Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008018.1 Hibiscus syriacus cultivar Beakdansim tig00110485_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: 927418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:428691 original size:32 final size:31
Alignment explanation
Indices: 428653--428729 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
428643 CGGGGTCGTG
*
428653 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** * **
428685 GGGCCTACCCGATAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
428716 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
428730 GTCACATTAG
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:429662 original size:29 final size:29
Alignment explanation
Indices: 429622--429749 Score: 179
Period size: 29 Copynumber: 4.4 Consensus size: 29
429612 TCGAAAATTC
*
429622 CCAA-AATATCACCTTTTTCAAAATATTT
1 CCAAGAATGTCACCTTTTTCAAAATATTT
*
429650 CCAAGAATGTCACATTTTTCAAAATATTT
1 CCAAGAATGTCACCTTTTTCAAAATATTT
*
429679 CCCAGAATGTCACCTTTTTCAAAATATTT
1 CCAAGAATGTCACCTTTTTCAAAATATTT
* *
429708 CTC-AGAATGTCACCTTTTTCAAAAAAATT
1 C-CAAGAATGTCACCTTTTTCAAAATATTT
*
429737 CCCAGAATGTCAC
1 CCAAGAATGTCAC
429750 TGGGTCGGGT
Statistics
Matches: 91, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
28 5 0.05
29 85 0.93
30 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (29 bp):
CCAAGAATGTCACCTTTTTCAAAATATTT
Found at i:429692 original size:58 final size:58
Alignment explanation
Indices: 429615--429749 Score: 209
Period size: 58 Copynumber: 2.3 Consensus size: 58
429605 TCCACATTCG
* *
429615 AAAATTCCCAAAATATCACCTTTTTCAAAATATTTC-CAAGAATGTCACATTTTTCAAA
1 AAAATTCCCAGAATGTCACCTTTTTCAAAATATTTCTC-AGAATGTCACATTTTTCAAA
* * *
429673 ATATTTCCCAGAATGTCACCTTTTTCAAAATATTTCTCAGAATGTCACCTTTTTCAAA
1 AAAATTCCCAGAATGTCACCTTTTTCAAAATATTTCTCAGAATGTCACATTTTTCAAA
429731 AAAATTCCCAGAATGTCAC
1 AAAATTCCCAGAATGTCAC
429750 TGGGTCGGGT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 68 0.99
59 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (58 bp):
AAAATTCCCAGAATGTCACCTTTTTCAAAATATTTCTCAGAATGTCACATTTTTCAAA
Found at i:429791 original size:16 final size:18
Alignment explanation
Indices: 429757--429792 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
429747 CACTGGGTCG
429757 GGTCTGGTCAACGGGTTC
1 GGTCTGGTCAACGGGTTC
429775 GGTC-GGTCAAC-GGTTC
1 GGTCTGGTCAACGGGTTC
429791 GG
1 GG
429793 GTCAGACCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.11, C:0.22, G:0.42, T:0.25
Consensus pattern (18 bp):
GGTCTGGTCAACGGGTTC
Found at i:429795 original size:17 final size:19
Alignment explanation
Indices: 429754--429795 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
429744 TGTCACTGGG
429754 TCGGGTCTGGTCAACGGGT
1 TCGGGTCTGGTCAACGGGT
429773 TC-GGTC-GGTCAAC-GGT
1 TCGGGTCTGGTCAACGGGT
429789 TCGGGTC
1 TCGGGTC
429796 AGACCGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 11 0.50
18 4 0.18
19 2 0.09
ACGTcount: A:0.10, C:0.24, G:0.40, T:0.26
Consensus pattern (19 bp):
TCGGGTCTGGTCAACGGGT
Found at i:435851 original size:29 final size:29
Alignment explanation
Indices: 435728--435922 Score: 178
Period size: 29 Copynumber: 6.6 Consensus size: 29
435718 CACATTCAAA
* * *
435728 AATTCTCAAAATGTCACCTTTTTTCAAAAT
1 AATTCCCAGAATGTCA-CATTTTTCAAAAT
** * *
435758 AATTCCCATCATATCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* **
435787 AATTCCCAGAATGTCAAAAAGAATTTCAAAAT
1 AATTCCCAGAATGTC--ACA-TTTTTCAAAAT
* *
435819 ATTTCTCAGAATGTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* *
435848 ATTTCCCAGAATATCACATTTTTCACAAA-
1 AATTCCCAGAATGTCACATTTTTCA-AAAT
*
435877 AATTCCCAGAATGTCACCTTTTTCACAAA-
1 AATTCCCAGAATGTCACATTTTTCA-AAAT
*
435906 AATTCTCAGAATGTCAC
1 AATTCCCAGAATGTCAC
435923 TGGGTCGGGT
Statistics
Matches: 138, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
29 98 0.71
30 17 0.12
31 1 0.01
32 22 0.16
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (29 bp):
AATTCCCAGAATGTCACATTTTTCAAAAT
Found at i:435884 original size:90 final size:89
Alignment explanation
Indices: 435722--435892 Score: 247
Period size: 90 Copynumber: 1.9 Consensus size: 89
435712 ATAGTCCACA
* ** *
435722 TTCAAAAATTCTCAAAATGTCACCTTTTTTCAAAATAATTCCCATCATATCACCTTTTTCAAAAT
1 TTCAAAAATTCTCAAAATGTCACCATTTTTCAAAATAATTCCCAGAATATCACATTTTTCAAAAT
435787 AATTCCCAGAATGTCAAAAAGAAT
66 AATTCCCAGAATGTCAAAAAGAAT
* *
435811 TTCAAAATATTTCTCAGAATGTCA-CATTTTTCAAAATATTTCCCAGAATATCACATTTTTCACA
1 TTCAAAA-A-TTCTCAAAATGTCACCATTTTTCAAAATAATTCCCAGAATATCACATTTTTCA-A
435875 AA-AATTCCCAGAATGTCA
63 AATAATTCCCAGAATGTCA
435893 CCTTTTTCAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
89 7 0.10
90 50 0.68
91 16 0.22
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (89 bp):
TTCAAAAATTCTCAAAATGTCACCATTTTTCAAAATAATTCCCAGAATATCACATTTTTCAAAAT
AATTCCCAGAATGTCAAAAAGAAT
Found at i:435908 original size:90 final size:86
Alignment explanation
Indices: 435722--435922 Score: 226
Period size: 90 Copynumber: 2.3 Consensus size: 86
435712 ATAGTCCACA
* * ** *
435722 TTCAAAAATTCTCAAAATGTCACCTTTTTTCAAAATAATTCCCATCATATCACCTTTTTCAAAAT
1 TTCAAAAATTCTCAGAATGTCA-CATTTTTCAAAATAATTCCCAGAATATCACATTTTTCAAAAT
*
435787 AATTCCCAGAATGTCAAAAAGAAT
65 AATTCCCAGAATGTC--AAACAAT
*
435811 TTCAAAATATTTCTCAGAATGTCACATTTTTCAAAATATTTCCCAGAATATCACATTTTTCACAA
1 TTCAAAA-A-TTCTCAGAATGTCACATTTTTCAAAATAATTCCCAGAATATCACATTTTTCA-AA
* **
435876 A-AATTCCCAGAATGTC-ACCTTT
63 ATAATTCCCAGAATGTCAAACAAT
435898 TTCACAAAAATTCTCAGAATGTCAC
1 TT--CAAAAATTCTCAGAATGTCAC
435923 TGGGTCGGGT
Statistics
Matches: 97, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
87 19 0.20
88 1 0.01
89 12 0.12
90 49 0.51
91 16 0.16
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (86 bp):
TTCAAAAATTCTCAGAATGTCACATTTTTCAAAATAATTCCCAGAATATCACATTTTTCAAAATA
ATTCCCAGAATGTCAAACAAT
Found at i:436820 original size:23 final size:23
Alignment explanation
Indices: 436794--436871 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
436784 CACCACAGCT
436794 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
436817 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
436840 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
436863 TATAATAAT
1 CAT-ATAAT
436872 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:437045 original size:101 final size:102
Alignment explanation
Indices: 436878--437093 Score: 335
Period size: 101 Copynumber: 2.1 Consensus size: 102
436868 TAATGTCCAT
* * *
436878 AAGGACCACATATCATTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
*
436943 GACTTCACACATGTTCCAAAGAATAC-ATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACAATATGTCCCG
* * * * *
436979 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATTAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
437044 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACA-ATATGTCCCG
437082 AAGGACCACATA
1 AAGGACCACATA
437094 GACCCTTGAC
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
101 83 0.81
103 20 0.19
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
GACTTCACACATGTTCCAAAGAATACAATATGTCCCG
Found at i:437962 original size:14 final size:14
Alignment explanation
Indices: 437943--437969 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
437933 TATTATTGGG
437943 ATGCATCGATGCAT
1 ATGCATCGATGCAT
437957 ATGCATCGATGCA
1 ATGCATCGATGCA
437970 CCAATTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (14 bp):
ATGCATCGATGCAT
Found at i:445040 original size:20 final size:20
Alignment explanation
Indices: 444996--445283 Score: 238
Period size: 20 Copynumber: 14.2 Consensus size: 20
444986 AATGACCAAC
*
444996 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
445015 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
445035 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
445055 AAAACCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
445075 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
445097 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
445117 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
445139 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
445159 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
445179 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
445199 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
445219 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
445239 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
445259 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
445279 AAAAT
1 AAAAT
445284 GAGTAAATTC
Statistics
Matches: 228, Mismatches: 20, Indels: 41
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.01
19 22 0.10
20 164 0.72
21 6 0.03
22 29 0.13
23 2 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:445189 original size:40 final size:40
Alignment explanation
Indices: 445073--445283 Score: 300
Period size: 40 Copynumber: 5.2 Consensus size: 40
445063 AACGGTCAAA
* *
445073 AGAAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTA
1 AGAAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTC
*
445115 AGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTC
445157 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCC
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT-C
* * *
445198 A-AGAATCGCAACGCGATT-CAGAAAATCGCAACGCGATTA
1 AGAAAATCGCAACGCGATTCCA-AGAATCGCAACGCGATTC
445237 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
445277 AGAAAAT
1 AGAAAAT
445284 GAGTAAATTC
Statistics
Matches: 153, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
39 3 0.02
40 94 0.61
41 4 0.03
42 52 0.34
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (40 bp):
AGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
Found at i:445223 original size:60 final size:58
Alignment explanation
Indices: 445077--445283 Score: 290
Period size: 60 Copynumber: 3.4 Consensus size: 58
445067 GTCAAAAGAA
* *
445077 AATCGCAACGCGATATTCCA-AGAATCGCAATGCGATTAAGAGAATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCG--ATT-CAGAAAATCGCAACGCGATT-A-AGAATCGCAACGCGA--TTCCAAG
445141 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATT--AAGAATCGCAACGCGATTCCAAG
445201 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAG--AATCGCAACGCGATTCCAAG
445261 AATCGCAACGCGATTCAGAAAAT
1 AATCGCAACGCGATTCAGAAAAT
445284 GAGTAAATTC
Statistics
Matches: 136, Mismatches: 3, Indels: 12
0.90 0.02 0.08
Matches are distributed among these distances:
58 3 0.02
60 85 0.62
61 2 0.01
62 33 0.24
63 1 0.01
64 12 0.09
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (58 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATTAAGAATCGCAACGCGATTCCAAG
Found at i:445390 original size:6 final size:6
Alignment explanation
Indices: 445379--445483 Score: 210
Period size: 6 Copynumber: 17.5 Consensus size: 6
445369 GACACGTATT
445379 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
445427 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
445475 ACCACG ACC
1 ACCACG ACC
445484 CGAGACGAGA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 99 1.00
ACGTcount: A:0.33, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:445992 original size:6 final size:6
Alignment explanation
Indices: 445981--446077 Score: 194
Period size: 6 Copynumber: 16.2 Consensus size: 6
445971 TCGTCTCGTC
445981 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
446029 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
446077 T
1 T
446078 AATACGTGTC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 91 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:446573 original size:20 final size:20
Alignment explanation
Indices: 446173--446600 Score: 407
Period size: 20 Copynumber: 21.2 Consensus size: 20
446163 GAATTTACTC
446173 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446193 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446213 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446233 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446253 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446273 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
