Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008211.1 Hibiscus syriacus cultivar Beakdansim tig00110833_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: 2208279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:225219 original size:20 final size:20
Alignment explanation
Indices: 225194--225231 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
225184 ATTGAGAAAG
225194 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
225214 GATGCATCGATGCACTCA
1 GATGCACCGATGCACTCA
225232 CCATATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:225275 original size:18 final size:18
Alignment explanation
Indices: 225215--225282 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
225205 GCACTCATTG
225215 ATGCATCGATGCACTCACC
1 ATGCATCGATGCACT-ACC
***
225234 AT--ATCGAATGCA-TTTT
1 ATGCATCG-ATGCACTACC
*
225250 ATGTATCGATGCACTACC
1 ATGCATCGATGCACTACC
*
225268 ATGCATCGATACACT
1 ATGCATCGATGCACT
225283 CATGTTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 9
0.69 0.15 0.17
Matches are distributed among these distances:
16 2 0.05
17 10 0.27
18 23 0.62
19 2 0.05
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (18 bp):
ATGCATCGATGCACTACC
Found at i:233543 original size:20 final size:20
Alignment explanation
Indices: 233518--233555 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
233508 ATTGAGAAAG
233518 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
233538 GATGCATCGATGCACTCA
1 GATGCACCGATGCACTCA
233556 CTATATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:233630 original size:64 final size:63
Alignment explanation
Indices: 233560--233716 Score: 201
Period size: 64 Copynumber: 2.5 Consensus size: 63
233550 CACTCACTAT
* * *
233560 ATCGAATACATTTTATGCATCGATGCACTTCCATGCATTGATACACTCAGG-TT-TTATGAAAAA
1 ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATACACTCAGGCTTGTT-TG--AAA
233623 C
63 C
* * *
233624 ATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTTAGGCTTGTTTGAAAC
1 ATCGAATGCATTTTATGCATCGATGCAC-TACCATGCATCGATACACTCAGGCTTGTTTGAAAC
*
233688 ATCGAATGCATTTTATGCATCGATCCACT
1 ATCGAATGCATTTTATGCATCGATGCACT
233717 CTTAGTGCAC
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 58 0.71
65 18 0.22
66 4 0.05
67 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATACACTCAGGCTTGTTTGAAAC
Found at i:233732 original size:64 final size:62
Alignment explanation
Indices: 233560--233735 Score: 171
Period size: 64 Copynumber: 2.7 Consensus size: 62
233550 CACTCACTAT
* * *
233560 ATCGAATACATTTTATGCATCGATGCACT-TCCATGCATTGATACACTCAGGTTTTATGAAAAAC
1 ATCGAATGCATTTTATGCATCGATCCACTCT-CATGCA-TGATGCACTCAGGTTTTATG-AAAAC
** *
233624 ATCGAATGCATTTTATGCATCGATGCACAGAC-CATGCATCGATGCACTTAGGCTTGTT-TG-AA
1 ATCGAATGCATTTTATGCATCGAT-C-CACTCTCATGCAT-GATGCACTCAGG-TT-TTATGAAA
233686 AC
61 AC
*
233688 ATCGAATGCATTTTATGCATCGATCCACTCTTAGTGCACTGATGCACT
1 ATCGAATGCATTTTATGCATCGATCCACTCTCA-TGCA-TGATGCACT
233736 AAGGGTCCAA
Statistics
Matches: 94, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
62 3 0.03
63 2 0.02
64 64 0.68
65 17 0.18
66 6 0.06
67 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (62 bp):
ATCGAATGCATTTTATGCATCGATCCACTCTCATGCATGATGCACTCAGGTTTTATGAAAAC
Found at i:237008 original size:35 final size:36
Alignment explanation
Indices: 236968--237039 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
236958 AGTAAGTAAA
*
236968 ACAATTCTAACAT-TTTTAACTTATTGGTGAAAACT
1 ACAATTCTAACATATTTTAACTTACTGGTGAAAACT
237003 ACAATTCTAACATATTTTAACTTACTGGTGAAAACT
1 ACAATTCTAACATATTTTAACTTACTGGTGAAAACT
237039 A
1 A
237040 TCTTTTCATG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 13 0.37
36 22 0.63
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (36 bp):
ACAATTCTAACATATTTTAACTTACTGGTGAAAACT
Found at i:243059 original size:16 final size:16
Alignment explanation
Indices: 243038--243068 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
243028 TATAAGATTT
*
243038 TTTATTATACTTATTA
1 TTTATTATAATTATTA
243054 TTTATTATAATTATT
1 TTTATTATAATTATT
243069 TGAAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTATAATTATTA
Found at i:243858 original size:25 final size:26
Alignment explanation
Indices: 243828--243906 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 26
243818 TTATATATGC
243828 AAAAAAAATTAAATAAATAAAATATT
1 AAAAAAAATTAAATAAATAAAATATT
* ** *
243854 -AAAAAATTTAAATACTTAAATAAATT
1 AAAAAAAATTAAATAAATAAA-ATATT
243880 AAAAAAATATTAAATATAATAAAATAT
1 AAAAAAA-ATTAAATA-AATAAAATAT
243907 AACTTAAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
25 17 0.41
26 4 0.10
27 6 0.15
28 10 0.24
29 4 0.10
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAAAAAATTAAATAAATAAAATATT
Found at i:243865 original size:17 final size:18
Alignment explanation
Indices: 243836--243883 Score: 66
Period size: 16 Copynumber: 2.8 Consensus size: 18
243826 GCAAAAAAAA
243836 TTAAATAAA-TAAAATA-
1 TTAAATAAATTAAAATAC
*
243852 TTAAA-AAATTTAAATAC
1 TTAAATAAATTAAAATAC
243869 TTAAATAAATTAAAA
1 TTAAATAAATTAAAA
243884 AAATATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 5 0.19
18 8 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAATAAATTAAAATAC
Found at i:243902 original size:20 final size:21
Alignment explanation
Indices: 243863--243903 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
243853 TAAAAAATTT
243863 AAATACTTAAATAAATTAAAA
1 AAATACTTAAATAAATTAAAA
243884 AAATA-TTAAATATAA-TAAAA
1 AAATACTTAAATA-AATTAAAA
243904 TATAACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATACTTAAATAAATTAAAA
Found at i:245095 original size:16 final size:14
Alignment explanation
Indices: 245084--245130 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
245074 TTAAAATCTT
245084 AAAAA-ATTAAAAA
1 AAAAATATTAAAAA
*
245097 AAAAATCTTAAAAA
1 AAAAATATTAAAAA
245111 ATTAAAATATTATAAAA
1 A--AAAATATTA-AAAA
245128 AAA
1 AAA
245131 CCTTTTCCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 5 0.18
14 8 0.29
15 2 0.07
16 8 0.29
17 5 0.18
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATATTAAAAA
Found at i:245100 original size:30 final size:30
Alignment explanation
Indices: 245064--245130 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
245054 ACTATTTTTG
* **
245064 AAAAAAATAT-TTAAAATCTTAAAAAATTA
1 AAAAAAAAATCTTAAAAAATTAAAAAATTA
*
245093 AAAAAAAAATCTTAAAAAATTAAAATATTA
1 AAAAAAAAATCTTAAAAAATTAAAAAATTA
*
245123 TAAAAAAA
1 AAAAAAAA
245131 CCTTTTCCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (30 bp):
AAAAAAAAATCTTAAAAAATTAAAAAATTA
Found at i:245101 original size:22 final size:22
Alignment explanation
Indices: 245076--245117 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
245066 AAAAATATTT
245076 AAAATCTTAAAAAATTAAAAAA
1 AAAATCTTAAAAAATTAAAAAA
245098 AAAATCTTAAAAAATTAAAA
1 AAAATCTTAAAAAATTAAAA
245118 TATTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATCTTAAAAAATTAAAAAA
Found at i:245546 original size:2 final size:2
Alignment explanation
Indices: 245539--245580 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
245529 TCGTCGGTTC
*
245539 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
245580 A
1 A
245581 ACGTTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251589 original size:17 final size:17
Alignment explanation
Indices: 251540--251596 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
251530 ACAATTGAGT
*
251540 AAAAAT-AAA-AAATAT
1 AAAAATGAAATAAATAA
251555 AAAAATGAAATAAGATAA
1 AAAAATGAAATAA-ATAA
251573 AAAAATGATAAT-AATAA
1 AAAAATGA-AATAAATAA
251590 AAAAATG
1 AAAAATG
251597 GGGTTAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
15 6 0.16
16 3 0.08
17 13 0.35
18 12 0.32
19 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (17 bp):
AAAAATGAAATAAATAA
Found at i:253977 original size:21 final size:21
Alignment explanation
Indices: 253951--253995 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
253941 GATTTCTGGG
* *
253951 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
253972 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
253993 CAA
1 CAA
253996 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:254604 original size:18 final size:18
Alignment explanation
Indices: 254581--254615 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
254571 CTAGGAGATT
254581 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
254599 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
254616 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:254701 original size:21 final size:22
Alignment explanation
Indices: 254672--254715 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
254662 GTTGTATGAT
254672 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
254693 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
254715 A
1 A
254716 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:255681 original size:149 final size:149
