Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008003.1 Hibiscus syriacus cultivar Beakdansim tig00110462_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: 3297763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:469646 original size:20 final size:20
Alignment explanation
Indices: 469608--469663 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
469598 GATAGTCAAA
* **
469608 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
469628 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
469648 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
469664 AAGTTTCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:469670 original size:20 final size:20
Alignment explanation
Indices: 469627--469670 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
469617 CGATAGTCAT
* *
469627 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
469647 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
469667 TTTC
1 TTTC
469671 ATAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:471423 original size:18 final size:18
Alignment explanation
Indices: 471400--471449 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
471390 TTTACTCGTA
471400 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
471418 ATTTCACTTATATTAACC
1 ATTTCACTTAGATTAACC
471436 ATTTCACTTAGATT
1 ATTTCACTTAGATT
471450 GCTTAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:471622 original size:20 final size:20
Alignment explanation
Indices: 471597--471744 Score: 215
Period size: 20 Copynumber: 7.4 Consensus size: 20
471587 TAGTTTACTT
471597 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
471617 TCGCAACGCGAAAACGACTA
1 TCGCAACGCGAAAATGACTA
*
471637 TCGCAACGCAAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
471657 TCGCAACGCGAAAACGACTA
1 TCGCAACGCGAAAATGACTA
*
471677 TCGCAACGCGAAAACGACTA
1 TCGCAACGCGAAAATGACTA
* *
471697 TTGCAACGCGAAAATAACTA
1 TCGCAACGCGAAAATGACTA
* **
471717 TCGCAATGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
471737 TCGCAACG
1 TCGCAACG
471745 AAAGAATCGT
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 114 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:471812 original size:20 final size:19
Alignment explanation
Indices: 471787--471853 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
471777 GGGATTCTCT
471787 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
*
471807 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-ATTCG
*
471827 CGTCGCGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
471845 TGTTGCGAT
1 CGTTGCGAT
471854 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.27
19 1 0.02
20 29 0.71
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:472395 original size:21 final size:22
Alignment explanation
Indices: 472371--472431 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 22
472361 CCCCTATCAT
472371 TCAAGAGGCCCCTATCATCC-C
1 TCAAGAGGCCCCTATCATCCGC
* * *
472392 TCAAGAGTCCCCTCTCA-CCGT
1 TCAAGAGGCCCCTATCATCCGC
* *
472413 TCAAGAGGCCACTGTCATC
1 TCAAGAGGCCCCTATCATC
472432 ATTGAAGAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.06
21 29 0.91
22 1 0.03
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.21
Consensus pattern (22 bp):
TCAAGAGGCCCCTATCATCCGC
Found at i:473891 original size:14 final size:14
Alignment explanation
Indices: 473854--473915 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
473844 TTGCTTGTTT
*
473854 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
473868 AACTGATTTGTAAA
1 AATTGATTTGTAAA
*
473882 AATTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
473897 TATTGATGTGTAAA
1 AATTGATTTGTAAA
473911 TAATT
1 -AATT
473916 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 24 0.63
15 14 0.37
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:474052 original size:20 final size:20
Alignment explanation
Indices: 474029--474067 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
474019 ATGTTAAACT
*
474029 CAAAATCGCAATGCGAAAGA
1 CAAAATCGCAACGCGAAAGA
474049 CAAAATCGCAACGCGAAAG
1 CAAAATCGCAACGCGAAAG
474068 TCAATTCGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.23, G:0.21, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACGCGAAAGA
Found at i:474128 original size:34 final size:36
Alignment explanation
Indices: 474071--474271 Score: 122
Period size: 34 Copynumber: 5.4 Consensus size: 36
474061 GCGAAAGTCA
* ** *
474071 ATTCGCGTTGCAATAGTTTAATACGCTTTGCGAT-T
1 ATTCGCGTTGCGATAGTCAAATACGCGTTGCGATAT
* *
474106 -TTCTCGTTGCGATAGTCAAATACCCGTTGCGATAAT
1 ATTCGCGTTGCGATAGTCAAATACGCGTTGCGAT-AT
* * *
474142 CAAATTCGCGTTGCGATACTCAAATTCGCGTTGCGATGTCAA
1 ---ATTCGCGTTGCGATAGTCAAATACGCGTTGCGA--T-AT
* * *
474184 ATTCGCGTTGCGATAGGCAAATTCGCATTGC-A-AT
1 ATTCGCGTTGCGATAGTCAAATACGCGTTGCGATAT
* * * * *
474218 TTTTGCGTTGCGATAGTCATATTCGTGTTGCGATAGT
1 ATTCGCGTTGCGATAGTCAAATACGCGTTGCGATA-T
474255 CAAATTCGCGTTGCGAT
1 ---ATTCGCGTTGCGAT
474272 TTTTGAGTTG
Statistics
Matches: 128, Mismatches: 24, Indels: 23
0.73 0.14 0.13
Matches are distributed among these distances:
34 53 0.41
35 1 0.01
36 2 0.02
37 1 0.01
38 1 0.01
39 28 0.22
40 40 0.31
42 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (36 bp):
ATTCGCGTTGCGATAGTCAAATACGCGTTGCGATAT
Found at i:474135 original size:20 final size:20
Alignment explanation
Indices: 474110--474313 Score: 200
Period size: 20 Copynumber: 10.8 Consensus size: 20
474100 GCGATTTTCT
* *
474110 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
474130 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
474150 CGTTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
474170 CGTTGCGAT-GTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
474189 CGTTGCGATAGGCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* * *
474209 CATTGC-A-A-T---TTTTG
1 CGTTGCGATAGTCAAATTCG
*
474223 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
474243 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
474263 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
474277 AGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
474297 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
474314 GAATGTGTAA
Statistics
Matches: 150, Mismatches: 21, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
14 19 0.13
15 1 0.01
16 2 0.01
17 1 0.01
18 2 0.01
19 19 0.13
20 106 0.71
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:474156 original size:54 final size:54
Alignment explanation
Indices: 474061--474313 Score: 269
Period size: 54 Copynumber: 4.6 Consensus size: 54
474051 AAATCGCAAC
* * ** * *
474061 GCGAAAGTC-AATTCGCGTTGCAATAGTTTAATACGCTTTGCGATTTTCT-CGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGCGTT
* * * *
474114 GCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGATACTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTTGCGTT
* * *
474174 GCGAT-GTCAAATTCGCGTTGCGATAGGCAAATTCGCATTGCAATTTTTGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
* * *
474227 GCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
*
474281 GCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
474314 GAATGTGTAA
Statistics
Matches: 165, Mismatches: 26, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
53 20 0.12
54 99 0.60
56 1 0.01
57 1 0.01
59 33 0.20
60 11 0.07
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (54 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
Found at i:474536 original size:140 final size:140
Alignment explanation
Indices: 474284--474553 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
474274 TTGAGTTGCG
*
474284 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
474349 TAGCAATGTTCAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
474414 AATACACATA
131 AATACACATA
474424 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
474489 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
474554 TACAACGTTT
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:474629 original size:6 final size:6
Alignment explanation
Indices: 474620--474653 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
474610 TTCTGATTGG
**
474620 GATTTT GATTTT GATTTT GATTGC GATTTT GATT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATT
474654 GCCTTTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.59
Consensus pattern (6 bp):
GATTTT
Found at i:474635 original size:12 final size:12
Alignment explanation
Indices: 474613--474655 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
474603 AAGCCGGTTC
*
474613 TGATTGGGATTT
1 TGATTGCGATTT
**
474625 TGATTTTGATTT
1 TGATTGCGATTT
474637 TGATTGCGATTT
1 TGATTGCGATTT
474649 TGATTGC
1 TGATTGC
474656 CTTTTTCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:476726 original size:15 final size:14
Alignment explanation
Indices: 476690--476726 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
476680 TCCCGTGGCA
476690 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
476704 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
476718 TTATTCTTC
1 TT-TTCTTC
476727 TTTTTCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.08, C:0.19, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:476952 original size:24 final size:24
Alignment explanation
Indices: 476925--476971 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
476915 CAAAATCCGA
476925 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
476949 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
476972 AATACCGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:477833 original size:20 final size:20
