Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008586.1 Hibiscus syriacus cultivar Beakdansim tig00111522_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: 346163
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:210380 original size:13 final size:13
Alignment explanation
Indices: 210362--210395 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
210352 AGATACACAG
*
210362 AGACGAGCAACAT
1 AGACGAGCAACAA
210375 AGACGAGCAACAA
1 AGACGAGCAACAA
210388 AGACGAGC
1 AGACGAGC
210396 CACGAACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.47, C:0.24, G:0.26, T:0.03
Consensus pattern (13 bp):
AGACGAGCAACAA
Found at i:211249 original size:17 final size:18
Alignment explanation
Indices: 211229--211264 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
211219 TTAATTATTG
211229 TTTAAAT-ATATTTTAAT
1 TTTAAATAATATTTTAAT
*
211246 TTTATATAATATTTTAAT
1 TTTAAATAATATTTTAAT
211264 T
1 T
211265 AGTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTAAATAATATTTTAAT
Found at i:211259 original size:18 final size:18
Alignment explanation
Indices: 211236--211293 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
211226 TTGTTTAAAT
211236 ATATTTTAATTTTATATA
1 ATATTTTAATTTTATATA
*
211254 ATATTTTAATTAGTAT-TA
1 ATATTTTAATT-TTATATA
*
211272 TTATTTT-ATTTTA-ATA
1 ATATTTTAATTTTATATA
211288 TATATT
1 -ATATT
211294 ATTTGATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 4 0.12
17 7 0.21
18 19 0.58
19 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATATTTTAATTTTATATA
Found at i:216452 original size:2 final size:2
Alignment explanation
Indices: 216445--216472 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
216435 TTATCCTTTA
216445 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
216473 CCTTGGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:216683 original size:16 final size:15
Alignment explanation
Indices: 216657--216688 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
216647 CTTATCCAAC
216657 AAAGAAAGAAGAAAA
1 AAAGAAAGAAGAAAA
216672 AAAGAGAAGAAGAAAA
1 AAAGA-AAGAAGAAAA
216688 A
1 A
216689 GGAAAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAAAA
Found at i:218949 original size:93 final size:93
Alignment explanation
Indices: 218785--219064 Score: 456
Period size: 93 Copynumber: 3.0 Consensus size: 93
218775 AGAAGACCCA
* *
218785 ATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAATCAA
218850 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGGAAGATGAATGTGCTC
*
218878 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAATCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAATCAA
218943 TCATTGAATTTGGAAGATGAATGTGCTC
66 TCATTGAATTTGGAAGATGAATGTGCTC
* * *
218971 ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATG-AACTC-CAAAATCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAAC-CACAGAATCA
* * *
219034 ATCATTGGATTTGAAAGATGAATTTGCTC
65 ATCATTGAATTTGGAAGATGAATGTGCTC
219063 AT
1 AT
219065 GGTAGAAATA
Statistics
Matches: 176, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
92 38 0.22
93 138 0.78
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (93 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACAGAATCAA
TCATTGAATTTGGAAGATGAATGTGCTC
Found at i:219171 original size:114 final size:114
Alignment explanation
Indices: 218967--219749 Score: 1372
Period size: 114 Copynumber: 6.9 Consensus size: 114
218957 AGATGAATGT
* *
218967 GCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
219031 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
66 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
* * *
219080 GCTCAATAGCATCTTCTAGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
*
219145 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGTG
66 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
*
219194 GCTCAATATCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
219259 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
66 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
*
219308 GCTCAATATCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
219373 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
66 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
219422 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
219487 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
66 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
* *
219536 GCTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
*
219601 TCAATCCTTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
66 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
* * *
219650 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAAC-CACAG
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATG-AACTC-CAA
* * * *
219714 AACCAATCATTGAATTTGGAAGATGAATGTGCTCAT
64 AATCAATCATTGGATTTGAAAGATGAATTTGCTCAT
219750 AGCATCTTTT
Statistics
Matches: 646, Mismatches: 21, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
113 4 0.01
114 606 0.94
115 36 0.06
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (114 bp):
GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAG
Found at i:219614 original size:342 final size:342
Alignment explanation
Indices: 218967--219946 Score: 1549
Period size: 342 Copynumber: 2.9 Consensus size: 342
218957 AGATGAATGT
* *
218967 GCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
*
219031 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTC
66 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTT
* *
219096 TAGAAGTGTTCTTTGAATTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTG
131 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTG
* * * *
219161 AAAGATGAATTTGCTCATGGTAGAAATAAGGTGGCTCAATATCATCTTTTGGAAGTGTTCTTTGA
196 AAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTAGAAGTGTTCTTTGA
219226 GTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTGCTC
261 GTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTGCTC
219291 ATGGTAGAAATAAGGAG
326 ATGGTAGAAATAAGGAG
*
219308 GCTCAATATCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