Alignment explanation
Indices: 255501--255804 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
255491 GAGTCGAGGG
255501 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
255566 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
255631 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
255650 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
255715 ACTTGATCCCTAGCATATGTATATGATTCTTAAATAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
255780 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
255799 TCTACG
1 TCTACG
255805 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:255827 original size:23 final size:23
Alignment explanation
Indices: 255783--255827 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
255773 ATTATTATAT
*
255783 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
255806 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
255828 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:256934 original size:7 final size:7
Alignment explanation
Indices: 256919--256956 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
256909 CGAAGAGAAG
256919 AAAAAAT
1 AAAAAAT
*
256926 AATAAAT
1 AAAAAAT
*
256933 AAAAAAA
1 AAAAAAT
256940 AAAAAAT
1 AAAAAAT
256947 AAAAAA-
1 AAAAAAT
256953 AAAA
1 AAAA
256957 TATTTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:256936 original size:14 final size:14
Alignment explanation
Indices: 256919--256956 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
256909 CGAAGAGAAG
* *
256919 AAAAAATAATAAAT
1 AAAAAAAAAAAAAT
256933 AAAAAAAAAAAAAT
1 AAAAAAAAAAAAAT
256947 AAAAAAAAAA
1 AAAAAAAAAA
256957 TATTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAAAAAAAAT
Found at i:256942 original size:18 final size:17
Alignment explanation
Indices: 256919--256956 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
256909 CGAAGAGAAG
*
256919 AAAAAATAATAAATAAAA
1 AAAAAAAAATAAA-AAAA
256937 AAAAAAAAATAAAAAAA
1 AAAAAAAAATAAAAAAA
256954 AAA
1 AAA
256957 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAAAAATAAAAAAA
Found at i:257043 original size:34 final size:33
Alignment explanation
Indices: 256952--257049 Score: 106
Period size: 34 Copynumber: 2.8 Consensus size: 33
256942 AAAATAAAAA
* * *
256952 AAAAATATTTTTAAAACCATATAATATATATTTTT
1 AAAAATATTTTTAAAACTATAT-A-ATATACTTTC
*
256987 AAAAATAGTTTTTAAAATTATATAATATACTTTC
1 AAAAATA-TTTTTAAAACTATATAATATACTTTC
* *
257021 AAAAATATTTTCCAAAACTATATATTATA
1 AAAAATATTTT-TAAAACTATATAATATA
257050 TATATGTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
33 4 0.07
34 29 0.54
35 8 0.15
36 13 0.24
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (33 bp):
AAAAATATTTTTAAAACTATATAATATACTTTC
Found at i:257102 original size:26 final size:26
Alignment explanation
Indices: 257065--257151 Score: 96
Period size: 24 Copynumber: 3.6 Consensus size: 26
257055 GTTTTCAAAA
*
257065 ATATTTTAAAAATATATATATTATAT
1 ATATTTTCAAAATATATATATTATAT
*
257091 ATATTTTCAAAA-A-CTATATTATAT
1 ATATTTTCAAAATATATATATTATAT
* *
257115 ATA-TAT--ATATATATATA-TATAT
1 ATATTTTCAAAATATATATATTATAT
257137 ATATTTTCAAAATAT
1 ATATTTTCAAAATAT
257152 TTTTAAAAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
21 2 0.04
22 9 0.18
23 8 0.16
24 13 0.27
25 6 0.12
26 11 0.22
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATTTTCAAAATATATATATTATAT
Found at i:257117 original size:2 final size:2
Alignment explanation
Indices: 257105--257140 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
257095 TTTCAAAAAC
257105 TA TA T- TA TA TA 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 TA TA TA TA TA TA T
257141 TTTCAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:257179 original size:34 final size:34
Alignment explanation
Indices: 257126--257209 Score: 116
Period size: 34 Copynumber: 2.4 Consensus size: 34
257116 TATATATATA
257126 TATATATATATATATTTTC-AAAATATTTTTAAAAAC
1 TATATAT-TATATA-TTTCAAAAATA-TTTTAAAAAC
*
257162 TATATATTATATATTTCAAAAATATTTTCAAAAC
1 TATATATTATATATTTCAAAAATATTTTAAAAAC
*
257196 TATATAATATATAT
1 TATATATTATATAT
257210 ATTTTCGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 26 0.58
35 12 0.27
36 7 0.16
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (34 bp):
TATATATTATATATTTCAAAAATATTTTAAAAAC
Found at i:257206 original size:83 final size:83
Alignment explanation
Indices: 257039--257212 Score: 216
Period size: 83 Copynumber: 2.1 Consensus size: 83
257029 TTTCCAAAAC
*
257039 TATATATTATATATATGTTTTCAAAAATATTTTAAAAATATATATATTATATATATTTTCAAAAA
1 TATATATTATATATATATTTTCAAAAATATTTTAAAAATATATATATTATATATATTTTCAAAAA
*
257104 CTATATTATATATATATA
66 CTATATTAAATATATATA
*
257122 TATATATATATATATATATTTTC-AAAATATTTTTAAAAA-CTATATA-T-TATATA-TTTCAAA
1 TATATAT-TATATATATATTTTCAAAAATA-TTTTAAAAATATATATATTATATATATTTTCAAA
*
257182 AA-TATTTTCAAAACTATATAATA
64 AACTATATT--AAA-TATAT-ATA
257205 TATATATT
1 TATATATT
257213 TTCGAAAACC
Statistics
Matches: 81, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
79 5 0.06
80 9 0.11
81 8 0.10
82 7 0.09
83 29 0.36
84 23 0.28
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.48
Consensus pattern (83 bp):
TATATATTATATATATATTTTCAAAAATATTTTAAAAATATATATATTATATATATTTTCAAAAA
CTATATTAAATATATATA
Found at i:257240 original size:157 final size:152
Alignment explanation
Indices: 256970--257257 Score: 379
Period size: 157 Copynumber: 1.9 Consensus size: 152
256960 TTTTAAAACC
256970 ATATAATATATATTTTTAAAAATAGTTTTTAAAATTATATAATATACTTTCAAAAATATTTTCCA
1 ATATAATATATATTTTTAAAAATAGTTTTTAAAATTATATAATATACTTTCAAAAATATTTTCCA
* *
257035 AAACTATATATTATATATATGTTTTCAAAAATATTTTAAAAATATATATATTATATATATTTTCA
66 AAACTATATA-TATATATATATTTTCAAAAAGATTTTAAAAATATATATATTATAT-T-TTTTCA
257100 AAAACTATATTATATATATATATAT
128 AAAACTATATTATATATATATATAT
* *
257125 ATATATATATATATATTTTCAAAATA-TTTTTAAAAACTATATATTATATA-TTTCAAAAATATT
1 ATATA-ATATATAT-TTTTAAAAATAGTTTTT-AAAA-T-TATATAATATACTTTCAAAAATATT
* * *
257188 TT-CAAAACTATATA-ATATATATATTTTCGAAAACCGCTTTCTACAAAT-TATATATTATATTT
61 TTCCAAAACTATATATATATATATATTTTC-AAAA-AGATTT-TAAAAATATATATATTATATTT
257250 TTTCAAAA
123 TTTCAAAA
257258 TATAATTTCA
Statistics
Matches: 118, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
155 27 0.23
156 18 0.15
157 41 0.35
158 22 0.19
159 10 0.08
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (152 bp):
ATATAATATATATTTTTAAAAATAGTTTTTAAAATTATATAATATACTTTCAAAAATATTTTCCA
AAACTATATATATATATATATTTTCAAAAAGATTTTAAAAATATATATATTATATTTTTTCAAAA
ACTATATTATATATATATATAT
Found at i:257277 original size:157 final size:159
Alignment explanation
Indices: 256970--257299 Score: 373
Period size: 157 Copynumber: 2.1 Consensus size: 159
256960 TTTTAAAACC
256970 ATATA-ATATATAT-TTTTAAAAATAGTTTTTAAAATTATATAATATACTTTCAAAAATATTTTC
1 ATATATATATATATATTTTAAAAATAGTTTTTAAAATTATATAATATACTTTCAAAAATATTTTC
* *
257033 CAAAACTATATATTATATATATGTTTTCAAAAATATTTTAAAAATATATATATTATATATATTTT
66 CAAAACTATATA-TATATATATATTTTCAAAAAGATTTTAAAAATATATATATTATATATATTTT
* *
257098 CAAAAACTATATTATATATATA-TATA-T-
130 CAAAAACTATATTAAAAATATATTATATTA
* *
257125 ATATATATATATATATTTTCAAAATA-TTTTTAAAAACTATATATTATATA-TTTCAAAAATATT
1 ATATATATATATATATTTTAAAAATAGTTTTT-AAAA-T-TATATAATATACTTTCAAAAATATT
* * *
257188 TT-CAAAACTATATA-ATATATATATTTTCGAAAACCGCTTTCTACAAAT-TATATATTATAT-T
63 TTCCAAAACTATATATATATATATATTTTC-AAAA-AGATTT-TAAAAATATATATATTATATAT
*
257249 -TTTTC-AAAA-TATAATTTCAAAAATTATATTGTATTA
125 ATTTTCAAAAACTAT-A-TT-AAAAA-TATATTATATTA
257285 ATATATATATATATA
1 ATATATATATATATA
257300 CATATAAATA
Statistics
Matches: 150, Mismatches: 10, Indels: 25
0.81 0.05 0.14
Matches are distributed among these distances:
153 3 0.02
154 5 0.03
155 25 0.17
156 21 0.14
157 45 0.30
158 25 0.17
159 11 0.07
160 15 0.10
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (159 bp):
ATATATATATATATATTTTAAAAATAGTTTTTAAAATTATATAATATACTTTCAAAAATATTTTC
CAAAACTATATATATATATATATTTTCAAAAAGATTTTAAAAATATATATATTATATATATTTTC
AAAAACTATATTAAAAATATATTATATTA
Found at i:263263 original size:37 final size:36
Alignment explanation
Indices: 263113--263282 Score: 195
Period size: 37 Copynumber: 4.7 Consensus size: 36
263103 ATATAGTTTT
*
263113 ATTTTGAATATATATAT-A-ATATAGTTTTTAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTAAAAC
* *
263147 ATTTT-AAAAAACTTATATAATATGTAGTTTTTAAAAAC
1 ATTTTGAAAATA--TATATAATATATAGTTTTT-AAAAC
*
263185 ATTTTGAAAATTTATATAATATATAGTTTTTAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTAAAAC
*
263221 ATTTTGAAAAATATATATAATATATAG-TTTTAAAATG
1 ATTTTG-AAAATATATATAATATATAGTTTTTAAAA-C
* *
263258 TTTTTGAAAATATATTATATTATAT
1 ATTTTGAAAATATA-TATAATATAT
263283 GGTATTGAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
33 4 0.03
34 5 0.04
35 5 0.04
36 28 0.24
37 61 0.52
38 10 0.09
39 4 0.03
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (36 bp):