Alignment explanation
Indices: 477787--477894 Score: 83
Period size: 20 Copynumber: 5.3 Consensus size: 20
477777 AAATTCAGTG
* * *
477787 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
477807 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* * *
477827 TTACGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
*
477847 TTGCGATAGTCGGAAAATCGCA
1 TTGCGATAGTC--ATAATCGCA
* * * *
477869 ATGCGATAATCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
477889 TTGCGA
1 TTGCGA
477895 ATCTGGAAAC
Statistics
Matches: 69, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.01
20 51 0.74
21 1 0.01
22 16 0.23
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:478234 original size:9 final size:9
Alignment explanation
Indices: 478220--478245 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
478210 TTTCTTGGCA
478220 TACCAGCTC
1 TACCAGCTC
478229 TACCAGCTC
1 TACCAGCTC
478238 TACCAGCT
1 TACCAGCT
478246 ATCCCCTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.12, T:0.23
Consensus pattern (9 bp):
TACCAGCTC
Found at i:494407 original size:2 final size:2
Alignment explanation
Indices: 494400--494429 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
494390 TAATCCATAA
494400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
494430 TATTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:494893 original size:14 final size:14
Alignment explanation
Indices: 494874--494901 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
494864 ATCATAACAA
494874 AATTATATAACTAT
1 AATTATATAACTAT
494888 AATTATATAACTAT
1 AATTATATAACTAT
494902 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:494979 original size:17 final size:18
Alignment explanation
Indices: 494952--494985 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
494942 AGCTTCTAAT
494952 TTTTGTTTAGTTCAAATA
1 TTTTGTTTAGTTCAAATA
494970 TTTT-TTTAGTTCAAAT
1 TTTTGTTTAGTTCAAAT
494986 TTCAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (18 bp):
TTTTGTTTAGTTCAAATA
Found at i:499506 original size:14 final size:14
Alignment explanation
Indices: 499489--499523 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
499479 CTCTTCAAAA
499489 ATATACCTATATAT
1 ATATACCTATATAT
499503 ATATACACCTATATAT
1 ATAT--ACCTATATAT
499519 ATATA
1 ATATA
499524 TATAATGGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.26
16 14 0.74
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATACCTATATAT
Found at i:499512 original size:16 final size:16
Alignment explanation
Indices: 499493--499523 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
499483 TCAAAAATAT
499493 ACCTATATATATATAC
1 ACCTATATATATATAC
499509 ACCTATATATATATA
1 ACCTATATATATATA
499524 TATAATGGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (16 bp):
ACCTATATATATATAC
Found at i:516193 original size:3 final size:3
Alignment explanation
Indices: 516185--516224 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
516175 CCCAGTCTCA
*
516185 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT
516225 CTAATCTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:516285 original size:33 final size:33
Alignment explanation
Indices: 516233--516323 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 33
516223 ATCTAATCTA
* * ** *
516233 AAAAACTCACTACCTATTAAATAATCATCCACT
1 AAAAACTCAATACCCATTAAATAAAAACCCACT
*
516266 AAAAATTCAATACCCATTAAATAAAAACCCACT
1 AAAAACTCAATACCCATTAAATAAAAACCCACT
**
516299 AAAAACT-AACTACATATTAAATAAA
1 AAAAACTCAA-TACCCATTAAATAAA
516324 GAAAACTTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (33 bp):
AAAAACTCAATACCCATTAAATAAAAACCCACT
Found at i:520659 original size:31 final size:31
Alignment explanation
Indices: 520623--520682 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
520613 TAAACTTAAG
520623 AGTTTTACAATACTAAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
* *
520654 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTAAAATTTAAATAATT
520683 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:520726 original size:22 final size:22
Alignment explanation
Indices: 520701--520975 Score: 307
Period size: 22 Copynumber: 12.6 Consensus size: 22
520691 TAAATAATTT
520701 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
520723 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
520745 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
***
520767 TTTTAAAAT-AATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
* * *
520788 TTTTAAAATAAATTAATCCATT
1 TTTTAAAATAAATCAATTCATA
**
520810 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATTCATA
*
520832 TTTTAAAATAAAT-AAATCTATA
1 TTTTAAAATAAATCAATTC-ATA
520854 TTTTAAAATAAATCAA-TCAATA
1 TTTTAAAATAAATCAATTC-ATA
520876 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
**
520898 TTTTAAAAT-AAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
*
520919 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
520941 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
520963 TTTTAAAATAAAT
1 TTTTAAAATAAAT
520976 TTTAAAATAG
Statistics
Matches: 218, Mismatches: 24, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
21 42 0.19
22 168 0.77
23 8 0.04
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:520749 original size:44 final size:43
Alignment explanation
Indices: 520701--520975 Score: 354
Period size: 44 Copynumber: 6.3 Consensus size: 43
520691 TAAATAATTT
*
520701 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-ATA
* ***
520745 TTTTAAAATAAATCAATCCATATTTTAAAATAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCATA
* * ***
520788 TTTTAAAATAAATTAATCCATTTTTTAAAATAAAATTTTTCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCATA
* *
520832 TTTTAAAATAAATAAATCTATATTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-ATA
* ***
520876 TTTTAAAATAAATCAATCTATATTTTAAAAT-AATTTTTCCATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-CATA
520919 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-ATA
520963 TTTTAAAATAAAT
1 TTTTAAAATAAAT
520976 TTTAAAATAG
Statistics
Matches: 204, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
43 76 0.37
44 128 0.63
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.43
Consensus pattern (43 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCATA
Found at i:520792 original size:65 final size:65
Alignment explanation
Indices: 520701--520978 Score: 371
Period size: 65 Copynumber: 4.2 Consensus size: 65
520691 TAAATAATTT
** *
520701 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAAT-TTTTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
520766 A
65 A
* * * ** *
520767 TTTTAAAATAATTTTTTCATATTTTAAAATAAATTAATCCATTTTTTAAAATAAAAT-TTTTCAT
1 TTTTAAAATAAATTTTTCATATTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCCAT
520831 A
65 A
*** * *
520832 TTTTAAAATAAATAAATCTATATTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCTAT
1 TTTTAAAATAAATTTTTC-ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
520897 A
65 A
*
520898 TTTTAAAAT-AATTTTTCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
1 TTTTAAAATAAATTTTT-CATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
520962 A
65 A
520963 TTTTAAAATAAATTTT
1 TTTTAAAATAAATTTT
520979 AAAATAGATT
Statistics
Matches: 183, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
65 116 0.63
66 67 0.37
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (65 bp):
TTTTAAAATAAATTTTTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
Found at i:520813 original size:109 final size:109
Alignment explanation
Indices: 520699--520975 Score: 414
Period size: 109 Copynumber: 2.5 Consensus size: 109
520689 ACTAAATAAT
*
520699 TTTTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCC
1 TTTTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCA
* ***
520764 ATATTTTAAAATAATTTTTTC-ATATTTTAAAATAAATTAATCCA
66 ATATTTTAAAATAAATCAATCTATATTTTAAAAT-AATTAATCCA
** *
520808 TTTTTTAAAATAAAAT-TTTTCATATTTTAAAATAAATAAATCTATATTTTAAAATAAATCAATC
1 TTTTTTAAAAT-AAATCAATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATC
**
520872 AATATTTTAAAATAAATCAATCTATATTTTAAAATAATTTTTCCA
65 AATATTTTAAAATAAATCAATCTATATTTTAAAATAATTAATCCA
* *
520917 TATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAT
1 TTTTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAAT
520976 TTTAAAATAG
Statistics
Matches: 150, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
108 4 0.03
109 130 0.87
110 16 0.11
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (109 bp):
TTTTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCA
ATATTTTAAAATAAATCAATCTATATTTTAAAATAATTAATCCA
Found at i:520999 original size:87 final size:84
Alignment explanation
Indices: 520742--520992 Score: 297
Period size: 87 Copynumber: 2.9 Consensus size: 84
520732 AAATCAATCT
* *** *
520742 ATATTTTAAAATAAATCAATCCATATTTTAAAATAATTTTTTCATATTTTAAAATAAATTAATCC
1 ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCATATTTTAAAATAAATTAA--A
*
520807 AT-TTTTTAAAATAAAATTTTTC
64 ATATATTTAAAAT--AATTTTTC
* * * **
520829 ATATTTTAAAATAAATAAATCTATATTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATC
1 ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-ATATTTTAAAATAAATTAAAA
520894 TATATTTTAAAATAATTTTTCC
65 TATA-TTTAAAATAATTTTT-C
520916 ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATATTTTAAAATAAATTTTAA
1 ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC-ATATTTTAAAATAAA--TTAA
*
520981 AATAGATTTAAA
63 AATATATTTAAA
520993 TGATTTTAAT
Statistics