219373 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTT
66 TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTT
219438 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTG
131 TGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTG
219503 AAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTAGAAGTGTTCTTTGA
196 AAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTAGAAGTGTTCTTTGA
*
219568 GTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCCTTGGATTTGAAAGATGAATTTGCTC
261 GTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTGCTC
219633 ATGGTAGAAATAAGGAG
326 ATGGTAGAAATAAGGAG
* * *
219650 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAAC-CACAG
1 GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATG-AACTC-CAA
* * *
219714 AACCAATCATTGAATTT----G--GAA---G---A---T-G-AAT---G-TGCTC-ATAGCATCT
64 AATCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCT
*
219757 TTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAACCAATCATTGGATT
129 TTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATT
219822 TGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTAGAAGTGTTCTTT
194 TGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTAGAAGTGTTCTTT
* * * * * * *
219887 GAGTTATCTGATCTGATTTGGTAGGAGCCCCAGAACCGATCATTGGAATTGAAAGATGAA
259 GAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAA
219947 CTGCATGATC
Statistics
Matches: 609, Mismatches: 27, Indels: 26
0.92 0.04 0.04
Matches are distributed among these distances:
321 190 0.31
322 4 0.01
323 1 0.00
326 3 0.00
327 1 0.00
328 1 0.00
331 1 0.00
334 1 0.00
337 3 0.00
339 1 0.00
341 4 0.01
342 379 0.62
343 20 0.03
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (342 bp):
GCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
TCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTT
TGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTG
AAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTCTAGAAGTGTTCTTTGA
GTTATCTGATCTGATTTGGTATGAACTCCAAAATCAATCATTGGATTTGAAAGATGAATTTGCTC
ATGGTAGAAATAAGGAG
Found at i:219896 original size:207 final size:207
Alignment explanation
Indices: 219536--219946 Score: 673
Period size: 207 Copynumber: 2.0 Consensus size: 207
219526 AAATAAGGAG
219536 GCTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
* * *
219601 TCAATCCTTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTT
66 CCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTC
* *
219666 TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAACCACAGAACCAATCATT-GAATT
131 TAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGATA-GAAACCACAGAACCAATCATTGGAA-T
*
219730 TGGAAGATGAATGT
194 TGAAAGATGAATGT
* *
219744 GCTC-ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
1 GCTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
219808 CCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTC
66 CCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTC
* * * * *
219873 TAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAGGAGCCCCAGAACCGATCATTGGAATTG
131 TAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGATAGAAACCACAGAACCAATCATTGGAATTG
219938 AAAGATGAA
196 AAAGATGAA
219947 CTGCATGATC
Statistics
Matches: 189, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
206 28 0.15
207 157 0.83
208 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (207 bp):
GCTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTATGAACTCCAAAA
CCAATCATTGGATTTGAAAGATGAATTTGCTCATGGTAGAAATAAGGAGGCTCAATAGCATCTTC
TAGAAGTGTTCTTTGAGTTATCTGATCTGATTTGATAGAAACCACAGAACCAATCATTGGAATTG
AAAGATGAATGT
Found at i:222950 original size:93 final size:92
Alignment explanation
Indices: 222782--222973 Score: 305
Period size: 93 Copynumber: 2.1 Consensus size: 92
222772 TATTTCTACC
* *
222782 ATGAGCAAATTCATCTTTCAAATCCAATGATTGGTTTTGGAGTTCATACCAAATCAGATCAGATA
1 ATGAGCAAATTCATCTTCCAAATCCAATGATTGGTTTTGGAGTTCATACCAAACCAGATCAGATA
222847 ACTCAAAGAACACTTCCAAAAGATGCT
66 ACTCAAAGAACACTTCCAAAAGATGCT
* * *
222874 ATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTGG-TTTCATACCAAACCAGATCAGA
1 ATGAGCAAATTCATCTTCCAAATCCAATGATTGGTT-T-TGGAGTTCATACCAAACCAGATCAGA
222938 TAACTCAAAGAACACTTCCAAAAGATGCT
64 TAACTCAAAGAACACTTCCAAAAGATGCT
222967 ATTGAGC
1 A-TGAGC
222974 CTCCTTATTT
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
92 33 0.36
93 51 0.55
94 8 0.09
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (92 bp):
ATGAGCAAATTCATCTTCCAAATCCAATGATTGGTTTTGGAGTTCATACCAAACCAGATCAGATA
ACTCAAAGAACACTTCCAAAAGATGCT
Found at i:223077 original size:114 final size:114
Alignment explanation
Indices: 222874--223656 Score: 1390
Period size: 114 Copynumber: 6.9 Consensus size: 114
222864 AAAAGATGCT
* * * * * *
222874 ATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTGG-TTTCATACCAAACCAGATCAGA
1 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATT-T-TGGAGTTCATACCAAATCAGATCAGA
222938 TAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACC
64 TAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACC
*
222989 ATGAGCAAATTCATCTTTCAAATCCAAGGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
1 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
* *
223054 ACTCAAAGAACACTTCTAGAAGATGCTATTGAGCCTCCTTATTTCTACC
66 ACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACC
223103 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
1 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
223168 ACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACC
66 ACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACC
223217 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
1 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
*
223282 ACTCAAAGAACACTTCCAAAAGATGATATTGAGCCTCCTTATTTCTACC
66 ACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACC
223331 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
1 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
* *
223396 ACTCAAAGAACACTTCCAAAAGATGATATTGAGCCACCTTATTTCTACC
66 ACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACC
223445 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
1 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
* *
223510 ATTCAAAGAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACC
66 ACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACC
223559 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
1 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
* *
223624 ATTCAAAGAACACTTCCAGAAGATGCTA-TGAGC
66 ACTCAAAGAACACTTCCAAAAGATGCTATTGAGC
223657 ACATTCATCT
Statistics
Matches: 649, Mismatches: 18, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
113 8 0.01
114 610 0.94
115 31 0.05
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.30
Consensus pattern (114 bp):
ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
ACTCAAAGAACACTTCCAAAAGATGCTATTGAGCCTCCTTATTTCTACC
Found at i:223728 original size:93 final size:93
Alignment explanation
Indices: 223559--223838 Score: 456
Period size: 93 Copynumber: 3.0 Consensus size: 93
223549 TATTTCTACC
* * * * *
223559 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATT-T-TGGAGTTCATACCAAATCAGATCAGA
1 ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGG-TTTCATACCAAACCAGATCAGA
*
223622 TAATTCAAAGAACACTTCCAGAAGATGCT
65 TAACTCAAAGAACACTTCCAGAAGATGCT
223651 ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGAT
1 ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGAT
*
223716 AACTCAAAGAACACTTCCAAAAGATGCT
66 AACTCAAAGAACACTTCCAGAAGATGCT
*
223744 ATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAGAT
1 ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGAT
*
223809 AACTCAAAGAACACTTCCAGAAGATACT
66 AACTCAAAGAACACTTCCAGAAGATGCT
223837 AT
1 AT
223839 TGGGTCTTCT
Statistics
Matches: 176, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
92 33 0.19
93 140 0.80
94 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (93 bp):
ATGAGCACATTCATCTTCCAAATTCAATGATTGATTCTGTGGTTTCATACCAAACCAGATCAGAT
AACTCAAAGAACACTTCCAGAAGATGCT
Found at i:225956 original size:16 final size:15
Alignment explanation
Indices: 225935--225966 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
225925 TCAATTTTCC
225935 TTTTTCTTCTTCTCTT
1 TTTTTCTTCTT-TCTT
225951 TTTTTCTTCTTTCTT
1 TTTTTCTTCTTTCTT
225966 T
1 T
225967 GTTGGATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTCTTTCTT
Found at i:226158 original size:2 final size:2
Alignment explanation
Indices: 226151--226185 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
226141 ACAACCAAGG
226151 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 A
226186 GGATAAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:231380 original size:18 final size:18
Alignment explanation
Indices: 231320--231379 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
231310 TAAATTAATC
*
231320 AAATAATATATTAAAAATA
1 AAATAATATA-TAAAATTA
*
231339 AAATAATA-ATACTAATTA
1 AAATAATATATA-AAATTA
*
231357 AAATATTATATAAAATTA
1 AAATAATATATAAAATTA
231375 AAATA
1 AAATA
231380 TATTTAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.06
18 22 0.63
19 11 0.31
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATATATAAAATTA
Found at i:232239 original size:13 final size:13
Alignment explanation
Indices: 232221--232254 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
232211 TGGGTTCGTG
*
232221 GCTCGTCTTTGTT
1 GCTCGTCTATGTT
232234 GCTCGTCTATGTT
1 GCTCGTCTATGTT
232247 GCTCGTCT
1 GCTCGTCT
232255 CTGTGTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.03, C:0.26, G:0.24, T:0.47
Consensus pattern (13 bp):
GCTCGTCTATGTT
Found at i:232717 original size:3 final size:3
Alignment explanation
Indices: 232709--232789 Score: 74
Period size: 3 Copynumber: 26.7 Consensus size: 3
232699 TTTTATTTTA
* * * *
232709 AAT AAT AAT ATTT AAT AAT ATT ATT AAT AAT AAT -AT ATAT AAT ATT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
** *
232755 AAT AAT AAT AAT AAT TTT AAT AAT AAA AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
232790 AACGAAATGA
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.03
3 56 0.89
4 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:235230 original size:20 final size:19
Alignment explanation
Indices: 235183--235221 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
235173 ATGACCAACA
*
235183 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
235202 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
235221 A
1 A
235222 TTATCGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:235349 original size:20 final size:20
Alignment explanation
Indices: 235326--235391 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
235316 GAATATGTAA
**
235326 ATCGCAACATGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
235346 ATCGCAATGCGATTCTGCCT
1 ATCGCAACGCGATTCTGACT
*
235366 ATCGTAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
235386 ATCGCA
1 ATCGCA
235392 TCACTGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:236492 original size:14 final size:14
Alignment explanation
Indices: 236463--236499 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
236453 AGAAAAACAA
236463 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
236478 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
236492 GAAGAAAA
1 GAAGAAAA
236500 TGTCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:238169 original size:18 final size:18
Alignment explanation
Indices: 238146--238185 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
238136 AGCAAAAGGC
*
238146 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
*
238164 AATCAAAATCCCAATCAC
1 AATCAAAATCCCAATCAA
238182 AATC
1 AATC
238186 GGCTTCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.28, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:238374 original size:20 final size:20
Alignment explanation
Indices: 238351--238675 Score: 343
Period size: 20 Copynumber: 16.9 Consensus size: 20
238341 TTACACATTC
* **
238351 ATTTGAATATCGCAACATGA
1 ATTTGACTATCGCAACGCGA
*
238371 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
238391 ATTTGACTATAGCAATGCGA
1 ATTTGACTATCGCAACGCGA
