Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000847.1 Hibiscus syriacus cultivar Beakdansim tig00001631_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: 265150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:180022 original size:3 final size:3
Alignment explanation
Indices: 180009--180045 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
179999 TAATTGGTAT
180009 ATG ATTG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG A-TG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
180046 CTATTGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:185993 original size:27 final size:27
Alignment explanation
Indices: 185950--186017 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
185940 ATATTGTCCA
*
185950 TACATTTAAAATATAATCCTCT-TCTTT
1 TACATTTAAAATTTAAT-CTCTATCTTT
* *
185977 TACTTTTAAAATTTAATCTTTATCTTT
1 TACATTTAAAATTTAATCTCTATCTTT
*
186004 TAGATTTAAAATTT
1 TACATTTAAAATTT
186018 TAAATTCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.53
Consensus pattern (27 bp):
TACATTTAAAATTTAATCTCTATCTTT
Found at i:186950 original size:8 final size:8
Alignment explanation
Indices: 186931--187056 Score: 90
Period size: 8 Copynumber: 15.8 Consensus size: 8
186921 TTCCCCGATC
*
186931 CTCAATCT
1 CTCAAACT
*
186939 CTTAAACT
1 CTCAAACT
* *
186947 CTTAAATT
1 CTCAAACT
186955 CTCAAACT
1 CTCAAACT
**
186963 CTTTAACT
1 CTCAAACT
* * *
186971 ATGAAATT
1 CTCAAACT
*
186979 ATCAAACT
1 CTCAAACT
186987 CTCAAACT
1 CTCAAACT
*
186995 TTCAAACT
1 CTCAAACT
*
187003 CTCAAATT
1 CTCAAACT
187011 CTCAAACT
1 CTCAAACT
**
187019 CTTTAACT
1 CTCAAACT
* *
187027 CTGAAATT
1 CTCAAACT
*
187035 ATCAAACT
1 CTCAAACT
*
187043 CTCAAATT
1 CTCAAACT
187051 CTCAAA
1 CTCAAA
187057 ATGACTCTTA
Statistics
Matches: 90, Mismatches: 28, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
8 90 1.00
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (8 bp):
CTCAAACT
Found at i:186964 original size:24 final size:24
Alignment explanation
Indices: 186931--187056 Score: 101
Period size: 24 Copynumber: 5.2 Consensus size: 24
186921 TTCCCCGATC
* *
186931 CTCAATCTCTTAAACTCTTAAATT
1 CTCAAACTCTCAAACTCTTAAATT
** * *
186955 CTCAAACTCTTTAACTATGAAATT
1 CTCAAACTCTCAAACTCTTAAATT
* *
186979 ATCAAACTCTCAAACT-TTCAAACT
1 CTCAAACTCTCAAACTCTT-AAATT
* * *
187003 CTCAAATTCTCAAACTCTTTAACT
1 CTCAAACTCTCAAACTCTTAAATT
* * * *
187027 CTGAAATTATCAAACTCTCAAATT
1 CTCAAACTCTCAAACTCTTAAATT
187051 CTCAAA
1 CTCAAA
187057 ATGACTCTTA
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
23 1 0.01
24 79 0.96
25 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (24 bp):
CTCAAACTCTCAAACTCTTAAATT
Found at i:187003 original size:56 final size:56
Alignment explanation
Indices: 186942--187056 Score: 196
Period size: 56 Copynumber: 2.1 Consensus size: 56
186932 TCAATCTCTT
*
186942 AAACTCTTAAATTCTCAAACTCTTTAACTATGAAATTATCAAACTCTCAAACTT-TC
1 AAACTCTCAAATTCTCAAACTCTTTAACTATGAAATTATCAAACTCTCAAA-TTCTC
*
186998 AAACTCTCAAATTCTCAAACTCTTTAACTCTGAAATTATCAAACTCTCAAATTCTC
1 AAACTCTCAAATTCTCAAACTCTTTAACTATGAAATTATCAAACTCTCAAATTCTC
187054 AAA
1 AAA
187057 ATGACTCTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 2 0.04
56 54 0.96
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (56 bp):
AAACTCTCAAATTCTCAAACTCTTTAACTATGAAATTATCAAACTCTCAAATTCTC
Found at i:190289 original size:21 final size:21
Alignment explanation
Indices: 190265--190318 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
190255 ACCGGCTGCA
*
190265 GTGGCATATGAAAGTTGGACG
1 GTGGCATATGAAAGTGGGACG
* *
190286 GTGGTATATGAAAGTGGGGCG
1 GTGGCATATGAAAGTGGGACG
* *
190307 GCGGCATCTGAA
1 GTGGCATATGAA
190319 CCAACGGACT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.41, T:0.22
Consensus pattern (21 bp):
GTGGCATATGAAAGTGGGACG
Found at i:191029 original size:2 final size:2
Alignment explanation
Indices: 191024--191059 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
191014 CACATATTTC
191024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
191060 GCCATTCTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:191977 original size:30 final size:30
Alignment explanation
Indices: 191918--192006 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
191908 CCCGAAGGAC
* * *
191918 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
191947 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
191977 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
192007 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:192042 original size:31 final size:31
Alignment explanation
Indices: 192002--192102 Score: 132
Period size: 31 Copynumber: 3.2 Consensus size: 31
191992 AAAGATCCTC
*
192002 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
192033 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
*
192064 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
192096 GGTAAAC
1 GGTAAAC
192103 CCTCGACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 33 0.56
32 26 0.44
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:193356 original size:21 final size:21
Alignment explanation
Indices: 193326--193370 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
193316 ATTCTGTCGT
* *
193326 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