Matches: 141, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
86 8 0.06
87 95 0.67
88 32 0.23
89 6 0.04
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (84 bp):
ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCATATTTTAAAATAAATTAAAAT
ATATTTAAAATAATTTTTC
Found at i:521696 original size:111 final size:111
Alignment explanation
Indices: 521496--521956 Score: 733
Period size: 111 Copynumber: 4.1 Consensus size: 111
521486 TTGTCGGTTT
* * * * *
521496 GTGTCGATACTTTATAAAAATATATTGATCAATTACAATATAACAGGTAAAAAATGACAAAATCG
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
*
521561 GTCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATATTGAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
521607 GTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
* * *
521672 GTCTATAAATGACAAAACATGTAAAGCGCTACAGGATATATTAAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
521718 GTGTCGATACTTTATAAAAATGTATCAATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
* *
521783 GTCTATAAATGATAAAATAGGTAAAGCGCTACCGGATATATTGAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
521829 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT--AAAAAATGACAAAAC
* * * *
521894 CGGTCTATAAATGACAAAACAAGTAAAGCGCTACCAGATATGTTGATA
64 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
521942 GTGTTGATACTTTAT
1 GTGTCGATACTTTAT
521957 TATAAGTATC
Statistics
Matches: 322, Mismatches: 26, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
111 252 0.78
113 70 0.22
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.26
Consensus pattern (111 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:522162 original size:182 final size:181
Alignment explanation
Indices: 521826--522282 Score: 752
Period size: 182 Copynumber: 2.5 Consensus size: 181
521816 GGATATATTG
*
521826 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAATATGACAA
** * * * *
521891 AATCGGTCTATAAATGACAAAACAAGTAAAGCGCTACCAGATATGTTGATAGTGTTGATACTTTA
65 AATCGGTCTCGAAATGACAAAAC-GGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTA
* *
521956 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
129 TTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
*
522009 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
522074 ACCGGTCTCGAAATGACAAAATCGGTAAAGAGCTACTAGATATGTTGAAAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAA-CGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
*
522139 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCTCCAAT
130 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
522191 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
522256 ATCGGTCTCGAAATGATAAAACCGGTA
66 ATCGGTCTCGAAATGACAAAA-CGGTA
522283 GTAAAAAAAT
Statistics
Matches: 256, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
182 204 0.80
183 52 0.20
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (181 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ATCGGTCTCGAAATGACAAAACGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTATT
ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
Found at i:523354 original size:30 final size:32
Alignment explanation
Indices: 523319--523386 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 32
523309 AAATGTTTTA
523319 TATTTTATAGT-AAT-ATAATTATATAAATAT
1 TATTTTATAGTAAATAATAATTATATAAATAT
* * * *
523349 TATTTTTTATTAAAATAATATTTATATAATTAT
1 TATTTTATAGT-AAATAATAATTATATAAATAT
523382 TATTT
1 TATTT
523387 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 9 0.29
32 3 0.10
33 19 0.61
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATTTTATAGTAAATAATAATTATATAAATAT
Found at i:525972 original size:35 final size:35
Alignment explanation
Indices: 525933--526032 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 35
525923 TAAATAAGAA
* *
525933 GAACGAAAGGAAGCATCAGCACTTTGGATTCAAGT
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
** *
525968 GAACGGAATAAAGCATC-GACACTTTCAATTCAAGT
1 GAACGGAAGGAAGCATCAG-CACTTTCGATTCAAGT
* *
526003 GAACGGGAGGAAGCATAAGCACTTTCGATT
1 GAACGGAAGGAAGCATCAGCACTTTCGATT
526033 TAATTGTTCA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
34 1 0.02
35 51 0.96
36 1 0.02
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:527462 original size:2 final size:2
Alignment explanation
Indices: 527457--527489 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
527447 ATCTTAGATT
*
527457 TC TC TC GC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
527490 TAGAAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.03, T:0.48
Consensus pattern (2 bp):
TC
Found at i:532062 original size:229 final size:229
Alignment explanation
Indices: 531662--532380 Score: 1354
Period size: 229 Copynumber: 3.1 Consensus size: 229
531652 GTTATATTGT
* * *
531662 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
531726 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
*
531791 TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
531856 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
531890 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
531955 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
532020 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
532085 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
* *
532119 AAAGTATATATCATTTTTATAAAAGTGTACATACTTATTTTACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
532184 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
532249 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-A
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
532313 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
532347 AATA-TATATATCATTTTTATAAAAGTGTCCATAC
1 AA-AGTATATATCATTTTTATAAAAGTGTCCATAC
532381 GTATAAAAGT
Statistics
Matches: 482, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
228 110 0.23
229 372 0.77
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (229 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:532452 original size:20 final size:19
Alignment explanation
Indices: 532429--532475 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
532419 CGATATACCA
532429 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
532449 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
532469 GGTAAAA
1 GGTAAAA
532476 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:532633 original size:20 final size:19
Alignment explanation
Indices: 532610--532656 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
532600 CGATATAACA
532610 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
532630 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
532650 GGTAAAA
1 GGTAAAA
532657 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:532658 original size:17 final size:19
Alignment explanation
Indices: 532619--532661 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
532609 AGGTAAAAAT
532619 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
532639 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
532656 ATGATA
1 ATGATA
532662 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:534901 original size:21 final size:21
Alignment explanation
Indices: 534877--534920 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
534867 AAGACAATCA
534877 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
534898 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
534919 AG
1 AG
534921 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:534996 original size:33 final size:33
Alignment explanation
Indices: 534954--535019 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
534944 AAATAGATGG
*
534954 AGTGGTGAAAGAAGTAGAGGTGTTGACGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAACGGGTGA
* * *
534987 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAACGGGTGA
535020 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAACGGGTGA
Found at i:537571 original size:199 final size:199
Alignment explanation
Indices: 536959--538927 Score: 3665
Period size: 199 Copynumber: 9.9 Consensus size: 199
536949 CAATATGGCC
* * *
536959 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
537024 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGATTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
537089 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
537154 TGGAA
195 TGGAA
* * *
537159 AACAGGGTGCAACCAAAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
537224 CCAAAAGTGTAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
537289 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
537354 TGGAA
195 TGGAA
*
537359 AACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
537424 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
537489 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
*
537554 GAAA
196 GGAA
537558 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
537623 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
537688 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
537753 GGAA
196 GGAA
* *
537757 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
537822 CCAAAAGTGTAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
537887 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
537952 TGGAA
195 TGGAA
*
537957 AACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
538022 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
538086 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
*
538151 GAAA
196 GGAA
538155 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
538220 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