238411 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
238431 ATATGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
238451 ATTTGACTATCGCAATGC-A
1 ATTTGACTATCGCAACGCGA
* *
238470 A----A-AATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
238485 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
238505 ATATGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
238525 ATTTGACTATCGCAATGC-A
1 ATTTGACTATCGCAACGCGA
*
238544 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
238559 ATTTGACTATCTCAACACGA
1 ATTTGACTATCGCAACGCGA
** *
238579 ATTTGAAAAGCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
238599 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
238619 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
238639 ATTTGATTATCGCAACAG-GA
1 ATTTGACTATCGCAAC-GCGA
238659 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
238676 AGAAAATCGC
Statistics
Matches: 253, Mismatches: 39, Indels: 27
0.79 0.12 0.08
Matches are distributed among these distances:
14 19 0.08
15 6 0.02
19 7 0.03
20 220 0.87
21 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:238490 original size:74 final size:74
Alignment explanation
Indices: 238402--238675 Score: 361
Period size: 74 Copynumber: 3.6 Consensus size: 74
238392 TTTGACTATA
238402 GCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGACTATCGCAAT
1 GCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGACTATCGCAAT
238467 GCAAAAATC
66 GCAAAAATC
238476 GCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGACTATCGCAAT
1 GCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGACTATCGCAAT
238541 GCAAAAATC
66 GCAAAAATC
* * * * ** * *
238550 GCAACGCGAATTTGACTATCTCAACACGAATTTGAAAAGCGCAACGCGAATTTGACTATCGCAAC
1 GCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGACTATCGCAA-
* * *
238615 GGGAATTTGACTATC
65 TGCAA----A-AATC
* *
238630 GCAATGCGAATTTGATTATCGCAACAG-GAATTTGACTATCGCAACG
1 GCAATGCGAATTTGACTATCGCAAC-GCGAATATGACTATCGCAACG
238676 AGAAAATCGC
Statistics
Matches: 175, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
74 130 0.74
75 3 0.02
79 1 0.01
80 41 0.23
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (74 bp):
GCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGACTATCGCAAT
GCAAAAATC
Found at i:238681 original size:94 final size:92
Alignment explanation
Indices: 238495--238714 Score: 234
Period size: 94 Copynumber: 2.3 Consensus size: 92
238485 ATTTGACTAT
* *
238495 CGCAACGCGAATATGACTATCGCAACGTGAATTTGACTATCGCAATGCAAAAATCGCAACGCGAA
1 CGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAATGCAAAAATCGCAACGCGAA
*
238560 TTTGACTATCTCAACACGAATTTGAAAAG
66 TTTGACTATCGCAACACGAA--TGAAAAG
* *
238589 CGCAACGCGAATTTGACTATCGCAACGGGAATTTGACTATCGCAATGCGAATTTGATTATCGCAA
1 CGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAATGC-AA----A-AATCGCAA
*
238654 CAG-GAATTTGACTATCGC-A-ACG-A-GAAAAT
60 C-GCGAATTTGACTATCGCAACACGAATGAAAAG
* * * *
238683 CGCAAAGTGTATTAGACTATCGCAACGCGAAT
1 CGCAACGCGAATTTGACTATCGCAACGCGAAT
238715 ATGATGCAGA
Statistics
Matches: 109, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
94 78 0.72
95 2 0.02
97 1 0.01
98 3 0.03
99 2 0.02
100 22 0.20
101 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.23
Consensus pattern (92 bp):
CGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAATGCAAAAATCGCAACGCGAA
TTTGACTATCGCAACACGAATGAAAAG
Found at i:240269 original size:21 final size:21
Alignment explanation
Indices: 240223--240302 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
240213 AGAATGTTGG
* * *
240223 GAGGGACCTCTTCAACGATGA
1 GAGGGGCCTCTTGAACGGTGA
* *
240244 CAGGGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTGAACGGTGA
* *
240265 GAGGGGACTCTTG-AGGGATGA
1 GAGGGGCCTCTTGAACGG-TGA
*
240286 TAGGGGCCTCTTGAACG
1 GAGGGGCCTCTTGAACG
240303 ATAGTATAGG
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 3 0.07
21 40 0.89
22 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.39, T:0.20
Consensus pattern (21 bp):
GAGGGGCCTCTTGAACGGTGA
Found at i:240318 original size:42 final size:42
Alignment explanation
Indices: 240239--240331 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
240229 CCTCTTCAAC
* * *
240239 GATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
* * * * **
240281 GATGATAGGGGCCTCTTGAACGATAGTATAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
240323 GATGACAGG
1 GATGACAGG
240332 TGAGTCGGGC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
Found at i:240827 original size:20 final size:20
Alignment explanation
Indices: 240802--240845 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
240792 AATAGTTTCT
240802 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
240822 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
240842 GAAA
1 GAAA
240846 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:240855 original size:20 final size:20
Alignment explanation
Indices: 240832--240900 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
240822 GAAACTTAAA
240832 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
240852 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
240872 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
240892 ATCGCAACG
1 ATCGCAACG
240901 GGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:240938 original size:20 final size:20
Alignment explanation
Indices: 240905--240944 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
240895 GCAACGGGAT
**
240905 AATCGCAATTCGAAAATAAA
1 AATCGCAACGCGAAAATAAA
*
240925 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAAATAAA
240945 TTCGTGTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAAAATAAA
Found at i:241023 original size:34 final size:34
Alignment explanation
Indices: 240951--241041 Score: 110
Period size: 34 Copynumber: 2.7 Consensus size: 34
240941 TAAATTCGTG
* *
240951 TTGCGATTTTCATTTTCGCATTGTGATTTTCACG
1 TTGCGATTTTCATTTTCGCATTGTGATTATCACA
* * *
240985 TTGCGGTTTTTATTTTCGCATTGTGATTATCCCA
1 TTGCGATTTTCATTTTCGCATTGTGATTATCACA
** *
241019 TTGCGATAGTCATTTCCGCATTG
1 TTGCGATTTTCATTTTCGCATTG