ATTTTGAAAATATATATAATATATAGTTTTTAAAAC
Found at i:263295 original size:74 final size:74
Alignment explanation
Indices: 263119--263282 Score: 224
Period size: 74 Copynumber: 2.2 Consensus size: 74
263109 TTTTATTTTG
* *
263119 AATATATATATAATATAGTTTTTAAAACATTTTAAAAAACTTATATAATATGTAGTTTTTAAAAA
1 AATATATATATTATATAGTTTTTAAAACATTTTAAAAAACTTATATAATATATAGTTTTTAAAAA
263184 CATTTTGAA
66 CATTTTGAA
* * *
263193 AATTTATATAATATATAGTTTTTAAAACATTTTGAAAAA-TATATATAATATATAG-TTTTAAAA
1 AATATATATATTATATAGTTTTTAAAACATTTTAAAAAACT-TATATAATATATAGTTTTTAAAA
***
263256 TGTTTTTGAA
65 ACATTTTGAA
263266 AATATATTATATTATAT
1 AATATA-TATATTATAT
263283 GGTATTGAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
73 21 0.27
74 57 0.73
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (74 bp):
AATATATATATTATATAGTTTTTAAAACATTTTAAAAAACTTATATAATATATAGTTTTTAAAAA
CATTTTGAA
Found at i:263390 original size:19 final size:19
Alignment explanation
Indices: 263343--263389 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
263333 AAATTTATTT
263343 TATTATTATTATATATTATA
1 TATT-TTATTATATATTATA
*
263363 TATTATATTA-ATATTA-A
1 TATTTTATTATATATTATA
263380 TATTTT-TTAT
1 TATTTTATTAT
263390 TTTTTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 3 0.12
17 6 0.25
18 6 0.25
19 5 0.21
20 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTATTATATATTATA
Found at i:263867 original size:16 final size:17
Alignment explanation
Indices: 263835--263868 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
263825 ATAGAGCAAC
263835 ACCACGAAATGCACAAAA
1 ACCACGAAA-GCACAAAA
263853 ACCACGAAA-CACAAAA
1 ACCACGAAAGCACAAAA
263869 CATAAGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.29, G:0.09, T:0.03
Consensus pattern (17 bp):
ACCACGAAAGCACAAAA
Found at i:270605 original size:23 final size:23
Alignment explanation
Indices: 270579--270647 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
270569 CACCACAGCT
*
270579 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
270602 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
270625 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
270648 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:270834 original size:103 final size:103
Alignment explanation
Indices: 270655--270875 Score: 345
Period size: 103 Copynumber: 2.1 Consensus size: 103
270645 CCATATAATA
* * * * *
270655 ATGT-CCATAAGGGCCACATATCATTCTTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGACCAAGTATGT
270719 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
65 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
* *
270758 ATGTCCCAAAGGACCACATATCATTCCTTAATAATCATATACATATGCCAAGGACCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGACCAAGTATGTG
*
270823 TCTCACCAGACTTCACACATGTTTCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
270861 ATGTCCCGAAGGACC
1 ATGTCCCAAAGGACC
270876 GCGTAGACCC
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
103 105 0.97
104 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGACCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:272483 original size:14 final size:14
Alignment explanation
Indices: 272464--272495 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
272454 TTTGGTAATC
272464 CGTTCATTTATCTT
1 CGTTCATTTATCTT
*
272478 CGTTCATTTATGTT
1 CGTTCATTTATCTT
272492 CGTT
1 CGTT
272496 TATGTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (14 bp):
CGTTCATTTATCTT
Found at i:272497 original size:24 final size:24
Alignment explanation
Indices: 272465--272519 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
272455 TTGGTAATCC
* *
272465 GTTCATTTATCTTCGTTCA-TTTAT
1 GTTCGTTTATCTTCATT-AGTTTAT
*
272489 GTTCGTTTATGTTCATTAGTTTAT
1 GTTCGTTTATCTTCATTAGTTTAT
272513 GTTCGTT
1 GTTCGTT
272520 CAGCCTAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.58
Consensus pattern (24 bp):
GTTCGTTTATCTTCATTAGTTTAT
Found at i:279325 original size:74 final size:75
Alignment explanation
Indices: 279242--279395 Score: 301
Period size: 74 Copynumber: 2.1 Consensus size: 75
279232 TCGCAATTTG
279242 GTTTTCTTTTATATTAAAAAAATAAAATTAAAGCGTCAACTTTATCTTGGTTGGCCTGCAATTA-
1 GTTTTCTTTTATATTAAAAAAATAAAATTAAAGCGTCAACTTTATCTTGGTTGGCCTGCAATTAT
279306 TTTTTTTATC
66 TTTTTTTATC
279316 GTTTTCTTTTATATTAAAAAAATAAAATTAAAGCGTCAACTTTATCTTGGTTGGCCTGCAATTAT
1 GTTTTCTTTTATATTAAAAAAATAAAATTAAAGCGTCAACTTTATCTTGGTTGGCCTGCAATTAT
279381 TTTTTTTATC
66 TTTTTTTATC
279391 GTTTT
1 GTTTT
279396 TTGACCTCTC
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 64 0.81
75 15 0.19
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (75 bp):
GTTTTCTTTTATATTAAAAAAATAAAATTAAAGCGTCAACTTTATCTTGGTTGGCCTGCAATTAT
TTTTTTTATC
Found at i:281231 original size:14 final size:15
Alignment explanation
Indices: 281208--281240 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
281198 CAGTTTGGTT
*
281208 AATTGTTTAAA-AAA
1 AATTGATTAAATAAA
281222 AATTGATTAAATAAA
1 AATTGATTAAATAAA
281237 AATT
1 AATT
281241 TCGATTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (15 bp):
AATTGATTAAATAAA
Found at i:281451 original size:20 final size:20
Alignment explanation
Indices: 281426--281463 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
281416 TTTTATTCAC
*
281426 GGAATATAAGATTACCAGTA
1 GGAATAAAAGATTACCAGTA
281446 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
281464 GGAATATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTA
Found at i:281467 original size:18 final size:19
Alignment explanation
Indices: 281426--281469 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
281416 TTTTATTCAC
*
281426 GGAATATAAGATTACCAGTA
1 GGAATAAAAGATTACCAG-A
281446 GGAATAAAAGATTACCAG-
1 GGAATAAAAGATTACCAGA
281464 GGAATA
1 GGAATA
281470 TGATTACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
20 17 0.74
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGA
Found at i:296321 original size:32 final size:32
Alignment explanation
Indices: 296278--296352 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
296268 TGTGTCTAAT
*
296278 TGATGACATGATATATATCACGT-AACCAAAAG
1 TGATGACATGATATATATCACATCAACC-AAAG
* * *
296310 TGATGATATGATATATGTCACATCATCCAAAG
1 TGATGACATGATATATATCACATCAACCAAAG
296342 TGATGACATGA
1 TGATGACATGA
296353 CATGTGTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 34 0.92
33 3 0.08
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (32 bp):
TGATGACATGATATATATCACATCAACCAAAG
Found at i:296374 original size:32 final size:32
Alignment explanation
Indices: 296306--296396 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
296296 CACGTAACCA
* * *
296306 AAAGTGATGATATGATATATGTCACATCATCC
1 AAAGTGATGATATGACATGTGTCACGTCATCC
* *
296338 AAAGTGATGACATGACATGTGTCACGTCAAT-G
1 AAAGTGATGATATGACATGTGTCACGTC-ATCC
*
296370 AAAGT-ATCGATGTGACATGTGTCACGT
1 AAAGTGAT-GATATGACATGTGTCACGT
296397 AACAAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.04
32 46 0.92
33 2 0.04
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (32 bp):
AAAGTGATGATATGACATGTGTCACGTCATCC
Found at i:296659 original size:21 final size:21
Alignment explanation
Indices: 296635--296677 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
296625 TTCAACAAAT
* * *
296635 CTCTTCATTAAACGGTCTTAA
1 CTCTTCATCAAAAGGTCATAA
296656 CTCTTCATCAAAAGGTCATAA
1 CTCTTCATCAAAAGGTCATAA
296677 C
1 C
296678 CTTTTGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (21 bp):
CTCTTCATCAAAAGGTCATAA
Found at i:297011 original size:21 final size:20
Alignment explanation
Indices: 296973--297011 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
296963 CCTTAACAAA
* *
296973 ACTTCCTCTTCTGTTTTCTG
1 ACTTCCTCATCTGATTTCTG
296993 ACTTCGCTCATCTGATTTC
1 ACTTC-CTCATCTGATTTC
297012 ATGTCAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.10, C:0.31, G:0.10, T:0.49
Consensus pattern (20 bp):
ACTTCCTCATCTGATTTCTG
Found at i:299455 original size:29 final size:30
Alignment explanation
Indices: 299396--299452 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
299386 TGTATGGTTT
299396 AAAAAAAATGAAAGTTTAGATACTAAAATG
1 AAAAAAAATGAAAGTTTAGATACTAAAATG
* * *
299426 AAAAAAACTGATAGTTTAGTTACTAAA
1 AAAAAAAATGAAAGTTTAGATACTAAA
299453 TGAGTAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.26
Consensus pattern (30 bp):
AAAAAAAATGAAAGTTTAGATACTAAAATG
Found at i:301853 original size:26 final size:24
Alignment explanation
Indices: 301821--301884 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 24
301811 ATTTTACGAA
301821 AATAATAAAATTATAATAATTATATT
1 AATAATAAAATTATAATAA-T-TATT
*
301847 AATAAT-ATATTAT-AT-ATTATT
1 AATAATAAAATTATAATAATTATT
*
301868 AA-AATAAAAATATAATA
1 AATAATAAAATTATAATA
301885 TCATATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 3 0.09
21 11 0.34
22 3 0.09
23 1 0.03
24 2 0.06
25 6 0.19
26 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AATAATAAAATTATAATAATTATT
