Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008186.1 Hibiscus syriacus cultivar Beakdansim tig00110793_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: 806808
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 3
Found at i:673527 original size:18 final size:18
Alignment explanation
Indices: 673504--673538 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
673494 AAGCCGGTTG
*
673504 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
673522 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
673539 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:676686 original size:20 final size:20
Alignment explanation
Indices: 676661--676788 Score: 107
Period size: 20 Copynumber: 6.3 Consensus size: 20
676651 GAAATTCAGT
*
676661 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
676681 GTTGCGATAGTTAGAATCGA
1 GTTGCGATAGTCAGAATCGC
**
676701 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
676722 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * * *
676742 ATTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAGAATCGC
* *
676762 ATTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
*
676782 ATTGCGA
1 GTTGCGA
676789 ATCTGGAAAC
Statistics
Matches: 88, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.03
20 68 0.77
21 15 0.17
22 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:678938 original size:21 final size:19
Alignment explanation
Indices: 678906--679221 Score: 218
Period size: 21 Copynumber: 15.3 Consensus size: 19
678896 CGTTGCGATT
678906 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
678925 TTGGAATAAATCGCAACACGAAC
1 TTGGACT--ATCGC-A-ACGAAC
* *
678948 TTCGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
678967 TTGGAATATATCGCAACGCGAAC
1 TTGG-A-CTATCGCAA--CGAAC
* *
678990 TTAGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
679009 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
679032 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
* * * **
679051 TTGGAATAAATTGCATCGCGATG
1 TTGGACT--ATCGCA--ACGAAC
*
679074 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
679093 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
679116 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
679135 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
*
679156 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
679175 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
* *
679198 TTGGACTATCGCAGCGAAT
1 TTGGACTATCGCAACGAAC
679217 TTGGA
1 TTGGA
679222 AAATCGCATT
Statistics
Matches: 233, Mismatches: 38, Indels: 52
0.72 0.12 0.16
Matches are distributed among these distances:
19 78 0.33
20 2 0.01
21 96 0.41
22 2 0.01
23 55 0.24
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:678971 original size:42 final size:42
Alignment explanation
Indices: 678909--679229 Score: 479
Period size: 42 Copynumber: 7.7 Consensus size: 42
678899 TGCGATTTTG
*
678909 GACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
678951 GACTATCGCAACGAATTTGGAATATATCGCAACGCGAACTTA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
678993 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * **
679035 GACTATCGCAACGAACTTGGAATAAATTGCATCGCGATGTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
679077 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
679119 GACTATCGCAACGAACTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
679159 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
679201 GACTATCGCAGCGAATTTGG-A-AAATCGCA
1 GACTATCGCAACGAACTTGGAATAAATCGCA
679230 TTGCGATAGT
Statistics
Matches: 257, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
40 45 0.18
41 1 0.00
42 211 0.82
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:679227 original size:19 final size:19
Alignment explanation
Indices: 679163--679229 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
679153 AACTTGGACT
*
679163 ATCGCAACGAATTTGGAATAA
1 ATCGCAGCGAATTTGG-A-AA
* **
679184 ATCGCAACGCGAACTTGGACT
1 ATCGC-A-GCGAATTTGGAAA
679205 ATCGCAGCGAATTTGGAAA
1 ATCGCAGCGAATTTGGAAA
679224 ATCGCA
1 ATCGCA