241042 CGATAGTCAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGTGATTATCACA
Found at i:241042 original size:20 final size:20
Alignment explanation
Indices: 241017--241065 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
241007 GTGATTATCC
241017 CATTGCGATAGTCATTTCCG
1 CATTGCGATAGTCATTTCCG
*
241037 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTCCG
241057 CATTGCGAT
1 CATTGCGAT
241066 TTTAAGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (20 bp):
CATTGCGATAGTCATTTCCG
Found at i:243019 original size:20 final size:20
Alignment explanation
Indices: 242976--243043 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
242966 GAAACTTAAA
* **
242976 ATCGCAACATGAAAATGAAA
1 ATCGCAACACGAAAATGACT
242996 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
** **
243016 ATCGCAATGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
243036 ATCGCAAC
1 ATCGCAAC
243044 GAGATAATCG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:243095 original size:14 final size:14
Alignment explanation
Indices: 243036--243096 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 14
243026 GAATTTGACT
*
243036 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
243050 ATCGCAACGCGAAATGAAC
1 ATCGCAA--CG--A-GAAA
243069 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
243083 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
243097 CTAAATTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 24 0.62
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 9 0.23
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:243571 original size:22 final size:22
Alignment explanation
Indices: 243494--243571 Score: 104
Period size: 22 Copynumber: 3.5 Consensus size: 22
243484 GATGGAGATA
*
243494 GACGGATTTCG-CTGGAGATAGG
1 GACGGATTTCGTC-GGAGATGGG
* *
243516 GACGGATTTCGCCGGAAATGGG
1 GACGGATTTCGTCGGAGATGGG
243538 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
243560 GACGGATGTCGT
1 GACGGATTTCGT
243572 TGTAGAGAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
22 49 0.98
23 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:243766 original size:20 final size:20
Alignment explanation
Indices: 243741--243805 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
243731 TTATCACAAC
*
243741 GCGATAGTTAGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
*
243761 GCGATAGTCAGAATTGCGTT
1 GCGATAGTCAGAATCGCGTT
*
243781 GCGATAGTCAAAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
243801 GCGAT
1 GCGAT
243806 TTACATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:243948 original size:19 final size:19
Alignment explanation
Indices: 243924--243960 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
243914 TTCGATAATG
*
243924 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
243943 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
243961 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:249684 original size:11 final size:11
Alignment explanation
Indices: 249668--249698 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
249658 GTCTTTATGA
249668 TGAAACAAATC
1 TGAAACAAATC
249679 TGAAACAAATC
1 TGAAACAAATC
249690 TGAAACAAA
1 TGAAACAAA
249699 CTCGATAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.16
Consensus pattern (11 bp):
TGAAACAAATC
Found at i:253047 original size:20 final size:20
Alignment explanation
Indices: 253022--253066 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
253012 TTATCCGGAA
*
253022 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGGAGTTT
253042 AAAAATCCGGTCTGGAGTTT
1 AAAAATCCGGTCTGGAGTTT
253062 AAAAA
1 AAAAA
253067 ATTGGATGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGGAGTTT
Found at i:253121 original size:17 final size:17
Alignment explanation
Indices: 253095--253127 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
253085 TTACCGGATT
253095 AAAAACCGGTTTTTTTA
1 AAAAACCGGTTTTTTTA
*
253112 AAAAATCGGTTTTTTT
1 AAAAACCGGTTTTTTT
253128 CAAACCGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (17 bp):
AAAAACCGGTTTTTTTA
Found at i:259785 original size:6 final size:6
Alignment explanation
Indices: 259774--259798 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
259764 AAACCTGCAA
259774 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
259799 GACGGGACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:260427 original size:20 final size:20
Alignment explanation
Indices: 260399--260474 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
260389 AAATTGGAGT
* *
260399 TCGCATTGCAAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
260419 TCGCGTTGCGAATTTGATTA
1 TCGCGTTGCGAATTTGACTA
* *
260439 TCGCGTTACGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
260459 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
260475 GAACCTGGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:260491 original size:40 final size:39
Alignment explanation
Indices: 260404--260493 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 39
260394 GGAGTTCGCA
* *
260404 TTGCAAATTTGACTATCGCGTTGCGAATTTGATTATCGCG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGA-TACCGCG
* * *
260444 TTACGAATTTGACTTTCGCGTTGCGAATTTGGA-ACCTGGG
1 TTGCGAATTTGACTATCGCGTTGCGAATTT-GATACC-GCG
260484 TTGCGAATTT
1 TTGCGAATTT
260494 ATTGGTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 2 0.05
40 38 0.90
41 2 0.05
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (39 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGATACCGCG
Found at i:261069 original size:15 final size:14
Alignment explanation
Indices: 261038--261071 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
261028 TTAAGATCAA
*
261038 ATTTAAAGTTTAGG
1 ATTTAAAGTTTAAG
261052 ATTTAAAGTTTTAAG
1 ATTTAAAG-TTTAAG
261067 ATTTA
1 ATTTA
261072 GAATTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
ATTTAAAGTTTAAG
Found at i:264593 original size:3 final size:3
Alignment explanation
Indices: 264585--264645 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
264575 TCCGAGAATA
* * * *
