Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007937.1 Hibiscus syriacus cultivar Beakdansim tig00110347_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: 820613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:189933 original size:35 final size:35
Alignment explanation
Indices: 189867--189935 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
189857 GTTTCAAAAA
* * *
189867 TGGTATCGATACTATCTTTATTGTATTGATACCCT
1 TGGTATCGATACTATCTTCATAGTATCGATACCCT
189902 TGGTATCGATACTATCTTCCA-AGTATCGATACCC
1 TGGTATCGATACTATCTT-CATAGTATCGATACCC
189936 CATGAATGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (35 bp):
TGGTATCGATACTATCTTCATAGTATCGATACCCT
Found at i:196931 original size:15 final size:15
Alignment explanation
Indices: 196911--196967 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
196901 TTTTATTAAC
* *
196911 ATGTGAATGTGTTCT
1 ATGTGAATATGTTAT
*
196926 ATGTGAAAATGTTAT
1 ATGTGAATATGTTAT
*
196941 ATGTGAATATGTTTT
1 ATGTGAATATGTTAT
* *
196956 ATATGAAAATGT
1 ATGTGAATATGT
196968 GCTAAGTGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (15 bp):
ATGTGAATATGTTAT
Found at i:196947 original size:30 final size:30
Alignment explanation
Indices: 196911--196986 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
196901 TTTTATTAAC
* *
196911 ATGTGAATGTGTTCTATGTGAAAATGTTAT
1 ATGTGAATATGTTCTATATGAAAATGTTAT
* **
196941 ATGTGAATATGTTTTATATGAAAATGTGCT
1 ATGTGAATATGTTCTATATGAAAATGTTAT
* *
196971 AAGTGAAAATGTTCTA
1 ATGTGAATATGTTCTA
196987 CGTGAAGATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (30 bp):
ATGTGAATATGTTCTATATGAAAATGTTAT
Found at i:196959 original size:17 final size:15
Alignment explanation
Indices: 196920--196983 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
196910 CATGTGAATG
*
196920 TGTTCTATGTGAAAA
1 TGTTATATGTGAAAA
*
196935 TGTTATATGTGAATA
1 TGTTATATGTGAAAA
* *
196950 TGTTTTATATGAAAA
1 TGTTATATGTGAAAA
** *
196965 TGTGCTAAGTGAAAA
1 TGTTATATGTGAAAA
196980 TGTT
1 TGTT
196984 CTACGTGAAG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.42
Consensus pattern (15 bp):
TGTTATATGTGAAAA
Found at i:196977 original size:15 final size:15
Alignment explanation
Indices: 196959--196992 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
196949 ATGTTTTATA
196959 TGAAAATGTGCTAAG
1 TGAAAATGTGCTAAG
* *
196974 TGAAAATGTTCTACG
1 TGAAAATGTGCTAAG
196989 TGAA
1 TGAA
196993 GATACCCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (15 bp):
TGAAAATGTGCTAAG
Found at i:197162 original size:25 final size:25
Alignment explanation
Indices: 197126--197200 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
197116 GAGTCGAGGG
*
197126 TTCTACGCGGTCTTTCGGGACAAAT
1 TTCTACGTGGTCTTTCGGGACAAAT
*
197151 TTCTACGTGGTCCTTCGGGACAAA-
1 TTCTACGTGGTCTTTCGGGACAAAT
* *
197175 TTATACGTGGT-TCTTCAGGACAAAT
1 TTCTACGTGGTCT-TTCGGGACAAAT
197200 T
1 T
197201 ATACATGGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
24 20 0.47
25 23 0.53
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (25 bp):
TTCTACGTGGTCTTTCGGGACAAAT
Found at i:197190 original size:24 final size:24
Alignment explanation
Indices: 197129--197204 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
197119 TCGAGGGTTC
* * *
197129 TACGCGGTCTTTCGGGACAAATTTC
1 TACGTGGTCCTTCGGGACAAA-TTA
197154 TACGTGGTCCTTCGGGACAAATTA
1 TACGTGGTCCTTCGGGACAAATTA
* *
197178 TACGTGGTTCTTCAGGACAAATTA
1 TACGTGGTCCTTCGGGACAAATTA
197202 TAC
1 TAC
197205 ATGGCACTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 27 0.59
25 19 0.41
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (24 bp):
TACGTGGTCCTTCGGGACAAATTA
Found at i:197214 original size:24 final size:24
Alignment explanation
Indices: 197143--197240 Score: 83
Period size: 24 Copynumber: 4.0 Consensus size: 24
197133 CGGTCTTTCG
* *
197143 GGACAAATTTCTACGTGGTC-CTTCG
1 GGACAAA-TTATACGTGG-CACTTCA
**
197168 GGACAAATTATACGTGGTTCTTCA
1 GGACAAATTATACGTGGCACTTCA
*
197192 GGACAAATTATACATGGCACTTCGA
1 GGACAAATTATACGTGGCACTTC-A
* * *
197217 TG-CATATTCTACGTGGCACTTCA
1 GGACAAATTATACGTGGCACTTCA
197240 G
1 G
197241 TGTAAACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.02
24 50 0.83
25 9 0.15
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (24 bp):
GGACAAATTATACGTGGCACTTCA
Found at i:211246 original size:22 final size:22
Alignment explanation
Indices: 211221--211274 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
211211 CGTTGATTAC
211221 CGTTGACCGGACCATTGACTGT
1 CGTTGACCGGACCATTGACTGT
*
211243 CGTTGACCGGACCGTTGACTGT
1 CGTTGACCGGACCATTGACTGT
211265 CGTTGACCGG
1 CGTTGACCGG
211275 TCGTTAACTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (22 bp):
CGTTGACCGGACCATTGACTGT
Found at i:215332 original size:27 final size:27
Alignment explanation
Indices: 215302--215386 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
215292 TGTGCAACTC
215302 ACCGAATTCATCATATGTTGATGAACA
1 ACCGAATTCATCATATGTTGATGAACA
* *
215329 ACCG-TTTCGA-CACTATG-TG-TGCAACTC
1 ACCGAATTC-ATCA-TATGTTGATG-AAC-A
* *
215356 ACTGAATTCATCATATGTTGATGAAAA
1 ACCGAATTCATCATATGTTGATGAACA
215383 ACCG
1 ACCG
215387 TTTCAGCACT
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
25 2 0.05
26 10 0.23
27 20 0.47
28 9 0.21
29 2 0.05
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.29
Consensus pattern (27 bp):
ACCGAATTCATCATATGTTGATGAACA
Found at i:215349 original size:54 final size:54
Alignment explanation
Indices: 215286--215533 Score: 336
Period size: 54 Copynumber: 4.6 Consensus size: 54
215276 ACCAAATGGA
* *
215286 ACTATGTGTGCAACTCACCGAATTCATCATATGTTGATGAACAACCGTTTCGAC
1 ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * *
215340 ACTATGTGTGCAACTCACTGAATTCATCATATGTTGATGAAAAACCGTTTC-AGC
1 ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGA-C
* * * * *
215394 ACTATATGTGCAACTCACAGAATCCATCATACGTTGATGAATAATCATTTCGAC
1 ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGAC
** *
215448 ACTATGTGTGCAACTCATGGAATTCATCATATGTTGATGAACAACCATTTCGGC
1 ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGAC
* * *
215502 ACTATATGTGCAACTCACAAAATTAATCATAT
1 ACTATGTGTGCAACTCACAGAATTCATCATAT
215534 TAACTTCTTA
Statistics
Matches: 170, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.01
54 168 0.99
55 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (54 bp):
ACTATGTGTGCAACTCACAGAATTCATCATATGTTGATGAACAACCATTTCGAC
Found at i:215531 original size:108 final size:108
Alignment explanation
Indices: 215286--215532 Score: 370
Period size: 108 Copynumber: 2.3 Consensus size: 108
215276 ACCAAATGGA
* * * *
215286 ACTATGTGTGCAACTCACCGAATTCATCATATGTTGATGAACAACCGTTTCGACACTATGTGTGC
1 ACTATATGTGCAACTCACAGAATTCATCATACGTTGATGAACAACCATTTCGACACTATGTGTGC
*
215351 AACTCACTGAATTCATCATATGTTGATGAAAAACCGTTTCAGC
66 AACTCACTGAATTCATCATATGTTGATGAAAAACCATTTCAGC
* * *
215394 ACTATATGTGCAACTCACAGAATCCATCATACGTTGATGAATAATCATTTCGACACTATGTGTGC
1 ACTATATGTGCAACTCACAGAATTCATCATACGTTGATGAACAACCATTTCGACACTATGTGTGC
* *
215459 AACTCA-TGGAATTCATCATATGTTGATGAACAACCATTTCGGC
66 AACTCACT-GAATTCATCATATGTTGATGAAAAACCATTTCAGC
* *
215502 ACTATATGTGCAACTCACAAAATTAATCATA
1 ACTATATGTGCAACTCACAGAATTCATCATA
215533 TTAACTTCTT
Statistics
Matches: 125, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
107 1 0.01
108 124 0.99
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (108 bp):
ACTATATGTGCAACTCACAGAATTCATCATACGTTGATGAACAACCATTTCGACACTATGTGTGC
AACTCACTGAATTCATCATATGTTGATGAAAAACCATTTCAGC
Found at i:219654 original size:25 final size:23
Alignment explanation
Indices: 219610--219655 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
219600 TTTTAAATAT
*
219610 ATATTTTTAAATTATTTGATTTA
1 ATATTTTTAAATTATATGATTTA
*
219633 ATATTTTTATATTTGATATGATT
1 ATATTTTTA-AATT-ATATGATT
219656 ATTAAAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 3 0.16
25 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (23 bp):
ATATTTTTAAATTATATGATTTA
Found at i:222285 original size:27 final size:27
Alignment explanation
Indices: 222239--222293 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
222229 CATGGAGACT
*
222239 AGATGGGTTAGGAGGATTTTGAGAAGA
1 AGATGGGTTAGGAGGATTTTGAAAAGA
222266 AGATGGGTT--GAGTGAGTTTTGAAAAGA
1 AGATGGGTTAGGAG-GA-TTTTGAAAAGA
222293 A
1 A
222294 TAATACAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 3 0.12
26 2 0.08
27 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.27
Consensus pattern (27 bp):
AGATGGGTTAGGAGGATTTTGAAAAGA
Found at i:224139 original size:6 final size:6
Alignment explanation
Indices: 224128--224158 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
224118 TCAATCAATG
224128 CTGCAC CTGCAC CTGCAC CTGCAC CTGCAC C
1 CTGCAC CTGCAC CTGCAC CTGCAC CTGCAC C
224159 AAACTCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (6 bp):
CTGCAC
Found at i:225496 original size:18 final size:18
Alignment explanation
Indices: 225454--225496 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
225444 TAAAATGCCA
225454 AATAATAATAAAACTTAT
1 AATAATAATAAAACTTAT
* * * *
225472 AAAAATAATAATATTTTT
