Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007833.1 Hibiscus syriacus cultivar Beakdansim tig00110177_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: 816380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:229360 original size:2 final size:2
Alignment explanation
Indices: 229348--229394 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
229338 TTAATACATC
* *
229348 TA TA CA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA TA -A GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
229389 TA TA TA
1 TA TA TA
229395 ATAAAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:229407 original size:14 final size:14
Alignment explanation
Indices: 229390--229463 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
229380 TATAAGATAT
229390 ATATAATAAAAATA
1 ATATAATAAAAATA
229404 ATATAAATAAAAA-A
1 ATAT-AATAAAAATA
* * *
229418 A-AGAAT-ATAGTA
1 ATATAATAAAAATA
229430 A-ATAAATAAAAA-A
1 ATAT-AATAAAAATA
229443 ATATAATTAAAAATA
1 ATATAA-TAAAAATA
229458 TATATA
1 -ATATA
229464 TAGGGGATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
11 2 0.04
12 6 0.13
13 8 0.17
14 16 0.35
15 9 0.20
16 5 0.11
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
ATATAATAAAAATA
Found at i:229407 original size:25 final size:27
Alignment explanation
Indices: 229359--229409 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
229349 ATACATATAT
* *
229359 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
229386 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
229410 ATAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:229413 original size:18 final size:17
Alignment explanation
Indices: 229386--229448 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 17
229376 ATGATATAAG
*
229386 ATATATATAATAAAAATA
1 ATATAAATAATAAAAA-A
*
229404 ATATAAATAAAAAAAAGAA
1 ATATAAAT-AATAAAA-AA
229423 TATAGTAAATAAATAAAAAA
1 -ATA-TAAAT-AATAAAAAA
229443 ATATAA
1 ATATAA
229449 TTAAAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 10 0.26
19 10 0.26
20 6 0.16
21 12 0.32
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
ATATAAATAATAAAAAA
Found at i:229431 original size:21 final size:21
Alignment explanation
Indices: 229392--229447 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
229382 TAAGATATAT
229392 ATAATAAAAATAATA-TAAATAA
1 ATAA-AAAAAT-ATAGTAAATAA
229414 A-AAAAAGAATATAGTAAATAA
1 ATAAAAA-AATATAGTAAATAA
229435 ATAAAAAAATATA
1 ATAAAAAAATATA
229448 ATTAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 6 0.19
21 19 0.61
22 6 0.19
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (21 bp):
ATAAAAAAATATAGTAAATAA
Found at i:236422 original size:41 final size:42
Alignment explanation
Indices: 236329--236425 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
236319 ATTTGTAAGT
* * * * *
236329 CCTTCGGGCCATCTGTAAGTCTTTCGAGCATGATGCTTAAAT
1 CCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATGCTTAAAG
*
236371 CCTTCAGGTCATCTGTAAGCCTTTCAAGCAAGATG-TTAAAG
1 CCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATGCTTAAAG
236412 CCTTCGGGTCATCT
1 CCTTCGGGTCATCT
236426 ATAAAACCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 18 0.38
42 30 0.62
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (42 bp):
CCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATGCTTAAAG
Found at i:236520 original size:34 final size:34
Alignment explanation
Indices: 236482--236564 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
236472 AAGCCTTTCG
236482 GGGGTTTCTTGATTTCTAAGAAACTAATCCTTCA
1 GGGGTTTCTTGATTTCTAAGAAACTAATCCTTCA
**
236516 GGGGTTTCTTGATAACTAAGAAACTAATCCTTCA
1 GGGGTTTCTTGATTTCTAAGAAACTAATCCTTCA
236550 GGGGTTTCTTGATTT
1 GGGGTTTCTTGATTT
236565 TTAAATCTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (34 bp):
GGGGTTTCTTGATTTCTAAGAAACTAATCCTTCA
Found at i:236701 original size:90 final size:90
Alignment explanation
Indices: 236534--237007 Score: 689
Period size: 90 Copynumber: 5.3 Consensus size: 90
236524 TTGATAACTA
* * * * *
236534 AGAAACTAATCCTTCAGGGGTTTCTTGATTTTTAAATCTTTCGGGCCATCCATAAGACCTTCAAT
1 AGAAACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
* *
236599 GTAGGATATTTTCAAATGAGATTTT
66 GCAGGATGTTTTCAAATGAGATTTT
* *
236624 AGAAACTAAGCATTCAGGGGTTTCTTGATTTGTAAGTCATTCGGGCCATCTATAAGACCTTCAGT
1 AGAAACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
*
236689 GCATGATGTTTTCAAATGAGATTTT
66 GCAGGATGTTTTCAAATGAGATTTT
* * * * * *
236714 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTATAAGTCCTTCGGGCTATCCATAAGACTTTTAGT
1 AGAAACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
*
236779 GCAGAATGTTTTCAAATGAGATTTT
66 GCAGGATGTTTTCAAATGAGATTTT
* * * * * *
236804 AGAAACTAAGCCTTCGGGGGTTTCTAGTTTTGTAAGTCCTTCGGGCCATCTATAAGACCTACAGT
1 AGAAACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
236869 GCAGGATGTTTTCAAATGAGATTTT
66 GCAGGATGTTTTCAAATGAGATTTT
*
236894 AGAAACTAAGCCTTC-GGAGGTTTCTTGATTTTTAAGTCATTCGGGCCATCCATAAGACCTTCAG
1 AGAAACTAAGCCTTCAGG-GGTTTCTTGATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAG
*
236958 TGCAGGACGTTTTCAAATGAGATTTT
65 TGCAGGATGTTTTCAAATGAGATTTT
*
236984 AGAAACTAAGCCTTTTAGGGGTTT
1 AGAAACTAAGCC-TTCAGGGGTTT
237008 TTTAATTATC
Statistics
Matches: 344, Mismatches: 37, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
89 2 0.01
90 333 0.97
91 7 0.02
92 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (90 bp):
AGAAACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
GCAGGATGTTTTCAAATGAGATTTT
Found at i:237321 original size:177 final size:177
Alignment explanation
Indices: 236894--237298 Score: 650
Period size: 177 Copynumber: 2.3 Consensus size: 177
236884 ATGAGATTTT
*
236894 AGAAACTAAGCCTTCGGAGGTTTCTTGATTTTTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
1 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
* * *
236959 GCAGGACGTTTTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTTTTAATTATCTCAAAA
66 GCATGATGTATTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTTTTAATTATCTCAAAA
* * *
237024 GAGTTGTTAAAGGAAGCTAAGCCTTTTAAGGGGTTCTTTGACAACTA
131 GAGTTATTAAAGGAAGCTAAGCCTATAAAGGGGTTCTTTGACAACTA
* * * *
237071 AAAAACTAAGTCTTCGGGGGTTTTTTGATTTGTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
1 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
* *
237136 GCATGATGTATTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGTTTTTTTAATTATCTTAAAA
66 GCATGATGTATTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTTTTAATTATCTCAAAA
237201 GAGTTATTAAAGGAAGCTAAGCCTAATAAAGGGGTT-TATTGACAACTA
131 GAGTTATTAAAGGAAGCTAAGCCT-ATAAAGGGGTTCT-TTGACAACTA
* *
237249 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAATCATTCGGGTCATC
1 AGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCATTCGGGCCATC
237299 AGTAAGTCTT
Statistics
Matches: 207, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
177 144 0.70
178 63 0.30
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (177 bp):
AGAAACTAAGCCTTCGGGGGTTTCTTGATTTTTAAGTCATTCGGGCCATCCATAAGACCTTCAGT
GCATGATGTATTCAAATGAGATTTTAGAAACTAAGCCTTTTAGGGGTTTTTTAATTATCTCAAAA
GAGTTATTAAAGGAAGCTAAGCCTATAAAGGGGTTCTTTGACAACTA
Found at i:237325 original size:22 final size:22
Alignment explanation
Indices: 237300--237362 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 22
237290 CGGGTCATCA
237300 GTAAGTCTTTCGAGCATGATGT
1 GTAAGTCTTTCGAGCATGATGT
* * * * *
237322 GTAAATCCTTC-AG-GTCATCT
1 GTAAGTCTTTCGAGCATGATGT
*
237342 GTAAGTCTTTCGAGCAAGATG
1 GTAAGTCTTTCGAGCATGATG
237363 ATAAGTCCTT
Statistics
Matches: 28, Mismatches: 11, Indels: 4
0.65 0.26 0.09
Matches are distributed among these distances:
20 13 0.46
21 4 0.14
22 11 0.39
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (22 bp):
GTAAGTCTTTCGAGCATGATGT
Found at i:237340 original size:42 final size:42
Alignment explanation
Indices: 237281--237362 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
237271 TCTTGATTTT
* *
237281 TAAATCATTCGGGTCATCAGTAAGTCTTTCGAGCATGATGTG
1 TAAATCATTCAGGTCATCAGTAAGTCTTTCGAGCAAGATGTG
* *
237323 TAAATCCTTCAGGTCATCTGTAAGTCTTTCGAGCAAGATG
1 TAAATCATTCAGGTCATCAGTAAGTCTTTCGAGCAAGATG
237363 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (42 bp):
TAAATCATTCAGGTCATCAGTAAGTCTTTCGAGCAAGATGTG
Found at i:237779 original size:105 final size:105
Alignment explanation
Indices: 237584--237819 Score: 382
Period size: 105 Copynumber: 2.2 Consensus size: 105
237574 AAAGATTATG
* * * *
237584 ATTCACTATAGAAGGAGGTAAACCAACATTTCTAGAAGAGTTCATAATGAGAAAAACTCGTCCTA
1 ATTCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAAAACTCGTCCTA
237649 AAGGAGAAAGTTCATAATGAAAAGAACTTGTTCCTTTTAA
66 AAGGAGAAAGTTCATAATGAAAAGAACTTGTTCCTTTTAA
* * *
237689 ATTCCCCACAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTA
1 ATTCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAAAACTCGTCCTA
* *
237754 AAGGTGAAAGTTCATAATGAGAAGAACTTGTTCCTTTTAA
66 AAGGAGAAAGTTCATAATGAAAAGAACTTGTTCCTTTTAA
*
237794 ATTCACCACAGAAGAAGGTGAACCAA
1 ATTCACCACAGAAGGAGGTGAACCAA
237820 AATTATTTTA
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
105 120 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (105 bp):
ATTCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAAAACTCGTCCTA
AAGGAGAAAGTTCATAATGAAAAGAACTTGTTCCTTTTAA
Found at i:240233 original size:14 final size:15
Alignment explanation
Indices: 240206--240234 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
240196 TTAAAGTTTA
240206 AAATATTATTATTAT
1 AAATATTATTATTAT
240221 AAATATT-TTATTAT
1 AAATATTATTATTAT
240235 TCAATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATATTATTATTAT
Found at i:240842 original size:2 final size:2
Alignment explanation
Indices: 240835--241215 Score: 191
Period size: 2 Copynumber: 191.5 Consensus size: 2
240825 TTATAAACTA
240835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
240877 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AA AT AT AA AC A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
240918 AT AT AT AT AT GAG CT AT AT AT AT AA ACT AT AT AGT TT AT AT GT
1 AT AT AT AT AT -AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
* * * *
240961 AT AA ACT AT AT AT AT AA AT -T AT AT AA AT CA- ACT AT AT AG AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT
* * * *
241002 AT AA ACT AT AT AT AT A- AT AT AT AT AT AT AT AT A- AG CT AC AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
241043 AT GT AT AA ACT AT AT AT GT A- AT CT AT AT AGT TT AT AT A- AA AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * *
241085 AT AT AT GT A- AT CT AT AT AGT TT AT AT AA ACT AT AT AT AT AA ACT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT A-T
* * * *
241129 AT AT AA AGT AT AT A- AT TT AT A- AA AT AT A- AT TT AT AT -T A-
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
241167 AT AT A- AT AT AT AT AC GT AT AA ACT AT AT AT AT -T TT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
*
241207 AA AT AT AT A
1 AT AT AT AT A
241216 GTTATTATAA
Statistics
Matches: 282, Mismatches: 67, Indels: 60
0.69 0.16 0.15
Matches are distributed among these distances:
1 16 0.06
2 252 0.89
3 14 0.05
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:240935 original size:13 final size:13
Alignment explanation
Indices: 240826--241133 Score: 163
