Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008338.1 Hibiscus syriacus cultivar Beakdansim tig00111059_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: 2210178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1177404 original size:19 final size:20
Alignment explanation
Indices: 1177359--1177408 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1177349 TTCGAGAATG
**
1177359 AAAATCGCAACGCAGAAATG
1 AAAATCGCAACGCAGAAACC
**
1177379 ACTATCGCAACGC-GAAACC
1 AAAATCGCAACGCAGAAACC
1177398 AAAATCGCAAC
1 AAAATCGCAAC
1177409 ACGATTTTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.46, C:0.28, G:0.16, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCAGAAACC
Found at i:1179349 original size:94 final size:94
Alignment explanation
Indices: 1179162--1179453 Score: 468
Period size: 94 Copynumber: 3.1 Consensus size: 94
1179152 TAGATTGCTT
* *
1179162 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1179223 ATTTTTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
1179252 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1179317 ATTTGTCTTTGTTTTGTCTTTTTGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1179346 AGTAAATTTGTTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1179411 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1179440 AGTAAATTTGTTCG
1 AGTAAATTTATTCG
1179454 TTTGTTCCAA
Statistics
Matches: 189, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
90 35 0.19
92 3 0.02
93 21 0.11
94 130 0.69
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1179934 original size:21 final size:21
Alignment explanation
Indices: 1179910--1179976 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1179900 TCATTCCTCG
1179910 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1179931 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1179952 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1179973 AGAG
1 AGAG
1179977 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1179934 original size:42 final size:42
Alignment explanation
Indices: 1179858--1179976 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1179848 GACTCGCCTG
* * * * * * *
1179858 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1179900 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1179942 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1179977 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1181346 original size:14 final size:14
Alignment explanation
Indices: 1181327--1181362 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1181317 ATTGTTTAAT
1181327 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1181341 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1181355 TGATTTGT
1 TGATTTGT
1181363 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1181485 original size:19 final size:19
Alignment explanation
Indices: 1181469--1181553 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
1181459 AAAAATGACT
*
1181469 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1181488 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1181507 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1181521 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
1181540 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1181554 CTAAATTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1181554 original size:19 final size:18
Alignment explanation
Indices: 1181469--1181563 Score: 90
Period size: 19 Copynumber: 5.3 Consensus size: 18
1181459 AAAAATGACT
*
1181469 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAAT-AAA
1181488 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAAT-AAA
* *
1181507 ATCGCAA--CG--AGAGA
1 ATCGCAACGCGAAATAAA
1181521 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAA-TAAA
1181540 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAA-TAAA
*
1181559 TTCGC
1 ATCGC
1181564 GTTGCGATTT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 50 0.77
ACGTcount: A:0.44, C:0.23, G:0.20, T:0.13
Consensus pattern (18 bp):
ATCGCAACGCGAAATAAA
Found at i:1181600 original size:33 final size:33
Alignment explanation
Indices: 1181563--1181689 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
1181553 ACTAAATTCG
* * *
1181563 CGTTGCGATTTTCATTTCGCTTTGCAATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1181596 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1181629 CATTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1181662 CGTTGCGATTTTCATTTCACATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1181690 AGTCATTTCC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1181622 original size:19 final size:19
Alignment explanation
Indices: 1181598--1181709 Score: 82
Period size: 19 Copynumber: 6.4 Consensus size: 19
1181588 AATTCCCTCG
1181598 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1181617 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
*
1181631 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1181650 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1181664 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
** *
1181683 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
1181703 TTGCGAT
1 TTGCGAT
1181710 AGACATTAAG
Statistics
Matches: 71, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
14 15 0.21
16 10 0.14
17 9 0.13
19 28 0.39
20 9 0.13
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1181708 original size:20 final size:20
Alignment explanation
Indices: 1181683--1181755 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
1181673 TCATTTCACA
*
1181683 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* **
1181703 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
1181723 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
1181744 TTGCGATAGTCA
1 TTGCGATAGTCA
1181756 AATGATTGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 12 0.29
22 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:1184239 original size:24 final size:24
Alignment explanation
Indices: 1184205--1184258 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1184195 CTGAAACATC
* *
1184205 ATCAAAATCTGAGTATTGACTAAT
1 ATCAAAATCTGAGTATTGACCAAG
* *
1184229 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
1184253 ATCAAA
1 ATCAAA
1184259 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:1185143 original size:20 final size:20
Alignment explanation
Indices: 1184997--1185143 Score: 172
Period size: 20 Copynumber: 7.3 Consensus size: 20
1184987 GATTCTGTAT
* *
1184997 TATCTCGTTGCGATAGTCA-
1 TATCGCGTTGCGAAAGTCAG
*
1185016 TAATCTCGTTGCGAAAGTCAG
1 T-ATCGCGTTGCGAAAGTCAG
*
1185037 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1185057 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1185077 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1185097 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1185118 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1185138 TATCGC
1 TATCGC
1185144 ATTGTGATTT
Statistics
Matches: 114, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.04
20 94 0.82
21 14 0.12
22 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1185211 original size:21 final size:20
Alignment explanation
Indices: 1185181--1185233 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 20
1185171 ATTTACTTAT
1185181 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GGAAAA
*
1185202 TCGCAATGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
1185223 TCGCATTGCGA
1 TCGCATTGCGA
1185234 TAGTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 24 0.83
22 4 0.14
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:1186376 original size:64 final size:65
Alignment explanation
Indices: 1186257--1186398 Score: 200
Period size: 64 Copynumber: 2.2 Consensus size: 65
1186247 TTTTTCAAAG
*
1186257 TGATGCATCGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTGGACATCGAATGCATT
1 TGATGCATCGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTGAACATCGAATGCATT
* **
1186322 TGATGCATCGATGCACC-ATCCATGTATCGATGCACTC-TGG-ATATTTTGAAACATCGAATGCA
1 TGATGCATCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCA
1186384 TT
64 TT
*
1186386 TCATGCATCGATG
1 TGATGCATCGATG
1186399 TACTCTTAGT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
63 6 0.09
64 46 0.66
65 18 0.26
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (65 bp):
TGATGCATCGATGCACCAATCCATGCATCGATGCACCATGGAATAAATTGAACATCGAATGCATT
Found at i:1192494 original size:20 final size:20
Alignment explanation
Indices: 1192469--1192507 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1192459 CTGAATTTAA
1192469 TATTTAAGTATGATGTTTTT
1 TATTTAAGTATGATGTTTTT
* *
1192489 TATTTAATTATGTTGTTTT
1 TATTTAAGTATGATGTTTT
1192508 CATGAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (20 bp):
TATTTAAGTATGATGTTTTT
Found at i:1194794 original size:65 final size:63
Alignment explanation
Indices: 1194725--1194884 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 63
1194715 AAATAAATTG
*
1194725 AACATCGAATGCATTTCATGCATCGATGCACATACTATCCATCGATGCACTCAGAG-T-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACA-ACCATCCATCGATGCACTCAG-GCTATTT-TG
1194788 AA
63 -A
* * * * *
1194790 AACATCGAATGCATTTGATGCATCGATACACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCA-CAACCATCCATCGATGCACTCAGGCTATTTTGA
* *
1194854 AACATCGAAAGCATTTCATGCATCAATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
1194885 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 28 0.34
65 48 0.59
66 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACAACCATCCATCGATGCACTCAGGCTATTTTGA
Found at i:1201094 original size:64 final size:63
Alignment explanation
Indices: 1201009--1201166 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
1200999 TTGTTTAAGG
* * * *
1201009 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * * *
1201073 TGCATCGATGCATAAGGAGTGCATTGATGCATCCCCATTAAATACAAACATTGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
1201137 TGCATCGATGCAT-GGTGTAGTGCATCGATG
1 TGCATCGATGCATAAG-G-AGTGCATCGATG
1201167 AATACCTTCA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.76
65 17 0.22
66 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:1202451 original size:30 final size:30
Alignment explanation
Indices: 1202399--1202494 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
1202389 ATAAGGAACA
* *
1202399 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTGTGACC
* *
1202430 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
* * *
1202460 TCTGGATAGTTACCG-GGGTCTTTGTGACC
1 TATGGACAGTTACCGAGGTTCTTTGTGACC
*
1202489 TCTGGA
1 TATGGA
1202495 TAGGTCATTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.32
30 29 0.52
31 9 0.16
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTGTGACC
Found at i:1204364 original size:14 final size:15
Alignment explanation
Indices: 1204338--1204366 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1204328 CTTGAAGGAG