1 AATAATAATAAAACTTAT
225490 AATAATA
1 AATAATA
225497 TTTTACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAATAATAAAACTTAT
Found at i:235196 original size:16 final size:16
Alignment explanation
Indices: 235175--235208 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
235165 TCCACCATAG
235175 TAAAATAATTTTTGGC
1 TAAAATAATTTTTGGC
*
235191 TAAAATAATTTTTTGC
1 TAAAATAATTTTTGGC
235207 TA
1 TA
235209 GCAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (16 bp):
TAAAATAATTTTTGGC
Found at i:242975 original size:31 final size:31
Alignment explanation
Indices: 242940--243004 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
242930 TTAAAACATT
* *
242940 ATTCTTAGTTTATTATTATTTAGGGATTAGA
1 ATTCTTAGTTTATTATTATTTAGGAATTAAA
242971 ATTCTTAGTTTATTATTATTTAGGAATTAAA
1 ATTCTTAGTTTATTATTATTTAGGAATTAAA
243002 ATT
1 ATT
243005 AGAACATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.52
Consensus pattern (31 bp):
ATTCTTAGTTTATTATTATTTAGGAATTAAA
Found at i:249546 original size:37 final size:37
Alignment explanation
Indices: 249496--249574 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
249486 TTGATTTACT
249496 GGTCATTAATATGGTGGTCTGTGATTGTGTATATTTC
1 GGTCATTAATATGGTGGTCTGTGATTGTGTATATTTC
249533 GGTCATTAATATGGTGGTCTGTGATTGTGTATATTTC
1 GGTCATTAATATGGTGGTCTGTGATTGTGTATATTTC
249570 GGTCA
1 GGTCA
249575 CTAACAATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.19, C:0.09, G:0.28, T:0.44
Consensus pattern (37 bp):
GGTCATTAATATGGTGGTCTGTGATTGTGTATATTTC
Found at i:256675 original size:18 final size:18
Alignment explanation
Indices: 256629--256681 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
256619 TTATCTTTAA
256629 AATTA-TTA-TTTATTAT
1 AATTATTTATTTTATTAT
* * * *
256645 TATTTTTTCTTTTTTTAT
1 AATTATTTATTTTATTAT
256663 AATTATTTATTTTATTAT
1 AATTATTTATTTTATTAT
256681 A
1 A
256682 TCTTCTCATC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 3 0.11
17 2 0.07
18 22 0.81
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
AATTATTTATTTTATTAT
Found at i:257076 original size:19 final size:19
Alignment explanation
Indices: 257052--257094 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
257042 GACATCATGA
257052 AGTTGGCAAAGGAATAGGC
1 AGTTGGCAAAGGAATAGGC
257071 AGTTGGCAAAGGAATAGGC
1 AGTTGGCAAAGGAATAGGC
257090 AGTTG
1 AGTTG
257095 ACGCGGATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.09, G:0.37, T:0.19
Consensus pattern (19 bp):
AGTTGGCAAAGGAATAGGC
Found at i:259769 original size:55 final size:55
Alignment explanation
Indices: 259705--260071 Score: 451
Period size: 55 Copynumber: 6.7 Consensus size: 55
259695 AATTGGTCTA
* ** * **
259705 CTCCCTATTCTTTCAGGGAGTATAAGACTCAAACAATCTTCAAAAAATGTGTTTG
1 CTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCTGAAAATGGGTCCG
* * * * *
259760 CTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTT-TAACAAACGTGTCCC
1 CTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCTGA-AAATGGGTCCG
* * *
259815 CTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTTTGAAAATAGGTTCG
1 CTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCTGAAAATGGGTCCG
* * *
259870 CTCCCTATTCTTTCAGGGAGTAT-AGAACTCCAACAATCTT-TGAAAATGGGTTCA
1 CTCCCTATTCTTTCAGGGAGTATAAG-ACTCGAACAATCTTCTGAAAATGGGTCCG
* * *
259924 CTCCCTATTCTTTCAGGGTGTAT-AGAACTCGAATAATCTTCTGAAAATGGGT-CT
1 CTCCCTATTCTTTCAGGGAGTATAAG-ACTCGAACAATCTTCTGAAAATGGGTCCG
*
259978 CTCCCTATTCTTTCAGGGAGTATAAAACTCGAACAATCTTCTGAAAATGGGTCCG
1 CTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCTGAAAATGGGTCCG
*
260033 CT-CCTATTCTTTCAGGGAGCAT-AGAACTCGAACAATCTT
1 CTCCCTATTCTTTCAGGGAGTATAAG-ACTCGAACAATCTT
260072 GATTTGCTTC
Statistics
Matches: 278, Mismatches: 27, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
53 1 0.00
54 134 0.48
55 141 0.51
56 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (55 bp):
CTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCTGAAAATGGGTCCG
Found at i:260134 original size:37 final size:37
Alignment explanation
Indices: 260071--260191 Score: 163
Period size: 37 Copynumber: 3.3 Consensus size: 37
260061 CGAACAATCT
** *
260071 TGATTTGCTTCACTACTCTTATGTGAAAGCTTATAGA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTATAGA
* *
260108 TTATTTCCTTCACTACTCTTCCGTGAAGGCTTATAGA
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTATAGA
* *
260145 TGATTTGCTTCACTACTTTTCCGTGAAGGCTTA-AGTT
1 TGATTTGCTTCACTACTCTTCCGTGAAGGCTTATAG-A
260182 TGATTTGCTT
1 TGATTTGCTT
260192 TGAAGGTCAA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
36 2 0.03
37 72 0.97
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (37 bp):
TGATTTGCTTCACTACTCTTCCGTGAAGGCTTATAGA
Found at i:261492 original size:7 final size:7
Alignment explanation
Indices: 261478--261521 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
261468 TATTTTTATT
261478 TTTC-TC
1 TTTCTTC
261484 TTTCTTC
1 TTTCTTC
261491 TTTCTTC
1 TTTCTTC
261498 TTTCTTC
1 TTTCTTC
261505 TTTCTTC
1 TTTCTTC
261512 TTTCTTC
1 TTTCTTC
261519 TTT
1 TTT
261522 TTTTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.11
7 33 0.89
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTCTTC
Found at i:261536 original size:14 final size:14
Alignment explanation
Indices: 261446--261536 Score: 56
Period size: 15 Copynumber: 6.1 Consensus size: 14
261436 TTGAACCCCC
*
261446 TTTTTATTCTTTTT
1 TTTTTTTTCTTTTT
*
261460 TTATTTTTTATTTTT
1 TT-TTTTTTCTTTTT
* *
261475 ATTTTTCTCTTTCTT
1 TTTTTTTTCTTT-TT
*
261490 CTTTCTTCTTTCTTCTT
1 -TTT-TT-TTTCTTTTT
* *
261507 TCTTCTTTCTTCTTT
1 TTTTTTTTCTT-TTT
*
261522 TTTTTTTTATTTTT
1 TTTTTTTTCTTTTT
261536 T
1 T
261537 CATTTTCTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
14 20 0.35
15 24 0.42
16 4 0.07
17 4 0.07
18 5 0.09
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTTCTTTTT
Found at i:261542 original size:14 final size:13
Alignment explanation
Indices: 261445--261542 Score: 67
Period size: 14 Copynumber: 7.5 Consensus size: 13
261435 CTTGAACCCC
*
261445 CTTTTTA-TTCTT
1 CTTTTTATTTTTT
261457 -TTTTTATTTTTT
1 CTTTTTATTTTTT
*
261469 ATTTTTATTTTTCT
1 CTTTTTATTTTT-T
* *
261483 CTTTCTTCTTTCTT
1 CTTT-TTATTTTTT
* *
261497 CTTTCTTCTTTCTT
1 CTTT-TTATTTTTT
*
261511 CTTTCTTCTTTTTT
1 CTTT-TTATTTTTT
261525 -TTTTTATTTTTT
1 CTTTTTATTTTTT
*
261537 CATTTT
1 CTTTTT
261543 CTTTCATTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
11 6 0.08
12 12 0.16
13 18 0.24
14 32 0.43
15 6 0.08
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTTTATTTTTT
Found at i:261543 original size:28 final size:28
Alignment explanation
Indices: 261447--261588 Score: 98
Period size: 28 Copynumber: 5.0 Consensus size: 28
261437 TGAACCCCCT
*
261447 TTTTATTCTTTT-TTTATTTTTTATTTTTA
1 TTTT-TTCTTTTCTTCATTTTTT-TTTTTA
* *
261476 -TTTTTCTCTTTCTTC-TTTCTTCTTTCTTC
1 TTTTTTCT-TTTCTTCATTT-TT-TTTTTTA
*
261505 TTTCTTC-TTTCTTC-TTTTTTTTTTTA
1 TTTTTTCTTTTCTTCATTTTTTTTTTTA
* *
261531 TTTTTTCATTTTCTTTCATTTTTCTTTTCA
1 TTTTTTC-TTTTC-TTCATTTTTTTTTTTA
*
261561 TTTTCTCATTTTC-TCATTTTCTTTTTTT
1 TTTTTTC-TTTTCTTCATTTT-TTTTTTT
261589 CTTTAAAAAA
Statistics
Matches: 91, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
26 11 0.12
27 6 0.07
28 30 0.33
29 16 0.18
30 28 0.31
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTTTCTTTTCTTCATTTTTTTTTTTA
Found at i:261558 original size:22 final size:24
Alignment explanation
Indices: 261533--261589 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
261523 TTTTTTTATT
261533 TTTTCATTTTCTTTCATTTT-TC-
1 TTTTCATTTTCTTTCATTTTCTCA
261555 TTTTCATTTTC--TCATTTTCTCA
1 TTTTCATTTTCTTTCATTTTCTCA
261577 TTTTC-TTTT-TTTC
1 TTTTCATTTTCTTTC
261590 TTTAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 7 0.23
21 6 0.19
22 18 0.58
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTTCATTTTCTTTCATTTTCTCA
Found at i:261564 original size:11 final size:11
Alignment explanation
Indices: 261533--261566 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
261523 TTTTTTTATT
261533 TTTTCATTTTC
1 TTTTCATTTTC
261544 -TTTCATTTTTC
1 TTTTCA-TTTTC
261555 TTTTCATTTTC
1 TTTTCATTTTC
261566 T
1 T
261567 CATTTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCATTTTC
Found at i:261571 original size:8 final size:8
Alignment explanation
Indices: 261530--261582 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
261520 TTTTTTTTTT
*
261530 ATTTTTTC
1 ATTTTCTC
261538 ATTTTCTTTC
1 ATTTTC--TC
261548 ATTTT-TC
1 ATTTTCTC
261555 --TTT-TC
1 ATTTTCTC
261560 ATTTTCTC
1 ATTTTCTC
261568 ATTTTCTC
1 ATTTTCTC
261576 ATTTTCT
1 ATTTTCT
261583 TTTTTTCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
5 5 0.13
7 5 0.13
8 22 0.56
10 7 0.18
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (8 bp):
ATTTTCTC
Found at i:261589 original size:30 final size:30
Alignment explanation
Indices: 261512--261589 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
261502 TTCTTTCTTC
*
261512 TTTCTTC-TTTTTTTTTTT-ATTTTTTCAT
1 TTTCTTCATTTTTTTTTTTCATTTTCTCAT
*
261540 TTTCTTTCA-TTTTTCTTTTCATTTTCTCAT
1 TTTC-TTCATTTTTTTTTTTCATTTTCTCAT
