338308 TTTTTGAAAACGCAAAATATATAGTTTTTTTAAAAA-A
1 TTTTTGAAAACGTATAATATATAG--TTTTTAAAAATA
* *
338345 ---TTGCAAACATATAATATATAGTTTTTGAAAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTT-AAAAATA
* *
338379 TTTTTGAAAACGTATTATATATTGTTTTTAAAAATA
1 TTTTTGAAAACGTATAATATATAGTTTTTAAAAATA
* * *
338415 CTTTTGAAAACGTATGATATATAGTTTTAAAAAA
1 TTTTTGAAAACGTATAATATATAGTTTTTAAAAA
338449 ATGACTTTGA
Statistics
Matches: 214, Mismatches: 25, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
32 5 0.02
33 5 0.02
34 18 0.08
35 57 0.27
36 64 0.30
37 57 0.27
38 8 0.04
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (36 bp):
TTTTTGAAAACGTATAATATATAGTTTTTAAAAATA
Found at i:338536 original size:9 final size:9
Alignment explanation
Indices: 338522--338582 Score: 67
Period size: 9 Copynumber: 7.2 Consensus size: 9
338512 GTTTACATTG
*
338522 TTATTTATC
1 TTATTTATT
338531 TTATTT-TT
1 TTATTTATT
*
338539 TTATTTTTT
1 TTATTTATT
338548 TTA-TT-TT
1 TTATTTATT
338555 TTATTTA-T
1 TTATTTATT
*
338563 GTATTTATT
1 TTATTTATT
338572 TTATTTATT
1 TTATTTATT
338581 TT
1 TT
338583 TTCAGGTCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
7 5 0.11
8 18 0.40
9 22 0.49
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (9 bp):
TTATTTATT
Found at i:338544 original size:17 final size:16
Alignment explanation
Indices: 338522--338581 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 16
338512 GTTTACATTG
338522 TTATTTATCTTATTTTT
1 TTATTTAT-TTATTTTT
*
338539 TTATTT-TTTTTATTTT
1 TTATTTATTTAT-TTTT
*
338555 TTATTTATGTATTTATT
1 TTATTTATTTATTT-TT
338572 TTATTTATTT
1 TTATTTATTT
338582 TTTCAGGTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 3 0.08
16 13 0.36
17 20 0.56
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (16 bp):
TTATTTATTTATTTTT
Found at i:338561 original size:4 final size:4
Alignment explanation
Indices: 338522--338581 Score: 59
Period size: 4 Copynumber: 14.5 Consensus size: 4
338512 GTTTACATTG
* * *
338522 TTAT TTAT CTTAT TTTT TTATT TTTT TTAT TT-T TTAT TTAT GTAT TTATT
1 TTAT TTAT -TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT TTAT TTA-T
338572 TTAT TTAT TT
1 TTAT TTAT TT
338582 TTTCAGGTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
3 3 0.07
4 32 0.70
5 11 0.24
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:343709 original size:26 final size:26
Alignment explanation
Indices: 343673--343757 Score: 120
Period size: 26 Copynumber: 3.3 Consensus size: 26
343663 AGGGCACTAA
*
343673 GTGTA-TATGGTGGGCTA-AACCTTAT
1 GTGTATTATGGTGGGC-ACGACCTTAT
343698 GTGTATTATGGTGGGCACGACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
* *
343724 GTGTATGATGGTGGGCACGATCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
343750 GTGTATTA
1 GTGTATTA
343758 GCACTTCGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
25 6 0.11
26 48 0.89
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (26 bp):
GTGTATTATGGTGGGCACGACCTTAT
Found at i:347336 original size:26 final size:26
Alignment explanation
Indices: 347300--347384 Score: 120
Period size: 26 Copynumber: 3.3 Consensus size: 26
347290 AGGGCACTAA
*
347300 GTGTA-TATGGTGGGCTA-AACCTTAT
1 GTGTATTATGGTGGGC-ACGACCTTAT
347325 GTGTATTATGGTGGGCACGACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
* *
347351 GTGTATGATGGTGGGCACGATCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
347377 GTGTATTA
1 GTGTATTA
347385 GCACTTCGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
25 6 0.11
26 48 0.89
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (26 bp):
GTGTATTATGGTGGGCACGACCTTAT
Found at i:350968 original size:26 final size:26
Alignment explanation
Indices: 350932--351016 Score: 120
Period size: 26 Copynumber: 3.3 Consensus size: 26
350922 AGGGCACTAA
*
350932 GTGTA-TATGGTGGGCTA-AACCTTAT
1 GTGTATTATGGTGGGC-ACGACCTTAT
350957 GTGTATTATGGTGGGCACGACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
* *
350983 GTGTATGATGGTGGGCACGATCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
351009 GTGTATTA
1 GTGTATTA
351017 GCACTTCGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
25 6 0.11
26 48 0.89
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.36
Consensus pattern (26 bp):
GTGTATTATGGTGGGCACGACCTTAT
Found at i:355585 original size:28 final size:27
Alignment explanation
Indices: 355527--355591 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
355517 CCTAATGAGA
* * *
355527 ATTTAGATTTTTAGATTTAGTCTTCAT
1 ATTTATATTTTTAGATTTAATCTTCAG
355554 ATTTATATCTTTTAGATTTAATACTT-AG
1 ATTTATAT-TTTTAGATTTAAT-CTTCAG
355582 ATTTATATTT
1 ATTTATATTT
355592 CACAATTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 9 0.27
28 21 0.64
29 3 0.09
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (27 bp):
ATTTATATTTTTAGATTTAATCTTCAG
Found at i:365211 original size:6 final size:6
Alignment explanation
Indices: 365200--365239 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
365190 ATACTTCTTT
365200 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TGTTTC- TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA T-TTTCA TTTT
365240 TTGTTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 3 0.09
6 26 0.79
7 4 0.12
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.70
Consensus pattern (6 bp):
TTTTCA
Found at i:365758 original size:25 final size:24
Alignment explanation
Indices: 365728--365800 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 24
365718 TCAAATTAGC
365728 TATCATCTTTTATAATGATATAAT
1 TATCATCTTTTATAATGATATAAT
* *
365752 ATATCATCTTTCATAAATGATATGAT
1 -TATCATCTTTTAT-AATGATATAAT
*
365778 TCATCATCTTATATAATCGATAT
1 T-ATCATCTTTTATAAT-GATAT
365801 GATGTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 16 0.39
26 25 0.61
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.45
Consensus pattern (24 bp):
TATCATCTTTTATAATGATATAAT
Found at i:367948 original size:44 final size:43
Alignment explanation
Indices: 367880--367964 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 43
367870 TGTCAAGATC
*
367880 TATGTTGGAGCTATTATCAACTTTTCCAACTTATTCCCTAAAAT
1 TATGTTGGAGCTATTACCAACTTTTCCAACTTATT-CCTAAAAT
* *
367924 TATGTTGGAGTTATTACCAGCTTTTCCAACTTATTCCTAAA
1 TATGTTGGAGCTATTACCAACTTTTCCAACTTATTCCTAAA
367965 TTTCCATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (43 bp):
TATGTTGGAGCTATTACCAACTTTTCCAACTTATTCCTAAAAT
Found at i:370112 original size:30 final size:30
Alignment explanation
Indices: 370076--370136 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
370066 ACGTTGGATC
370076 GATCAACAAGTTGTAAAGTGATGGTGGTGG
1 GATCAACAAGTTGTAAAGTGATGGTGGTGG
370106 GATCAACAAGTTGTAAAGTGATGGTGGTGG
1 GATCAACAAGTTGTAAAGTGATGGTGGTGG
370136 G
1 G
370137 CCTTGCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.07, G:0.38, T:0.26
Consensus pattern (30 bp):
GATCAACAAGTTGTAAAGTGATGGTGGTGG
Found at i:372175 original size:21 final size:22
Alignment explanation
Indices: 372129--372175 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
372119 ACATGATATT
*
372129 TAATATATATATTTCATAATCA
1 TAATATATATATTTCATAATAA
* *
372151 -AATATGTCTATTT-ATAATAA
1 TAATATATATATTTCATAATAA
372171 TAATA
1 TAATA
372176 CTGATTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (22 bp):
TAATATATATATTTCATAATAA
Found at i:381271 original size:20 final size:21
Alignment explanation