264585 TAT TAT TAT TAT TAT TAT TAT CAT TAT TA- TAC TAC AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
264632 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
264646 CAAATATTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:264703 original size:15 final size:15
Alignment explanation
Indices: 264680--264717 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
264670 GTTACAAATG
264680 AAGACCCGAAGGCCC
1 AAGACCCGAAGGCCC
* *
264695 AAGATCCGAAGGCCT
1 AAGACCCGAAGGCCC
264710 AAGACCCG
1 AAGACCCG
264718 TGCCAGGCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.26, T:0.05
Consensus pattern (15 bp):
AAGACCCGAAGGCCC
Found at i:266366 original size:24 final size:24
Alignment explanation
Indices: 266339--266397 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
266329 CAATAAGTCA
*
266339 GAAAATATTTTCTTAACTGATTAG
1 GAAAGTATTTTCTTAACTGATTAG
*
266363 GAAAGTATATTCTTAACTGATTAG
1 GAAAGTATTTTCTTAACTGATTAG
266387 GAAAGTATTTT
1 GAAAGTATTTT
266398 AAATCATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (24 bp):
GAAAGTATTTTCTTAACTGATTAG
Found at i:276129 original size:42 final size:42
Alignment explanation
Indices: 276022--276131 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
276012 TCTAGAATGT
* * * *
276022 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTATTGAACGA
* * ** *
276064 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTATTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTATTGAACGA
276106 TAGGG-GAGGCCTCTTGAACGATGACA
1 T-GGGAGAGGCCTCTTGAACGATGACA
276132 TGTGAGTTGG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
42 48 0.91
43 5 0.09
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTATTGAACGA
Found at i:276636 original size:20 final size:20
Alignment explanation
Indices: 276613--276701 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
276603 GAAACTTAAA
276613 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
276633 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
276653 ATCGCAATGC-AAATTTACCT
1 ATCGCAACGCGAAAATGA-CT
* **
276673 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
276693 ATCGCAACG
1 ATCGCAACG
276702 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 5 0.08
20 51 0.84
21 5 0.08
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:276779 original size:53 final size:52
Alignment explanation
Indices: 276708--276833 Score: 128
Period size: 53 Copynumber: 2.4 Consensus size: 52
276698 AACGAGAGAA
* ** *
276708 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTT-TCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTCGCATTACGATT-TTGTCGTTGCGATAGTC-AAT
* * * ** *
276761 TCGTATTGCGATAGTCATTTTCGCGTTACGATTTTGTTGTTGCGATTTTCATT
1 TCGCATTGCGATAGTCA-TTTCGCATTACGATTTTGTCGTTGCGATAGTCAAT
276814 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
276834 TAGCGTTGCG
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
52 3 0.05
53 33 0.55
54 24 0.40
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATAGTCATTTCGCATTACGATTTTGTCGTTGCGATAGTCAAT
Found at i:276783 original size:20 final size:20
Alignment explanation
Indices: 276746--276885 Score: 107
Period size: 20 Copynumber: 7.3 Consensus size: 20
276736 GATTCTTTCG
** *
276746 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCA
*
276766 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
276786 TTACGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
276800 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
276819 TTGCGATAGTCATTTTAGCG
1 TTGCGATAGTCATTTTCGCA
**
276839 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCA
*
276859 TTGCGATAGTCATTTTCACA
1 TTGCGATAGTCATTTTCGCA
276879 TTGCGAT
1 TTGCGAT
276886 TGTAAACTAT
Statistics
Matches: 96, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
14 6 0.06
16 6 0.06
17 4 0.04
18 1 0.01
19 10 0.10
20 69 0.72
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:276886 original size:93 final size:87
Alignment explanation
Indices: 276714--276886 Score: 238
Period size: 93 Copynumber: 1.9 Consensus size: 87
276704 AGAATCGCAA
276714 TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGTATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGTATTGCGATAGTCAT
* *
276779 TTTCGCGTTACGATTTTGTTGT
66 TTTCACATTACGATTTTGTTGT
** *
276801 TGCGATTTTCATTTCGCATTGCGATAGTCATTTTAGCGTTGCGATAGTCATTTTCGTGTTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT--TC--TTT--CGTTGCGATAGTCAAATTCGTATTGCGAT
*
276866 AGTCATTTTCACATTGCGATT
60 AGTCATTTTCACATTACGATT
276887 GTAAACTATT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
87 25 0.34
89 2 0.03
91 3 0.04
93 44 0.59
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGTATTGCGATAGTCAT
TTTCACATTACGATTTTGTTGT
Found at i:278794 original size:20 final size:20
Alignment explanation
Indices: 278711--278797 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 20
278701 GAAACTTAAA
* **
278711 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATTTGACT
278731 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
278751 ATCGCAAAGC-AA---GA--
1 ATCGCAACGCGAATTTGACT
*
278765 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
278785 ATCGCAACGCGAA
1 ATCGCAACGCGAA
278798 ATGAAAATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
14 8 0.15
15 2 0.04
16 2 0.04
18 2 0.04
19 2 0.04
20 38 0.70
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:279208 original size:22 final size:22
Alignment explanation
Indices: 279148--279213 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
279138 TGACCGTGAA
* * *
279148 TGATTTCGCCGGAGATAGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
279170 TGATATCGTCGAAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
279192 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
279214 GGATGTCGCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.24, C:0.15, G:0.36, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:279435 original size:20 final size:20
Alignment explanation
Indices: 279412--279504 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
279402 CGATAGTCAG
*