Found at i:301924 original size:10 final size:11
Alignment explanation
Indices: 301843--301932 Score: 50
Period size: 11 Copynumber: 8.5 Consensus size: 11
301833 ATAATAATTA
301843 TATTA-ATAAT
1 TATTATATAAT
301853 ATATTATAT-AT
1 -TATTATATAAT
301864 TATTA-A-AAT
1 TATTATATAAT
* **
301873 AAAAATATAA-
1 TATTATATAAT
301883 TATCATATATAAT
1 TAT--TATATAAT
*
301896 TATAATATAAT
1 TATTATATAAT
*
301907 TGAGTATAT-AT
1 T-ATTATATAAT
301918 TATTATATAA-
1 TATTATATAAT
301928 TATTA
1 TATTA
301933 AAAATATAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 19
0.67 0.11 0.21
Matches are distributed among these distances:
9 5 0.08
10 18 0.30
11 21 0.35
12 13 0.22
13 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (11 bp):
TATTATATAAT
Found at i:301964 original size:27 final size:27
Alignment explanation
Indices: 301914--301965 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
301904 AATTGAGTAT
*
301914 ATATTATTATATAATATTAAAAATATA
1 ATATTATTAAATAATATTAAAAATATA
*
301941 ATATTATTAAAT-TTATTAATAAATA
1 ATATTATTAAATAATATTAA-AAATA
301966 AATGAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATTATTAAATAATATTAAAAATATA
Found at i:302186 original size:2 final size:2
Alignment explanation
Indices: 302179--302212 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
302169 CGAATACCAA
302179 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
302213 TTCCTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:302688 original size:12 final size:12
Alignment explanation
Indices: 302671--302696 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
302661 TATTCGAGAA
302671 CAAGACGTAAAG
1 CAAGACGTAAAG
302683 CAAGACGTAAAG
1 CAAGACGTAAAG
302695 CA
1 CA
302697 CGAATAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.19, G:0.23, T:0.08
Consensus pattern (12 bp):
CAAGACGTAAAG
Found at i:303965 original size:22 final size:23
Alignment explanation
Indices: 303932--303987 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
303922 ATATTATAAA
303932 AATATTTATTTATCT-TTTAAAAT
1 AATA-TTATTTATCTATTTAAAAT
*
303955 CAA-ATTATTTATTTATTTAAAAT
1 -AATATTATTTATCTATTTAAAAT
303978 AATATTATTT
1 AATATTATTT
303988 TAAAATTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 11 0.38
23 16 0.55
24 2 0.07
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATTATTTATCTATTTAAAAT
Found at i:304113 original size:23 final size:22
Alignment explanation
Indices: 304086--304184 Score: 98
Period size: 23 Copynumber: 4.5 Consensus size: 22
304076 TAATTTTAGA
304086 ATAATATTATTTAAAATAAATC
1 ATAATATTATTTAAAATAAATC
*
304108 ATTAATATTATTTAAAATAAATAA
1 A-TAATATTATTTAAAATAAAT-C
*
304132 ATAATATGATTTTAAAATTAAAT-
1 ATAATATTA-TTTAAAA-TAAATC
*
304155 A-AATA-T-TTTAAAATAATTTC
1 ATAATATTATTTAAAATAA-ATC
304175 ATAATATTAT
1 ATAATATTAT
304185 AAATATATTT
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
18 3 0.05
19 8 0.12
20 1 0.02
21 4 0.06
22 6 0.09
23 29 0.45
24 8 0.12
25 5 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (22 bp):
ATAATATTATTTAAAATAAATC
Found at i:304162 original size:19 final size:21
Alignment explanation
Indices: 304129--304168 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
304119 TTAAAATAAA
304129 TAAATAATATGATTTTAAAAT
1 TAAATAATATGATTTTAAAAT
304150 TAAATAA-AT-ATTTTAAAAT
1 TAAATAATATGATTTTAAAAT
304169 AATTTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 2 0.11
21 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAATAATATGATTTTAAAAT
Found at i:304198 original size:20 final size:20
Alignment explanation
Indices: 304156--304231 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 20
304146 AAATTAAATA
*
304156 AATATTTTAAA-ATAATTTCAT
1 AATATTATAAATAT-ATTT-AT
304177 AATATTATAAATATATTTAT
1 AATATTATAAATATATTTAT
*
304197 AATA--ATAATATAAATTTTAT
1 AATATTATAA-ATATA-TTTAT
304217 AAATATATATAAATA
1 -AATAT-TATAAATA
304232 ATTATTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.09
19 4 0.09
20 11 0.24
21 18 0.39
22 2 0.04
23 3 0.07
24 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATTATAAATATATTTAT
Found at i:304236 original size:20 final size:21
Alignment explanation
Indices: 304165--304241 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 21
304155 AAATATTTTA
304165 AAATAATT-TCATAATAT-TAT
1 AAATAATTAT-ATAATATATAT
304185 AAATATATT-TATAATAATAATAT
1 AAATA-ATTATATAAT-AT-ATAT
*
304208 AAAT-TTTATA-AATATATAT
1 AAATAATTATATAATATATAT
*
304227 AAATAATTATTTAAT
1 AAATAATTATATAAT
304242 TTTTTATTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
19 8 0.17
20 16 0.34
21 14 0.30
22 2 0.04
23 7 0.15
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATAATTATATAATATATAT
Found at i:304945 original size:21 final size:21
Alignment explanation
Indices: 304920--304968 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
304910 ATCATCATTC
*
304920 ATTATGAATCATCACATCAAT
1 ATTATAAATCATCACATCAAT
* *
304941 ATTATAAATGATCACCTCAAT
1 ATTATAAATCATCACATCAAT
304962 ATTATAA
1 ATTATAA
304969 CGATCAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (21 bp):
ATTATAAATCATCACATCAAT
Found at i:307064 original size:157 final size:154
Alignment explanation
Indices: 306913--307593 Score: 764
Period size: 157 Copynumber: 4.4 Consensus size: 154
306903 TTTAAGTCAA
* * * *
306913 TTTTTTACCAAATATTAATCACGTGCTCATAAACCATC-ATAGAATCCATAT-TTACTTTCAATT
1 TTTTTTACCAAAT-TTAA-CACATGCTCATATACCA-CAATAGAATACATATGTAAC-TTCAATT
* * * *
306976 TCTCTTTTTGATGATAGA-TTTTTTATTTTTTAATTTAGT-CCTTAATTTTTCATAATTTCTTTA
62 TCTCTTTTTGATAATA-ATTTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTTCCTTA
*
307039 TTTTTTCAATTCATCCTTTATTTTAAGTT
126 TTTCTTCAATTCATCCTTTATTTTAAGTT
* * * * *
307068 TATTTTACCAAATTTAAACAATATGCTCATATACCACAATATAATAAATATGTAACTTCAATTTT
1 TTTTTTACCAAATTT-AAC-ACATGCTCATATACCACAATAGAATACATATGTAACTTCAATTTC
* * *
307133 TCTTTTTG---ATAGTTTTTTTATTTTTCAATTTAGTCCCTCACTTTTTTATAATTTCCTTATTT
64 TCTTTTTGATAATAATTTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTTCCTTATTT
* * * *
307195 -TTAAAATTCATTCTTTATTCTAAGTCC
129 CTT-CAATTCATCCTTTATTTTAAGT-T
* * * * *
307222 GTTTTTACCAAATTT--GA-A--C-CATAT-GCTC-ATAGAATACCTATGTAACTTCAATTTCTC
1 TTTTTTACCAAATTTAACACATGCTCATATACCACAATAGAATACATATGTAACTTCAATTTCTC
** *
307279 TTTTTGGCAATAATTTTTTTATTTTTCAATTTAGTCTCTCAATTTTTCATAATTTCCTTATTTCT
66 TTTTTGATAATAATTTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTTCCTTATTTCT
307344 TCAATTCATCCTTTATTTTAAGTTTT
131 TCAATTCATCCTTTATTTTAAG--TT
* * *
307370 TTTTTTACCAAATTTGAACATATGCTCATATACCACAATAGAATACATATATAACTTCAATTCCT
1 TTTTTTACCAAATTT-AACACATGCTCATATACCACAATAGAATACATATGTAACTTCAATTTCT
* *
307435 CTTTTTGATAATAATTTTTTTATTTTTCAATTTAGTCCCTCATTTTTTCATAATTTCCTTACTTC
65 CTTTTTGATAATAATTTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTTCCTTATTTC
*
307500 TTGAATTCATCCTTTATTTTAAGTATT
130 TTCAATTCATCCTTTATTTTAAG--TT
* *
307527 TTTTTTACCAAATTTAAACCACATGCTCATATACCACAATAAAATATATTATGTAACTTCAATTT
1 TTTTTTACCAAATTT-AA-CACATGCTCATATACCACAATAGAATACA-TATGTAACTTCAATTT
307592 CT
63 CT
307594 ACTCTTTTAC
Statistics
Matches: 445, Mismatches: 56, Indels: 46
0.81 0.10 0.08
Matches are distributed among these distances:
144 31 0.07
145 2 0.00
146 5 0.01
147 69 0.16
148 16 0.04
149 2 0.00
150 1 0.00
151 1 0.00
152 26 0.06
153 42 0.09
154 18 0.04
155 58 0.13
156 5 0.01
157 127 0.29
158 26 0.06
159 16 0.04
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (154 bp):
TTTTTTACCAAATTTAACACATGCTCATATACCACAATAGAATACATATGTAACTTCAATTTCTC
TTTTTGATAATAATTTTTTTATTTTTCAATTTAGTCCCTCAATTTTTCATAATTTCCTTATTTCT
TCAATTCATCCTTTATTTTAAGTT
Found at i:307509 original size:304 final size:300
Alignment explanation
Indices: 306969--307557 Score: 846
Period size: 304 Copynumber: 1.9 Consensus size: 300
306959 CATATTTACT
** * *
306969 TTCAATTTCTCTTTTTGATGATAGATTTTTTATTTTTTAATTTAGTCCTTAATTTTTCATAATTT
1 TTCAATTTCTCTTTTTGACAATAGATTTTTTATTTTTCAATTTAGTCCTCAATTTTTCATAATTT
* *
307034 CTTTATTTTTTCAATTCATCCTTTATTTTAAGTTTATTTTACCAAATTTAAACAATATGCTCATA
66 CCTTATTTCTTCAATTCATCCTTTATTTTAAGTTTATTTTACCAAATTTAAACAATATGCTCATA
* * ** *
307099 TACCACAATATAATAAATATGTAACTTCAATTTTTCTTTTTGATAGTTTTTTTATTTTTCAATTT
131 TACCACAATAGAATAAATATATAACTTCAATTCCTCTTTTTGATAATTTTTTTATTTTTCAATTT
* *
307164 AGTCCCTCACTTTTTTATAATTTCCTTATTTTTAAAATTCATTCTTTATTCTAAGT-CCGTTTTT
196 AGTCCCTCACTTTTTTATAATTTCCTTATTCTTAAAATTCATCCTTTATTCTAAGTACCGTTTTT
* *
307228 ACCAAATTTGAACCATATGCTCATAGAATACCTATGTAAC
261 ACCAAATTTAAACCACATGCTCATAGAATACCTATGTAAC
*
307268 TTCAATTTCTCTTTTTGGCAATA-ATTTTTTTATTTTTCAATTTAGTCTCTCAATTTTTCATAAT
1 TTCAATTTCTCTTTTTGACAATAGA-TTTTTTATTTTTCAATTTAGTC-CTCAATTTTTCATAAT
* *
307332 TTCCTTATTTCTTCAATTCATCCTTTATTTTAAGTTTTTTTTTTACCAAATTTGAAC-ATATGCT
64 TTCCTTATTTCTTCAATTCATCCTTTATTTTAAG--TTTATTTTACCAAATTTAAACAATATGCT
*
307396 CATATACCACAATAGAATACATATATAACTTCAATTCCTCTTTTTGATAATAATTTTTTTATTTT