* *
446293 ATTTTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446313 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446333 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
446353 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446373 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
446393 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446413 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
446433 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446453 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
446475 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446495 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
446517 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
446537 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
446557 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
446577 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
446596 ATTTT
1 ATTTT
446601 GTTGGTCATT
Statistics
Matches: 340, Mismatches: 39, Indels: 59
0.78 0.09 0.13
Matches are distributed among these distances:
17 1 0.00
18 2 0.01
19 28 0.08
20 256 0.75
21 24 0.07
22 28 0.08
25 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:449556 original size:26 final size:27
Alignment explanation
Indices: 449522--449573 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
449512 TATTTAAATT
449522 TTTTCCCTTTTAGTTTCATTTT-TATGG
1 TTTTCCCTTTTAGTTTC-TTTTCTATGG
*
449549 TTTT-CCTTTTTGTTTCTTTTCTATG
1 TTTTCCCTTTTAGTTTCTTTTCTATG
449574 ATTAAGTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 15 0.65
27 4 0.17
ACGTcount: A:0.08, C:0.15, G:0.10, T:0.67
Consensus pattern (27 bp):
TTTTCCCTTTTAGTTTCTTTTCTATGG
Found at i:449849 original size:102 final size:102
Alignment explanation
Indices: 449735--449941 Score: 299
Period size: 102 Copynumber: 2.0 Consensus size: 102
449725 TGATGCAGTA
* * * *
449735 GAAGAGAAAATTAGGCAAGTTGATCCAAGAGGGCAAAATGTGC-ATAGTGTTCTCAAGCCAGATG
1 GAAGAAAAAATTAGACAAGTTAATCCAAGAGGGCAAAATGTGCAAT-GTGTTCTCAAACCAGATG
449799 AAGATGAGCGTGTAGATGTACATACAAGTACTGATGCT
65 AAGATGAGCGTGTAGATGTACATACAAGTACTGATGCT
* ** *
449837 GAAGAAAAAATTAGACAATTTAATCCAAGAGGGCATCATGTGCAATGTTTTCTCAAACCAGATGA
1 GAAGAAAAAATTAGACAAGTTAATCCAAGAGGGCAAAATGTGCAATGTGTTCTCAAACCAGATGA
* * *
449902 AGATGGGCGTGTAGTTGTACATATAAGTACTGATGCT
66 AGATGAGCGTGTAGATGTACATACAAGTACTGATGCT
449939 GAA
1 GAA
449942 TCCAAGTTGG
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 91 0.98
103 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (102 bp):
GAAGAAAAAATTAGACAAGTTAATCCAAGAGGGCAAAATGTGCAATGTGTTCTCAAACCAGATGA
AGATGAGCGTGTAGATGTACATACAAGTACTGATGCT
Found at i:450913 original size:156 final size:154
Alignment explanation
Indices: 450509--450931 Score: 566
Period size: 156 Copynumber: 2.7 Consensus size: 154
450499 TTTTAGGGGG
* * *
450509 TGGATTTAAATACTGCTGAGAATAAGGGTGATGCCTCAGAAGCCCTTTCACAGGCATTGCAAGAA
1 TGGATTTAAATACTGCTGAGACTAAAGGTGATGCCTCAGAAGCCCTTGCACAGGCATTGCAAGAA
* * * *
450574 AAGGTTTCAGATGTTTATTCTGT-CT-T-TGGTGTCTGGTAATTTATATATTTCTATTTATATCC
66 AAGGTTTTAGATGTTTCTTCTGTCCTGTCTGGTTTCTGGTAATTTATACATTTCTATTTATATCC
**
450636 ATCATATTTTGTAGAGGGATTTGC
131 ATCATATTTTGTAGAGGGACATGC
* * * * *
450660 TCGATTCAAATACTGCTGAGACT-AAGCTTAATGCCTCAGAAGCCCTTGCAAAGGCATTGCAAGA
1 TGGATTTAAATACTGCTGAGACTAAAG-GTGATGCCTCAGAAGCCCTTGCACAGGCATTGCAAGA
* * * *
450724 AAAGGTTTTAGACGTTTCTTTTCTCTGTGGTCTGGTTTCTGGTAATTTATACATTTCTATTTATA
65 AAAGGTTTTAGATGTTTCTTCTGTC-CT-GTCTGGTTTCTGGTAATTTATACATTTCTATTTATA
*
450789 TCCATCATATTTTGTAGAGGGGCATGC
128 TCCATCATATTTTGTAGAGGGACATGC
*
450816 TGGATTTAAATACTGCTGAGACTAAAGGTGACGCCTCAGAAGCCCTTGCACAGGCATTGCAAGAA
1 TGGATTTAAATACTGCTGAGACTAAAGGTGATGCCTCAGAAGCCCTTGCACAGGCATTGCAAGAA
* * *
450881 AAGGTTTTAGATGATTCTTCTGTCACTAGTCTGGTTTCTGGAAATTCATAC
66 AAGGTTTTAGATGTTTCTTCTGTC-CT-GTCTGGTTTCTGGTAATTTATAC
450932 CTTGTTTTCT
Statistics
Matches: 231, Mismatches: 34, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
150 2 0.01
151 72 0.31
153 1 0.00
155 1 0.00
156 152 0.66
157 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (154 bp):
TGGATTTAAATACTGCTGAGACTAAAGGTGATGCCTCAGAAGCCCTTGCACAGGCATTGCAAGAA
AAGGTTTTAGATGTTTCTTCTGTCCTGTCTGGTTTCTGGTAATTTATACATTTCTATTTATATCC
ATCATATTTTGTAGAGGGACATGC
Found at i:455272 original size:103 final size:105
Alignment explanation
Indices: 455093--455558 Score: 381
Period size: 103 Copynumber: 4.5 Consensus size: 105
455083 CAAAGTTTGC
* ** * * *
455093 CTTGTATTTATACACATAT-ATAACTATATATAAGATGAATAAACTCGGGTGAGTGTCGGATTTG
1 CTTGTATTTATACACATATCA-AACTATATATCAGATGGTTAAACTCGAGTGAGTGTCGAATTTA
* * *
455157 GATATGTGTCCTACATGGTATGCTCAAATATTTCT-AA-GT
65 GACATGTATCCTACATAGTATGCTCAAATATTTCTGAATGT
* *
455196 CTTGTATTTATACACATATCAAACTAAATATCAGATGGTTGAACTCGAGTGAGTGTCGAATTTAG
1 CTTGTATTTATACACATATCAAACTATATATCAGATGGTTAAACTCGAGTGAGTGTCGAATTTAG
* * * * *
455261 ACATGAATCCTACATGGAATGC-C-TA-ATTTCTGGATGT
66 ACATGTATCCTACATAGTATGCTCAAATATTTCTGAATGT
* * * * * *
455298 -TTG---TTATACACACATCTAACTATATATCATATGGTTGAACTCGAATGAATGTC-AGATTTA
1 CTTGTATTTATACACATATCAAACTATATATCAGATGGTTAAACTCGAGTGAGTGTCGA-ATTTA
* * * * * *
455358 GACGTGTATCCTATATAATATGCTTAATTTTTTTCT-ATATTTGT
65 GACATGTATCCTACATAGTATGCTCAA-ATATTTCTGA-A--TGT
* * * * *
455402 CTTGTATTTTATACACATCT-AAATTATATATCATATGGTTAAACTCGAGCGAGTGTCGGATTT-
1 CTTGTA-TTTATACACATATCAAACTATATATCAGATGGTTAAACTCGAGTGAGTGTCGAATTTA
*
455465 GAACATG--TCCTACATAGTATGCTCAAAT-TTTTTGAAATTTGT
65 G-ACATGTATCCTACATAGTATGCTCAAATATTTCTG-AA--TGT
* * *
455507 CTTGCATTTATACAAATATCTAACTATATATCAGATGGTTAAACTCGAGTGA
1 CTTGTATTTATACACATATCAAACTATATATCAGATGGTTAAACTCGAGTGA
455559 ACGTTAGATT
Statistics
Matches: 289, Mismatches: 53, Indels: 40
0.76 0.14 0.10
Matches are distributed among these distances:
97 1 0.00
98 66 0.23
100 6 0.02
101 5 0.02
102 9 0.03
103 73 0.25
104 19 0.07
105 43 0.15
106 17 0.06
107 1 0.00
108 39 0.13
109 10 0.03
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (105 bp):
CTTGTATTTATACACATATCAAACTATATATCAGATGGTTAAACTCGAGTGAGTGTCGAATTTAG
ACATGTATCCTACATAGTATGCTCAAATATTTCTGAATGT
Found at i:455386 original size:98 final size:98
Alignment explanation
Indices: 455203--455387 Score: 239
Period size: 98 Copynumber: 1.9 Consensus size: 98
455193 AGTCTTGTAT
* * *
455203 TTATACACATATCAAACTAAATATCAGATGGTTGAACTCGAGTGAGTGTCGAATTTAGACATGAA
1 TTATACACACATCAAACTAAATATCAGATGGTTGAACTCGAATGAATGTCGAATTTAGACATGAA
*
455268 TCCTACATGGAATGCCTAATTTCTGGATGTTTG
66 TCCTACATGAAATGCCTAATTTCTGGATGTTTG
* * * * *
455301 TTATACACACATCTAACTATATATCATATGGTTGAACTCGAATGAATGTC-AGATTTAGACGTGT
1 TTATACACACATCAAACTAAATATCAGATGGTTGAACTCGAATGAATGTCGA-ATTTAGACATGA
* *
455365 ATCCTATAT-AATATGCTTAATTT
65 ATCCTACATGAA-ATGCCTAATTT
455388 TTTTCTATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
97 2 0.03
98 72 0.97
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (98 bp):
TTATACACACATCAAACTAAATATCAGATGGTTGAACTCGAATGAATGTCGAATTTAGACATGAA
TCCTACATGAAATGCCTAATTTCTGGATGTTTG
Found at i:455549 original size:105 final size:107
Alignment explanation
Indices: 455301--455575 Score: 290
Period size: 105 Copynumber: 2.6 Consensus size: 107
455291 TGGATGTTTG
* ** *
455301 TTATACACACATCTAACTATATATCATATGGTTGAACTCGAATGAATGTCAGATTTAGACGTGTA
1 TTATACA-ACATCTAACTATATATCATATGGTTAAACTCGAGCGAATGTCAGATTTAGACATG-A
* * * * * *
455366 TCCTATATAATATGCTTAATTTTTTTCTATATTTGTCTTGTATT
64 TCCTACATAATATGCTCAAATTTTTTCGAAATTTGTCTTGCATT
* * *
455410 TTATAC-ACATCTAAATTATATATCATATGGTTAAACTCGAGCGAGTGTCGGATTT-GAACATG-
1 TTATACAACATCT-AACTATATATCATATGGTTAAACTCGAGCGAATGTCAGATTTAG-ACATGA
*
455472 TCCTACATAGTATGCTCAAATTTTTT-GAAATTTGTCTTGCA-T
64 TCCTACATAATATGCTCAAATTTTTTCGAAATTTGTCTTGCATT
* * * * * *
455514 TTATACAAATATCTAACTATATATCAGATGGTTAAACTCGAGTGAACGTTAGATTTCGACAT
1 TTATAC-AACATCTAACTATATATCATATGGTTAAACTCGAGCGAATGTCAGATTTAGACAT
455576 ATGCCCGATG
Statistics
Matches: 139, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
104 7 0.05
105 51 0.37
106 28 0.20
107 7 0.05
108 40 0.29
109 6 0.04
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.40
Consensus pattern (107 bp):
TTATACAACATCTAACTATATATCATATGGTTAAACTCGAGCGAATGTCAGATTTAGACATGATC
CTACATAATATGCTCAAATTTTTTCGAAATTTGTCTTGCATT
Found at i:457123 original size:16 final size:16
Alignment explanation
Indices: 457102--457137 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
457092 AACAGATGCA
457102 ATTCAGATCATTTT-GG
1 ATTCAGAT-ATTTTCGG
457118 ATTCAGATATTTTCGG
1 ATTCAGATATTTTCGG
457134 ATTC
1 ATTC
457138 GAATTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (16 bp):
ATTCAGATATTTTCGG
Found at i:470861 original size:208 final size:206
Alignment explanation
Indices: 470491--470884 Score: 596
Period size: 208 Copynumber: 1.9 Consensus size: 206
470481 GATTTAGTAG
* *
470491 CAGTATAAAAAATATGGATTCATATCAAATTGATGCCTCAGAATCAATACTTTGAGAGAATCATC
1 CAGTACAAAAAATATGGATTCATATCAAATTGATGCCTCAGAATCAATACTTCGAGAGAATCATC
*
470556 AGAGAAAGAAACCTCAGATGGTACGGACAAATGATTGAACATCACAGGCAATCAAGAATCAGAAT
66 AGAGAAAGAAACCTCAGATGGTACGGAAAAATGATTGAACATCACAGGCAATCAAGAATCAGAAT
* * *
470621 ATAATAACAAAACGCTATTCAAATTTGAGTATAGCAAGAGAA-AAACAGAATCCTCTGCCTTAAA
131 ATAATAACAAAACGCTATACAAATTCGAGTATACCAAGAGAAGAAACAGAATCCTCTGCCTTAAA
470685 TAATCATACCA
196 TAATCATACCA
470696 CAGTACAAAAAATACATGGATTCATATCAAATTGATGCCTCAGAATCAA-ATCTTCGAGAGAATA
1 CAGTACAAAAAAT--ATGGATTCATATCAAATTGATGCCTCAGAATCAATA-CTTCGAGAGAAT-
* * * *
470760 CATCAGAGAAAGAAATCTCAGATGGTACGGAAAAATGTTTGAACGTCACAGGCAATCAAGATTCA
62 CATCAGAGAAAGAAACCTCAGATGGTACGGAAAAATGATTGAACATCACAGGCAATCAAGAATCA
* * * *
470825 GAATATAATAACATAACG-TAATAGAAATTCGAGTATACCGAGAGAAGAAATAGAATCCTC
127 GAATATAATAACAAAACGCT-ATACAAATTCGAGTATACCAAGAGAAGAAACAGAATCCTC
470885 CGTATGAAAG
Statistics
Matches: 169, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
205 12 0.07
206 1 0.01
207 46 0.27
208 98 0.58
209 12 0.07
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (206 bp):
CAGTACAAAAAATATGGATTCATATCAAATTGATGCCTCAGAATCAATACTTCGAGAGAATCATC
AGAGAAAGAAACCTCAGATGGTACGGAAAAATGATTGAACATCACAGGCAATCAAGAATCAGAAT
ATAATAACAAAACGCTATACAAATTCGAGTATACCAAGAGAAGAAACAGAATCCTCTGCCTTAAA
TAATCATACCA
Found at i:471394 original size:19 final size:19
Alignment explanation
Indices: 471356--471394 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
471346 AAAATATTTT
* *
471356 AAATATAAATCTAATTATA
1 AAATATAAATCGAATAATA
*
471375 AAATATAACTCGAATAATA
1 AAATATAAATCGAATAATA
471394 A
1 A
471395 TTCTAAACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATATAAATCGAATAATA
Found at i:472422 original size:26 final size:26
Alignment explanation
Indices: 472367--472423 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
472357 CCAAATTATC
* * *
472367 TTTTTTTTTAATTTAGGTGCTTAATT
1 TTTTTTATCAATTTAGGTGCTTAATG
472393 TTTTTTATCAATTTAGGTG-TCTAATG
1 TTTTTTATCAATTTAGGTGCT-TAATG
472419 TTTTT
1 TTTTT
472424 AATATTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.19, C:0.05, G:0.12, T:0.63
Consensus pattern (26 bp):
TTTTTTATCAATTTAGGTGCTTAATG
Found at i:473731 original size:27 final size:27
Alignment explanation
Indices: 473699--473759 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
473689 AATAATAACA
*
473699 TTAAACATATAAATTGACAAAA-ATAAT
1 TTAAACATATAAA-TGAAAAAATATAAT
*
473726 TTAAACATCTAAATGAAAAAATTATAAT
1 TTAAACATATAAATGAAAAAA-TATAAT
473754 TTAAAC
1 TTAAAC
473760 CATTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 7 0.23
27 12 0.40
28 11 0.37
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.31
Consensus pattern (27 bp):
TTAAACATATAAATGAAAAAATATAAT
Found at i:475047 original size:87 final size:87
Alignment explanation
Indices: 474901--475074 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
474891 TTGTCATTGG
474901 TCGGTTTATATAGTTTATAAGGACAAAATTTACTTCCACAATTCCATTTTTGGTTTTCCTTACAA
1 TCGGTTTATATAGTTTATAAGGACAAAATTTACTTCCACAATTCCATTTTTGGTTTTCCTTACAA
474966 TTCCTTTTATGTCATTAGAAGC
66 TTCCTTTTATGTCATTAGAAGC
474988 TCGGTTTATATAGTTTATAAGGACAAAATTTACTTCCACAATTCCATTTTTGGTTTTCCTTACAA
1 TCGGTTTATATAGTTTATAAGGACAAAATTTACTTCCACAATTCCATTTTTGGTTTTCCTTACAA
475053 TTCCTTTTATGTCATTAGAAGC