Indices: 381243--381285 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
381233 AATTTTGAGT
*
381243 TTTGAAATTAAT-TTCTTATA
1 TTTGAAATTAATGGTCTTATA
* *
381263 TTTGGAATTCATGGTCTTATA
1 TTTGAAATTAATGGTCTTATA
381284 TT
1 TT
381286 CCAAATACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (21 bp):
TTTGAAATTAATGGTCTTATA
Found at i:384499 original size:14 final size:15
Alignment explanation
Indices: 384472--384500 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
384462 AATTACCAAT
384472 TTCCATTGAAATATC
1 TTCCATTGAAATATC
384487 TTCCATT-AAATATC
1 TTCCATTGAAATATC
384501 CCCTAGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.41
Consensus pattern (15 bp):
TTCCATTGAAATATC
Found at i:391730 original size:2 final size:2
Alignment explanation
Indices: 391718--391835 Score: 101
Period size: 2 Copynumber: 62.0 Consensus size: 2
391708 CCCATTTAAA
391718 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** *
391759 -T AT -T CAT -T CAT AA ACT CG AA AT A- AT -T AT AT AT AT AT AT
1 AT AT AT -AT AT -AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
391797 AT -T AT AT AG AT AT AT AT AT AT AT AT -T AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
391836 TCATAACTCG
Statistics
Matches: 95, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
1 9 0.09
2 84 0.88
3 2 0.02
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:396578 original size:33 final size:33
Alignment explanation
Indices: 396541--396606 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
396531 CAAAGCTCCT
396541 AAAAATTCTTCTTCCCTTGATATTTGTTACGTG
1 AAAAATTCTTCTTCCCTTGATATTTGTTACGTG
396574 AAAAATTCTTCTTCCCTTGATATTTGTTACGTG
1 AAAAATTCTTCTTCCCTTGATATTTGTTACGTG
396607 TGTGAATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (33 bp):
AAAAATTCTTCTTCCCTTGATATTTGTTACGTG
Found at i:406448 original size:2 final size:2
Alignment explanation
Indices: 406441--406466 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
406431 ATTTCATTTC
406441 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
406467 CACCGACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:407879 original size:129 final size:129
Alignment explanation
Indices: 407664--407921 Score: 498
Period size: 129 Copynumber: 2.0 Consensus size: 129
407654 AATCTATAGA
*
407664 TTGGGACTTTTGCCCCAAAGTGAAACATTGGTGCCAAAATGCTAAAAAAATAAGGATCAAAATGA
1 TTGGGACTTTTGCCCCAAAGTGAAACATTGGTGCCAAAATACTAAAAAAATAAGGATCAAAATGA
407729 TCATTTTGGTAAGTTGGGGTGGGGCTAATTTTGGTATTATGCATATTTTATTTCTATTTTGGTC
66 TCATTTTGGTAAGTTGGGGTGGGGCTAATTTTGGTATTATGCATATTTTATTTCTATTTTGGTC
*
407793 TTGGGCCTTTTGCCCCAAAGTGAAACATTGGTGCCAAAATACTAAAAAAATAAGGATCAAAATGA
1 TTGGGACTTTTGCCCCAAAGTGAAACATTGGTGCCAAAATACTAAAAAAATAAGGATCAAAATGA
407858 TCATTTTGGTAAGTTGGGGTGGGGCTAATTTTGGTATTATGCATATTTTATTTCTATTTTGGTC
66 TCATTTTGGTAAGTTGGGGTGGGGCTAATTTTGGTATTATGCATATTTTATTTCTATTTTGGTC
407922 ATCTACTTAT
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 127 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.36
Consensus pattern (129 bp):
TTGGGACTTTTGCCCCAAAGTGAAACATTGGTGCCAAAATACTAAAAAAATAAGGATCAAAATGA
TCATTTTGGTAAGTTGGGGTGGGGCTAATTTTGGTATTATGCATATTTTATTTCTATTTTGGTC
Found at i:408053 original size:3 final size:3
Alignment explanation
Indices: 408040--408070 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
408030 TTTCCACTTA
408040 ATT AGTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
408071 TATAAGATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:409243 original size:18 final size:18
Alignment explanation
Indices: 409222--409258 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
409212 GGCGTAATGA
409222 CGTTGGCTGGCTCCTAGG
1 CGTTGGCTGGCTCCTAGG
409240 CGTTGGCTGGCTCCTAGG
1 CGTTGGCTGGCTCCTAGG
409258 C
1 C
409259 ATTTGCCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.30, G:0.38, T:0.27
Consensus pattern (18 bp):
CGTTGGCTGGCTCCTAGG
Found at i:410175 original size:23 final size:23
Alignment explanation
Indices: 410149--410198 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
410139 ATCAAGTACA
*
410149 ATAACATATTAGGTACCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
** *
410172 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
410195 ATAA
1 ATAA
410199 TAAAATAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTACCGCTTAT
Found at i:410205 original size:23 final size:23
Alignment explanation
Indices: 410158--410206 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
410148 AATAACATAT
**
410158 TAGGTACCGCTTATATAATGTAA
1 TAGGTACCGCTTATATAATAAAA
*
410181 TAGGTAGCGCTTATATAATAAAA
1 TAGGTACCGCTTATATAATAAAA
410204 TAG
1 TAG
410207 ATTAATTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (23 bp):
TAGGTACCGCTTATATAATAAAA
Found at i:410262 original size:23 final size:23
Alignment explanation
Indices: 410236--410285 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
410226 ATCAAGCACA
* *
410236 ATAACATATTAGGTACCGCTTAT
1 ATAACATAATAGGTACCACTTAT
** *
410259 ATAATGTAATAGGTAGCACTTAT
1 ATAACATAATAGGTACCACTTAT
410282 ATAA
1 ATAA
410286 TAAAATAGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTACCACTTAT
Found at i:410292 original size:23 final size:23
Alignment explanation
Indices: 410245--410293 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
410235 AATAACATAT
* **
410245 TAGGTACCGCTTATATAATGTAA
1 TAGGTACCACTTATATAATAAAA
*
410268 TAGGTAGCACTTATATAATAAAA
1 TAGGTACCACTTATATAATAAAA
410291 TAG
1 TAG
410294 ATTAATTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (23 bp):
TAGGTACCACTTATATAATAAAA
Found at i:410380 original size:87 final size:87
Alignment explanation
Indices: 410132--410372 Score: 428
Period size: 87 Copynumber: 2.8 Consensus size: 87
410122 ATTTAACCGG
*
410132 AAACATTATCAAGTACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATAT
1 AAACATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATAT
*
410197 AATAAAATAGATTAATTACTGA
66 AATAAAATAGATTAATTACTAA
*
410219 AAACATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTATAT
1 AAACATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATAT
410284 AATAAAATAGATTAATTACTAA
66 AATAAAATAGATTAATTACTAA
* * *
410306 AAACATTATCAAGCACAACAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATAT
1 AAACATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATAT
410371 AA
66 AA
410373 CGTAATAGGT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 147 1.00
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.30
Consensus pattern (87 bp):
AAACATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATAT
AATAAAATAGATTAATTACTAA
Found at i:410395 original size:25 final size:23
Alignment explanation
Indices: 410332--410394 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
410322 AACAACATAT
410332 TAGGTAGCGCTTATATAACGTAA
1 TAGGTAGCGCTTATATAACGTAA
410355 TAGGTAGCGCTTATATAACGTAA
1 TAGGTAGCGCTTATATAACGTAA
*
410378 TAGGTAGCGTTTATATA
1 TAGGTAGCGCTTATATA
410395 TTAAAATATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAACGTAA
Found at i:412698 original size:17 final size:17
Alignment explanation
Indices: 412676--412712 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
412666 GCCAAAGGAA
412676 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
412693 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
412710 GTC
1 GTC