127 CATATACCACAATAGAATAAATATATAACTTCAATTCCTCTTTTTG---ATAATTTTTTTATTTT
* *
307461 TCAATTTAGTCCCTCA-TTTTTTCATAATTTCCTTACTTCTT-GAATTCATCCTTTATTTTAAGT
189 TCAATTTAGTCCCTCACTTTTTT-ATAATTTCCTTA-TTCTTAAAATTCATCCTTTATTCTAAGT
***
307524 ATTTTTTTTACCAAATTTAAACCACATGCTCATA
252 ACCGTTTTTACCAAATTTAAACCACATGCTCATA
307558 TACCACAATA
Statistics
Matches: 256, Mismatches: 24, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
298 1 0.00
299 41 0.16
300 47 0.18
301 48 0.19
302 19 0.07
303 6 0.02
304 62 0.24
305 32 0.12
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (300 bp):
TTCAATTTCTCTTTTTGACAATAGATTTTTTATTTTTCAATTTAGTCCTCAATTTTTCATAATTT
CCTTATTTCTTCAATTCATCCTTTATTTTAAGTTTATTTTACCAAATTTAAACAATATGCTCATA
TACCACAATAGAATAAATATATAACTTCAATTCCTCTTTTTGATAATTTTTTTATTTTTCAATTT
AGTCCCTCACTTTTTTATAATTTCCTTATTCTTAAAATTCATCCTTTATTCTAAGTACCGTTTTT
ACCAAATTTAAACCACATGCTCATAGAATACCTATGTAAC
Found at i:309573 original size:23 final size:23
Alignment explanation
Indices: 309547--309595 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
309537 AGCGTTTACG
* *
309547 AACATGTTCTTTTAATATTTGCC
1 AACATATTCGTTTAATATTTGCC
* *
309570 AACATATTCGTTTAATGTTTGGC
1 AACATATTCGTTTAATATTTGCC
309593 AAC
1 AAC
309596 TAACACACTT
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:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (23 bp):
AACATATTCGTTTAATATTTGCC
Found at i:315507 original size:49 final size:50
Alignment explanation
Indices: 315452--315553 Score: 161
Period size: 49 Copynumber: 2.1 Consensus size: 50
315442 TTTCTATAGT
*
315452 ATTGAATGATAGTTAAGTAAAATTTCAAAT-AAAATAGACTGTTAATTGA
1 ATTGAATGATAATTAAGTAAAATTTCAAATAAAAATAGACTGTTAATTGA
* * *
315501 ATTGAATGATAATTAAGTAAAATTTTAAATAAAAATATAGTGTTAATTGA
1 ATTGAATGATAATTAAGTAAAATTTCAAATAAAAATAGACTGTTAATTGA
315551 ATT
1 ATT
315554 AATTGTTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
49 28 0.58
50 20 0.42
ACGTcount: A:0.48, C:0.02, G:0.13, T:0.37
Consensus pattern (50 bp):
ATTGAATGATAATTAAGTAAAATTTCAAATAAAAATAGACTGTTAATTGA
Found at i:323144 original size:16 final size:16
Alignment explanation
Indices: 323123--323154 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
323113 AATGAATAAA
323123 GTTCATTAATTTGTAC
1 GTTCATTAATTTGTAC
323139 GTTCATTAATTTGTAC
1 GTTCATTAATTTGTAC
323155 CATGGTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
GTTCATTAATTTGTAC
Found at i:327328 original size:29 final size:27
Alignment explanation
Indices: 327294--327349 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
327284 TTTTCCACCC
327294 AAAAATTT-ATAAAACTTCATATTTTTTAA
1 AAAAATTTCA-AAAA-TTCAT-TTTTTTAA
327323 AAAAATTTCAAAAATTCATTTTTTTAA
1 AAAAATTTCAAAAATTCATTTTTTTAA
327350 TATCAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 8 0.31
28 5 0.19
29 12 0.46
30 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAAATTTCAAAAATTCATTTTTTTAA
Found at i:337147 original size:15 final size:16
Alignment explanation
Indices: 337127--337162 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
337117 TTAATATGTG
337127 ATAAAAATAAAAAT-A
1 ATAAAAATAAAAATAA
*
337142 ATAAAAATATAAATAA
1 ATAAAAATAAAAATAA
337158 ATAAA
1 ATAAA
337163 TATTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAAAATAAAAATAA
Found at i:337604 original size:21 final size:21
Alignment explanation
Indices: 337580--337635 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
337570 AATGATTAAG
*
337580 ACCTTTCGATGAAATGACATA
1 ACCTTTCGATGAAAGGACATA
* * *
337601 ACCTTTCAATTAAAGGACTTA
1 ACCTTTCGATGAAAGGACATA
* *
337622 TCCTTTTGATGAAA
1 ACCTTTCGATGAAA
337636 AGTACTTAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (21 bp):
ACCTTTCGATGAAAGGACATA
Found at i:337642 original size:22 final size:22
Alignment explanation
Indices: 337612--337677 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
337602 CCTTTCAATT
* *
337612 AAAGGACTTATCCTTTTGATGA
1 AAAGGACTTAACCTTTTCATGA
* *
337634 AAAGTACTTAACTTTTTCATG-
1 AAAGGACTTAACCTTTTCATGA
* **
337655 AAAGGATTTAATATTTTCATGA
1 AAAGGACTTAACCTTTTCATGA
337677 A
1 A
337678 GAGAATTGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (22 bp):
AAAGGACTTAACCTTTTCATGA
Found at i:337658 original size:21 final size:21
Alignment explanation
Indices: 337612--337677 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
337602 CCTTTCAATT
* *
337612 AAAGGACTT-ATCCTTTTGATG
1 AAAGGACTTAAT-ATTTTCATG
*
337633 AAAAGTACTTAACT-TTTTCATG
1 -AAAGGACTTAA-TATTTTCATG
*
337655 AAAGGATTTAATATTTTCATG
1 AAAGGACTTAATATTTTCATG
337676 AA
1 AA
337678 GAGAATTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 19 0.51
22 15 0.41
23 1 0.03
24 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (21 bp):
AAAGGACTTAATATTTTCATG
Found at i:339840 original size:13 final size:13
Alignment explanation
Indices: 339822--339846 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339812 AATATCATTT
339822 GCAAGTTATCCAC
1 GCAAGTTATCCAC
339835 GCAAGTTATCCA
1 GCAAGTTATCCA
339847 TGTAAACTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (13 bp):
GCAAGTTATCCAC
Found at i:340627 original size:21 final size:21
Alignment explanation
Indices: 340580--340634 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
340570 AAGAACTTAT
*
340580 CCTTTTGATGAAAAGTGATTAA
1 CCTTTTCATGAAAAGT-ATTAA
340602 CCTTTTCATGAAAAG-ATTTAA
1 CCTTTTCATGAAAAGTA-TTAA
*
340623 TCTTTTCATGAA
1 CCTTTTCATGAA
340635 GAGAATTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
22 14 0.47
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
CCTTTTCATGAAAAGTATTAA
Found at i:345467 original size:23 final size:22
Alignment explanation
Indices: 345441--345495 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
345431 GGTTCTACGC
*
345441 GGTCCTTCGGGACAATTCTATGT
1 GGTCCTTCGGAAC-ATTCTATGT
*
345464 GGTCCTTCAGAACATTCTATGT
1 GGTCCTTCGGAACATTCTATGT
345486 GG-CACTTCGG
1 GGTC-CTTCGG
345496 TGTAATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 16 0.57
23 11 0.39
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (22 bp):
GGTCCTTCGGAACATTCTATGT
Found at i:345483 original size:22 final size:23
Alignment explanation
Indices: 345441--345487 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
345431 GGTTCTACGC
* *
345441 GGTCCTTCGGGACAATTCTATGT
1 GGTCCTTCAGAACAATTCTATGT
345464 GGTCCTTCAGAAC-ATTCTATGT
1 GGTCCTTCAGAACAATTCTATGT
345486 GG
1 GG
345488 CACTTCGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (23 bp):
GGTCCTTCAGAACAATTCTATGT
Found at i:345779 original size:65 final size:65
Alignment explanation
Indices: 345696--345828 Score: 225
Period size: 68 Copynumber: 2.0 Consensus size: 65
345686 TTCTAAATGG
345696 TTTTGCATAGTGACTGATAATGATA-T-TGATGATGATGATGATACATATTATATATATGTGCAC
1 TTTTGCATAGTGACTGATAATGATATTATGATGATGATGATGATACATATTATATATATGTGCAC
345759 TTTTGCATAGTGACAATGATAATGATATTGATGATGATGATGATGATACATATTATATATATGTG
1 TTTTGCATAGTGAC--TGATAATGATATT-ATGATGATGATGATGATACATATTATATATATGTG
345824 CAC
63 CAC
345827 TT
1 TT
345829 ATGCTTTTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
63 14 0.22
65 11 0.17
66 1 0.02
68 39 0.60
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.40
Consensus pattern (65 bp):
TTTTGCATAGTGACTGATAATGATATTATGATGATGATGATGATACATATTATATATATGTGCAC
Found at i:359561 original size:11 final size:11
Alignment explanation
Indices: 359535--359568 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
359525 ACTATTTATT
*
359535 ATATTTATAAAA
1 ATATTTA-ATAA
359547 ATATTTAATAA
1 ATATTTAATAA
359558 ATATTTAATAA
1 ATATTTAATAA
359569 TATAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATTTAATAA
Found at i:359568 original size:24 final size:26
Alignment explanation
Indices: 359506--359568 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 26
359496 CAATATTAAA
359506 AATAAATATTTAA-AAAAGTACTATTT
1 AATAAATATTTAATAAAAG-ACTATTT
*
359532 -AT-TATATTT-ATAAAA-A-TATTT
1 AATAAATATTTAATAAAAGACTATTT
359553 AATAAATATTTAATAA
1 AATAAATATTTAATAA
359569 TATAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
21 5 0.16
22 3 0.10
23 7 0.23
24 14 0.45
25 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
AATAAATATTTAATAAAAGACTATTT
Found at i:359636 original size:19 final size:18
Alignment explanation
Indices: 359608--359656 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
359598 AATATATTTA
359608 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAATG
359626 AAAACATATAAAATAAATG
1 AAAACA-ATAAAATAAATG
359645 AAAA-AATAAAAT
1 AAAACAATAAAAT
359657 TAAAAATCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.23
18 7 0.23
19 16 0.53
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAACAATAAAATAAATG
Found at i:360443 original size:18 final size:18
Alignment explanation
Indices: 360420--360456 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
360410 TATAGTTTGT
*
360420 TTTTTTTTTCTTTCTCTG