279412 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
279432 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
279452 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
279472 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
279492 ATTAGTATTGCGA
1 ATTCGCATTGCGA
279505 ATTAGGAAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:289102 original size:46 final size:45
Alignment explanation
Indices: 288970--289095 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 45
288960 GATAAACTGG
* * *
288970 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATTTTGGT
289014 AAAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGT
1 AAAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTATTTTGGT
*
289060 AAAATAAGCTTACGAGATTATGGGATAAATGGTAAG
1 AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
289096 AGATTTTATC
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
44 24 0.32
45 12 0.16
46 40 0.53
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATTTTGGT
Found at i:293970 original size:119 final size:119
Alignment explanation
Indices: 293757--293995 Score: 435
Period size: 119 Copynumber: 2.0 Consensus size: 119
293747 AGAAACACTG
293757 TGGTGTGGATAAAAGAAGAAGAAAGCCACTTCCTCCATTATTGCAAGTACAGAGAATGAGATGGC
1 TGGTGTGGATAAAAGAAGAAGAAAGCCACTTCCTCCATTATTGCAAGTACAGAGAATGAGATGGC
*
293822 TGGGGATGTAGACGATGACTTCACGAAAGAGAATG-CAGATACTATAATGACGTT
66 TGGGGATGTAGACGATGACTTCACCAAAGAGAATGCCA-ATACTATAATGACGTT
*
293876 TGGTGTGGATAAAAGAAGAAGAAAGCCACTTCCTCCATTATTGCAAGTGCAGAGAATGAGATGGC
1 TGGTGTGGATAAAAGAAGAAGAAAGCCACTTCCTCCATTATTGCAAGTACAGAGAATGAGATGGC
*
293941 TGGGGATTTAGACGATGACTTCACCAAAGAGAATGCCAATACTATAATGACGTT
66 TGGGGATGTAGACGATGACTTCACCAAAGAGAATGCCAATACTATAATGACGTT
293995 T
1 T
293996 TCTTGTATGG
Statistics
Matches: 116, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
119 114 0.98
120 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (119 bp):
TGGTGTGGATAAAAGAAGAAGAAAGCCACTTCCTCCATTATTGCAAGTACAGAGAATGAGATGGC
TGGGGATGTAGACGATGACTTCACCAAAGAGAATGCCAATACTATAATGACGTT
Found at i:296032 original size:35 final size:35
Alignment explanation
Indices: 295986--296125 Score: 194
Period size: 36 Copynumber: 3.9 Consensus size: 35
295976 AGATGAACAA
295986 TTGAATCGAAAGTG-CGGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTC-GATGCTTCCTTCCGTTCAC
* *
296021 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTC-AC
296057 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
* *
296092 TTTGAATCGAAAGTG-CTAATGCTTCCTTTCGTTC
1 -TTGAATCGAAAGTGTC-GATGCTTCCTTCCGTTC
296126 TTCTTATTCA
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
35 32 0.34
36 63 0.66
ACGTcount: A:0.19, C:0.24, G:0.20, T:0.37
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
Found at i:296130 original size:72 final size:71
Alignment explanation
Indices: 295986--296130 Score: 240
Period size: 72 Copynumber: 2.0 Consensus size: 71
295976 AGATGAACAA
*
295986 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCAATGCTTCCTTTCG
296051 TTCTTC
66 TTCTTC
296057 TTGAATCGAAAGTGTC-GATGCTTCCTTCCGTTCACTTTGAATCGAAAGTG-CTAATGCTTCCTT
1 TTGAATCGAAAGTG-CGGATGCTTCCTTCCGTTCAC-TTGAATCGAAAGTGTC-AATGCTTCCTT
296120 TCGTTCTTC
63 TCGTTCTTC
296129 TT
1 TT
296131 ATTCACCTTC
Statistics
Matches: 70, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
71 34 0.49
72 36 0.51
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (71 bp):
TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCAATGCTTCCTTTCG
TTCTTC
Found at i:301467 original size:2 final size:2
Alignment explanation
Indices: 301460--301488 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
301450 AAAACCCAAT
301460 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
301489 TTATTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:302144 original size:44 final size:44
Alignment explanation
Indices: 302078--302174 Score: 167
Period size: 44 Copynumber: 2.2 Consensus size: 44
302068 GACCTTTTAA
*
302078 ATTTAAATTGTAAGTTACTGTTAAAGTTGCATATGATTGGATTG
1 ATTTAAATTGTAAGTTAATGTTAAAGTTGCATATGATTGGATTG
* *
302122 ATTTAAATTGTAAGTTAATGTTATAGTTGCATTTGATTGGATTG
1 ATTTAAATTGTAAGTTAATGTTAAAGTTGCATATGATTGGATTG
302166 ATTTAAATT
1 ATTTAAATT
302175 ATATATTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (44 bp):
ATTTAAATTGTAAGTTAATGTTAAAGTTGCATATGATTGGATTG
Found at i:302292 original size:66 final size:66
Alignment explanation
Indices: 302186--302316 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
302176 TATATTATAA
*
302186 ATGATAAATTATTTCATGGACTCTTTCCACTACGTCATAATGTTAATCTAGTTTGGATTAAGGCA
1 ATGATAAATTATTTCATGGACTCTTTCCACTACGTCATAATGTTAATCTAGTTTGAATTAAGGCA
302251 T
66 T
*
302252 ATGATAAATTATTTCATGGACTCTTTCCACTACGTCATAATGTTAATCTAGTTTGAATTGAGGCA
1 ATGATAAATTATTTCATGGACTCTTTCCACTACGTCATAATGTTAATCTAGTTTGAATTAAGGCA
302317 GATGCACTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (66 bp):
ATGATAAATTATTTCATGGACTCTTTCCACTACGTCATAATGTTAATCTAGTTTGAATTAAGGCA
T
Found at i:311687 original size:30 final size:30
Alignment explanation
Indices: 311611--311694 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 30
311601 CTCCTCATCT
* * *
311611 TCTTCTTTGTGTTTGCTTACTTCTTCCTGC
1 TCTTCTTCGTGTTTGCTTGCTTCATCCTGC
*
311641 TCCTCCTCTTCGTGTTTGCTTGTTTCATCCTGC
1 T-CT--TCTTCGTGTTTGCTTGCTTCATCCTGC
*
311674 TCTTCTTCATGTTTGCTTGCT
1 TCTTCTTCGTGTTTGCTTGCT
311695 CCTTCATACT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 17 0.38
31 2 0.04
32 2 0.04
33 24 0.53
ACGTcount: A:0.04, C:0.29, G:0.14, T:0.54
Consensus pattern (30 bp):
TCTTCTTCGTGTTTGCTTGCTTCATCCTGC
Found at i:311701 original size:33 final size:32
Alignment explanation
Indices: 311611--311706 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 32
311601 CTCCTCATCT
* * * *
311611 TCTTCTTTGTGTTTGCTTACTTCTTCCTGCTCC
1 TCTTCTTCGTGTTTGCTTGC-TCTTCATCCTCC
* *
311644 TCCTCTTCGTGTTTGCTTG-T-TTCATCCTGC
1 TCTTCTTCGTGTTTGCTTGCTCTTCATCCTCC
* *
311674 TCTTCTTCATGTTTGCTTGCTCCTTCATACTCC
1 TCTTCTTCGTGTTTGCTTGCT-CTTCATCCTCC
311707 ATGTCTTCAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
30 24 0.48
31 2 0.04