Period size: 13 Copynumber: 23.0 Consensus size: 13
240816 ATGTAGTTAT
240826 TATAAACTA-ATA
1 TATAAACTATATA
*
240838 TATATA-TATATA
1 TATAAACTATATA
*
240850 TATATA-TATATA
1 TATAAACTATATA
*
240862 TATATA-TATATA
1 TATAAACTATATA
*
240874 TATATA-TATATA
1 TATAAACTATATA
*
240886 TATATA-TATATA
1 TATAAACTATATA
* *
240898 TATACA-TATAAA
1 TATAAACTATATA
240910 TATAAACAATATATA
1 TATAAAC--TATATA
* *
240925 TATGAGCTATATA
1 TATAAACTATATA
240938 TATAAACTATATA
1 TATAAACTATATA
*
240951 GT-T----TATATG
1 -TATAAACTATATA
240960 TATAAACTATATA
1 TATAAACTATATA
*
240973 TATAAATTATATA
1 TATAAACTATATA
* *
240986 AATCAACTATATAGA
1 TATAAACTATAT--A
241001 TATAAACTATATA
1 TATAAACTATATA
*
241014 TATAATATATATATA
1 TATAA-A-CTATATA
*
241029 TATATAAGCTACATATG
1 TATA-AA-CT--ATATA
241046 TATAAACTATATA
1 TATAAACTATATA
* *
241059 TGTAATCTATATAGTTTA
1 TATAAAC--TATA---TA
*
241077 TATAAAATATATA
1 TATAAACTATATA
* *
241090 TGTAATCTATATAGTTTA
1 TATAAAC--TATA---TA
241108 TATAAACTATATA
1 TATAAACTATATA
241121 TATAAACTATATA
1 TATAAACTATATA
241134 AAGTATATAA
Statistics
Matches: 237, Mismatches: 32, Indels: 53
0.74 0.10 0.16
Matches are distributed among these distances:
8 1 0.00
9 6 0.03
11 2 0.01
12 71 0.30
13 80 0.34
14 2 0.01
15 43 0.18
16 11 0.05
17 8 0.03
18 13 0.05
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (13 bp):
TATAAACTATATA
Found at i:241014 original size:11 final size:11
Alignment explanation
Indices: 240994--241215 Score: 66
Period size: 11 Copynumber: 20.6 Consensus size: 11
240984 TAAATCAACT
*
240994 ATATAGATATAA
1 ATATATATAT-A
241006 ACTATATATATA
1 A-TATATATATA
241018 ATATATATAT-
1 ATATATATATA
241028 ATATATA-AGCTA
1 ATATATATA--TA
*
241040 CATATGTATA-A
1 -ATATATATATA
*
241051 ACTATATATGTA
1 A-TATATATATA
*
241063 ATCTATATAGT-
1 ATATATATA-TA
*
241074 -T-TATATAAA
1 ATATATATATA
*
241083 ATATATATGTA
1 ATATATATATA
*
241094 ATCTATATAGT-
1 ATATATATA-TA
241105 -T-TATATA-A
1 ATATATATATA
241113 ACTATATATATA
1 A-TATATATATA
241125 A-ACTATATA-A
1 ATA-TATATATA
241135 AGTATATA-AT-
1 A-TATATATATA
* *
241145 TTATAAAATATA
1 ATAT-ATATATA
*
241157 ATTTATAT-TA
1 ATATATATATA
241167 ATATA-ATAT-
1 ATATATATATA
**
241176 ATATACGTATA
1 ATATATATATA
241187 A-ACTATATATA
1 ATA-TATATATA
* * *
241198 TTTTATATAAA
1 ATATATATATA
241209 ATATATA
1 ATATATA
241216 GTTATTATAA
Statistics
Matches: 155, Mismatches: 25, Indels: 61
0.64 0.10 0.25
Matches are distributed among these distances:
9 23 0.15
10 29 0.19
11 76 0.49
12 12 0.08
13 14 0.09
14 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (11 bp):
ATATATATATA
Found at i:241021 original size:9 final size:9
Alignment explanation
Indices: 241009--241215 Score: 54
Period size: 9 Copynumber: 22.0 Consensus size: 9
240999 GATATAAACT
241009 ATATATATA
1 ATATATATA
241018 ATATATAT-
1 ATATATATA
241026 ATATATATA
1 ATATATATA
*
241035 AGCTACATAT-
1 A--TATATATA
* *
241045 GTATAAACT-
1 ATATATA-TA
*
241054 ATATATGTA
1 ATATATATA
*
241063 ATCTATATA
1 ATATATATA
* *
241072 GTTTATATAAA
1 --ATATATATA
241083 ATATATATGTA
1 ATATATA--TA
*
241094 ATCTATATA
1 ATATATATA
* *
241103 GTTTATATAA
1 ATATATAT-A
241113 ACTATATATA
1 A-TATATATA
*
241123 TAAACTATATA
1 -ATA-TATATA
241134 A-AGTATATA
1 ATA-TATATA
241143 AT-T-TATA
1 ATATATATA
241150 A-A-ATATA
1 ATATATATA
*
241157 ATTTATATTA
1 ATATATA-TA
241167 ATATA-ATA
1 ATATATATA
241175 TATATACGTATAA
1 -ATATA--TAT-A
241188 ACTATATATA
1 A-TATATATA
* *
241198 TTTTATATA
1 ATATATATA
*
241207 AAATATATA
1 ATATATATA
241216 GTTATTATAA
Statistics
Matches: 145, Mismatches: 28, Indels: 50
0.65 0.13 0.22
Matches are distributed among these distances:
7 10 0.07
8 16 0.11
9 65 0.45
10 11 0.08
11 35 0.24
12 3 0.02
13 5 0.03
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (9 bp):
ATATATATA
Found at i:241088 original size:31 final size:31
Alignment explanation
Indices: 241046--241133 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
241036 GCTACATATG
241046 TATAAACTATATATGTAATCTATATAGTTTA
1 TATAAACTATATATGTAATCTATATAGTTTA
*
241077 TATAAAATATATATGTAATCTATATAGTTTA
1 TATAAACTATATATGTAATCTATATAGTTTA
* *
241108 TATAAACTATATATATAAACTATATA
1 TATAAACTATATATGTAATCTATATA
241134 AAGTATATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (31 bp):
TATAAACTATATATGTAATCTATATAGTTTA
Found at i:241177 original size:54 final size:54
Alignment explanation
Indices: 241098--241237 Score: 140
Period size: 54 Copynumber: 2.5 Consensus size: 54
241088 TATGTAATCT
* *
241098 ATATAGTTTATATAAACTATATATATAAACTATATAAAGTATATA-ATTTATAAA
1 ATATAATTTATATAAACTATATATATAAAC-ATATAAACTATATATATTTATAAA
* * *
241152 ATATAATTTATATTAA-TATAATATATATACGTATAAACTATATATATTTTATATAAA
1 ATATAATTTATATAAACTAT-ATATATAAACATATAAACTATATATA--TT-TATAAA
* *
241209 ATATATAGTTATTATAAACTACATATATA
1 ATATA-ATTTA-TATAAACTATATATATA
241238 TGTAACCTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
53 15 0.21
54 24 0.34
56 2 0.03
57 11 0.16
58 4 0.06
59 12 0.17
60 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (54 bp):
ATATAATTTATATAAACTATATATATAAACATATAAACTATATATATTTATAAA
Found at i:241187 original size:37 final size:35
Alignment explanation
Indices: 241146--241215 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
241136 GTATATAATT
* *
241146 TATAAAATATAATTTATATTAATATAATATATATACG
1 TATAAAATAT-ATATAT-TTAATATAAAATATATACG
* *
241183 TATAAACTATATATATTTTATATAAAATATATA
1 TATAAAATATATATATTTAATATAAAATATATA
241216 GTTATTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 15 0.52
36 5 0.17
37 9 0.31
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (35 bp):
TATAAAATATATATATTTAATATAAAATATATACG
Found at i:241283 original size:58 final size:57
Alignment explanation
Indices: 241221--241353 Score: 198
Period size: 56 Copynumber: 2.4 Consensus size: 57
241211 ATATAGTTAT
* * * *
241221 TATAAACTACATATATATGTAACCTATAGTTTATAAAGAATAGTTTATATATAATTTA
1 TATAAACTA-ATATATATATAACCTATAGTCTATAAACAATAGTTGATATATAATTTA
241279 TATAAACT-ATATATATATAACCTATAGTCTATAAACAATAGTTGATATATAATTTA
1 TATAAACTAATATATATATAACCTATAGTCTATAAACAATAGTTGATATATAATTTA
*
241335 TATAAACT-ATATATGTATA
1 TATAAACTAATATATATATA
241354 GACACAGTTG
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 62 0.89
58 8 0.11
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.41
Consensus pattern (57 bp):
TATAAACTAATATATATATAACCTATAGTCTATAAACAATAGTTGATATATAATTTA
Found at i:241534 original size:2 final size:2
Alignment explanation
Indices: 241522--241576 Score: 58
Period size: 2 Copynumber: 27.0 Consensus size: 2
241512 ATAAACTATG
**
241522 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TCA CC TA TA -A TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
*
241565 TA TG TA TA TA TA
1 TA TA TA TA TA TA
241577 CAATCTGTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 1 0.02
2 40 0.91
3 3 0.07
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:241736 original size:21 final size:21
Alignment explanation
Indices: 241710--241757 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
241700 ATTAGTGTAC
* *
241710 TATATAGTTTATAACCTATAG
1 TATATAATTTATAAACTATAG
241731 TATATAATTTATAAACTATAG
1 TATATAATTTATAAACTATAG
*
241752 TTTATA
1 TATATA
241758 TTAATGTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (21 bp):
TATATAATTTATAAACTATAG
Found at i:241818 original size:15 final size:15
Alignment explanation
Indices: 241768--241818 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
241758 TTAATGTACT
*
241768 ATATAGTTTATATTA
1 ATATAATTTATATTA
* *
241783 ATGTTAA-TTATCTTA
1 AT-ATAATTTATATTA
241798 ACTATAATTTATATTA
1 A-TATAATTTATATTA
241814 ATATA
1 ATATA
241819 GTATATAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:241837 original size:36 final size:36
Alignment explanation
Indices: 241797--241929 Score: 143
Period size: 36 Copynumber: 3.9 Consensus size: 36
241787 TAATTATCTT
241797 AACTATAATTTATATTAATATAGTATATAGTTTATA
1 AACTATAATTTATATTAATATAGTATATAGTTTATA
* * * *
241833 AACTATAATTTGTATTAATGTAGTAGATATTTTATA
1 AACTATAATTTATATTAATATAGTATATAGTTTATA
* ** *
241869 AACTATAGTTTATATT-AT-TA-T-TA-A-AATATT
1 AACTATAATTTATATTAATATAGTATATAGTTTATA
*
241899 AACTATAGTTTATATTAATATAGTATATAGT
1 AACTATAATTTATATTAATATAGTATATAGT
241930 ATTTGTTGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
30 19 0.24
31 3 0.04
32 3 0.04
33 2 0.03
34 4 0.05
35 3 0.04
36 46 0.57
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (36 bp):
AACTATAATTTATATTAATATAGTATATAGTTTATA
Found at i:241922 original size:15 final size:16
Alignment explanation
Indices: 241894--241927 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
241884 TATTATTAAA
*
241894 ATATTAACTATAGTTT
1 ATATTAACTATAGTAT
241910 ATATTAA-TATAGTAT
1 ATATTAACTATAGTAT
241925 ATA
1 ATA
241928 GTATTTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
ATATTAACTATAGTAT
Found at i:248106 original size:21 final size:21
Alignment explanation
Indices: 248080--248119 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
248070 CCCCCTTTGA
*
248080 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
248101 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
248120 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:251665 original size:31 final size:31
Alignment explanation
Indices: 251549--251784 Score: 108
Period size: 29 Copynumber: 7.8 Consensus size: 31
251539 TTAATTATAG
* **
251549 TTTATAAACCATATACTATATTAATATTAAT
1 TTTATAAACTATATTTTATATTAATATTAAT
* * * *
251580 TATATTAACTATAGTTTATAAACTATACTATATAA-
1 TTTATAAACTATA-TTT-TATA-T-TAATAT-TAAT
* *
251615 TTTATAAAATATA-GTTATATTAATATTAAT
1 TTTATAAACTATATTTTATATTAATATTAAT
* *
251645 TTTATAGACTATATTTTATATT-A-ATTACAA
1 TTTATAAACTATATTTTATATTAATATTA-AT
*
251675 ATTATAAACTATA--TTATATTAATA-TAAGT
1 TTTATAAACTATATTTTATATTAATATTAA-T
** * *
251704 TGACATTAA-TAT-TAATTATATTAATATTAA-
1 T-TTATAAACTATAT-TTTATATTAATATTAAT
*
251734 -TTATAATA-TATAATTTATATTAATATTAA-
1 TTTATAA-ACTATATTTTATATTAATATTAAT
251763 -TTATAAA-TGATA-TTTATATTAA
1 TTTATAAACT-ATATTTTATATTAA
251785 CTCTATTAAT
Statistics
Matches: 157, Mismatches: 29, Indels: 41
0.69 0.13 0.18
Matches are distributed among these distances:
28 23 0.15
29 41 0.26
30 34 0.22
31 29 0.18
32 7 0.04
33 4 0.03
34 1 0.01
35 15 0.10
36 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTATAAACTATATTTTATATTAATATTAAT
Found at i:251717 original size:6 final size:6
Alignment explanation
Indices: 251708--251763 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
251698 ATAAGTTGAC
251708 ATTAAT ATT-A- ATT-AT ATTAAT ATTAAT -TATAAT ATATAAT -TT-AT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT-TAAT AT-TAAT ATTAAT
251752 ATTAAT ATTAAT
1 ATTAAT ATTAAT
251764 TATAAATGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 6 0.14
5 8 0.18
6 24 0.55
7 6 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTAAT
Found at i:251765 original size:44 final size:44
Alignment explanation
Indices: 251603--251767 Score: 135
Period size: 44 Copynumber: 3.8 Consensus size: 44
251593 GTTTATAAAC
* * *
251603 TATACTATATAATTTATA-AAATA-TAGTTATATTAATATTAAT
1 TATAATATATAATTTATATTAATATTAATTATATTAATATTAAT
* * * **
251645 TTTATAGACTATATTTTATATTAATTACAAATTATA--AACTA-T-AT
1 TATA-ATA-TATAATTTATATTAA-TATTAATTATATTAA-TATTAAT
* * *
251689 TATATTAATATAAGTTGACATTAATATTAATTATATTAATATTAAT
1 TATAAT-ATATAA-TTTATATTAATATTAATTATATTAATATTAAT