1 TTTTTTTTTCTGTCTCTG
360438 TTTTTTTTTCTGTCTCTG
1 TTTTTTTTTCTGTCTCTG
360456 T
1 T
360457 CTCTAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (18 bp):
TTTTTTTTTCTGTCTCTG
Found at i:360486 original size:18 final size:18
Alignment explanation
Indices: 360421--360489 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
360411 ATAGTTTGTT
360421 TTTTTTTTCTTTCTCTG--
1 TTTTTTTT-TTTCTCTGCC
360438 TTTTTTTTTCTGTCTCTGTCTC
1 TTTTTTTTT-T-TCTCTG-C-C
**
360460 TAGTTTTTTTTCTCTGCC
1 TTTTTTTTTTTCTCTGCC
360478 TTTTTTTTTTTC
1 TTTTTTTTTTTC
360490 AGGTTCGGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.02
17 9 0.21
18 17 0.40
19 1 0.02
20 6 0.14
21 1 0.02
22 7 0.17
ACGTcount: A:0.01, C:0.19, G:0.07, T:0.72
Consensus pattern (18 bp):
TTTTTTTTTTTCTCTGCC
Found at i:360948 original size:3 final size:3
Alignment explanation
Indices: 360930--361012 Score: 116
Period size: 3 Copynumber: 27.7 Consensus size: 3
360920 ATTATTTATT
* *
360930 TAA TATA TAT TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA T-A TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
360975 TAA TAA TAA T-A TAAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TA
361013 TGGATAAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
3 63 0.88
4 5 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:361622 original size:113 final size:113
Alignment explanation
Indices: 361326--361869 Score: 903
Period size: 113 Copynumber: 4.9 Consensus size: 113
361316 TGATAGTATC
* *
361326 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
** * * *
361390 TCATTATGAACCTTCTCTGGCAA---AAAT-AATCAAGTGATGAATTC
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
*
361434 AAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
361494 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
361542 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
361607 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
361655 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
361720 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
*
361768 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCATCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
361833 TCATTATGAA-CTTATCTGGCAATGAATGATCCATCAA
66 TCATTATGAACCTTCTCTGGCAATG-TTGATCCATCAA
361870 GTGGATTTGA
Statistics
Matches: 416, Mismatches: 10, Indels: 15
0.94 0.02 0.03
Matches are distributed among these distances:
104 43 0.10
105 6 0.01
107 2 0.00
108 51 0.12
109 29 0.07
112 19 0.05
113 266 0.64
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (113 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
Found at i:362920 original size:167 final size:167
Alignment explanation
Indices: 362597--363013 Score: 716
Period size: 167 Copynumber: 2.5 Consensus size: 167
362587 GTAGTTCTTA
*
362597 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-AGCAAATTCATCTTCCC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
362661 AATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
66 AATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
362726 GAACGAATTCATCTTCTAAATTCAATGATTGGTTCTG
131 GAACAAATTCATCTTCCAAATTCAATGATTGGTTCTG
*
362763 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCC
*
362827 AAACTCAATGATT-GTTCTGTCT-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
65 AAATTCAATGATTGGTTCTG-CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
*
362890 ATTGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG
129 A-TGAACAAATTCATCTTCCAAATTCAATGATTGGTTCTG
*
362930 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
362995 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
363014 AGATATCACA
Statistics
Matches: 236, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
166 94 0.40
167 136 0.58
168 6 0.03
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (167 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
AATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
GAACAAATTCATCTTCCAAATTCAATGATTGGTTCTG
Found at i:362981 original size:84 final size:84
Alignment explanation
Indices: 362597--363013 Score: 707
Period size: 83 Copynumber: 5.0 Consensus size: 84
362587 GTAGTTCTTA
*
362597 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-AGCAAATTCATCTTCCC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
362661 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
* * * *
362680 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACGAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
362744 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
*
362763 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCC
*
362827 AAACTCAATGATT-GTTCTG
65 AAATTCAATGATTGGTTCTG
* *
362846 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
362911 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
*
362930 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
362995 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
363014 AGATATCACA
Statistics
Matches: 314, Mismatches: 15, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
82 2 0.01
83 196 0.62
84 116 0.37
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
AATTCAATGATTGGTTCTG
Found at i:364146 original size:1 final size:1
Alignment explanation
Indices: 364140--364191 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
364130 TTTTCTTCTC
* * * * * *
364140 TTTTTTTTTATTTTCTTTTTTTCTATTTTTTTATTTTTTTTTATTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
364192 AATTCTCTTC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:364153 original size:10 final size:10
Alignment explanation
Indices: 364140--364192 Score: 70
Period size: 10 Copynumber: 5.0 Consensus size: 10
364130 TTTTCTTCTC
364140 TTTTTTTTTA
1 TTTTTTTTTA
*
364150 TTTTCTTTTTT
1 TTTT-TTTTTA
364161 TCTATTTTTTTA
1 T-T-TTTTTTTA
364173 TTTTTTTTTA
1 TTTTTTTTTA
364183 TTTTTTTTTA
1 TTTTTTTTTA
364193 ATTCTCTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 22 0.58
11 7 0.18
12 7 0.18
13 2 0.05
ACGTcount: A:0.09, C:0.04, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:364156 original size:25 final size:23
Alignment explanation
Indices: 364128--364181 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
364118 CCTTGACCCC
*
364128 TCTTTTCTTCTCTTTTTTTTTATTT
1 TCTTTT-TT-TCTATTTTTTTATTT
364153 TCTTTTTTTCTATTTTTTTATTT
1 TCTTTTTTTCTATTTTTTTATTT
364176 T-TTTTT
1 TCTTTTT
364182 ATTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.18
23 15 0.54
24 2 0.07
25 6 0.21
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (23 bp):
TCTTTTTTTCTATTTTTTTATTT
Found at i:364171 original size:18 final size:18
Alignment explanation
Indices: 364150--364189 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
364140 TTTTTTTTTA
*
364150 TTTTCTTTTTTTCTATTT
1 TTTTATTTTTTTCTATTT
*
364168 TTTTATTTTTTTTTATTT
1 TTTTATTTTTTTCTATTT
364186 TTTT
1 TTTT
364190 TTAATTCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTATTTTTTTCTATTT
Found at i:375525 original size:13 final size:13
Alignment explanation
Indices: 375501--375535 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
375491 TATTTATTAT
375501 ATATTT-ATAAAA
1 ATATTTAATAAAA
375513 ATATTTAAT-AAA
1 ATATTTAATAAAA
375525 ATATTTAATAA
1 ATATTTAATAA
375536 TATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTAATAAAA
Found at i:375603 original size:19 final size:18
Alignment explanation
Indices: 375575--375623 Score: 82
Period size: 19 Copynumber: 2.7 Consensus size: 18
375565 AATATATTTA
375575 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAATG
375593 AAAACATATAAAATAAATG
1 AAAACA-ATAAAATAAATG
375612 AAAA-AATAAAAT
1 AAAACAATAAAAT
375624 TAAAAATCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.23
18 7 0.23
19 16 0.53
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAACAATAAAATAAATG
Found at i:375865 original size:29 final size:30
Alignment explanation
Indices: 375820--375878 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
375810 TATTTTAATA
375820 TGAAGGACTAAAATAAATAAAATTA-AAATT
1 TGAAGGACTAAAATAAA-AAAATTATAAATT
* *
375850 TGAA-GACTAAATTAAAAATATTATAAATT
1 TGAAGGACTAAAATAAAAAAATTATAAATT
375879 CAATTTAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (30 bp):
TGAAGGACTAAAATAAAAAAATTATAAATT
Found at i:376169 original size:13 final size:13
Alignment explanation
Indices: 376151--376180 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
376141 CGCGAGTTCT
376151 GCCGCCGACCACC
1 GCCGCCGACCACC
*
376164 GCCGCCGGCCACC
1 GCCGCCGACCACC
376177 GCCG
1 GCCG
376181 GCCACCGCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.60, G:0.30, T:0.00
Consensus pattern (13 bp):
GCCGCCGACCACC
Found at i:376457 original size:18 final size:18
Alignment explanation
Indices: 376431--376501 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 18
376421 TGGTATAGTT
*
376431 TGTTTTTTTTTTCTTTCTC