1204338 ATGAAATAAGAAGAA
1 ATGAAATAAGAAGAA
1204353 ATGAAA-AAGAAGAA
1 ATGAAATAAGAAGAA
1204367 TGGAGAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.21, T:0.10
Consensus pattern (15 bp):
ATGAAATAAGAAGAA
Found at i:1208116 original size:24 final size:24
Alignment explanation
Indices: 1208011--1208110 Score: 155
Period size: 24 Copynumber: 4.2 Consensus size: 24
1208001 TCCAAACGTA
* * * *
1208011 ATGATGATACCCCGAATCACAAAG
1 ATGACGATACCCCGTATCGCAGAG
1208035 ATGACGATACCCCGTATCGCAGAG
1 ATGACGATACCCCGTATCGCAGAG
1208059 ATGACGATACCCCGTATCGCAGAG
1 ATGACGATACCCCGTATCGCAGAG
*
1208083 ATAACGATACCCCGTATCGCAGAG
1 ATGACGATACCCCGTATCGCAGAG
1208107 ATGA
1 ATGA
1208111 TAATACTATC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (24 bp):
ATGACGATACCCCGTATCGCAGAG
Found at i:1209403 original size:20 final size:20
Alignment explanation
Indices: 1209375--1209430 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1209365 AATTTTCTCC
*
1209375 AAGGGATCGATCCTTTTAGA
1 AAGGAATCGATCCTTTTAGA
1209395 AAGGAATCGATCCTTTTAGA
1 AAGGAATCGATCCTTTTAGA
*
1209415 AAAGAATCGATCCTTT
1 AAGGAATCGATCCTTT
1209431 ATTGGACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (20 bp):
AAGGAATCGATCCTTTTAGA
Found at i:1209982 original size:15 final size:15
Alignment explanation
Indices: 1209945--1209990 Score: 62
Period size: 14 Copynumber: 3.2 Consensus size: 15
1209935 CTTGAAGGAG
1209945 ATGAAAGAAGAAGAA
1 ATGAAAGAAGAAGAA
1209960 ATG-AAGAAGAAG-A
1 ATGAAAGAAGAAGAA
1209973 ATGAAGAGAAG-AGAA
1 ATGAA-AGAAGAAGAA
1209988 ATG
1 ATG
1209991 GGAAGAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 12 0.43
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (15 bp):
ATGAAAGAAGAAGAA
Found at i:1211203 original size:23 final size:23
Alignment explanation
Indices: 1211167--1211235 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1211157 CACCACAGCT
* * *
1211167 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * *
1211190 CGTAGAATTACACCGTAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
*
1211213 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
1211236 TATAAGGTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:1211634 original size:2 final size:2
Alignment explanation
Indices: 1211627--1211651 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1211617 TGTCTTATCC
1211627 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1211652 TCACATGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1212914 original size:64 final size:63
Alignment explanation
Indices: 1212826--1212986 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 63
1212816 TTCCTTTGAA
* * *
1212826 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAA-GGG
* ** * ** *
1212890 GTGCATCGATTCACTCCTTATGCATCGATGTACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGG
* *
1212954 ATGCATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCAC-TCCTATGCATCGATACAC
1212987 ACTGAACAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 2 0.03
64 68 0.86
65 9 0.11
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:1214526 original size:23 final size:23
Alignment explanation
Indices: 1214482--1214545 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1214472 CAGCTCATAT
*
1214482 AAATGCACCGAAGTACCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
1214505 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
1214528 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
1214546 TATACGGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:1215018 original size:2 final size:2
Alignment explanation
Indices: 1215011--1215061 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1215001 ATTCATCTTC
1215011 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1215053 AT AT AT AT A
1 AT AT AT AT A
1215062 ATTTTTCCTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1216269 original size:64 final size:65
Alignment explanation
Indices: 1216160--1216320 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
1216150 TTCCCTTGAA
* * *
1216160 GTGCATCGATGCACAACC-CATGCATCGATACACCAATCACCTTCGATGTTTTCA-TTTTAAGGG
1 GTGCATCGATGCACATCCTCATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAA-GG
1216223 G
65 G
* * ** *
1216224 GTGCATCGATGCAC-TCCTCATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACATCCTCATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGG
* *
1216288 GTGCATCGATGCACTTCCT-GTGCATCGATACAC
1 GTGCATCGATGCACATCCTCATGCATCGATACAC
1216321 ACTGAACAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.02
64 72 0.86
65 10 0.12
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCACATCCTCATGCATCGATACACCAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:1220423 original size:21 final size:21
Alignment explanation
Indices: 1220394--1220433 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1220384 CAACCACTTT
1220394 TATTA-TTTTATTATTTTTTGG
1 TATTATTTTTA-TATTTTTTGG
*
1220415 TATTTTTTTTATATTTTTT
1 TATTATTTTTATATTTTTT
1220434 AGTTATACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (21 bp):
TATTATTTTTATATTTTTTGG
Found at i:1221754 original size:20 final size:19
Alignment explanation
Indices: 1221708--1221746 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1221698 TGATTATTAT
*
1221708 ATTATTATTTTATTTAACA
1 ATTATTATTTTATTGAACA
1221727 ATTAATTATTTTATTAGAAC
1 ATT-ATTATTTTATT-GAAC
1221747 TCTTATTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 11 0.65
21 3 0.18
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTATTATTTTATTGAACA
Found at i:1222585 original size:4 final size:4
Alignment explanation
Indices: 1222576--1222609 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1222566 TTTTATTCAA
*
1222576 TATT TATT TATT TATT TATTT TATT CATT TATT T
1 TATT TATT TATT TATT TA-TT TATT TATT TATT T
1222610 TCATTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1222600 original size:13 final size:13
Alignment explanation
Indices: 1222576--1222610 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1222566 TTTTATTCAA
1222576 TATTTA-TTTATT
1 TATTTATTTTATT
1222588 TATTTATTTTATT
1 TATTTATTTTATT
*
1222601 CATTTATTTT
1 TATTTATTTT
1222611 CATTAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:1223041 original size:22 final size:22
Alignment explanation
Indices: 1223015--1223059 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1223005 CCCTTATTTG
1223015 TTCAATGTTGGTCCTCAAGAAT
1 TTCAATGTTGGTCCTCAAGAAT
1223037 TTCAATGTTGGTCCTCAAGAAT
1 TTCAATGTTGGTCCTCAAGAAT
1223059 T
1 T
1223060 CCTCAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (22 bp):
TTCAATGTTGGTCCTCAAGAAT
Found at i:1226420 original size:2 final size:2
Alignment explanation
Indices: 1226415--1226457 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1226405 ATAGTGTGTG
1226415 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1226457 T
1 T
1226458 TTATTATTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1226585 original size:17 final size:17
Alignment explanation
Indices: 1226563--1226606 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
1226553 TTGAGAAATT
*
1226563 TTGAGAATATAGGGAAA
1 TTGAGAATAGAGGGAAA
1226580 TTGAGAATTTAGAGGGAAA
1 TTGAGAA--TAGAGGGAAA
1226599 TTGAGAAT
1 TTGAGAAT
1226607 TTAGAGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.33
19 16 0.67
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (17 bp):
TTGAGAATAGAGGGAAA
Found at i:1226595 original size:19 final size:19
Alignment explanation
Indices: 1226573--1226619 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1226563 TTGAGAATAT
1226573 AGGGAAATTGAGAATTTAG
1 AGGGAAATTGAGAATTTAG
1226592 AGGGAAATTGAGAATTTAG
1 AGGGAAATTGAGAATTTAG
*
1226611 AGAGAAATT
1 AGGGAAATT
1226620 TAGAGGGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.26
Consensus pattern (19 bp):
AGGGAAATTGAGAATTTAG
Found at i:1227391 original size:21 final size:21
Alignment explanation
Indices: 1227367--1227416 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1227357 AAAAATCCTG
1227367 AACCCTAAAGC-CTAAACTT-TA
1 AACCCTAAA-CACTAAA-TTATA
1227388 AACCCTAAACACTAAATTATA
1 AACCCTAAACACTAAATTATA
1227409 AACCCTAA
1 AACCCTAA
1227417 TGTAAATGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.48, C:0.28, G:0.02, T:0.22
Consensus pattern (21 bp):
AACCCTAAACACTAAATTATA
Found at i:1227867 original size:21 final size:21
Alignment explanation
Indices: 1227841--1227900 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
1227831 AGAAACCATG
*
1227841 AAACCCTAAATCCTAAATCA-T
1 AAACCCTAAATCATAAA-CAGT
1227862 AAACCCTAAATCATAAACAGT
1 AAACCCTAAATCATAAACAGT
1227883 AAACCCTAAA-CTATAAAC
1 AAACCCTAAATC-ATAAAC
1227901 CCCTAGTAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 3 0.08
21 33 0.92
ACGTcount: A:0.52, C:0.27, G:0.02, T:0.20
Consensus pattern (21 bp):
AAACCCTAAATCATAAACAGT
Found at i:1227869 original size:14 final size:14
Alignment explanation
Indices: 1227847--1227879 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1227837 CATGAAACCC
*
1227847 TAAATCCTAAATCA
1 TAAACCCTAAATCA
1227861 TAAACCCTAAATCA
1 TAAACCCTAAATCA
1227875 TAAAC
1 TAAAC
1227880 AGTAAACCCT
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:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:1228534 original size:14 final size:14
Alignment explanation
Indices: 1228517--1228589 Score: 76
Period size: 14 Copynumber: 5.2 Consensus size: 14
1228507 ATAGAAATTC
*
1228517 TAAACCTTAAATCA
1 TAAACCTTAAACCA
* *
1228531 TAAATCTTAAACCC
1 TAAACCTTAAACCA
*
1228545 TAAACTTTAAACCA
1 TAAACCTTAAACCA
*
1228559 TAAACATTAAA-CA
1 TAAACCTTAAACCA
*
1228572 CTAAACCATAAACCA
1 -TAAACCTTAAACCA
1228587 TAA
1 TAA
1228590 TATAAATGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
13 2 0.04
14 44 0.92
15 2 0.04
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:1228560 original size:28 final size:28
Alignment explanation
Indices: 1228516--1228589 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
1228506 TATAGAAATT
* *
1228516 CTAAACCTTAAATCATAAATC-TTAAACC
1 CTAAACCTTAAACCATAAA-CATTAAACA
*
1228544 CTAAACTTTAAACCATAAACATTAAACA
1 CTAAACCTTAAACCATAAACATTAAACA
*
1228572 CTAAACCATAAACCATAA
1 CTAAACCTTAAACCATAA
1228590 TATAAATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (28 bp):
CTAAACCTTAAACCATAAACATTAAACA
Found at i:1228562 original size:21 final size:21
Alignment explanation
Indices: 1228538--1228585 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1228528 TCATAAATCT
**
1228538 TAAACCCTAAACTTTAAACCA
1 TAAACCCTAAACACTAAACCA
**
1228559 TAAACATTAAACACTAAACCA
1 TAAACCCTAAACACTAAACCA
1228580 TAAACC
1 TAAACC
1228586 ATAATATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAACCCTAAACACTAAACCA
Found at i:1228586 original size:7 final size:7
Alignment explanation
Indices: 1228517--1228589 Score: 51
Period size: 7 Copynumber: 10.4 Consensus size: 7
1228507 ATAGAAATTC
*
1228517 TAAACCT
1 TAAACCA