251735 TATAATATATAATTTATATTAATATTAATTATA
1 TATAATATATAATTTATATTAATATTAATTATA
251768 AATGATATTT
Statistics
Matches: 93, Mismatches: 18, Indels: 22
0.70 0.14 0.17
Matches are distributed among these distances:
42 3 0.03
43 14 0.15
44 45 0.48
45 14 0.15
46 11 0.12
47 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (44 bp):
TATAATATATAATTTATATTAATATTAATTATATTAATATTAAT
Found at i:251827 original size:20 final size:20
Alignment explanation
Indices: 251802--251840 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
251792 AATTAAATAA
251802 TTTATTAATATAAATTATAG
1 TTTATTAATATAAATTATAG
251822 TTTATTAATATAAATTATA
1 TTTATTAATATAAATTATA
251841 TAGGGATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTATTAATATAAATTATAG
Found at i:252598 original size:30 final size:30
Alignment explanation
Indices: 252562--252637 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
252552 CATCTTCTGT
* *
252562 AACCCAAACTCGAACTCGAACCCGAATACG
1 AACCCAAACTCGAACCCGAACCCGAACACG
* * * *
252592 AACCCAAACCCGAACCCGAATCTGAACATG
1 AACCCAAACTCGAACCCGAACCCGAACACG
252622 AACCCAAACTCGAACC
1 AACCCAAACTCGAACC
252638 TAAAAACAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.41, C:0.38, G:0.12, T:0.09
Consensus pattern (30 bp):
AACCCAAACTCGAACCCGAACCCGAACACG
Found at i:252636 original size:12 final size:12
Alignment explanation
Indices: 252622--252761 Score: 99
Period size: 12 Copynumber: 11.9 Consensus size: 12
252612 TCTGAACATG
*
252622 AACCCAAACTCG
1 AACCCAAACTCA
* **
252634 AACCTAAAAACA
1 AACCCAAACTCA
**
252646 AACCCAAACTTG
1 AACCCAAACTCA
* *
252658 AA-CCAAAATCC
1 AACCCAAACTCA
*
252669 AATCCAAACT-A
1 AACCCAAACTCA
*
252680 AACCCAAACCCA
1 AACCCAAACTCA
*
252692 AACCCAAACCCA
1 AACCCAAACTCA
*
252704 AACCCAAAC-CC
1 AACCCAAACTCA
*
252715 AACCCAAACCCA
1 AACCCAAACTCA
252727 AACCCAAA-TCCA
1 AACCCAAACT-CA
* *
252739 AACCCGAACCCA
1 AACCCAAACTCA
*
252751 AATCCAAACTC
1 AACCCAAACTC
252762 GAAATTAAAA
Statistics
Matches: 99, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
11 26 0.26
12 73 0.74
ACGTcount: A:0.49, C:0.41, G:0.02, T:0.07
Consensus pattern (12 bp):
AACCCAAACTCA
Found at i:252675 original size:23 final size:24
Alignment explanation
Indices: 252622--252700 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 24
252612 TCTGAACATG
252622 AACCCAAACTCGAACCTAAAAACA
1 AACCCAAACTCGAACCTAAAAACA
* * *
252646 AACCCAAACTTGAACC-AAAATCC
1 AACCCAAACTCGAACCTAAAAACA
* * * **
252669 AATCCAAACT-AAACCCAAACCCA
1 AACCCAAACTCGAACCTAAAAACA
252692 AACCCAAAC
1 AACCCAAAC
252701 CCAAACCCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 4 0.09
23 26 0.58
24 15 0.33
ACGTcount: A:0.52, C:0.37, G:0.03, T:0.09
Consensus pattern (24 bp):
AACCCAAACTCGAACCTAAAAACA
Found at i:252690 original size:6 final size:6
Alignment explanation
Indices: 252679--252759 Score: 128
Period size: 6 Copynumber: 13.7 Consensus size: 6
252669 AATCCAAACT
252679 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC -AACCC AAACCC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* * *
252726 AAACCC AAATCC AAACCC GAACCC AAATCC AAAC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAAC
252760 TCGAAATTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.49, C:0.47, G:0.01, T:0.02
Consensus pattern (6 bp):
AAACCC
Found at i:256853 original size:22 final size:22
Alignment explanation
Indices: 256825--256885 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
256815 GGGTCTACGC
256825 GGTCCTTCGGGACAAATACATA
1 GGTCCTTCGGGACAAATACATA
*
256847 GGTCCTTTGGGACAAATACATA
1 GGTCCTTCGGGACAAATACATA
*
256869 GGTCATTCGGGACAAAT
1 GGTCCTTCGGGACAAAT
256886 TTCATATGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATACATA
Found at i:257622 original size:21 final size:21
Alignment explanation
Indices: 257596--257635 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
257586 CCGAAATTAC
257596 TGTAGCAAGGTATCGATACAA
1 TGTAGCAAGGTATCGATACAA
*
257617 TGTAGCAGGGTATCGATAC
1 TGTAGCAAGGTATCGATAC
257636 CCCTATAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (21 bp):
TGTAGCAAGGTATCGATACAA
Found at i:257699 original size:22 final size:22
Alignment explanation
Indices: 257671--257729 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
257661 CATTTGGTAC
257671 TGTTCACGGTACTGTTCATTAA
1 TGTTCACGGTACTGTTCATTAA
*
257693 TGTTCACAGTACTGTTCATTAA
1 TGTTCACGGTACTGTTCATTAA
*
257715 TTTTCACGGTACTGT
1 TGTTCACGGTACTGT
257730 ACATACCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (22 bp):
TGTTCACGGTACTGTTCATTAA
Found at i:258472 original size:60 final size:60
Alignment explanation
Indices: 258337--258472 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
258327 ACATATAAAA
*
258337 AATCGAGTG-ACCATTTTATAATTTTTAATAGTCGAAGTACTCAACAAAATAATATTCTAT
1 AATCGAG-GAACCATTTTATAACTTTTAATAGTCGAAGTACTCAACAAAATAATATTCTAT
* * * * *
258397 AATTGAGGGATCATTTTATAACTTTTAATAGTCAGATG-ACTCAATAAAATAATA-TCATAT
1 AATCGAGGAACCATTTTATAACTTTTAATAGTC-GAAGTACTCAACAAAATAATATTC-TAT
*
258457 AGTCGAGGAACCATTT
1 AATCGAGGAACCATTT
258473 ATGTACTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 3 0.05
60 58 0.91
61 3 0.05
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (60 bp):
AATCGAGGAACCATTTTATAACTTTTAATAGTCGAAGTACTCAACAAAATAATATTCTAT
Found at i:260864 original size:20 final size:20
Alignment explanation
Indices: 260839--260885 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
260829 TGTTTTTCAT
**
260839 ATTTTAAAGGCTTTAAACAC
1 ATTTTAAACACTTTAAACAC
* *
260859 ATTTTAAACACTTTAAATAT
1 ATTTTAAACACTTTAAACAC
260879 ATTTTAA
1 ATTTTAA
260886 TTAACTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (20 bp):
ATTTTAAACACTTTAAACAC
Found at i:263978 original size:22 final size:22
Alignment explanation
Indices: 263945--264005 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
263935 GGGTATACAC
* *
263945 AGTCCTTCGGGACAAATATATA
1 AGTCATTCGGGACAAATACATA
* * *
263967 GGTTATTTGGGACAAATACATA
1 AGTCATTCGGGACAAATACATA
263989 AGTCATTCGGGACAAAT
1 AGTCATTCGGGACAAAT
264006 TTCATATGCC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (22 bp):
AGTCATTCGGGACAAATACATA
Found at i:265938 original size:133 final size:133
Alignment explanation
Indices: 265700--265966 Score: 534
Period size: 133 Copynumber: 2.0 Consensus size: 133
265690 ATATATCAAT
265700 AGCATACTTTCGATAAATTAGGCTTGAAGTATTCTAATTTCTTTAGCGTTCAGGGTATTTTTCTC
1 AGCATACTTTCGATAAATTAGGCTTGAAGTATTCTAATTTCTTTAGCGTTCAGGGTATTTTTCTC
265765 CTTTGATCATTAGAGGTTATTATAGTTATTACAAATCTCGAAGACATTTCAGTAATTTCTTTCAA
66 CTTTGATCATTAGAGGTTATTATAGTTATTACAAATCTCGAAGACATTTCAGTAATTTCTTTCAA
265830 TTC
131 TTC
265833 AGCATACTTTCGATAAATTAGGCTTGAAGTATTCTAATTTCTTTAGCGTTCAGGGTATTTTTCTC
1 AGCATACTTTCGATAAATTAGGCTTGAAGTATTCTAATTTCTTTAGCGTTCAGGGTATTTTTCTC
265898 CTTTGATCATTAGAGGTTATTATAGTTATTACAAATCTCGAAGACATTTCAGTAATTTCTTTCAA
66 CTTTGATCATTAGAGGTTATTATAGTTATTACAAATCTCGAAGACATTTCAGTAATTTCTTTCAA
265963 TTC
131 TTC
265966 A
1 A
265967 ATCCTATGTA
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 134 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (133 bp):
AGCATACTTTCGATAAATTAGGCTTGAAGTATTCTAATTTCTTTAGCGTTCAGGGTATTTTTCTC
CTTTGATCATTAGAGGTTATTATAGTTATTACAAATCTCGAAGACATTTCAGTAATTTCTTTCAA
TTC
Found at i:266028 original size:20 final size:20
Alignment explanation
Indices: 266003--266048 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
265993 TCCAATATGT
266003 CCTTTCGGAGTTATTTTTCA
1 CCTTTCGGAGTTATTTTTCA
266023 CCTTTCGGAGTTATTTTTCA
1 CCTTTCGGAGTTATTTTTCA
266043 CCTTTC
1 CCTTTC
266049 AAAAAAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.24, G:0.13, T:0.50
Consensus pattern (20 bp):
CCTTTCGGAGTTATTTTTCA
Found at i:270104 original size:58 final size:58
Alignment explanation
Indices: 269984--270118 Score: 180
Period size: 58 Copynumber: 2.3 Consensus size: 58
269974 ACCGTTGACC
* *** *
269984 GGTGCTATTTTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTTTGGTAATTAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGAAATG
* * * *
270042 GGTGCGATTCTGGTAATTAATTCGGTTTTGGTGCTATTCTGGTAATTAATTCGAAATG
1 GGTGCTATTTTGGTAATTAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGAAATG
*
270100 GGTGCTATTTTAGTAATTA
1 GGTGCTATTTTGGTAATTA
270119 TTTTAAAAAG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (58 bp):
GGTGCTATTTTGGTAATTAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGAAATG
Found at i:270108 original size:29 final size:29
Alignment explanation
Indices: 269984--270094 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
269974 ACCGTTGACC
* * *
269984 GGTGCTATTTTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAATTAATTCGGTTTT
*
270013 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAATTAATTCGGTTTT
*
270042 GGTGCGATTCTGGTAATTAATTCGGTTTT
1 GGTGCTATTCTGGTAATTAATTCGGTTTT
270071 GGTGCTATTCTGGTAATTAATTCG
1 GGTGCTATTCTGGTAATTAATTCG
270095 AAATGGGTGC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAATTAATTCGGTTTT
Found at i:281621 original size:8 final size:8
Alignment explanation
Indices: 281608--281647 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
281598 TCTTTCATTT
281608 AAAAAAAG
1 AAAAAAAG
281616 AAAAAAAG
1 AAAAAAAG
*
281624 ATAAAAAG
1 AAAAAAAG
281632 --AAAAAG
1 AAAAAAAG
281638 AAAAAAAG
1 AAAAAAAG
281646 AA
1 AA
281648 GCATAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 6 0.21
8 23 0.79
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:281637 original size:14 final size:14
Alignment explanation
Indices: 281608--281647 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
281598 TCTTTCATTT
281608 AAAAAAAGAAAAAAAG
1 AAAAAAAG--AAAAAG
*
281624 ATAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
281638 AAAAAAAGAA
1 AAAAAAAGAA
281648 GCATAATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 15 0.68
16 7 0.32
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:281667 original size:26 final size:27
Alignment explanation
Indices: 281633--281699 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 27
281623 GATAAAAAGA
281633 AAAAGAAAAAAAG-AAGCATA-ATTGTGC
1 AAAA-AAAAAAAGAAAG-ATAGATTGTGC
281660 AAAAAAAAAAAGAAAGATAGATTGTGC
1 AAAAAAAAAAAGAAAGATAGATTGTGC
*
281687 AATGAAAAAAAAG
1 AA-AAAAAAAAAG
281700 TTATATGGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
26 11 0.31
27 16 0.44
28 9 0.25
ACGTcount: A:0.64, C:0.04, G:0.18, T:0.13
Consensus pattern (27 bp):
AAAAAAAAAAAGAAAGATAGATTGTGC
Found at i:285896 original size:28 final size:23
Alignment explanation
Indices: 285838--285885 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
285828 TCAACGCTTT
285838 TGCTTGTTGTAGATTTTCTTTTC
1 TGCTTGTTGTAGATTTTCTTTTC
285861 TGCTTGTTGTAGATTTTCTTTTC
1 TGCTTGTTGTAGATTTTCTTTTC
285884 TG
1 TG
285886 TCTTCCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.08, C:0.12, G:0.19, T:0.60
Consensus pattern (23 bp):
TGCTTGTTGTAGATTTTCTTTTC
Found at i:287932 original size:20 final size:20
Alignment explanation
Indices: 287907--287953 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
287897 TGTTTTTCTT
287907 ATTTTAAA-AGCTTTAAACAC
1 ATTTTAAACA-CTTTAAACAC
* *
287927 ATTTTAAACACTTTAAATAT
1 ATTTTAAACACTTTAAACAC
287947 ATTTTAA
1 ATTTTAA
287954 TTAACTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTTAAACACTTTAAACAC
Found at i:291049 original size:22 final size:22
Alignment explanation
Indices: 291024--291084 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
291014 GGGTATACGC
291024 GGTCCTTCGGGACAAATACATA
1 GGTCCTTCGGGACAAATACATA
*
291046 GGTCCTTTGGGACAAATACATA
1 GGTCCTTCGGGACAAATACATA
*
291068 GGTCATTCGGGACAAAT
1 GGTCCTTCGGGACAAAT
291085 TTCATATGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATACATA
Found at i:291097 original size:23 final size:22
Alignment explanation
Indices: 291029--291098 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
291019 TACGCGGTCC
291029 TTCGGGACAAATACATAGGTCC-
1 TTCGGGACAAATACATAGG-CCA
* *
291051 TTTGGGACAAATACATAGGTCA
1 TTCGGGACAAATACATAGGCCA
* *
291073 TTCGGGACAAATTTCATATGCCA
1 TTCGGGACAAA-TACATAGGCCA
291096 TTC
1 TTC
291099 AGTGGGACTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.70
23 11 0.28
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (22 bp):
TTCGGGACAAATACATAGGCCA
Found at i:291887 original size:12 final size:12
Alignment explanation
Indices: 291870--291902 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
291860 TAGCATTCAT
291870 TACTGTTCAC-G
1 TACTGTTCACAG
291881 ATACTGTTCACAG
1 -TACTGTTCACAG
291894 TACTGTTCA
1 TACTGTTCA
291903 TCAATATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.36
Consensus pattern (12 bp):
TACTGTTCACAG
Found at i:292667 original size:60 final size:60
Alignment explanation
Indices: 292532--292667 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
292522 ACATATAAAA
* *
292532 AATCGAGTG-ACCATTTTATAATTTTTAATAGTCGAAGTACTCAACAAAATAAATTTCTAT
1 AATCGAG-GAACCATTTTATAACTTTTAATAGTCGAAGTACTCAACAAAATAAATATCTAT
* * * * *
292592 AATTGAGGGATCATTTTATAACTTTTAATAGTCGGA-TGACTCAATAAAAT-AATATCATAT
1 AATCGAGGAACCATTTTATAACTTTTAATAGTCGAAGT-ACTCAACAAAATAAATATC-TAT
*
292652 AGTCGAGGAACCATTT
1 AATCGAGGAACCATTT
292668 ATGTACTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
59 7 0.11
60 56 0.89
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (60 bp):
AATCGAGGAACCATTTTATAACTTTTAATAGTCGAAGTACTCAACAAAATAAATATCTAT
Found at i:301661 original size:22 final size:22
Alignment explanation
Indices: 301636--301686 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
301626 AAATTTTGGC
**
301636 TTTTTTGTTTTTTTGTTTTGATT
1 TTTTTTGCCTTTTT-TTTTGATT
301659 TTTTTTGCCTTTTTTTTTG-TT
1 TTTTTTGCCTTTTTTTTTGATT
301680 TTTTTTG
1 TTTTTTG
301687 AAACAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 5 0.19
23 12 0.46
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.82
Consensus pattern (22 bp):
TTTTTTGCCTTTTTTTTTGATT
Found at i:303891 original size:20 final size:20
Alignment explanation
Indices: 303866--303912 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
303856 TGTTTTTCAT
303866 ATTTTAAA-AGCTTTAAACAC
1 ATTTTAAACA-CTTTAAACAC
* *
303886 ATTTTAAACACTTTAAATAT
1 ATTTTAAACACTTTAAACAC
303906 ATTTTAA
1 ATTTTAA
303913 TTAACTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTTAAACACTTTAAACAC
Found at i:304777 original size:66 final size:66
Alignment explanation
Indices: 304666--304793 Score: 238
Period size: 66 Copynumber: 1.9 Consensus size: 66
304656 ATTTTACGAG
*
304666 AATGTAGTATGGTGATTTATAGACTCACGAAGATACCCGCTCTTGATCACTATTGAGTTTCAGTA
1 AATGCAGTATGGTGATTTATAGACTCACGAAGATACCCGCTCTTGATCACTATTGAGTTTCAGTA
304731 A
66 A
*
304732 AATGCAGTATGGTGATTTATAGACTGACGAAGATACCCGCTCTTGATCACTATTGAGTTTCA
1 AATGCAGTATGGTGATTTATAGACTCACGAAGATACCCGCTCTTGATCACTATTGAGTTTCA
304794 TTGTTTGACT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (66 bp):
AATGCAGTATGGTGATTTATAGACTCACGAAGATACCCGCTCTTGATCACTATTGAGTTTCAGTA
A
Found at i:306783 original size:13 final size:13
Alignment explanation
Indices: 306765--306789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
306755 TGTCTATGAG
306765 AAGATATAAGAAT
1 AAGATATAAGAAT
306778 AAGATATAAGAA
1 AAGATATAAGAA
306790 ATGTAATAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (13 bp):
AAGATATAAGAAT
Found at i:307044 original size:22 final size:22
Alignment explanation
Indices: 307016--307071 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
307006 TACGCGGCCC
307016 TTCGGGACAAATACATAGGTCCA
1 TTCGGGACAAATACATAGGT-CA
307039 TT-GGGACAAATACATAGGTCA
1 TTCGGGACAAATACATAGGTCA
307060 TTCGGGACAAAT
1 TTCGGGACAAAT
307072 TTTATATGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.12
22 26 0.81
23 2 0.06
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (22 bp):
TTCGGGACAAATACATAGGTCA
Found at i:308962 original size:20 final size:20
Alignment explanation
Indices: 308937--308984 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
308927 TCCTGTATGT
308937 CCTTTCGGAGTTATTTTTCA
1 CCTTTCGGAGTTATTTTTCA
308957 CCTTTCGGAGTTATTTTTCA
1 CCTTTCGGAGTTATTTTTCA
308977 CCTTTCGG
1 CCTTTCGG
308985 GAAAGTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (20 bp):
CCTTTCGGAGTTATTTTTCA
Found at i:320058 original size:12 final size:12
Alignment explanation
Indices: 320041--320070 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
320031 TAGGGCCATT
320041 AGTTTTACATCA
1 AGTTTTACATCA
*
320053 AGTTTTACATTA
1 AGTTTTACATCA
320065 AGTTTT
1 AGTTTT
320071 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:325630 original size:18 final size:18
Alignment explanation
Indices: 325607--325645 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
325597 ATAACTAAAA
325607 TTGATTAAATTAT-GTATT
1 TTGATTAAATT-TCGTATT
*
325625 TTGATTATATTTCGTATT
1 TTGATTAAATTTCGTATT
325643 TTG
1 TTG
325646 TGGATTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.59
Consensus pattern (18 bp):
TTGATTAAATTTCGTATT
Found at i:326058 original size:12 final size:12
Alignment explanation
Indices: 326041--326070 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
326031 TAGGGCCATT
326041 AGTTTTACATCA
1 AGTTTTACATCA
*
326053 AGTTTTACATTA
1 AGTTTTACATCA
326065 AGTTTT
1 AGTTTT
326071 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:332080 original size:12 final size:12
Alignment explanation
Indices: 332063--332093 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
332053 TAGGGCCATT
332063 AGTTTTACATCA
1 AGTTTTACATCA
*
332075 AGTTTTACATTA
1 AGTTTTACATCA
332087 AGTTTTA
1 AGTTTTA
332094 TTTATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:336910 original size:24 final size:24
Alignment explanation
Indices: 336883--336981 Score: 60
Period size: 24 Copynumber: 4.2 Consensus size: 24
336873 ATAATGGAAT
336883 TAATAAAGGGGATAATAATATAAG
1 TAATAAAGGGGATAATAATATAAG
* ** * *
336907 TAATGAAAAGAAATAATAAGA-ATG
1 TAAT-AAAGGGGATAATAATATAAG
* * * ** *
336931 AAATGAA--TGATTAATAATGGAAT
1 TAATAAAGGGGA-TAATAATATAAG
336954 TAATAAAGGGGATAATAATATAAG
1 TAATAAAGGGGATAATAATATAAG
336978 TAAT
1 TAAT
336982 GAAAAGAAAT
Statistics
Matches: 51, Mismatches: 19, Indels: 10
0.64 0.24 0.12
Matches are distributed among these distances:
21 1 0.02
22 6 0.12
23 8 0.16
24 22 0.43
25 14 0.27
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (24 bp):
TAATAAAGGGGATAATAATATAAG
Found at i:336930 original size:19 final size:19
Alignment explanation
Indices: 336902--337010 Score: 56
Period size: 19 Copynumber: 4.9 Consensus size: 19
336892 GGATAATAAT
336902 ATAAGTAATGAAAAGAAATA
1 ATAAG-AATGAAAAGAAATA
*
336922 ATAAGAATGAAATGAATGATTA
1 ATAAGAATGAAAAGAA--A-TA
*
336944 ATAATGGAATTAATAAAGGGGATAATA
1 ATAA--GAA-TGA-AAA---GA-AATA
336971 ATATAAGTAATGAAAAGAAATA
1 AT--AAG-AATGAAAAGAAATA
*
336993 ATAAGAATGAAATGAAAT
1 ATAAGAATGAAAAGAAAT
337011 GAAATAAGGA
Statistics
Matches: 70, Mismatches: 5, Indels: 29
0.67 0.05 0.28
Matches are distributed among these distances:
19 22 0.31
20 8 0.11
21 1 0.01
22 12 0.17
23 2 0.03
24 3 0.04
25 2 0.03
26 5 0.07
27 7 0.10
28 3 0.04
29 4 0.06
30 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (19 bp):
ATAAGAATGAAAAGAAATA
Found at i:336946 original size:71 final size:71
Alignment explanation
Indices: 336849--337008 Score: 302
Period size: 71 Copynumber: 2.2 Consensus size: 71
336839 TGGGTTGCAA
*
336849 AATAAGATAAGAAATGAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAA
1 AATAAGA-ATGAAATGAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAA
336914 AAGAAAT
65 AAGAAAT
336921 AATAAGAATGAAATGAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAA
1 AATAAGAATGAAATGAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAA
336986 AGAAAT
66 AGAAAT
336992 AATAAGAATGAAATGAA
1 AATAAGAATGAAATGAA
337009 ATGAAATAAG
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
71 80 0.92
72 7 0.08
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.24
Consensus pattern (71 bp):
AATAAGAATGAAATGAATGATTAATAATGGAATTAATAAAGGGGATAATAATATAAGTAATGAAA
AGAAAT
Found at i:337009 original size:24 final size:24
Alignment explanation
Indices: 336908--337017 Score: 75
Period size: 24 Copynumber: 4.6 Consensus size: 24
336898 TAATATAAGT
336908 AATGAAAAGAAATAATAAGAATGA
1 AATGAAAAGAAATAATAAGAATGA
* * *
336932 AATG-AATGATTAATAAT-GGAAT-T
1 AATGAAAAGA--AATAATAAGAATGA
* ** * * *
336955 AAT-AAAGGGGATAATAATATAAGT
1 AATGAAAAGAAATAATAAGA-ATGA
336979 AATGAAAAGAAATAATAAGAATGA
1 AATGAAAAGAAATAATAAGAATGA
*
337003 AATGAAATGAAATAA
1 AATGAAAAGAAATAA
337018 GGATGGGATA
Statistics
Matches: 63, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
21 5 0.08
22 1 0.02
23 11 0.17
24 28 0.44
25 18 0.29
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (24 bp):
AATGAAAAGAAATAATAAGAATGA
Found at i:339097 original size:20 final size:20
Alignment explanation
Indices: 339072--339118 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
339062 TGTTTTTCAA
339072 ATTTTAAA-AGCTTTAAACAC
1 ATTTTAAACA-CTTTAAACAC
* *
339092 ATTTTAAACACTTTAAATAT
1 ATTTTAAACACTTTAAACAC
339112 ATTTTAA
1 ATTTTAA
339119 TTAACTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTTAAACACTTTAAACAC
Found at i:340051 original size:3 final size:3
Alignment explanation
Indices: 340039--340074 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
340029 CTTCTAATTC
340039 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
340075 CAGTGAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:340726 original size:60 final size:60
Alignment explanation
Indices: 340662--340782 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
340652 AAATATAAAA
* * *
340662 AATTGAGCGA-CTAATTTGTAATTTTTAATAGTCGAAGAAATCAACAAAATAATATCCTAT
1 AATTGAGCGATC-AATTTATAAATTTTAATAGTCGAAGAAATCAACAAAATAATATCATAT
* * * * *
340722 AATTGAGGGATCATTTTATAAATTTTAATAGTCGAATAACTCAATAAAATAATATCATAT
1 AATTGAGCGATCAATTTATAAATTTTAATAGTCGAAGAAATCAACAAAATAATATCATAT
340782 A
1 A
340783 GTCGATGAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 51 0.98
61 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.35
Consensus pattern (60 bp):
AATTGAGCGATCAATTTATAAATTTTAATAGTCGAAGAAATCAACAAAATAATATCATAT
Found at i:340797 original size:60 final size:60
Alignment explanation
Indices: 340684--340797 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
340674 AATTTGTAAT
* * * *
340684 TTTTAATAGTCGAAGAAATCAACAAAATAATATCCTATAATTGAGGGATCATTTTATAAA
1 TTTTAATAGTCGAAGAAATCAACAAAATAATATCATATAATCGAGGAACCATTTTATAAA
* * * * *
340744 TTTTAATAGTCGAATAACTCAATAAAATAATATCATATAGTCGATGAACCATTT
1 TTTTAATAGTCGAAGAAATCAACAAAATAATATCATATAATCGAGGAACCATTT
340798 ATGTACTTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (60 bp):