261570 TTTC-TCATTTTCTTTTTTTC
1 TTTCTTCATTTT-TTTTTTTC
261590 TTTAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 7 0.17
29 15 0.36
30 20 0.48
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTCTTCATTTTTTTTTTTCATTTTCTCAT
Found at i:286693 original size:50 final size:51
Alignment explanation
Indices: 286621--286725 Score: 176
Period size: 50 Copynumber: 2.1 Consensus size: 51
286611 TCAAAAATTT
* * *
286621 TATATGTAAGGTGTGAATTGTATTGTGAGTAATTAAAAATGATTCT-ATTA
1 TATATGTAAGGTGTGAATTGTATTATGAGTAATTAAAAAAGATTCTCAATA
286671 TATATGTAAGGTGTGAATTGTATTATGAGTAATTAAAAAAGATTCTCAATA
1 TATATGTAAGGTGTGAATTGTATTATGAGTAATTAAAAAAGATTCTCAATA
286722 TATA
1 TATA
286726 CTACCTGGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 44 0.86
51 7 0.14
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.40
Consensus pattern (51 bp):
TATATGTAAGGTGTGAATTGTATTATGAGTAATTAAAAAAGATTCTCAATA
Found at i:287712 original size:2 final size:2
Alignment explanation
Indices: 287705--287745 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
287695 ACAAGTTTTC
287705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
287746 ACAGTCAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:293873 original size:22 final size:22
Alignment explanation
Indices: 293839--293894 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
293829 TTGGTATATG
* *
293839 TATATGATTCTTAAGG-AATTT
1 TATATGGTACTTAAGGAAATTT
*
293860 CTATATGGTACTTATGGACAATTT
1 -TATATGGTACTTAAGGA-AATTT
293884 TATATGGTACT
1 TATATGGTACT
293895 ACGGTGCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.45
23 11 0.38
24 5 0.17
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (22 bp):
TATATGGTACTTAAGGAAATTT
Found at i:293905 original size:23 final size:24
Alignment explanation
Indices: 293855--293898 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
293845 ATTCTTAAGG
*
293855 AATTTCTATATGGTACTTATGGAC
1 AATTTCTATATGGTACTTACGGAC
293879 AATTT-TATATGGTAC-TACGG
1 AATTTCTATATGGTACTTACGG
293899 TGCAATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 10 0.53
24 5 0.26
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (24 bp):
AATTTCTATATGGTACTTACGGAC
Found at i:293929 original size:24 final size:24
Alignment explanation
Indices: 293902--293953 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
293892 ACTACGGTGC
*
293902 AATTCTACGCGGCACTTCGGTACA
1 AATTCTACGCGACACTTCGGTACA
* *
293926 AATTCTACGTGACACTTCGGTGCA
1 AATTCTACGCGACACTTCGGTACA
293950 AATT
1 AATT
293954 TATACGAGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (24 bp):
AATTCTACGCGACACTTCGGTACA
Found at i:299690 original size:14 final size:17
Alignment explanation
Indices: 299658--299692 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
299648 TTCCAGACAA
299658 TTCATCTTCTTATCTTC
1 TTCATCTTCTTATCTTC
*
299675 TTCATCTTCTTCTCTTC
1 TTCATCTTCTTATCTTC
299692 T
1 T
299693 CCAATGTGAA
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:0.09, C:0.31, G:0.00, T:0.60
Consensus pattern (17 bp):
TTCATCTTCTTATCTTC
Found at i:300510 original size:24 final size:24
Alignment explanation
Indices: 300483--300528 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
300473 ATAAGTCTAG
* * *
300483 ATTTAATACTTTGATACATGATTC
1 ATTTAATAATATGAAACATGATTC
*
300507 ATTTCATAATATGAAACATGAT
1 ATTTAATAATATGAAACATGAT
300529 ATGAGTTCAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (24 bp):
ATTTAATAATATGAAACATGATTC
Found at i:300905 original size:24 final size:24
Alignment explanation
Indices: 300854--300919 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
300844 TAATTTTATA
*
300854 TGGCACTACGGTGC-AATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
* *
300877 CGGCACTTCGGTGCAAATTCTTCG
1 TGGCACTTCGGTGCAAATTCTACG
*
300901 TGGCACTTCAGTGCAAATT
1 TGGCACTTCGGTGCAAATT
300920 TATACGAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 12 0.32
24 25 0.68
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:301489 original size:21 final size:22
Alignment explanation
Indices: 301459--301506 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
301449 AGCAGTACTT
*
301459 TAGCA-GGTATCGGTA-CACTC
1 TAGCATGGTATCGATACCACTC
*
301479 TAGCATGGTATCGATACCCCTC
1 TAGCATGGTATCGATACCACTC
301501 TAGCAT
1 TAGCAT
301507 TGTGAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.21
21 9 0.38
22 10 0.42
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (22 bp):
TAGCATGGTATCGATACCACTC
Found at i:301524 original size:18 final size:18
Alignment explanation
Indices: 301501--301543 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
301491 GATACCCCTC
*
301501 TAGCATTGTGAAAAATTT
1 TAGCATTATGAAAAATTT
301519 TAGCATTATGAAAAATTT
1 TAGCATTATGAAAAATTT
301537 TAGCATT
1 TAGCATT
301544 TGGTACTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (18 bp):
TAGCATTATGAAAAATTT
Found at i:302782 original size:27 final size:29
Alignment explanation
Indices: 302723--302783 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 29
302713 GAGAAGCTTT
*
302723 TTTTTATTTTATATTAACAAATACTTTAA
1 TTTTTATTTTATATGAACAAATACTTTAA
302752 --TTTA-TTTATTATGAA-AAATA-TTTAA
1 TTTTTATTTTA-TATGAACAAATACTTTAA
302777 TTTTTAT
1 TTTTTAT
302784 ACATTTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
25 5 0.19
26 9 0.33
27 13 0.48
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTTATTTTATATGAACAAATACTTTAA
Found at i:305244 original size:25 final size:25
Alignment explanation
Indices: 305212--305261 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
305202 AAGGCCATTC
305212 TCATTGAATTAATATATATATATAT
1 TCATTGAATTAATATATATATATAT
305237 TCATTGAATTAATATATATATATAT
1 TCATTGAATTAATATATATATATAT
305262 ATATCTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
TCATTGAATTAATATATATATATAT
Found at i:308880 original size:83 final size:84
Alignment explanation
Indices: 308776--308929 Score: 247
Period size: 83 Copynumber: 1.8 Consensus size: 84
308766 AAGGACAAAG
* * *
308776 TTTGGGAGGTTATTTGGATTAAGTTCATCTATCTAAAGTGCAATATTTTATGTGGAGGTTGATG-
1 TTTGAGAGGTTATTTGGATTAAGTCCATCTACCTAAAGTGCAATATTTTATGTGGAGGTTGATGT
308840 CTTGGAAGACTGAACTTTA
66 CTTGGAAGACTGAACTTTA
* * *
308859 TTTGAGAGGTTATTTGGATTAAGTCCATCTCCCTAAAGTGCAATCTTTTATGTGGAGGTTGGTGT
1 TTTGAGAGGTTATTTGGATTAAGTCCATCTACCTAAAGTGCAATATTTTATGTGGAGGTTGATGT
308924 CTTGGA
66 CTTGGA
308930 GGTTATGGCT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
83 58 0.91
84 6 0.09
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (84 bp):
TTTGAGAGGTTATTTGGATTAAGTCCATCTACCTAAAGTGCAATATTTTATGTGGAGGTTGATGT
CTTGGAAGACTGAACTTTA
Found at i:310995 original size:23 final size:24
Alignment explanation
Indices: 310967--311044 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
310957 AGTCAACTAT
310967 GGTCAAAGTCAACGGGTCGGGTCA
1 GGTCAAAGTCAACGGGTCGGGTCA
*
310991 -GTCAAAGTTAACGGGTCGGGTCA
1 GGTCAAAGTCAACGGGTCGGGTCA
*
311014 GGTCAAA--CAATTTGGGTCGGGTCA
1 GGTCAAAGTCAA--CGGGTCGGGTCA
311038 GGTCAAA
1 GGTCAAA
311045 CAGTTCGGGC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.04
23 22 0.46
24 24 0.50
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.21
Consensus pattern (24 bp):
GGTCAAAGTCAACGGGTCGGGTCA
Found at i:311030 original size:24 final size:24
Alignment explanation
Indices: 311002--311066 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
310992 TCAAAGTTAA
311002 CGGGTCGGGTCAGGTCAAACAATT
1 CGGGTCGGGTCAGGTCAAACAATT
* *
311026 TGGGTCGGGTCAGGTCAAACAGTT
1 CGGGTCGGGTCAGGTCAAACAATT
311050 CGGG-CTGGGTCAGGTCA
1 CGGGTC-GGGTCAGGTCA
311067 CGGTTGGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.20, C:0.20, G:0.38, T:0.22
Consensus pattern (24 bp):
CGGGTCGGGTCAGGTCAAACAATT
Found at i:314260 original size:31 final size:31
Alignment explanation
Indices: 314225--314308 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
314215 GGAGTACCTT
* *
314225 GGGGCCTGAGAGCCTACCCAAGATAATTCTC
1 GGGGCCTGAGAGCCTACCCAAGAAAAATCTC
*
314256 GGGGCCAT-AGAGGCTTACCCAAGAAAAATCTC
1 GGGGCC-TGAGA-GCCTACCCAAGAAAAATCTC
*
314288 GGGGCC-GCAAAGCCTACCCAA
1 GGGGCCTG-AGAGCCTACCCAA
314309 AGCTTGCCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
31 18 0.41
32 26 0.59
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGGCCTGAGAGCCTACCCAAGAAAAATCTC
Found at i:315162 original size:23 final size:22
Alignment explanation
Indices: 315131--315192 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
315121 AGTCAACTCT
*
315131 GGTCAAAGTCAACGGGTCGGGTC
1 GGTCAAAGTCAACGGGTC-AGTC
*
315154 GGTTAAAGTCAACGGGTCAGTC
1 GGTCAAAGTCAACGGGTCAGTC
315176 GGTCAAAGTCAACGGGT
1 GGTCAAAGTCAACGGGT
315193 TGAGTCGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.19
Consensus pattern (22 bp):
GGTCAAAGTCAACGGGTCAGTC
Found at i:315183 original size:22 final size:23
Alignment explanation
Indices: 315131--315205 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
315121 AGTCAACTCT
*
315131 GGTCAAAGTCAACGGGTCGGGTC
1 GGTCAAAGTCAACGGGTCGAGTC
*
315154 GGTTAAAGTCAACGGGTC-AGTC
1 GGTCAAAGTCAACGGGTCGAGTC
*
315176 GGTCAAAGTCAACGGGTTGAGTC
1 GGTCAAAGTCAACGGGTCGAGTC