193347 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
193368 TTG
1 TTG
193371 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:195820 original size:20 final size:20
Alignment explanation
Indices: 195795--195834 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
195785 CGAAAACCAA
195795 GCGTGCCGGAGAGTGACTTT
1 GCGTGCCGGAGAGTGACTTT
195815 GCGTGCCGGAGAGTGACTTT
1 GCGTGCCGGAGAGTGACTTT
195835 CTTTAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.20, G:0.40, T:0.25
Consensus pattern (20 bp):
GCGTGCCGGAGAGTGACTTT
Found at i:198127 original size:194 final size:196
Alignment explanation
Indices: 197785--198174 Score: 766
Period size: 194 Copynumber: 2.0 Consensus size: 196
197775 TGAGGTTGTT
197785 TAAGCTGGACATAAACATGATGACTGAGATATGATAGTCGTTTAAGATTTTGAGATCAAGTTTTA
1 TAAGCTGGACATAAACATGATGACTGAGATATGATAGTCGTTTAAGATTTTGAGATCAAGTTTTA
197850 TTGTATCACAGTCAATGAGTTAACGTTAAGATCAGAATACCGTCTATTTTTAACAGAAAATGACG
66 TTGTATCACAGTCAATGAGTTAACGTTAAGATCAGAATACCGTCTATTTTTAACAGAAAATGACG
197915 AGTTTGGAAAATAATAAATAGTT-GGTGATCATTTTGTAACTTTTAATAGTCGAGGAACTTGACC
131 AGTTTGGAAAATAATAAATAGTTGGGTGATCATTTTGTAACTTTTAATAGTCGAGGAACTTGACC
197979 A
196 A
197980 TAAGCTGGACAT-AACATGATGACTGAGATATGATAGTCGTTTAAGATTTTGAGATCAAGTTTTA
1 TAAGCTGGACATAAACATGATGACTGAGATATGATAGTCGTTTAAGATTTTGAGATCAAGTTTTA
198044 TTGTATCACAGTCAATGAGTTAACGTTAAGATCAGAATACCGTCTATTTTTAACAGAAAATGACG
66 TTGTATCACAGTCAATGAGTTAACGTTAAGATCAGAATACCGTCTATTTTTAACAGAAAATGACG
198109 AGTTTGGAAAATAATAAATAGTTGGGTGATCATTTTGTAACTTTTAATAGTCGAGGAACTTGACC
131 AGTTTGGAAAATAATAAATAGTTGGGTGATCATTTTGTAACTTTTAATAGTCGAGGAACTTGACC
198174 A
196 A
198175 AGCAACACTC
Statistics
Matches: 194, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
194 140 0.72
195 54 0.28
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (196 bp):
TAAGCTGGACATAAACATGATGACTGAGATATGATAGTCGTTTAAGATTTTGAGATCAAGTTTTA
TTGTATCACAGTCAATGAGTTAACGTTAAGATCAGAATACCGTCTATTTTTAACAGAAAATGACG
AGTTTGGAAAATAATAAATAGTTGGGTGATCATTTTGTAACTTTTAATAGTCGAGGAACTTGACC
A
Found at i:199376 original size:29 final size:29
Alignment explanation
Indices: 199334--199391 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
199324 AGGCCGGACA
199334 CTGAAGATGGCACCCGCCTGGATGAGGCG
1 CTGAAGATGGCACCCGCCTGGATGAGGCG
199363 CTGAAGATGGCACCCGCCTGGATGAGGCG
1 CTGAAGATGGCACCCGCCTGGATGAGGCG
199392 AGATATAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.28, G:0.38, T:0.14
Consensus pattern (29 bp):
CTGAAGATGGCACCCGCCTGGATGAGGCG
Found at i:201766 original size:39 final size:39
Alignment explanation
Indices: 201723--201820 Score: 196
Period size: 39 Copynumber: 2.5 Consensus size: 39
201713 CTATCCGAGT
201723 AACCATCAGTAACTTAGTATTAAACTTGCCTATGTCAAC
1 AACCATCAGTAACTTAGTATTAAACTTGCCTATGTCAAC
201762 AACCATCAGTAACTTAGTATTAAACTTGCCTATGTCAAC
1 AACCATCAGTAACTTAGTATTAAACTTGCCTATGTCAAC
201801 AACCATCAGTAACTTAGTAT
1 AACCATCAGTAACTTAGTAT
201821 CCAAAGGCGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (39 bp):
AACCATCAGTAACTTAGTATTAAACTTGCCTATGTCAAC
Found at i:202579 original size:16 final size:17
Alignment explanation
Indices: 202558--202589 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
202548 AGCTTTTCAT
202558 TCAATTTTG-GTTCGGG
1 TCAATTTTGAGTTCGGG
202574 TCAATTTTGAGTTCGG
1 TCAATTTTGAGTTCGG
202590 ATCTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (17 bp):
TCAATTTTGAGTTCGGG
Found at i:209485 original size:11 final size:11
Alignment explanation
Indices: 209460--209495 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
209450 ATATTTAGTG
*
209460 TTATT-ATAAA
1 TTATTAATATA
209470 TTATTAATATA
1 TTATTAATATA
209481 TTATTAATATA
1 TTATTAATATA
209492 TTAT
1 TTAT
209496 GTATCAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATTAATATA
Found at i:210186 original size:21 final size:21
Alignment explanation
Indices: 210160--210207 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
210150 GTTTCTAAAT
210160 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
210181 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
210202 TCGCAA
1 TCGCAA
210208 TGAGATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:210250 original size:21 final size:19
Alignment explanation
Indices: 210216--210323 Score: 90
Period size: 21 Copynumber: 5.3 Consensus size: 19
210206 AATGAGATTT
*
210216 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
210235 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
210258 TCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
* * *
210277 TCGAAGTTCGCGTTGTGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
210300 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
210319 TCCAA
1 TCCAA
210324 AATCGCAAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
19 23 0.32
21 30 0.42
23 18 0.25
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:210268 original size:42 final size:42
Alignment explanation
Indices: 210215--210323 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
210205 CAATGAGATT
210215 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
* * *
210257 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
210299 TTCCAAATTCGTTGCGATAGTCCAA
1 TTCCAAATTCGTTGCGATAGTCCAA