TTTTAATAGTCGAAGAAATCAACAAAATAATATCATATAATCGAGGAACCATTTTATAAA
Found at i:354850 original size:12 final size:12
Alignment explanation
Indices: 354833--354862 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
354823 TAGGGCCATT
354833 AGTTTTACATCA
1 AGTTTTACATCA
*
354845 AGTTTTACATTA
1 AGTTTTACATCA
354857 AGTTTT
1 AGTTTT
354863 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:359580 original size:28 final size:29
Alignment explanation
Indices: 359549--359618 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
359539 AAAAGACAAA
359549 AAAGAAAAAAAAAG-AAGCA-AAATTGTGC
1 AAAGAAAAAAAAAGAAAG-ATAAATTGTGC
* * *
359577 AAAG-GAAATAAAGAAAGATAGATTGTGC
1 AAAGAAAAAAAAAGAAAGATAAATTGTGC
*
359605 AATGAAAAAAAAAG
1 AAAGAAAAAAAAAG
359619 TTATATGGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
27 8 0.24
28 18 0.55
29 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.20, T:0.13
Consensus pattern (29 bp):
AAAGAAAAAAAAAGAAAGATAAATTGTGC
Found at i:365507 original size:6 final size:6
Alignment explanation
Indices: 365492--365528 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
365482 GTTGTTTTTA
365492 TTTA-T TTTATT TTTATT TTTATT TTTA-T TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
365529 TTCCTTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:365508 original size:11 final size:11
Alignment explanation
Indices: 365492--365528 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
365482 GTTGTTTTTA
365492 TTTATTTTATT
1 TTTATTTTATT
365503 TTTATTTTTATT
1 TTTA-TTTTATT
365515 TTTATTTTATT
1 TTTATTTTATT
365526 TTT
1 TTT
365529 TTCCTTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:365536 original size:18 final size:18
Alignment explanation
Indices: 365492--365528 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
365482 GTTGTTTTTA
365492 TTTA-TTTTATTTTTATT
1 TTTATTTTTATTTTTATT
365509 TTTATTTTTA-TTTTATT
1 TTTATTTTTATTTTTATT
365526 TTT
1 TTT
365529 TTCCTTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTATTTTTATTTTTATT
Found at i:366717 original size:13 final size:12
Alignment explanation
Indices: 366699--366741 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
366689 TCTTTCATTG
366699 AAAAAAAAAGACA
1 AAAAAAAAAGA-A
366712 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
366724 AAAGAAAAAGAA
1 AAAAAAAAAGAA
366736 AAAAAA
1 AAAAAA
366742 GAAGCAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.88, C:0.02, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:366725 original size:6 final size:6
Alignment explanation
Indices: 366699--366738 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
366689 TCTTTCATTG
*
366699 AAAA-A AAAAGA CAAAAAA AAAAGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA -AAAAGA AAAAGA AAAAGA AAAAGA AAAA
366739 AAAGAAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 4 0.13
6 22 0.71
7 5 0.16
ACGTcount: A:0.88, C:0.03, G:0.10, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:366750 original size:12 final size:12
Alignment explanation
Indices: 366699--366750 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
366689 TCTTTCATTG
366699 AAAAAAAAAGACA
1 AAAAAAAAAG-CA
366712 AAAAAAAAAG-A
1 AAAAAAAAAGCA
366723 AAAAGAAAAAG-A
1 AAAA-AAAAAGCA
366735 AAAAAAAGAAGCA
1 AAAAAAA-AAGCA
366748 AAA
1 AAA
366751 TTGTGCAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.22
12 14 0.39
13 14 0.39
ACGTcount: A:0.85, C:0.04, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGCA
Found at i:366750 original size:25 final size:24
Alignment explanation
Indices: 366699--366750 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
366689 TCTTTCATTG
366699 AAAAAAAAAGACAAAAAAAAAAGA
1 AAAAAAAAAGACAAAAAAAAAAGA
* *
366723 AAAAGAAAAAGA-AAAAAAAGAAGC
1 AAAA-AAAAAGACAAAAAAAAAAGA
366747 AAAA
1 AAAA
366751 TTGTGCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.85, C:0.04, G:0.12, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAGACAAAAAAAAAAGA
Found at i:366760 original size:27 final size:28
Alignment explanation
Indices: 366730--366796 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
366720 AGAAAAAGAA
366730 AAAGAAAAAAAAG-AAGCA-AAATTGTGC
1 AAAGAAAAAAAAGAAAG-ATAAATTGTGC
* * *
366757 AAAGGAAATAAAGAAAGATAGATTGTGC
1 AAAGAAAAAAAAGAAAGATAAATTGTGC
*
366785 AATGAAAAAAAA
1 AAAGAAAAAAAA
366797 AAGTTATATG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 12 0.38
28 20 0.62
ACGTcount: A:0.63, C:0.04, G:0.19, T:0.13
Consensus pattern (28 bp):
AAAGAAAAAAAAGAAAGATAAATTGTGC
Found at i:367852 original size:12 final size:12
Alignment explanation
Indices: 367835--367864 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
367825 TAGGGCCATT
367835 AGTTTTACATCA
1 AGTTTTACATCA
*
367847 AGTTTTACATTA
1 AGTTTTACATCA
367859 AGTTTT
1 AGTTTT
367865 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:373115 original size:20 final size:20
Alignment explanation
Indices: 373090--373136 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
373080 TGTTTTTCAA
373090 ATTTTAAA-AGCTTTAAACAC
1 ATTTTAAACA-CTTTAAACAC
* *
373110 ATTTTAAACACTTTAAATAT
1 ATTTTAAACACTTTAAACAC
373130 ATTTTAA
1 ATTTTAA
373137 TTAACTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTTAAACACTTTAAACAC
Found at i:374723 original size:60 final size:60
Alignment explanation
Indices: 374659--374779 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
374649 AAATATAAAA
* * *
374659 AATTGAGCGACCAATTTGTAATTTTTAATAGTCGAA-GAAATCAACAAAATAATATCCTAT
1 AATTGAGCGACCAATTTATAAATTTTAATAGTCGAATG-AATCAACAAAATAATATCATAT
* * * * *
374719 AATTGAGGGATCATTTTATAAATTTTAATAGTCGAATGACTCAATAAAATAATATCATAT
1 AATTGAGCGACCAATTTATAAATTTTAATAGTCGAATGAATCAACAAAATAATATCATAT
374779 A
1 A
374780 GTCGAGGAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 51 0.98
61 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.34
Consensus pattern (60 bp):
AATTGAGCGACCAATTTATAAATTTTAATAGTCGAATGAATCAACAAAATAATATCATAT
Found at i:374794 original size:60 final size:60
Alignment explanation
Indices: 374681--374794 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
374671 AATTTGTAAT
* * * *
374681 TTTTAATAGTCGAAGAAATCAACAAAATAATATCCTATAATTGAGGGATCATTTTATAAA
1 TTTTAATAGTCGAAGAAATCAACAAAATAATATCATATAATCGAGGAACCATTTTATAAA
* * *
374741 TTTTAATAGTCGAATG-ACTCAATAAAATAATATCATATAGTCGAGGAACCATTT
1 TTTTAATAGTCGAA-GAAATCAACAAAATAATATCATATAATCGAGGAACCATTT
374795 ATGTACTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 45 0.98
61 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (60 bp):
TTTTAATAGTCGAAGAAATCAACAAAATAATATCATATAATCGAGGAACCATTTTATAAA
Found at i:381397 original size:20 final size:20
Alignment explanation
Indices: 381368--381415 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
381358 TCCAGTATGT
*
381368 CCTTTTGGAGTTATTTTTCA
1 CCTTTCGGAGTTATTTTTCA
381388 CCTTTCGGAGTTATTTTTCA
1 CCTTTCGGAGTTATTTTTCA
381408 CCTTTCGG
1 CCTTTCGG
381416 GAAAGTATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.21, G:0.17, T:0.50
Consensus pattern (20 bp):
CCTTTCGGAGTTATTTTTCA
Found at i:384997 original size:95 final size:95
Alignment explanation
Indices: 384830--385007 Score: 248
Period size: 95 Copynumber: 1.9 Consensus size: 95
384820 GATGAAGTGA
* * * *
384830 CATGTGCCACATTATCACTTATATACACATGGCACATGATATACCATCACTTTTATACATATGAC
1 CATGGGCCACATCATCACTTATATACACATGGCACATGACATACCATCACTTTTATACATATAAC
* * *
384895 ATATGTCAGGTTATCACTCTAAACATGTGG
66 ACATGTCAAGTCATCACTCTAAACATGTGG
* * * *
384925 CATGGGCCACATCATCACTTATATATACGTGGCACATGACATACCATCATTTTTGTACATATAAC
1 CATGGGCCACATCATCACTTATATACACATGGCACATGACATACCATCACTTTTATACATATAAC
*
384990 ACCTGTCAAGTCATCACT
66 ACATGTCAAGTCATCACT
385008 TTCGACACAT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
95 71 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.31
Consensus pattern (95 bp):
CATGGGCCACATCATCACTTATATACACATGGCACATGACATACCATCACTTTTATACATATAAC
ACATGTCAAGTCATCACTCTAAACATGTGG
Found at i:404519 original size:16 final size:18
Alignment explanation
Indices: 404488--404529 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
404478 TGCAGACGAT
*
404488 ATAATTAAAACAATTAA-
1 ATAATAAAAACAATTAAC
404505 ATAATAAAAAC-ATTAAC
1 ATAATAAAAACAATTAAC
404522 A-AATAAAA
1 ATAATAAAA
404530 TAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAATAAAAACAATTAAC
Found at i:404568 original size:19 final size:19
Alignment explanation
Indices: 404530--404569 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
404520 ACAAATAAAA
* *
404530 TAAATAAAAAGTTCATAAT
1 TAAATAAAAACTTCACAAT
*
404549 TAAATAAAAACTTTACAAT
1 TAAATAAAAACTTCACAAT
404568 TA
1 TA
404570 CTGCTAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAATAAAAACTTCACAAT
Found at i:404592 original size:79 final size:84
Alignment explanation
Indices: 404507--404692 Score: 276
Period size: 79 Copynumber: 2.3 Consensus size: 84
404497 ACAATTAAAT
*
404507 AATAAAAACATTAACAAATAAAATAAATAAAAAGT-T-CATAATTAAATAAAAACTTTACAATTA
1 AATAAAAACATTAACAAATAAAATAAATAAAAAATATACATAATTAAATAAAAACTTTACAATTA
404570 CTGCT-A-AAA-AAAATTA
66 CTGCTAACAAACAAAATTA
* *
404586 AATAAAAATATTAACAAATAAAATAAATAAAAAATATATATAATTAAATAAAAACTTTACAATTA
1 AATAAAAACATTAACAAATAAAATAAATAAAAAATATACATAATTAAATAAAAACTTTACAATTA
*
404651 CTGGTAAACAAACAAAATTA
66 CTGCT-AACAAACAAAATTA
404671 AATAAAAACATT-ACAAACTAAA
1 AATAAAAACATTAACAAA-TAAA
404693 CAACTCTATC
Statistics
Matches: 95, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
79 33 0.35
80 1 0.01
81 30 0.32
83 1 0.01
84 8 0.08
85 22 0.23
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (84 bp):
AATAAAAACATTAACAAATAAAATAAATAAAAAATATACATAATTAAATAAAAACTTTACAATTA
CTGCTAACAAACAAAATTA
Found at i:405123 original size:21 final size:21
Alignment explanation
Indices: 405099--405139 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
405089 ATCTGACTCG
* * *
405099 GCTATGGTGGCATCTGATATA
1 GCTACGGTGACATATGATATA
405120 GCTACGGTGACATATGATAT
1 GCTACGGTGACATATGATAT
405140 GGAAGCAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (21 bp):
GCTACGGTGACATATGATATA
Found at i:405195 original size:21 final size:21
Alignment explanation
Indices: 405171--405227 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
405161 ACTGCGGTGG
405171 CATCTGAAATGGTTGTGGTAC
1 CATCTGAAATGGTTGTGGTAC
* *
405192 CATCTGATATGGTTGTGGTGC
1 CATCTGAAATGGTTGTGGTAC
* *
405213 CATCTAAAACGGTTG
1 CATCTGAAATGGTTG
405228 CGGAATGTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (21 bp):
CATCTGAAATGGTTGTGGTAC
Found at i:406929 original size:16 final size:16
Alignment explanation
Indices: 406910--406952 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
406900 TTGCAAAAAG
406910 TAATAAAAATTTAGTA
1 TAATAAAAATTTAGTA
406926 TAAT-AAAATTTAGTA
1 TAATAAAAATTTAGTA
*
406941 AAATAATAAATT
1 TAATAA-AAATT
406953 ATTAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 14 0.58
16 5 0.21
17 5 0.21
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (16 bp):
TAATAAAAATTTAGTA
Found at i:410142 original size:3 final size:3
Alignment explanation
Indices: 410134--410204 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
410124 TTAATATATT
410134 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
410181 TAA TAA TAA T-A TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
410205 TAATTAATAT