538285 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
538350 GGAA
196 GGAA
* * *
538354 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCAAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC-GAAC
538419 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
538484 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
538549 TGGAA
195 TGGAA
538554 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
538619 CAAAAGTATAATGTATTATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
538684 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
*
538749 GAAA
196 GGAA
*
538753 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
538818 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
*
538883 AACATGTCTAAATAATGTGTCGACACGT--TTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACAC-TAATTTAGTTTGTGTCGATA
538928 CTAATTTAAA
Statistics
Matches: 1731, Mismatches: 34, Indels: 10
0.98 0.02 0.01
Matches are distributed among these distances:
198 213 0.12
199 872 0.50
200 646 0.37
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
GGAA
Found at i:537828 original size:399 final size:398
Alignment explanation
Indices: 536959--538927 Score: 3665
Period size: 399 Copynumber: 4.9 Consensus size: 398
536949 CAATATGGCC
* * *
536959 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
537024 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGATTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
537089 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
* *
537154 TGGAAAACAGGGTGCAACCAAAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
195 TGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
* *
537219 GAAAACCAAAAGTGTAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTA
260 G-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTA
537284 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGA
324 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGA
537349 ATGAATGGAA
389 ATGAATGGAA
*
537359 AACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
537424 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
537489 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
*
537554 GAAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
537619 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATG
537684 AGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAAT
326 AGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAAT
537749 GAATGGAA
391 GAATGGAA
* *
537757 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
537822 CCAAAAGTGTAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
537887 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
*
537952 TGGAAAACAGGATGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
195 TGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
538017 GAACCCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAAGTTTACCGGTTTTAT
260 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTAT
538081 GAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAA
325 GAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAA
*
538146 TGAATGAAA
390 TGAATGGAA
538155 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
538220 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
538285 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
*
538350 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCA
196 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC-
* *
538415 AAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTAT
260 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTAT
538480 GAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAA
325 GAGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAA
538545 TGAATGGAA
390 TGAATGGAA
538554 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
538619 CAAAAGTATAATGTATTATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
538684 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
* *
538749 GAAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
196 GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
538814 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATG
261 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATG
*
538879 AGAGAACATGTCTAAATAATGTGTCGACACGT--TTTAGTTTGTGTCGATA
326 AGAGAATATGTCTAAATAATGTGTCGACAC-TAATTTAGTTTGTGTCGATA
538928 CTAATTTAAA
Statistics
Matches: 1532, Mismatches: 33, Indels: 11
0.97 0.02 0.01
Matches are distributed among these distances:
397 211 0.14
398 482 0.31
399 781 0.51
400 58 0.04
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (398 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
GGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAAT
GAATGGAA
Found at i:540412 original size:6 final size:6
Alignment explanation
Indices: 540388--540470 Score: 58
Period size: 6 Copynumber: 13.3 Consensus size: 6
540378 AGCGGTCGCA
* * * * * *
540388 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** *
540436 GGCGAT GAAGAT GATGACGAT GAAGAT GATGAT GA
1 GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT GA
540471 TGAAGATGGT
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
6 52 0.88
7 1 0.02
8 1 0.02
9 5 0.08
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.19
Consensus pattern (6 bp):
GAAGAT
Found at i:540442 original size:36 final size:36
Alignment explanation
Indices: 540391--540467 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
540381 GGTCGCAGAA
* *
540391 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGAAGAC
* * *
540427 GATGAAGCTGGCGATGAAGATGATGACGATGAAGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGAAGAC
540463 GATGA
1 GATGA
540468 TGATGAAGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.09, G:0.35, T:0.19
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGAAGAC
Found at i:540458 original size:15 final size:15
Alignment explanation
Indices: 540418--540478 Score: 83
Period size: 15 Copynumber: 4.3 Consensus size: 15
540408 AGATGACGAT
540418 GATGATGACGATGAA
1 GATGATGACGATGAA
*
540433 GCTG--G-CGATGAA
1 GATGATGACGATGAA
540445 GATGATGACGATGAA
1 GATGATGACGATGAA
*
540460 GATGATGATGATGAA
1 GATGATGACGATGAA
540475 GATG
1 GATG
540479 GTGATCCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.25
13 1 0.03
14 1 0.03
15 28 0.70
ACGTcount: A:0.36, C:0.07, G:0.36, T:0.21
Consensus pattern (15 bp):
GATGATGACGATGAA
Found at i:540466 original size:18 final size:18
Alignment explanation
Indices: 540388--540470 Score: 82
Period size: 18 Copynumber: 4.8 Consensus size: 18
540378 AGCGGTCGCA
*
540388 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
540406 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
540424 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
540442 GAAGAT---GATGACGAT
1 GAAGATGAAGATGACGAT
*
540457 GAAGATGATGATGA
1 GAAGATGAAGATGA
540471 TGAAGATGGT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
15 13 0.25
18 38 0.75
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:540471 original size:6 final size:6
Alignment explanation
Indices: 540403--540483 Score: 54
Period size: 6 Copynumber: 13.5 Consensus size: 6
540393 TGAAGCTGAC
* * * * * ** *
540403 GATGAA GATGAC GATGAT GATGAC GATGAA GCTGGC GATGAA GATGAT
1 GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT
* * * *
540451 GACGAT GAAGAT GATGAT GATGAA GATGGT GAT
1 GATGAT GATGAT GATGAT GATGAT GATGAT GAT
540484 CCAAACAAGT
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.22
Consensus pattern (6 bp):
GATGAT
Found at i:540478 original size:12 final size:12
Alignment explanation
Indices: 540391--540470 Score: 88
Period size: 12 Copynumber: 6.4 Consensus size: 12
540381 GGTCGCAGAA
*
540391 GATGAAGCTGAC
1 GATGAAGATGAC
540403 GATGAAGATGAC
1 GATGAAGATGAC
*
540415 GATGATGATGAC
1 GATGAAGATGAC
* *
540427 GATGAAGCTGGC
1 GATGAAGATGAC
540439 GATGAAGATGATGAC
1 GATG-A-A-GATGAC
*
540454 GATGAAGATGAT
1 GATGAAGATGAC
540466 GATGA
1 GATGA
540471 TGAAGATGGT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
12 45 0.79
13 2 0.04
14 2 0.04
15 8 0.14
ACGTcount: A:0.36, C:0.09, G:0.35, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:540483 original size:15 final size:15
Alignment explanation
Indices: 540439--540483 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
540429 TGAAGCTGGC
*
540439 GATGAAGATGATGAC
1 GATGAAGATGATGAT
540454 GATGAAGATGATGAT
1 GATGAAGATGATGAT
*
540469 GATGAAGATGGTGAT
1 GATGAAGATGATGAT
540484 CCAAACAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.36, T:0.24
Consensus pattern (15 bp):
GATGAAGATGATGAT
Found at i:542258 original size:181 final size:182
Alignment explanation
Indices: 541952--542475 Score: 838
Period size: 183 Copynumber: 2.9 Consensus size: 182
541942 CTTTTAACAT
** * * * *
541952 ATTATAATAAAATAGGTAAATTTGTAATGCT-ATCGGTATAAATATACCCGTTTTATGCGCGAAT
1 ATTATAATGTAATAGATAAATTTGTAAT-ATAACCGGTATAAATATACCGGTTTTATGCGCGAAT
*
542016 AGGTCTACAACCTATATCGACACTTTTTAATCTTGTGTCGGTACTTTATGTCCAGATTGG-A-AA
65 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAA
* * *
542079 AAATGTGTCGATACATTGTTAAAAAGTGTCGACATTTACATATCGGAACCCATA
130 AAATGTGTCGATACATT-TAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
542133 ATTATAATGTAATAGATAAATTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAAATTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
542198 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
*
542263 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATAC-ATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