210324 AATCGCAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (42 bp):
TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
Found at i:210801 original size:3 final size:3
Alignment explanation
Indices: 210793--210886 Score: 100
Period size: 3 Copynumber: 30.7 Consensus size: 3
210783 TTCATTTAAA
* *
210793 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
210841 AAT TACT AAT T-T TAT TATT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT T-AT TAT TAT TA
210887 CAAACGGCCA
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.03
3 66 0.87
4 8 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:212087 original size:18 final size:19
Alignment explanation
Indices: 212060--212100 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
212050 TTAATTTTAT
*
212060 TTTTCGTTTATTTATA-TG
1 TTTTCATTTATTTATATTG
*
212078 TTTTCATTTATTTTTATTG
1 TTTTCATTTATTTATATTG
212097 TTTT
1 TTTT
212101 TAAATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.73
Consensus pattern (19 bp):
TTTTCATTTATTTATATTG
Found at i:214407 original size:8 final size:7
Alignment explanation
Indices: 214383--214424 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
214373 CTTTCATACA
214383 TGCA-TT
1 TGCATTT
214389 TGCATTT
1 TGCATTT
214396 TGCATCTT
1 TGCAT-TT
214404 TGCATTT
1 TGCATTT
* *
214411 TTCATTG
1 TGCATTT
214418 TGCATTT
1 TGCATTT
214425 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:214407 original size:15 final size:14
Alignment explanation
Indices: 214383--214424 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
214373 CTTTCATACA
214383 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
214396 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
214411 TTCATTGTGCATTT
1 TGCATTTTGCATTT
214425 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:214512 original size:26 final size:25
Alignment explanation
Indices: 214483--214540 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
214473 CATTCACATA
*
214483 TTTACATTTGAATTTGCATTTGCATT
1 TTTACATTTGAATTTACATTTGCA-T
* * *
214509 TTTACGTTTGTATTTACATTTTCAT
1 TTTACATTTGAATTTACATTTGCAT
214534 TTTACAT
1 TTTACAT
214541 ATTTGGTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.57
Consensus pattern (25 bp):
TTTACATTTGAATTTACATTTGCAT
Found at i:216165 original size:11 final size:11
Alignment explanation
Indices: 216149--216176 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
216139 TTATCCTTTA
216149 ATATATATTAT
1 ATATATATTAT
216160 ATATATATTAT
1 ATATATATTAT
216171 ATATAT
1 ATATAT
216177 CCTTTGTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATATATTAT
Found at i:218741 original size:81 final size:83
Alignment explanation
Indices: 218604--219072 Score: 695
Period size: 81 Copynumber: 5.7 Consensus size: 83
218594 CATTAACTGA
* * *
218604 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
218669 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTGG
* * *
218687 AAGATGAA-TTGTTAATAGCATCTTCT-GAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
218750 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTGG
* *
218768 AAGATGAATGTGCTCATAGCA--TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
218830 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTGG
*
218849 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
218913 AATCAATCATTGAATTTGG
65 AACCAATCATTGAATTTGG
*
218932 AAGATGAATTTGCTAATAG-ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
218996 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTGG
* * *
219014 -AGATGAATTTGCTCATAGCATCTTCTGGAAGTATTC-TTGAGTTATTTGATCTGGTTTGG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
219073 TAGGAACTAC
Statistics
Matches: 360, Mismatches: 19, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
80 7 0.02
81 167 0.46
82 98 0.27
83 88 0.24
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAATTTGG
Found at i:218922 original size:164 final size:165
Alignment explanation
Indices: 218604--219069 Score: 680
Period size: 164 Copynumber: 2.8 Consensus size: 165
218594 CATTAACTGA
* * *
218604 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTT-TAGCAG
1 AAGATGAATTTGCTAATAGCA-CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAG
**
218668 AACCAATCATTGAATTGGGAAGATGAA-TTGTTAATAGCATCTTCT-GAAGTGTTCTTTGAGTTA
64 AACCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
* *
218731 TCTGACCTGGTTTAGCAGAACCAATCATTGAATTGGG
129 TCTGATCTGGTTGAGCAGAACCAATCATTGAATTGGG
* *
218768 AAGATGAATGTGCTCATAGCA-TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 AAGATGAATTTGCTAATAGCACTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
218832 CCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 CCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
218897 TGATCTGGTTG-GACAGAATCAATCATTGAATTTGG
131 TGATCTGGTTGAG-CAGAACCAATCATTGAATTGGG
*
218932 AAGATGAATTTGCTAATAG-ATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAA
1 AAGATGAATTTGCTAATAGCA-CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
* * *
218995 AACCAATCATTGAATTTAG-AGATGAATTTGCTCATAGCATCTTCTGGAAGTATTC-TTGAGTTA
64 AACCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
219058 TTTGATCTGGTT
129 TCTGATCTGGTT
219070 TGGTAGGAAC
Statistics