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:410779 original size:113 final size:113
Alignment explanation
Indices: 410519--411088 Score: 858
Period size: 113 Copynumber: 5.0 Consensus size: 113
410509 ATCTCCTTCT
* * * *
410519 GTGATAGAATT-ATGCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCA
1 GTGAT-GAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
410583 GATGAGTTCTTCTCATTATGAA-CTTCTCTGGAAATGCTGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGATAATCCATCAA
* * *
410631 TTGATGAATTCATGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* *
410696 ATGAGTTATTCTCATTATGAACCTTCTCTGGCAAA-AATAATCCATCAA
66 ATGAGTTCTTCTCATTATGAACCTTCTCTGG-AAATGATAATCCATCAA
* ** *
410744 GTGATGAATTCAGACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAG
1 GTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * *
410809 ATGAGTTCTTCTTATTATGAACTTTCTCTAGAAAAGATAATCCATCAA
66 ATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGATAATCCATCAA
* * *
410857 TTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
1 -GTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
410922 GATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGCTAATCCATCAA
65 GATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGATAATCCATCAA
*
410971 GTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
411036 ATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGATAATCCTTCAA
66 ATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGATAATCCATCAA
*
411084 ATGAT
1 GTGAT
411089 AGATTTGAAT
Statistics
Matches: 415, Mismatches: 38, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
111 5 0.01
112 77 0.19
113 229 0.55
114 104 0.25
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
GTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACCTTCTCTGGAAATGATAATCCATCAA
Found at i:410918 original size:227 final size:225
Alignment explanation
Indices: 410533--411088 Score: 891
Period size: 227 Copynumber: 2.5 Consensus size: 225
410523 TAGAATTATG
* * *
410533 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
410598 TTATGAACTTCTCTGGAAATGCTGATCCATCAATTGATGAATTCATGTAAAAGGTTGAACAAATT
66 TTATGAACTTCTCTGGAAATGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATT
410663 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACCTTCTCTGGC
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACCTTCTCTGG-
410728 AAA-AATAATCCATCAAGTGATGAATTCAGA
195 AAATAATAATCCATCAAGTGATGAATTCAGA
* *
410758 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
410823 TTATGAACTTTCTCTAGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAA
66 TTATGAAC-TTCTCTGGAAATGATAATCCATCAA-TTGATGAATTCAGGTAAAAGGTTGAACAAA
* *
410888 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
129 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACCTTCTCTG
** *
410953 GAAATGCTAATCCATCAAGTGATGAATTCAGG
194 GAAATAATAATCCATCAAGTGATGAATTCAGA
*
410985 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
411049 ATTATGAACCTTCTCTGGAAATGATAATCCTTCAAATGAT
65 ATTATGAA-CTTCTCTGGAAATGATAATCCATCAATTGAT
411089 AGATTTGAAT
Statistics
Matches: 304, Mismatches: 22, Indels: 9
0.91 0.07 0.03
Matches are distributed among these distances:
225 68 0.22
226 31 0.10
227 204 0.67
228 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (225 bp):
CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTCTCTGGAAATGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTATGAACCTTCTCTGGA
AATAATAATCCATCAAGTGATGAATTCAGA
Found at i:413127 original size:7 final size:7
Alignment explanation
Indices: 413115--413144 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
413105 TTGACCCCCC
413115 TTTTTCT
1 TTTTTCT
413122 TTTTTCT
1 TTTTTCT
413129 TTTTTCT
1 TTTTTCT
413136 TTTTT-T
1 TTTTTCT
413142 TTT
1 TTT
413145 CTTCAAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTCT
Found at i:423757 original size:13 final size:15
Alignment explanation
Indices: 423735--423771 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
423725 TTTGACAGAA
423735 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
423747 AAATAAAATACTTGC
1 AAATAAAATACTTGC
423762 AAATAAAATA
1 AAATAAAATA
423772 AAGCATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:425966 original size:12 final size:11
Alignment explanation
Indices: 425960--426032 Score: 71
Period size: 12 Copynumber: 6.5 Consensus size: 11
425950 TTAATATATT
425960 TAATAATAATAA
1 TAATAAT-ATAA
425972 TAATAATGATAA
1 TAATAAT-ATAA
425984 TAATAATA-AA
1 TAATAATATAA
425994 -AATAATAATAA
1 TAATAAT-ATAA
*
426005 TTATAATAATAA
1 TAATAAT-ATAA
426017 TAATAAT-TAA
1 TAATAATATAA
426027 TTAATA
1 -TAATA
426033 TGGGTAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
9 6 0.11
10 6 0.11
11 8 0.15
12 34 0.63
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (11 bp):
TAATAATATAA
Found at i:425968 original size:3 final size:3
Alignment explanation
Indices: 425960--426023 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
425950 TTAATATATT
* * *
425960 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA AAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
426008 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
426024 TAATTAATAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:431332 original size:37 final size:37
Alignment explanation
Indices: 431291--431365 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
431281 TTCGGAACCT
*
431291 TTAACTTAATTTGATCTGTTTCTCTTTTCGATCTTTA
1 TTAACTTAATTTGATCTGTATCTCTTTTCGATCTTTA
431328 TTAACTTAATTTGATCTGTATCTCTTTTCGATCTTTA
1 TTAACTTAATTTGATCTGTATCTCTTTTCGATCTTTA
431365 T
1 T
431366 CAGACACTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.56
Consensus pattern (37 bp):
TTAACTTAATTTGATCTGTATCTCTTTTCGATCTTTA
Found at i:431366 original size:17 final size:17
Alignment explanation
Indices: 431311--431366 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
431301 TTGATCTGTT
431311 TCTCTTTTCGATCTTTA
1 TCTCTTTTCGATCTTTA
* *
431328 T-TAACTTAATTTGATCTGTA
1 TCT--CTT--TTCGATCTTTA
431348 TCTCTTTTCGATCTTTA
1 TCTCTTTTCGATCTTTA
431365 TC
1 TC
431367 AGACACTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 1 0.03
17 12 0.40
18 3 0.10
19 3 0.10
20 10 0.33
21 1 0.03
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (17 bp):
TCTCTTTTCGATCTTTA
Found at i:437002 original size:200 final size:197
Alignment explanation
Indices: 436350--437067 Score: 867
Period size: 199 Copynumber: 3.6 Consensus size: 197
436340 AGCGCTTGTA
* **
436350 TTGACCTATTTTCTAAGT-AAACCGGTATATTTATACCGGTAACATTACAAATTTACCTATTACA
1 TTGACCTATTTTCTAA-TAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACA
* * *
436414 TTATAATTATCGGTTTCGATGTTTTTTGGATTGATACAATTT--TAAATGTATCAACACTTTATG
65 TTATAATTATC-GTTTCGATGTTTTTTGGATCGATAC-TTTTAATAAATGTATCGACACTTTATG
* * * *
436477 CTTGCACCTCGTTGGGCATTCATTCTGGAAAAAAATATCGACACAAACTTAAAAAGTGTCGATAC
128 CGTGCACCTCTTTGGGCATTCATTCTGGACAAAAATATCGACACAAA-TTAACAAGTGTCGATAC
436542 ATTAT-
192 ATTATG
* * * * *
436547 TTAGACCTATTTTCTCATAAAATCGGTATATTTATATCGGGTACATTGTAAATTTACCTATCACA
1 TT-GACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACA
* * * *
436612 TTGTAATTTTCGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTCTATGCG
65 TTATAATTATCGTTTCGATGTTTTTTGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG
* * * *
436677 TGCA-CTCCGTTT-GGCATTCATTATGGACAAAATGTATCAACACAAATTTAACAAGTGTTGATA
130 TGCACCT-C-TTTGGGCATTCATTCTGGACAAAA-ATATCGACACAAA-TTAACAAGTGTCGATA
*
436740 CTTTATG
191 CATTATG
* * * *
436747 TTGACCTATTTTCTCATAAAACCAGTATATTTATATCGGTTACATTGTAAATTTACATATTACAT
1 TTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
**
436812 TATAATTATCGTTTCGATGTTTTTAAGATCGATACTTTTAATAAATGTATCGACACTTTATGCGT
66 TATAATTATCGTTTCGATGTTTTTTGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGT
* *
436877 GCACCTCATTTGGGCATTCATTCTGGACAATAAATATTGACACAAATTCCACAAGTGTCGATACA
131 GCACCTC-TTTGGGCATTCATTCTGGACAA-AAATATCGACACAAATT-AACAAGTGTCGATACA
436942 TTATG
193 TTATG
* * * * *
436947 TTGATCTGTTTTCTAAT-TAACCAGGTATATTTATACCCGTTACATTGTTAATTTACCTATTACA
1 TTGACCTATTTTCTAATAAAACC-GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACA
* * * * *
437011 TTATAATTATTAGTTTTGATGTTTTTTGGGTAGATACTTGTAGA-AAATGTATCGACA
65 TTATAATTA-TCGTTTCGATGTTTTTTGGATCGATACTTTTA-ATAAATGTATCGACA
437068 TATATTTAGG
Statistics
Matches: 447, Mismatches: 59, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
196 3 0.01
197 28 0.06
198 104 0.23
199 163 0.36
200 108 0.24
201 40 0.09
202 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
TTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
TATAATTATCGTTTCGATGTTTTTTGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGT
GCACCTCTTTGGGCATTCATTCTGGACAAAAATATCGACACAAATTAACAAGTGTCGATACATTA
TG
Found at i:440575 original size:201 final size:200
Alignment explanation
Indices: 440219--441158 Score: 1275
Period size: 201 Copynumber: 4.8 Consensus size: 200
440209 TATAATGGAT
* *
440219 AAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAAACCTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATC
** ** *
440284 AATATATTTATACCAATTATATTACAAAATTACCTATTACATTATAATTATGAATTTCGATGTTT
66 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGATGTTT
* * *
440349 TTTAGATCGACACCTTTTGAAAATGTATCGACACTTTATGCTTTCACCCTATTTTGGCATCCATT
131 TTGAGATCGACA-CTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTTGGCATCCATT
440414 CTATAC
195 CTATAC
*
440420 AAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATATTGTAGACCTATTCTCTCATAAAATC
1 AAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATC
* * *
440485 GGTATATTTATATCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTT
66 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGATGTTT
* * * *
440550 TTGGGATTGACACGTTTTAAAAATGTATCGACACTTTATGAGTTCACCCTTTTTTGGCATCCATT
131 TTGAGATCGACAC-TTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTTGGCATCCATT
440615 CTATAC
195 CTATAC
* *
440621 AAAAAGTATCGACACAAAATTAAAAAATGTTGATACATGTTGTAGACCTATTCTCTCATAAAATC
1 AAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATC
* *
440686 GATATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGATATTT
66 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGATGTTT
*
440751 TCGAGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTTGGCATCCATT
131 TTGAGATCGACAC-TTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTTGGCATCCATT
440816 C--T--
195 CTATAC
* *
440818 -----GTA-C-A-A-AAAATTAAAAAGTGTTGATACATATTGTAGACCTATTCTCTCATAAAATC
1 AAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATC
*
440874 GGTATATTTATATCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGA-----
66 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGATGTTT
*
440934 -T--G-T------TTTTG---A-G-ATCGACACTTTATGCGTTCACCCTTTTTTGGCATACATTC
131 TTGAGATCGACACTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTTGGCATCCATTC
*
440984 TGTAC
196 TATAC
*
440989 AAAAAGTATCGACACGAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAA-C
1 AAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATC
* * *
441053 TGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATATT
66 -GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGATGTT
* *
441118 TTT-AGGATCGACTCATTTTTAAAATGTATCGACACTTTATG
130 TTTGA-GATCGACAC-TTTTGAAAATGTATCGACACTTTATG