* * *
542316 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAAATTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
542381 TGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
542446 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATA-CATTTAAAAAAGTGTCG
542476 GTAATTTTAA
Statistics
Matches: 319, Mismatches: 19, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
180 1 0.00
181 114 0.36
182 1 0.00
183 199 0.62
184 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (182 bp):
ATTATAATGTAATAGATAAATTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
AATGTGTCGATACATTTAAAAAAGTGTCGACATTTACACATCGGAACCCAGA
Found at i:544947 original size:25 final size:25
Alignment explanation
Indices: 544919--544983 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
544909 TTATCATTAA
*
544919 ATTTAGGTATGTACAATAACTGCAT
1 ATTTAGGTATGTACAATAACTACAT
****
544944 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
544969 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
544984 TCTTTTGAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:545361 original size:23 final size:23
Alignment explanation
Indices: 545330--545402 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
545320 ATAGGTAAAC
*
545330 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
545353 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
545376 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
545399 ATAT
1 ATAT
545403 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:545851 original size:18 final size:18
Alignment explanation
Indices: 545830--545866 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
545820 GTAATTGGAG
545830 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
545848 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
545866 T
1 T
545867 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:545874 original size:24 final size:24
Alignment explanation
Indices: 545822--545868 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
545812 TTTCATATGT
* *
545822 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
545846 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
545869 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:546167 original size:39 final size:39
Alignment explanation
Indices: 546124--546210 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
546114 TCCGATGCTC
*
546124 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
546163 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
546202 ATCAAAATC
1 ATCAAAATC
546211 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:546663 original size:23 final size:23
Alignment explanation
Indices: 546632--546704 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
546622 ATAGGTAAAA
*
546632 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
546655 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
546678 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
546701 ATAT
1 ATAT
546705 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:547093 original size:23 final size:23
Alignment explanation
Indices: 547062--547134 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
547052 ATAGGTAAAA
*
547062 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
547085 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
547108 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
547131 ATAT
1 ATAT
547135 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:547231 original size:430 final size:430
Alignment explanation
Indices: 546431--547483 Score: 2000
Period size: 430 Copynumber: 2.5 Consensus size: 430
546421 TAATTTTGTA
546431 AAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATG
1 AAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATG
*
546496 AAATTATTAAATTAATATTGTAAGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAA
66 AAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAA
*
546561 TTAAATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAG
131 TTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAG
546626 GTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATA
196 GTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATA
546691 GGTAGTGGTTATATTGTAAAGTGTATATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGG
261 GGTAGTGGTTATATTGTAAAGTGTATATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGG
* *
546756 AAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGCGT
326 AAAACATTAATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGT
546821 CTAATGATTTATTTTTTACGTTACGATATATATTATTATT
391 CTAATGATTTATTTTTTACGTTACGATATATATTATTATT
546861 AAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATG
1 AAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATG
546926 AAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAA
66 AAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAA
*
546991 TTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATAGACACTTTCAATATAATAG
131 TTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAG
547056 GTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATA
196 GTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATA
*
547121 GGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGG
261 GGTAGTGGTTATATTGTAAAGTGTATATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGG
547186 AAAACATTAATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGT
326 AAAACATTAATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGT
547251 CTAATGATTTATTTTTTACGTTACGATATATATTATTATT
391 CTAATGATTTATTTTTTACGTTACGATATATATTATTATT
* *
547291 AAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAATAATTTTTTGTGCAAATA
1 AAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATG
*
547356 AAATTATTAAATTAATATTGTAGGTGGAAAACATGAAATACTATT-AAAAAAATTGAAACATAAA
66 AAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAA
* *
547420 TTACATAACTTTAAAAGAAGTATCGGTCTTTTTTATAAAAAGTATGGACACTTTCAATATAATA
131 TTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
547484 TAATGTAATA
Statistics
Matches: 611, Mismatches: 12, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
429 80 0.13
430 531 0.87
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (430 bp):
AAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATG
AAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAA
TTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAG
GTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATA
GGTAGTGGTTATATTGTAAAGTGTATATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGG
AAAACATTAATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGT
CTAATGATTTATTTTTTACGTTACGATATATATTATTATT
Found at i:547339 original size:30 final size:29
Alignment explanation
Indices: 547280--547346 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
547270 GTTACGATAT
* *
547280 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
547310 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
547340 ATTTTTT
1 ATATTTT
547347 GTGCAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:548235 original size:183 final size:183
Alignment explanation
Indices: 547922--548289 Score: 605
Period size: 183 Copynumber: 2.0 Consensus size: 183
547912 TTTAAATTTT
* * *
547922 AAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
*
547987 TTTAAGATCCAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAAATATATAAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATATATAAAATTTT
*
548052 TATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTT-AATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
* *
548105 AAATATTAAATATATTATATATAACATTTGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
* * *
548170 TTTAAGAT-CAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAAAGTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAA-TATATAAAATTT
*
548234 TTATTTTATAATTATATATTATTTAAATTATTTATAAACTTTTTTTGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
548288 AA
1 AA
548290 CATTTAATTT
Statistics
Matches: 172, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
182 47 0.27
183 125 0.73
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.41
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:551559 original size:4 final size:4
Alignment explanation
Indices: 551550--551574 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
551540 ATCAACTTGG
551550 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
551575 TCTTATTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:553000 original size:32 final size:33
Alignment explanation
Indices: 552932--553000 Score: 79
Period size: 34 Copynumber: 2.1 Consensus size: 33
552922 TATCTCTTAG
* **
552932 TTTTTTAAAATTATTTAATTTGATTGTTTTAATT
1 TTTTTTAAAATAATTTAA-TTGATTACTTTAATT
*
552966 TTTTTTAATATAATTTAA-TGATTACTTT-ATT
1 TTTTTTAAAATAATTTAATTGATTACTTTAATT
552997 TTTT
1 TTTT
553001 ATGGAATTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 7 0.23
32 8 0.26
34 16 0.52
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (33 bp):
TTTTTTAAAATAATTTAATTGATTACTTTAATT
Found at i:562888 original size:20 final size:20
Alignment explanation
Indices: 562863--562900 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
562853 TTTGGTTCAC
562863 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTATCAGTG
562883 GGAATGTAAGATTATCAG
1 GGAATGTAAGATTATCAG
562901 GGACTAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (20 bp):
GGAATGTAAGATTATCAGTG
Found at i:564537 original size:19 final size:19
Alignment explanation