315199 GGGTCAA
1 -GGTCAA
315206 TCAGTTTGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
22 19 0.41
23 21 0.46
24 6 0.13
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.20
Consensus pattern (23 bp):
GGTCAAAGTCAACGGGTCGAGTC
Found at i:319348 original size:21 final size:21
Alignment explanation
Indices: 319306--319348 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
319296 TTTATGGGCT
* * *
319306 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
319327 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
319348 A
1 A
319349 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:320990 original size:23 final size:23
Alignment explanation
Indices: 320960--321020 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
320950 ACATTTTATA
320960 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
320983 TGGCACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
*
321006 TGGCACTTAGGTGCA
1 TGGCACTTCGGTGCA
321021 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:324246 original size:70 final size:70
Alignment explanation
Indices: 324133--324273 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
324123 ATCTAGGCAA
*
324133 GTAAACAAAGAGTAAAGTAAAGAGAAAGGGGAAAACAAAAGAATGTGGGCTTTAAGATGATTTAT
1 GTAAACAAAGAGTAAAGTAAAGAGAAAGGGGAAAACAAAAGAATGTGGGCTTTAAGATGATTTAG
324198 CCCTT
66 CCCTT
324203 GTAAACAAAGAGTAAAGTAAAGAGAAAGGGGAAAACAAAAGAATGTGGGCTTTAAGATGATTTAG
1 GTAAACAAAGAGTAAAGTAAAGAGAAAGGGGAAAACAAAAGAATGTGGGCTTTAAGATGATTTAG
324268 CCCTT
66 CCCTT
324273 G
1 G
324274 ACCAAGAAGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.21
Consensus pattern (70 bp):
GTAAACAAAGAGTAAAGTAAAGAGAAAGGGGAAAACAAAAGAATGTGGGCTTTAAGATGATTTAG
CCCTT
Found at i:348072 original size:23 final size:23
Alignment explanation
Indices: 348044--348130 Score: 129
Period size: 23 Copynumber: 3.7 Consensus size: 23
348034 GAATATGTTC
*
348044 ATGAACACGTTCGTGAACATTAA
1 ATGAACATGTTCGTGAACATTAA
* *
348067 ACGAACATGTTCATGAACATATAA
1 ATGAACATGTTCGTGAACAT-TAA
348091 ATGAACATGTTCGTGAACATTAA
1 ATGAACATGTTCGTGAACATTAA
*
348114 ATGAACATATTCGTGAA
1 ATGAACATGTTCGTGAA
348131 TAATAAATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
23 36 0.63
24 21 0.37
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (23 bp):
ATGAACATGTTCGTGAACATTAA
Found at i:348086 original size:12 final size:12
Alignment explanation
Indices: 348032--348110 Score: 61
Period size: 12 Copynumber: 6.7 Consensus size: 12
348022 TGAATGCTAA
*
348032 ATGAATATGTTC
1 ATGAACATGTTC
*
348044 ATGAACACGTTC
1 ATGAACATGTTC
* **
348056 GTGAACAT-TAA
1 ATGAACATGTTC
*
348067 ACGAACATGTTC
1 ATGAACATGTTC
* **
348079 ATGAACATATAA
1 ATGAACATGTTC
348091 ATGAACATGTTC
1 ATGAACATGTTC
*
348103 GTGAACAT
1 ATGAACAT
348111 TAAATGAACA
Statistics
Matches: 48, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
11 7 0.15
12 41 0.85
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (12 bp):
ATGAACATGTTC
Found at i:348095 original size:47 final size:46
Alignment explanation
Indices: 348044--348138 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 46
348034 GAATATGTTC
*
348044 ATGAACACGTTCGTGAACATTAAACGAACATGTTCATGAACATATAA
1 ATGAACACGTTCGTGAACATTAAACGAACATATTCATGAACA-ATAA
* * * *
348091 ATGAACATGTTCGTGAACATTAAATGAACATATTCGTGAATAATAA
1 ATGAACACGTTCGTGAACATTAAACGAACATATTCATGAACAATAA
348137 AT
1 AT
348139 AAACGAACAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 6 0.14
47 37 0.86
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (46 bp):
ATGAACACGTTCGTGAACATTAAACGAACATATTCATGAACAATAA
Found at i:348168 original size:30 final size:30
Alignment explanation
Indices: 348132--348243 Score: 120
Period size: 30 Copynumber: 3.7 Consensus size: 30
348122 ATTCGTGAAT
*
348132 AATAAATAAACGAACATGAACACCTTCAAA
1 AATAAATAAACGAACACGAACACCTTCAAA
* * **
348162 AATAAATAAACGAACATGAACACGATATTGAA
1 AATAAATAAACGAACACGAACAC-CT-TCAAA
* *
348194 AAT--TTAAATGAACACGAACACCTTCAAA
1 AATAAATAAACGAACACGAACACCTTCAAA
*
348222 AATAAATAAAAGAACACGAACA
1 AATAAATAAACGAACACGAACA
348244 TAACCTTGTT
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
28 6 0.09
29 1 0.01
30 53 0.79
31 1 0.01
32 6 0.09
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (30 bp):
AATAAATAAACGAACACGAACACCTTCAAA
Found at i:356797 original size:27 final size:26
Alignment explanation
Indices: 356766--356820 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
356756 CATGAAATAA
*
356766 AATTAAGCAAGGATAAATATATAAGAT
1 AATTAAGCAAGGATAAATAAATAA-AT
*
356793 AATTAAGCAATGATAAATAAATAAAT
1 AATTAAGCAAGGATAAATAAATAAAT
356819 AA
1 AA
356821 ATACATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.25
Consensus pattern (26 bp):
AATTAAGCAAGGATAAATAAATAAAT
Found at i:357245 original size:14 final size:14
Alignment explanation
Indices: 357226--357271 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
357216 CACACAAAAT
357226 TTAAATAAATGACA
1 TTAAATAAATGACA
*
357240 TTAAATGAAA--A-T
1 TTAAAT-AAATGACA
357252 TTAAATAAATGACA
1 TTAAATAAATGACA
357266 TTAAAT
1 TTAAAT
357272 GAAAATCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
11 3 0.12
12 6 0.23
13 2 0.08
14 12 0.46
15 3 0.12
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (14 bp):
TTAAATAAATGACA
Found at i:357250 original size:26 final size:26
Alignment explanation
Indices: 357221--357277 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
357211 AAAACCACAC
357221 AAAATTTAAATAAATGACATTAAATG
1 AAAATTTAAATAAATGACATTAAATG
357247 AAAATTTAAATAAATGACATTAAATG
1 AAAATTTAAATAAATGACATTAAATG
357273 AAAAT
1 AAAAT
357278 CATCTGCCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.30
Consensus pattern (26 bp):
AAAATTTAAATAAATGACATTAAATG
Found at i:357277 original size:16 final size:16
Alignment explanation
Indices: 357232--357277 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
357222 AAATTTAAAT
357232 AAATGACATTAAATGA
1 AAATGACATTAAATGA
357248 AAAT----TTAAAT--
1 AAATGACATTAAATGA
357258 AAATGACATTAAATGA
1 AAATGACATTAAATGA
357274 AAAT
1 AAAT
357278 CATCTGCCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 12
0.67 0.00 0.33
Matches are distributed among these distances:
10 4 0.17
12 6 0.25
14 6 0.25
16 8 0.33
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.28
Consensus pattern (16 bp):
AAATGACATTAAATGA
Found at i:357634 original size:68 final size:70
Alignment explanation
Indices: 357525--357657 Score: 191
Period size: 68 Copynumber: 1.9 Consensus size: 70
357515 TTAACATTTA
*
357525 TGGTAAAAGTGTCCAACAATAACAAAACCGATAGCGCCTAATAATGTTTCCGATCAT-TTTTACC
1 TGGTAAAAGTGTCCAACAATAACAAAACCGATAGCACCTAATAATGTTTCCGATCATATTTTACC
357589 AAATC
66 AAATC
* * * *
357594 TGGTAAAA-TG-CCTAATAATAACAAAATCGGTAGCATCTAATAATGTTTCCGATCATATTTTAC
1 TGGTAAAAGTGTCC-AACAATAACAAAACCGATAGCACCTAATAATGTTTCCGATCATATTTTAC
357657 C
65 C
357658 GGTTTTATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 2 0.04
68 40 0.70
69 15 0.26
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (70 bp):
TGGTAAAAGTGTCCAACAATAACAAAACCGATAGCACCTAATAATGTTTCCGATCATATTTTACC
AAATC
Found at i:365934 original size:31 final size:31
Alignment explanation
Indices: 365899--365974 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
365889 CTAACGTGAC
**
365899 TCTTGGGTAAGCTTTACGGCCCTGAAATCAT
1 TCTTGGGTAAGCCCTACGGCCCTGAAATCAT
* * * *
365930 TCTTGGGTAGGCCCTGCGGCCCTGAGATCTT
1 TCTTGGGTAAGCCCTACGGCCCTGAAATCAT
*
365961 TCTTGGGTAGGCCC
1 TCTTGGGTAAGCCC
365975 CGTGGCCTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.14, C:0.26, G:0.29, T:0.30
Consensus pattern (31 bp):
TCTTGGGTAAGCCCTACGGCCCTGAAATCAT
Found at i:365987 original size:31 final size:31
Alignment explanation
Indices: 365915--366001 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
365905 GTAAGCTTTA
* *
365915 CGGCCCTGA-AATCATTCTTGGGTAGGCCCTG
1 CGGCCCTGAGAA-CTTTCTTGGGTAGGCCCCG
*
365946 CGGCCCTGAGATCTTTCTTGGGTAGGCCCCG
1 CGGCCCTGAGAACTTTCTTGGGTAGGCCCCG
* * *
365977 TGGCCTTGAGAACTTTATTGGGTAG
1 CGGCCCTGAGAACTTTCTTGGGTAG
366002 ACTCTCAGGC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 47 0.98
32 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.31, T:0.29
Consensus pattern (31 bp):
CGGCCCTGAGAACTTTCTTGGGTAGGCCCCG
Found at i:366151 original size:14 final size:14
Alignment explanation
Indices: 366132--366159 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
366122 ATGGTTTTAA
366132 AAGAAGTAGATATT
1 AAGAAGTAGATATT
366146 AAGAAGTAGATATT
1 AAGAAGTAGATATT
366160 CGTGAGACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
AAGAAGTAGATATT
Found at i:366904 original size:18 final size:18
Alignment explanation
Indices: 366882--366934 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
366872 TTATGATATT
*
366882 TTGATGTGGTATTGTTACA
1 TTGATGTCGTATTGTTA-A
* *
366901 -TGATGTTGTAATGTTAA
1 TTGATGTCGTATTGTTAA
366918 TTGATGTCGTAGTTGTT
1 TTGATGTCGTA-TTGTT
366935 GTTGTGCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 23 0.82
19 4 0.14
ACGTcount: A:0.21, C:0.04, G:0.26, T:0.49
Consensus pattern (18 bp):