679230 TTGCGATAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
19 16 0.43
20 1 0.03
21 10 0.27
22 2 0.05
23 8 0.22
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (19 bp):
ATCGCAGCGAATTTGGAAA
Found at i:679271 original size:21 final size:21
Alignment explanation
Indices: 679225--679273 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
679215 ATTTGGAAAA
*
679225 TCGCATTGCGATAGTCAAAGT
1 TCGCGTTGCGATAGTCAAAGT
*
679246 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCAAAGT
679267 TCGCGTT
1 TCGCGTT
679274 TCGAATCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCAAAGT
Found at i:679918 original size:10 final size:10
Alignment explanation
Indices: 679903--679931 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
679893 TTAGAACATT
679903 GATTTAGAGG
1 GATTTAGAGG
679913 GATTTAGAGG
1 GATTTAGAGG
679923 GATTTAGAG
1 GATTTAGAG
679932 AGTTTGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (10 bp):
GATTTAGAGG
Found at i:681175 original size:21 final size:21
Alignment explanation
Indices: 681149--681204 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
681139 GGGAGTGTCA
*
681149 GTGCATCGATGCATACCCATT
1 GTGCATCGATGCATACCCATG
681170 GTGCATCGATGCATACCCATG
1 GTGCATCGATGCATACCCATG
*
681191 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
681205 CAGTGTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (21 bp):
GTGCATCGATGCATACCCATG
Found at i:681296 original size:18 final size:17
Alignment explanation
Indices: 681242--681290 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
681232 TTAGACCCTT
* *
681242 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
681260 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
681278 AGTGCATTCGATG
1 AGTGCA-TCGATG
681291 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:681460 original size:65 final size:65
Alignment explanation
Indices: 681262--681471 Score: 218
Period size: 65 Copynumber: 3.2 Consensus size: 65
681252 TGCACTAAGA
* * ** *
681262 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCAT-GACT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGATT
681325 G
65 G
* * *
681326 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-ATGCATCGGTGCATGG-
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGA
681388 TAT-
63 T-TG
* *
681391 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGGATT
681455 G
65 G
*
681456 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
681472 CTCTGAAAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 50 0.42
65 60 0.50
66 2 0.02
67 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGATTG
Found at i:687648 original size:22 final size:22
Alignment explanation
Indices: 687623--687668 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
687613 GTTTATAAAT
*
687623 AGGGAATCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
687645 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
687667 AG
1 AG
687669 TACTTCCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCTAC
Found at i:688204 original size:22 final size:22
Alignment explanation
Indices: 688173--688244 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
688163 CTGAGTGGCA
*
688173 TATGAAATTTGTCCCGAAGGGCC
1 TATG-AATTTGTCCCGAAGGACC
* *
688196 TGTGAATTTGTCCCGAAGAACC
1 TATGAATTTGTCCCGAAGGACC
*
688218 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
688239 TATGAA
1 TATGAA
688245 ACCCTCGACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.45
22 20 0.48
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:688229 original size:21 final size:21
Alignment explanation
Indices: 688203--688243 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
688193 GCCTGTGAAT
688203 TTGTCCCGAAGAACCTATGAG
1 TTGTCCCGAAGAACCTATGAG
*
688224 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGAACCTATGA
688244 AACCCTCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TTGTCCCGAAGAACCTATGAG
Found at i:696021 original size:19 final size:19
Alignment explanation
Indices: 695984--696023 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
695974 GGTCCTTGAG
*