412713 GGTCAGACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.46, T:0.19
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:420848 original size:110 final size:110
Alignment explanation
Indices: 420648--420922 Score: 433
Period size: 110 Copynumber: 2.5 Consensus size: 110
420638 TCGGGTTGTT
* * * *
420648 ACAAAACCAGTTTCATTATGACAAAAATGATAAAATTTACATGATATGTTTAAAGTATCGATCAT
1 ACAAAA-CAGTTTCATTATGACAAAAACGGTAAAATTTACATGATATGTTGAAAATATCGATCAT
*
420713 TTTATAAAAAAGATAGATACTTTACAATATAACATGTAAAAATATG
65 TTTATAAAAAAGATAGATACTTTACAATATAACATATAAAAATATG
* *
420759 ACAAAACAGTTTCATTATGACAAAAACGGTAAAATTTACTTGATATGTTGAAAATATCGATCCTT
1 ACAAAACAGTTTCATTATGACAAAAACGGTAAAATTTACATGATATGTTGAAAATATCGATCATT
*
420824 TTATAAAAAGGATAGATACTTTACAATATAACATATAAAAATATG
66 TTATAAAAAAGATAGATACTTTACAATATAACATATAAAAATATG
* * *
420869 ACAAAACTAGTTTCATTATTACAAAACCGGTAAAATTTACCTGATATGTTGAAA
1 ACAAAAC-AGTTTCATTATGACAAAAACGGTAAAATTTACATGATATGTTGAAA
420923 GTATAAATAC
Statistics
Matches: 152, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
110 103 0.68
111 49 0.32
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (110 bp):
ACAAAACAGTTTCATTATGACAAAAACGGTAAAATTTACATGATATGTTGAAAATATCGATCATT
TTATAAAAAAGATAGATACTTTACAATATAACATATAAAAATATG
Found at i:421596 original size:111 final size:111
Alignment explanation
Indices: 421386--421755 Score: 494
Period size: 111 Copynumber: 3.3 Consensus size: 111
421376 TAGCGCCTAT
* * * * *
421386 AAAGTATCGAT-ACTTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATATG-ACA
1 AAAGTATTGATCATTTTATAAAAATG-ATCGATACTTTACAATATAACATGTAAAAATATGAAAA
*
421449 AACCAGTTTTATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
65 AATCAGTTTTATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
* *
421496 AAAGTATTGATCATTTTATAAAAAAGATAGATACTTTACAATATAACATGTAAAAATATGAAAAA
1 AAAGTATTGATCATTTTATAAAAATGATCGATACTTTACAATATAACATGTAAAAATATGAAAAA
* * * * *
421561 ATTAATTTCATTATGACAAAAAGGGTAAAAATTACCTGATATGTTG
66 ATCAGTTTTATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
* * * * *
421607 AAAGTATTGATCCTTTTATAAAAGTGATCGATACTTTACAATATAATATGTATAAATATGACAAA
1 AAAGTATTGATCATTTTATAAAAATGATCGATACTTTACAATATAACATGTAAAAATATGAAAAA
* *
421672 ATCAGTTTTATTATGACAAAACCGGTAAAATTTACCTGATATATTG
66 ATCAGTTTTATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
* *
421718 AAAGTATAT-ATACTTTTTATAAAAAGGATCGATACTTT
1 AAAGTAT-TGAT-CATTTTATAAAAATGATCGATACTTT
421756 TTTGAAAGTT
Statistics
Matches: 226, Mismatches: 30, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
110 41 0.18
111 161 0.71
112 24 0.11
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (111 bp):
AAAGTATTGATCATTTTATAAAAATGATCGATACTTTACAATATAACATGTAAAAATATGAAAAA
ATCAGTTTTATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
Found at i:427407 original size:17 final size:17
Alignment explanation
Indices: 427375--427423 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
427365 AATATTTCTA
*
427375 ATTTAAAATATAAAATT
1 ATTTAAAAAATAAAATT
*
427392 ATTTAAAAAATTAAA-T
1 ATTTAAAAAATAAAATT
*
427408 A--TCAAAAATAAAATT
1 ATTTAAAAAATAAAATT
427423 A
1 A
427424 AATGACTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 10 0.37
15 2 0.07
16 2 0.07
17 13 0.48
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAAAATAAAATT
Found at i:427553 original size:21 final size:24
Alignment explanation
Indices: 427505--427562 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
427495 AAATTAAACT
*
427505 AAATAAATATTATAAAGTCTCATAA
1 AAATAAA-ATTTTAAAGTCTCATAA
427530 AAATAAAATTTTAAAGT-T-ATAA
1 AAATAAAATTTTAAAGTCTCATAA
*
427552 AATTAAAATTT
1 AAATAAAATTT
427563 ATGTATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 14 0.45
23 1 0.03
24 9 0.29
25 7 0.23
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (24 bp):
AAATAAAATTTTAAAGTCTCATAA
Found at i:432541 original size:26 final size:26
Alignment explanation
Indices: 432490--432587 Score: 126
Period size: 26 Copynumber: 3.7 Consensus size: 26
432480 ATGAATAGTG
* *
432490 AACAGTACCCCCGTGAAAAGTGAACAGT
1 AACAGTA--CCCGTGAACAGTAAACAGT
432518 AACAGTACCCGTGAACAGTAAACAGT
1 AACAGTACCCGTGAACAGTAAACAGT
* *
432544 AACAGTA-CCGTGAATAGTAAATAGT
1 AACAGTACCCGTGAACAGTAAACAGT
*
432569 AACAATACCCGTGAACAGT
1 AACAGTACCCGTGAACAGT
432588 GGGAGAATCG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
25 22 0.35
26 34 0.54
28 7 0.11
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.17
Consensus pattern (26 bp):
AACAGTACCCGTGAACAGTAAACAGT
Found at i:437616 original size:18 final size:20
Alignment explanation
Indices: 437590--437630 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
437580 TGACTAATAA
437590 TTTCAACTAAC-TTGA-TTC
1 TTTCAACTAACATTGATTTC
*
437608 TTTCTACTAACATTGATTTC
1 TTTCAACTAACATTGATTTC
437628 TTT
1 TTT
437631 TTGTTTGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 4 0.20
20 6 0.30
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTCAACTAACATTGATTTC
Found at i:441774 original size:52 final size:52
Alignment explanation
Indices: 441675--441945 Score: 190
Period size: 58 Copynumber: 5.0 Consensus size: 52
441665 TGATAGGATG
* * *
441675 TTTTCAAATGAAGTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATA
1 TTTTCAAATG-AGTTTT--TAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATA
* * *
441730 TTTTCAAATGGGTTTTTAGAAACTAAGCCTAATTTTCAGTGGTTTCTTGAGGA
1 TTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGA-TA
* * * * * * *
441783 TGATTTCCAATGAATTTTCAAAAGAAGCCAAGCCTAATTTTTAGGGGTTTCTTGATG
1 T--TTTCAAATGAGTTTT---TAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATA
* * *
441840 TTTTTAAATGAG-TTTTA-AAACTAAGCCTGATTTTCAGGTGTTTCGTGATGACTA
1 TTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTC-T--TGA-TA
* * * *
441894 TTTCCCAA-GAATTTTTAAAGAAACTAAACCTAATTATT-AGGGGTTTCTTGAT
1 TTTTCAAATGAGTTTTT--AGAAACTAAGCCTAATT-TTCAGGGGTTTCTTGAT
441946 GAGAACTGAA
Statistics
Matches: 168, Mismatches: 33, Indels: 32
0.72 0.14 0.14
Matches are distributed among these distances:
50 22 0.13
51 2 0.01
52 30 0.18
53 8 0.05
54 21 0.12
55 30 0.18
56 2 0.01
57 22 0.13
58 31 0.18
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (52 bp):
TTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATA
Found at i:441830 original size:110 final size:107
Alignment explanation
Indices: 441669--441945 Score: 353
Period size: 110 Copynumber: 2.6 Consensus size: 107
441659 GCTCCTTGAT
* *
441669 AGGATGTTTTCAAATGAAGTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATATTTT
1 AGGATGATTTCCAATGAA-TTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATATTTT
* *
441734 CAAATGGGTTTTTAGAAACTAAGCCTAATTTTCA-GTGGTTTCTTG
65 CAAATGAG-TTTTA-AAACTAAGCCTAATTTTCAGGT-GTTTCGTG
* *
441779 AGGATGATTTCCAATGAATTTTCAAAAGAAGCCAAGCCTAATTTTTAGGGGTTTCTTGATGTTTT
1 AGGATGATTTCCAATGAATTTT-AAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATATTTT
* *
441844 TAAATGAGTTTTAAAACTAAGCCTGATTTTCAGGTGTTTCGTG
65 CAAATGAGTTTTAAAACTAAGCCTAATTTTCAGGTGTTTCGTG
* * * * *
441887 ATGACT-ATTTCCCAA-GAATTTTTAAAGAAACTAAACCTAATTATTAGGGGTTTCTTGAT
1 AGGA-TGATTT-CCAATGAATTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGAT
441946 GAGAACTGAA
Statistics
Matches: 149, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
107 32 0.21
108 39 0.26
109 16 0.11
110 62 0.42
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (107 bp):
AGGATGATTTCCAATGAATTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATATTTTC
AAATGAGTTTTAAAACTAAGCCTAATTTTCAGGTGTTTCGTG
Found at i:442267 original size:39 final size:39
Alignment explanation
Indices: 442178--442719 Score: 856
Period size: 39 Copynumber: 14.0 Consensus size: 39
442168 AGGGATCAAC
*
442178 ATCTCACTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
442216 ATCTCGCTTGAGATAGTTTCACTCGAAACATAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
442255 ATCTCGCTTGAGATAGTTTCACTCAAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
442294 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
442333 ATCTCGGTTGAGATAGTTTCACTCGAAGCATAAGTTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
442372 ATCTCGCTTGAGATAGTTTCACTGGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
442411 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
442449 ATCTCACTTGAGATAGTTTCACTCAAAATAGTAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
442488 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
442527 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
442566 ATCTTGCTTGAGATAGTTTCACTTGAAATAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
442605 ATCTCGCTTGAGATAGTTTCACTCAAAACAGAAG-TTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
442643 TTCTTGCTTAAGATAGTTTCACTCGAAACATAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
442682 ATCTCACTTGAGATAGTTTCACTCGAAACAGAAGATTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
442720 ATTTCCCTTT
Statistics
Matches: 460, Mismatches: 41, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
38 99 0.22
39 361 0.78
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:442513 original size:194 final size:193
Alignment explanation
Indices: 442178--442719 Score: 845
Period size: 194 Copynumber: 2.8 Consensus size: 193
442168 AGGGATCAAC
*
442178 ATCTCACTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCTCGCTTGAGATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
* *
442242 AACATAAGATTTTATCTCGCTTGAGATAGTTTCACTCAAAACAGAAGATTTTATCTCGCTTGAGA
66 AACAAAAGA-TTTATCTCGCTTGAGATAGTTTCACTCAAAATAG-AGATTTTATCTCGCTTGAGA
* * * *
442307 TAGTTTCACTCGAAACAGAAGATTTTATCTCGGTTGAGATAGTTTCACTCGAAGCATAAGTTTTT
129 TAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
442372 ATCTCGCTTGAGATAGTTTCACTGGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
*
442437 AACAAAAGATTTATCTCACTTGAGATAGTTTCACTCAAAATAGTAGATTTTATCTCGCTTGAGAT
66 AACAAAAGATTTATCTCGCTTGAGATAGTTTCACTCAAAATAG-AGATTTTATCTCGCTTGAGAT
442502 AGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
130 AGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
442566 ATCTTGCTTGAGATAGTTTCACTTGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCAA
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
* * * * * *
442631 AACAGAAGTTTTTTCTTGCTTAAGATAGTTTCACTCGAAACATA-AGATTTTATCTCACTTGAGA
66 AACAAAAGATTTATCTCGCTTGAGATAGTTTCACTC-AAA-ATAGAGATTTTATCTCGCTTGAGA
442695 TAGTTTCACTCGAAACAGAAGATTT
129 TAGTTTCACTCGAAACAGAAGATTT
442720 ATTTCCCTTT
Statistics
Matches: 322, Mismatches: 23, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
194 279 0.87
195 40 0.12
196 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (193 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA
AACAAAAGATTTATCTCGCTTGAGATAGTTTCACTCAAAATAGAGATTTTATCTCGCTTGAGATA
GTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:442677 original size:22 final size:22
Alignment explanation
Indices: 442651--442717 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
442641 TTTTCTTGCT
442651 TAAGATAGTTTCACTCGAAACA
1 TAAGATAGTTTCACTCGAAACA
*
442673 TAAGAT--TTT-ATCTC---ACT
1 TAAGATAGTTTCA-CTCGAAACA
*
442690 TGAGATAGTTTCACTCGAAACA
1 TAAGATAGTTTCACTCGAAACA
*
442712 GAAGAT
1 TAAGAT
442718 TTATTTCCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 14
0.63 0.10 0.27
Matches are distributed among these distances:
17 7 0.21
19 7 0.21
20 7 0.21
22 12 0.36
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (22 bp):
TAAGATAGTTTCACTCGAAACA
Found at i:442865 original size:59 final size:59
Alignment explanation
Indices: 442794--442929 Score: 164
Period size: 59 Copynumber: 2.3 Consensus size: 59
442784 AGGTAGAATC
* * ** * *
442794 ACAACACTTCGAATCAGCGACGCCCCACTTGAGGGATCAACATTTCCTTTGCTCGACTA
1 ACAACACTTCGAATCAGCAACACCCCACCAGAGGGATCAACATTTCCTATACTCGACTA
* ** * *
442853 ACAACACTTCGAATCAGCAACACCCCACCAGAGGGGTTGACATTTCCTATACTCGATTC
1 ACAACACTTCGAATCAGCAACACCCCACCAGAGGGATCAACATTTCCTATACTCGACTA
*
442912 ATAACACTTCGAATCAGC
1 ACAACACTTCGAATCAGC
442930 CATGTCTCAT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (59 bp):
ACAACACTTCGAATCAGCAACACCCCACCAGAGGGATCAACATTTCCTATACTCGACTA
Found at i:450018 original size:42 final size:42
Alignment explanation
Indices: 449959--450040 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
449949 CTTGGAATGT
* *
449959 TGGGGCATGCTGAAGGCCCATTTTAGTCAGAAATAATCCATG
1 TGGGGCATGCTGAAGGCCCATTTTAGACAAAAATAATCCATG
* *
450001 TGGGGCATGTTGAAGGCCCATTTTAGACAAAAATGATCCA
1 TGGGGCATGCTGAAGGCCCATTTTAGACAAAAATAATCCA
450041 AGTAGGATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (42 bp):
TGGGGCATGCTGAAGGCCCATTTTAGACAAAAATAATCCATG
Found at i:450717 original size:22 final size:22
Alignment explanation
Indices: 450682--450736 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
450672 CATATCTAAA
* *
450682 TTTTCTAATGATGATAGATTCTC
1 TTTTC-AAAGATGATAAATTCTC
450705 TTTTCAAAGATGATAAATTCTC
1 TTTTCAAAGATGATAAATTCTC
450727 TTTTCAAAGA
1 TTTTCAAAGA
450737 CAAAGCTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 25 0.83
23 5 0.17
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (22 bp):
TTTTCAAAGATGATAAATTCTC
Found at i:451396 original size:45 final size:44
Alignment explanation
Indices: 451332--451484 Score: 148
Period size: 45 Copynumber: 3.4 Consensus size: 44
451322 AAATTTCGCT
*
451332 CTCCACGAAAGAGTAGTGGAATAGATTTTTCAGAAAAGTATTAAA
1 CTCCACGGAAGAGTAGTGGAATAGATTTTTCA-AAAAGTATTAAA
* * ** * * *
451377 CTCCACGGAAGAGTAGTGGAAGAAAATTCAATCCAAAA-T-CTGAA
1 CTCCACGGAAGAGTAGTGGAA-TAGATT-TTTCAAAAAGTATTAAA
* * * *
451421 TTCCACGGAAGAGTGGTGGAATAGGTTTTTCAACAAAGTATAAAA
1 CTCCACGGAAGAGTAGTGGAATAGATTTTTCAA-AAAGTATTAAA
451466 CTCCACGGAAGAGTAGTGG
1 CTCCACGGAAGAGTAGTGG
451485 GAGCAAATTC
Statistics
Matches: 82, Mismatches: 21, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
42 3 0.04
43 6 0.07
44 23 0.28
45 40 0.49
46 8 0.10
47 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (44 bp):
CTCCACGGAAGAGTAGTGGAATAGATTTTTCAAAAAGTATTAAA
Found at i:451440 original size:89 final size:89
Alignment explanation
Indices: 451333--451496 Score: 258
Period size: 89 Copynumber: 1.8 Consensus size: 89
451323 AATTTCGCTC
*
451333 TCCACGAAAGAGTAGTGGAATAGATTTTTCAGA-AAAGTATTAAACTCCACGGAAGAGTAGTGGA
1 TCCACGAAAGAGTAGTGGAATAGATTTTTCA-ACAAAGTATAAAACTCCACGGAAGAGTAGTGGA
451397 AGAAAATTCAATCCAAAATCTGAAT
65 AGAAAATTCAATCCAAAATCTGAAT
* * * *
451422 TCCACGGAAGAGTGGTGGAATAGGTTTTTCAACAAAGTATAAAACTCCACGGAAGAGTAGTGGGA
1 TCCACGAAAGAGTAGTGGAATAGATTTTTCAACAAAGTATAAAACTCCACGGAAGAGTAGTGGAA
*
451487 GCAAATTCAA
66 GAAAATTCAA
451497 CTTTGAATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
88 1 0.01
89 67 0.99
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (89 bp):
TCCACGAAAGAGTAGTGGAATAGATTTTTCAACAAAGTATAAAACTCCACGGAAGAGTAGTGGAA