TTGATGTCGTATTGTTAA
Found at i:376117 original size:15 final size:15
Alignment explanation
Indices: 376097--376127 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
376087 AATGTTTTGT
376097 CCCAATCGTGCTGCA
1 CCCAATCGTGCTGCA
376112 CCCAATCGTGCTGCA
1 CCCAATCGTGCTGCA
376127 C
1 C
376128 TCTTTTCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (15 bp):
CCCAATCGTGCTGCA
Found at i:376338 original size:21 final size:21
Alignment explanation
Indices: 376308--376357 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
376298 ATCACGTATA
376308 TTAAT-TTTAGAATTTA-TGAT
1 TTAATATTTAGAATTTAGTG-T
**
376328 TTAATATTTAGGGTTTAGTGT
1 TTAATATTTAGAATTTAGTGT
376349 TTAATATTT
1 TTAATATTT
376358 TAAGATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 19 0.73
22 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (21 bp):
TTAATATTTAGAATTTAGTGT
Found at i:391443 original size:19 final size:19
Alignment explanation
Indices: 391416--391461 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
391406 AAAAGTAACA
*
391416 GAAAGAAATCAAATTCTTT
1 GAAATAAATCAAATTCTTT
391435 GAAATAAATCAAATTCTTT
1 GAAATAAATCAAATTCTTT
391454 GAAATAAA
1 GAAATAAA
391462 AGAGAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (19 bp):
GAAATAAATCAAATTCTTT
Found at i:391741 original size:24 final size:24
Alignment explanation
Indices: 391708--391762 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
391698 AAAATGATTA
* *
391708 TTTTCTAAGAAAGAGAGAAAATAT
1 TTTTCAAAGAAAGAGAGAAAACAT
*
391732 TTTTCAAAGAAGGAGAGAAAACAT
1 TTTTCAAAGAAAGAGAGAAAACAT
391756 TTTTCAA
1 TTTTCAA
391763 GTGAAGAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.29
Consensus pattern (24 bp):
TTTTCAAAGAAAGAGAGAAAACAT
Found at i:391982 original size:83 final size:83
Alignment explanation
Indices: 391881--392166 Score: 423
Period size: 83 Copynumber: 3.5 Consensus size: 83
391871 TAATATCTGA
* * **
391881 AAATAGATAATAATATCTTTAAAATTTAAAATATTAAATCTGAGAGTTTTACTTTAACCAAAACT
1 AAATAGATTATAATATCTTTTAAATTTAAAATATTAAATCTGAGAGTTTTACTCCAACCAAAACT
*
391946 CTTTTAATATTTAAATTT
66 CTTTTAATATCTAAATTT
* * * * *
391964 AAACATATTATAATATCTTTTAAATTTATAATATTAAATCTGATAGTTTTACTCCAACCGAAACT
1 AAATAGATTATAATATCTTTTAAATTTAAAATATTAAATCTGAGAGTTTTACTCCAACCAAAACT
392029 CTTTTAATATCTAAATTT
66 CTTTTAATATCTAAATTT
* *
392047 AAATAGATTATAATATCTTTTAAATTTATAATATTAAACCTGAGAGTTTTACTCCAACCAAAACT
1 AAATAGATTATAATATCTTTTAAATTTAAAATATTAAATCTGAGAGTTTTACTCCAACCAAAACT
392112 CTTTTAATATCTAAATTT
66 CTTTTAATATCTAAATTT
**
392130 AAATAGAAAATAATAT-TATTTAAATTT-AAATATTAAA
1 AAATAGATTATAATATCT-TTTAAATTTAAAATATTAAA
392167 CATATATTCC
Statistics
Matches: 184, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
82 10 0.05
83 174 0.95
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (83 bp):
AAATAGATTATAATATCTTTTAAATTTAAAATATTAAATCTGAGAGTTTTACTCCAACCAAAACT
CTTTTAATATCTAAATTT
Found at i:396966 original size:3 final size:3
Alignment explanation
Indices: 396932--396994 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
396922 CAATTTACTT
* * * *
396932 TTA TTA TTG TTA TTT TTA TTTA TTA ATA TTA TTA TTA TACA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA
396979 TTA TTTA TTA TTA TTA
1 TTA -TTA TTA TTA TTA
396995 AATAAATATT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
3 41 0.84
4 8 0.16
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:396975 original size:13 final size:13
Alignment explanation
Indices: 396959--396994 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
396949 ATTTATTAAT
396959 ATTATTATTATAC
1 ATTATTATTATAC
**
396972 ATTATTATTATTT
1 ATTATTATTATAC
396985 ATTATTATTA
1 ATTATTATTA
396995 AATAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATTATTATAC
Found at i:396994 original size:16 final size:16
Alignment explanation
Indices: 396935--396994 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
396925 TTTACTTTTA
* *
396935 TTATTGTTATTTTTAT
1 TTATTATTATTATTAT
*
396951 TTATTAATATTATTA-
1 TTATTATTATTATTAT
*
396966 TTATACATTATTATTAT
1 TTAT-TATTATTATTAT
396983 TTATTATTATTA
1 TTATTATTATTA
396995 AATAAATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 4 0.11
16 28 0.78
17 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:398247 original size:14 final size:13
Alignment explanation
Indices: 398212--398237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
398202 TATAATTTTA
398212 CATTTTAATCATT
1 CATTTTAATCATT
398225 CATTTTAATCATT
1 CATTTTAATCATT
398238 AGTTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
CATTTTAATCATT
Found at i:398337 original size:17 final size:16
Alignment explanation
Indices: 398317--398361 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
398307 ATTATTGTAA
*
398317 TATTTTTATTATATTAT
1 TATTATTATT-TATTAT
*
398334 TATTATTATTTATTTT
1 TATTATTATTTATTAT
398350 TAATTATTATTT
1 T-ATTATTATTT
398362 TATATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTATTTATTAT
Found at i:398534 original size:113 final size:112
Alignment explanation
Indices: 398417--398638 Score: 247
Period size: 113 Copynumber: 2.0 Consensus size: 112
398407 TAAAATCCTA
** *
398417 TATTTCATAAAATATTTA-TAATCATATTTTAA-T-ATATATTTATTTTTTTAATAT-TAAGAAA
1 TATTTCATAAAATATAAATTAAT--TATTTTAATTAAT-TATTTA-TTTTTTAATATCAAAGAAA
* ** *
398478 A-AGATTGTCTTAAAACACCTAGAAGTTTGTTTTCTGATATTTTTAAATATCC
62 AGA-ACTGTCTTAAAACACCTAGAAG-TCATTTTCTGATATTTCTAAATATCC
* * *
398530 TATTTTATAAATTATAAATTAATTGTTTTAATTAATTATTTATTTTTTAATATCAAAGAAAAGAA
1 TATTTCATAAAATATAAATTAATTATTTTAATTAATTATTTATTTTTTAATATCAAAGAAAAGAA
**
398595 CTGTCTTAAGGCACCTAGAAGTCATTTTCTGATATTTCTAAATA
66 CTGTCTTAAAACACCTAGAAGTCATTTTCTGATATTTCTAAATA
398639 AATAAATATC
Statistics
Matches: 92, Mismatches: 12, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
112 38 0.41
113 47 0.51
114 7 0.08
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.46
Consensus pattern (112 bp):
TATTTCATAAAATATAAATTAATTATTTTAATTAATTATTTATTTTTTAATATCAAAGAAAAGAA
CTGTCTTAAAACACCTAGAAGTCATTTTCTGATATTTCTAAATATCC
Found at i:399212 original size:26 final size:26
Alignment explanation
Indices: 399156--399226 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
399146 TTTTCTTTTA
* *
399156 AATTTTATTACTTATTATTTTTATATT
1 AATTTTATTAATT-TTATTTTGATATT
399183 -ATTTTATTAATTTT-TTTTGAGTATT
1 AATTTTATTAATTTTATTTTGA-TATT
399208 AATTTTAATT-ATTTTATTT
1 AATTTT-ATTAATTTTATTT
399227 ATCTGTTAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 5 0.13
25 6 0.16
26 21 0.55
27 6 0.16
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (26 bp):
AATTTTATTAATTTTATTTTGATATT
Found at i:406771 original size:114 final size:114
Alignment explanation
Indices: 406571--406790 Score: 305
Period size: 114 Copynumber: 1.9 Consensus size: 114
406561 CATGTTCTCA
* * * *
406571 TAGTAGAAATAAGAAGACCTAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTAATTT
1 TAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTAAGTTATCTGATATAATTC
* * *
406636 GGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTGCTCG
66 GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCG
* * * * **
406685 TAGTAGAAATAAGGAGGCCCAATAACATCTTTTGGAAGTGTTCTTTGAGTTATCTGATATGGTTC
1 TAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTAAGTTATCTGATATAATTC
* *
406750 GGTAGGAACCCCATAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
406791 CTGCATGATC
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
114 91 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAACATCTTCTGGAAGTGTTCTTTAAGTTATCTGATATAATTC
GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCG
Found at i:408939 original size:54 final size:54
Alignment explanation
Indices: 408857--409011 Score: 247
Period size: 54 Copynumber: 2.9 Consensus size: 54
408847 GAAATCTTGG
408857 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
1 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* *
408911 CAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* * * * *
408965 CAGAAGCCACAGGAAAGGTTGAATGCGCTGTCAAATGTTTTATGAAC
1 CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
409012 CTGCTATTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.25
Consensus pattern (54 bp):
CAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:409422 original size:22 final size:22
Alignment explanation
Indices: 409367--409446 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
409357 TACATCTGCA
* * *
409367 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGACAAATTCT
** * *
409389 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGACAAATTCT
* * *
409411 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGACAAATTCT
409433 CTTTTCAAAGATGA
1 CTTTTCAAAGATGA
409447 AAGCTTTATG
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGACAAATTCT
Found at i:410242 original size:157 final size:158
Alignment explanation
Indices: 409956--410262 Score: 562
Period size: 157 Copynumber: 1.9 Consensus size: 158
409946 TTATCTTGAG
* *
409956 ATTGGAGCATGTTACCCAATCAATATGTTATTTTGAAACATAATGAGAAAACGATTTTCATAGTT