Matches: 277, Mismatches: 18, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
162 62 0.22
163 40 0.14
164 117 0.42
165 54 0.19
166 4 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (165 bp):
AAGATGAATTTGCTAATAGCACTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
CCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTGAGCAGAACCAATCATTGAATTGGG
Found at i:219034 original size:245 final size:245
Alignment explanation
Indices: 218604--219069 Score: 742
Period size: 245 Copynumber: 1.9 Consensus size: 245
218594 CATTAACTGA
*
218604 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTGAGCAGA
*
218669 ACCAATCATTGAATTGGGAAGATGAATTGTTAATAGCATCTTCTGAAGTGTTCTTTGAGTTATCT
66 ACCAATCATTGAATTGGGAAGATGAATTGCTAATAGCATCTTCTGAAGTGTTCTTTGAGTTATCT
* *
218734 GACCTGGTTTAGCAGAACCAATCATTGAATTGGGAAGATGAATGTGCTCATAGCA-TTCTGGAAG
131 GACCTGGTTTAGCAAAACCAATCATTGAATTGAGAAGATGAATGTGCTCATAGCACTTCTGGAAG
*
218798 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTAG
196 TATTC-TTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTAG
*
218849 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG-GACAG
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTGAG-CAG
* *
218913 AATCAATCATTGAATTTGGAAGATGAATTTGCTAATAG-ATCTTCTGGAAGTGTTCTTTGAGTTA
65 AACCAATCATTGAATTGGGAAGATGAA-TTGCTAATAGCATCTTCT-GAAGTGTTCTTTGAGTTA
* * * *
218977 TCTGATCTGGTTTGGCAAAACCAATCATTGAATTTAG-AGATGAATTTGCTCATAGCATCTTCTG
128 TCTGACCTGGTTTAGCAAAACCAATCATTGAATTGAGAAGATGAATGTGCTCATAGCA-CTTCTG
*
219041 GAAGTATTCTTGAGTTATTTGATCTGGTT
192 GAAGTATTCTTGAGTTATCTGATCTGGTT
219070 TGGTAGGAAC
Statistics
Matches: 203, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
244 1 0.00
245 111 0.55
246 78 0.38
247 13 0.06
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (245 bp):
AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTGAGCAGA
ACCAATCATTGAATTGGGAAGATGAATTGCTAATAGCATCTTCTGAAGTGTTCTTTGAGTTATCT
GACCTGGTTTAGCAAAACCAATCATTGAATTGAGAAGATGAATGTGCTCATAGCACTTCTGGAAG
TATTCTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAATTTAG
Found at i:220064 original size:35 final size:35
Alignment explanation
Indices: 220013--220079 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
220003 TTCAACCAGA
220013 AATAGAATATTGGGGCATT-TTGAAGGCTCATAGC
1 AATAGAATATTGGGGCATTCTTGAAGGCTCATAGC
* *
220047 AATATGAATATTTGGGCATTCTTGTAGGCTCAT
1 AATA-GAATATTGGGGCATTCTTGAAGGCTCAT
220080 CTTAACAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 4 0.14
35 14 0.48
36 11 0.38
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (35 bp):
AATAGAATATTGGGGCATTCTTGAAGGCTCATAGC
Found at i:220323 original size:73 final size:73
Alignment explanation
Indices: 220172--220332 Score: 191
Period size: 73 Copynumber: 2.2 Consensus size: 73
220162 AAGCAAATAT
* * *
220172 TGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAATATTTATCA
1 TGGGGCATGCTG-AAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
220237 GCAAAATGC
65 GCAAAATGC
* * ** * *
220246 TGGGGCATGCTGAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACACTTGTATT
1 TGGGGCATGCTGAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACA-TT-TATC
*
220311 AGC-CAATG-
64 AGCAAAATGC
220319 TGGGGCATGCTGAA
1 TGGGGCATGCTGAA
220333 GGCCTATATC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
73 51 0.68
74 18 0.24
75 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (73 bp):
TGGGGCATGCTGAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCAG
CAAAATGC
Found at i:221630 original size:22 final size:22
Alignment explanation
Indices: 221604--221658 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
221594 ATCTACACTC
*
221604 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
221626 TTCAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
221648 TTCAAAGATGA
1 TTCAAAGATGA
221659 AAACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:222336 original size:17 final size:17
Alignment explanation
Indices: 222283--222339 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
222273 TTTTCCAGAG
222283 GAAGTTCATAATGAGAA
1 GAAGTTCATAATGAGAA
* *
222300 GAACTT-ATCTGAAGGAAGAA
1 GAAGTTCA--T-AATG-AGAA
222320 GAAGTTCATAATGAGAA
1 GAAGTTCATAATGAGAA
222337 GAA
1 GAA
222340 CTTGTTTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
16 1 0.03
17 12 0.39
18 4 0.13
19 4 0.13
20 9 0.29
21 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.25, T:0.21
Consensus pattern (17 bp):
GAAGTTCATAATGAGAA
Found at i:222351 original size:110 final size:110
Alignment explanation
Indices: 222112--223246 Score: 1239
Period size: 110 Copynumber: 10.3 Consensus size: 110
222102 AAACTCATTT
* * * ** * * ** *
222112 GAAGAACTTGTTCAACTTTTTGCTTAAATTTATCACCCGGTGGATCAGCAGTGT-CAGTTAGAGT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCA-TTTCCAGAGAAAGT
*
222176 TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGA
65 TCATAATGAGAAGAACTCATCTG-A-AGGAAGAAGAAGTTCATAATGA
* * * * * * *** *
222224 GAAGAATTTGTTCAACCTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTT
*
222289 CATAATGAGAAGAACTTATCTGAAGGAAGAAGAAGTTCATAATGA
66 CATAATGAGAAGAACTCATCTGAAGGAAGAAGAAGTTCATAATGA
* * * * *
222334 GAAGAACTTGTTTAACCTTTTGCTTGAATTCATCACTTGATGGATTATCATTGCC--AGAAGGTT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTT
*
222397 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
66 CATAATGAGAAGAACTCATCT---GAAGGAAGAAGAAGTTCATAATGA
* ** * *
222445 GAAGAATTTGTTC-ACCTTTTGCTCAAATCCATCA-TTCGATGGATCAGTATTTCCAGAGAAAGT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTT-GATGGATCAGCATTTCCAGAGAAAGT
222508 TCATAATGAGAAGAACTCATCTGAAGAGAAGGAAGAAGTTCATAAT-A
65 TCATAATGAGAAGAACTCATCTGAAG-GAA-GAAGAAGTTCATAATGA
* * * *
222555 GAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGA-AAAGTT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTT
*
222619 CATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGA
66 CATAATGAGAAGAACTCATCTG-A-AGGAAGAAGAAGTTCATAATGA
* * * *
222666 GAAGAACTTGTTTAACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCC--AGAAAGTT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTT
222729 CATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAA-TTCATAATGA
66 CATAATGAGAAGAACTCATCTG-A-AGGAAGAAGAAGTTCATAATGA
* * * * *
222775 GAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGAT-ATCATTGCCAGAGAAGGTT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTT
222839 CAT-ATGAGAAGAACTCATCTGAA-GAAGGAAGAAGAATTCATAATGA
66 CATAATGAGAAGAACTCATCTGAAGGAA-GAAGAAG--TTCATAATGA
* ** *
222885 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA-TTCGATGGATCAGCATTTCCAGAGAAAGT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTT-GATGGATCAGCATTTCCAGAGAAAGT
222949 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
65 TCATAATGAGAAGAACTCATCT---GAAGGAAGAAGAAGTTCATAATGA
* * * * *
222998 GAAG-ACTTGTTCAACTTTTTGCTTAAATTCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTT
223062 CATAAT--G-AG-A---A---GAAGGAAGAAGAAGTTCATAATGA
66 CATAATGAGAAGAACTCATCTGAAGGAAGAAGAAGTTCATAATGA
* * * * * *
223097 GAAGAATTTGTTCAACC-TTTGCTTGAATTCATCATTTGATGGATCAACATTGCGAG-GTAGAGT
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAG-AAAGT
*
223160 TCATAATGAGAAGAACTCTTCATCTGAAGAAGAAAGAAGAAGTTCATAATAA
65 TCATAATGAGAAGAA--C-TCATCTGAAG--G-AAGAAGAAGTTCATAATGA
*
223212 GAAGAACTTGTTCAA-CTTTTGCAT-AATTCTATCAC
1 GAAGAACTTGTTCAACCTTTTGCTTGAATTC-ATCAC
223247 AGAAAGGAGA
Statistics
Matches: 879, Mismatches: 95, Indels: 95
0.82 0.09 0.09
Matches are distributed among these distances:
98 1 0.00
99 72 0.08
100 10 0.01
101 1 0.00
102 2 0.00
103 1 0.00
105 1 0.00
106 3 0.00
107 7 0.01
108 35 0.04
109 81 0.09
110 256 0.29
111 158 0.18
112 173 0.20
113 16 0.02
114 7 0.01
115 52 0.06
116 3 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (110 bp):
GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCAGCATTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGGAAGAAGAAGTTCATAATGA
Found at i:222701 original size:332 final size:332
Alignment explanation
Indices: 222173--223233 Score: 1393
Period size: 332 Copynumber: 3.2 Consensus size: 332
222163 TGTCAGTTAG
* *
222173 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAA-GAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGA-GAAGGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * * * ** *
222237 AACCTTTTCCCTGAATTCATTACTTGATGAATTATTTTTTCCAGAGGAAGTTCATAATGAGAAGA
65 AACCTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGA
222302 ACTTATCTG-A-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTC
130 ACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTC
* * *
222365 ATCACTTGATGGATTATCATTGCCAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
195 ATCACTTGATGGATTAACATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
** *
222430 AGAAATTCATAATGAGAAGAATTTGTTC-ACCTTTTGCTCAAATCCATCATTCGATGGATCAGTA
260 AG-AATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATT-GATGGATCA-TA
*
222494 TTTCCAGAGAA
322 TTGCCAGAGAA
222505 AGTTCATAATGAGAAGAACTCATCTGAAGAGAAGGAAGAAGTTCATAAT-AGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGAAGGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
222569 ACTTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGA-AAAGTTCATAATGAGAAGAA
66 ACCTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
*
222633 CTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATTCA
131 CTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCA
222698 TCACTTGATGGATTAACATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAA
196 TCACTTGATGGATTAACATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
*
222762 GAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGGAT-ATCATT
261 GAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCA-TTGATGGATCAT-ATT
222826 GCCAGAGAA
324 GCCAGAGAA
* *
222835 GGTTCAT-ATGAGAAGAACTCATCTG-A-AGAAGGAAGAAGAATTCATAATGAGAAGAATTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGAAGGAAGAAG--TTCATAATGAGAAGAACTTGTT
* * * *
222897 CAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAG
64 CAACCTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
* * * *
222962 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAG-ACTTGTTCAACTTTTTGCTTAAAT
129 AACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAAT
* * * * *
223026 TCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAG-A---A---G--GAA-G
193 TCATCACTTGATGGATTAACATTTCC--AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
223081 AAGAAG--TTCATAATGAGAAGAATTTGTTCAACC-TTTGCTTGAATTCATCATTTGATGGATCA