*
1228524 TAAATCA
1 TAAACCA
* *
1228531 TAAATCT
1 TAAACCA
*
1228538 TAAACCC
1 TAAACCA
**
1228545 TAAACTT
1 TAAACCA
1228552 TAAACCA
1 TAAACCA
1228559 TAAA-CA
1 TAAACCA
1228565 TTAAA-CA
1 -TAAACCA
1228572 CTAAACCA
1 -TAAACCA
1228580 TAAACCA
1 TAAACCA
1228587 TAA
1 TAA
1228590 TATAAATGTA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
6 2 0.04
7 50 0.93
8 2 0.04
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACCA
Found at i:1228770 original size:14 final size:14
Alignment explanation
Indices: 1228751--1228821 Score: 61
Period size: 14 Copynumber: 5.7 Consensus size: 14
1228741 TATTGTTTTT
1228751 TATATAAATTAAAC
1 TATATAAATTAAAC
1228765 TATAT-AATT----
1 TATATAAATTAAAC
1228774 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1228788 TATATTAATT----
1 TATATAAATTAAAC
1228798 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1228812 TATATTAATT
1 TATATAAATT
1228822 TTCCTTTGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 18
0.68 0.05 0.27
Matches are distributed among these distances:
9 5 0.11
10 13 0.29
13 4 0.09
14 23 0.51
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:1228801 original size:24 final size:24
Alignment explanation
Indices: 1228749--1228822 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
1228739 AATATTGTTT
1228749 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1228772 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1228796 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1228820 TTT
1 TTT
1228823 TCCTTTGCAT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 20 0.40
24 30 0.60
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1228872 original size:25 final size:22
Alignment explanation
Indices: 1228844--1228891 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 22
1228834 ATTAATCATG
1228844 TTTTATCTAATTTATATTTAAATAA
1 TTTTAT-TAATTT-TA-TTAAATAA
1228869 TTTTATTAATTTTATTAAATAA
1 TTTTATTAATTTTATTAAATAA
1228891 T
1 T
1228892 AGGTCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 2 0.09
24 6 0.26
25 6 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATTAATTTTATTAAATAA
Found at i:1228931 original size:29 final size:28
Alignment explanation
Indices: 1228862--1228934 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
1228852 AATTTATATT
*
1228862 TAAATAATTTTATTAATTTTATTAAATAA
1 TAAAT-ATTTTATTAATTTAATTAAATAA
** * *
1228891 TAGGTCTATTTATTAATTTAATTATCATAA
1 TAAATAT-TTTATTAATTTAATTA-AATAA
1228921 TAAATATTTTATTA
1 TAAATATTTTATTA
1228935 TAACATTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
28 1 0.03
29 25 0.74
30 8 0.24
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (28 bp):
TAAATATTTTATTAATTTAATTAAATAA
Found at i:1232016 original size:21 final size:21
Alignment explanation
Indices: 1231975--1232018 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
1231965 TTGGTTCACG
1231975 AAAAAATAAATATTTAAATTAA
1 AAAAAATAAATATTT-AATTAA
1231997 AAAAATATAAATATTT-ATTAA
1 AAAAA-ATAAATATTTAATTAA
1232018 A
1 A
1232019 TATTTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 5 0.24
23 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAATAAATATTTAATTAA
Found at i:1238587 original size:21 final size:21
Alignment explanation
Indices: 1238562--1238609 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1238552 CCTAATATTG
1238562 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
1238583 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
1238604 CAATGT
1 CAATGT
1238610 TTGAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:1245359 original size:27 final size:27
Alignment explanation
Indices: 1245317--1245368 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1245307 AATAATTTGC
1245317 GTGACTCGGAAATATTGTTAAACAGCA
1 GTGACTCGGAAATATTGTTAAACAGCA
* * *
1245344 GTGAGTCGGAAGTATTGTTTAACAG
1 GTGACTCGGAAATATTGTTAAACAG
1245369 GTTTCAATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (27 bp):
GTGACTCGGAAATATTGTTAAACAGCA
Found at i:1248745 original size:17 final size:19
Alignment explanation
Indices: 1248709--1248745 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1248699 GTTGGTAAGT
1248709 ATTTTTAAATATTAATTTA
1 ATTTTTAAATATTAATTTA
*
1248728 ATTTTTTAAT-TT-ATTTA
1 ATTTTTAAATATTAATTTA
1248745 A
1 A
1248746 ATCAAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTAAATATTAATTTA
Found at i:1259151 original size:17 final size:18
Alignment explanation
Indices: 1259118--1259152 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1259108 TATTATTTCC
1259118 TTCCCTCTTCACTTAGTTA
1 TTCCCTCTT-ACTTAGTTA
1259137 TTCCCTCTT-CTTAGTT
1 TTCCCTCTTACTTAGTT
1259153 CTTCTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.11, C:0.31, G:0.06, T:0.51
Consensus pattern (18 bp):
TTCCCTCTTACTTAGTTA
Found at i:1267008 original size:24 final size:24
Alignment explanation
Indices: 1266968--1267013 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1266958 CTCTGAACAA
*
1266968 GTTTTGTAATGTTTAAACGTATTT
1 GTTTTGTAATGTGTAAACGTATTT
*
1266992 GTTTTGTAAATG-GTAAATGTAT
1 GTTTTGT-AATGTGTAAACGTAT
1267014 AGAGATGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (24 bp):
GTTTTGTAATGTGTAAACGTATTT
Found at i:1267133 original size:22 final size:21
Alignment explanation
Indices: 1267075--1267139 Score: 112
Period size: 21 Copynumber: 3.0 Consensus size: 21
1267065 TGTAGCAGTA
1267075 CTGTAGCAGGGAATCGGTTCC
1 CTGTAGCAGGGAATCGGTTCC
*
1267096 CTGTAGCATGGAATCGGTTCC
1 CTGTAGCAGGGAATCGGTTCC
1267117 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCA-GGGAATCGGTTCC
1267139 C
1 C
1267140 CTCTGACAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 28 0.68
22 13 0.32
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (21 bp):
CTGTAGCAGGGAATCGGTTCC
Found at i:1274920 original size:32 final size:32
Alignment explanation
Indices: 1274868--1274962 Score: 111
Period size: 32 Copynumber: 3.0 Consensus size: 32
1274858 GTCAATATCA
* * *
1274868 GGTCGGATCAAAATCAGATCAGTTGATTTTTG
1 GGTCGGGTCAATATCGGATCAGTTGATTTTTG
* *
1274900 GGTCGGGTTAATATCGGATCAGTTAGA-TTTCG
1 GGTCGGGTCAATATCGGATCAGTT-GATTTTTG
**
1274932 GGTCGGGTCAATATCGGATTTGTTGATTTTT
1 GGTCGGGTCAATATCGGATCAGTTGATTTTT
1274963 TGTTTAGGTC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 2 0.04
32 48 0.92
33 2 0.04
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (32 bp):
GGTCGGGTCAATATCGGATCAGTTGATTTTTG
Found at i:1275291 original size:19 final size:19
Alignment explanation
Indices: 1275267--1275319 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1275257 GATAAATAAA
1275267 TATTTTTTATTAAAAAATT
1 TATTTTTTATTAAAAAATT
** *
1275286 TATTTTCAATT-ATAAATT
1 TATTTTTTATTAAAAAATT
1275304 TAATATTTTTATTAAA
1 T-AT-TTTTTATTAAA
1275320 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
18 7 0.28
19 11 0.44
20 6 0.24
21 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTTTATTAAAAAATT
Found at i:1275580 original size:18 final size:19
Alignment explanation
Indices: 1275543--1275580 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1275533 TTTTAAACTT
* *
1275543 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
1275562 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
1275580 T
1 T
1275581 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:1275691 original size:32 final size:33
Alignment explanation
Indices: 1275655--1275722 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
1275645 ATTTCAATAT
*
1275655 GTTCGGGTTGCTTTC-GAGTCGGGTT-AAATTCG
1 GTTCGGGTTGCTTTCGGA-TCAGGTTAAAATTCG
*
1275687 GTTCGGGTTGCTTTTGGATCAGGTTAAAATTCG
1 GTTCGGGTTGCTTTCGGATCAGGTTAAAATTCG
1275720 GTT
1 GTT
1275723 AAGATTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.15, C:0.13, G:0.32, T:0.40
Consensus pattern (33 bp):
GTTCGGGTTGCTTTCGGATCAGGTTAAAATTCG
Found at i:1284832 original size:24 final size:23
Alignment explanation
Indices: 1284800--1284866 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 23
1284790 ATAAAACATT
1284800 AATTAAATATTTATATATTTTATAA
1 AATT-AATATTTATATATTTTA-AA
* *
1284825 AATTAATATTAATTTATTTTAAA
1 AATTAATATTTATATATTTTAAA
1284848 AATTAA-ATTTATGATATTT
1 AATTAATATTTAT-ATATTT
1284867 ATTACAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.14
23 13 0.35
24 15 0.41
25 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
AATTAATATTTATATATTTTAAA
Found at i:1285258 original size:71 final size:72
Alignment explanation
Indices: 1285070--1285633 Score: 771
Period size: 71 Copynumber: 7.7 Consensus size: 72
1285060 TTAAAATAAA
* *
1285070 TAAA-AAAAAATTATATTTTAAATTCTAAGGATAAAATTTTAATTTTAATTTGATTTTATTAATT
1 TAAATAAAAAATTATATTTTAAATTATAAGGATAAAATATTAATTTTAATTTGA--TT-TTAA-T
1285134 AATTATTTATT
62 AATTATTTATT
*
1285145 TAAATAAAAAATTATATTTTAAATTATAAGGAAAAAATATTAATTTTAATTTGATTTTAATAATT
1 TAAATAAAAAATTATATTTTAAATTATAAGGATAAAATATTAATTTTAATTTGATTTTAATAATT
1285210 ATTTATT
66 ATTTATT
* * *
1285217 TAAA-CAAAAATTATATTTTAAATTATAAGGATATAATATTAA-TTTAATTT-AATTTAATTAAT
1 TAAATAAAAAATTATATTTTAAATTATAAGGATAAAATATTAATTTTAATTTGATTTTAA-TAAT
1285279 TATTTATT
65 TATTTATT
* * *
1285287 GAAATAAATAAAAATATATATTTTAAATTATAAGGATAGAATATTAACTTTAATTTGATTTTTAT
1 TAAAT--A-AAAAAT-TATATTTTAAATTATAAGGATAAAATATTAATTTTAATTTGA---TT-T
**
1285352 TAATTAATTATTTAAA
58 TAA-TAATTATTTATT
*
1285368 TAAATAAAAAATTATATTTTAAATTATAAGGATAGAATATTAATTTTAATTTGATTTTAATAATT
1 TAAATAAAAAATTATATTTTAAATTATAAGGATAAAATATTAATTTTAATTTGATTTTAATAATT
1285433 ATTTATT
66 ATTTATT
* * * *
1285440 TAAA-CAAAAATTATATTTTAAATTATAAGGATATAATATTAA-TTTAATTTAATTTTATTAATT
1 TAAATAAAAAATTATATTTTAAATTATAAGGATAAAATATTAATTTTAATTTGATTTTAATAATT
1285503 ATTTATT
66 ATTTATT
* * *
1285510 TAAATAAAAAATTATATTTTAAATTATAAGGATAGAATATTAATTTTGATTTGATTTTATTAATT
1 TAAATAAAAAATTATATTTTAAATTATAAGGATAAAATATTAATTTTAATTTGATTTTAATAATT
1285575 ATTTATT
66 ATTTATT
* *
1285582 TAAATAAAAAAATATATTTTAAATTATAAGGATAAAATATTAATATTAATTT
1 TAAATAAAAAATTATATTTTAAATTATAAGGATAAAATATTAATTTTAATTT
1285634 AATTAATTAA
Statistics
Matches: 445, Mismatches: 29, Indels: 33
0.88 0.06 0.07
Matches are distributed among these distances:
69 6 0.01
70 53 0.12
71 107 0.24
72 104 0.23
73 8 0.02
74 10 0.02
75 34 0.08
76 54 0.12
77 42 0.09
78 6 0.01
79 1 0.00
80 1 0.00
81 19 0.04
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.48
Consensus pattern (72 bp):
TAAATAAAAAATTATATTTTAAATTATAAGGATAAAATATTAATTTTAATTTGATTTTAATAATT
ATTTATT
Found at i:1285382 original size:223 final size:222
Alignment explanation
Indices: 1285051--1285633 Score: 939
Period size: 223 Copynumber: 2.6 Consensus size: 222
1285041 TATAATTTGC
* * * *
1285051 AATTATTTATTAAAATAAATAAAAAAAAATTATATTTTAAATTCTAAGGATAAAATTTTAATTTT
1 AATTATTTATTAAAATAAAT--AAAAATA-TATATTTTAAATTATAAGGATAGAATATTAATTTT
** *
1285116 AATTTGATTTTATTAATTAATTATTTATTTAAATAAAAAATTATATTTTAAATTATAAGGAAAAA
63 AATTTGATTTTATTAATTAATTATTTAAATAAATAAAAAATTATATTTTAAATTATAAGGATAAA
1285181 ATATTAATTTTAATTTGATTTTAATAATTATTTATTTAAACAAAAATTATATTTTAAATTATAAG