1 ATTGGAGCATGTTACCCAATCAACATGTTACTTTGAAACATAATGAGAAAACGATTTTCATAGTT
410021 TCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCTTAG-TTTTTT
66 TCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCTTAGTTTTTTT
410085 TACTTAGTAAACTATTTCCAACAACCTT
131 TACTTAGTAAACTATTTCCAACAACCTT
*
410113 ATTGGGGCATGTTACCCAATCAACATGTTACTTTGAAACATAATGAGAAAACGATTTTCATAGTT
1 ATTGGAGCATGTTACCCAATCAACATGTTACTTTGAAACATAATGAGAAAACGATTTTCATAGTT
*
410178 TCTCATTTTATCTTTTTTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCTTAGTTTTTTT
66 TCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCTTAG-TTTTTT
410243 TTACTTAGTAAACTATTTCC
130 TTACTTAGTAAACTATTTCC
410263 CACATCTGTA
Statistics
Matches: 144, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
157 119 0.83
159 25 0.17
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (158 bp):
ATTGGAGCATGTTACCCAATCAACATGTTACTTTGAAACATAATGAGAAAACGATTTTCATAGTT
TCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCTTAGTTTTTTT
TACTTAGTAAACTATTTCCAACAACCTT
Found at i:410364 original size:76 final size:76
Alignment explanation
Indices: 410265--411099 Score: 1555
Period size: 76 Copynumber: 11.0 Consensus size: 76
410255 CTATTTCCCA
410265 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
410330 ACCCTCAGGGT
66 ACCCTCAGGGT
* * ** *
410341 CATCTGTAAGTCTTGTAGTGCATGATGTCTCCAAAAAGCCTTTAGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
410406 ACCCTCAGGGT
66 ACCCTCAGGGT
410417 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
410482 ACCCTCAGGGT
66 ACCCTCAGGGT
*
410493 CATCTGTAAGTCCTACAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
410558 ACCCTCAGGGT
66 ACCCTCAGGGT
410569 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
410634 ACCCTCAGGGT
66 ACCCTCAGGGT
410645 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
410710 ACCCTCAGGGT
66 ACCCTCAGGGT
410721 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
410786 ACCCTCAGGGT
66 ACCCTCAGGGT
*
410797 CATCTGTAAGTCCTGCAGTGCATGATGTCTCC-AAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
410861 ACCCTCAGGGT
66 ACCCTCAGGGT
410872 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
410937 ACCCTCAGGTT
66 ACCCTCAGGGT
*
410948 CATCTGTAAGTCCTGTAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
411013 ACCCTCAGGGT
66 ACCCTCAGGGT
* *
411024 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
411089 ACCCTCGGGGT
66 ACCCTCAGGGT
411100 TATTCATAAG
Statistics
Matches: 737, Mismatches: 21, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 0.10
76 663 0.90
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCCTCAGGGT
Found at i:411292 original size:3 final size:3
Alignment explanation
Indices: 411258--411320 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
411248 CAATTTACTT
* * * *
411258 TTA TTA TTG TTA TTT TTA TTTA TTA ATA TTA TTA TTA TACA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA
411305 TTA TTTA TTA TTA TTA
1 TTA -TTA TTA TTA TTA
411321 AATAAATATT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
3 41 0.84
4 8 0.16
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:411301 original size:13 final size:13
Alignment explanation
Indices: 411285--411320 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
411275 ATTTATTAAT
411285 ATTATTATTATAC
1 ATTATTATTATAC
**
411298 ATTATTATTATTT
1 ATTATTATTATAC
411311 ATTATTATTA
1 ATTATTATTA
411321 AATAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTATTATTATAC
Found at i:411320 original size:16 final size:16
Alignment explanation
Indices: 411261--411320 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
411251 TTTACTTTTA
* *
411261 TTATTGTTATTTTTAT
1 TTATTATTATTATTAT
*
411277 TTATTAATATTATTA-
1 TTATTATTATTATTAT
*
411292 TTATACATTATTATTAT
1 TTAT-TATTATTATTAT
411309 TTATTATTATTA
1 TTATTATTATTA
411321 AATAAATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 4 0.11
16 28 0.78
17 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:412589 original size:18 final size:18
Alignment explanation
Indices: 412540--412589 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
412530 TTTAGTTTTT
412540 ATAATTTTACATTTTAATC
1 ATAATTTT-CATTTTAATC
412559 ATTAA-TTTCATTTTAATC
1 A-TAATTTTCATTTTAATC
*
412577 ATAATTTTTATTT
1 ATAATTTTCATTT
412590 GACTATGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 18 0.64
19 4 0.14
20 3 0.11
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (18 bp):
ATAATTTTCATTTTAATC
Found at i:412656 original size:12 final size:11
Alignment explanation
Indices: 412639--412730 Score: 75
Period size: 12 Copynumber: 8.4 Consensus size: 11
412629 TTATTTCCTT
412639 TTATTTTAATCA
1 TTATTTTAAT-A
412651 TTATTTGTAATA
1 TTATTT-TAATA
*
412663 TTATTTTATTA
1 TTATTTTAATA
*
412674 TTA--TTATTA
1 TTATTTTAATA
*
412683 TTATTATTATTA
1 TTATT-TTAATA
412695 TTATTTT-AT-
1 TTATTTTAATA
*
412704 TTGTTTTAATTA
1 TTATTTTAA-TA
*
412716 TTATTTTATTA
1 TTATTTTAATA
412727 TTAT
1 TTAT
412731 AAATATATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
9 15 0.22
10 2 0.03
11 16 0.24
12 31 0.46
13 4 0.06
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.67
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:412674 original size:3 final size:3
Alignment explanation
Indices: 412661--412730 Score: 85
Period size: 3 Copynumber: 24.0 Consensus size: 3
412651 TTATTTGTAA
412661 TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
412706 GTTT TAAT TAT TAT T-T TAT TAT TAT
1 -TAT T-AT TAT TAT TAT TAT TAT TAT
412731 AAATATATAT
Statistics
Matches: 60, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
2 7 0.12
3 50 0.83
4 3 0.05
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:412686 original size:32 final size:32
Alignment explanation
Indices: 412644--412730 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 32
412634 TCCTTTTATT
* *
412644 TTAATCATTATTTGTAATATTATTTTATTAT-TA
1 TTAATTATTATTT-TATTATTATTTTATT-TGTA
*
412677 TT-ATTATTATTATTATTATTATTTTATTTGTT
1 TTAATTATTATT-TTATTATTATTTTATTTGTA
412709 TTAATTATTATTTTATTATTAT
1 TTAATTATTATTTTATTATTAT
412731 AAATATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
31 1 0.02
32 35 0.73
33 12 0.25
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (32 bp):
TTAATTATTATTTTATTATTATTTTATTTGTA
Found at i:412923 original size:20 final size:19
Alignment explanation
Indices: 412898--412939 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
412888 CTATTTTATA
412898 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
412918 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
412937 AAT
1 AAT
412940 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:413024 original size:113 final size:111
Alignment explanation
Indices: 412803--413024 Score: 243
Period size: 112 Copynumber: 2.0 Consensus size: 111
412793 AATAATCATA
* *
412803 TTTTAATATATATTTATTTTTTAATATTAAGAAAAAGACTGTCTTAAAACACCTAGAAGTCTGTT
1 TTTTAATATATATTTATTTTTTAATATAAAGAAAAAGACTGTCTTAAAACACCTAGAAGTCTATT
* * ** * * *
412868 TTCTGATATTTTTAAATATCCTATTTTATAAATTATATATTAATTG
66 TTCTGATATTTCTAAAGATAATAATATATAAATTATAAATTAATTG
* ** *
412914 TTTTAATTATTTATTTATTTTTTAATATCAAAG-AAAAGAGCTGTCTTAAGGCATCTAGAAGTC-
1 TTTTAA-TATATATTTATTTTTTAATAT-AAAGAAAAAGA-CTGTCTTAAAACACCTAGAAGTCT
* *
412977 ATTTTCTGATATTTCTAAAGA-AATAAATATCTTAATGTATAAATTAAT
63 ATTTTCTGATATTTCTAAAGATAAT-AATATATAAAT-TATAAATTAAT
413025 AGATTTTCTT
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
111 7 0.08
112 51 0.56
113 33 0.36
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (111 bp):
TTTTAATATATATTTATTTTTTAATATAAAGAAAAAGACTGTCTTAAAACACCTAGAAGTCTATT
TTCTGATATTTCTAAAGATAATAATATATAAATTATAAATTAATTG
Found at i:413092 original size:6 final size:7
Alignment explanation
Indices: 413074--413103 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
413064 AATTATATAT
413074 ATTTTTA
1 ATTTTTA
413081 ATTTTTA
1 ATTTTTA
413088 ATTTTTA
1 ATTTTTA
413095 ATTTTTA
1 ATTTTTA
413102 AT
1 AT
413104 AATAGAGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:418335 original size:29 final size:30
Alignment explanation
Indices: 418264--418341 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 30
418254 TTTCAAACCG
*
418264 AATTAATCGCTACCCGAATATTGAAAAAAA
1 AATTAATCGTTACCCGAATATTGAAAAAAA
418294 AACGTTAATCGTTACCCGAATATT-AAAAAAA
1 AA--TTAATCGTTACCCGAATATTGAAAAAAA
* * *
418325 TATTAACCGTTCCCCGA
1 AATTAATCGTTACCCGA
418342 TCGAACTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 13 0.31
30 2 0.05
31 8 0.19
32 19 0.45
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (30 bp):
AATTAATCGTTACCCGAATATTGAAAAAAA
Found at i:423853 original size:19 final size:19
Alignment explanation
Indices: 423829--423914 Score: 82
Period size: 19 Copynumber: 4.2 Consensus size: 19
423819 GCGTTTTTGA
*
423829 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
423848 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
423869 AAAAACATGTTGTTGCGATAGTG
1 --AAA-ATG-TGTTGCGATAGTG
* *
423892 AAAAAGTGTTGCTATAGTG
1 AAAATGTGTTGCGATAGTG
423911 AAAA
1 AAAA
423915 ATCCAAAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