Indices: 564513--564560 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
564503 TAAAAAATTT
564513 ATTAAAAATATTTTTATTC
1 ATTAAAAATATTTTTATTC
*
564532 ATTAAAAATATTTTTATTT
1 ATTAAAAATATTTTTATTC
*
564551 AGTAAAAATA
1 ATTAAAAATA
564561 ATGATTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTAAAAATATTTTTATTC
Found at i:581483 original size:45 final size:45
Alignment explanation
Indices: 581434--581523 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
581424 TTGTCAAATT
581434 TCTCTCTTTCACTCTCAAAACAACAGAAAATGGAAAACACAGTAC
1 TCTCTCTTTCACTCTCAAAACAACAGAAAATGGAAAACACAGTAC
*
581479 TCTCTCTTTCACTCTCAAGACAACAGAAAATGGAAAACACAGTAC
1 TCTCTCTTTCACTCTCAAAACAACAGAAAATGGAAAACACAGTAC
581524 GGATACAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.41, C:0.27, G:0.10, T:0.22
Consensus pattern (45 bp):
TCTCTCTTTCACTCTCAAAACAACAGAAAATGGAAAACACAGTAC
Found at i:581621 original size:18 final size:18
Alignment explanation
Indices: 581598--581633 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
581588 TTTTAAATAT
*
581598 ATATATAAAATTTTTAAA
1 ATATATAAAAGTTTTAAA
*
581616 ATATATAATAGTTTTAAA
1 ATATATAAAAGTTTTAAA
581634 TTTTGAAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATATAAAAGTTTTAAA
Found at i:582635 original size:22 final size:22
Alignment explanation
Indices: 582607--582655 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
582597 AATGTCTGTT
582607 TCTTGTAGGAACCTCCAAGAAA
1 TCTTGTAGGAACCTCCAAGAAA
582629 TCTTGTAGGAACCTCCAAGAAA
1 TCTTGTAGGAACCTCCAAGAAA
582651 TCTTG
1 TCTTG
582656 AGCACTGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (22 bp):
TCTTGTAGGAACCTCCAAGAAA
Found at i:588106 original size:18 final size:19
Alignment explanation
Indices: 588068--588108 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
588058 CCTGTATTTG
*
588068 TTTTTCTTTTACACTATTC
1 TTTTTCTTTTACACTACTC
*
588087 TTTTTCTTTT-CATTACTC
1 TTTTTCTTTTACACTACTC
588105 TTTT
1 TTTT
588109 ATTCTTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTCTTTTACACTACTC
Found at i:588337 original size:7 final size:7
Alignment explanation
Indices: 588327--588379 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
588317 TAAAACCTCA
588327 AAACTTT
1 AAACTTT
588334 AAACTTT
1 AAACTTT
*
588341 AAACTCT
1 AAACTTT
*
588348 AAAATTT
1 AAACTTT
588355 AAA-TTT
1 AAACTTT
588361 AAACTTTT
1 AAAC-TTT
*
588369 AAACTCT
1 AAACTTT
588376 AAAC
1 AAAC
588380 ACCTAATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
6 6 0.15
7 27 0.68
8 7 0.17
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (7 bp):
AAACTTT
Found at i:588363 original size:20 final size:22
Alignment explanation
Indices: 588326--588379 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
588316 CTAAAACCTC
588326 AAAACTTTAAACTTTAAACTCT
1 AAAACTTTAAACTTTAAACTCT
*
588348 AAAA-TTTAAA-TTTAAACTTT
1 AAAACTTTAAACTTTAAACTCT
* *
588368 TAAACTCTAAAC
1 AAAACTTTAAAC
588380 ACCTAATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 12 0.44
21 11 0.41
22 4 0.15
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAACTTTAAACTTTAAACTCT
Found at i:588387 original size:28 final size:27
Alignment explanation
Indices: 588316--588400 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 27
588306 CAAATAAATC
588316 CTAAAACCTCAAAACTTTAAACTTTAAACT
1 CTAAAACCT--AAA-TTTAAACTTTAAACT
**
588346 CTAAAATTTAAATTTAAACTTTTAAACT
1 CTAAAACCTAAATTTAAAC-TTTAAACT
* *
588374 CTAAACACCTAATTTCTAAACCTTAAA
1 CTAAA-ACCTAAATT-TAAACTTTAAA
588401 TAGAATAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 7 0.15
28 16 0.35
29 11 0.24
30 12 0.26
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (27 bp):
CTAAAACCTAAATTTAAACTTTAAACT
Found at i:593825 original size:6 final size:6
Alignment explanation
Indices: 593814--593839 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
593804 ATGATGGTTG
593814 AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AA
593840 TAAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:595463 original size:34 final size:35
Alignment explanation
Indices: 595402--595485 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 35
595392 TCTAAAGTAT
* * * *
595402 TTTTTTTTACCAAAGTAAGTACCTAAAGT-TATAA
1 TTTTTTTTATCAAAATAAGAACATAAAGTATATAA
*
595436 TTTTTTTTATCAAAATAAGAACATAAAGTATTTAA
1 TTTTTTTTATCAAAATAAGAACATAAAGTATATAA
*
595471 -TTTTTTTATCTAAAT
1 TTTTTTTTATCAAAAT
595486 TCTAAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 39 0.91
35 4 0.09
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.46
Consensus pattern (35 bp):
TTTTTTTTATCAAAATAAGAACATAAAGTATATAA
Found at i:595593 original size:29 final size:30
Alignment explanation
Indices: 595561--595649 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
595551 CTTTAGAAGT
595561 CTATTTTGACAAAAAAATACTTTAAG-TAC
1 CTATTTTGACAAAAAAATACTTTAAGATAC
** *
595590 CTATTTTGATCAAAATGATAACTTT-AGATAT
1 CTATTTTGA-CAAAAAAAT-ACTTTAAGATAC
* * *
595621 TTATTTTAACAAAAAATTACTTTAA-ATAC
1 CTATTTTGACAAAAAAATACTTTAAGATAC
595650 GTAAAAGAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
29 17 0.36
30 16 0.34
31 14 0.30
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (30 bp):
CTATTTTGACAAAAAAATACTTTAAGATAC
Found at i:596546 original size:16 final size:15
Alignment explanation
Indices: 596522--596557 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
596512 ATTATATAAA
*
596522 ATATAATGAATTATTT
1 ATATTATGAATTA-TT
596538 ATATTATGAATTATT
1 ATATTATGAATTATT
596553 ATATT
1 ATATT
596558 TTGTATTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATTATGAATTATT
Found at i:596708 original size:15 final size:15
Alignment explanation
Indices: 596688--596744 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
596678 AATCGGGTAG
*
596688 CGGGTACCCGACTAC
1 CGGGTACCCGAATAC
*
596703 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AATA-C
* *
596720 CGGATACCCGATTAC
1 CGGGTACCCGAATAC
596735 CGGGTACCCG
1 CGGGTACCCG
596745 TAACATCCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.23, C:0.37, G:0.26, T:0.14
Consensus pattern (15 bp):
CGGGTACCCGAATAC
Found at i:596736 original size:32 final size:32
Alignment explanation
Indices: 596692--596754 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
596682 GGGTAGCGGG
596692 TACCCGACTACCGGGTACCCGCAAAATCCGGA
1 TACCCGACTACCGGGTACCCGCAAAATCCGGA
* * *
596724 TACCCGATTACCGGGTACCCGTAACATCCGG
1 TACCCGACTACCGGGTACCCGCAAAATCCGG
596755 GTCGGGACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.37, G:0.22, T:0.16
Consensus pattern (32 bp):
TACCCGACTACCGGGTACCCGCAAAATCCGGA
Found at i:596756 original size:17 final size:16
Alignment explanation
Indices: 596688--596756 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
596678 AATCGGGTAG
**
596688 CGGGTACCCGACTA-C
1 CGGGTACCCGAAAATC
596703 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
* **
596720 CGGATACCCGATTA-C
1 CGGGTACCCGAAAATC
*
596735 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
596752 CGGGT
1 CGGGT
596757 CGGGACACGG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:596813 original size:15 final size:15
Alignment explanation
Indices: 596793--596834 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
596783 CCCGGAAGTT
596793 TCGGGTACCCGAAAA
1 TCGGGTACCCGAAAA
596808 TCGGGTACCCGAAAA
1 TCGGGTACCCGAAAA
*
596823 TCCGGATACCCG
1 T-CGGGTACCCG
596835 GATTTGCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (15 bp):
TCGGGTACCCGAAAA
Found at i:597491 original size:15 final size:17
Alignment explanation
Indices: 597466--597505 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
597456 AATCCTTATT
597466 TTTTTTGAATAAAT-TA
1 TTTTTTGAATAAATATA
597482 TTTTTT-AATAAATATA
1 TTTTTTGAATAAATATA
597498 TTATTTTG
1 TT-TTTTG
597506 GGTCAGATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 10 0.48
17 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTTTTGAATAAATATA
Found at i:605919 original size:296 final size:298
Alignment explanation
Indices: 605354--605950 Score: 1126
Period size: 296 Copynumber: 2.0 Consensus size: 298
605344 TTTTCGTAAG
* *
605354 CTTGTTTTCGTATCTGATCTCGTTATCTAATATAAATGTGAAGCTGACTGGCTGTGCATCTAATT
1 CTTGTTTTCGTATCTGATCTCGTTATCTAATATAAATGTGAAGCTAACTGGCTGCGCATCTAATT
605419 CTAATCATTAACTAGATGATTCATCAGTAGTTGAAGTAGGAAGTGTTGATTGGGGTTCTTTTTAA
66 CTAATCATTAACTAGATGATTCATCAGTAGTT--AGTAGGAAGTGTTGATTGGGGTTCTTTTTAA
*
605484 TCAAATATTGTGATTAGTAAATCGAATAAATCGATGAGGTAGGCCAACAGGAATGCTGGGTTTCT
129 TCAAATATTGGGATTAGTAAATCGAATAAATCGATGAGGTAGGCCAACAGGAATGCTGGGTTTCT
605549 TTAACCTAATTCAAGACTAATTCCAGCATATGCCAACTATTCTGAAGTGACAATTTTAAACATAT
194 TTAACCTAATTCAAGACTAATTCCAGCATATGCCAACTATTCTGAAGTGACAATTTTAAACATAT
605614 CTATTAGCCCATCATAGGCTTCTGAATCTGAATAAACTTC
259 CTATTAGCCCATCATAGGCTTCTGAATCTGAATAAACTTC
605654 CTTGTTTTCGTATCTGATCTCGTTATC-AATATAAATGTGAAGCTAACTGGCTGCGCATCTAATT
1 CTTGTTTTCGTATCTGATCTCGTTATCTAATATAAATGTGAAGCTAACTGGCTGCGCATCTAATT
605718 CTAATCATTAACTAGATGATTCATCAGTAGTT-GTAGGAAGTGTTGATTGGGGTTCTTTTTAATC
66 CTAATCATTAACTAGATGATTCATCAGTAGTTAGTAGGAAGTGTTGATTGGGGTTCTTTTTAATC
*
605782 AAATATTGGGATTAGTAAGTCGAATAAATCGATGAGGTAGGCCAACAGGAATGCTGGGTTTCTTT
131 AAATATTGGGATTAGTAAATCGAATAAATCGATGAGGTAGGCCAACAGGAATGCTGGGTTTCTTT
605847 AACCTAATTCAAGACTAATTCCAGCATATGCCAACTATTCTGAAGTGACAATTTTAAACATATCT
196 AACCTAATTCAAGACTAATTCCAGCATATGCCAACTATTCTGAAGTGACAATTTTAAACATATCT
605912 ATTAGCCCATCATAGGCTTCTGAATCTGAATAAACTTC
261 ATTAGCCCATCATAGGCTTCTGAATCTGAATAAACTTC
605950 C
1 C
605951 GATGGGCTGT
Statistics
Matches: 293, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