1 TGTTTTTTTTTT-TGTCTC
376450 TGTTTTTTTTTTTGTCTC
1 TGTTTTTTTTTTTGTCTC
*
376468 TGTCTCTAGTTTTTTT-TCTC
1 TGT-T-T-TTTTTTTTGTCTC
376488 TGCCTTTTTTTTTT
1 TG--TTTTTTTTTT
376502 CAGGTTCGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 8 0.18
19 19 0.43
20 8 0.18
21 8 0.18
22 1 0.02
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.75
Consensus pattern (18 bp):
TGTTTTTTTTTTTGTCTC
Found at i:376461 original size:22 final size:25
Alignment explanation
Indices: 376426--376484 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
376416 ATCGTTGGTA
*
376426 TAGTTTGTTTTTTTT-T-TCTTTCTC
1 TAGTTT-TTTTTTTTGTCTCTGTCTC
376450 T-GTTTTTTTTTTTGTCTCTGTCTC
1 TAGTTTTTTTTTTTGTCTCTGTCTC
376474 TAGTTTTTTTT
1 TAGTTTTTTTT
376485 CTCTGCCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 8 0.26
23 5 0.16
24 9 0.29
25 9 0.29
ACGTcount: A:0.03, C:0.12, G:0.10, T:0.75
Consensus pattern (25 bp):
TAGTTTTTTTTTTTGTCTCTGTCTC
Found at i:376473 original size:24 final size:22
Alignment explanation
Indices: 376433--376484 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 22
376423 GTATAGTTTG
376433 TTTTTTTTTTCTTTCTCT-GTT
1 TTTTTTTTTTCTTTCTCTAGTT
376454 TTTTTTTTTGTCTCTGTCTCTAGTT
1 TTTTTTTTT-TCT-T-TCTCTAGTT
376479 TTTTTT
1 TTTTTT
376485 CTCTGCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.33
22 3 0.11
23 1 0.04
24 5 0.19
25 9 0.33
ACGTcount: A:0.02, C:0.13, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTTTTTTCTTTCTCTAGTT
Found at i:376500 original size:20 final size:19
Alignment explanation
Indices: 376433--376501 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
376423 GTATAGTTTG
376433 TTTTTTTTTTCTTTCTCTG-
1 TTTTTTTTTT-TTTCTCTGC
*
376452 TTTTTTTTTTTGTCTCTGTC
1 TTTTTTTTTTTTTCTCTG-C
* **
376472 TCTAGTTTTTTTTCTCTGCC
1 TTTTTTTTTTTTTCTCTG-C
376492 TTTTTTTTTT
1 TTTTTTTTTT
376502 CAGGTTCGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
18 7 0.18
19 10 0.26
20 22 0.56
ACGTcount: A:0.01, C:0.16, G:0.07, T:0.75
Consensus pattern (19 bp):
TTTTTTTTTTTTTCTCTGC
Found at i:376962 original size:3 final size:3
Alignment explanation
Indices: 376954--377021 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
376944 AATATATATT
* *
376954 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
377002 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
377022 TGGATAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:380850 original size:3 final size:3
Alignment explanation
Indices: 380842--380901 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
380832 CCAATTCTCA
380842 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
380890 TTC TTC TTC TTC
1 TTC TTC TTC TTC
380902 CTTTCCAAGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:383031 original size:23 final size:22
Alignment explanation
Indices: 383005--383047 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
382995 AATTTGGTTT
383005 TAAAACATTAATAGGTTTTAAGG
1 TAAAA-ATTAATAGGTTTTAAGG
* *
383028 TAAAATTTATTAGGTTTTAA
1 TAAAAATTAATAGGTTTTAA
383048 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (22 bp):
TAAAAATTAATAGGTTTTAAGG
Found at i:383128 original size:14 final size:14
Alignment explanation
Indices: 383111--383141 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
383101 AATAAACATA
383111 AACGAACATAAATG
1 AACGAACATAAATG
*
383125 AACGACCATAAATG
1 AACGAACATAAATG
383139 AAC
1 AAC
383142 ATATTATTGA
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:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:383406 original size:3 final size:3
Alignment explanation
Indices: 383398--383456 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
383388 GAGTATTTAC
383398 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
383446 TAT TAT TAT TA
1 TAT TAT TAT TA
383457 GTGTTATTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:383518 original size:20 final size:20
Alignment explanation
Indices: 383472--383518 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
383462 ATTTGAATAG
383472 TTATAAACTATGAAAAATGTA
1 TTATAAACTA-GAAAAATGTA
*
383493 AT-TAAACTA-AAAAATGATA
1 TTATAAACTAGAAAAATG-TA
383512 TTATAAA
1 TTATAAA
383519 TCAGAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.32
19 3 0.14
20 11 0.50
21 1 0.05
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (20 bp):
TTATAAACTAGAAAAATGTA
Found at i:384594 original size:17 final size:17
Alignment explanation
Indices: 384569--384603 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
384559 AATTAGTCAC
*
384569 TCAATATTAACCGATGT
1 TCAACATTAACCGATGT
384586 TCAACATTAACCGATGT
1 TCAACATTAACCGATGT
384603 T
1 T
384604 AATGTGGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (17 bp):
TCAACATTAACCGATGT
Found at i:386405 original size:6 final size:6
Alignment explanation
Indices: 386362--386402 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
386352 AGAGAACTCT
*
386362 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTT CTTCT
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCT
386403 TCTGAAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (6 bp):
CTTCTC
Found at i:394519 original size:23 final size:22
Alignment explanation
Indices: 394473--394519 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
394463 AGAATGTCAT
*
394473 GAGGGAACCGATACCCCCACAG
1 GAGGGAACCGATACCCCCAAAG
*
394495 GAGGGAACCGATTCCCCCTAAAG
1 GAGGGAACCGATACCCCC-AAAG
394518 GA
1 GA
394520 AAGTTGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.32, C:0.32, G:0.28, T:0.09
Consensus pattern (22 bp):
GAGGGAACCGATACCCCCAAAG
Found at i:396122 original size:23 final size:23
Alignment explanation
Indices: 396070--396134 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
396060 ACATTATTAT
396070 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
*** *
396093 GCAGCACTCCGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
* *
396116 ATGGCACTTCGGTACAATT
1 ATGGCACTACGGTGCAATT
396135 ATACGAGCTG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:402331 original size:19 final size:21
Alignment explanation
Indices: 402307--402345 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
402297 CATAGTTAAT
402307 AATTTAAGA-G-TGAGTGATA
1 AATTTAAGATGATGAGTGATA
402326 AATTTAAGATGATGAGTGAT
1 AATTTAAGATGATGAGTGAT
402346 TTGAGGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (21 bp):
AATTTAAGATGATGAGTGATA
Found at i:406115 original size:24 final size:24
Alignment explanation
Indices: 406083--406132 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
406073 CACAAATACG
406083 ATTGAGAGTATTGAACGTTCAGTT
1 ATTGAGAGTATTGAACGTTCAGTT
*
406107 ATTGAGAGTGTTGAACGTTCAGTT
1 ATTGAGAGTATTGAACGTTCAGTT
406131 AT
1 AT
406133 CCATTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (24 bp):
ATTGAGAGTATTGAACGTTCAGTT
Found at i:411618 original size:12 final size:12
Alignment explanation
Indices: 411601--411628 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
411591 ACCGTTAGGA
411601 AATTAAATTTAT
1 AATTAAATTTAT
411613 AATTAAATTTAT
1 AATTAAATTTAT
411625 AATT
1 AATT
411629 TATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAAATTTAT
Found at i:411812 original size:54 final size:56
Alignment explanation
Indices: 411675--411814 Score: 150
Period size: 54 Copynumber: 2.5 Consensus size: 56
411665 CTATTATTTA
* *
411675 TAATTTATATATATATTTAATAAAATTTGTATACAAATAAATTTAATATATATTGGCC
1 TAATCTATATATATATTTAAT-AAATTTGTACACAAATAAATTTAATATATATT-GCC
* *
411733 T--TCT-TGTATA-ATTTAATATATATTTGTACACAAAT-AATTTAATATAGT-TT-TC
1 TAATCTATATATATATTTAATA-A-ATTTGTACACAAATAAATTTAATATA-TATTGCC
411785 TAATCTATATATATATTTAATAAATTTGTA
1 TAATCTATATATATATTTAATAAATTTGTA
411815 TAATTTAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
52 2 0.03
53 1 0.01
54 31 0.44
55 25 0.36
56 10 0.14
58 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (56 bp):
TAATCTATATATATATTTAATAAATTTGTACACAAATAAATTTAATATATATTGCC
Found at i:411833 original size:11 final size:10
Alignment explanation
Indices: 411766--411842 Score: 54
Period size: 10 Copynumber: 7.8 Consensus size: 10
411756 TTGTACACAA
411766 ATAATTTAAT
1 ATAATTTAAT
*
411776 ATAGTTT--T
1 ATAATTTAAT
* *
411784 CTAATCTATAT
1 ATAATTTA-AT
411795 ATATATTTAAT
1 ATA-ATTTAAT
*
411806 A-AATTT-GT
1 ATAATTTAAT
411814 ATAATTTAAT
1 ATAATTTAAT
411824 ATATATTTAAT
1 ATA-ATTTAAT
*
411835 AAAATTTA
1 ATAATTTA
411843 TTACCAAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
8 7 0.14
9 9 0.18
10 16 0.31
11 15 0.29
12 4 0.08
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (10 bp):
ATAATTTAAT
Found at i:414138 original size:20 final size:20
Alignment explanation
Indices: 414080--414139 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
414070 CCATATTTAC
* *
414080 GAACATTCCATGATGTTCTA
1 GAACCTTCCATAATGTTCTA
* * *
414100 GAACTTTCTATAATATTCTA
1 GAACCTTCCATAATGTTCTA