128 ATATTAATTTTAATTTGATTTTAATAATTATTTATTTAAACAAAAATTATATTTTAAATTATAAG
1285246 GATATAATATTAATTTAATTTAATTTAATT
193 GATATAATATTAATTTAATTTAATTTAATT
* *
1285276 AATTATTTATTGAAATAAATAAAAATATATATTTTAAATTATAAGGATAGAATATTAACTTTAAT
1 AATTATTTATTAAAATAAATAAAAATATATATTTTAAATTATAAGGATAGAATATTAATTTTAAT
*
1285341 TTGATTTTTATTAATTAATTATTTAAATAAATAAAAAATTATATTTTAAATTATAAGGATAGAAT
66 TTGA-TTTTATTAATTAATTATTTAAATAAATAAAAAATTATATTTTAAATTATAAGGATAAAAT
1285406 ATTAATTTTAATTTGATTTTAATAATTATTTATTTAAACAAAAATTATATTTTAAATTATAAGGA
130 ATTAATTTTAATTTGATTTTAATAATTATTTATTTAAACAAAAATTATATTTTAAATTATAAGGA
*
1285471 TATAATATTAATTTAATTTAATTTTATT
195 TATAATATTAATTTAATTTAATTTAATT
* *
1285499 AATTATTTATTTAAAT--A-AAAAAT-TATATTTTAAATTATAAGGATAGAATATTAATTTTGAT
1 AATTATTTATTAAAATAAATAAAAATATATATTTTAAATTATAAGGATAGAATATTAATTTTAAT
*
1285560 TTGATTTTATTAATTATTTATTTAAAT--A-AAAAAA-TATATTTTAAATTATAAGGATAAAATA
66 TTGATTTTATTAATTAATTATTTAAATAAATAAAAAATTATATTTTAAATTATAAGGATAAAATA
*
1285621 TTAATATTAATTT
131 TTAATTTTAATTT
1285634 AATTAATTAA
Statistics
Matches: 340, Mismatches: 17, Indels: 13
0.92 0.05 0.04
Matches are distributed among these distances:
214 38 0.11
215 6 0.02
216 1 0.00
218 22 0.06
219 40 0.12
220 6 0.02
221 1 0.00
222 38 0.11
223 169 0.50
225 19 0.06
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (222 bp):
AATTATTTATTAAAATAAATAAAAATATATATTTTAAATTATAAGGATAGAATATTAATTTTAAT
TTGATTTTATTAATTAATTATTTAAATAAATAAAAAATTATATTTTAAATTATAAGGATAAAATA
TTAATTTTAATTTGATTTTAATAATTATTTATTTAAACAAAAATTATATTTTAAATTATAAGGAT
ATAATATTAATTTAATTTAATTTAATT
Found at i:1285425 original size:38 final size:38
Alignment explanation
Indices: 1285306--1285427 Score: 97
Period size: 38 Copynumber: 3.2 Consensus size: 38
1285296 AAAAATATAT
*
1285306 ATTTTAAATTATAAGGATAGAATATTAACTTTAATTTG
1 ATTTTAAATTATAAGGATAGAATATTAATTTTAATTTG
* ** ** * ***
1285344 ATTTT-TATTAATTAATTATTTAA-ATAAATAAAAAATTAT-
1 ATTTTAAATT-A-TAAGGATAGAATATTAAT-TTTAATT-TG
1285383 ATTTTAAATTATAAGGATAGAATATTAATTTTAATTTG
1 ATTTTAAATTATAAGGATAGAATATTAATTTTAATTTG
1285421 ATTTTAA
1 ATTTTAA
1285428 TAATTATTTA
Statistics
Matches: 58, Mismatches: 19, Indels: 14
0.64 0.21 0.15
Matches are distributed among these distances:
37 4 0.07
38 28 0.48
39 22 0.38
40 4 0.07
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.48
Consensus pattern (38 bp):
ATTTTAAATTATAAGGATAGAATATTAATTTTAATTTG
Found at i:1288466 original size:14 final size:15
Alignment explanation
Indices: 1288447--1288497 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1288437 AATTATACCA
*
1288447 TTACTCACTTA-ATT
1 TTACTCACTCATATT
*
1288461 TTACTCTCTCATATT
1 TTACTCACTCATATT
*
1288476 TTACTCTCTCATATT
1 TTACTCACTCATATT
1288491 TTACTCA
1 TTACTCA
1288498 TTACATTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 9 0.27
15 24 0.73
ACGTcount: A:0.24, C:0.25, G:0.00, T:0.51
Consensus pattern (15 bp):
TTACTCACTCATATT
Found at i:1288478 original size:15 final size:15
Alignment explanation
Indices: 1288458--1288496 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
1288448 TACTCACTTA
1288458 ATTTTACTCTCTCAT
1 ATTTTACTCTCTCAT
1288473 ATTTTACTCTCTCAT
1 ATTTTACTCTCTCAT
1288488 ATTTTACTC
1 ATTTTACTC
1288497 ATTACATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTTACTCTCTCAT
Found at i:1288719 original size:19 final size:18
Alignment explanation
Indices: 1288677--1288719 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1288667 ATTATATCCT
*
1288677 TAAATTATACTTAAATTC
1 TAAATTATACTTAAACTC
*
1288695 TCAAATTATATTGTAAACTC
1 T-AAATTATACT-TAAACTC
1288715 TAAAT
1 TAAAT
1288720 CTCAAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 13 0.62
20 7 0.33
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (18 bp):
TAAATTATACTTAAACTC
Found at i:1290745 original size:22 final size:23
Alignment explanation
Indices: 1290702--1290753 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1290692 GTTAATTTTT
1290702 TAATAATTATTTATTATAAAAATA
1 TAAT-ATTATTTATTATAAAAATA
1290726 TAATATTATTATATT-T-AAAATA
1 TAATATTATT-TATTATAAAAATA
*
1290748 TTATAT
1 TAATAT
1290754 AGTTGAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 11 0.42
23 7 0.27
24 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAATA
Found at i:1311230 original size:17 final size:16
Alignment explanation
Indices: 1311208--1311268 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 16
1311198 CAAAAACTCA
1311208 AAAATCATAACCCATT
1 AAAATCATAACCCATT
1311224 GAAAATCATAAGCTCCA-T
1 -AAAATCATAA-C-CCATT
*
1311242 AAAATCATAACCC-TAC
1 AAAATCATAACCCAT-T
1311258 AAAATCATAAC
1 AAAATCATAAC
1311269 ACCGACACTC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
15 2 0.05
16 12 0.31
17 20 0.51
18 2 0.05
19 3 0.08
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAATCATAACCCATT
Found at i:1311707 original size:43 final size:42
Alignment explanation
Indices: 1311610--1312040 Score: 381
Period size: 43 Copynumber: 10.1 Consensus size: 42
1311600 TGAGAACAAA
* * *
1311610 AAACGCCGCAATAGGTCAAGATCTATCGCA--GTTTTTGGGAAC
1 AAACGCCGCAAAAGGTC-ATATCTATAGCAGCGTTTTT-GGAAC
*
1311652 AAACGCCGCAAAAGGTCATTATCTATAGCATCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCA-TATCTATAGCAGCGTTTTTGGAAC
* * * * *
1311695 AAACGCCACAAAAGGTTAATATTTATAGC-GACATTTTAGGAAC
1 AAACGCCGCAAAAGG-TCATATCTATAGCAG-CGTTTTTGGAAC
* * * *
1311738 AAACACCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGTAAC
1 AAACGCCGCAAAAGG-TCATATCTATAGCAGCGTTTTTGGAAC
* * *
1311781 AAACGCCGCAAAAGGTTGATATCTATAGCGGCGTTTTTGTAAC
1 AAACGCCGCAAAAGG-TCATATCTATAGCAGCGTTTTTGGAAC
* * *
1311824 AAACACCGCAAAAGGTCAGATCTATAGCGGCG-TTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCAGCGTTTTTGGA-AC
* *
1311866 AAACGACGCAAAAGGTCATATCTATAGCTGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCATATCTATAGCAGCGTTTTTGGAAC
* * *
1311908 AAACTCCACAAAAGATCGATATCTATAGCGATG-G--TTTGGAAC
1 AAACGCCGCAAAAGGTC-ATATCTATAGC-A-GCGTTTTTGGAAC
* * * * *
1311950 AAACGCTGCAAAAGGTTAGATCTATAGCGGCGTTTTTTGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCAGCGTTTTTGGA-AC
** * * * *
1311993 AAACGCCGCAAAATATTAGATCTATAGCGGTGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCATATCTATAGCAGCGTTTTTGGA-AC
1312036 AAACG
1 AAACG
1312041 TTGCTATTAC
Statistics
Matches: 331, Mismatches: 43, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 17 0.05
42 110 0.33
43 191 0.58
44 10 0.03
45 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCATATCTATAGCAGCGTTTTTGGAAC
Found at i:1315415 original size:22 final size:22
Alignment explanation
Indices: 1315375--1315431 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1315365 AATATATGGT
* *
1315375 ATGAAGAGTACTGTAAACAATA
1 ATGAACAGTACTATAAACAATA
* *
1315397 ATGAACAGTACTATGAACAGTA
1 ATGAACAGTACTATAAACAATA
1315419 ACGTGAACAGTAC
1 A--TGAACAGTAC
1315432 CGAATGCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 19 0.66
24 10 0.34
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (22 bp):
ATGAACAGTACTATAAACAATA
Found at i:1315500 original size:20 final size:21
Alignment explanation
Indices: 1315464--1315505 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
1315454 TTACTTCAGG
*
1315464 GGTATCGATACCCCTGCTACA
1 GGTACCGATACCCCTGCTACA
1315485 GGTACCGATA-CCCTGCTACA
1 GGTACCGATACCCCTGCTACA
1315505 G
1 G
1315506 TACTCCTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTACCGATACCCCTGCTACA
Found at i:1319056 original size:32 final size:32
Alignment explanation
Indices: 1318937--1319061 Score: 114
Period size: 31 Copynumber: 4.0 Consensus size: 32
1318927 AACCTCGGTA
* * *
1318937 ACTGTCCATAAG-TCCTGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCC-GTAGAACATAGGTAAT
* * *
1318968 AATGTCTATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* * *
1318999 ACTGTACATATGTCCCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTCCGTAGA-ACATAGGTAAT
*
1319031 TCTGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTTCCGTAGAACATAGGTAA
1319062 ACCCTCGACT
Statistics
Matches: 73, Mismatches: 16, Indels: 9
0.74 0.16 0.09
Matches are distributed among these distances:
30 3 0.04
31 39 0.53
32 29 0.40
33 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:1319326 original size:19 final size:17
Alignment explanation
Indices: 1319285--1319329 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1319275 GCTACCGTTT
1319285 TATCACATATCATGTTA
1 TATCACATATCATGTTA
* *
1319302 TTTCACATATACACTTTTA
1 TATCACATAT-CA-TGTTA
1319321 TATCACATA
1 TATCACATA
1319330 AACTCATATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 12 0.52
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.42
Consensus pattern (17 bp):
TATCACATATCATGTTA
Found at i:1319743 original size:2 final size:2
Alignment explanation
Indices: 1319736--1319789 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1319726 ACTTATGTTC
1319736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1319778 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1319790 TTCACACAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1321185 original size:41 final size:41
Alignment explanation
Indices: 1321064--1321210 Score: 97
Period size: 42 Copynumber: 3.5 Consensus size: 41
1321054 ACAACATTTA
* * * **
1321064 TATAAAAACGCCGCTAAAGTACTAATCTATCGCGGCGTTTG
1 TATAAAAACGCCACTAAAGTATTACTCTATCGTAGCGTTTG
* *
1321105 TTAGAAAAATGCCACTATAAACG-A-TAC-CTAT--TACGGCGTTTG
1 -TATAAAAACGCCAC--TAAA-GTATTACTCTATCGTA--GCGTTTG
* *
1321147 TATAAAAACGCCGCTAAAGTATTACTCTATCGTAGCGTTTA
1 TATAAAAACGCCACTAAAGTATTACTCTATCGTAGCGTTTG
* *
1321188 TTTAAGAAACACCACTAAAGTAT
1 TATAA-AAACGCCACTAAAGTAT
1321211 CGTTTTGTGG
Statistics
Matches: 81, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
38 1 0.01
39 5 0.06
40 3 0.04
41 25 0.31
42 37 0.46
43 4 0.05
44 5 0.06
45 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (41 bp):
TATAAAAACGCCACTAAAGTATTACTCTATCGTAGCGTTTG
Found at i:1321185 original size:83 final size:83
Alignment explanation
Indices: 1320946--1321189 Score: 282
Period size: 83 Copynumber: 3.0 Consensus size: 83
1320936 TTTTTTTTGC
*
1320946 AAAAATGCCAC--TAAA-GAACCCTATTACGGTGTTTATATTAAAAACGCCGCTAAAGTACT-CT
1 AAAAATGCCACTATAAACGAACCCTATTACGGCGTTTATA-TAAAAACGCCGCTAAAGTACTACT
* ** * *
1321007 TTATTATGGCATTTATTGG
65 CTATCGTGGCGTTTATTAG
* * ** * *
1321026 AAAAACGCCACTATGAACGAACCCTATTACAACATTTATATAAAAACGCCGCTAAAGTACTAATC
1 AAAAATGCCACTATAAACGAACCCTATTACGGCGTTTATATAAAAACGCCGCTAAAGTACTACTC
* *
1321091 TATCGCGGCGTTTGTTAG
66 TATCGTGGCGTTTATTAG
* *
1321109 AAAAATGCCACTATAAACGATA-CCTATTACGGCGTTTGTATAAAAACGCCGCTAAAGTATTACT
1 AAAAATGCCACTATAAACGA-ACCCTATTACGGCGTTTATATAAAAACGCCGCTAAAGTACTACT
*
1321173 CTATCGTAGCGTTTATT
65 CTATCGTGGCGTTTATT
1321190 TAAGAAACAC
Statistics
Matches: 134, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
80 10 0.07
82 24 0.18
83 99 0.74
84 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (83 bp):
AAAAATGCCACTATAAACGAACCCTATTACGGCGTTTATATAAAAACGCCGCTAAAGTACTACTC