441159 AGAAACTTTA
Statistics
Matches: 658, Mismatches: 45, Indels: 72
0.85 0.06 0.09
Matches are distributed among these distances:
167 39 0.06
168 1 0.00
169 2 0.00
172 5 0.01
176 3 0.00
177 1 0.00
178 1 0.00
179 3 0.00
180 103 0.16
186 1 0.00
188 107 0.16
189 2 0.00
190 1 0.00
191 1 0.00
192 3 0.00
196 4 0.01
199 2 0.00
200 2 0.00
201 377 0.57
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (200 bp):
AAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATC
GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGATGTTT
TTGAGATCGACACTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTTGGCATCCATTC
TATAC
Found at i:440885 original size:188 final size:184
Alignment explanation
Indices: 440611--441158 Score: 677
Period size: 188 Copynumber: 3.0 Consensus size: 184
440601 TTTTGGCATC
* * *
440611 CATTCTATACAAAAAGTATCGACACAAAATTAAAAAATGTTGATACATGTTGTAGACCTATTCTC
1 CATTCTGTACAAAAAGTATCGACAAAAAATTAAAAAGTGTTGATACATGTTGTAGACCTATTCTC
*
440676 TCATAAAATCGATATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGAT
66 TCATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGAT
440741 TTCGATATTTTCGAGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCAC-
131 TTCGATATTTT-GAGATCGACACTTTTTGAAAATGTATCGACACTTTATG-G--CACA
* * * * *** *
440798 CCTTTTTTGGCATCCA-T-TCTGTACAAAAAATTAAAAAGTGTTGATACATATTGTAGACCTATT
1 CATTCTGT-ACAAAAAGTATC-G-ACAAAAAATTAAAAAGTGTTGATACATGTTGTAGACCTATT
*
440861 CTCTCATAAAATCGGTATATTTATATCGGTTATATTACAAAATTACCTATTACATTATAATTATG
63 CTCTCATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATG
* * * * * *
440926 GATTTCGATGTTTTTGAGATCGACACTTTATG----CGT-TC-ACCCTTTTTTGGCATA
128 GATTTCGAT-ATTTTGAGATCGACACTTTTTGAAAATGTATCGACAC-TTTATGGCACA
** *
440979 CATTCTGTACAAAAAGTATCGACACGAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTC
1 CATTCTGTACAAAAAGTATCGACAAAAAATTAAAAAGTGTTGATACATGTTGTAGACCTATTCTC
*
441044 TCATAAAA-CTGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGG
66 TCATAAAATC-GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGA
* * *
441108 TTTCAATATTTTTAGGATCGACTCATTTTT-AAAATGTATCGACACTTTATG
130 TTTCGATATTTTGA-GATCGACAC-TTTTTGAAAATGTATCGACACTTTATG
441159 AGAAACTTTA
Statistics
Matches: 305, Mismatches: 39, Indels: 36
0.80 0.10 0.09
Matches are distributed among these distances:
179 6 0.02
180 119 0.39
181 11 0.04
182 6 0.02
183 7 0.02
184 4 0.01
185 7 0.02
186 5 0.02
187 7 0.02
188 129 0.42
189 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (184 bp):
CATTCTGTACAAAAAGTATCGACAAAAAATTAAAAAGTGTTGATACATGTTGTAGACCTATTCTC
TCATAAAATCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGAT
TTCGATATTTTGAGATCGACACTTTTTGAAAATGTATCGACACTTTATGGCACA
Found at i:441073 original size:180 final size:180
Alignment explanation
Indices: 440576--441129 Score: 724
Period size: 180 Copynumber: 3.0 Consensus size: 180
440566 TTAAAAATGT
440576 ATCGACACTTTATGAGTTCACCCTTTTTTGGCATCCATTCTATACAAAAAGTATCGACACAAAAT
1 ATCGACACTTTATGAGTTCACCCTTTTTTGGCATCCATTCTATACAAAAAGTATCGACACAAAAT
* *
440641 TAAAAAATGTTGATACATGTTGTAGACCTATTCTCTCATAAAATCGATATATTTATACCGGTTAT
66 TAAAAAGTGTTGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCGGTTAT
*
440706 ATTACAAAATTACCTATTACATTATAATTATGGATTTCGATATTTTCGAG
131 ATTACAAAATTACCTATTACATTATAATTATGGATTTCGATATTTTTGAG
* * * * * * * ***
440756 ATCGACACTTTTTGAAAATGTATCGACAC-TTTATGCGTTCA-CCCTTTTTTGGCATCCA-T-TC
1 ATCGACACTTTATG---A-GT-TC-ACCCTTTTTTG-G--CATCCATTCTAT-ACAAAAAGTATC
* *
440817 TGTACAAAAAATTAAAAAGTGTTGATACATATTGTAGACCTATTCTCTCATAAAATCGGTATATT
56 -G-ACACAAAATTAAAAAGTGTTGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTATATT
* *
440882 TATATCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGATGTTTTTGAG
119 TATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGATTTCGATATTTTTGAG
* * * *
440944 ATCGACACTTTATGCGTTCACCCTTTTTTGGCATACATTCTGTACAAAAAGTATCGACACGAAAT
1 ATCGACACTTTATGAGTTCACCCTTTTTTGGCATCCATTCTATACAAAAAGTATCGACACAAAAT
*
441009 TAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAA-CTGGTATATTTATACCGGTTA
66 TAAAAAGTGTTGATACATGTTGTAGACCTATTCTCTCATAAAATC-GGTATATTTATACCGGTTA
* *
441073 TATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATATTTTT-AGG
130 TATTACAAAATTACCTATTACATTATAATTATGGATTTCGATATTTTTGA-G
441124 ATCGAC
1 ATCGAC
441130 TCATTTTTAA
Statistics
Matches: 319, Mismatches: 37, Indels: 36
0.81 0.09 0.09
Matches are distributed among these distances:
179 2 0.01
180 136 0.43
181 7 0.02
182 6 0.02
183 8 0.03
184 4 0.01
185 7 0.02
186 6 0.02
187 8 0.03
188 135 0.42
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (180 bp):
ATCGACACTTTATGAGTTCACCCTTTTTTGGCATCCATTCTATACAAAAAGTATCGACACAAAAT
TAAAAAGTGTTGATACATGTTGTAGACCTATTCTCTCATAAAATCGGTATATTTATACCGGTTAT
ATTACAAAATTACCTATTACATTATAATTATGGATTTCGATATTTTTGAG
Found at i:444224 original size:21 final size:21
Alignment explanation
Indices: 444200--444242 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
444190 ATAAATAGTA
* *
444200 TCGACACAAATTTTATAAGTG
1 TCGACACAAATTTCAGAAGTG
444221 TCGACACAAATTTCAGAAGTG
1 TCGACACAAATTTCAGAAGTG
444242 T
1 T
444243 TGATACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (21 bp):
TCGACACAAATTTCAGAAGTG
Found at i:444569 original size:200 final size:199
Alignment explanation
Indices: 444216--445345 Score: 1491
Period size: 200 Copynumber: 5.7 Consensus size: 199
444206 CAAATTTTAT
* * * * * * *
444216 AAGTGTCGACACAAATTTCAGAAGTGTTGATACAT-TATGTAGACATATTTTCTCATAAAATCGA
1 AAGTATCGACACAAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTTTCTCATAAAACCGG
* * * * *
444280 TATAGTTATACTGGTTACATTGAAAATTTACCTATTAAATTTTAATTATGGGTTTCGATGTTTTT
65 TATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
*
444345 GGGATCGACACTTTCTAAAAATGTATCGACACTTTATAGGTGCACCCTTTTTGGCTTTGATTCTG
130 GGGATCGACACTTTCTAAAAATGTATCGACACTTTAT-GGTACACCCTTTTTGGCTTTGATTCTG
*
444410 GCCCAA
194 GACCAA
** *
444416 AAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATGCTCTCATAAAACCAGT
1 AAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTTTCTCATAAAACCGGT
* * *
444481 ATATTTATACCGGTTGCATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTA
66 ATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* * * * * * * *
444546 GGATCGATACTTTTTATAAATGTATCGACACTATATGGGTACACCCTTTTGGGCATTCATTATGG
131 GGATCGACACTTTCTAAAAATGTATCGACACTTTAT-GGTACACCCTTTTTGGCTTTGATTCTGG
444611 A-CAA
195 ACCAA
* * *
444615 ATAATATCGACACAAATTTCAGAAGTGTCGATACAT-TATGTAGACCTATTTTCTCATAAAACCG
1 A-AGTATCGACACAAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTTTCTCATAAAACCG
* * *
444679 GTATAGTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTT
64 GTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * * *
444744 TGGGATCGACACTTTCTAAAAATGTATCGATACTTTATGGGTGCACACTTTTTGGGGTTTGATTC
129 TGGGATCGACACTTTCTAAAAATGTATCGACACTTTAT-GGTACACCCTTTTT-GGCTTTGATTC
*
444809 TAGACCAA
192 TGGACCAA
* *
444817 AAGTATCGACACGAATTCCACAAGTATCGATACATGTTGTAGACCTATTTTCTCATAAAACCGGT
1 AAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTTTCTCATAAAACCGGT
** *
444882 ATATTTATATTGGTTACATTGAAAAATTACATATTACATTATAATTATGGGTTTCGATGTTTTTG
66 ATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* * * * * * * * *
444947 GGATCGACACTTTTTGAAAATGTATCGACACTATATGCATTCACCATTTTTGGCATTCATTATGG
131 GGATCGACACTTTCTAAAAATGTATCGACACTTTATG-GTACACCCTTTTTGGCTTTGATTCTGG
*
445012 ACAAA
195 ACCAA
* * * * *
445017 AAGTATCGACACAATATT-AAAAAGTGTCGATACATGTTATAGACCTATTTT-TCATAAAACTGA
1 AAGTATCGACACAA-ATTCCACAAGTGTCGATACATGTTGTAGACCTATTTTCTCATAAAACCGG
* * *
445080 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTT
65 TATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
*
445145 GGGATCGACACTTTCTAAAAATGTATCGACACTTTATGAGTACACGCTTTTTGATG-TTTGATTC
130 GGGATCGACACTTTCTAAAAATGTATCGACACTTTATG-GTACACCCTTTTTG--GCTTTGATTC
445209 TGGACCAA
192 TGGACCAA
** * *
445217 AAGTATCGACAGGAATTCCACAAGTGTCGATACATGTTGTAGATCTATTCTCTCATAAAACCGGT
1 AAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTTTCTCATAAAACCGGT
*
445282 ATATTTATACCGGTTATATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGAT-TTTTTG
66 ATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
445346 AGATTAATAT
Statistics
Matches: 801, Mismatches: 117, Indels: 24
0.85 0.12 0.03
Matches are distributed among these distances:
199 122 0.15
200 437 0.55
201 237 0.30
202 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (199 bp):
AAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTTTCTCATAAAACCGGT
ATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTTCTAAAAATGTATCGACACTTTATGGTACACCCTTTTTGGCTTTGATTCTGGA
CCAA
Found at i:445114 original size:400 final size:400
Alignment explanation
Indices: 444221--445394 Score: 1756
Period size: 400 Copynumber: 2.9 Consensus size: 400
444211 TTTATAAGTG
* * * *
444221 TCGACACAAATTTCAGAAGTGTTGATACATTATGTAGACATATTTTCTCATAAAA-TCGATATAG
1 TCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACT-GATATAG
* * *
444285 TTATACTGGTTACATTGAAAATTTACCTATTAAATTTTAATTATGGGTTTCGATGTTTTTGGGAT
65 TTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGAT
* * * *
444350 CGACACTTTCTAAAAATGTATCGACACTTTATAGGTGCACCCTTTTT-GGCTTTGATTCTGGCCC
130 CGACACTTTCTAAAAATGTATCGACACTTTATGGGTGCACACTTTTTGGGGTTTGATTCTGGACC
* * *
444414 AAAAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATGCTCTCATAAAACCA
195 AAAAGTATCGACACGAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
* *
444479 GTATATTTATACCGGTTGCATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTC
260 GTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * * * *
444544 TAGGATCGATACTTTTTATAAATGTATCGACACTATATGGGTACACCCTTTTGGGCATTCATTAT
325 TGGGATCGATACTTTTTATAAATGTATCGACACTATAT-GCTTCACCATTTTTGGCATTCATTAT
444609 GGACAAATAATA
389 GGACAAATAATA
* * * *
444621 TCGACACAAATTTCAGAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATAGT
1 TCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACTGATATAGT
*
444686 TATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGGGATC
66 TATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATC
* *
444751 GACACTTTCTAAAAATGTATCGATACTTTATGGGTGCACACTTTTTGGGGTTTGATTCTAGACCA
131 GACACTTTCTAAAAATGTATCGACACTTTATGGGTGCACACTTTTTGGGGTTTGATTCTGGACCA
* *
444816 AAAGTATCGACACGAATTCCACAAGTATCGATACATGTTGTAGACCTATTTTCTCATAAAACCGG
196 AAAGTATCGACACGAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGG
** *
444881 TATATTTATATTGGTTACATTGAAAAATTACATATTACATTATAATTATGGGTTTCGATGTTTTT
261 TATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
*
444946 GGGATCGACACTTTTTGA-AAATGTATCGACACTATATGCATTCACCATTTTTGGCATTCATTAT
326 GGGATCGATACTTTTT-ATAAATGTATCGACACTATATGC-TTCACCATTTTTGGCATTCATTAT
445010 GGACAAA-AAGTA
389 GGACAAATAA-TA
*
445022 TCGACAC-AATATTAAAAAGTGTCGATACATGT-TATAGACCTATTTT-TCATAAAACTGATATA
1 TCGACACAAAT-TTAAAAAGTGTCGATACAT-TATGTAGACCTATTTTCTCATAAAACTGATATA
* * *
445084 TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTTTTGGGA
64 GTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGA
* * * **
445149 TCGACACTTTCTAAAAATGTATCGACACTTTATGAGTACACGCTTTTTGATGTTTGATTCTGGAC
129 TCGACACTTTCTAAAAATGTATCGACACTTTATGGGTGCACACTTTTTGGGGTTTGATTCTGGAC
* *
445214 CAAAAGTATCGACAGGAATTCCACAAGTGTCGATACATGTTGTAGATCTATTCTCTCATAAAACC
194 CAAAAGTATCGACACGAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACC
*
445279 GGTATATTTATACCGGTTATATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGAT-TTT
259 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* ** *
445343 TTGAGATTAATATTTTTTATAAATGTATCGACAC-ATATGCTT-ACCTATTTTT
324 TTGGGATCGATACTTTTTATAAATGTATCGACACTATATGCTTCACC-ATTTTT
445395 TGGAAACTTT
Statistics
Matches: 706, Mismatches: 59, Indels: 21
0.90 0.08 0.03
Matches are distributed among these distances:
396 3 0.00
397 8 0.01
398 7 0.01
399 30 0.04
400 421 0.60
401 235 0.33
402 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (400 bp):
TCGACACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACTGATATAGT
TATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATC
GACACTTTCTAAAAATGTATCGACACTTTATGGGTGCACACTTTTTGGGGTTTGATTCTGGACCA
AAAGTATCGACACGAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGG
TATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTT
GGGATCGATACTTTTTATAAATGTATCGACACTATATGCTTCACCATTTTTGGCATTCATTATGG
ACAAATAATA
Found at i:445244 original size:601 final size:600
Alignment explanation
Indices: 444216--445345 Score: 1592
Period size: 601 Copynumber: 1.9 Consensus size: 600
444206 CAAATTTTAT
* * * * * *
444216 AAGTGTCGACACAAATTTCAGAAGTGTTGATACATTATGTAGACATATTTTCTCATAAAATCGAT
1 AAGTATCGACACAAATTCCACAAGTATCGATACATTATGTAGACATATTTTCTCATAAAACCGAT
* * *
444281 ATAGTTATACTGGTTACATTGAAAATTTACCTATTAAATTTTAATTATGGGTTTCGATGTTTTTG
66 ATAGTTATACTGGTTACATTGAAAAATTACATATTAAATTATAATTATGGGTTTCGATGTTTTTG
* * * * * *
444346 GGATCGACACTTTCTAAAAATGTATCGACACTTTATAGGTGCACCCTTTTTGGCTTTGATTCTGG
131 GGATCGACACTTTCTAAAAATGTATCGACACTATATAGATGCACCATTTTTGGCATTCATTATGG
* * * * *
444411 CCCAAAAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATGCTCTCATAAAA
196 ACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATGTTATAGACCTATGCTCTCATAAAA
* *
444476 CCAGTATATTTATACCGGTTGCATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
261 CCAGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATGT
* * * *
444541 TTCTAGGATCGATACTTTTTATAAATGTATCGACACTATATGGGTACACCCTTTTGGGCATTCAT
326 TTCTAGGATCGACACTTTCTAAAAATGTATCGACACTATATGAGTACACCCTTTTGGGCATTCAT
* * *
444606 TATGGACAAATAATATCGACACAAATTTCAGAAGTGTCGATACAT-TATGTAGACCTATTTTCTC
391 TATGGACAAATAATATCGACACAAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTCTCTC
*
444670 ATAAAACCGGTATAGTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTT
455 ATAAAACCGGTATAGTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTT
*
444735 TGATGTTTTTGGGATCGACACTTTCTAAAAATGTATCGATACTTTATGGGTGCACACTTTTTGGG
520 CGAT-TTTTTGGGATCGACACTTTCTAAAAATGTATCGATACTTTATGGGTGCACACTTTTTGGG
444800 GTTTGATTCTAGACCAA
584 GTTTGATTCTAGACCAA
* * *
444817 AAGTATCGACACGAATTCCACAAGTATCGATACATGT-TGTAGACCTATTTTCTCATAAAACCGG
1 AAGTATCGACACAAATTCCACAAGTATCGATACAT-TATGTAGACATATTTTCTCATAAAACCGA
* * *
444881 TATATTTATATTGGTTACATTGAAAAATTACATATTACATTATAATTATGGGTTTCGATGTTTTT
65 TATAGTTATACTGGTTACATTGAAAAATTACATATTAAATTATAATTATGGGTTTCGATGTTTTT
* * *
444946 GGGATCGACACTTTTTGAAAATGTATCGACACTATAT-GCATTCACCATTTTTGGCATTCATTAT
130 GGGATCGACACTTTCTAAAAATGTATCGACACTATATAG-ATGCACCATTTTTGGCATTCATTAT
* *
445010 GGACAAAAAGTATCGACACAATATT-AAAAAGTGTCGATACATGTTATAGACCTAT-TTTTCATA
194 GGACAAAAAGTATCGACACAA-ATTCAAAAAGTGTCGATACATGTTATAGACCTATGCTCTCATA
* * *
445073 AAA-CTGATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCG
258 AAACCAG-TATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCG
* * * * *
445137 ATGTTTTTGGGATCGACACTTTCTAAAAATGTATCGACACTTTATGAGTACACGCTTTTTGATG-
322 ATGTTTCTAGGATCGACACTTTCTAAAAATGTATCGACACTATATGAGTACAC-CCTTTTG-GGC
* * * * ** *
445201 TTTGATTCTGGACCAAA-AGTATCGACAGGAATTCCACAAGTGTCGATACATGTTGTAGATCTAT
385 ATTCATTATGGA-CAAATAATATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTAT
* *
445265 TCTCTCATAAAACCGGTATATTTATACCGGTTATATTGAAAAATTACCTATTACATTATAATTAT
449 TCTCTCATAAAACCGGTATAGTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTAT
445330 GGGTTTCGATTTTTTG
514 GGGTTTCGATTTTTTG
445346 AGATTAATAT
Statistics
Matches: 462, Mismatches: 59, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
599 2 0.00
600 115 0.25
601 335 0.73
602 10 0.02
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (600 bp):
AAGTATCGACACAAATTCCACAAGTATCGATACATTATGTAGACATATTTTCTCATAAAACCGAT
ATAGTTATACTGGTTACATTGAAAAATTACATATTAAATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTTCTAAAAATGTATCGACACTATATAGATGCACCATTTTTGGCATTCATTATGG
ACAAAAAGTATCGACACAAATTCAAAAAGTGTCGATACATGTTATAGACCTATGCTCTCATAAAA
CCAGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATGT
TTCTAGGATCGACACTTTCTAAAAATGTATCGACACTATATGAGTACACCCTTTTGGGCATTCAT
TATGGACAAATAATATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCA
TAAAACCGGTATAGTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTC
GATTTTTTGGGATCGACACTTTCTAAAAATGTATCGATACTTTATGGGTGCACACTTTTTGGGGT
TTGATTCTAGACCAA
Found at i:445773 original size:18 final size:19
Alignment explanation
Indices: 445725--445770 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
445715 ATTACATTCA
* *
445725 TATAAAAAATTATTAATCG
1 TATACAAAATTATAAATCG
*
445744 TATACAAAATTATAAATCT
1 TATACAAAATTATAAATCG
445763 TATACAAA
1 TATACAAA
445771 TTAACCCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.35
Consensus pattern (19 bp):
TATACAAAATTATAAATCG
Found at i:447356 original size:18 final size:18
Alignment explanation
Indices: 447335--447373 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
447325 TCTTCCTCAT
447335 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
447353 TTCCTCCCTCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
447371 TTC
1 TTC
447374 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:448260 original size:26 final size:26
Alignment explanation
Indices: 448230--448283 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
448220 TCGACAACGT
*
448230 ACTTTTCCATTCTACTACAGCAACAA
1 ACTTTTCCATTCGACTACAGCAACAA
448256 ACTTTTCCATTCGACTACAGCAACAA
1 ACTTTTCCATTCGACTACAGCAACAA
448282 AC
1 AC
448284 AAACAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.31, G:0.06, T:0.28
Consensus pattern (26 bp):
ACTTTTCCATTCGACTACAGCAACAA
Found at i:448837 original size:182 final size:182
Alignment explanation
Indices: 448505--448898 Score: 603
Period size: 182 Copynumber: 2.2 Consensus size: 182
448495 TATTTCGTTG
* * * *
448505 AAAGTATCGATAATTTATTATTAACGTATCGACACTTTCAATATATTCGATAGCTCTTTACCGGT
1 AAAGTGTCGAT-ACTTA-TATTAAAGTATCGACACTTTCAATATATTCGATAGCTCTATACCGGT
*
448570 TTTATCATTTCAAGACCAGTTTTGTCATATTTTTACATGTTATATCATTATGGATCGATACATTT
64 TTTATCATTTCAAGACCAGTTTTATCATATTTTTACATGTTATATCATTATGGATCGATACATTT
* *
448635 TTATAAAGTATCGACACTTTATAGGAGTTAAAACTGCTTCTCTTTTAAATTAAC
129 TTATAAAGTATCAACACTTTATAGGAGTTAAAACTGCTTATCTTTTAAATTAAC
* *
448689 AAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTT
1 AAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAATATATTCGATAGCTCTATACCGGTTT
* * * *
448754 TGTCCTTT-AGAGACTCA-TTTTATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTT
66 TATCATTTCA-AGAC-CAGTTTTATCATATTTTTACATGTTATATCATTATGGATCGATACATTT
* *
448817 TTATAAAGTATCAACACTTTATAGGCGTTAAAACTGCTTATCTTTTAAATTCAC
129 TTATAAAGTATCAACACTTTATAGGAGTTAAAACTGCTTATCTTTTAAATTAAC
448871 AAAGTGTCGATACTTATATTAAAGTATC
1 AAAGTGTCGATACTTATATTAAAGTATC
448899 TACATTGTAA
Statistics
Matches: 193, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
181 1 0.01
182 176 0.91
183 6 0.03
184 10 0.05
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (182 bp):
AAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAATATATTCGATAGCTCTATACCGGTTT
TATCATTTCAAGACCAGTTTTATCATATTTTTACATGTTATATCATTATGGATCGATACATTTTT
ATAAAGTATCAACACTTTATAGGAGTTAAAACTGCTTATCTTTTAAATTAAC
Found at i:451080 original size:21 final size:21
Alignment explanation
Indices: 451029--451082 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
451019 AAATCAGTTC
451029 CCAGAATCGCAATGCGATAGT
1 CCAGAATCGCAATGCGATAGT
* * **
451050 ACA-AATTCGCATTGCGATTTT
1 CCAGAA-TCGCAATGCGATAGT
451071 CCAGAATCGCAA
1 CCAGAATCGCAA
451083 CGCAAATATG
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
CCAGAATCGCAATGCGATAGT
Found at i:451100 original size:20 final size:20
Alignment explanation
Indices: 451075--451127 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
451065 GATTTTCCAG
451075 AATCGCAACGC-AA-ATATGAA
1 AATCGCAACGCGAACATAT--A
451095 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
451115 AATCGCAACGCGA
1 AATCGCAACGCGA
451128 TTCTGACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 25 0.81
21 2 0.06
22 4 0.13
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:451196 original size:20 final size:20
Alignment explanation
Indices: 451173--451327 Score: 104
Period size: 20 Copynumber: 7.7 Consensus size: 20
451163 ACATGTATCC
*
451173 GTAAATTGCAACGACAATAT
1 GTAAATCGCAACGACAATAT
*
451193 GTAAAATCGCAACG-C-GTAT
1 GT-AAATCGCAACGACAATAT
* *
451212 CCGTAAATCGCAACGAGAATAC
1 --GTAAATCGCAACGACAATAT
* *
451234 GTAAATCGCAACG-CGTATCT
1 GTAAATCGCAACGAC-AATAT
* *
451254 GTAAATCGCAACGAGAATAC
1 GTAAATCGCAACGACAATAT
* *
451274 GTAAATCGCAATG-C-GTAT
1 GTAAATCGCAACGACAATAT
* *
451292 CCGTAAATCGCAATGACAATAC
1 --GTAAATCGCAACGACAATAT
451314 GTAAAATCGCAACG
1 GT-AAATCGCAACG
451328 TTTATCCATA
Statistics
Matches: 103, Mismatches: 20, Indels: 23
0.71 0.14 0.16
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 71 0.69
21 23 0.22
22 4 0.04
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
GTAAATCGCAACGACAATAT
Found at i:451318 original size:60 final size:61
Alignment explanation
Indices: 451136--451327 Score: 185
Period size: 60 Copynumber: 3.1 Consensus size: 61
451126 GATTCTGACT
* * * * * *
451136 ATCGCAATGAGTATCCGTAAAATCACAAC-ATGTATCCGTAAATTGCAACGACAATATGTAAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGA-GTATCCGTAAATCGCAACGACAATACGTAAA
* * * * * *
451198 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACG-C-GTATCTGT-AA
1 ATCGCAACGAGAATACGTAAATCGCAACGAGTATCCGTAAATCGCAACGACAATA-C-GTAAA
* * *
451258 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCGCAATGACAATACGTAAA
1 ATCGCAACGAGAATACGTAAATCGCAACGAGTATCCGTAAATCGCAACGACAATACGTAAA
451319 ATCGCAACG
1 ATCGCAACG
451328 TTTATCCATA
Statistics
Matches: 107, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
59 2 0.02
60 46 0.43
61 40 0.37
62 19 0.18
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (61 bp):
ATCGCAACGAGAATACGTAAATCGCAACGAGTATCCGTAAATCGCAACGACAATACGTAAA
Found at i:451341 original size:41 final size:41
Alignment explanation
Indices: 451136--451347 Score: 257
Period size: 40 Copynumber: 5.2 Consensus size: 41
451126 GATTCTGACT
* * * * **
451136 ATCGCAATGAGTATCCGTAAAATCACAACATGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
451177 ATTGCAACGACAATATGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
451218 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
451258 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * ** *
451298 ATCGCAATGACAATACGTAAAATCGCAACGTTTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
451339 ATCGAAACG
1 ATCGCAACG
451348 TGATCTCCGG
Statistics
Matches: 147, Mismatches: 23, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
40 75 0.51
41 72 0.49
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Done.