GAAAATTCAATCCAAAATCTGAAT
Found at i:453483 original size:15 final size:16
Alignment explanation
Indices: 453464--453511 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
453454 TTATATAGTT
453464 TTAATATTAAATATTA
1 TTAATATTAAATATTA
* *
453480 -TAATAGTATTAATAATA
1 TTAATA-T-TAAATATTA
453497 TTAATATTAAATATT
1 TTAATATTAAATATT
453512 TAGTATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
15 5 0.20
16 7 0.28
17 8 0.32
18 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TTAATATTAAATATTA
Found at i:453489 original size:18 final size:18
Alignment explanation
Indices: 453465--453511 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 18
453455 TATATAGTTT
453465 TAATATTAAATATTATAA
1 TAATATTAAATATTATAA
* *
453483 TAGTATT-AATA--ATAT
1 TAATATTAAATATTATAA
453498 TAATATTAAATATT
1 TAATATTAAATATT
453512 TAGTATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
15 9 0.39
16 4 0.17
17 4 0.17
18 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAATATTAAATATTATAA
Found at i:455737 original size:15 final size:16
Alignment explanation
Indices: 455718--455769 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 16
455708 TTGTTTTTAC
455718 TTTTTACTTTTTATT-A
1 TTTTTA-TTTTTATTAA
455734 TTTTTATTTTTATTAA
1 TTTTTATTTTTATTAA
*
455750 TTTTATTATGTTTATTAA
1 -TTT-TTATTTTTATTAA
455768 TT
1 TT
455770 GTTTTGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
15 8 0.25
16 7 0.22
17 5 0.16
18 12 0.38
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTTATTTTTATTAA
Found at i:456860 original size:18 final size:19
Alignment explanation
Indices: 456827--456863 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
456817 CCTAAAACTT
456827 AATATTTTGATAAAAATAA
1 AATATTTTGATAAAAATAA
*
456846 AATATTTT-ATTAAAATAA
1 AATATTTTGATAAAAATAA
456864 CCCTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AATATTTTGATAAAAATAA
Found at i:463315 original size:15 final size:15
Alignment explanation
Indices: 463274--463306 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
463264 AGTTATAAAT
*
463274 TAAAAT-TATAGTGA
1 TAAAATATATTGTGA
463288 TAAAATATATTGTGA
1 TAAAATATATTGTGA
463303 TAAA
1 TAAA
463307 TATTTTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (15 bp):
TAAAATATATTGTGA
Found at i:463717 original size:2 final size:2
Alignment explanation
Indices: 463712--463740 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
463702 AATTTCTGTG
463712 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 A
463741 ATTCAATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:464472 original size:22 final size:22
Alignment explanation
Indices: 464431--464474 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
464421 TATAGATTTA
* *
464431 AAATTTAAAATATACAAAAAAT
1 AAATATAAAAAATACAAAAAAT
464453 AAATATAAAAAATACTAAAAAA
1 AAATATAAAAAATAC-AAAAAA
464475 ACTGAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATATAAAAAATACAAAAAAT
Found at i:465462 original size:24 final size:23
Alignment explanation
Indices: 465428--465472 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
465418 TATGATTTTG
*
465428 TTTAATATTTAATTTATTGTTATA
1 TTTAATATTTAAATT-TTGTTATA
*
465452 TTTAATTTTTAAATTTTGTTA
1 TTTAATATTTAAATTTTGTTA
465473 CAAGTTGGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTAATATTTAAATTTTGTTATA
Found at i:467379 original size:2 final size:2
Alignment explanation
Indices: 467348--467396 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
467338 TATCATAATC
* * * * *
467348 AT AT AT TT AT AT TT AT AT GT GT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
467390 AT AT AT A
1 AT AT AT A
467397 GTTATGACAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:469085 original size:18 final size:19
Alignment explanation
Indices: 469039--469085 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
469029 TTTAAAATAT
*
469039 AATTTTAGTTATCATAACCA
1 AATTTTAGTTATAATAA-CA
469059 ATTATTTTAGTTATAATAA-A
1 A--ATTTTAGTTATAATAACA
469079 AATTTTA
1 AATTTTA
469086 AATAAAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 6 0.25
20 3 0.12
22 15 0.62
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (19 bp):
AATTTTAGTTATAATAACA
Found at i:469301 original size:22 final size:23
Alignment explanation
Indices: 469276--469334 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
469266 AATCAATTAG
*
469276 AACAAGTT-TATTTAGTCAAAAT
1 AACAAGTTAAATTTAGTCAAAAT
469298 AACATA-TTAAATTTAGTCAAAAT
1 AACA-AGTTAAATTTAGTCAAAAT
469321 AA-AAGTTAAATTTA
1 AACAAGTTAAATTTA
469335 TTTTGTCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.03
22 16 0.48
23 16 0.48
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (23 bp):
AACAAGTTAAATTTAGTCAAAAT
Found at i:469311 original size:23 final size:22
Alignment explanation
Indices: 469285--469334 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 22
469275 GAACAAGTTT
469285 ATTTAGTCAAAATAACATA-TTAA
1 ATTTAGTCAAAATAA-A-AGTTAA
469308 ATTTAGTCAAAATAAAAGTTAA
1 ATTTAGTCAAAATAAAAGTTAA
469330 ATTTA
1 ATTTA
469335 TTTTGTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.04
22 10 0.38
23 15 0.58
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (22 bp):
ATTTAGTCAAAATAAAAGTTAA
Found at i:469498 original size:32 final size:35
Alignment explanation
Indices: 469453--469537 Score: 86
Period size: 39 Copynumber: 2.4 Consensus size: 35
469443 TTAAAATATT
* *
469453 ATTTCGTCCCAATAACA-AA-TTGTA-ACAAAATG
1 ATTTAGTCACAATAACATAAGTTGTAGACAAAATG
*
469485 ATTTAGTCACAATAACACGTTAAGTTTTATGACAAAATG
1 ATTTAGTCACAATAACA---TAAGTTGTA-GACAAAATG
469524 ATTTAGTCACAATA
1 ATTTAGTCACAATA
469538 GTAAAAAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 15 0.35
36 2 0.05
37 4 0.09
39 22 0.51
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (35 bp):
ATTTAGTCACAATAACATAAGTTGTAGACAAAATG
Found at i:469613 original size:32 final size:32
Alignment explanation
Indices: 469574--469705 Score: 112
Period size: 32 Copynumber: 4.1 Consensus size: 32
469564 GTCCCAATGT
469574 TTTATCAAAATGAAAAATTGTGACAAAT-TT-A
1 TTTATCAAAAT-AAAAATTGTGACAAATATTAA
* *
469605 TTTAATCAAAATAACAAATTATAACAAATATTAA
1 TTT-ATCAAAATAA-AAATTGTGACAAATATTAA
** *
469639 TTTATCATTATAAAAATTGTGACAAATAAT-A
1 TTTATCAAAATAAAAATTGTGACAAATATTAA
* * *
469670 TTCTTTCACAATAATAAATTGTAACAAA-ATT-A
1 TT-TATCAAAATAA-AAATTGTGACAAATATTAA
469702 TTTA
1 TTTA
469706 GTCACAGTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
31 9 0.11
32 47 0.57
33 22 0.27
34 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (32 bp):
TTTATCAAAATAAAAATTGTGACAAATATTAA
Found at i:469689 original size:65 final size:62
Alignment explanation
Indices: 469586--469705 Score: 152
Period size: 65 Copynumber: 1.9 Consensus size: 62
469576 TATCAAAATG
*
469586 AAAAATTGTGACAAATTTATTTAATCAAAATAACAAATTATAACAAATATTAATTTATCATTAT
1 AAAAATTGTGACAAATATATTTAATCAAAATAACAAATTATAACAAA-ATT-ATTTATCATTAT
* * * *
469650 AAAAATTGTGACAAATAATATTCT-TTCACAATAATAAATTGTAACAAAATTATTTA
1 AAAAATTGTGACAAAT-ATATT-TAATCAAAATAACAAATTATAACAAAATTATTTA
469706 GTCACAGTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
63 5 0.10
64 19 0.39
65 24 0.49
66 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (62 bp):
AAAAATTGTGACAAATATATTTAATCAAAATAACAAATTATAACAAAATTATTTATCATTAT
Found at i:469717 original size:64 final size:64
Alignment explanation