TATCGTGGCGTTTATTAG
Found at i:1321740 original size:17 final size:16
Alignment explanation
Indices: 1321720--1321799 Score: 67
Period size: 17 Copynumber: 4.8 Consensus size: 16
1321710 ATTTTGTGGA
1321720 GGTTATGATTTTTAATG
1 GGTTATGATTTTT-ATG
1321737 GGTTATGA-TTTT-TG
1 GGTTATGATTTTTATG
*
1321751 GGTTTTTGA-TTTTATG
1 GG-TTATGATTTTTATG
*
1321767 GAGCTTATGATTTTCAATGG
1 G-G-TTATGATTTT-TAT-G
1321787 GGTTATGATTTTT
1 GGTTATGATTTTT
1321800 GAGTTTTTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
14 4 0.08
15 9 0.17
16 7 0.13
17 14 0.27
18 13 0.25
19 3 0.06
20 2 0.04
ACGTcount: A:0.19, C:0.03, G:0.25, T:0.54
Consensus pattern (16 bp):
GGTTATGATTTTTATG
Found at i:1321743 original size:49 final size:49
Alignment explanation
Indices: 1321671--1321799 Score: 161
Period size: 49 Copynumber: 2.6 Consensus size: 49
1321661 CAGAGAACAG
* * *
1321671 GGTTATGCTTTTT-ATGAGGTTATGATTTTTACCTTTTTTATTTTGTGGA
1 GGTTATGATTTTTAATG-GGTTATGATTTTTACCTTTTTGATTTTATGGA
***
1321720 GGTTATGATTTTTAATGGGTTATGATTTTTGGGTTTTTGATTTTATGGA
1 GGTTATGATTTTTAATGGGTTATGATTTTTACCTTTTTGATTTTATGGA
* *
1321769 GCTTATGATTTTCAATGGGGTTATGATTTTT
1 GGTTATGATTTTTAAT-GGGTTATGATTTTT
1321800 GAGTTTTTGG
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 53 0.76
50 17 0.24
ACGTcount: A:0.18, C:0.04, G:0.23, T:0.55
Consensus pattern (49 bp):
GGTTATGATTTTTAATGGGTTATGATTTTTACCTTTTTGATTTTATGGA
Found at i:1321865 original size:6 final size:6
Alignment explanation
Indices: 1321845--1321888 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1321835 AAGAAGAAGA
* * *
1321845 AGAAGG AGAAGG AGAATG AGAATG AGAATG AGAAAG AGAA-G AGA
1 AGAATG AGAATG AGAATG AGAATG AGAATG AGAATG AGAATG AGA
1321889 GTTGACGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.07
Consensus pattern (6 bp):
AGAATG
Found at i:1321865 original size:12 final size:11
Alignment explanation
Indices: 1321830--1321888 Score: 55
Period size: 12 Copynumber: 5.0 Consensus size: 11
1321820 TTCCAGAAGG
1321830 AGGAGAAGAAGA
1 AGGAGAAG-AGA
*
1321842 AGAAGAAGGAGA
1 AGGAGAA-GAGA
1321854 AGGAGAATGAGA
1 AGGAGAA-GAGA
*
1321866 ATGAGAATGAGA
1 AGGAGAA-GAGA
*
1321878 AAGAGAAGAGA
1 AGGAGAAGAGA
1321889 GTTGACGGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
11 4 0.10
12 36 0.88
13 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.39, T:0.05
Consensus pattern (11 bp):
AGGAGAAGAGA
Found at i:1321866 original size:18 final size:17
Alignment explanation
Indices: 1321830--1321885 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
1321820 TTCCAGAAGG
*
1321830 AGGAGAAGAAGAAGAAGA
1 AGGAGAAGGAGAAG-AGA
1321848 AGGAGAAGGAGAATGAGA
1 AGGAGAAGGAGAA-GAGA
* *
1321866 ATGAGAATGAGAAAGAGA
1 AGGAGAAGGAG-AAGAGA
1321884 AG
1 AG
1321886 AGAGTTGACG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 29 0.91
19 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.05
Consensus pattern (17 bp):
AGGAGAAGGAGAAGAGA
Found at i:1324791 original size:16 final size:16
Alignment explanation
Indices: 1324762--1324809 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1324752 AAAATAATAA
1324762 AATAAAAATATAATATT
1 AATAAAAAT-TAATATT
*
1324779 AATAAGAATTAATATT
1 AATAAAAATTAATATT
* *
1324795 AATAATAATAAATAT
1 AATAAAAATTAATAT
1324810 AGGACGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 20 0.71
17 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
AATAAAAATTAATATT
Found at i:1324967 original size:37 final size:37
Alignment explanation
Indices: 1324921--1324992 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
1324911 AGTACCTAAG
*
1324921 TTAATAGTTTTGGTCTGTTTTAATATCTAAACTTTAA
1 TTAATAGTTTTGGTCCGTTTTAATATCTAAACTTTAA
* *
1324958 TTAATAGTTTTGGTCCGTTTTAGTATCTGAACTTT
1 TTAATAGTTTTGGTCCGTTTTAATATCTAAACTTT
1324993 CAATATTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (37 bp):
TTAATAGTTTTGGTCCGTTTTAATATCTAAACTTTAA
Found at i:1325161 original size:14 final size:14
Alignment explanation
Indices: 1325142--1325172 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1325132 TTATTTTTTC
*
1325142 AATATGACCTTCCT
1 AATATGACATTCCT
1325156 AATATGACATTCCT
1 AATATGACATTCCT
1325170 AAT
1 AAT
1325173 TCAGAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (14 bp):
AATATGACATTCCT
Found at i:1325278 original size:26 final size:26
Alignment explanation
Indices: 1325239--1325289 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1325229 TGATGTTGAC
*
1325239 GTGATAGTTCACGTCTTTAATATGAT
1 GTGATAGTTCACGTCCTTAATATGAT
* *
1325265 GTGATCGTTTACGTCCTTAATATGA
1 GTGATAGTTCACGTCCTTAATATGA
1325290 CGTTTACAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (26 bp):
GTGATAGTTCACGTCCTTAATATGAT
Found at i:1330525 original size:17 final size:17
Alignment explanation
Indices: 1330496--1330529 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1330486 TAAGAACTTG
1330496 ATTTGAAATTTTTGAAT
1 ATTTGAAATTTTTGAAT
1330513 ATTTGGAAA-TTTTGAAT
1 ATTT-GAAATTTTTGAAT
1330530 CTTCAAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATTTGAAATTTTTGAAT
Found at i:1331149 original size:12 final size:12
Alignment explanation
Indices: 1331132--1331156 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1331122 TGATGATGGT
1331132 TCTCCAACGTCA
1 TCTCCAACGTCA
1331144 TCTCCAACGTCA
1 TCTCCAACGTCA
1331156 T
1 T
1331157 TTATGTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.08, T:0.28
Consensus pattern (12 bp):
TCTCCAACGTCA
Found at i:1334543 original size:20 final size:20
Alignment explanation
Indices: 1334507--1334544 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1334497 CCGTTAAACA
*
1334507 GGGGGAATCGGTACCCTCTG
1 GGGGGAATCAGTACCCTCTG
*
1334527 GGGGGAATCAGTTCCCTC
1 GGGGGAATCAGTACCCTC
1334545 CGAGCAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.26, G:0.37, T:0.21
Consensus pattern (20 bp):
GGGGGAATCAGTACCCTCTG
Found at i:1334693 original size:12 final size:12
Alignment explanation
Indices: 1334678--1334702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1334668 AATACTTTGT
1334678 AAAATTTGTTTA
1 AAAATTTGTTTA
1334690 AAAATTTGTTTA
1 AAAATTTGTTTA
1334702 A
1 A
1334703 GTATAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
AAAATTTGTTTA
Found at i:1336188 original size:60 final size:60
Alignment explanation
Indices: 1336076--1336188 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
1336066 ATAGCTTGGA
* * *
1336076 GATGAAAATGAAATGTTCAAAAGTTTGAGGACTAATTTAGAATAATATTCATAGTTTAAG
1 GATGAAAATGAAATATTCAAAAGTTTGAGGACTAATTTAAAATAATAGTCATAGTTTAAG
* **
1336136 GATGAAATTGAAATATTTTAAAGTTT-AGGGACTAATTTAAAATGAA-AGTCATA
1 GATGAAAATGAAATATTCAAAAGTTTGA-GGACTAATTTAAAAT-AATAGTCATA
1336189 AATTAAGGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.02
60 42 0.93
61 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (60 bp):
GATGAAAATGAAATATTCAAAAGTTTGAGGACTAATTTAAAATAATAGTCATAGTTTAAG
Found at i:1337727 original size:23 final size:23
Alignment explanation
Indices: 1337680--1337728 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1337670 AATAACATAT
* **
1337680 TAGGTAGCGCTTACATAATGTAA
1 TAGGTAACGCTTACATAATAAAA
*
1337703 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACGCTTACATAATAAAA
1337726 TAG
1 TAG
1337729 ACATTTAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (23 bp):
TAGGTAACGCTTACATAATAAAA
Found at i:1338223 original size:199 final size:196
Alignment explanation
Indices: 1337741--1338445 Score: 737
Period size: 199 Copynumber: 3.5 Consensus size: 196
1337731 ATTTAACTCA
** * *
1337741 TATATTTATACCGG-TAGCATTGTAAATTTACCTATTGTATTATAATTATTGGTTTCGTTGTTTT
1 TATATTTATACCGGTTA-CATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATATTTT
*
1337805 T-TGGATCGATATAATTTTAAATGTATCGACACTTTATTCTTGCACCTCGTTGGGCATTCCTAAT
65 TGTGGATCGATACAATTTTAAATGTATCGACACTTTATTCTTGCACCTCGTTGGGCATT-C--AT
* *
1337869 TCATTCTGGAAAAAAGTATCGACACAAACTATAAAGGTGTCGATACATTATTTAGACCTATTTTC
127 T-A---TGGAAAAAAGTATCGACACAAA-T-TAAAAGTGTCGATACTTTATTT-GACCTATTTTC
*
1337934 TCATAAAATCGG
185 TCATAAAACCGG
* * * *
1337946 TATATTTATACCGGGTACATTGTAAATTTACCTATAACATTGTAATT-TTTGTTTCGATATTTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATATTTTT
* * * *
1338010 TTGGATCAATACAATTTTAAATGTATTGACACGTTATTCTTGCACCTCGTTGGGCATTCATTATG
66 GTGGATCGATACAATTTTAAATGTATCGACACTTTATTCTTGCACCTCGTTGGGCATTCATTATG
* *
1338075 GATCAAATGTATCGACACAAATTACACAAGTGTCGATACTTTATTCTGACCTATTTTCTCATAAA
131 GA-AAAAAGTATCGACACAAATTA-A-AAGTGTCGATACTTTATT-TGACCTATTTTCTCATAAA
1338140 ACCGG
192 ACCGG
* * * *
1338145 TAAATTTAAACCGGTTACATTGTAAATTGACCTATTACATTATAATTATCGGTTTCGATATTTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATATTTTT
* * * * * * *
1338210 GT-GATCGATACAATTTTAAATGTATCGACACTTTATGCGTGAACAT-GTTTGTGCTTTC-TTTT
66 GTGGATCGATACAATTTTAAATGTATCGACACTTTATTCTTGCACCTCG-TTGGGCATTCATTAT
* * * * * *
1338272 GGAAAAAAGTATCGCCACAAACTTAAAAAGTGTCGATACTTTATGTTGACATGTTTTATAAT-TA
130 GGAAAAAAGTATCGACACAAA-TT-AAAAGTGTCGATACTTTAT-TTGACCTATTTTCTCATAAA
1338336 ACCGG
192 ACCGG
* * * ** * * *
1338341 TATATGTATACTGGTTACATTGTTAATTTAAATATTACATTATAAATATTTGTTTCGATGTTTTT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATATTTTT
* * *
1338406 G-GGGTCGATAC-TTTTTGAAAATGTATCGACAC-ATATTCTT
66 GTGGATCGATACAATTTT--AAATGTATCGACACTTTATTCTT
1338446 ACATATGTAT
Statistics
Matches: 426, Mismatches: 60, Indels: 37
0.81 0.11 0.07
Matches are distributed among these distances:
195 4 0.01
196 73 0.17
197 60 0.14
198 17 0.04
199 141 0.33
200 17 0.04
201 1 0.00
202 3 0.01
204 15 0.04
205 93 0.22
206 2 0.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (196 bp):
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATATTTTT
GTGGATCGATACAATTTTAAATGTATCGACACTTTATTCTTGCACCTCGTTGGGCATTCATTATG
GAAAAAAGTATCGACACAAATTAAAAGTGTCGATACTTTATTTGACCTATTTTCTCATAAAACCG
G
Found at i:1340236 original size:199 final size:199
Alignment explanation
Indices: 1339843--1340699 Score: 1188
Period size: 199 Copynumber: 4.3 Consensus size: 199
1339833 AGACATTTGG
* * *
1339843 TTATAATTAT-GTTTTTCGTTGTTTTTGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTT
1 TTATAATTATAG-TTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT-TT
* * * *
1339907 A-TGCACTTGGTTTTTTAAAATATAGTCTGGACAAAAATGTATCGAAACTTGATGTATTTGTGTC
64 AGTGCACTTGG--TTTTAAAATACAGTCTGGACAAAAA-GTATCGACACTTGTTATATTTGTGTC
** * * * * *
1339971 GATACTTCATGTATACCTGTTTTCTCATAAACCGGTACATTTAGACCGGTTACATTGTTAATTTA
126 GATACTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGATAATTTA
1340036 CCTATTACA
191 CCTATTACA
*
1340045 TTATAATTATAGTTTTCGATATTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
1 TTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
* * *
1340110 TGCACTTGGTTTTGAAATACATTCTGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
66 TGCACTTGGTTTTAAAATACAGTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
* * *
1340175 TTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGTTTACA-TGAATAATTTACCTA