256 AAGAAGAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCA-TTGATGGATC-
* * *
223143 ACATTGCGAG-GTAG
319 ATATTGCCAGAG-AA
* *
223157 AGTTCATAATGAGAAGAACTCTTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAG-AGAAGGAAGAAGTTCATAATGAGAAGAACTTG
223222 TTCAA-CTTTTGC
62 TTCAACCTTTTGC
223234 ATAATTCTAT
Statistics
Matches: 657, Mismatches: 48, Indels: 54
0.87 0.06 0.07
Matches are distributed among these distances:
321 26 0.04
322 41 0.06
323 11 0.02
324 8 0.01
325 2 0.00
326 15 0.02
327 36 0.05
328 1 0.00
329 39 0.06
330 123 0.19
331 156 0.24
332 179 0.27
333 20 0.03
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (332 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGAAGGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTTAAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
CTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCA
TCACTTGATGGATTAACATTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
GAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTGATGGATCATATTGC
CAGAGAA
Found at i:223076 original size:99 final size:99
Alignment explanation
Indices: 222971--223174 Score: 295
Period size: 99 Copynumber: 2.1 Consensus size: 99
222961 GAACTCATCT
*
222971 GAAGAAGGAAGAAGAAGTTCATAATGAGAAG-ACTTGTTCAACTTTTTGCTTAAATTCATCATTT
1 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-CTTTGCTTAAATTCATCATTT
* * *
223035 AATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGA
65 AATGGATCAACATTGCCAG-GTAAAGTTCATAATGA
* * *
223070 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTGCTTGAATTCATCATTTG
1 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTTAAATTCATCATTTA
* *
223135 ATGGATCAACATTGCGAGGTAGAGTTCATAATGA
66 ATGGATCAACATTGCCAGGTAAAGTTCATAATGA
223169 GAAGAA
1 GAAGAA
223175 CTCTTCATCT
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
98 1 0.01
99 83 0.88
100 10 0.11
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (99 bp):
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTTAAATTCATCATTTA
ATGGATCAACATTGCCAGGTAAAGTTCATAATGA
Found at i:223628 original size:3 final size:3
Alignment explanation
Indices: 223620--223709 Score: 96
Period size: 3 Copynumber: 30.7 Consensus size: 3
223610 TTCATTTAAA
* * *
223620 TAT TAT TAT TAT TAT TAT TA- TAT TAT AAT TAT TA- TAT AAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
223666 TAC TAT T-T TAT TAT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
223710 CAAACGGGCC
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
2 6 0.08
3 63 0.88
4 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:223645 original size:17 final size:17
Alignment explanation
Indices: 223619--223707 Score: 90
Period size: 17 Copynumber: 5.1 Consensus size: 17
223609 TTTCATTTAA
223619 ATATTATTATTATTATT
1 ATATTATTATTATTATT
*
223636 AT-TATATTATAATTATT
1 ATAT-TATTATTATTATT
* * *
223653 ATATAATTATAATTACT
1 ATATTATTATTATTATT
* *
223670 ATTTTATTATTATTACTA
1 ATATTATTATTATTA-TT
223688 ATATTATTATTAATTATT
1 ATATTATTATT-ATTATT
223706 AT
1 AT
223708 TACAAACGGG
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
16 1 0.02
17 39 0.67
18 14 0.24
19 4 0.07
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTATTATTATTATT
Found at i:224902 original size:19 final size:18
Alignment explanation
Indices: 224866--224914 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
224856 TAGATTTTTA
*
224866 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
224883 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
224902 ATTTTATTGTTTT
1 ATTTTATTGTTTT
224915 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:225826 original size:12 final size:12
Alignment explanation
Indices: 225809--225847 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
225799 TCTCGTCTCG
225809 GGTCGGGGTCGT
1 GGTCGGGGTCGT
225821 GGTCGGGGTCGT
1 GGTCGGGGTCGT
*
225833 GGTCGTGGTCGT
1 GGTCGGGGTCGT
225845 GGT
1 GGT
225848 AATACATGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.56, T:0.28
Consensus pattern (12 bp):
GGTCGGGGTCGT
Found at i:225844 original size:6 final size:6
Alignment explanation
Indices: 225809--225847 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
225799 TCTCGTCTCG
* *
225809 GGTCGG GGTCGT GGTCGG GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
225848 AATACATGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.15, G:0.56, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:225960 original size:19 final size:19
Alignment explanation
Indices: 225936--226002 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
225926 TCGTTGCGAT
*
225936 TTTGGACTACCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
225955 TTTGGAATAAATCGCAAAGCGAA
1 TTTGGACT--ATCGC-AA-CGAA
* *
225978 CTTGGACTATCGCAACAAA
1 TTTGGACTATCGCAACGAA
225997 TTTGGA
1 TTTGGA
226003 ATAAATCGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 15 0.39
20 2 0.05
21 9 0.24
22 2 0.05
23 10 0.26
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:225999 original size:42 final size:42
Alignment explanation
Indices: 225937--226018 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
225927 CGTTGCGATT
*
225937 TTGGACTACCGCAACGAATTTGGAATAAATCGCAAAGCGAAC
1 TTGGACTACCGCAACAAATTTGGAATAAATCGCAAAGCGAAC