Indices: 469586--469718 Score: 148
Period size: 64 Copynumber: 2.1 Consensus size: 64
469576 TATCAAAATG
* *
469586 AAAAATTGTGACAAATTTATTTAATCAAAATAACAAATTATAACAAATATTAATTTATCATTAT
1 AAAAATTGTGACAAATATATTTAATCAAAATAACAAATTATAACAAATATTAATTTATCATCAT
* * * *
469650 AAAAATTGTGACAAATAATATTCT-TTCACAATAATAAATTGTAACAAA-ATT-ATTTAGTCA-C
1 AAAAATTGTGACAAAT-ATATT-TAATCAAAATAACAAATTATAACAAATATTAATTTA-TCATC
469711 AGT
63 A-T
469714 AAAAA
1 AAAAA
469719 GTTATAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
63 6 0.10
64 28 0.47
65 24 0.41
66 1 0.02
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (64 bp):
AAAAATTGTGACAAATATATTTAATCAAAATAACAAATTATAACAAATATTAATTTATCATCAT
Found at i:470282 original size:2 final size:2
Alignment explanation
Indices: 470275--470300 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
470265 CTTGTAGTGA
470275 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
470301 TCAATCAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:472370 original size:18 final size:18
Alignment explanation
Indices: 472347--472381 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
472337 TTAGAATTTG
472347 TCCCGAAGGATCACTATA
1 TCCCGAAGGATCACTATA
472365 TCCCGAAGGATCACTAT
1 TCCCGAAGGATCACTAT
472382 CCATAGGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (18 bp):
TCCCGAAGGATCACTATA
Found at i:476240 original size:108 final size:109
Alignment explanation
Indices: 476024--476298 Score: 333
Period size: 108 Copynumber: 2.5 Consensus size: 109
476014 GCTCATTGAT
* * * *
476024 AGGATGTTTTCAAATTAACTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATATTTT
1 AGGATGATTTCCAATGAATTTTTAAAAGAAGCTAAGCCTAA-TTTTAGGGGTTTCTTGATATTTT
* * *
476089 CAAAAGCATTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTG
65 CAAAAGCATTTTTAGAAACTAAACCTAATTTTCAGGGGTTTCTTG
* * *
476134 AGGATGATTTCCAATGAATTTTTAAAAGAAGTTAATCCTAATTTTAGGGGTTTCTTGATGTTTT-
1 AGGATGATTTCCAATGAATTTTTAAAAGAAGCTAAGCCTAATTTTAGGGGTTTCTTGATATTTTC
* * *
476198 AAATG-AGTTTTTGGAAACTAAACTTAATTTTCCA-GGGTTTCTTG
66 AAAAGCA-TTTTTAGAAACTAAACCTAATTTT-CAGGGGTTTCTTG
* * * *
476242 ATGATTATTTCCAAAGAATTTTT-AAAGAAGCTAAGCCTAATTATTAGGGGCTTCTTG
1 AGGATGATTTCCAATGAATTTTTAAAAGAAGCTAAGCCTAATT-TTAGGGGTTTCTTG
476299 TTGAAAATTG
Statistics
Matches: 143, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
107 18 0.13
108 67 0.47
109 23 0.16
110 35 0.24
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.41
Consensus pattern (109 bp):
AGGATGATTTCCAATGAATTTTTAAAAGAAGCTAAGCCTAATTTTAGGGGTTTCTTGATATTTTC
AAAAGCATTTTTAGAAACTAAACCTAATTTTCAGGGGTTTCTTG
Found at i:476469 original size:41 final size:41
Alignment explanation
Indices: 476356--476474 Score: 105
Period size: 43 Copynumber: 2.8 Consensus size: 41
476346 AGGGTTTCTT
* *
476356 GATGAGTAAGTCCTTCAGGCCATCAATAAATCTTTAGGGAAG
1 GATGA-TAAGTCCTTCAGGCCATCAATAAGTCTTTAGGCAAG
* * * * * *
476398 GATGTTTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAA-
1 GATG--ATAAGTCCTTCAGGCCATCAATAAGTCTTTAG-GCAAG
* *
476441 GATGATAAGTCCTTCAGGCCATCCATAAGACTTT
1 GATGATAAGTCCTTCAGGCCATCAATAAGTCTTT
476475 TGGGCATGGA
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
41 24 0.40
42 4 0.07
43 29 0.48
44 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (41 bp):
GATGATAAGTCCTTCAGGCCATCAATAAGTCTTTAGGCAAG
Found at i:476642 original size:39 final size:39
Alignment explanation
Indices: 476553--477579 Score: 1371
Period size: 39 Copynumber: 26.5 Consensus size: 39
476543 AGGGATCAAC
* *
476553 ATCTCGCTTGAGATAGTTTCACTCGAAATAGAATA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
476591 ATCTCTCTTGAGATAGTTTCACTCGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
476630 ATCTCGCTTGAGATAGTTTCACTCAAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
** * *
476668 ATCTCATTTGAGATAGTTTCACTAGAAATAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
476707 ATCTCGCTTGAGA-AGGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATA-GTTTCACTCGAAACAGAAGATTTT
* *
476746 ATCTCACTTGAGATAGTTTCACTCGAAACAGAAGAATTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
476785 ATGTCGCTTGAGATAGTTTCACTCGAAACGGAATATTCT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
476824 ATCTCGCATGAGATAAGATAGTTTCACTCGAAAAAGAAGTTTTT
1 ATCTCGC-T----TGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
476868 ATCTCGTTTGAGATAGTTCCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
476907 ATCTCGATTGAGATAGTTTCACTCGAAATAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
476946 ATCTCACTTGAGATAGTTTCACTCTAAACATAATATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
476985 ATCTCGCTTGAGATAGTTTCACTCTAAACA-AATAATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAA-GATTTT
* * * *
477024 ATCTCACTTAAGATAGTTTCACTTGAAACAGAATATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
477063 ATGTCGCTTGAGATAGTTTTACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
477101 ATCTCGCTTGAGATAATTTAACTCGAAATAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
477139 ATCTCGCTTGAGATAGTTTCACTC-AACACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAA-ACAGAAGATTTT
* * * *
477177 ATGTCGCTTGAGATAGGTTCAC-CCAAACAGTAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
477215 ATCTCGCTTAAGATAGTTTCACTCGAAACAGAAGTTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
477254 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* ** *
477292 ATCTCGCTTGAGATAATTGAACTCGAAACATAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
477330 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
477368 ATCTCGCTTGAGATAGGTTCACCCG-AACAGTAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
477406 ATCTCGCTTAATATAGTTTCACTCGAAACAGAAGTTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
477445 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
477484 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
477523 ATCTCGCTTGAGATAGTTTCACTCGAAATAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
477561 ATCTCTCTTGAGATTGTTT
1 ATCTCGCTTGAGATAGTTT
477580 TTCTTAAAGA
Statistics
Matches: 871, Mismatches: 101, Indels: 34
0.87 0.10 0.03
Matches are distributed among these distances:
37 18 0.02
38 318 0.37
39 499 0.57
40 4 0.00
43 1 0.00
44 31 0.04
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:477119 original size:19 final size:20
Alignment explanation
Indices: 477060--477154 Score: 65
Period size: 19 Copynumber: 5.0 Consensus size: 20
477050 AACAGAATAT
* *
477060 TTTATGTCGCTTGAGATAGT
1 TTTATCTCGCTTGAGATAGA
****
477080 TTTA-CTCGAAACAGA-AGA
1 TTTATCTCGCTTGAGATAGA
477098 TTTATCTCGCTTGAGATA-A
1 TTTATCTCGCTTGAGATAGA
* **
477117 TTTAACTCGAAAT-AGA-AGA
1 TTTATCTCG-CTTGAGATAGA
477136 TTTATCTCGCTTGAGATAG
1 TTTATCTCGCTTGAGATAG
477155 TTTCACTCAA
Statistics
Matches: 53, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
18 8 0.15
19 37 0.70
20 8 0.15
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (20 bp):
TTTATCTCGCTTGAGATAGA
Found at i:477297 original size:19 final size:19
Alignment explanation
Indices: 477275--477373 Score: 51
Period size: 19 Copynumber: 5.2 Consensus size: 19
477265 GATAGTTTCA
477275 CTCGAAACAGAAGATTTAT
1 CTCGAAACAGAAGATTTAT
**** * *
477294 CTCGCTTGAGATA-ATTGAA
1 CTCGAAACAGA-AGATTTAT
*
477313 CTCGAAACATAAGATTTAT
1 CTCGAAACAGAAGATTTAT
****
477332 CTCGCTTGAGATAG-TTTCA-
1 CTCGAAACAGA-AGATTT-AT
477351 CTCGAAACAGAAGATTTAT