131 TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTG-ATAATTTACCTA
1340239 TTACA
195 TTACA
* * * * *
1340244 TTAAAATTATATTTTTCGATGTTTTCGGAATCGACACTTGTTTTAAATGTATCGACAC-TTTTAT
1 TTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA-
* * * *
1340308 GTGCACTTGGTTCTAAAATACATTCTGGACCAAAAGTATCGACACTTGTTCTATTTGTGTCGATA
65 GTGCACTTGGTTTTAAAATACAGTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATA
* * * *
1340373 CTATTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTATATTGCTAATTTACCTA
130 CTTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGATAATTTACCTA
1340438 TTACA
195 TTACA
*
1340443 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTAT--ATGTATCGACACTTTTTAG
1 TTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
* * *
1340506 TGCACTTGGTTTTGAAATACAGTCTGGAGAAAAAGTATCGACACTTGTTAGATTTGTGTCGATAC
66 TGCACTTGGTTTTAAAATACAGTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
* ** *
1340571 TTTTTGTACACATGTTTTCTCAAAAACCAGTATATTTAGACCTTTTACA-TGAATAATTTACCTC
131 TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTG-ATAATTTACCTA
1340635 TTACA
195 TTACA
* * *
1340640 TTATAATTATATTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTT
1 TTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTT
1340700 GTTTTATTTG
Statistics
Matches: 586, Mismatches: 60, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
196 2 0.00
197 169 0.29
198 12 0.02
199 312 0.53
200 23 0.04
201 3 0.01
202 64 0.11
203 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (199 bp):
TTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
TGCACTTGGTTTTAAAATACAGTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGATAC
TTTTTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGGTTACATTGATAATTTACCTAT
TACA
Found at i:1340595 original size:396 final size:399
Alignment explanation
Indices: 1339847--1340699 Score: 1338
Period size: 396 Copynumber: 2.1 Consensus size: 399
1339837 ATTTGGTTAT
* * * * * *
1339847 AATTATGTTTTTCGTTGTTTTTGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTTATGCA
1 AATTATATTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTATGCA
* * *
1339912 CTTGGTTTTTTAAAATATAGTCTGGACAAAAATGTATCGAAACTTGATGTATTTGTGTCGATACT
66 CTTGG-TTTCTAAAATACAGTCTGGACAAAAATGTATCGAAACTTGATCTATTTGTGTCGATACT
* * * *
1339977 TCATGTATACCTGTTTTCTCATAAACCGGTACATTTAGACCGGTTACATTGTTAATTTACCTATT
130 TCATGTACACATGTTTTCTCAAAAACCGGTACATTTAGACCGGTTACATTGCTAATTTACCTATT
1340042 ACATTATAATTATAGTTTTCGATATTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTT
195 ACATTATAATTATAGTTTTCGATATTTTTGGGATCGACACTTGTTAT-AATGTATCGACACTTTT
* *
1340107 TAGTGCACTTGGTTTTGAAATACATTCTGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGA
259 TAGTGCACTTGGTTTTGAAATACAGTCTGGAGAAAAAGTATCGACACTTGTTAGATTTGTGTCGA
* **
1340172 TACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGTTTACATGAATAATTTACC
324 TACTTTTTGTACACATGTTTTCTCAAAAACCAGTATATTTAGACCGTTTACATGAATAATTTACC
1340237 TATTACATTAA
389 TATTACATTAA
* *
1340248 AATTATATTTTTCGATGTTTTCGGAATCGACACTTGTTTTAAATGTATCGACACTTT-TATGTGC
1 AATTATATTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGT-TATGC
* * * *
1340312 ACTTGG-TTCTAAAATACATTCTGGACCAAAA-GTATCGACACTTGTTCTATTTGTGTCGATACT
65 ACTTGGTTTCTAAAATACAGTCTGGACAAAAATGTATCGAAACTTGATCTATTTGTGTCGATACT
* * * *
1340375 AT-TTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTATATTGCTAATTTACCTAT
130 -TCATGTACACATGTTTTCTCAAAAACCGGTACATTTAGACCGGTTACATTGCTAATTTACCTAT
* *
1340439 TACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTAT-ATGTATCGACACTTTT
194 TACATTATAATTATAGTTTTCGATATTTTTGGGATCGACACTTGTTATAATGTATCGACACTTTT
1340503 TAGTGCACTTGGTTTTGAAATACAGTCTGGAGAAAAAGTATCGACACTTGTTAGATTTGTGTCGA
259 TAGTGCACTTGGTTTTGAAATACAGTCTGGAGAAAAAGTATCGACACTTGTTAGATTTGTGTCGA
*
1340568 TACTTTTTGTACACATGTTTTCTCAAAAACCAGTATATTTAGACCTTTTACATGAATAATTTACC
324 TACTTTTTGTACACATGTTTTCTCAAAAACCAGTATATTTAGACCGTTTACATGAATAATTTACC
* *
1340633 TCTTACATTAT
389 TATTACATTAA
1340644 AATTATATTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTT
1 AATTATATTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTT
1340700 GTTTTATTTG
Statistics
Matches: 416, Mismatches: 34, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
396 204 0.49
398 129 0.31
399 22 0.05
400 1 0.00
401 60 0.14
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (399 bp):
AATTATATTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTTGTTATGCA
CTTGGTTTCTAAAATACAGTCTGGACAAAAATGTATCGAAACTTGATCTATTTGTGTCGATACTT
CATGTACACATGTTTTCTCAAAAACCGGTACATTTAGACCGGTTACATTGCTAATTTACCTATTA
CATTATAATTATAGTTTTCGATATTTTTGGGATCGACACTTGTTATAATGTATCGACACTTTTTA
GTGCACTTGGTTTTGAAATACAGTCTGGAGAAAAAGTATCGACACTTGTTAGATTTGTGTCGATA
CTTTTTGTACACATGTTTTCTCAAAAACCAGTATATTTAGACCGTTTACATGAATAATTTACCTA
TTACATTAA
Found at i:1341058 original size:28 final size:28
Alignment explanation
Indices: 1341023--1341091 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
1341013 TAATTTTACT
*
1341023 AACAAGAAACTAATTTTTTTTTATAAGG
1 AACAAGAAACTAATTTTTTTTGATAAGG
1341051 AACAAGAAACTAATTTTTTTTGATAAGG
1 AACAAGAAACTAATTTTTTTTGATAAGG
1341079 AACAAGAAACTAA
1 AACAAGAAACTAA
1341092 ATGAGCATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.32
Consensus pattern (28 bp):
AACAAGAAACTAATTTTTTTTGATAAGG
Found at i:1343076 original size:15 final size:15
Alignment explanation
Indices: 1343052--1343093 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1343042 AGGAGGTTGT
1343052 GGTTGAGAAGAGCTG
1 GGTTGAGAAGAGCTG
* *
1343067 GGTTGGGAAGAGGTG
1 GGTTGAGAAGAGCTG
1343082 GGTTGAGAAGAG
1 GGTTGAGAAGAG
1343094 ATTTGAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.52, T:0.19
Consensus pattern (15 bp):
GGTTGAGAAGAGCTG
Found at i:1343743 original size:182 final size:182
Alignment explanation
Indices: 1343531--1343985 Score: 716
Period size: 182 Copynumber: 2.5 Consensus size: 182
1343521 TCTATTTACT
* * *
1343531 GGTTTTGTCA-TTTTGAGAGCGGTTTTATCATATTTTTACCTGTTATATTGTTCTGGATCGATAC
1 GGTTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * *
1343595 ATTTTCATAAAGTGTCGACACTTTTTAAGCGCTATATCTTCTTCTCTTTTAAATTCATAAAGAGT
66 ATTTTCATAAAGTGTCGACACTTTTTAAGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGAGT
* *
1343660 CGATACTT-ATATTAAATTATCGACACTTTCAACATATCCGGTAATTTTTTCC
131 CGATA-TTAATATTAAATTATCGACACTTTCAACATATCCGGTAACTTTGTCC
* * * **
1343712 GGTTTTGTCATTTTTTAGATCAGTTTTATCATATTTTTACCTGTTATATTGGTAACGATCGATAC
1 GGTTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* *
1343777 ATTTTAATAAAGTGTCGACACTTTTTAAGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGT
66 ATTTTCATAAAGTGTCGACACTTTTTAAGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGAGT
* * *
1343842 CGATATTAATATTAAATTATCGACACTTTCAATATATTCGGTAACTTTGTCT
131 CGATATTAATATTAAATTATCGACACTTTCAACATATCCGGTAACTTTGTCC
1343894 GGTTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 GGTTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
*
1343959 ATTTTCATAAAATGTCGACACTTTTTA
66 ATTTTCATAAAGTGTCGACACTTTTTA
1343986 GTTTAATTTC
Statistics
Matches: 248, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 12 0.05
182 236 0.95
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (182 bp):
GGTTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
ATTTTCATAAAGTGTCGACACTTTTTAAGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGAGT
CGATATTAATATTAAATTATCGACACTTTCAACATATCCGGTAACTTTGTCC
Found at i:1344142 original size:163 final size:163
Alignment explanation
Indices: 1343824--1344145 Score: 427
Period size: 163 Copynumber: 2.0 Consensus size: 163
1343814 CTTATTCTCT
*
1343824 TTTAAATTCAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAATATATTCGGTAACTT
1 TTTAAATTCAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAACATATTCGGTAACTT
* * *
1343889 TGTCTGGTTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATGGATC
66 TGTCTGGTTTTGTCAATTTTGAGACCAGTTTTATCATATTTTTACATGTTATATTGTTATGAATC
* *
1343954 GATACATTTTCATAAAATGTCGACACTTTTTAG
131 AATACATTTTCATAAAATATCGACACTTTTTAG
* *
1343987 TTTAATTTCAGAAAGTGTCGATACTT-ATATTAAATTATCGACACTTTCAACATA-TCTGGTATC
1 TTTAAATTCAGAAAGTGTCGATA-TTAATATTAAATTATCGACACTTTCAACATATTC-GGTAAC
* * * * *
1344050 GTTT-TACTGGTTTTGTTAATTTTGGGACCTGTTTTATCATATTTTTACATTTTATATTGTTGTG
64 -TTTGT-CTGGTTTTGTCAATTTTGAGACCAGTTTTATCATATTTTTACATGTTATATTGTTATG
* ** *
1344114 AATCAATA-TTTTTTTTAAAGTATCGACACTTT
127 AATCAATACATTTTCATAAAATATCGACACTTT
1344146 ATAGGCGCTA
Statistics
Matches: 138, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
162 2 0.01
163 74 0.54
164 62 0.45
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (163 bp):
TTTAAATTCAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAACATATTCGGTAACTT
TGTCTGGTTTTGTCAATTTTGAGACCAGTTTTATCATATTTTTACATGTTATATTGTTATGAATC
AATACATTTTCATAAAATATCGACACTTTTTAG
Found at i:1344495 original size:182 final size:181
Alignment explanation
Indices: 1343987--1344853 Score: 1057
Period size: 182 Copynumber: 4.8 Consensus size: 181
1343977 CACTTTTTAG
* * * *
1343987 TTTAATTTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCTGGTATCGT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACTT
* * * * * *
1344052 TTTACTGGTTTTGTTAATTTTGGGACCTGTTTTATCATATTTTTACATTTTATATTGTTGTGAAT
66 TTTTC-GGTTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGTTATGGAT
* * ** *
1344117 CAATA-TTTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
130 CGATACATTTTCATAAAGTATCGACACTTTATAAGCGCTATAACTT-TTCTCT
* * **
1344169 TTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACACTTTCAATATATCCGGTAGTTT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTA-ACT
* *
1344234 TTTTTACTGGTTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATAGTTATGG
65 TTTTT-C-GGTTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGTTATGG
* * * *
1344299 ATCGATACATTTTCATAAAGTGTCGATACTTTTTAAGCGCAATAACTTTTTCTCT
128 ATCGATACATTTTCATAAAGTATCGACACTTTATAAGCGCTATAAC-TTTTCTCT
* *
1344354 TTTAAATTCAGAAAGTGTCGATATTTATATTAAATTATCGACACTTTTAACATATCCGGTAACTT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACTT
* * * *
1344419 TTTTCGATTTTGTCATTTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGGTAAGGATC
66 TTTTCGGTTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGTTATGGATC
* * *
1344484 GATACATTTTCATAAAGTGTCGACACTTT-TTAGATGCTATAACTTATTCTCT
131 GATACATTTTCATAAAGTATCGACACTTTATAAG-CGCTATAACTT-TTCTCT
* *
1344536 TTTAAATTCAGAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAATATATCCGGTAACTT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACTT
* * * *
1344601 TTTCCGGTTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACATGTTATATTGTTGTGGATC
66 TTTTCGGTTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGTTATGGATC
** * * *
1344666 GATGTATTTT-TTAAAGTATCGACACTTTATAGGCGCTATAAC--CTCTCT
131 GATACATTTTCATAAAGTATCGACACTTTATAAGCGCTATAACTTTTCTCT
* * *
1344714 TTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACAC--TCGACACATATCTGGTAGC