66 TTCCTTTTATGTCATTAGAAGC
475075 CTAAATAATC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (87 bp):
TCGGTTTATATAGTTTATAAGGACAAAATTTACTTCCACAATTCCATTTTTGGTTTTCCTTACAA
TTCCTTTTATGTCATTAGAAGC
Found at i:477157 original size:18 final size:18
Alignment explanation
Indices: 477136--477180 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
477126 TTTCGTCCCA
477136 TATATATATTTT-TTTAAT
1 TATATAT-TTTTATTTAAT
*
477154 TATATATTTTTATTTATT
1 TATATATTTTTATTTAAT
477172 TACTATATT
1 TA-TATATT
477181 CGTCCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 14 0.58
19 6 0.25
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATATATTTTTATTTAAT
Found at i:477158 original size:20 final size:21
Alignment explanation
Indices: 477135--477224 Score: 59
Period size: 20 Copynumber: 4.5 Consensus size: 21
477125 ATTTCGTCCC
477135 ATATATATAT-TTTTTTAATT
1 ATATATATATCTTTTTTAATT
* *
477155 ATATAT-T-T-TTATTTATTT
1 ATATATATATCTTTTTTAATT
* *
477173 ACTATAT-TCGTCCTTTTTTATTT
1 A-TATATAT-AT-CTTTTTTAATT
*
477196 ATAT-TATATCATTTTT-ATT
1 ATATATATATCTTTTTTAATT
477215 ATATATATAT
1 ATATATATAT
477225 ATATATATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
18 10 0.18
19 13 0.23
20 17 0.30
21 3 0.05
22 4 0.07
23 10 0.18
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (21 bp):
ATATATATATCTTTTTTAATT
Found at i:477209 original size:14 final size:13
Alignment explanation
Indices: 477191--477239 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
477181 CGTCCTTTTT
477191 TATTTATATTATA
1 TATTTATATTATA
*
477204 TCATTTTTATTATA
1 T-ATTTATATTATA
*
477218 TATATATATATATA
1 TATTTATAT-TATA
477232 TATTTATA
1 TATTTATA
477240 GATGTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 7 0.23
14 23 0.77
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTTATATTATA
Found at i:477216 original size:23 final size:23
Alignment explanation
Indices: 477148--477228 Score: 64
Period size: 23 Copynumber: 3.5 Consensus size: 23
477138 TATATATTTT
477148 TTTA-ATTATAT-ATTTTTATTTA
1 TTTATATTATATCATTTTTA-TTA
*
477170 TTTACTA-TAT-TCGTCCTTTT-TTA
1 TTTA-TATTATATCAT--TTTTATTA
477193 TTTATATTATATCATTTTTATTA
1 TTTATATTATATCATTTTTATTA
*
477216 TATATATATATAT
1 TTTATAT-TATAT
477229 ATATATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
22 11 0.23
23 23 0.49
24 9 0.19
25 4 0.09
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (23 bp):
TTTATATTATATCATTTTTATTA
Found at i:477392 original size:17 final size:17
Alignment explanation
Indices: 477356--477395 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
477346 TATATATATA
*
477356 TATTATATTTTTTACTT
1 TATTTTATTTTTTACTT
477373 TATTTTATTTTTT-CTAT
1 TATTTTATTTTTTACT-T
477390 TATTTT
1 TATTTT
477396 TTTCTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTTTATTTTTTACTT
Found at i:477609 original size:11 final size:10
Alignment explanation
Indices: 477572--477630 Score: 50
Period size: 11 Copynumber: 5.7 Consensus size: 10
477562 TTTTTTAACA
477572 TTTTATTCATT
1 TTTTATT-ATT
*
477583 TTGT-TTA-T
1 TTTTATTATT
477591 TTTTATTATT
1 TTTTATTATT
477601 TTTTCATTATT
1 TTTT-ATTATT
*
477612 TTTTACTTGTT
1 TTTTA-TTATT
477623 TTGTTATT
1 TT-TTATT
477631 TTCCATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 4 0.10
9 4 0.10
10 8 0.20
11 21 0.52
12 3 0.08
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (10 bp):
TTTTATTATT
Found at i:480158 original size:27 final size:27
Alignment explanation
Indices: 480120--480181 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
480110 TCTCAAACCT
*
480120 CAAAATAAAATACCTTGTTTCTTTACC
1 CAAAATAAAATACCTTGATTCTTTACC
480147 CAAAATAAAATACCTTGATTCTTTACC
1 CAAAATAAAATACCTTGATTCTTTACC
480174 CAAAATAA
1 CAAAATAA
480182 CTCATGGTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (27 bp):
CAAAATAAAATACCTTGATTCTTTACC
Found at i:480822 original size:21 final size:20
Alignment explanation
Indices: 480798--480847 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
480788 ATCAGAACAA
*
480798 AAAGAAAAAAGAGAAAAAAGC
1 AAAGAAAAAAGA-AAAAAAAC
* *
480819 AAAGAGAAAATAAAAAAAAC
1 AAAGAAAAAAGAAAAAAAAC
480839 AAAGGAAAA
1 AAA-GAAAA
480848 TTGAAGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAGAAAAAAGAAAAAAAAC
Found at i:480836 original size:20 final size:19
Alignment explanation
Indices: 480811--480848 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
480801 GAAAAAAGAG
*
480811 AAAAAAGCAAAGAGAAAATA
1 AAAAAAACAAAG-GAAAATA
480831 AAAAAAACAAAGGAAAAT
1 AAAAAAACAAAGGAAAAT
480849 TGAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (19 bp):
AAAAAAACAAAGGAAAATA
Found at i:481035 original size:69 final size:69
Alignment explanation
Indices: 480924--481057 Score: 252
Period size: 69 Copynumber: 1.9 Consensus size: 69
480914 CAAACTATGT
480924 GATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCATCAA
1 GATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCATCAA
480989 ATGA
66 ATGA
480993 GATTGATCAAGCACAATCA-TTTCTGAATCACTGAATCACTTCACTCGAAGATCATAGAGCATCA
1 GATTGATCAAGCACAATCATTTTC-GAATCACTGAATCACTTCACTCGAAGATCATAGAGCATCA
481057 A
65 A
481058 GAGAGAGACA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
68 4 0.06
69 60 0.94
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (69 bp):
GATTGATCAAGCACAATCATTTTCGAATCACTGAATCACTTCACTCGAAGATCATAGAGCATCAA
ATGA
Found at i:482048 original size:32 final size:33
Alignment explanation
Indices: 481978--482087 Score: 125
Period size: 32 Copynumber: 3.4 Consensus size: 33
481968 GGCATCTTGA
* *
481978 AGATTCAACATCAAATGTTGGGGGTATGTTTTTT
1 AGATTCAACATCAAATGTT-GGGGCATGTTTTTG
*
482012 AGATTTAACATCAAATGTTGGGGCAT-TTTTTG
1 AGATTCAACATCAAATGTTGGGGCATGTTTTTG
* * * **
482044 AGATTCAACATCGAATATTGGGGCATCTTTGGG
1 AGATTCAACATCAAATGTTGGGGCATGTTTTTG
482077 A-ATTCAACATC
1 AGATTCAACATC
482088 CTGATGCAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 38 0.57
33 11 0.16
34 18 0.27
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (33 bp):
AGATTCAACATCAAATGTTGGGGCATGTTTTTG
Found at i:482723 original size:106 final size:106
Alignment explanation
Indices: 482597--482919 Score: 468
Period size: 106 Copynumber: 3.0 Consensus size: 106
482587 ATATCGTGCC
482597 ACTCGAGACAACACAAGTTCAAC-TCTACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTC-ACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
482661 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
482703 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
482768 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * **
482809 ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTTGCTGTCAACAAATAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
** * * ** *
482874 AGCTCCAGAGCCAATTTTAACTTCATGGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
482915 ACTCG
1 ACTCG
482920 GAACGATACA
Statistics
Matches: 196, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
106 194 0.99
107 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.22
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:483258 original size:37 final size:37
Alignment explanation
Indices: 483214--483286 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
483204 CCTTAAAATG
* * *
483214 AATTTTATCTCGATTGAGATAGTTTCCCTTGAAACAA
1 AATTTTATCTCCATTGAGACAGTTTCCATTGAAACAA
* *
483251 AATTTTATCTCCCTTGAGACAGTTTCTATTGAAACA
1 AATTTTATCTCCATTGAGACAGTTTCCATTGAAACA
483287 TAAACATTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (37 bp):
AATTTTATCTCCATTGAGACAGTTTCCATTGAAACAA
Found at i:483262 original size:102 final size:102
Alignment explanation
Indices: 483119--483489 Score: 512
Period size: 102 Copynumber: 3.6 Consensus size: 102
483109 ACTAATTTAT
* * ** * * *
483119 TCTCCCTTGAGATACTTTCTTTTGGAACTAAAA-TTTGTCTCCCTTAAGACAGTTTCTCTTGAAA
1 TCTCTCTTGAGATAGTTTCCCTTGAAAC-AAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAA
* * *
483183 CATAAACATTAAAAACATTTCCCTTAAAATGAATTTTA
65 CATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
** *
483221 TCTCGATTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTATTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAAC
483286 ATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
66 ATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
* * **
483323 TCTCTCTTGAGATAGTTTCCCTTTAAATAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAAC
* *
483388 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
66 ATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
* * * *
483425 TCTCTCTTGAGACAGTTTCACTTGAAAC-AAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAAC
483489 A
66 A
483490 AAATATTTGA
Statistics
Matches: 239, Mismatches: 29, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
101 37 0.15
102 202 0.85
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (102 bp):
TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCTCTTGAAAC
ATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
Found at i:483369 original size:37 final size:36
Alignment explanation
Indices: 483302--483386 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 36
483292 ATTGAAAACA
* * * *
483302 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTTGCCTCCCTTGAGACAG
*
483338 TTTCCCTTTAAATAAAATTTTGCCTCCCTTGAGACAG
1 TTTCCCTTGAAAT-AAATTTTGCCTCCCTTGAGACAG
*
483375 TTTCTCTTGAAA
1 TTTCCCTTGAAA
483387 CATAAACATT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 12 0.29
37 29 0.71
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGCCTCCCTTGAGACAG
Found at i:483457 original size:36 final size:36
Alignment explanation
Indices: 483404--483491 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
483394 ATTGAAAACA
* *
483404 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
* *
483440 TTTCACTTGAAACAAATTTTATCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
483476 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
483492 ATATTTGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
Found at i:483578 original size:121 final size:122
Alignment explanation
Indices: 483445--483666 Score: 365
Period size: 121 Copynumber: 1.8 Consensus size: 122
483435 GACAGTTTCA
*
483445 CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTT
1 CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTTT
*
483510 -TTAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
66 CTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
* * *
483566 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTTT
1 CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTTT
* *
483631 CCTAAAACAAATTTTGTCTCCCTTGTGACAGTTTCT
66 -CTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCT
483667 ATTGAAACAC
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
121 61 0.66
123 31 0.34
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (122 bp):
CTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTTGAATATATTTTT
CTAAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
Found at i:483674 original size:65 final size:67
Alignment explanation
Indices: 483570--483732 Score: 206
Period size: 65 Copynumber: 2.4 Consensus size: 67
483560 GTCTCTCTTG
* * ** *
483570 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTTTCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCATTGAAACACAAAATCTTCAAATTTA-TTTCCC
483633 -TA
65 TTA
* *
483635 AAACAAATTTTGTCTCCCTTGTGACAGTTTCTATTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCATTGAAACACAAAATCTTCAAATTTATTTCCCT
483700 TA
66 TA
* *
483702 AAACAAAATTTTGTTTCCCTTGAGACCGTTT
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTT
483733 TTCATGAAAC
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 32 0.38
66 7 0.08
67 22 0.26
68 23 0.27
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCATTGAAACACAAAATCTTCAAATTTATTTCCCT
TA
Found at i:488104 original size:3 final size:3
Alignment explanation
Indices: 488096--488180 Score: 143
Period size: 3 Copynumber: 28.0 Consensus size: 3
488086 AATATTTATT
488096 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
488144 TGTA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
488181 CAAACTAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 75 0.97