19 32 0.57
20 2 0.04
21 4 0.07
23 5 0.09
24 3 0.05
25 10 0.18
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:424349 original size:20 final size:20
Alignment explanation
Indices: 424324--424388 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
424314 TACCACCAGT
*
424324 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATAGTCAAAATCG
* **
424344 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--TAGTCAAAATCG
*
424365 CGTTGCAATAGTCAAAATCG
1 CGTTGCGATAGTCAAAATCG
424385 CGTT
1 CGTT
424389 ACGAATCTGG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.09
20 17 0.49
21 12 0.34
22 3 0.09
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAAATCG
Found at i:424442 original size:19 final size:19
Alignment explanation
Indices: 424418--424454 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
424408 TGCGATACTG
* *
424418 GAGATCGCGTTGTGATTTA
1 GAGATCGCATTGCGATTTA
424437 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
424455 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:430459 original size:18 final size:18
Alignment explanation
Indices: 430438--430490 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
430428 TTTTTGAAAT
430438 TTTTATTTTTAAATAAAA
1 TTTTATTTTTAAATAAAA
430456 TTTTTATTTTTAAA-AAAA
1 -TTTTATTTTTAAATAAAA
**
430474 CATT-TTTTT-AATAAAA
1 TTTTATTTTTAAATAAAA
430490 T
1 T
430491 ATCATAATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 2 0.07
16 9 0.30
17 2 0.07
18 4 0.13
19 13 0.43
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTATTTTTAAATAAAA
Found at i:430466 original size:20 final size:19
Alignment explanation
Indices: 430434--430480 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
430424 ATAATTTTTG
*
430434 AAATTTTTATTTTTAAATA
1 AAATTTTTATTTTTAAAAA
430453 AAATTTTTATTTTTAAAAA
1 AAATTTTTATTTTTAAAAA
430472 AACATTTTT
1 AA-ATTTTT
430481 TTAATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATTTTTATTTTTAAAAA
Found at i:430692 original size:30 final size:30
Alignment explanation
Indices: 430613--430685 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
430603 CTCCATTATC
430613 GGGATTAAATCCCAGTATGATGCCCTTGAA
1 GGGATTAAATCCCAGTATGATGCCCTTGAA
430643 GGGATTAAATCCCAGTATGATGCCCTTGAA
1 GGGATTAAATCCCAGTATGATGCCCTTGAA
430673 GGGATTAAATCCC
1 GGGATTAAATCCC
430686 GATATGAACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (30 bp):
GGGATTAAATCCCAGTATGATGCCCTTGAA
Found at i:431820 original size:17 final size:17
Alignment explanation
Indices: 431789--431822 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
431779 CCAATAATTT
431789 AATTTATAAAAATTTAA
1 AATTTATAAAAATTTAA
431806 AATTT-TAAAAGATTTAA
1 AATTTATAAAA-ATTTAA
431823 TGTATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AATTTATAAAAATTTAA
Found at i:433974 original size:30 final size:30
Alignment explanation
Indices: 433940--434023 Score: 159
Period size: 30 Copynumber: 2.8 Consensus size: 30
433930 CGGTAGTTAT
433940 TTAAACTGATTCATTAATTTAAATAACTAC
1 TTAAACTGATTCATTAATTTAAATAACTAC
*
433970 TTAAACTGATTCATTAATTTAGATAACTAC
1 TTAAACTGATTCATTAATTTAAATAACTAC
434000 TTAAACTGATTCATTAATTTAAAT
1 TTAAACTGATTCATTAATTTAAAT
434024 CCCGCGTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (30 bp):
TTAAACTGATTCATTAATTTAAATAACTAC
Found at i:435146 original size:17 final size:17
Alignment explanation
Indices: 435124--435162 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
435114 TAATCTACCG
435124 ATGTTGAAAACATTTTC
1 ATGTTGAAAACATTTTC
*
435141 ATGTTGAAAACATTTTG
1 ATGTTGAAAACATTTTC
435158 ATGTT
1 ATGTT
435163 TCGATATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (17 bp):
ATGTTGAAAACATTTTC
Found at i:435558 original size:65 final size:65
Alignment explanation
Indices: 435438--435586 Score: 185
Period size: 65 Copynumber: 2.3 Consensus size: 65
435428 TTTCGAATAC
* * * * ***
435438 AATTTATGCACCGATGCAC-AGTCATGCATCGATGCACTCTGGATTTTATTAAAACATCGAATTG
1 AATTTGTGCACCGATGCACAAGCCATGCATCGATGCACCCAGGATTTTATTAAAACATCGAAGCA
* * *
435502 ATTTTGTGCACCGATGCACAAGCCATGCATCGATGCACCCAGGCTATTT-TTGAAACATCGAAGC
1 AATTTGTGCACCGATGCACAAGCCATGCATCGATGCACCCAGGAT-TTTATTAAAACATCGAAGC
435566 A
65 A
435567 AATTTGTGCACCGATGCACA
1 AATTTGTGCACCGATGCACA
435587 CCCTAGTGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 17 0.24
65 52 0.72
66 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (65 bp):
AATTTGTGCACCGATGCACAAGCCATGCATCGATGCACCCAGGATTTTATTAAAACATCGAAGCA
Found at i:443723 original size:21 final size:21
Alignment explanation
Indices: 443681--443724 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
443671 ACCTCGGGAG
*
443681 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
443702 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
443723 CT
1 CT
443725 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:444879 original size:65 final size:63
Alignment explanation
Indices: 444760--444969 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
444750 TTTATCAAAG
* *
444760 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
444822 ATT
61 ATT
* *
444825 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
444889 T
63 T
* * * * * *
444890 TGATGCATCGATCCACCAACCATGCATCGATGCATTCTGGCTATTTTGAAACATCGAATGAACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
444954 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
444970 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 46 0.37
65 69 0.56
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:446081 original size:453 final size:453
Alignment explanation
Indices: 445234--446142 Score: 1368
Period size: 453 Copynumber: 2.0 Consensus size: 453
445224 ATCAAAGAGA
* *
445234 AAGCATCAAACCTCAAGTTTGAGCATTTCAATCCTATTTTTCATTCAATATTCATTTTGCTTTCA
1 AAGCATCAAACCTCAAGTTTGAGCATTTCAAGCCTA-TTTTCATTAAATATTCATTTTGCTTTCA
* *
445299 ATAACACTACTTGTACTCAATTGTATTCATTTTTAGTGTTCTTTTCTTTGTTCTAGAATTGTGCA
65 AGAACACTACTTGTACTCAATTGTATTCATTTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCA
* *
445364 AACAATCTGCCTTGTGAGGATTTCCTTGTAAGTTTGCAAATTTGTAATCTTCTCTTTGAGAAAGA
130 AACAATCTGCCTTGTGAGGATTTCCTTGTAAGTTTACAAATTTATAATCTTCTCTTTGAGAAAGA
*
445429 GTGTTCTCAAGAATTGGGGTATATTCTTGAGGGAGTTGTAAGGTTATCTCTTTGGCCTCAAAATA
195 GTGTTCTCAAGAATTGGGGTATATTCTTGAGGGAGTTGTAAGGTTATCTCTTTGGCCTCAAAAGA
**
445494 AAGAACAAATTGGTGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGAC
260 AAGAACAAATTCATGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGAC
*
445559 TTTGATTGAGAAAGTCGAACCACTCTAAATCATTGTACAATTACTTTCAATTTTCTGCAAAAGCT
325 TTTGATTGAGAAAGTCGAACCACTCTAAATCATTGTACAAATACTTTCAATTTTCTGCAAAAGCT
** *
445624 TCCACCAAAATTTTAATTGCCAATTCA-CCCCTCTTGGCCGATTCTGTCGATCGATTAACTCAAC
390 TCCACCAAAATTTT-ATTGCCAATTCACCCCCTCTTGGCCGATTCCATCGATCGATTAACACAAC
*
445688 AAGCATCAAACCTCAAGTTTGAGCATTTTCAAGCCTA-TTTCCTTAAATATTCATTTTTGCTTTC
1 AAGCATCAAACCTCAAGTTTGAGCA-TTTCAAGCCTATTTTCATTAAATATTCA-TTTTGCTTTC
*
445752 AAGAACACTTA-TTGTGCTCAATTGTATT-ATTCTTGAGTGTTC-TTTCTTTGTTCTAGAATTGT
64 AAGAACAC-TACTTGTACTCAATTGTATTCATT-TTGAGTGTTCTTTTCTTTGTTCTAGAATTGT
* * * *
445814 GCAAAC-ATCTTGCCTTGTGAGGATTTTCTTGTAAGTTTACAAAATTTATATTGTTCTCTTTGGG
127 GCAAACAATC-TGCCTTGTGAGGATTTCCTTGTAAGTTTAC-AAATTTATAATCTTCTCTTTGAG
* * * * *
445878 AGAGAGTGTTCTCAAGAATTTGGGGTATAATTCTTGTGGTATTTGTAAGGTTA-CTCTTTGTCCT
190 AAAGAGTGTTCTCAAGAA-TTGGGGTAT-ATTCTTGAGGGAGTTGTAAGGTTATCTCTTTGGCCT
445942 CAAAAGAAAG-ACAAATTCATGAATTTG-TGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGA
253 CAAAAGAAAGAACAAATTCATGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGA
* * * * * *
446005 CGTAGACTTTGGTTGAGAAAGTCGAACTACTCTAAATCGTTGTGCAAATATTTTCAATTTTCTGT
318 CGTAGACTTTGATTGAGAAAGTCGAACCACTCTAAATCATTGTACAAATACTTTCAATTTTCTGC
* * *
446070 AAAAGCTTCCACCGAACTTTTATTGCCAATTCACCCCCTCTTGGCCTATTCCATCGATCGATTAA
383 AAAAGCTTCCACCAAAATTTTATTGCCAATTCACCCCCTCTTGGCCGATTCCATCGATCGATTAA
446135 CACAAC
448 CACAAC
446141 AA
1 AA
446143 TCGAGAATGT
Statistics
Matches: 413, Mismatches: 33, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
452 15 0.04
453 219 0.53
454 118 0.29
455 40 0.10
456 21 0.05
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (453 bp):
AAGCATCAAACCTCAAGTTTGAGCATTTCAAGCCTATTTTCATTAAATATTCATTTTGCTTTCAA
GAACACTACTTGTACTCAATTGTATTCATTTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAA
ACAATCTGCCTTGTGAGGATTTCCTTGTAAGTTTACAAATTTATAATCTTCTCTTTGAGAAAGAG
TGTTCTCAAGAATTGGGGTATATTCTTGAGGGAGTTGTAAGGTTATCTCTTTGGCCTCAAAAGAA
AGAACAAATTCATGAATTTGTTGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACT
TTGATTGAGAAAGTCGAACCACTCTAAATCATTGTACAAATACTTTCAATTTTCTGCAAAAGCTT
CCACCAAAATTTTATTGCCAATTCACCCCCTCTTGGCCGATTCCATCGATCGATTAACACAAC
Found at i:454168 original size:14 final size:14
Alignment explanation
Indices: 454151--454182 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
454141 CTTTTTATTT
*
454151 TTTTTAATTTAATA
1 TTTTTAATTTAAAA
454165 TTTTTAATTTAAAA
1 TTTTTAATTTAAAA
454179 TTTT
1 TTTT
454183 CATATTCTCT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTAATTTAAAA
Found at i:454253 original size:21 final size:20
Alignment explanation
Indices: 454228--454277 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
454218 ATATTCTATT
*
454228 AATTAAAAATAAAATAATTAA
1 AATTAAAAATAAAAT-ATGAA
*
454249 AATTAATTAATAAAATATGAA
1 AATTAA-AAATAAAATATGAA
454270 AA-TAAAAA
1 AATTAAAAA
454278 CTAATCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 12 0.48
22 8 0.32
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AATTAAAAATAAAATATGAA
Found at i:455121 original size:2 final size:2
Alignment explanation
Indices: 455114--455139 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
455104 TTTTTAACTT
455114 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
455140 ATTTAATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:468376 original size:23 final size:23
Alignment explanation
Indices: 468350--468403 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
468340 AATTCGCAAT
468350 CTTTATATAAATAAAATAGTGTA
1 CTTTATATAAATAAAATAGTGTA
* *
468373 CTTTATAGAAATAAAATATTGTA
1 CTTTATATAAATAAAATAGTGTA
468396 CTTTATAT
1 CTTTATAT
468404 TAAAAAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (23 bp):
CTTTATATAAATAAAATAGTGTA
Found at i:472445 original size:3 final size:3
Alignment explanation
Indices: 472439--472474 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
472429 TTTACTCATT
*
472439 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
472475 AAAAAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:474510 original size:14 final size:14
Alignment explanation
Indices: 474473--474510 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
474463 TCTCTATTAA
*
474473 TTATAAATTAAAAT
1 TTATAATTTAAAAT
474487 TTATATATTTAAAAT
1 TTATA-ATTTAAAAT
474502 TTATAATTT
1 TTATAATTT
474511 TTTTCTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATAATTTAAAAT
Found at i:477881 original size:15 final size:15
Alignment explanation
Indices: 477861--477892 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
477851 ATCAATACCT
477861 TTTTGCATACATACA
1 TTTTGCATACATACA
*
477876 TTTTGCATACATTCA
1 TTTTGCATACATACA
477891 TT
1 TT
477893 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:485227 original size:13 final size:13
Alignment explanation
Indices: 485209--485307 Score: 82
Period size: 13 Copynumber: 7.7 Consensus size: 13
485199 TATTATGCTT
485209 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
* *
485222 GAAGAAAGAAAAG
1 GAAGAAAAAAAAA
*
485235 GAAAAAAGAAAAAA
1 GAAGAAA-AAAAAA
*
485249 GAA-AAAGAAAAA
1 GAAGAAAAAAAAA
485261 G-AGAAAAAAGAAA
1 GAAGAAAAAA-AAA
485274 GAA-AAAAGAGAAAA
1 GAAGAAAA-A-AAAA
*
485288 GAA-AAAAAGAAA
1 GAAGAAAAAAAAA
485300 -AAGAAAAA
1 GAAGAAAAA
485308 GGGGGGTCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
11 3 0.04
12 19 0.27
13 29 0.41
14 19 0.27
15 1 0.01
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:485231 original size:7 final size:7
Alignment explanation
Indices: 485209--485305 Score: 68
Period size: 6 Copynumber: 15.0 Consensus size: 7
485199 TATTATGCTT
485209 GAAGAAA
1 GAAGAAA
*
485216 -AAAAAA
1 GAAGAAA
485222 GAAGAAA
1 GAAGAAA
*
485229 GAA-AAG
1 GAAGAAA
*
485235 GAAAAAA
1 GAAGAAA
*
485242 GAAAAAA
1 GAAGAAA
485249 GAA-AAA
1 GAAGAAA
485255 GAA-AAA
1 GAAGAAA
485261 G-AGAAA
1 GAAGAAA
*
485267 AAAGAAA
1 GAAGAAA
*
485274 GAAAAAA
1 GAAGAAA
485281 G-AGAAAA
1 GAAG-AAA
485288 GAA-AAA
1 GAAGAAA
485294 -AAGAAA
1 GAAGAAA
485300 -AAGAAA
1 GAAGAAA
485306 AAGGGGGGTC
Statistics
Matches: 75, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
5 3 0.04
6 36 0.48
7 35 0.47
8 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:485241 original size:20 final size:19
Alignment explanation
Indices: 485216--485307 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 19
485206 CTTGAAGAAA
*
485216 AAAAAAGAAGAAAGAAAAGG
1 AAAAAAGAAAAAAGAAAA-G
485236 AAAAAAGAAAAAAGAAAAAG
1 AAAAAAGAAAAAAG-AAAAG
485256 AAAAAGAGAAAAAAG-AAAG
1 AAAAA-AGAAAAAAGAAAAG
* *
485275 AAAAAAGAGAAAAGAAAAAA
1 AAAAAAGAAAAAAG-AAAAG
485295 AGAAAAAGAAAAA
1 A-AAAAAGAAAAA
485308 GGGGGGTCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
18 8 0.13
19 9 0.14
20 23 0.37
21 23 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAAAGAAAAG
Found at i:485307 original size:7 final size:7
Alignment explanation
Indices: 485216--485307 Score: 97
Period size: 7 Copynumber: 13.7 Consensus size: 7
485206 CTTGAAGAAA
485216 AAAAAAG
1 AAAAAAG
*
485223 AAGAAAG
1 AAAAAAG
*
485230 -AAAAGG
1 AAAAAAG
485236 AAAAAAG
1 AAAAAAG
485243 AAAAAAG
1 AAAAAAG
485250 -AAAAAG
1 AAAAAAG
485256 AAAAAGAG
1 AAAAA-AG
485264 AAAAAAG
1 AAAAAAG
485271 ---AAAG
1 AAAAAAG
485275 AAAAAAG
1 AAAAAAG
*
485282 AGAAAAG
1 AAAAAAG
485289 AAAAAA-
1 AAAAAAG
485295 AGAAAAAG
1 A-AAAAAG
485303 AAAAA
1 AAAAA
485308 GGGGGGTCAA
Statistics
Matches: 71, Mismatches: 6, Indels: 16
0.76 0.06 0.17
Matches are distributed among these distances:
4 4 0.06
6 11 0.15
7 48 0.68
8 8 0.11
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:486752 original size:94 final size:92
Alignment explanation
Indices: 486614--486829 Score: 308
Period size: 94 Copynumber: 2.3 Consensus size: 92
486604 CTGGTTTAGT
* * *
486614 AAAATCAATCATT-GAATTTGGAAGAGGAATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAG
1 AAAACCAATCATTGGAA-TTGAAAGATGAATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAG
* * *
486678 TTATCTGATCTGGTTTGGTATGAACCCC
65 TTATCTGATCTGGTTCGGTAGGAACCAC
* *
486706 GAAAAACCAATCATTGGACTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGA
1 --AAAACCAATCATTGGAATTGAAAGATGAATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGA
486771 GTTATCTGATCTGGTTCGGTAGGAACCAC
64 GTTATCTGATCTGGTTCGGTAGGAACCAC
* *
486800 AGAACCAATCATTGGAATTAAAAGATGAAT
1 AAAACCAATCATTGGAATTGAAAGATGAAT
486830 TACATGATCG
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
92 27 0.25
94 81 0.74
95 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (92 bp):
AAAACCAATCATTGGAATTGAAAGATGAATGTGCTCATAACATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGGTTCGGTAGGAACCAC
Found at i:487719 original size:24 final size:23
Alignment explanation
Indices: 487676--487720 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
487666 GTTCATAATG
*
487676 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
487699 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
487721 AATTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:487723 original size:113 final size:114
Alignment explanation
Indices: 487510--488521 Score: 1396
Period size: 113 Copynumber: 8.8 Consensus size: 114
487500 TAGCAAAGAT
* * * *
487510 TCAAATCCATCATTTGATGGATTAGCATTTTCCAATTCGAGTTCATAATGAGAAGAACTCAGCAT
1 TCAAATCCATCACTTGATGGATCAGC-TTTTCCAGTTCGAGTTCATAATGAGAAGAACT--TCAT
*
487575 TTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
63 CTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
487627 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
487691 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
* *
487740 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAATTCATAATGAGAAGAACTCATCATT
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACT--TCATC
487805 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
64 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
487856 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
487920 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
487969 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
*
488033 AAGAAGGAATAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
*
488082 TCAAATTCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAA-TTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
* * **
488146 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAT
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
* * * **** * *
488195 TCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTT-ATCTA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
* * **
488259 AAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTAT
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
* * * **** *
488307 TCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTT-ATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
* * *** * *
488371 AAG-AGGAAGAAGAAGTTCACAATGAGAAGAGCCTGTTCAACCTTTTAC
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
* * * *
488419 AT-AATTTTATCACAT-ACATGTTAGCATCAGCTTTTGCAGTTCGAGTTCATAATGAGAAGAACT
1 -TCAA----ATC-CATCACTTGAT-GGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACT
* * *
488482 CATCATCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGA
59 --TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGA
488522 GCTTATTCAA
Statistics
Matches: 835, Mismatches: 45, Indels: 26
0.92 0.05 0.03
Matches are distributed among these distances:
112 153 0.18
113 440 0.53
114 3 0.00
115 2 0.00
116 146 0.17
117 58 0.07
119 1 0.00
120 7 0.01
121 25 0.03
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (114 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGC
Done.