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTC-A-ACATATCCGGTAAC
* * * * * * **
1344777 GTTTTATCGGTTTTGTC-ATTTTGGGACCGGTTTTGTCATATTTGTACATGTAATATTACTATGG
64 -TTTTTTCGGTTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGTTATGG
* *
1344841 AGCGATCCATTTT
128 ATCGATACATTTT
1344854 TCATTTGTAT
Statistics
Matches: 599, Mismatches: 76, Indels: 24
0.86 0.11 0.03
Matches are distributed among these distances:
176 2 0.00
177 1 0.00
178 106 0.18
179 14 0.02
181 29 0.05
182 282 0.47
183 6 0.01
184 64 0.11
185 93 0.16
186 2 0.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (181 bp):
TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACTT
TTTTCGGTTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGTTATGGATC
GATACATTTTCATAAAGTATCGACACTTTATAAGCGCTATAACTTTTCTCT
Found at i:1344507 original size:530 final size:533
Alignment explanation
Indices: 1343506--1344819 Score: 1735
Period size: 530 Copynumber: 2.5 Consensus size: 533
1343496 TAATTCTGGA
* * *
1343506 TCAACATAT-TCGGTATCTATTTACTGGTTTTG-TCATTTTGAGAGCGGTTTTATCATATTTTTA
1 TCAACATATCT-GGTATCT-TTTACTGGTTTTGTTAATTTTGAGACCAGTTTTATCATATTTTTA
* * * ** * * * *
1343569 CCTGTTATATTGTTCTGGATCGATACATTTTCATAAAGTGTCGACACTTTTTAAGCGCTATATCT
64 CATGTTATATTGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACT
* **
1343634 TCTTCTCTTTTAAATTCATAAAGAGTCGATACTTATATTAAATTATCGACACTTTCAACATATCC
128 TCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACACTTTCAACATATCC
* * * *
1343699 GGTAATTTTTTCCGGTTTTGTCATTTTTTAGATCAGTTTTATCATATTTTTACCTGTTATATTGG
193 GGTAATTTTTTCCGGTTTTGTCAATTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATAGG
*
1343764 TAACGATCGATACATTTTAATAAAGTGTCGACACTTTTTAAGCGCTATAACTTATTCTCTTTTAA
258 TAACGATCGATACATTTTAATAAAGTGTCGACACTTTTTAAGCGCAATAACTTATTCTCTTTTAA
* *
1343829 ATTCAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAATATATTCGGTAACTTTGTCT
323 ATTCAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAACATATCCGGTAACTTTGTCT
* * * *
1343894 GGTTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
388 GATTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACATGTTATATTGGTAAGGATCGATAC
*
1343959 ATTTTCATAAAATGTCGACACTTTTTAG-T-T-T-A-A-T-TTCAGAAAGTGTCGATACTTATAT
453 ATTTTCATAAAATGTCGACACTTTTTAGATCTATAATATTATTCAGAAAGTGTCGATACTAATAT
1344017 TAAATTATCGACACTT
518 TAAATTATCGACACTT
* *
1344033 TCAACATATCTGGTATCGTTTTACTGGTTTTGTTAATTTTGGGACCTGTTTTATCATATTTTTAC
1 TCAACATATCTGGTATC-TTTTACTGGTTTTGTTAATTTTGAGACCAGTTTTATCATATTTTTAC
* * *
1344098 ATTTTATATTGTTGTGAATCAATATTTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTC
65 ATGTTATATTGTTGTGGATCGATATTTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTC
*
1344163 TTCTCTTTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACACTTTCAATATATCCGG
130 TTCTCTTTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGG
* * *
1344228 TAGTTTTTTTTACTGGTTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATAG
195 TA--ATTTTTT-CCGGTTTTGTCAATTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATAG
* ** * * *
1344293 TTATGGATCGATACATTTTCATAAAGTGTCGATACTTTTTAAGCGCAATAACTTTTTCTCTTTTA
257 GTAACGATCGATACATTTTAATAAAGTGTCGACACTTTTTAAGCGCAATAACTTATTCTCTTTTA
* * *
1344358 AATTCAGAAAGTGTCGATATTTATATTAAATTATCGACACTTTTAACATATCCGGTAACTTT-TT
322 AATTCAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAACATATCCGGTAACTTTGTC
*
1344422 TCGATTTTGTCATTTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGGTAAGGATCGAT
387 T-GATTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACATGTTATATTGGTAAGGATCGAT
*
1344487 ACATTTTCATAAAGTGTCGACACTTTTTAGATGCTATAACTTATTCTCTTTTAAATTCAGAAAGT
451 ACATTTTCATAAAATGTCGACACTTTTTAGAT-CTATAA--TA-------TT--ATTCAGAAAGT
1344552 GTCGATACTAATATTAAATTATCGACACTT
504 GTCGATACTAATATTAAATTATCGACACTT
* * * * * * *
1344582 TCAATATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACA
1 TCAACATATCTGGTATCTTTTACTGGTTTTGTTAATTTTGAGACCAGTTTTATCATATTTTTACA
* *
1344647 TGTTATATTGTTGTGGATCGATGTATTTTTTAAAGTATCGACACTTTATAGGCGCTATAAC--C-
66 TGTTATATTGTTGTGGATCGATATTTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCT
*
1344709 TCTCTTTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACAC--TCGACACATATCTG
131 TCTCTTTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACACTTTC-A-ACATATCCG
* * * * *
1344772 GTAGCGTTTTAT-CGGTTTTGTC-ATTTTGGGACCGGTTTTGTCATATTT
194 GTA--ATTTTTTCCGGTTTTGTCAATTTTGAGACCAGTTTTATCATATTT
1344820 GTACATGTAA
Statistics
Matches: 690, Mismatches: 69, Indels: 41
0.86 0.09 0.05
Matches are distributed among these distances:
527 125 0.18
528 49 0.07
529 8 0.01
530 250 0.36
531 1 0.00
533 1 0.00
534 1 0.00
535 1 0.00
538 1 0.00
542 23 0.03
543 11 0.02
544 1 0.00
545 65 0.09
546 2 0.00
548 98 0.14
549 53 0.08
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (533 bp):
TCAACATATCTGGTATCTTTTACTGGTTTTGTTAATTTTGAGACCAGTTTTATCATATTTTTACA
TGTTATATTGTTGTGGATCGATATTTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCT
TCTCTTTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGT
AATTTTTTCCGGTTTTGTCAATTTTGAGACCAGTTTTATCATATTTTTACCTGTTATATAGGTAA
CGATCGATACATTTTAATAAAGTGTCGACACTTTTTAAGCGCAATAACTTATTCTCTTTTAAATT
CAGAAAGTGTCGATATTAATATTAAATTATCGACACTTTCAACATATCCGGTAACTTTGTCTGAT
TTTGTCATTTTTGAGACCAGTTTTATCATATTTTTACATGTTATATTGGTAAGGATCGATACATT
TTCATAAAATGTCGACACTTTTTAGATCTATAATATTATTCAGAAAGTGTCGATACTAATATTAA
ATTATCGACACTT
Found at i:1344764 original size:367 final size:364
Alignment explanation
Indices: 1343987--1344833 Score: 1091
Period size: 367 Copynumber: 2.3 Consensus size: 364
1343977 CACTTTTTAG
* * *
1343987 TTTAATTTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCTGGTATCGT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
* * * * * **
1344052 TTTACTGGTTTTGTTAATTTTGGGACCTGTTTTATCATATTTTTACATTTTATATTGTTGTGAAT
66 TTTACTGATTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGGTAAGAAT
* ** * *
1344117 CAATATTTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAA
131 CAATAATTTTCATAAAGTATCGACACTTTATAGACGCTATAACTTATTCTCTTTTAAATTCAGAA
* * ** *
1344182 AGTTTCGATACTTATATTAAATTATCGACACTTTCAATATATCCGGTAGTTTTTTTTACTGGTTT
196 AGTGTCGATACTAATATTAAATTATCGACACTTTCAATATATCCGGTAG-ACTTTTTACCGGTTT
* *
1344247 TGTCAATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATAGTTATGGATCGATACATTTT
260 TGTCAATTTTGAGACCAGTTTTATCATATTTTTACATGTTATATAGTTATGGATCGATACATTTT
* * * *
1344312 CATAAAGTGTCGATACTTTTTAAGCGCAATAACTTTTTCTCT
325 CATAAAGTATCGACACTTTATAAGCGCAATAAC--TCTCTCT
* * *
1344354 TTTAAATTCAGAAAGTGTCGATATTTATATTAAATTATCGACACTTTTAACATATCCGGTAACTT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
* * *
1344419 TTTTC-GATTTTGTCATTTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGGTAAGGAT
66 TTTACTGATTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGGTAAGAAT
* * * *
1344483 CGATACATTTTCATAAAGTGTCGACACTTTTTAGATGCTATAACTTATTCTCTTTTAAATTCAGA
131 CAATA-ATTTTCATAAAGTATCGACACTTTATAGACGCTATAACTTATTCTCTTTTAAATTCAGA
1344548 AAGTGTCGATACTAATATTAAATTATCGACACTTTCAATATATCCGGTA-ACTTTTT-CCGGTTT
195 AAGTGTCGATACTAATATTAAATTATCGACACTTTCAATATATCCGGTAGACTTTTTACCGGTTT
* * * **
1344611 TGTCATTTTTGAGACCAGTTTTATCATATTTTTACATGTTATATTGTTGTGGATCGATGTATTTT
260 TGTCAATTTTGAGACCAGTTTTATCATATTTTTACATGTTATATAGTTATGGATCGATACATTTT
* * *
1344676 -TTAAAGTATCGACACTTTATAGGCGCTATAAC-CTCTCT
325 CATAAAGTATCGACACTTTATAAGCGCAATAACTCTCTCT
* * *
1344714 TTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACAC--TCGACACATATCTGGTAGC
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTC-A-ACATATCCGGTAAC
* * * * * *
1344777 GTTTTA-TCGGTTTTGTC-ATTTTGGGACCGGTTTTGTCATATTTGTACATGTAATATT
64 GTTTTACT-GATTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATT
1344834 ACTATGGAGC
Statistics
Matches: 417, Mismatches: 58, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
358 1 0.00
359 1 0.00
360 97 0.23
361 8 0.02
363 26 0.06
364 64 0.15
365 5 0.01
366 54 0.13
367 161 0.39
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (364 bp):
TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
TTTACTGATTTTGTCAATTTTGAGACCTGTTTTATCATATTTTTACATGTTATATTGGTAAGAAT
CAATAATTTTCATAAAGTATCGACACTTTATAGACGCTATAACTTATTCTCTTTTAAATTCAGAA
AGTGTCGATACTAATATTAAATTATCGACACTTTCAATATATCCGGTAGACTTTTTACCGGTTTT
GTCAATTTTGAGACCAGTTTTATCATATTTTTACATGTTATATAGTTATGGATCGATACATTTTC
ATAAAGTATCGACACTTTATAAGCGCAATAACTCTCTCT
Found at i:1364144 original size:13 final size:13
Alignment explanation
Indices: 1364089--1364153 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
1364079 TATATTTTAA
1364089 TTATTTATTATAT
1 TTATTTATTATAT
* *
1364102 TTAATAATTA-A-
1 TTATTTATTATAT
1364113 -TA-TTATTA-A-
1 TTATTTATTATAT
1364122 TTA-TTATTATAT
1 TTATTTATTATAT
1364134 TTATTTATTATAT
1 TTATTTATTATAT
*
1364147 TCATTTA
1 TTATTTA
1364154 ATTTTTATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
9 6 0.14
10 10 0.23
11 1 0.02
12 4 0.09
13 23 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTTATTATAT
Found at i:1364144 original size:16 final size:16
Alignment explanation
Indices: 1364058--1364144 Score: 79
Period size: 16 Copynumber: 5.3 Consensus size: 16
1364048 ACCTATTTTA
*
1364058 ATTACTATATTT-ATAT
1 ATTATTATATTTAAT-T
*
1364074 ATTACTATATTTTAATT
1 ATTATTATA-TTTAATT
*
1364091 ATTTATTATATTTAATA
1 A-TTATTATATTTAATT
*
1364108 ATTAATAT-TATTAATT
1 ATTATTATAT-TTAATT
*
1364124 ATTATTATATTTATTT
1 ATTATTATATTTAATT
1364140 ATTAT
1 ATTAT
1364145 ATTCATTTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
15 1 0.02
16 37 0.62
17 13 0.22
18 9 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATTATATTTAATT
Found at i:1365042 original size:16 final size:16
Alignment explanation
Indices: 1365000--1365045 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1364990 AGAATTGGGA
* *
1365000 TGAGATTTGAAAGAGT
1 TGAGAGTTGAGAGAGT
1365016 TGAGAGTTGAGAGAGCT
1 TGAGAGTTGAGAGAG-T
1365033 TGA-AGTTGAGAGA
1 TGAGAGTTGAGAGA
1365046 ATAAAAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 23 0.85
17 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.37, T:0.26
Consensus pattern (16 bp):
TGAGAGTTGAGAGAGT
Found at i:1367456 original size:29 final size:29
Alignment explanation
Indices: 1367421--1367502 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1367411 AAACTAAATT
*
1367421 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1367450 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1367479 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1367503 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1372224 original size:29 final size:29
Alignment explanation
Indices: 1372189--1372270 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1372179 AAACTAAATT
*
1372189 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1372218 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1372247 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1372271 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1375495 original size:178 final size:178