4 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:488631 original size:46 final size:46
Alignment explanation
Indices: 488409--489319 Score: 1355
Period size: 46 Copynumber: 20.0 Consensus size: 46
488399 TCAAAAAGCT
* *
488409 CCCGAAGG-TTTTAAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
488454 CCCAAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
488499 CCCGAAGG-TTCTGAAAACATCATGCACTGAAGCG-CTTACAAATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAG-GACTTACAGATGA
* * * *
488544 CCCGAAGG-TTTTAAAAACAGCATGCACTAAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
488589 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* * *
488635 CCCGAAGG-TTTTGAAAAACATCATTCACTAAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTG-AAAACATCATGCACTGAAGGACTTACAGATGA
* * *
488681 CCTGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATAA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
488727 CCCAAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
488773 CCC-AGAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGA-AGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
488818 CCCGAAGGTTTTTGATAACATAATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
488864 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
488910 CCC-AGAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGA-AGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
488955 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
489001 CCCGAAGGTTTTTGATAACATCATGCATTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
489047 CCCAAAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGG
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
489092 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGG
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
489138 CCCGAA-GTTTTTGAAAAACATCATACACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTG-AAAACATCATGCACTGAAGGACTTACAGATGA
489184 CCCGAAGGTTTTT-AATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAA-AACATCATGCACTGAAGGACTTACAGATGA
* *
489230 CCCGGAGG-TTTTGAAAACATCATGCACTGAAGAACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
*
489275 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATG
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATG
489320 TTGGAAATAG
Statistics
Matches: 795, Mismatches: 54, Indels: 33
0.90 0.06 0.04
Matches are distributed among these distances:
44 1 0.00
45 309 0.39
46 474 0.60
47 11 0.01
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (46 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:488803 original size:183 final size:181
Alignment explanation
Indices: 488409--489319 Score: 1364
Period size: 183 Copynumber: 5.0 Consensus size: 181
488399 TCAAAAAGCT
* * *
488409 CCCGAAGGTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGATAACAT
* *
488474 CATGCACTGAAGGGCTTACAGATGACCCGAAGGTTCTGAAAACATCATGCACTGAAGCG-CTTAC
66 CATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAG-GACTTAC
* * * * * *
488538 AAATGACCCGAAGG-TTTTAAAAACAGCATGCACTAAAGGGCTTACAGATGA
130 AGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
* * *
488589 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAAC
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG-ATAAC
* * * * *
488654 ATCATTCACTAAAGGGCTTACAGATGACCTGAAGGTTTTTGATAACATCATGCACTGAAGGACTT
64 ATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTT
* *
488719 ACAGATAACCCAAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
128 ACAGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
488773 CCC-AGAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGATAAC
1 CCCGA-AGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGATAAC
* *
488837 ATAATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTT
64 ATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTGAAGGACTT
*
488902 ACAGATGACCC-AGAGG-TTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
128 ACAGATGACCCGA-AGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
* *
488955 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
1 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGATAAC
* *
489020 ATCATGCATTGAAGGACTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGACTTA
64 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTA
* *
489085 CAGATGGCCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGG
129 CAGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
* * *
489138 CCCGAAGTTTTTGAAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTTAATAAC
1 CCCGAAGGTTTTG-AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGATAAC
* *
489203 ATCATGCACTGAAGGACTTACAGATGACCCGGAGGTTTTGAAAACATCATGCACTGAAGAACTTA
64 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTA
489268 CAGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATG
129 CAGATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATG
489320 TTGGAAATAG
Statistics
Matches: 672, Mismatches: 46, Indels: 23
0.91 0.06 0.03
Matches are distributed among these distances:
180 8 0.01
181 46 0.07
182 127 0.19
183 448 0.67
184 43 0.06
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (181 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGATAACAT
CATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACA
GATGACCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
Found at i:488859 original size:137 final size:137
Alignment explanation
Indices: 488409--489319 Score: 1424
Period size: 137 Copynumber: 6.7 Consensus size: 137
488399 TCAAAAAGCT
* * * * *
488409 CCCGAAGG-TTTTAAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG-TTTTGAAAAC
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
* *
488472 ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTCTGAAAACATCATGCACTGAAGCG-CTT
66 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAG-GACTT
*
488536 ACAAATGA
130 ACAGATGA
* * * * *
488544 CCCGAAGG-TTTTAAAAACAGCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTTGATAAC
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
* * *
488608 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAAACATCATTCACTAAAGGGCTT
66 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTG-AAAACATCATGCACTGAAGGACTT
488673 ACAGATGA
130 ACAGATGA
* * *
488681 CCTGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATAACCCAAAGGTTTTTGATAAC
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
*
488746 ATCATGCACTGAAGGACTTACAGATGACCC-AGAGGTTTTGAAAACATCATGCACTGAAGGGCTT
66 ATCATGCACTGAAGGACTTACAGATGACCCGA-AGGTTTTGAAAACATCATGCACTGAAGGACTT
488810 ACAGATGA
130 ACAGATGA
*
488818 CCCGAAGGTTTTTGATAACATAATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
488883 ATCATGCACTGAAGGACTTACAGATGACCC-AGAGGTTTTGAAAACATCATGCACTGAAGGACTT
66 ATCATGCACTGAAGGACTTACAGATGACCCGA-AGGTTTTGAAAACATCATGCACTGAAGGACTT
488947 ACAGATGA
130 ACAGATGA
488955 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
* *
489020 ATCATGCATTGAAGGACTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGACTTA
66 ATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTA
*
489085 CAGATGG
131 CAGATGA
* *
489092 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGGCCCGAA-GTTTTTGAAAAA
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTG-ATAA
* * *
489156 CATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTTAATAACATCATGCACTGAAGGACT
65 CATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAA-AACATCATGCACTGAAGGACT
489221 TACAGATGA
129 TACAGATGA
* * *
489230 CCCGGAGG-TTTTGAAAACATCATGCACTGAAGAACTTACAGATGACCCGAAGGTTTTTGATAAC
1 CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
489294 ATCATGCACTGAAGGACTTACAGATG
66 ATCATGCACTGAAGGACTTACAGATG
489320 TTGGAAATAG
Statistics
Matches: 725, Mismatches: 42, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
135 50 0.07
136 55 0.08
137 489 0.67
138 131 0.18
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (137 bp):
CCCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGATAAC
ATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTA
CAGATGA
Found at i:490020 original size:19 final size:21
Alignment explanation
Indices: 489973--490027 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
489963 GAAATCCAAT
*
489973 AAATCTTTCATCTTTGAAAAG
1 AAATCTATCATCTTTGAAAAG
489994 AGAATCTATCATCTTTG-AAA-
1 A-AATCTATCATCTTTGAAAAG
490014 AAATCTATCATCTT
1 AAATCTATCATCTT
490028 CGAAGAATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.41
20 1 0.03
21 4 0.12
22 14 0.44
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATCTATCATCTTTGAAAAG
Found at i:501553 original size:3 final size:3
Alignment explanation
Indices: 501545--501589 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
501535 AATATTTATT
*
501545 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
501590 GCAAACTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:501906 original size:20 final size:18
Alignment explanation
Indices: 501883--501937 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
501873 TATTCCTCCT
501883 TTTTTATTTATATTATATCA
1 TTTTTA-TTATA-TATATCA
501903 TTTTTATTATATATATC-
1 TTTTTATTATATATATCA
*
501920 TTGTATCATTATATATAT
1 TT-T-TTATTATATATAT
501938 ATATATATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 2 0.06
18 7 0.22
19 17 0.53
20 6 0.19
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTATTATATATATCA
Found at i:502060 original size:32 final size:36
Alignment explanation
Indices: 501981--502054 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 36
501971 ATTTACTATG
*
501981 TATATATTTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATTTTCTTAATATTATATTTTATA-GTTTT
*
502018 TATATATATTTTCTTAATATTCTATTTT-T-GTTTT
1 TATATATATTTTCTTAATATTATATTTTATAGTTTT
502052 TAT
1 TAT
502055 TTATTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 8 0.23
36 1 0.03
37 26 0.74
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (36 bp):
TATATATATTTTCTTAATATTATATTTTATAGTTTT
Found at i:502243 original size:19 final size:19
Alignment explanation
Indices: 502219--502255 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
502209 ATTTTTATTA
502219 TTTTTTAATTTCTTTTACC
1 TTTTTTAATTTCTTTTACC
* *
502238 TTTTTTTATTTTTTTTAC
1 TTTTTTAATTTCTTTTAC
502256 TCCATTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTAATTTCTTTTACC
Found at i:502321 original size:19 final size:17
Alignment explanation
Indices: 502299--502335 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
502289 TTTTTTAACA
502299 TTTTATTCATTTTGTTTAT
1 TTTTATT-ATTTT-TTTAT
502318 TTTTATTATTTTTTTAT
1 TTTTATTATTTTTTTAT
502335 T
1 T
502336 ATTTTTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTATTATTTTTTTAT
Found at i:502333 original size:11 final size:11
Alignment explanation
Indices: 502317--502342 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
502307 ATTTTGTTTA
502317 TTTTTATTATT
1 TTTTTATTATT
502328 TTTTTATTATT
1 TTTTTATTATT
502339 TTTT
1 TTTT
502343 ACGTGTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTATTATT
Found at i:504434 original size:159 final size:158
Alignment explanation
Indices: 504146--504520 Score: 503
Period size: 159 Copynumber: 2.4 Consensus size: 158
504136 CATAATTTCA
* *
504146 TTATTTCTTCAATTCCTC-TTTCATTTTAAGTCCATTTTTTACTAAATTTGAACTACATGCTCCT
1 TTATTTCTTCAATTTCTCATTT-ATTTTAAGTCCATTTTTTACCAAATTTGAACTACATGCTCCT
** *
504210 AAACCATAGTAGAATACATGTGTTCTTTCAATTTCTATTTTTGATAACAAATTATTTATTTTTCA
65 AAACCATAGTAGAATACATGTGAACTTTCAATTCCTATTTTTGATAACAAATTATTTATTTTTCA
*
504275 ATTTAGTCCTTCAATTTTTCACAATCTCC
130 ATATAGTCCTTCAATTTTTCACAATCTCC
* * *
504304 TTATTTCTTCAATTTTTCATTTATTTTAAGTCCCTTTTTTTTACCAAATTTG-AGTCACATGCTC
1 TTATTTCTTCAATTTCTCATTTATTTTAAGT-CC-ATTTTTTACCAAATTTGAACT-ACATGCTC
* *
504368 CTAAA-CATAGTAGAATACATGTGAACTTTCAATTCCTCTTTTTGATAACAAATTTTTTATTTTT
63 CTAAACCATAGTAGAATACATGTGAACTTTCAATTCCTATTTTTGATAACAAATTATTTATTTTT
*
504432 CAATATAGTCCTTCAATTTTTCATAATCTCC
128 CAATATAGTCCTTCAATTTTTCACAATCTCC
* * * * *
504463 TTATTCCTTCAATTTGTGATTTA---TAAGT-CACGTTTTTACCAAATTTGAACCACATGCT
1 TTATTTCTTCAATTTCTCATTTATTTTAAGTCCA-TTTTTTACCAAATTTGAACTACATGCT
504521 TATATAACAC