* *
225979 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGA
1 TTGGACTACCGCAACAAATTTGGAATAAATCGCAAAGCGA
226019 TAGTCGAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (42 bp):
TTGGACTACCGCAACAAATTTGGAATAAATCGCAAAGCGAAC
Found at i:226010 original size:21 final size:21
Alignment explanation
Indices: 225946--226015 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
225936 TTTGGACTAC
225946 CGCAACGAATTTGGAATAAAT
1 CGCAACGAATTTGGAATAAAT
* *
225967 CGCAAAGCGAACTTGGACT--AT
1 CGC-AA-CGAATTTGGAATAAAT
*
225988 CGCAACAAATTTGGAATAAAT
1 CGCAACGAATTTGGAATAAAT
226009 CGCAACG
1 CGCAACG
226016 CGATAGTCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 9 0.23
20 2 0.05
21 16 0.41
22 2 0.05
23 10 0.26
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (21 bp):
CGCAACGAATTTGGAATAAAT
Found at i:229311 original size:14 final size:14
Alignment explanation
Indices: 229294--229340 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
229284 ATTTAATAAA
*
229294 TAAATTTTATATTT
1 TAAATTTTATATCT
* *
229308 TAAATCTGATATCT
1 TAAATTTTATATCT
*
229322 TAAATTTTAAATCT
1 TAAATTTTATATCT
229336 TAAAT
1 TAAAT
229341 ATAATTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (14 bp):
TAAATTTTATATCT
Found at i:229989 original size:35 final size:35
Alignment explanation
Indices: 229942--230027 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
229932 AAAACAGTCA
* * *
229942 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
229977 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
230012 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
230028 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:230021 original size:21 final size:21
Alignment explanation
Indices: 229996--230038 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
229986 TTCTAAACCC
229996 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
230017 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
230038 T
1 T
230039 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:230192 original size:16 final size:18
Alignment explanation
Indices: 230160--230193 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
230150 TATTAATGTA
230160 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
230178 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
230194 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:230870 original size:128 final size:129
Alignment explanation
Indices: 230661--230906 Score: 422
Period size: 128 Copynumber: 1.9 Consensus size: 129
230651 AATTTTCTTC
* * *
230661 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
230726 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACC-AATTGATAGCATATATAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAA
* * * *
230789 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
230854 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
230907 TATATAATAA
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
128 103 0.94
129 7 0.06
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (129 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAA
Found at i:233959 original size:64 final size:63
Alignment explanation
Indices: 233874--234034 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
233864 TTGTTTAAGG
* * * *
233874 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* *
233938 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
* *
234002 TGCATCAATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
234035 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:235575 original size:149 final size:149
Alignment explanation
Indices: 235401--235715 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
235391 GAGTCGAGGG
* *
235401 TCTACGCGGTCTTTCGGGATATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTATGTGGAACATGTGTGAAGTATTGAAAGACACAT
235466 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
* *
235531 TATGGCACTACGGTGCAAT
131 TATGACACTACAGTGCAAT
235550 TCTACGCGGTCCTTCGGGATATATATATATTATGTGGAACATGTGTGAAGTATTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTATGTGGAACATGTGTGAAGTATTGAAAGACACAT
235615 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
235680 TATGACACTACAGTGCAAT
131 TATGACACTACAGTGCAAT
235699 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
235716 TGCAATTATA
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTATGTGGAACATGTGTGAAGTATTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGACACTACAGTGCAAT
Found at i:239210 original size:65 final size:65
Alignment explanation
Indices: 239050--239210 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
239040 TTGTTTAAGG
* * * **
239050 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
239113 A
65 A
*
239114 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
239178 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
239211 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:240774 original size:147 final size:148
Alignment explanation
Indices: 240578--240878 Score: 568
Period size: 147 Copynumber: 2.0 Consensus size: 148
240568 GAGTCGAGGG
240578 TCTACGCGGTCCTTCGGGATATATGTATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATA-GTATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