414120 GAACCTTCCA-AAGTGTTCTA
1 GAACCTTCCATAA-TGTTCTA
414140 TAACATTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
GAACCTTCCATAATGTTCTA
Found at i:416270 original size:2 final size:2
Alignment explanation
Indices: 416263--416300 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
416253 TCACGAGGTA
416263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
416301 GTTTACTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:425394 original size:2 final size:2
Alignment explanation
Indices: 425387--425432 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
425377 TCACTAGATT
425387 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
425429 TA TA
1 TA TA
425433 ATTTTTAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:429537 original size:3 final size:3
Alignment explanation
Indices: 429529--429569 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
429519 TCAGTTCATT
*
429529 TTA TTA TTA TTAA TTA TTA AT- TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
429570 AATAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:431676 original size:20 final size:21
Alignment explanation
Indices: 431653--431704 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
431643 AGAAATTAAA
431653 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
431673 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
431695 -ATT-ATTTATT
1 AATTCATTTATT
431705 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:436410 original size:19 final size:18
Alignment explanation
Indices: 436386--436425 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
436376 CTCATCCAGC
* *
436386 AAAGAAAGAAGAAGAAGAA
1 AAAGAAAAAAAAAG-AGAA
436405 AAAGAAAAAAAAAGAGAA
1 AAAGAAAAAAAAAGAGAA
436423 AAA
1 AAA
436426 AGGAAAATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAAAGAGAA
Found at i:438141 original size:157 final size:158
Alignment explanation
Indices: 437854--438170 Score: 627
Period size: 157 Copynumber: 2.0 Consensus size: 158
437844 GAGATAACCA
437854 GTTTTACCATCAACTAAACCTTTCCATAGGTTAAGGAAGAGTGAGATATGGCAGTGTGTATTTTG
1 GTTTTACCATCAACTAAACCTTTCCATAGGTTAAGGAAGAGTGAGATATGGCAGTGTGTATTTTG
437919 GAGCAGCAGAAGAGACAGCTGTCGTAGCAGTCATTACAAGAAAATGCACCAATAAAAATCTTCTA
66 GAGCAGCAGAAGAGACAGCTGTCGTAGCAGTCATTACAAGAAAATGCACCAATAAAAATCTTCTA
437984 GTTAATCATGATGATGTTTATGCTTCCG
131 GTTAATCATGATGATGTTTATGCTTCCG
438012 GTTTTACCATCAACTAAACCTTTCCATA-GTTAAGGAAGAGTGAGATATGGCAGTGTGTATTTTG
1 GTTTTACCATCAACTAAACCTTTCCATAGGTTAAGGAAGAGTGAGATATGGCAGTGTGTATTTTG
438076 GAGCAGCAGAAGAGACAGCTGTCGTAGCAGTCATTACAAGAAAATGCACCAATAAAAATCTTCTA
66 GAGCAGCAGAAGAGACAGCTGTCGTAGCAGTCATTACAAGAAAATGCACCAATAAAAATCTTCTA
438141 GTTAATCATGATGATGTTTATGCTTCCG
131 GTTAATCATGATGATGTTTATGCTTCCG
438169 GT
1 GT
438171 AAGATTGTTA
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
157 131 0.82
158 28 0.18
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (158 bp):
GTTTTACCATCAACTAAACCTTTCCATAGGTTAAGGAAGAGTGAGATATGGCAGTGTGTATTTTG
GAGCAGCAGAAGAGACAGCTGTCGTAGCAGTCATTACAAGAAAATGCACCAATAAAAATCTTCTA
GTTAATCATGATGATGTTTATGCTTCCG
Found at i:439124 original size:84 final size:83
Alignment explanation
Indices: 438816--439122 Score: 501
Period size: 84 Copynumber: 3.7 Consensus size: 83
438806 TGGAACAAAT
*
438816 ATAATGTGCTCAATAGCATCTTTTGGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAATGTGCTCAATAGCATCTTCT-GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-
438881 CAATCATTGAATTTTGGAAGA
64 CAATCATTGAA-TTTGGAAGA
438902 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
*
438967 ATCATTGAATTTAGAAG-
66 ATCATTGAATTTGGAAGA
* *
438984 ATAAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAAC
1 AT-AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
439048 TAATCATTGAATTTGGAAGA
65 -AATCATTGAATTTGGAAGA
* *
439068 ATAATGTGTTCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGGTT
1 ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
439123 TGGTAGGAAC
Statistics
Matches: 209, Mismatches: 8, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
82 55 0.26
83 35 0.17
84 57 0.27
85 39 0.19
86 23 0.11
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (83 bp):
ATAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACA
ATCATTGAATTTGGAAGA
Found at i:441698 original size:21 final size:22
Alignment explanation
Indices: 441670--441723 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
441660 ATCTACACTC
*
441670 TTCAAAGATGATAGA-TCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
441691 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
441713 TTCAAAGATGA
1 TTCAAAGATGA
441724 AAACTTTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:442313 original size:112 final size:111
Alignment explanation
Indices: 442116--442771 Score: 803
Period size: 109 Copynumber: 6.0 Consensus size: 111
442106 TAGCAAAGAT
* * *
442116 TCAAATCCATCATTCAATGGATCAACA-TTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATT-GATGGATCATCATTTCCAGAG--AAGTTCATAATGAGAAGAACTCATCTG
* *
442179 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * *
442228 TCAAATCCATCATTCGATGGATTGA-CATTTCCATAGAAGTTCATAATGAGAAGAACTCATATGA
1 TCAAATCCATCATT-GATGGA-TCATCATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGA
442292 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
** *
442340 TTGAATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 TCAAATCCATCA-TTGATGGATCATCATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGA
442405 AGAAGGAAGAAGAAGTTC---AT-AGAAGAATTTGTTCAACCTTTTAC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
** * *
442449 TTGAATCTATTATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCA-TTGATGGATCATCATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGA
*
442514 AGAAGGAAGAAG-AGTTCATAATGAGAAG-ATTTGTTCAACCTTTT-G
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * * * * *
442559 TCTGAATTCATCACTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAA-AAGAAGAACTCATCTG
1 TC-AAATCCATCATTGATGGATCATCATTT-CCAGAGAA-GTTCATAATGAGAAGAACTCATCTG
442622 AAGAA-G--GAAGAAGTTCATAAT---AAGAATTTGTTCAACC-TTTAC
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
* * * * *
442664 TCAAATCCATCACTGATGGAACAGCTTTTCTAGAGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 TCAAATCCATCATTGATGGATCATCATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
442729 AAGGAAGAAGAAGTTCATAATAAGAAGAA-TTGTTCAACTTTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
442772 GCATAATTCT
Statistics
Matches: 485, Mismatches: 34, Indels: 52
0.85 0.06 0.09
Matches are distributed among these distances:
103 8 0.02
104 50 0.10
105 19 0.04
106 4 0.01
107 25 0.05
108 6 0.01
109 132 0.27
110 35 0.07
111 27 0.06
112 125 0.26
113 53 0.11
114 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (111 bp):
TCAAATCCATCATTGATGGATCATCATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
Found at i:442473 original size:109 final size:110
Alignment explanation
Indices: 442119--442746 Score: 732
Period size: 112 Copynumber: 5.7 Consensus size: 110
442109 CAAAGATTCA
** * **
442119 AATCCATCATTCAATGGATCAACA-TTCCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
442182 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCA
65 AAGGAAGAAGAAGTTC---ATGAGAAGAATTTGTTCAACCTTTTACTTG
* * * *
442231 AATCCATCATTCGATGGATTGA-CATTTCCATAG-AAGTTCATAATGAGAAGAACTCATATGAAG
1 AATCCATCATTTGATGGA-TCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
442294 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTG
65 AAGGAAGAAGAAGTTC---ATGAGAAGAATTTGTTCAACCTTTTACTTG
*
442343 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
442408 AGGAAGAAGAAGTTCAT-AGAAGAATTTGTTCAACCTTTTACTTG
66 AGGAAGAAGAAGTTCATGAGAAGAATTTGTTCAACCTTTTACTTG
* *
442452 AATCTATTATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
442517 AGGAAGAAG-AGTTCATAATGAGAAG-ATTTGTTCAACCTTTT-GTCTG
66 AGGAAGAAGAAGTTC---ATGAGAAGAATTTGTTCAACCTTTTACT-TG
* * * * * *
442563 AATTCATCA-CTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAA-AAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGATCATCATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * **
442625 AA-G--GAAGAAGTTCATAATAAGAATTTGTTCAACC-TTTACTCA
65 AAGGAAGAAGAAGTTCATGAGAAGAATTTGTTCAACCTTTTACTTG
* * * * *
442667 AATCCATCA-CTGATGGAACAGCTTTTCTAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
442730 AGGAAGAAGAAGTTCAT
66 AGGAAGAAGAAGTTCAT
442747 AATAAGAAGA
Statistics
Matches: 459, Mismatches: 38, Indels: 43
0.85 0.07 0.08
Matches are distributed among these distances:
103 9 0.02
104 51 0.11
105 18 0.04
106 4 0.01
107 17 0.04
108 6 0.01
109 121 0.26
110 29 0.06
111 28 0.06
112 124 0.27
113 51 0.11
114 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (110 bp):
AATCCATCATTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATGAGAAGAATTTGTTCAACCTTTTACTTG
Done.