Alignment explanation
Indices: 1375196--1375555 Score: 632
Period size: 178 Copynumber: 2.0 Consensus size: 178
1375186 CGTGCTCCTA
1375196 AACTATCATAGAATACTTATGCACTTTTAATTCCTATTTTTATAACAAATTTTATATTTTTCAAT
1 AACTATCATAGAATACTTATGCACTTTTAATTCCTATTTTTATAACAAATTTTATATTTTTCAAT
* * *
1375261 TTAGTCCCTCAACTTTGCATGATTTTCTTATTTCTTTAATTCGTCCTTCATTTTATGTCTGTTTT
66 TTAGTCCCTCAACTTTGCATGATTTTCTTATTTCTCTAATTCATCCTTCATTTTATGTATGTTTT
* *
1375326 TAATCAAATTTGAACTACATGATCCCCTTAACTATAGAATACCCATGT
131 TAATCAAATTTGAACTACATGATCCCCTTAACTAGAGAATACCCAGGT
* *
1375374 AACTATCATAGAATACTTATGTACTTTTAATT-CTCATTTTTATTACAAATTTTATATTTTTCAA
1 AACTATCATAGAATACTTATGCACTTTTAATTCCT-ATTTTTATAACAAATTTTATATTTTTCAA
*
1375438 TTTAGTCCCTCAACTTTTCATGATTTTCTTATTTCTCTAATTCATCCTTCATTTTATGTATGTTT
65 TTTAGTCCCTCAACTTTGCATGATTTTCTTATTTCTCTAATTCATCCTTCATTTTATGTATGTTT
1375503 TTAATCAAATTTGAACTACATGATCCCCTTAACTAGAGAATACCCAGGT
130 TTAATCAAATTTGAACTACATGATCCCCTTAACTAGAGAATACCCAGGT
1375552 AACT
1 AACT
1375556 TTAAGTTCTA
Statistics
Matches: 173, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
177 2 0.01
178 171 0.99
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (178 bp):
AACTATCATAGAATACTTATGCACTTTTAATTCCTATTTTTATAACAAATTTTATATTTTTCAAT
TTAGTCCCTCAACTTTGCATGATTTTCTTATTTCTCTAATTCATCCTTCATTTTATGTATGTTTT
TAATCAAATTTGAACTACATGATCCCCTTAACTAGAGAATACCCAGGT
Found at i:1377565 original size:23 final size:23
Alignment explanation
Indices: 1377535--1377578 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1377525 TCTTCATTTC
1377535 TTGGATATCTAGGCGTCTTCATG
1 TTGGATATCTAGGCGTCTTCATG
1377558 TTGGATATCTAGGCGTCTTCA
1 TTGGATATCTAGGCGTCTTCA
1377579 ATGCAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (23 bp):
TTGGATATCTAGGCGTCTTCATG
Found at i:1379864 original size:24 final size:24
Alignment explanation
Indices: 1379837--1379884 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1379827 TTTTTACTAC
1379837 TAAATAATTATTAGTAATAATTAT
1 TAAATAATTATTAGTAATAATTAT
* * * *
1379861 TAAATCATTGTTTGTAATTATTAT
1 TAAATAATTATTAGTAATAATTAT
1379885 AATTTCATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (24 bp):
TAAATAATTATTAGTAATAATTAT
Found at i:1380148 original size:23 final size:23
Alignment explanation
Indices: 1380118--1380162 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1380108 AACATAGCAA
1380118 ATGAAGACGCCTAGATATCCAAC
1 ATGAAGACGCCTAGATATCCAAC
*
1380141 ATGAAGACTCCTAGATATCCAA
1 ATGAAGACGCCTAGATATCCAA
1380163 GAAATGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (23 bp):
ATGAAGACGCCTAGATATCCAAC
Found at i:1380662 original size:24 final size:25
Alignment explanation
Indices: 1380628--1380674 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
1380618 AAGTTTCAAT
1380628 GTCATTTAGTTTAGA-ATTAAATAAA
1 GTCATTTAGTTTA-ATATTAAATAAA
1380653 GTCA-TTAGTTTAATATTAAATA
1 GTCATTTAGTTTAATATTAAATA
1380675 GTGCATAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 1 0.05
24 16 0.76
25 4 0.19
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (25 bp):
GTCATTTAGTTTAATATTAAATAAA
Found at i:1385941 original size:231 final size:231
Alignment explanation
Indices: 1385538--1385989 Score: 886
Period size: 231 Copynumber: 2.0 Consensus size: 231
1385528 AAGATAATAT
1385538 ATTCATGAGTTTAAAATAAAGTTATGGCTAGAGTATAAAACAAGGATATATAAATAATACATGAC
1 ATTCATGAGTTTAAAATAAAGTTATGGCTAGAGTATAAAACAAGGATATATAAATAATACATGAC
1385603 ATTTAAAAGAAAACTCAAGACGTAATCTGCTACTCTGGATGTCTGAAATATCCTTAGCTACGATA
66 ATTTAAAAGAAAACTCAAGACGTAATCTGCTACTCTGGATGTCTGAAATATCCTTAGCTACGATA
1385668 TGCTTCCCGATTGCTTCTCCTAACGACTTGCACACGGAAACAAATTTCAAACGTTGAGCTTATTA
131 TGCTTCCCGATTGCTTCTCCTAACGACTTGCACACGGAAACAAATTTCAAACGTTGAGCTTATTA
1385733 GTTTAGTGCCACACTAACAATAAAACAAGGATATAC
196 GTTTAGTGCCACACTAACAATAAAACAAGGATATAC
1385769 ATTCATGAGTTTAAAATAAAGTTATGGCTAGAGTATAAAACAAGGATATATAAATAATACATGAC
1 ATTCATGAGTTTAAAATAAAGTTATGGCTAGAGTATAAAACAAGGATATATAAATAATACATGAC
*
1385834 ATTTAAAAGAAAACTCAAGACGTAATCTGCTACTCTGGATGTCTGAAATGTCCTTAGCTACGATA
66 ATTTAAAAGAAAACTCAAGACGTAATCTGCTACTCTGGATGTCTGAAATATCCTTAGCTACGATA
*
1385899 TGCTTCCCGATTGCTTCTCCTAACGACTTGCACACGGAAACAAATTTCGAACGTTGAGCTTATTA
131 TGCTTCCCGATTGCTTCTCCTAACGACTTGCACACGGAAACAAATTTCAAACGTTGAGCTTATTA
1385964 GTTTAGTGCCACACTAACAATAAAAC
196 GTTTAGTGCCACACTAACAATAAAAC
1385990 CATACTAAAA
Statistics
Matches: 219, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
231 219 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (231 bp):
ATTCATGAGTTTAAAATAAAGTTATGGCTAGAGTATAAAACAAGGATATATAAATAATACATGAC
ATTTAAAAGAAAACTCAAGACGTAATCTGCTACTCTGGATGTCTGAAATATCCTTAGCTACGATA
TGCTTCCCGATTGCTTCTCCTAACGACTTGCACACGGAAACAAATTTCAAACGTTGAGCTTATTA
GTTTAGTGCCACACTAACAATAAAACAAGGATATAC
Found at i:1389548 original size:23 final size:23
Alignment explanation
Indices: 1389522--1389580 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1389512 CTGGTAGACC
*
1389522 CATGAAAGTGACATTGTCATGTG
1 CATGAAAGAGACATTGTCATGTG
* *
1389545 CATGGATGAGACATTGTCATGTG
1 CATGAAAGAGACATTGTCATGTG
*
1389568 CATGAATGAGACA
1 CATGAAAGAGACA
1389581 CTATTATCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (23 bp):
CATGAAAGAGACATTGTCATGTG
Found at i:1395053 original size:16 final size:17
Alignment explanation
Indices: 1395032--1395072 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
1395022 ATCAACTGCA
1395032 AAGGAGACATGGCATT-
1 AAGGAGACATGGCATTC
1395048 AAGGAGACATGGCATTC
1 AAGGAGACATGGCATTC
1395065 AA-GAGACA
1 AAGGAGACA
1395073 GAAACATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (17 bp):
AAGGAGACATGGCATTC
Found at i:1397787 original size:17 final size:18
Alignment explanation
Indices: 1397767--1397804 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1397757 ATTCTCTCAT
*
1397767 CTTTTCTT-TTCTTCTTC
1 CTTTTCTTCATCTTCTTC
1397784 C-TTTCTTCATCTTCTTC
1 CTTTTCTTCATCTTCTTC
1397801 CTTT
1 CTTT
1397805 CAAGTGCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 6 0.33
17 10 0.56
18 2 0.11
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (18 bp):
CTTTTCTTCATCTTCTTC
Found at i:1403403 original size:3 final size:3
Alignment explanation
Indices: 1403388--1403418 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1403378 TGTCACATAC
*
1403388 ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1403419 AATAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:1403527 original size:16 final size:16
Alignment explanation
Indices: 1403502--1403538 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1403492 AACCCAATCC
*
1403502 AGGCCTAAATCCGAGA
1 AGGCCCAAATCCGAGA
1403518 AGGCCCAAATCCGAGA
1 AGGCCCAAATCCGAGA
1403534 AGGCC
1 AGGCC
1403539 TAATGCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.27, T:0.08
Consensus pattern (16 bp):
AGGCCCAAATCCGAGA
Found at i:1404412 original size:329 final size:329
Alignment explanation
Indices: 1403794--1404449 Score: 1152
Period size: 329 Copynumber: 2.0 Consensus size: 329
1403784 CGCACACGTC
* * * *
1403794 GTTGCCGTATGGCGAGTCAGCACCATAGCTTCGGTGACTCACCGAGGGCCACTTTTGTGATCGGT
1 GTTGCCCTATGGCGAGTCACCACCATAGCTTCGGTGACTCACCGAGGGCCACTTTTGTGACCAGT
* *
1403859 TTGAGAGCAACATCGATGAGGCCTATAAAAAGGCCATCCACCAGTCTTGAAAAAAAGGACATAGA
66 TTGAGAGCAACATCGATGAGGCCTATAAAAAGACCATCCACCAGTCTTGAAAAAAAGGACAGAGA
* *
1403924 GAGCCAAGCAACGCAACAATCAATGATAACCATTCGGAAATAAGCAAAAGAAAGTAGAAAAGGGC
131 GAGCCAAGCAACGCAACAATCAATGATAACCATTCGGAAATAAGCAAAAGAAAGAAGAAAAAGGC
*
1403989 TTACTAAGGTCGAAGGAGCTTCCACACATCATCAGAACTTTCGAATTTCGAAGGTAAAAACTTCA
196 TTACTAAGGTCGAAGGAGCTTCCACACATCATCAGAACTTTAGAATTTCGAAGGTAAAAACTTCA
*
1404054 GATCTAGCCTGATTGATTCATTTTTAGGACAAAGTGGGCTTAGATCTGAGTTTAGGGTAAATAGA
261 GATCTAGCCTGATTGATTCATTTTTAGGACAAAGTAGGCTTAGATCTGAGTTTAGGGTAAATAGA
1404119 GGTT
326 GGTT
* * * *
1404123 GTTGCCCTATGGTGAGTCACCACCATAGTTTCGGTGATTCACCGAGGGCCACTTTTGTGACCATT
1 GTTGCCCTATGGCGAGTCACCACCATAGCTTCGGTGACTCACCGAGGGCCACTTTTGTGACCAGT
*
1404188 TTGAGAGCAACATCGATGAGGCCTATAAAACGACCATCCACCAGTCTTGAAAAAAAGGACAGAGA
66 TTGAGAGCAACATCGATGAGGCCTATAAAAAGACCATCCACCAGTCTTGAAAAAAAGGACAGAGA
1404253 GAGCCAAGCAACGCAACAATCAATGATAACCATTCGGAAATAAGCAAAAGAAAGAAGAAAAAGGC
131 GAGCCAAGCAACGCAACAATCAATGATAACCATTCGGAAATAAGCAAAAGAAAGAAGAAAAAGGC
*
1404318 TTATTAAGGTCGAAGGAGCTTCCACACATCATCAGAACTTTTAG-ATTTCGAAGGTAAAAACTTC
196 TTACTAAGGTCGAAGGAGCTTCCACACATCATCAGAAC-TTTAGAATTTCGAAGGTAAAAACTTC
1404382 AGATCTAGCCTGATTGATTCATTTTTAGGACAAAGTAGGCTTAGATCTGAGTTTAGGGTAAATAG
260 AGATCTAGCCTGATTGATTCATTTTTAGGACAAAGTAGGCTTAGATCTGAGTTTAGGGTAAATAG
1404447 AGG
325 AGG
1404450 GTCGATTTGG
Statistics
Matches: 310, Mismatches: 16, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
329 306 0.99
330 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (329 bp):
GTTGCCCTATGGCGAGTCACCACCATAGCTTCGGTGACTCACCGAGGGCCACTTTTGTGACCAGT
TTGAGAGCAACATCGATGAGGCCTATAAAAAGACCATCCACCAGTCTTGAAAAAAAGGACAGAGA
GAGCCAAGCAACGCAACAATCAATGATAACCATTCGGAAATAAGCAAAAGAAAGAAGAAAAAGGC
TTACTAAGGTCGAAGGAGCTTCCACACATCATCAGAACTTTAGAATTTCGAAGGTAAAAACTTCA
GATCTAGCCTGATTGATTCATTTTTAGGACAAAGTAGGCTTAGATCTGAGTTTAGGGTAAATAGA
GGTT
Found at i:1405362 original size:11 final size:12
Alignment explanation
Indices: 1405324--1405365 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 12
1405314 ATATTTTAAA
1405324 TTTATTACTTTAAT
1 TTTATT-CTTT-AT
1405338 TATTATTCTTTAT
1 T-TTATTCTTTAT
1405351 TTTATT-TTTAT
1 TTTATTCTTTAT
1405362 TTTA
1 TTTA
1405366 ATTACATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.33
12 5 0.19
13 3 0.11
14 5 0.19
15 5 0.19
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATTCTTTAT
Found at i:1405671 original size:21 final size:21
Alignment explanation
Indices: 1405628--1405695 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
1405618 CTTTCCAATT
** *
1405628 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
1405648 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1405669 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
1405690 TCGCAA
1 TCGCAA
1405696 CGTGATACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 12 0.27
21 32 0.73
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:1405713 original size:41 final size:42
Alignment explanation
Indices: 1405668--1405823 Score: 137
Period size: 41 Copynumber: 3.8 Consensus size: 42
1405658 AATTTGGAAA
* ** *
1405668 ATCGCAATGCGAAT-TTGGAAAATCGCAACGTGATACTGACT
1 ATCGCAATGCGAATAATACAAAATCGCAACGCGATACTGACT
1405709 ATCGCAATGCG-ATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAATGCGAATAATACAAAATCGCAACGCGATACTGACT
* * * **
1405750 TTCGCAACGCG-ATACTTAC--TTTCGCAACGCGATACTGACT
1 ATCGCAATGCGAATA-ATACAAAATCGCAACGCGATACTGACT
* * *
1405790 TTCGCAA--CGAGATAATACATAATCGCAATGCGAT
1 ATCGCAATGCGA-ATAATACAAAATCGCAACGCGAT
1405824 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
38 2 0.02
39 3 0.03
40 31 0.32
41 57 0.59
42 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (42 bp):
ATCGCAATGCGAATAATACAAAATCGCAACGCGATACTGACT
Done.