1 CTCGAAACAGAAGATTTAT
477370 CTCG
1 CTCG
477374 CTTGAGATAG
Statistics
Matches: 52, Mismatches: 22, Indels: 12
0.60 0.26 0.14
Matches are distributed among these distances:
18 4 0.08
19 44 0.85
20 4 0.08
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (19 bp):
CTCGAAACAGAAGATTTAT
Found at i:477678 original size:59 final size:57
Alignment explanation
Indices: 477601--477788 Score: 207
Period size: 59 Copynumber: 3.2 Consensus size: 57
477591 AACTGCACCT
* * *
477601 CACATGAGGGATTAACATTTCCTTAGCTAGATTCACAACACTTCGAATCAACAATGCCC
1 CACATGAGGGA-TAACATTTCCTT-GCTCGATTCATAACACTTCGAATCAGCAATGCCC
* * * * *
477660 CACTTGAGGGATCAACATTTCATTTGCTCGACTCATAACACTTCGAATCAGCAACGCAC
1 CACATGAGGGAT-AACATTTC-CTTGCTCGATTCATAACACTTCGAATCAGCAATGCCC
* * *
477719 CACCA-GAAGGGATGACATTTCCTGTGCTCGATTCATAACACTTCGAATCAGCCATGCCT
1 CA-CATG-AGGGATAACATTTCCT-TGCTCGATTCATAACACTTCGAATCAGCAATGCCC
477778 CACATGAGGGA
1 CACATGAGGGA
477789 ACAATATTCC
Statistics
Matches: 107, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
58 9 0.08
59 89 0.83
60 9 0.08
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (57 bp):
CACATGAGGGATAACATTTCCTTGCTCGATTCATAACACTTCGAATCAGCAATGCCC
Found at i:479174 original size:132 final size:132
Alignment explanation
Indices: 478934--479194 Score: 386
Period size: 132 Copynumber: 2.0 Consensus size: 132
478924 CGGCAGGGGA
* *
478934 AGAGGGGAGAGAATTTATATATATATTTTTTGTGTTTGGCTTAAAATGAAATAAAAAAAAAGTTT
1 AGAGGGGAGAGAA-TTATATATATATTTTTTATGTTTGGCTTAAAATGAAATAAAAAAAAAATTT
*
478999 TGAATATATAGGGTAAGTCAAGGGTCTAATTATGTTAAAGCCCCTGAACCTTTGCCTTGTTTTTA
65 TGAATATATAGGGTAAGTCAAGGGTCTAATTACGTTAAAGCCCCTGAACCTTTGCCTTGTTTTTA
479064 CAG
130 CAG
479067 AGAGGGGAGAGAA-T-T-TATAT-TTTTTTATGTTTGGCTTAAAATGAAATAAAAAAAACAAAAT
1 AGAGGGGAGAGAATTATATATATATTTTTTATGTTTGGCTTAAAATGAAAT--AAAAAA-AAAAT
* * * *
479128 TTTGGTATATATAGGGTAAGTCAAGGGTCTTATTGCGTTAAGGCCCCTGAACCTTTGCCTTGTTT
63 TTT-GAATATATAGGGTAAGTCAAGGGTCTAATTACGTTAAAGCCCCTGAACCTTTGCCTTGTTT
479193 TT
127 TT
479195 GTAGTTTGGT
Statistics
Matches: 117, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
128 26 0.22
129 5 0.04
130 7 0.06
131 8 0.07
132 58 0.50
133 13 0.11
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (132 bp):
AGAGGGGAGAGAATTATATATATATTTTTTATGTTTGGCTTAAAATGAAATAAAAAAAAAATTTT
GAATATATAGGGTAAGTCAAGGGTCTAATTACGTTAAAGCCCCTGAACCTTTGCCTTGTTTTTAC
AG
Found at i:485350 original size:21 final size:21
Alignment explanation
Indices: 485324--485377 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
485314 TGAACCCTTG
485324 GTATCGATACTTTTTTAATAA
1 GTATCGATACTTTTTTAATAA
485345 GTATCGATACTTTTTTAATAA
1 GTATCGATACTTTTTTAATAA
485366 GTATCGATACTT
1 GTATCGATACTT
485378 ATCCATCGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (21 bp):
GTATCGATACTTTTTTAATAA
Found at i:485734 original size:17 final size:16
Alignment explanation
Indices: 485696--485734 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
485686 CCACTCTGAT
*
485696 TAAAAAATTTGGATAT
1 TAAAAAATTTGGATAC
485712 TCAAAAAATTTGGATACC
1 T-AAAAAATTTGGATA-C
485730 TAAAA
1 TAAAA
485735 TAATGATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.90
18 1 0.05
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (16 bp):
TAAAAAATTTGGATAC
Found at i:489782 original size:129 final size:130
Alignment explanation
Indices: 489547--489805 Score: 493
Period size: 129 Copynumber: 2.0 Consensus size: 130
489537 CTCGTTCTTC
489547 AACCGTTGTTTTGGTAAGCCTTCGATAATTTTCTGGCCATTTCAATTTGTTTCGGCTTGATATCT
1 AACCGTTGTTTTGGTAAGCCTTCGATAATTTTCTGGCCATTTCAATTTGTTTCGGCTTGATATCT
489612 GAACTGTTATTGATTGATTTTGGCAAGTGACTGAACATGGACTAATTGGCACCCCT-AATCATCT
66 GAACTGTTATTGATTGATTTTGGCAAGTGACTGAACATGGACTAATTGGCACCCCTAAATCATCT
*
489676 AACCTTTGTTTTGGTAAGCCTTCGATAATTTTCTGGCCATTTCAATTTGTTTCGGCTTGATATCT
1 AACCGTTGTTTTGGTAAGCCTTCGATAATTTTCTGGCCATTTCAATTTGTTTCGGCTTGATATCT
*
489741 GAACTGTTATTGATTGATTTTGGCAAGTGACTGAACATGGACTAATTGGCAGCCCTAAATCATCT
66 GAACTGTTATTGATTGATTTTGGCAAGTGACTGAACATGGACTAATTGGCACCCCTAAATCATCT
489806 CCATCGCCAC
Statistics
Matches: 127, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
129 119 0.94
130 8 0.06
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (130 bp):
AACCGTTGTTTTGGTAAGCCTTCGATAATTTTCTGGCCATTTCAATTTGTTTCGGCTTGATATCT
GAACTGTTATTGATTGATTTTGGCAAGTGACTGAACATGGACTAATTGGCACCCCTAAATCATCT
Found at i:494148 original size:15 final size:15
Alignment explanation
Indices: 494128--494157 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
494118 ATCGTGAATA
494128 TTAAATAAATAAATT
1 TTAAATAAATAAATT
494143 TTAAATAAATAAATT
1 TTAAATAAATAAATT
494158 CACAAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAATAAATAAATT
Found at i:494175 original size:29 final size:29
Alignment explanation
Indices: 494138--494193 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
494128 TTAAATAAAT
* *
494138 AAATTTTAAATAAATAAATTCACAAACAA
1 AAATGTTAAACAAATAAATTCACAAACAA
* *
494167 AAATGTTAAACGAATATATTCACAAAC
1 AAATGTTAAACAAATAAATTCACAAAC
494194 GTTAAATGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (29 bp):
AAATGTTAAACAAATAAATTCACAAACAA
Found at i:496393 original size:131 final size:132
Alignment explanation
Indices: 496159--496492 Score: 424
Period size: 131 Copynumber: 2.6 Consensus size: 132
496149 TTTAAGAGTA
* * * * *
496159 AAAATGATAATATCT-GATTATTTTCAATCAAGAATAAATGACCTTT-ATTGCATTACAACAATC
1 AAAATGATAATATCTAAATTATTTACAATCGAGAATAAATGACCTTTCA-TGCATTAAAACATTC
* * *
496222 ATTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGTCTTAAAATTCAATATCGATTCAA
65 ATTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGCCTTAAAAATCAATATCAATTCAA
*
496287 GTG
130 GAG
* *
496290 AAAATGATAATAT-TAAATTATTTACAATCGAGAATAAATGACCTTTCGTACATTAAAACATTCA
1 AAAATGATAATATCTAAATTATTTACAATCGAGAATAAATGACCTTTCATGCATTAAAACATTCA
** * *
496354 TTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGCCTTAAAAATCGGTATTAATTCGAG
66 TTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGCCTTAAAAATCAATATCAATTCAAG
496419 AG
131 AG
* * * * * * * *
496421 AAAACGACAATATCCAAA-CATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCATTCA
1 AAAATGATAATATCTAAATTATTTACAATCGAGAATAAATGACCTTTCATGCATTAAAACATTCA
496485 TTTATTAC
66 TTTATTAC
496493 TCCGACCAAA
Statistics
Matches: 175, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
130 1 0.01
131 171 0.98
132 3 0.02
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (132 bp):
AAAATGATAATATCTAAATTATTTACAATCGAGAATAAATGACCTTTCATGCATTAAAACATTCA
TTTATTACCCCAATTGAAATAAAGAGATATTACTATTTCGCCTTAAAAATCAATATCAATTCAAG
AG
Found at i:498607 original size:3 final size:3
Alignment explanation
Indices: 498599--498653 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
498589 ATGTATTTAT
* * *
498599 TAA TAA TAA TAT TAA TAA TAA TAA CAT TAA TAA TAA TAA -AA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
498644 TAA T-A TAA TA
1 TAA TAA TAA TA
498654 GTATAATAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:498619 original size:15 final size:15
Alignment explanation
Indices: 498599--498653 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
498589 ATGTATTTAT
498599 TAATAATAATATTAA
1 TAATAATAATATTAA
*
498614 TAATAATAACATTAA
1 TAATAATAATATTAA
*
498629 TAATAATAAAATTAA
1 TAATAATAATATTAA
498644 TAAT-ATAATA
1 TAATAATAATA