Statistics
Matches: 192, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
154 23 0.12
155 1 0.01
156 5 0.03
158 25 0.13
159 110 0.57
160 28 0.15
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.47
Consensus pattern (158 bp):
TTATTTCTTCAATTTCTCATTTATTTTAAGTCCATTTTTTACCAAATTTGAACTACATGCTCCTA
AACCATAGTAGAATACATGTGAACTTTCAATTCCTATTTTTGATAACAAATTATTTATTTTTCAA
TATAGTCCTTCAATTTTTCACAATCTCC
Found at i:504810 original size:2 final size:2
Alignment explanation
Indices: 504803--504828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
504793 TGAAAGAATA
504803 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
504829 TATGGTTAGA
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:506249 original size:30 final size:29
Alignment explanation
Indices: 506209--506378 Score: 214
Period size: 30 Copynumber: 5.7 Consensus size: 29
506199 TGGTCCGAAC
*
506209 TATATTTTTAAGTTAAGATAAGAATAAAT
1 TATATTTTTAAGTTAAGATAAGAATAAAA
* *
506238 TATATTTTTTAAGTTAAGATAAAGACTAGAA
1 TATA-TTTTTAAGTTAAGAT-AAGAATAAAA
* *
506269 TATATTTTTATGTTAAGATAAGAATAAAC
1 TATATTTTTAAGTTAAGATAAGAATAAAA
*
506298 TATATTTTTAAGGTTAAAATAAGAATAAAA
1 TATATTTTTAA-GTTAAGATAAGAATAAAA
* * *
506328 TATATTTAATAAGTTAAAATAAAAATAAAA
1 TATATTT-TTAAGTTAAGATAAGAATAAAA
506358 TATATTTTTAATGTTAAGATA
1 TATATTTTTAA-GTTAAGATA
506379 TAAAATTAAT
Statistics
Matches: 122, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
29 24 0.20
30 84 0.69
31 14 0.11
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.40
Consensus pattern (29 bp):
TATATTTTTAAGTTAAGATAAGAATAAAA
Found at i:506372 original size:90 final size:89
Alignment explanation
Indices: 506206--506378 Score: 258
Period size: 90 Copynumber: 1.9 Consensus size: 89
506196 TAATGGTCCG
* * ** * * *
506206 AACTATATTTTTAAGTTAAGATAAGAATAAATTATATTTTTTAAGTTAAGATAAAGACTAGAATA
1 AACTATATTTTTAAGTTAAAATAAGAATAAAATATATTTAATAAGTTAAAATAAAGAATAAAATA
506271 TATTTTTATGTTAAGATAAGAATA
66 TATTTTTATGTTAAGATAAGAATA
506295 AACTATATTTTTAAGGTTAAAATAAGAATAAAATATATTTAATAAGTTAAAATAAA-AATAAAAT
1 AACTATATTTTTAA-GTTAAAATAAGAATAAAATATATTTAATAAGTTAAAATAAAGAATAAAAT
506359 ATATTTTTAATGTTAAGATA
65 ATATTTTT-ATGTTAAGATA
506379 TAAAATTAAT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
89 28 0.37
90 47 0.63
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (89 bp):
AACTATATTTTTAAGTTAAAATAAGAATAAAATATATTTAATAAGTTAAAATAAAGAATAAAATA
TATTTTTATGTTAAGATAAGAATA
Found at i:513553 original size:2 final size:2
Alignment explanation
Indices: 513546--513581 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
513536 TCTTCTAAAA
513546 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
513582 ATATTTTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:513670 original size:4 final size:4
Alignment explanation
Indices: 513661--513695 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
513651 CGGAAGTAAT
* *
513661 TTTA TTTA TTTA TTTA TTTA TTCA TTCA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
513696 TGAATAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:514215 original size:26 final size:25
Alignment explanation
Indices: 514181--514230 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
514171 TATTTTAATT
514181 TTTTATTTATAATATTGAAATTTTA
1 TTTTATTTATAATATTGAAATTTTA
** *
514206 TTTTAGTTTATGTTATTGTAATTTT
1 TTTTA-TTTATAATATTGAAATTTT
514231 TTTACAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (25 bp):
TTTTATTTATAATATTGAAATTTTA
Found at i:517465 original size:15 final size:13
Alignment explanation
Indices: 517436--517467 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
517426 GATTCCAACT
517436 AACAACACGAAAC
1 AACAACACGAAAC
517449 AACAACACGAAA-
1 AACAACACGAAAC
517461 AACAACA
1 AACAACA
517468 GGAGAATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.66, C:0.28, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAACACGAAAC
Found at i:526794 original size:8 final size:7
Alignment explanation
Indices: 526764--526793 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
526754 CATACCCCTT
526764 AAAATAA
1 AAAATAA
526771 AAAATAA
1 AAAATAA
526778 AAAATAA
1 AAAATAA
526785 ATAAATAA
1 A-AAATAA
526793 A
1 A
526794 TTATGTCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAATAA
Found at i:527519 original size:50 final size:50
Alignment explanation
Indices: 527444--527542 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
527434 TAAAACACTC
527444 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
1 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
* *
527494 TAGAAGCTTGTGGAAGAGTGTGGAATCTTTTGGAATATTCTGGAGATGT
1 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGT
527543 GTGGAACCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.27, C:0.08, G:0.32, T:0.32
Consensus pattern (50 bp):
TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
Found at i:527558 original size:50 final size:50
Alignment explanation
Indices: 527444--527558 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 50
527434 TAAAACACTC
* *
527444 TAGAAGCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
1 TAGAACCTTATGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
* * * * *
527494 TAGAAGCTTGTGGAAGAGTGTGGAATCTTTTGGAATATTCTGGAGATGTG
1 TAGAACCTTATGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
*
527544 TGGAACCTTATGGAA
1 TAGAACCTTATGGAA
527559 TAATATAGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.28, C:0.09, G:0.32, T:0.31
Consensus pattern (50 bp):
TAGAACCTTATGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTA
Found at i:532159 original size:49 final size:50
Alignment explanation
Indices: 532056--532170 Score: 142
Period size: 49 Copynumber: 2.3 Consensus size: 50
532046 TAGAAGCTTT
* *
532056 TGGAAGAGTGTGGAATCCTCTGGAATATTCTAGAGATGTATAAAATCTTG
1 TGGAAGAGTGTGGAATCCTCTGGAATATTCTAGAGATGTATAAAACCTTA
* * * * **
532106 TGGAAGAGTGT-GAATCCTTTGGATTATTCTGGAGATGTGTGGAACCTTA
1 TGGAAGAGTGTGGAATCCTCTGGAATATTCTAGAGATGTATAAAACCTTA
*
532155 TGGAAGAGTATGGAAT
1 TGGAAGAGTGTGGAAT
532171 AATATGGAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 40 0.73
50 15 0.27
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (50 bp):
TGGAAGAGTGTGGAATCCTCTGGAATATTCTAGAGATGTATAAAACCTTA
Found at i:533417 original size:21 final size:21
Alignment explanation
Indices: 533393--533460 Score: 59
Period size: 25 Copynumber: 3.0 Consensus size: 21
533383 TTCATCACCC
533393 ATAATTTATTATTTTTATTTT
1 ATAATTTATTATTTTTATTTT
533414 ATAATTTAAATT-TTTTTATTTATT
1 ATAATTT--ATTATTTTTA-TT-TT
533438 ATTAAAGTTTA-TATTTTTATTTT
1 A-T-AA-TTTATTATTTTTATTTT
533461 CTGTCAACTT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
21 7 0.18
22 6 0.15
23 7 0.18
24 6 0.15
25 8 0.21
26 2 0.05
27 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (21 bp):
ATAATTTATTATTTTTATTTT
Found at i:537867 original size:12 final size:12
Alignment explanation
Indices: 537850--537907 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
537840 TAAGTGTACT
537850 TCTAAATCACCC
1 TCTAAATCACCC
*
537862 TCTAAATCA-CA
1 TCTAAATCACCC
* *
537873 TGCAAAATC-GCC
1 T-CTAAATCACCC
537885 TGCTAAATCACCC
1 T-CTAAATCACCC
537898 TCTAAATCAC
1 TCTAAATCAC
537908 ATGCAAAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 2 0.05
12 33 0.87
13 3 0.08
ACGTcount: A:0.36, C:0.34, G:0.05, T:0.24
Consensus pattern (12 bp):
TCTAAATCACCC
Found at i:537898 original size:36 final size:36
Alignment explanation
Indices: 537851--537926 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
537841 AAGTGTACTT
*
537851 CTAAATCACCCTCTAAATCACATGCAAAATCGCCTG
1 CTAAATCACCCTCTAAATCACATGCAAAATCACCTG
537887 CTAAATCACCCTCTAAATCACATGCAAAATCACCTG
1 CTAAATCACCCTCTAAATCACATGCAAAATCACCTG
537923 CTAA
1 CTAA
537927 GCCATTTGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.38, C:0.33, G:0.07, T:0.22
Consensus pattern (36 bp):
CTAAATCACCCTCTAAATCACATGCAAAATCACCTG
Found at i:537926 original size:24 final size:24
Alignment explanation
Indices: 537863--537955 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 24
537853 AAATCACCCT
* * * *
537863 CTAAATCACATGCAAAATCGCCTG
1 CTAAATCACCTGCTAAATCACATG
537887 CTAAATCACCCT-CTAAATCACATG
1 CTAAATCA-CCTGCTAAATCACATG
* ** **
537911 CAAAATCACCTGCTAAGCCATTTG
1 CTAAATCACCTGCTAAATCACATG
*
537935 CTAAATCGCCTGCTAAATCAC
1 CTAAATCACCTGCTAAATCAC
537956 CTGTAGGCGC
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
23 3 0.06
24 48 0.91
25 2 0.04
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.24
Consensus pattern (24 bp):
CTAAATCACCTGCTAAATCACATG
Found at i:539422 original size:21 final size:21
Alignment explanation
Indices: 539396--539439 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
539386 CTTTTGTCTC
539396 AATTAGCCTTAGAATTAAGTT
1 AATTAGCCTTAGAATTAAGTT
539417 AATTAGCCTTAGAATTAAGTT
1 AATTAGCCTTAGAATTAAGTT
539438 AA
1 AA
539440 GTGTATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (21 bp):
AATTAGCCTTAGAATTAAGTT
Found at i:547551 original size:3 final size:3
Alignment explanation
Indices: 547543--547799 Score: 461
Period size: 3 Copynumber: 86.7 Consensus size: 3
547533 CTTAAGTTTA
547543 TAT TAT TAT TAT TAT TAT TAT TAT 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
547591 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
547637 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
547683 TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
547730 TAT TAT TA- TAT TAT TAT TAT TAT 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
547777 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
547800 CTATAAATAT
Statistics
Matches: 247, Mismatches: 0, Indels: 14
0.95 0.00 0.05
Matches are distributed among these distances:
2 10 0.04
3 231 0.94
4 6 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:552048 original size:39 final size:40
Alignment explanation
Indices: 551910--552067 Score: 169
Period size: 39 Copynumber: 3.9 Consensus size: 40
551900 GTTAGTTGTT
* * *
551910 GGGACGACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCTAA
1 GGGATGACACTGCTCATACGTGATGAAGAGATCTGGTCG----A
* * * * *
551954 GGG-TGACACGGTTCCTACGTGATGAGGAAATCTGGTCGA
1 GGGATGACACTGCTCATACGTGATGAAGAGATCTGGTCGA
551993 GGGATGACACTGCTCATACGTGATGAAGAGATCTGGTCG-
1 GGGATGACACTGCTCATACGTGATGAAGAGATCTGGTCGA
*
552032 GGGATGACAC-GACTCATACGTGATGAAGAGTTCTGG
1 GGGATGACACTG-CTCATACGTGATGAAGAGATCTGG
552068 CCATCTTTAG
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
38 1 0.01
39 37 0.38
40 30 0.31
43 27 0.28
44 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (40 bp):
GGGATGACACTGCTCATACGTGATGAAGAGATCTGGTCGA
Found at i:552195 original size:134 final size:130
Alignment explanation
Indices: 551959--552210 Score: 341
Period size: 134 Copynumber: 1.9 Consensus size: 130
551949 TCTAAGGGTG
551959 ACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACACTGCTCATACGTGATGAAGAGA
1 ACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACACTGCTCATACGTGATGAAGAGA
**
552024 TCTGGTCGGGGATGACACGACTCATACGTGATGAAGAGTTC-TGGCCATCTTTAGGAAGGGCGAT
66 TCTAATCGGGGATGACACGACTCATACGTGATGAAGAGTTCTTGGCCAT-TTTAGGAAGGGCGAT
552088 A
130 A
** * *
552089 ACACGGTTCCTACGTGATGAGGATGTCTGGTTATC-ATGGGGTGACAC-GACTCCTACGTGATGA
1 ACACGGTTCCTACGTGATGAGGAAATCTGG---TCGA-GGGATGACACTG-CTCATACGTGATGA
*
552152 GGAGATCTAATCAGGGGATGACACTG-CTCATACGTGATGAAGAGTTCTTGGCCATTTTA
61 AGAGATCTAATC-GGGGATGACAC-GACTCATACGTGATGAAGAGTTCTTGGCCATTTTA
552211 TAGCGATAAT
Statistics
Matches: 107, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
130 28 0.26
132 2 0.02
133 33 0.31
134 36 0.34
135 8 0.07
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (130 bp):
ACACGGTTCCTACGTGATGAGGAAATCTGGTCGAGGGATGACACTGCTCATACGTGATGAAGAGA
TCTAATCGGGGATGACACGACTCATACGTGATGAAGAGTTCTTGGCCATTTTAGGAAGGGCGATA
Found at i:552217 original size:130 final size:127
Alignment explanation
Indices: 551910--552253 Score: 344
Period size: 130 Copynumber: 2.7 Consensus size: 127
551900 GTTAGTTGTT
* * * * * * *
551910 GGGACGACACTGCTCATACGTGATGAAGAGTTCGGGTC-GTCTAAG-GGTGACACGGTTCCTACG
1 GGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCATTTTAAGCGATAACACGGTTCCTACG
* **