33 24 0.48
ACGTcount: A:0.05, C:0.31, G:0.12, T:0.51
Consensus pattern (32 bp):
TCTTCTTCGTGTTTGCTTGCTCTTCATCCTCC
Found at i:322855 original size:5 final size:5
Alignment explanation
Indices: 322841--322884 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
322831 GTCCGTCTGT
* * *
322841 CTCGT CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
322885 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.05, C:0.41, G:0.36, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:323146 original size:6 final size:6
Alignment explanation
Indices: 322886--323142 Score: 325
Period size: 6 Copynumber: 42.8 Consensus size: 6
322876 CTCGGCTCGT
* *
322886 GGTCGT GGTCGT GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * * *
322934 GCTCGT GGTCGA GGTCGA GGTCGA GATCGT GGTCGA GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * *
322982 GATCGA GGTCGA GGTCGA GGTCGA GGTCGT GGTCGT GGTCGA GGTCGA
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * *
323030 GGTCGA GGTCGT GGTCGT GGTCGA GGTCGA GGTCGA GGTCGA GGTCGT
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* * * * * * *
323078 GGTCGT GGTCGT GGTCGT GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA GGTCGA
* *
323126 GGTCGT GGTCGT GGTCG
1 GGTCGA GGTCGA GGTCG
323143 TGGTAATACG
Statistics
Matches: 233, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 233 1.00
ACGTcount: A:0.10, C:0.17, G:0.49, T:0.24
Consensus pattern (6 bp):
GGTCGA
Found at i:323146 original size:24 final size:24
Alignment explanation
Indices: 322886--323142 Score: 361
Period size: 24 Copynumber: 10.7 Consensus size: 24
322876 CTCGGCTCGT
322886 GGTCGTGGTCGTGGTCGAGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
* *
322910 GGTCGAGGTCGAGGTCGAGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
* *
322934 GCTCGTGGTCGAGGTCGAGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
* *
322958 GATCGTGGTCGAGGTCGAGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
* * *
322982 GATCGAGGTCGAGGTCGAGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
323006 GGTCGTGGTCGTGGTCGAGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
* *
323030 GGTCGAGGTCGTGGTCGTGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
* * *
323054 GGTCGAGGTCGAGGTCGAGGTCGT
1 GGTCGTGGTCGTGGTCGAGGTCGA
*
323078 GGTCGTGGTCGTGGTCGTGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
* *
323102 GGTCGTGGTCGTGGTCGTGGTCGT
1 GGTCGTGGTCGTGGTCGAGGTCGA
323126 GGTCGTGGTCGTGGTCG
1 GGTCGTGGTCGTGGTCG
323143 TGGTAATACG
Statistics
Matches: 214, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 214 1.00
ACGTcount: A:0.10, C:0.17, G:0.49, T:0.24
Consensus pattern (24 bp):
GGTCGTGGTCGTGGTCGAGGTCGA
Found at i:328999 original size:5 final size:5
Alignment explanation
Indices: 328980--329028 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
328970 GTCCGTCCGT
* * * *
328980 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CTCGG CTCGG CTTGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
329029 TGGTCGTGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.04, C:0.39, G:0.37, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:329037 original size:6 final size:6
Alignment explanation
Indices: 329026--329122 Score: 122
Period size: 6 Copynumber: 16.2 Consensus size: 6
329016 TCGGCTTGGC
* * * *
329026 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* * * *
329074 TCGAGG TCGTGG TCGTGG TCGAGT TCGTGG TCATGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
329122 T
1 T
329123 AATAGGTGTC
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.07, C:0.16, G:0.47, T:0.29
Consensus pattern (6 bp):
TCGTGG
Found at i:329062 original size:24 final size:24
Alignment explanation
Indices: 329030--329118 Score: 142
Period size: 24 Copynumber: 3.7 Consensus size: 24
329020 CTTGGCTCGT
329030 GGTCGTGGTCGTGGTCGAGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
*
329054 GGTCGTGGTCGAGGTCGAGGTCGA
1 GGTCGTGGTCGTGGTCGAGGTCGA
* *
329078 GGTCGTGGTCGTGGTCGAGTTCGT
1 GGTCGTGGTCGTGGTCGAGGTCGA
*
329102 GGTCATGGTCGTGGTCG
1 GGTCGTGGTCGTGGTCG
329119 TGGTAATAGG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.08, C:0.17, G:0.48, T:0.27
Consensus pattern (24 bp):
GGTCGTGGTCGTGGTCGAGGTCGA
Found at i:335007 original size:5 final size:5
Alignment explanation
Indices: 334988--335031 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
334978 GTCCGTCTGT
* * * *
334988 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CTCGG CTTGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
335032 TGGTCGTGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.05, C:0.39, G:0.36, T:0.20
Consensus pattern (5 bp):
CTCGG
Found at i:335040 original size:6 final size:6
Alignment explanation
Indices: 335029--335119 Score: 128
Period size: 6 Copynumber: 15.2 Consensus size: 6
335019 TCGGCTTGGC
* * *
335029 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
* * *
335077 TCGTGG TCGAGT TCGTGG TCATGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
335120 AATACGTGTC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.05, C:0.16, G:0.47, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:340995 original size:6 final size:6
Alignment explanation
Indices: 340984--341032 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
340974 TCGGCTCGGC
*
340984 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
341032 T
1 T
341033 TGAGTCGTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.02, C:0.16, G:0.49, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:341020 original size:24 final size:24
Alignment explanation
Indices: 340988--341042 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
340978 CTCGGCTCGT
340988 GGTCGTGGTCGTGGTCGTGGTCGA
1 GGTCGTGGTCGTGGTCGTGGTCGA
*
341012 GGTCGTGGTCGTGGTCGTGGTTGA
1 GGTCGTGGTCGTGGTCGTGGTCGA
341036 -GTCGTGG
1 GGTCGTGG
341043 AATAGTGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 7 0.23
24 23 0.77
ACGTcount: A:0.04, C:0.15, G:0.51, T:0.31
Consensus pattern (24 bp):
GGTCGTGGTCGTGGTCGTGGTCGA
Done.