695984 TTATTTAAATTATATTTTA
1 TTATTTAAATTATAATTTA
696003 TTATTTAAATT-TAAATTTA
1 TTATTTAAATTAT-AATTTA
696022 TT
1 TT
696024 GTAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATTTAAATTATAATTTA
Found at i:706635 original size:22 final size:21
Alignment explanation
Indices: 706610--706650 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
706600 TATACAAAAT
706610 TATTTTTATTAAATATTTTTGA
1 TATTTTTATTAAAT-TTTTTGA
*
706632 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
706651 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:715939 original size:21 final size:21
Alignment explanation
Indices: 715913--716223 Score: 312
Period size: 21 Copynumber: 14.5 Consensus size: 21
715903 GTTTTCATAT
*
715913 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
715934 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
715955 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
715976 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
715997 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
716018 TCGTAATGCGAA-TATGGACTA
1 TCGCAATGCGAACT-TCGACTA
*
716039 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
716059 TCGCAATGCGATAGTCGAAGTTCG-CGT-
1 TCGCAATGCGA-A--C----TTCGAC-TA
* * **
716086 T-GCAATAGTCGAATTTGGAAAA
1 TCGCAAT-G-CGAACTTCGACTA
*
716108 TCGCAATGTGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
716129 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
716150 TCGTAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
716171 TCGCAATACGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
716192 TCGTAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
716213 TCGCATTGCGA
1 TCGCAATGCGA
716224 TTTACATATT
Statistics
Matches: 247, Mismatches: 25, Indels: 36
0.80 0.08 0.12
Matches are distributed among these distances:
20 14 0.06
21 212 0.86
22 2 0.01
23 5 0.02
26 5 0.02
27 4 0.02
28 5 0.02
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:716245 original size:174 final size:174
Alignment explanation
Indices: 715933--716256 Score: 512
Period size: 174 Copynumber: 1.9 Consensus size: 174
715923 AACTTCGACT
*
715933 ATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTAT
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTAT
* *
715998 CGCAATGCGAACTTGGACTATCGTAATGCGAATATGGACTATCGCAATGCGAATATGTAAATCGC
66 CGCAATACGAACTTGGACTATCGTAATGCGAATATCGACTATCGCAATGCGAATATGTAAATCGC
*
716063 AATGCGATAGTCGAAGTTCGCGTTGCAATAGTCGAATTTGGAAA
131 AATGCGATAGTCCAAGTTCGCGTTGCAATAGTCGAATTTGGAAA
* *
716107 ATCGCAATGTGAACTTCGACTATCGCAATGCGAACTTCGACTATCGTAATGCGAACTTCGACTAT
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTAT
*
716172 CGCAATACGAACTTGGACTATCGTAATGCGAACT-TCGACTATCGCATTGCG-AT-T-TACATAT
66 CGCAATACGAACTTGGACTATCGTAATGCGAA-TATCGACTATCGCAATGCGAATATGTA-A-A-
*
716233 TCGCATTGCGATAGTCCAAGTTCG
127 TCGCAATGCGATAGTCCAAGTTCG
716257 TATTGCGATA
Statistics
Matches: 138, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
171 2 0.01
172 2 0.01
173 3 0.02
174 130 0.94
175 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (174 bp):
ATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTAT
CGCAATACGAACTTGGACTATCGTAATGCGAATATCGACTATCGCAATGCGAATATGTAAATCGC
AATGCGATAGTCCAAGTTCGCGTTGCAATAGTCGAATTTGGAAA
Found at i:716261 original size:21 final size:21
Alignment explanation
Indices: 716232--716306 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
716222 GATTTACATA
716232 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
716253 TTCGTATTGCGATAATCTAAG
1 TTCGCATTGCGATAGTCCAAG
*
716274 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
716295 TTCGCGTTGCGA
1 TTCGCATTGCGA
716307 ATCTGGAAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:716518 original size:30 final size:31
Alignment explanation
Indices: 716484--716547 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
716474 AAAAAAATTA
716484 AATGACTCAAC-AAATAAAAAGGTGCGAACC
1 AATGACTCAACAAAATAAAAAGGTGCGAACC
* *
716514 AATGACTCAACAAAATAAAATGGTGTGAACC
1 AATGACTCAACAAAATAAAAAGGTGCGAACC
716545 AAT
1 AAT
716548 AATCAATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 11 0.35