551973 TGATGAGGAAATCTGG---TCGAGGGATGACACTGCTCATACGTGATGAAGAGATCTGGTCG
66 TGATGAGGAAGTCTGGTTATCGAGGGATGACACTGCTCATACGTGATGAAGAGATCTAATCG
552032 GGGATGACAC-GACTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGT
1 GGGATGACACTG-CTCATACGTGATGAAGAGTTCTGGCCAT-TTT---AA--GCGATAACACGGT
* * * *
552096 TCCTACGTGATGAGGATGTCTGGTTATC-ATGGGGTGACAC-GACTCCTACGTGATGAGGAGATC
59 TCCTACGTGATGAGGAAGTCTGGTTATCGA-GGGATGACACTG-CTCATACGTGATGAAGAGATC
552159 TAATCAG
122 TAATC-G
* **
552166 GGGATGACACTGCTCATACGTGATGAAGAGTTCTTGGCCATTTTATAGCGATAATATAGTTCCTA
1 GGGATGACACTGCTCATACGTGATGAAGAGTTC-TGGCCATTTTA-AGCGATAACACGGTTCCTA
* * *
552231 CGTAATGAGGACGGCTGGTTATC
64 CGTGATGAGGAAGTCTGGTTATC
552254 TAATGTTGAC
Statistics
Matches: 184, Mismatches: 20, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
121 1 0.01
122 33 0.18
124 2 0.01
127 2 0.01
129 1 0.01
130 65 0.35
131 1 0.01
132 3 0.02
133 33 0.18
134 35 0.19
135 8 0.04
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (127 bp):
GGGATGACACTGCTCATACGTGATGAAGAGTTCTGGCCATTTTAAGCGATAACACGGTTCCTACG
TGATGAGGAAGTCTGGTTATCGAGGGATGACACTGCTCATACGTGATGAAGAGATCTAATCG
Found at i:552272 original size:130 final size:129
Alignment explanation
Indices: 551997--552289 Score: 317
Period size: 130 Copynumber: 2.2 Consensus size: 129
551987 GGTCGAGGGA
* * **
551997 TGACACTGCTCATACGTGATGAAGAGATCTGGTCGGGGATGACACGACTCATACGTGATGAAGAG
1 TGACA-TGCTCCTACGTGATGAGGAGATCTAATCGGGGATGACACGACTCATACGTGATGAAGAG
* * * *
552062 TTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGATGTCTGGTTATCATG
65 TTCTGGCCATCTTTA-GAA-GGCGATAACACAGTTCCTACGTAATGAGGACGGCTGGTTATCAT-
552127 GGG
127 GGG
*
552130 TGACACGACTCCTACGTGATGAGGAGATCTAATCAGGGGATGACACTG-CTCATACGTGATGAAG
1 TGACATG-CTCCTACGTGATGAGGAGATCTAATC-GGGGATGACAC-GACTCATACGTGATGAAG
* * *
552194 AGTTCTTGGCCAT-TTTA-TA-GCGATAATATAGTTCCTACGTAATGAGGACGGCTGGTTATCTA
63 AGTTC-TGGCCATCTTTAGAAGGCGATAACACAGTTCCTACGTAATGAGGACGGCTGGTTATC--
*
552256 AT-GT
125 ATGGG
* *
552260 TGACGTTGCTCCTACATGATGAGGAGATCT
1 TGAC-ATGCTCCTACGTGATGAGGAGATCT
552290 GGTCAGCTGA
Statistics
Matches: 137, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
130 61 0.45
131 1 0.01
132 4 0.03
133 27 0.20
134 36 0.26
135 8 0.06
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (129 bp):
TGACATGCTCCTACGTGATGAGGAGATCTAATCGGGGATGACACGACTCATACGTGATGAAGAGT
TCTGGCCATCTTTAGAAGGCGATAACACAGTTCCTACGTAATGAGGACGGCTGGTTATCATGGG
Found at i:554070 original size:83 final size:86
Alignment explanation
Indices: 553924--554096 Score: 291
Period size: 83 Copynumber: 2.0 Consensus size: 86
553914 TTAATCGTTG
553924 TTCAAATTCAATGCATTATCTGTGATGATCCTTTCAGGTGTTCCATATCTACAAATGATTCTCTC
1 TTCAAATTCAATGCATTATCTGTGATGATCCTTTCA-G-GTTCCATATCTACAAATGATTCTCTC
553989 TTTAGAAATCTGCACA-TGCTCC
64 TTTAGAAATCTGCACACTGCTCC
554011 TTCAAATTCAATGCATTATCT-TGATGATCCTTTCA-GTTCCATATCTAC-AATGATTTCTCTCT
1 TTCAAATTCAATGCATTATCTGTGATGATCCTTTCAGGTTCCATATCTACAAATGA-TTCTCTCT
554073 TTAGAAATCTGCACACTGCTCC
65 TTAGAAATCTGCACACTGCTCC
554095 TT
1 TT
554097 TTGTGACATT
Statistics
Matches: 84, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
82 5 0.06
83 36 0.43
84 8 0.10
86 14 0.17
87 21 0.25
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (86 bp):
TTCAAATTCAATGCATTATCTGTGATGATCCTTTCAGGTTCCATATCTACAAATGATTCTCTCTT
TAGAAATCTGCACACTGCTCC
Found at i:560484 original size:30 final size:30
Alignment explanation
Indices: 560449--560511 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
560439 TTAAATTCGA
**
560449 ATGCATATTATTGGTAATGTGCTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
* * *
560479 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCATATTATTGGTAATGCACTATAAATG
560509 ATG
1 ATG
560512 AATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (30 bp):
ATGCATATTATTGGTAATGCACTATAAATG
Found at i:564969 original size:12 final size:12
Alignment explanation
Indices: 564949--564984 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
564939 ATATGAACAT
*
564949 CAAATAAAATAA
1 CAAAAAAAATAA
564961 CAAAAAAAATAA
1 CAAAAAAAATAA
*
564973 CAATAAAAATAA
1 CAAAAAAAATAA
564985 TTTCTATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (12 bp):
CAAAAAAAATAA
Found at i:570260 original size:30 final size:29
Alignment explanation
Indices: 570221--570306 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 29
570211 GATCATTACG
570221 TTATCATTTGTTACAAAATAGTCACTAACA
1 TTATCATTTGTTACAAAATA-TCACTAACA
* * *
570251 TTATTATTTGTGACAAAATTATCACTAACG
1 TTATCATTTGTTACAAAA-TATCACTAACA
*
570281 TTATCGTTTGTTACAAAATGATCACT
1 TTATCATTTGTTACAAAAT-ATCACT
570307 CGTCGTTAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.02
30 45 0.94
31 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (29 bp):
TTATCATTTGTTACAAAATATCACTAACA
Found at i:571194 original size:30 final size:30
Alignment explanation
Indices: 571157--571335 Score: 295
Period size: 30 Copynumber: 6.0 Consensus size: 30
571147 ACAATGAGTT
* *
571157 ACCATTTTGTAGCAAACGATAATGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
**
571187 ATTATTTTGTAACAAACGATAACGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
571217 ACCATTTTGTAACAAACGATAACGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
571247 ACCATTTTGTAACAAACGATAACGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
*
571277 ACCATTTTGTAACAAACGATAAAGTTAGTG
1 ACCATTTTGTAACAAACGATAACGTTAGTG
* *
571307 ATCATTTTGTAACAAACGATAATGTTAGT
1 ACCATTTTGTAACAAACGATAACGTTAGT
571336 AACAATTTGT
Statistics
Matches: 140, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 140 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (30 bp):
ACCATTTTGTAACAAACGATAACGTTAGTG
Found at i:578373 original size:31 final size:31
Alignment explanation
Indices: 578338--578414 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
578328 TTATGAGCAA
* *
578338 ACACTTTGATCTGACCCGACATGATAAGTAT
1 ACACTATGATCCGACCCGACATGATAAGTAT
578369 ACACTATGATCCGACCCGACATGATAAGTAT
1 ACACTATGATCCGACCCGACATGATAAGTAT
578400 ACACTATGATCCGAC
1 ACACTATGATCCGAC
578415 TCGATCCAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (31 bp):
ACACTATGATCCGACCCGACATGATAAGTAT
Found at i:584573 original size:25 final size:26
Alignment explanation
Indices: 584545--584595 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
584535 TCTTAAATCA
584545 TTTGATTTTTT-TTCTT-ATATACTTT
1 TTTGATTTTTTCTTCTTCATA-ACTTT
*
584570 TTTGTTTTTTTCTTCTTCATAACTTT
1 TTTGATTTTTTCTTCTTCATAACTTT
584596 CTCATTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 10 0.43
26 10 0.43
27 3 0.13
ACGTcount: A:0.14, C:0.12, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTGATTTTTTCTTCTTCATAACTTT
Found at i:588267 original size:13 final size:13
Alignment explanation
Indices: 588249--588273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
588239 ATTTTAGGGA
588249 TTTCTCTTCTCCT
1 TTTCTCTTCTCCT
588262 TTTCTCTTCTCC
1 TTTCTCTTCTCC
588274 GCAACAGCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTCTCTTCTCCT
Found at i:592658 original size:19 final size:19
Alignment explanation
Indices: 592602--592658 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 19
592592 CTATTATTTG
** *
592602 ATTAGTTAGGCTGTTGTTA
1 ATTAGTTAGATTGTTATTA
592621 ATTAGTTAGATTGCAGTTATTA
1 ATTAGTTAGATT---GTTATTA
592643 ATTAGTTAGATTGTTA
1 ATTAGTTAGATTGTTA
592659 GTTAGGCTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 14 0.44
22 18 0.56
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (19 bp):
ATTAGTTAGATTGTTATTA
Found at i:593805 original size:2 final size:2
Alignment explanation
Indices: 593798--593823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
593788 CATACTTTCC
593798 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
593824 TCATTTTTTT
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:610803 original size:21 final size:21
Alignment explanation
Indices: 610777--610821 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
610767 TAAAATTATG
610777 TATAATATTATATTTAAATTT
1 TATAATATTATATTTAAATTT
*
610798 TATAATATTATATTTTAATTT
1 TATAATATTATATTTAAATTT
610819 TAT
1 TAT
610822 TTTAATAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATAATATTATATTTAAATTT
Found at i:616586 original size:19 final size:19
Alignment explanation
Indices: 616564--616607 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
616554 TATAAGGTAG
616564 TATATATATATA-TAG-TATT
1 TATAT-TATATAGTAGATA-T
616583 TATATTATATAGTAGATAT
1 TATATTATATAGTAGATAT
616602 TATATT
1 TATATT
616608 TAAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 15 0.65
20 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
TATATTATATAGTAGATAT
Found at i:616650 original size:44 final size:47
Alignment explanation
Indices: 616567--616666 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 47
616557 AAGGTAGTAT
* *
616567 ATATATATATAGTATTTATATTATATAGTAGATATTATATTTAAAA-
1 ATATATATATAGTATTTATATAATATAGTAGATAGTATATTTAAAAC
* *
616613 ATATATATAGTAGT-TTTTTA-AATATA-TATATAGTATATTTAAAATC
1 ATATATATA-TAGTATTTATATAATATAGTAGATAGTATATTTAAAA-C
616659 ATATATAT
1 ATATATAT
616667 TTTTAATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 16 0.34
45 5 0.11
46 22 0.47
47 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (47 bp):
ATATATATATAGTATTTATATAATATAGTAGATAGTATATTTAAAAC
Found at i:616662 original size:23 final size:22
Alignment explanation
Indices: 616567--616666 Score: 96
Period size: 23 Copynumber: 4.5 Consensus size: 22
616557 AAGGTAGTAT
**
616567 ATATATATATAGTAT-TTATATT
1 ATATATATATAGTATATT-TAAA
* *
616589 ATATAGTAGATATTATATTTAAA
1 ATATA-TATATAGTATATTTAAA
* *
616612 A-ATATATATAGTAGTTTTTTAA
1 ATATATATATAGTA-TATTTAAA
616634 ATATATATATAGTATATTTAAA
1 ATATATATATAGTATATTTAAA
616656 ATCATATATAT
1 AT-ATATATAT
616667 TTTTAATTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
21 7 0.11
22 23 0.37
23 31 0.49
24 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (22 bp):
ATATATATATAGTATATTTAAA
Found at i:616970 original size:2 final size:2
Alignment explanation
Indices: 616813--616954 Score: 89
Period size: 2 Copynumber: 72.0 Consensus size: 2
616803 TTATACTTAC
* * *
616813 AT AT CAT AT CT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
616856 AT AT -T AT AT AG AT AT -T AT AT TT A- AA AT AT AT AT AGT AGT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT
* * * * * *
616896 CT TT AA AT AT AT AT AG A- AT TT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
616937 AT A- AT AT AGT AT TT AT AT
1 AT AT AT AT A-T AT AT AT AT
616955 TAAGGTATTA
Statistics
Matches: 109, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
1 6 0.06
2 95 0.87
3 8 0.07
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:616983 original size:19 final size:18
Alignment explanation
Indices: 616827--616983 Score: 97
Period size: 16 Copynumber: 9.1 Consensus size: 18
616817 CATATCTATG
616827 TATATATATATATA-TA-
1 TATATATATATATAGTAT
*
616843 TATATATATATTTA-TAT
1 TATATATATATATAGTAT
*
616860 TATATAGATAT-TA-TAT
1 TATATATATATATAGTAT
*
616876 T-TAAAATATATATAGTAGTT
1 TAT-ATATATATATAGTA--T
* * *
616896 CTTTAAATATATATAGAAT
1 -TATATATATATATAGTAT
616915 T-TATATATATATA-TA-
1 TATATATATATATAGTAT
*
616930 TATATTTATAATATAGTAT
1 TATATATAT-ATATAGTAT
*
616949 T-TATAT-TA-A-GGTAT
1 TATATATATATATAGTAT
616963 TATATATACTATATAGTAT
1 TATATATA-TATATAGTAT
616982 TA
1 TA
616984 CATTACCTAT
Statistics
Matches: 113, Mismatches: 11, Indels: 31
0.73 0.07 0.20
Matches are distributed among these distances:
14 5 0.04
15 8 0.07
16 35 0.31
17 31 0.27
18 10 0.09
19 8 0.07
20 1 0.01
21 14 0.12
22 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (18 bp):
TATATATATATATAGTAT
Found at i:617026 original size:27 final size:27
Alignment explanation
Indices: 616996--617067 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
616986 TTACCTATTC
616996 TATTTTATTTTATTATAATA-TAT-TA
1 TATTTTATTTTATTATAATATTATATA
*
617021 TGTATTTATATTTA-TACTAATATTATATA
1 TAT-TTTAT-TTTATTA-TAATATTATATA
617050 TATTTGTATTTATATTAT
1 TATTT-TATTT-TATTAT
617068 TATTTTTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
25 2 0.05
26 7 0.19
27 9 0.24
28 7 0.19