296 199 0.68
299 67 0.23
300 27 0.09
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (298 bp):
CTTGTTTTCGTATCTGATCTCGTTATCTAATATAAATGTGAAGCTAACTGGCTGCGCATCTAATT
CTAATCATTAACTAGATGATTCATCAGTAGTTAGTAGGAAGTGTTGATTGGGGTTCTTTTTAATC
AAATATTGGGATTAGTAAATCGAATAAATCGATGAGGTAGGCCAACAGGAATGCTGGGTTTCTTT
AACCTAATTCAAGACTAATTCCAGCATATGCCAACTATTCTGAAGTGACAATTTTAAACATATCT
ATTAGCCCATCATAGGCTTCTGAATCTGAATAAACTTC
Found at i:607132 original size:2 final size:2
Alignment explanation
Indices: 607125--607161 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
607115 AAAGGAAAAA
607125 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
607162 TTTTCTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:607661 original size:4 final size:4
Alignment explanation
Indices: 607652--607747 Score: 192
Period size: 4 Copynumber: 24.0 Consensus size: 4
607642 TTACAGGAAC
607652 TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG
1 TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG
607700 TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG
1 TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG TAGG
607748 GGTGTCCAAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 92 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
TAGG
Found at i:608086 original size:20 final size:20
Alignment explanation
Indices: 608042--608097 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 20
608032 TGTTTGAATC
*
608042 AAATTAATTAGATATTATTT
1 AAATTAATTATATATTATTT
608062 --A-TAATTATATATTATTT
1 AAATTAATTATATATTATTT
* *
608079 AAATTAATTGTAAATTATT
1 AAATTAATTATATATTATT
608098 ATTTTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 15 0.50
18 1 0.03
19 1 0.03
20 13 0.43
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
AAATTAATTATATATTATTT
Found at i:616288 original size:18 final size:21
Alignment explanation
Indices: 616265--616312 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 21
616255 TCTTTTTTTC
616265 ATTTTATTTA-TATTA-T-TT
1 ATTTTATTTATTATTATTATT
616283 ATTTTA-TTATTATTATTATT
1 ATTTTATTTATTATTATTATT
616303 ATTTTATTTA
1 ATTTTATTTA
616313 CAATTTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.12
18 11 0.42
19 1 0.04
20 8 0.31
21 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTATTTATTATTATTATT
Found at i:620992 original size:20 final size:20
Alignment explanation
Indices: 620964--621002 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
620954 ATTCCCTCAT
620964 TTTGAGACATTGAAACATTC
1 TTTGAGACATTGAAACATTC
*
620984 TTTGTGACATTGAAACATT
1 TTTGAGACATTGAAACATT
621003 GCATTTATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTGAGACATTGAAACATTC
Found at i:621622 original size:11 final size:11
Alignment explanation
Indices: 621577--621624 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
621567 TGCATAGTAC
**
621577 AAAGAAAAATC
1 AAAGAAAAAGA
621588 AAAGAAAAATAGCA
1 AAAG-AAAA-AG-A
621602 AAAGAAAAAGA
1 AAAGAAAAAGA
621613 AAAGAAAAAGA
1 AAAGAAAAAGA
621624 A
1 A
621625 GACAAAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 17 0.53
12 6 0.19
13 5 0.16
14 4 0.12
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:622834 original size:6 final size:6
Alignment explanation
Indices: 622823--622982 Score: 284
Period size: 6 Copynumber: 26.2 Consensus size: 6
622813 ACATACATAC
622823 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
622871 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
*
622919 ATACAT ATACAT ATATAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
622967 ACATACAT GATACAT A
1 --ATACAT -ATACAT A
622983 AATTTTGCAT
Statistics
Matches: 149, Mismatches: 3, Indels: 4
0.96 0.02 0.03
Matches are distributed among these distances:
6 137 0.92
7 6 0.04
8 6 0.04
ACGTcount: A:0.50, C:0.16, G:0.01, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:624223 original size:66 final size:65
Alignment explanation
Indices: 624078--624234 Score: 172
Period size: 66 Copynumber: 2.4 Consensus size: 65
624068 TTTGATTATT
* ** * *
624078 TTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGAAAGTTTTTCGTAAAAAATCATCTTTGAGTCT
1 TTTCTTTTGAAACAAA-TTTTGTCTCTCTTGAGAAAGTTTCTAATAAAAAACCAACTTTGAGTCT
624143 A
65 A
* * * * *
624144 TTTATATTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAAAACCAACATTTGAGAT-
1 TTTCTTTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTAATAAAAAACCAAC-TTTGAG-TC
*
624208 TG
64 TA
*
624210 TTTCTTTTGAAACAAATTTGGTCTC
1 TTTCTTTTGAAACAAATTTTGTCTC
624235 ACTTAAGATG
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
65 32 0.43
66 41 0.55
67 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (65 bp):
TTTCTTTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTAATAAAAAACCAACTTTGAGTCTA
Found at i:624409 original size:74 final size:70
Alignment explanation
Indices: 624317--624452 Score: 184
Period size: 74 Copynumber: 1.9 Consensus size: 70
624307 TGAGAAAAAA
* *
624317 AAAATCTTTGAGTTTGTTTCTT-TGGAAACAAAATTTACCATCTTTGAGTTTGTTTCCCTTGAAA
1 AAAATCTTTGAGTATGTTT-TTCTGGAAACAAAA---A-CATCTTTGAGTTTGTTTCCCTCGAAA
624381 CAAAACAAAC
61 CAAAACAAAC
* *
624391 AAAATCTTTGAGTATGTTTTTCTTGAAACAAAAACATCTTTGAGTTTGTTTCTCTCGAAACA
1 AAAATCTTTGAGTATGTTTTTCTGGAAACAAAAACATCTTTGAGTTTGTTTCCCTCGAAACA
624453 CCGATCTTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 26 0.46
71 1 0.02
73 2 0.04
74 28 0.49
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (70 bp):
AAAATCTTTGAGTATGTTTTTCTGGAAACAAAAACATCTTTGAGTTTGTTTCCCTCGAAACAAAA
CAAAC
Found at i:624433 original size:32 final size:33
Alignment explanation
Indices: 624383--624452 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
624373 CCTTGAAACA
* *
624383 AAACAAACAAAATCTTTGAGTATGTTTTTCTTG
1 AAACAAACAAAATCTTTGAGTATGTTTCTCTCG
* *
624416 AAACAAA-AACATCTTTGAGTTTGTTTCTCTCG
1 AAACAAACAAAATCTTTGAGTATGTTTCTCTCG
624448 AAACA
1 AAACA
624453 CCGATCTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (33 bp):
AAACAAACAAAATCTTTGAGTATGTTTCTCTCG
Found at i:624564 original size:63 final size:64
Alignment explanation
Indices: 624456--624575 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 64
624446 CGAAACACCG
624456 ATCTTTGAGAACGTTTCCCTTAAACACAAATTTTGTCTCGCTCGAGACAGTTTCCTTTACATGTC
1 ATCTTTGAGAACGTTTCCCTTAAACACAAATTTTGTCTCGCTCGAGACA-TTTCCTTTACATGTC
* * * ** *
624521 ATCTTTGAG-TCGTTTCCCTTTAA-ACGAATTTTGTCTCTTTCGAGACATTTGCTTT
1 ATCTTTGAGAACGTTTCCCTTAAACACAAATTTTGTCTCGCTCGAGACATTTCCTTT
624576 TGAAAAACAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
62 7 0.14
63 21 0.43
64 12 0.24
65 9 0.18
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (64 bp):
ATCTTTGAGAACGTTTCCCTTAAACACAAATTTTGTCTCGCTCGAGACATTTCCTTTACATGTC
Found at i:624616 original size:29 final size:29
Alignment explanation
Indices: 624579--624636 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
624569 TTGCTTTTGA
624579 AAAACATCATCCTTGAGTCT-GTTTCTTTT
1 AAAACATCATCCTTGAGT-TGGTTTCTTTT
*
624608 AAAACATCATCTTTGAGTTGGTTTCTTTT
1 AAAACATCATCCTTGAGTTGGTTTCTTTT
624637 GAAATCAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (29 bp):
AAAACATCATCCTTGAGTTGGTTTCTTTT
Found at i:625078 original size:6 final size:5
Alignment explanation
Indices: 625056--625126 Score: 58
Period size: 6 Copynumber: 13.6 Consensus size: 5
625046 TTTCCGGGTC
*
625056 TTTT- TTTTCA TTTTA -TTTA TATTA -TTTA TTTTA TTATTA TTATTA
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TT-TTA
625101 TTATTA TTATTA TTATTA TTTTA TTT
1 TT-TTA TT-TTA TT-TTA TTTTA TTT
625127 ACAATTTACA
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
4 11 0.18
5 16 0.27
6 33 0.55
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:625081 original size:3 final size:3
Alignment explanation
Indices: 625075--625125 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
625065 ATTTTATTTA
625075 TAT TATT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
625120 T-T TAT T
1 TAT TAT T
625126 TACAATTTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:625088 original size:18 final size:17
Alignment explanation
Indices: 625065--625125 Score: 88
Period size: 18 Copynumber: 3.5 Consensus size: 17
625055 CTTTTTTTTC
625065 ATTTTATT-TATATTATTT
1 ATTTTATTAT-TATTA-TT
625083 ATTTTATTATTATTATT
1 ATTTTATTATTATTATT
625100 ATTATTATTATTATTATT
1 ATT-TTATTATTATTATT
625118 ATTTTATT
1 ATTTTATT
625126 TACAATTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.24
18 30 0.73
19 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTATTATTATTATT
Found at i:629860 original size:21 final size:21
Alignment explanation
Indices: 629821--629860 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
629811 TTTAAATGTT
*
629821 TTTATTTATTTCGATATTTTA
1 TTTATTTATTTCGACATTTTA
629842 TTTATTTATTCTC-ACATTT
1 TTTATTTATT-TCGACATTT
629861 AGTATTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTATTTATTTCGACATTTTA
Found at i:630791 original size:16 final size:16
Alignment explanation
Indices: 630770--630805 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
630760 TATGTTACAT
*
630770 GTGTCATAGTATTAAA
1 GTGTCATAGAATTAAA
*
630786 GTGTCATTGAATTAAA
1 GTGTCATAGAATTAAA
630802 GTGT
1 GTGT
630806 ATATATCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (16 bp):
GTGTCATAGAATTAAA
Found at i:633262 original size:13 final size:13
Alignment explanation
Indices: 633232--633263 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
633222 TTAAATGTTT
633232 TAAAATTTAATAA
1 TAAAATTTAATAA
633245 T-AAATTTAATAA
1 TAAAATTTAATAA
633257 TAAAATT
1 TAAAATT
633264 AAAATTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAAATTTAATAA
Found at i:635217 original size:3 final size:3
Alignment explanation
Indices: 635201--635280 Score: 76
Period size: 3 Copynumber: 25.3 Consensus size: 3
635191 TCTACAAAAA
635201 TAT T-T TAT TA- TAT TAT TATT TATT TATT TATT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TA-T TAT TAT TAT TAT TAT
635247 TAAT TAT TATT TATT TAT TAT TAT TAT TAT TAT T
1 T-AT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT T
635281 TATTTATTGT
Statistics
Matches: 71, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.08
3 40 0.56
4 25 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:635225 original size:4 final size:4
Alignment explanation
Indices: 635204--635288 Score: 66
Period size: 4 Copynumber: 23.5 Consensus size: 4
635194 ACAAAAATAT
635204 TTTA -TTA TATTA -TTA TTTA TTTA TTTA TTTA -TTA -TTA -TTA TATTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
*
635249 ATTA -TTA TTTA TTTA -TTA -TTA -TTA -TTA -TTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
635289 GTATACCTTA
Statistics
Matches: 73, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
3 33 0.45
4 34 0.47
5 6 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:635247 original size:23 final size:23
Alignment explanation
Indices: 635204--635288 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 23
635194 ACAAAAATAT
635204 TTTATTATATTATTATT-TATTTA
1 TTTATT-TATTATTATTATATTTA
*
635227 TTTATTTATTATTATTATATTAA
1 TTTATTTATTATTATTATATTTA
635250 TTATTATTTATTTATTATTATTATTATTA
1 -T-TTATTTA-TTATTATTA-TA-T-TTA
635279 TTTATTTATT
1 TTTATTTATT
635289 GTATACCTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
22 10 0.19
23 11 0.21
24 1 0.02
25 7 0.13
26 11 0.21
27 9 0.17
28 2 0.04
29 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTATTTATTATTATTATATTTA
Found at i:635299 original size:23 final size:23
Alignment explanation
Indices: 635211--635278 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 23
635201 TATTTTATTA
635211 TATTATTATTTATTTATTTATT--
1 TATTATTA-TTATTTATTTATTAG
* *
635233 TATTATTATTATATTAATTATTATT
1 TATTATTATTAT-TTATTTATTA-G
635258 TATTTATTATTA-TTA-TTATTA
1 TA-TTATTATTATTTATTTATTA
635279 TTTATTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
21 4 0.10
22 16 0.40
23 6 0.15
24 3 0.08
25 2 0.05
26 9 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TATTATTATTATTTATTTATTAG
Found at i:635565 original size:24 final size:24
Alignment explanation
Indices: 635524--635610 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 24
635514 ACATAGGTCT
* *
635524 CGTTCGTTCAT-TTACGTTCGTGAA
1 CGTTCGTTTATGTT-CGTTCGTGTA
* *
635548 CGTTCGGTTATGTTCGTTTG-GTTA
1 CGTTCGTTTATGTTCGTTCGTG-TA
*
635572 TGTTCGTTTATGTTCGTTCGAT-TA
1 CGTTCGTTTATGTTCGTTCG-TGTA
635596 CGTTCGTTTATGTTC
1 CGTTCGTTTATGTTC
635611 ATTCATTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.02
24 48 0.94
25 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.49
Consensus pattern (24 bp):
CGTTCGTTTATGTTCGTTCGTGTA
Found at i:635570 original size:14 final size:14
Alignment explanation
Indices: 635548--635580 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
635538 CGTTCGTGAA
*
635548 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
635562 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
635576 CGTTT
1 CGTTT
635581 ATGTTCGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:636380 original size:16 final size:16
Alignment explanation
Indices: 636355--636400 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
636345 CCAACGTTTA
636355 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
636371 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
636387 TGTTCGTTTATGTT
1 TGTTCGTTTATGTT
636401 TGTTTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.59
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:636498 original size:16 final size:16
Alignment explanation
Indices: 636473--636505 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
636463 AAAAAAATTT
636473 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
636489 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
636505 T
1 T
636506 TTATGTTCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:636502 original size:10 final size:10
Alignment explanation
Indices: 636489--636519 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
636479 TTTATGTTCG
636489 TGTTCGTTTA
1 TGTTCGTTTA
636499 TGTTCGTTTA
1 TGTTCGTTTA
636509 TGTTCGTTTA
1 TGTTCGTTTA
636519 T
1 T
636520 TTATTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:637467 original size:17 final size:17
Alignment explanation
Indices: 637433--637473 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
637423 TACAAGGGAT
*
637433 TTAGAATCTGTGAAGAA
1 TTAGAATCTGTCAAGAA
*
637450 TTAGAATCTGTCAGGAA
1 TTAGAATCTGTCAAGAA
*
637467 TTGGAAT
1 TTAGAAT
637474 TCAATTCCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (17 bp):
TTAGAATCTGTCAAGAA
Found at i:657423 original size:20 final size:20
Alignment explanation
Indices: 657398--657442 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
657388 TTCACGAGTT
*
657398 CGTTCGATTAATTTGATTTA
1 CGTTCGATTAATGTGATTTA
657418 CGTTCGATTAATGTGATTTA
1 CGTTCGATTAATGTGATTTA
*
657438 TGTTC
1 CGTTC
657443 CTAGTTAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.49
Consensus pattern (20 bp):
CGTTCGATTAATGTGATTTA
Found at i:657794 original size:41 final size:41
Alignment explanation
Indices: 657737--657818 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
657727 TCAAAAAACA
657737 TAAATTTTGGTCACTGAAACATTGAATGTCGTTAGTGTGAT
1 TAAATTTTGGTCACTGAAACATTGAATGTCGTTAGTGTGAT
**
657778 TAAATTTTGGTCACTGAAATGTTGAATGTCGTTAGTGTGAT
1 TAAATTTTGGTCACTGAAACATTGAATGTCGTTAGTGTGAT
657819 AACGTGACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (41 bp):
TAAATTTTGGTCACTGAAACATTGAATGTCGTTAGTGTGAT
Found at i:661548 original size:26 final size:26
Alignment explanation
Indices: 661500--661550 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
661490 TTTTTACCTC
661500 TTAAAATTTATAAGTTCATCTCCCTT
1 TTAAAATTTATAAGTTCATCTCCCTT
661526 TTAAAATTTTATAAGTTCA-CTCCCT
1 TTAAAA-TTTATAAGTTCATCTCCCT
661551 CTAATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (26 bp):
TTAAAATTTATAAGTTCATCTCCCTT
Found at i:671378 original size:24 final size:24
Alignment explanation
Indices: 671343--671388 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
671333 GTATGCATGA
671343 AAAGCTTGAAGTA-AACAAAGAAGT
1 AAAGCTTGAAGTATAA-AAAGAAGT
671367 AAAGCATT-AAGTATAAAAAGAA
1 AAAGC-TTGAAGTATAAAAAGAA
671389 TACAAAGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.59, C:0.07, G:0.17, T:0.17
Consensus pattern (24 bp):
AAAGCTTGAAGTATAAAAAGAAGT
Found at i:675894 original size:78 final size:78
Alignment explanation
Indices: 675807--675958 Score: 218
Period size: 78 Copynumber: 1.9 Consensus size: 78
675797 TTCTATAATC
* * *
675807 ATTAATAGATAAATTAGTCATTTAAATCACAC-AATGATTATATAA-AGAAAATATTAAAAATTT
1 ATTAATAGATAAACTAGTCACTTAAATCACACAAAT-ATCATATAAGA-AAAATATTAAAAATTT
675870 AATTAAATAAATTTA
64 AATTAAATAAATTTA
* * *
675885 ATTAATAGATAAACTAGTCACTTAAATCACACAAATATCATATGAGAAAAATGTTAAAACTTTAA
1 ATTAATAGATAAACTAGTCACTTAAATCACACAAATATCATATAAGAAAAATATTAAAAATTTAA
675950 TTAAATAAA
66 TTAAATAAA
675959 CTTGAATAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
78 62 0.94
79 4 0.06
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (78 bp):
ATTAATAGATAAACTAGTCACTTAAATCACACAAATATCATATAAGAAAAATATTAAAAATTTAA
TTAAATAAATTTA
Found at i:676829 original size:21 final size:20
Alignment explanation
Indices: 676796--676838 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
676786 TGATGTTATT
*
676796 TTAATTTATTTTTGTATATA
1 TTAATTTAATTTTGTATATA
*
676816 TTAATTTTAATTTTGTTTATA
1 TTAA-TTTAATTTTGTATATA
676837 TT
1 TT
676839 TTGACAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTAATTTAATTTTGTATATA
Found at i:677845 original size:19 final size:19
Alignment explanation
Indices: 677809--677845 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
677799 ATGACCAACA
* *
677809 AAATCGCAATGCGGTCTCT
1 AAATCGCAACGCGATCTCT
677828 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
677846 CAGTATCGCA
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:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:678539 original size:20 final size:20
Alignment explanation
Indices: 678493--678567 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
678483 ACGCGATTTT
678493 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
**
678513 AAATTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
* **
678533 ATTTTCGTG-TGCGATTTTC
1 ATTTTCGCGTTGCGATAGTC
*
678552 ATTTTCGTGTTGCGAT
1 ATTTTCGCGTTGCGAT
678568 TTTAAGTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.36
20 30 0.64
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGTC
Found at i:678568 original size:20 final size:20
Alignment explanation
Indices: 678485--678570 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
678475 AAATCGCTAC
678485 GCGATTTT-ATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** **
678504 GCGATAGTCAAATTCGCGTT
1 GCGATTTTCATTTTCGCGTT
** *
678524 GCGATAGTCATTTTCGTG-T
1 GCGATTTTCATTTTCGCGTT
*
678543 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
678563 GCGATTTT
1 GCGATTTT
678571 AAGTTTCAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
19 23 0.41
20 33 0.59
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.45
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Done.