498654 GTATAATAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
14 5 0.14
15 32 0.86
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATAATAATATTAA
Found at i:499043 original size:134 final size:132
Alignment explanation
Indices: 498793--499248 Score: 534
Period size: 134 Copynumber: 3.4 Consensus size: 132
498783 ATATGATAAG
* * *
498793 GGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTGCACTGTCAC
1 GGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTACAATGTCAC
* * * * * * * * *
498858 TCACGAAAGATTGAATCAAGGCAGATTTATTCCTCTATCACTTAAGGAATATTAAATCTTAGAAG
66 TCA-GGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTT-GAAG
498923 AGAA
129 AGAA
* * *
498927 GGATTTGTTCCGCTTCGTCTTGAGGGAAAATCAGACATGGGGACGTTGATTCATTACAATGTCAC
1 GGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTACAATGTCAC
* * *
498992 TAAGGGAAGATTGAATCGAGGCAGACTTGTTACAATATTACTCAGGGAATATCAAATCTTGAAAG
66 TCA-GGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTG-AAG
*
499057 AGAG
129 AGAA
* * * * * * * * * * *
499061 GGATCTATTCCACTTCTTCTTAAGTGAAAATCAGATTTAGCGACATTGATTCATTCCAGTGTCAC
1 GGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTACAATGTCAC
* *
499126 TCAGGAAGATTGAATAGAGGCAGACTTGTTCCACTTTTACTCAGGGAATATCAAATCTTGGAAGA
66 TCAGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTT-GAAGA
*
499191 GAT
130 GAA
* * * *
499194 GGATATGTTCAGCTTCTTTTTGAGGGAAAATCAAATATGGGTACGTTGATTCATT
1 GGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATT
499249 CCACTATTCT
Statistics
Matches: 268, Mismatches: 52, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
133 101 0.38
134 167 0.62
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (132 bp):
GGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTACAATGTCAC
TCAGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAATATCAAATCTTGAAGAG
AA
Found at i:500502 original size:6 final size:6
Alignment explanation
Indices: 500491--500622 Score: 64
Period size: 6 Copynumber: 21.7 Consensus size: 6
500481 TTATTTATTC
500491 TTTCTT TTTC-T TTTCTT TCGTT-TT TTT-TT CTTT-TT TTTCATT TTTCATT
1 TTTCTT TTTCTT TTTCTT T--TTCTT TTTCTT -TTTCTT TTTC-TT TTTC-TT
* * *
500540 TTT-TT CATTCTT TTTCTT TTTCTTTT TTTCCTT TTTCCTT TTCCTT TTCCTT
1 TTTCTT -TTTCTT TTTCTT TTTC--TT TTT-CTT TTT-CTT TTTCTT TTTCTT
* * *
500592 TTT-TT ATT-TT TTTATT TTT-TT CTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
500623 AGGCAAAGTA
Statistics
Matches: 105, Mismatches: 8, Indels: 26
0.76 0.06 0.19
Matches are distributed among these distances:
5 26 0.25
6 43 0.41
7 28 0.27
8 7 0.07
9 1 0.01
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:500514 original size:16 final size:15
Alignment explanation
Indices: 500488--500582 Score: 83
Period size: 16 Copynumber: 6.2 Consensus size: 15
500478 TTTTTATTTA
500488 TTCTTTCTTTTTCTT
1 TTCTTTCTTTTTCTT
500503 TTCTTTCGTTTTT-TT
1 TTCTTTC-TTTTTCTT
500518 TTCTTT-TTTTTCATTT
1 TTCTTTCTTTTTC--TT
*
500534 TTCATT-TTTTTCATT
1 TTCTTTCTTTTTC-TT
500549 CTT-TTTCTTTTTCTT
1 -TTCTTTCTTTTTCTT
500564 TT-TTTCCTTTTTCCTT
1 TTCTTT-CTTTTT-CTT
500580 TTC
1 TTC
500583 CTTTTCCTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
13 5 0.07
14 5 0.07
15 27 0.40
16 31 0.46
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (15 bp):
TTCTTTCTTTTTCTT
Found at i:500520 original size:20 final size:20
Alignment explanation
Indices: 500495--500575 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
500485 TTATTCTTTC
*
500495 TTTTTCTTTTCTTTCGTTTT
1 TTTTTCTTTTCTTTCATTTT
*
500515 TTTTTCTTTTTTTTCATTTT
1 TTTTTCTTTTCTTTCATTTT
* * *
500535 TCATTT-TTTTCATTCTTTTT
1 T-TTTTCTTTTCTTTCATTTT
*
500555 CTTTTTCTTTT-TTTCCTTTT
1 -TTTTTCTTTTCTTTCATTTT
500575 T
1 T
500576 CCTTTTCCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 40 0.82
21 8 0.16
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTCTTTCATTTT
Found at i:500535 original size:36 final size:35
Alignment explanation
Indices: 500477--500568 Score: 100
Period size: 35 Copynumber: 2.6 Consensus size: 35
500467 TTGAACCCTC
* *
500477 TTTTTTATTTATTCTTTCTTTTTC-TTTTCTTTCGTTT
1 TTTTTTCTTT-TTCTTTCTTTTTCATTTT-TTTC-ATT
500514 TTTTTTCTTTTT-TTTCATTTTTCATTTTTTTCATT
1 TTTTTTCTTTTTCTTTC-TTTTTCATTTTTTTCATT
*
500549 CTTTTTCTTTTTCTTT-TTTT
1 TTTTTTCTTTTTCTTTCTTTT
500569 CCTTTTTCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
34 4 0.08
35 17 0.35
36 15 0.31
37 13 0.27
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.80
Consensus pattern (35 bp):
TTTTTTCTTTTTCTTTCTTTTTCATTTTTTTCATT
Found at i:500566 original size:40 final size:40
Alignment explanation
Indices: 500501--500581 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
500491 TTTCTTTTTC
*
500501 TTTTCTTTCGTTTTTTTTTCTTTTTTTTCATTTTTCATTT
1 TTTTCATTCGTTTTTTTTTCTTTTTTTTCATTTTTCATTT
* * *
500541 TTTTCATTCTTTTTCTTTTTC-TTTTTTTCCTTTTTCCTTT
1 TTTTCATTCGTTTT-TTTTTCTTTTTTTTCATTTTTCATTT
500581 T
1 T
500582 CCTTTTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 30 0.83
41 6 0.17
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (40 bp):
TTTTCATTCGTTTTTTTTTCTTTTTTTTCATTTTTCATTT
Found at i:500567 original size:26 final size:26
Alignment explanation
Indices: 500492--500621 Score: 81
Period size: 25 Copynumber: 4.9 Consensus size: 26
500482 TATTTATTCT
500492 TTCTTTTTCTTTTCTTTCGTTTTTTTTTC
1 TTCTTTTTC-TTT-TTTC-TTTTTTTTTC
* * *
500521 TTTTTTTTCATTTTTC-ATTTTTTTC
1 TTCTTTTTCTTTTTTCTTTTTTTTTC
*
500546 ATTCTTTTTC-TTTTTCTTTTTTTCCTTT
1 -TTCTTTTTCTTTTTTCTTTTTTT--TTC
* * *
500574 TTCCTTTTCCTTTTCCTTTTTTTATT-
1 TTCTTTTTCTTTTTTCTTTTTTT-TTC
* *
500600 TT-TTTAT-TTTTTTCTTCTTTTT
1 TTCTTTTTCTTTTTTCTTTTTTTT
500622 CAGGCAAAGT
Statistics
Matches: 82, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
23 1 0.01
24 11 0.13
25 17 0.21
26 15 0.18
27 14 0.17
28 16 0.20
29 8 0.10
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (26 bp):
TTCTTTTTCTTTTTTCTTTTTTTTTC
Found at i:500593 original size:40 final size:39
Alignment explanation
Indices: 500511--500610 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 39
500501 TTTTCTTTCG
*
500511 TTTTTTTTTCTTTTTTTTCATTTTTCATTTTTTTCATTCT
1 TTTTTTTTTCTTTTTTTTCATTTTTCATTTTTTT-ATCCT
* *
500551 TTTTCTTTTTC-TTTTTTTCCTTTTTCCTTTTCCTTT-TCCT
1 TTTT-TTTTTCTTTTTTTTCATTTTTCATTTT--TTTATCCT
*
500591 TTTTTTATTTTTTTATTTTT
1 TTTTTT-TTTCTTT-TTTTT
500611 TTCTTCTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
39 2 0.04
40 32 0.64
41 8 0.16
42 8 0.16
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (39 bp):
TTTTTTTTTCTTTTTTTTCATTTTTCATTTTTTTATCCT
Found at i:500602 original size:15 final size:15
Alignment explanation
Indices: 500477--500602 Score: 55
Period size: 16 Copynumber: 7.8 Consensus size: 15
500467 TTGAACCCTC
500477 TTTTTTATTTATT-CT
1 TTTTTTATTT-TTCCT
500492 TTCTTTT-TCTTTT-CT
1 TT-TTTTAT-TTTTCCT
*
500507 TTCGTTTT-TTTTTCTT
1 TT--TTTTATTTTTCCT
*
500523 TTTTTTCATTTTTCAT
1 TTTTTT-ATTTTTCCT
*
500539 TTTTTTCATTCTTTTTCT
1 TTTTTT-A-T-TTTTCCT
500557 TTTTCTT-TTTTTCCT
1 TTTT-TTATTTTTCCT
*
500572 TTTTCCTTTTCCTTTTCCT
1 TTTT--TTAT--TTTTCCT
500591 TTTTTTATTTTT
1 TTTTTTATTTTT
500603 TTATTTTTTT
Statistics
Matches: 91, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
14 4 0.04
15 27 0.30
16 33 0.36
17 5 0.05
18 9 0.10
19 13 0.14
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.79
Consensus pattern (15 bp):
TTTTTTATTTTTCCT
Done.