29 10 0.27
30 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (27 bp):
TATTTTATTTTATTATAATATTATATA
Found at i:617071 original size:27 final size:27
Alignment explanation
Indices: 616996--617071 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
616986 TTACCTATTC
* *
616996 TATTTTATTT-TATTATAATATATTATG
1 TATTTTATTTATATTATTAT-TATTATA
* *
617023 TATTTATATTTATACTAATATTA-TATA
1 TATTT-TATTTATATTATTATTATTATA
617050 TATTTGTATTTATATTATTATT
1 TATTT-TATTTATATTATTATT
617072 TTTGTTTTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 27 0.68
28 7 0.17
29 6 0.15
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (27 bp):
TATTTTATTTATATTATTATTATTATA
Found at i:618343 original size:19 final size:20
Alignment explanation
Indices: 618303--618343 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
618293 ACATTGAGAG
618303 TTTATAAAATAATCATTAAA
1 TTTATAAAATAATCATTAAA
* *
618323 TTTATTAAATTATCA-TAAA
1 TTTATAAAATAATCATTAAA
618342 TT
1 TT
618344 GTGATCGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTATAAAATAATCATTAAA
Found at i:628718 original size:29 final size:31
Alignment explanation
Indices: 628686--628747 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 31
628676 TATCTATTAG
628686 TAAATTTATAA-TTTTTTAA-AAATAATTTT
1 TAAATTTATAATTTTTTTAAGAAATAATTTT
*
628715 TAAATTTGTAATTTTTTTAATGAAATAATTTT
1 TAAATTTATAATTTTTTTAA-GAAATAATTTT
628747 T
1 T
628748 TAAGATAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.34
30 8 0.28
32 11 0.38
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (31 bp):
TAAATTTATAATTTTTTTAAGAAATAATTTT
Found at i:637172 original size:12 final size:12
Alignment explanation
Indices: 637155--637182 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
637145 GCATACACAC
637155 ACATGCATGCAT
1 ACATGCATGCAT
637167 ACATGCATGCAT
1 ACATGCATGCAT
637179 ACAT
1 ACAT
637183 ACATAACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (12 bp):
ACATGCATGCAT
Found at i:639663 original size:24 final size:24
Alignment explanation
Indices: 639636--639688 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
639626 TAAGCCTTGC
639636 ATTCCAGCTATGTTTGCAAATTTA
1 ATTCCAGCTATGTTTGCAAATTTA
*** *
639660 ATTCCTTTTATTTTTGCAAATTTA
1 ATTCCAGCTATGTTTGCAAATTTA
639684 ATTCC
1 ATTCC
639689 TTTTATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (24 bp):
ATTCCAGCTATGTTTGCAAATTTA
Found at i:639689 original size:24 final size:24
Alignment explanation
Indices: 639648--639697 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
639638 TCCAGCTATG
639648 TTTGCAAATTTAATTCCTTTTATT
1 TTTGCAAATTTAATTCCTTTTATT
639672 TTTGCAAATTTAATTCCTTTTATT
1 TTTGCAAATTTAATTCCTTTTATT
639696 TT
1 TT
639698 CAAGGTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTGCAAATTTAATTCCTTTTATT
Found at i:640117 original size:29 final size:30
Alignment explanation
Indices: 640080--640136 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
640070 TTTCATTTTC
*
640080 TTTACTATTATTAT-TTTTTTTTCTTTCTGA
1 TTTACTATTATTATATTTTTCTT-TTTCTGA
*
640110 TTTA-TATTTTTATATTTTTCTTTTTCT
1 TTTACTATTATTATATTTTTCTTTTTCT
640137 TTCCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.74
Consensus pattern (30 bp):
TTTACTATTATTATATTTTTCTTTTTCTGA
Found at i:641101 original size:162 final size:163
Alignment explanation
Indices: 640831--641156 Score: 572
Period size: 162 Copynumber: 2.0 Consensus size: 163
640821 GTGAATTTAT
640831 TCACCGTGCGGGCATAGGAATGTGTCCTCTCGAGTTTAACTTAGTCCACACAAGCTTGTAATAGG
1 TCACCGTGCGGGCATAGGAATGTGTCCTCTCGAGTTTAACTTAGTCCACAC-AGCTTGTAATAGG
640896 CTTAGGACTAAGGTCTGGCAAGCCCAAGGGGCACCGGCAAGGAGAACTCGAGTACCTTTTTAGAA
65 CTTAGGACTAAGGTCTGGCAAGCCCAAGGGGCACCGGCAAGGAGAACTCGAGTACCTTTTTAGAA
640961 CCT-AACCGGGAGAGTGGCAGGGAATTAGAGCTCA
130 CCTAAACCGGGAGAGT-GCAGGGAATTAGAGCTCA
640995 TCACCGTGCGGGCATAAGGGAATGTGTCCTCTCGAGTTTAACTTAGT-C-CAC-GCTTGTAATAG
1 TCACCGTGCGGGCAT-A-GGAATGTGTCCTCTCGAGTTTAACTTAGTCCACACAGCTTGTAATAG
641057 GCTTAGGACTAAGGGTCTGGCAAGCCCAAGGGGCACC-GCAAGGAGAACTCGAGTACCTTTTTAG
64 GCTTAGGACTAA-GGTCTGGCAAGCCCAAGGGGCACCGGCAAGGAGAACTCGAGTACCTTTTTAG
641121 AACCTAAACCGGGAGAGTGCAGGGAATTAGAGCTCA
128 AACCTAAACCGGGAGAGTGCAGGGAATTAGAGCTCA
641157 CCCCGAGACC
Statistics
Matches: 158, Mismatches: 0, Indels: 10
0.94 0.00 0.06
Matches are distributed among these distances:
162 73 0.46
163 36 0.23
164 18 0.11
165 2 0.01
166 29 0.18
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (163 bp):
TCACCGTGCGGGCATAGGAATGTGTCCTCTCGAGTTTAACTTAGTCCACACAGCTTGTAATAGGC
TTAGGACTAAGGTCTGGCAAGCCCAAGGGGCACCGGCAAGGAGAACTCGAGTACCTTTTTAGAAC
CTAAACCGGGAGAGTGCAGGGAATTAGAGCTCA
Found at i:644301 original size:106 final size:106
Alignment explanation
Indices: 644164--647312 Score: 4993
Period size: 106 Copynumber: 30.6 Consensus size: 106
644154 AAAAGTTGTC
**
644164 TGTCAATAAATAACTT-TCCAATTTCAGAGCCAATTTCAACTTCA-AAGCGAAGGATATTGGACT
1 TGTCAATAACCAACTTCT-CAATTTCAGAGCCAATTTCAACTTCACAA-CGAAGGATATTGGACT
* *
644227 CCAGACAACGTATGTTCAACTTCACGACGAAGGGACCGCTGGT
64 CCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
644270 TGTCAATAACCAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
644335 AGACAACGTAAGTTCAACTTCACGACGAAGGGACTGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
644376 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
644441 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
644482 TATCAAT-A--AA-----CAATTTC----CTAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
644535 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
644576 TGTCAATAACCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
644641 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
644682 TGTCAATAACCAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
644747 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
644788 TGTCAATAACCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
644853 AGACAACGTAAGTTCAACTTCACGACAAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
644894 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGATGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
644959 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
645000 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
645065 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
645106 TGTCAAT-A--AA-----CAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
645159 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
645200 TGTCAAT-A--AA-----CAATTTC----CTAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
645253 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGC----
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
**
645290 TGTCAATAACCAACTTCTCAAACTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
645355 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
645396 TGTCAATAACCAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
645461 AGACAACGTAAGTT---CTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
645499 TGTCAATAACCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
645564 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
645605 TGTCAATAACCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
645670 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
645711 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGATGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
645776 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
645817 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
645882 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
645923 T-TCAAT-A--AA-----CAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
645975 AGACAACGCAAGTTC-ACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
646015 TGTCAAT-A--AA-----CAATTTC----CTAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
646068 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
646109 TGTCAATAACCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
646174 AGACAACGTAAGTTCAACTTCATGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
646215 TGTCAATAACCAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
646279 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
646320 TGTCAATAACCAACTTCTCAAATTT-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TGTCAATAACCAACTTCTC-AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
*
646384 CAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGT
65 CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
646426 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGATGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
646491 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
646532 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
646596 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
646637 TGTCAAT-A--AA-----CAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGCACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
646690 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
646731 TGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCT
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
646796 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
646837 TGTCAGTAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
646902 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
646943 TGTCAAT-A--AA-----CAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
646996 AGATAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
647037 TGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCT
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
647102 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
647143 TGTCAGTAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
647208 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
** * * ** * * *
647249 TGTCAATAAATAA-TTTTCCAGTCCCAGAACCAATTTCAACTTCACATCGGAGGATATTGGACTC
1 TGTCAATAACCAACTTCT-CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
647313 GGAACAATAC
Statistics
Matches: 2889, Mismatches: 78, Indels: 152
0.93 0.03 0.05
Matches are distributed among these distances:
90 7 0.00
91 1 0.00
92 26 0.01
93 144 0.05
94 416 0.14
95 4 0.00
97 22 0.01
98 26 0.01
102 102 0.04
103 107 0.04
104 2 0.00
105 169 0.06
106 1860 0.64
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:644471 original size:43 final size:43
Alignment explanation
Indices: 644410--644565 Score: 127
Period size: 43 Copynumber: 3.4 Consensus size: 43
644400 CAGAGCCAAT
644410 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** * * *
644453 TTCAACTTCACGACGAAGGGACCGCTGGTTA-TCAATAAACAATTTC-CTAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG--ACTC--CAGACAA---CGC-AAG
*
644504 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
644547 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
644566 GACCGCTGGT
Statistics
Matches: 85, Mismatches: 16, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
43 37 0.44
44 3 0.04
45 3 0.04
46 7 0.08
47 2 0.02
48 7 0.08
49 3 0.04
50 4 0.05
51 19 0.22
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:644748 original size:306 final size:306
Alignment explanation
Indices: 644193--647264 Score: 4983
Period size: 306 Copynumber: 10.0 Consensus size: 306
644183 AATTTCAGAG
*
644193 CCAATTTCAACTTCA-AAGCGAAGGATATTGGACTCCAGACAACGTATGTTCAACTTCACGACGA
1 CCAATTTCAACTTCACAA-CGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGA
*
644257 AGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAG
65 AGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
* * * *
644322 GATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAAC
130 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACC
644387 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
195 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
*
644452 GTTCAACTTCACGACGAAGGGACCGCTGGTTATCAATAAACAATTTC
260 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
*
644499 CTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
*
644564 GGGACCGCTGGTTGTCAATAACCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
*
644629 ATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
* *