240643 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGAACATTATTA
240708 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
*
240727 TCTACGCGGTCCTTCGGGATATA-TATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
1 TCTACGCGGTCCTTCGGGATATAGTATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACATA
240791 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGAACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGAACATTATTAT
240856 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
240874 TCTAC
1 TCTAC
240879 ACGGCACTTC
Statistics
Matches: 150, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
147 127 0.85
149 23 0.15
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGATATAGTATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGAACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:243323 original size:29 final size:29
Alignment explanation
Indices: 243229--243325 Score: 74
Period size: 29 Copynumber: 3.3 Consensus size: 29
243219 CTATAACCTT
*
243229 TATTTTAAATTAGTCCTTAAACTTTTGAA
1 TATTCTAAATTAGTCCTTAAACTTTTGAA
* * * **
243258 TATTCCAATTTCA-TCAC-GAAAC-TACGAA
1 TATTCTAAATT-AGTC-CTTAAACTTTTGAA
243286 TCTCATTCTAAATTAGTCCTTAAACTTTTGAA
1 --T-ATTCTAAATTAGTCCTTAAACTTTTGAA
243318 TATTCTAA
1 TATTCTAA
243326 TTTCATCCCT
Statistics
Matches: 49, Mismatches: 11, Indels: 16
0.64 0.14 0.21
Matches are distributed among these distances:
28 4 0.08
29 21 0.43
30 6 0.12
31 14 0.29
32 4 0.08
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (29 bp):
TATTCTAAATTAGTCCTTAAACTTTTGAA
Found at i:243338 original size:29 final size:29
Alignment explanation
Indices: 243246--243339 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
243236 AATTAGTCCT
* *
243246 TAAACTTTTGAATATTCCAATTTCATCAC
1 TAAACTTTTGAATATTCTAATTTCATCCC
* ** * *
243275 GAAAC-TACGAATCTCATTCTAAATT-AGTCCT
1 TAAACTTTTGAA--T-ATTCTAATTTCA-TCCC
243306 TAAACTTTTGAATATTCTAATTTCATCCC
1 TAAACTTTTGAATATTCTAATTTCATCCC
243335 TAAAC
1 TAAAC
243340 CATGACCATC
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
28 4 0.09
29 21 0.45
30 4 0.09
31 14 0.30
32 4 0.09
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.38
Consensus pattern (29 bp):
TAAACTTTTGAATATTCTAATTTCATCCC
Found at i:243358 original size:60 final size:59
Alignment explanation
Indices: 243229--243394 Score: 190
Period size: 60 Copynumber: 2.8 Consensus size: 59
243219 CTATAACCTT
* * * *
243229 TATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCACGAAACTACGAATC
1 TATTATAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCGAAACCACGAATC
* * *
243288 TCATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCTAAACCATGACCATC
1 T-ATTATAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCGAAACCACGA--ATC
** ** *
243350 T-TTATAAATCGGTCCCCAAACTTTTGAATATCCTAATTTCATCCC
1 TATTATAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCC
243395 CGAATTAATC
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 1 0.01
60 87 0.95
62 4 0.04
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.39
Consensus pattern (59 bp):
TATTATAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCCGAAACCACGAATC
Found at i:253912 original size:6 final size:6
Alignment explanation
Indices: 253896--253939 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
253886 TTTTACCTAG
* * *
253896 GGTGCCT GGTGCT GGTGCT GGTGCG GGTGCG GGTGCC GGTGCT G
1 GGTG-CT GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT GGTGCT G
253940 CTTGAGCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (6 bp):
GGTGCT
Found at i:254656 original size:76 final size:75
Alignment explanation
Indices: 254530--254669 Score: 253
Period size: 76 Copynumber: 1.9 Consensus size: 75
254520 ACAGACCACG
254530 GACAGCTGGTTGTGTTGGGTTGGGATTAGGGCTGAACAACGAAAGTGAGAAAATCGAAAAATATG
1 GACAGCTGGTTGTGTTGGGTTGGGATTAGGGCTGAACAACGAAAGTGAGAAAATC-AAAAATATG
254595 CATTGATCACA
65 CATTGATCACA
* *
254606 GACAGTTGGTTGTGTTGGGTTGGGATTAGGGCTGATCAACGAAAGTGAGAAAATCAAAAATATG
1 GACAGCTGGTTGTGTTGGGTTGGGATTAGGGCTGAACAACGAAAGTGAGAAAATCAAAAATATG
254670 TTTCACATAA
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
75 9 0.15
76 53 0.85
ACGTcount: A:0.34, C:0.10, G:0.31, T:0.25
Consensus pattern (75 bp):
GACAGCTGGTTGTGTTGGGTTGGGATTAGGGCTGAACAACGAAAGTGAGAAAATCAAAAATATGC
ATTGATCACA
Found at i:255475 original size:40 final size:40
Alignment explanation
Indices: 255431--255510 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
255421 TCAAAGGACT
255431 TAATAAAATAATATCATATAGTCAAAGGACCATTTATGTA
1 TAATAAAATAATATCATATAGTCAAAGGACCATTTATGTA
* * * *
255471 TAATAAAATAGTATCCTATAGTCCAATGACCATTTATGTA
1 TAATAAAATAATATCATATAGTCAAAGGACCATTTATGTA
255511 CTTTACCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (40 bp):
TAATAAAATAATATCATATAGTCAAAGGACCATTTATGTA
Found at i:256616 original size:24 final size:23
Alignment explanation
Indices: 256584--256631 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
256574 ATCAATACTC
256584 TTTCAAGAGTATCGATACTTTAGG
1 TTTCAAGAGTATCGATA-TTTAGG
256608 TTTCAAGAGTATCGATATTTAGG
1 TTTCAAGAGTATCGATATTTAGG
256631 T
1 T
256632 CATAGTTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (23 bp):
TTTCAAGAGTATCGATATTTAGG
Done.