644694 ACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
196 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
644759 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAAATTC
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-A--AA-----CAATTTC
644813 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
*
644878 CAAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
62 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
* *
644943 ATGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
127 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
645008 ACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
192 ACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
645073 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
257 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
*
645123 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
*
645188 GGGACCGCTGGTTGTCAAT-A--AA-----CAATTTC----CTAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
*
645241 ATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGC----TGTCAATAACCA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
** *
645302 ACTTCTCAAACTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
196 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
645367 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-A--AA-----CAATTTC
645421 AAAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTT---CTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
*
645483 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
62 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
*
645548 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
127 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
*
645613 ACCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
192 ACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
645678 TAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTC
257 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-A--AA-----CAATTTC
* *
645736 AGAGCCAATTTCAACTTCACAACGATGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 ----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
645801 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
62 CGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
645866 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTT-TCAAT-
127 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
645929 A--AA-----CAATTTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
192 ACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
645983 CAAGTTC-ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
257 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
*
646032 CTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
*
646097 GGGACCGCTGGTTGTCAATAACCAACTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
646162 ATATTGGACTCCAGACAACGTAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAACCA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
* *
646227 ACTTCTCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGTAAG
196 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
646291 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCAACTTCTCAAATTTAGAG
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT-A--AA-----C-AATTT---C
646349 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
*
646414 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGATGG
66 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
646479 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
646544 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGCAAG
196 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
646608 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
* *
646654 CCAATTTCAACTTCACAACGAAGGATATTGCACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
* *
646719 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
* * *
646784 ATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGTAAACA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
646849 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
196 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
646914 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
* *
646960 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
* *
647025 GGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGG
66 GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
* * *
647090 ATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAGTAAACA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
*
647155 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
196 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
647220 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTT
261 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
647265 TCCAGTCCCA
Statistics
Matches: 2627, Mismatches: 68, Indels: 142
0.93 0.02 0.05
Matches are distributed among these distances:
290 110 0.04
291 1 0.00
292 178 0.07
293 7 0.00
294 70 0.03
296 9 0.00
298 14 0.01
299 31 0.01
300 1 0.00
301 9 0.00
302 51 0.02
303 3 0.00
304 54 0.02
305 341 0.13
306 733 0.28
307 9 0.00
308 7 0.00
309 9 0.00
310 6 0.00
311 72 0.03
313 1 0.00
314 15 0.01
315 183 0.07
316 2 0.00
317 294 0.11
318 417 0.16
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (306 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAACCA
ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC
Found at i:645095 original size:43 final size:43
Alignment explanation
Indices: 645034--645283 Score: 151
Period size: 43 Copynumber: 5.4 Consensus size: 43
645024 CAGAGCCAAT
645034 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
645077 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
645128 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * *
645171 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC-CTAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGC-AAG
*
645222 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
645265 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
645284 GACCGCTGTC
Statistics
Matches: 149, Mismatches: 40, Indels: 36
0.66 0.18 0.16
Matches are distributed among these distances:
43 57 0.38
44 6 0.04
45 6 0.04
46 14 0.09
48 14 0.09
49 6 0.04
50 7 0.05
51 39 0.26
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:645912 original size:43 final size:43
Alignment explanation
Indices: 645851--646098 Score: 149
Period size: 43 Copynumber: 5.4 Consensus size: 43
645841 CAGAGCCAAT
645851 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
645894 TTCAACTTCACGACGAAGGGACCGCTGGTTTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGGACTC--CAGACAA---CGCAAG
645944 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * *
645987 TTC-ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTC-CTAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGC-AAG
*
646037 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
646080 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
646099 GACCGCTGGT
Statistics
Matches: 147, Mismatches: 40, Indels: 36
0.66 0.18 0.16
Matches are distributed among these distances:
42 12 0.08
43 47 0.32
44 6 0.04
45 7 0.05
46 10 0.07
47 10 0.07
48 7 0.05
49 7 0.05
50 29 0.20
51 12 0.08
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:646720 original size:43 final size:43
Alignment explanation
Indices: 646566--646720 Score: 127
Period size: 43 Copynumber: 3.4 Consensus size: 43
646556 CAGAGCCAAT
*
646566 TTCAACTTCACAACGAAGGATA-TGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGCACTCCAGACAACGCAAG
* * * * * *
646608 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAT--AAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA----T-ATTG-CACTCCAGACAA---CGCAAG
646659 TTCAACTTCACAACGAAGGATATTGCACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGCACTCCAGACAACGCAAG
*
646702 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
646721 GACCGCTGGT
Statistics
Matches: 86, Mismatches: 14, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
42 16 0.19
43 25 0.29
44 3 0.03
45 3 0.03
46 6 0.07
47 1 0.01
48 5 0.06
49 2 0.02
50 5 0.06
51 20 0.23
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGCACTCCAGACAACGCAAG
Found at i:646932 original size:43 final size:43
Alignment explanation
Indices: 646871--647026 Score: 132
Period size: 43 Copynumber: 3.4 Consensus size: 43
646861 CAGAGCCAAT
646871 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
646914 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
*
646965 TTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
647008 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
647027 GACCGCTGGT
Statistics
Matches: 83, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
43 38 0.46
44 3 0.04
45 3 0.04
46 6 0.07
48 7 0.08
49 3 0.04
50 3 0.04
51 20 0.24
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:647816 original size:14 final size:14
Alignment explanation
Indices: 647799--647841 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
647789 GTCCCTTTTA
647799 TTTTTATAATATAC
1 TTTTTATAATATAC
*
647813 TTTTGATTAATATTA-
1 TTTTTA-TAATA-TAC
647828 TTTTTATAATATAC
1 TTTTTATAATATAC
647842 ATTATTGCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 10 0.42
16 2 0.08
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (14 bp):
TTTTTATAATATAC
Found at i:648733 original size:24 final size:24
Alignment explanation
Indices: 648706--648758 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
648696 TAAGCCTTGC
648706 ATTCCAGCTATGTTTGCAAATTTA
1 ATTCCAGCTATGTTTGCAAATTTA
*** *
648730 ATTCCTTTTATTTTTGCAAATTTA
1 ATTCCAGCTATGTTTGCAAATTTA
648754 ATTCC
1 ATTCC
648759 TTTTATTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (24 bp):
ATTCCAGCTATGTTTGCAAATTTA
Found at i:648759 original size:24 final size:24
Alignment explanation
Indices: 648718--648766 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
648708 TCCAGCTATG
648718 TTTGCAAATTTAATTCCTTTTATT
1 TTTGCAAATTTAATTCCTTTTATT
648742 TTTGCAAATTTAATTCCTTTTATT
1 TTTGCAAATTTAATTCCTTTTATT
648766 T
1 T
648767 CAAGGTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTGCAAATTTAATTCCTTTTATT
Found at i:649197 original size:28 final size:29
Alignment explanation
Indices: 649161--649215 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
649151 TTTCATTTTC
*
649161 TTTACTATTATTAT-TTTTTTTCTTTCTGA
1 TTTACTATTATTATATTTTCTT-TTTCTGA
*
649190 TTTA-TATTTTTATATTTTCTTTTTCT
1 TTTACTATTATTATATTTTCTTTTTCT
649216 TTCCTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTACTATTATTATATTTTCTTTTTCTGA
Found at i:652216 original size:20 final size:20
Alignment explanation
Indices: 652159--652209 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
652149 ATCCTATTCC
*
652159 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTTTATTCCCA
652179 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
652199 CTGGTAATCTT
1 CTGGTAATCTT
652210 ACATTCCGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:652486 original size:25 final size:25
Alignment explanation
Indices: 652452--652504 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
652442 CGTAACATTG
652452 AATAAATTTATGTGATTTATAATTT
1 AATAAATTTATGTGATTTATAATTT
652477 AATAAATTTATGTGATTTATAATTT
1 AATAAATTTATGTGATTTATAATTT
652502 AAT
1 AAT
652505 TTCTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (25 bp):
AATAAATTTATGTGATTTATAATTT
Found at i:652988 original size:5 final size:5
Alignment explanation
Indices: 652978--653002 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
652968 CATCAATAAT
652978 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
653003 TTCATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:653560 original size:14 final size:14
Alignment explanation
Indices: 653541--653571 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
653531 CCCCGACTAA
653541 TAAAATATTGTAGT
1 TAAAATATTGTAGT
653555 TAAAATATTGTAGT
1 TAAAATATTGTAGT
653569 TAA
1 TAA
653572 TATTGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (14 bp):
TAAAATATTGTAGT
Done.