31 20 0.65
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.17
Consensus pattern (31 bp):
AATGACTCAACAAAATAAAAAGGTGCGAACC
Found at i:728125 original size:11 final size:11
Alignment explanation
Indices: 728111--728168 Score: 73
Period size: 11 Copynumber: 5.4 Consensus size: 11
728101 TGTTAGAGTA
728111 TTATTAGTTTG
1 TTATTAGTTTG
728122 TTATTAGTTTG
1 TTATTAGTTTG
* *
728133 TTA-TGGGTTG
1 TTATTAGTTTG
* *
728143 TTATTAGCTGG
1 TTATTAGTTTG
728154 TTATTAGTTTG
1 TTATTAGTTTG
728165 TTAT
1 TTAT
728169 GTTGGTTACT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 8 0.21
11 31 0.79
ACGTcount: A:0.17, C:0.02, G:0.22, T:0.59
Consensus pattern (11 bp):
TTATTAGTTTG
Found at i:729698 original size:36 final size:36
Alignment explanation
Indices: 729646--729846 Score: 339
Period size: 36 Copynumber: 5.6 Consensus size: 36
729636 CAAAAGTTTG
*
729646 TTCCGATTCAAGTCGAACGGAGGGAAGCATCTGCAC
1 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
* *
729682 TTCCGATTCAAATCGAACGGAGGGAAGCATCGACAC
1 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
*
729718 TTCCGATTCAAGTTGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
*
729754 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
* *
729790 TTCCGATTCAAGTCGAACGGAAGGAAGCATCAGCAC
1 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
729826 TTCCGATTCAAGTCGAACGGA
1 TTCCGATTCAAGTCGAACGGA
729847 AGGATGTGTC
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 156 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.18
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
Found at i:730389 original size:11 final size:11
Alignment explanation
Indices: 730375--730432 Score: 73
Period size: 11 Copynumber: 5.4 Consensus size: 11
730365 TGTTAGAGTA
730375 TTATTAGTTTG
1 TTATTAGTTTG
730386 TTATTAGTTTG
1 TTATTAGTTTG
* *
730397 TTA-TGGGTTG
1 TTATTAGTTTG
* *
730407 TTATTAGCTGG
1 TTATTAGTTTG
730418 TTATTAGTTTG
1 TTATTAGTTTG
730429 TTAT
1 TTAT
730433 GTTGGTTACT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 8 0.21
11 31 0.79
ACGTcount: A:0.17, C:0.02, G:0.22, T:0.59
Consensus pattern (11 bp):
TTATTAGTTTG
Found at i:734276 original size:2 final size:2
Alignment explanation
Indices: 734269--734293 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
734259 ATATAGTGAT
734269 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
734294 TTGTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:737159 original size:26 final size:25
Alignment explanation
Indices: 737073--737159 Score: 60
Period size: 25 Copynumber: 3.5 Consensus size: 25
737063 GATAGATTTT
* *
737073 TTTTATTATATTT-ATATTTACTTTA
1 TTTTGTTAAATTTAATA-TTACTTTA
737098 TTTTGTTAAATTGTAAT-TT--TTTA
1 TTTTGTTAAATT-TAATATTACTTTA
*
737121 TTATT-TCT-CATTTAATACTTACTTTA
1 TT-TTGT-TAAATTTAATA-TTACTTTA
737147 TTTTGTTAAATTT
1 TTTTGTTAAATTT
737160 GTTGGACTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 19
0.68 0.06 0.27
Matches are distributed among these distances:
22 4 0.08
23 10 0.21
24 5 0.10
25 15 0.31
26 12 0.25
27 2 0.04
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.64
Consensus pattern (25 bp):
TTTTGTTAAATTTAATATTACTTTA
Found at i:739965 original size:26 final size:26
Alignment explanation
Indices: 739936--739986 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
739926 GTTAATGGCA
739936 ACAATGATGTTGGAAATCTATATTGC
1 ACAATGATGTTGGAAATCTATATTGC
739962 ACAATGATGTTGGAAATCTATATTG
1 ACAATGATGTTGGAAATCTATATTG
739987 TAACGACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (26 bp):
ACAATGATGTTGGAAATCTATATTGC
Found at i:740706 original size:46 final size:47
Alignment explanation
Indices: 740639--740746 Score: 182
Period size: 48 Copynumber: 2.3 Consensus size: 47
740629 ACGTAGTATC
*
740639 TGCCCCGCGCTATATAAAATTATGT-GTAAAGGTATGTCGCGGTACA
1 TGCCCCGCGCTATATAAAATTATGTAGTAAAGGTATGTCACGGTACA
*
740685 TGCCCCGCGCTATATAAAATTATGTGAGTAAAGGTATGTCACGGTACC
1 TGCCCCGCGCTATATAAAATTATGT-AGTAAAGGTATGTCACGGTACA
740733 TGCCCCGCGCTATA
1 TGCCCCGCGCTATA
740747 CTCCTACGTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
46 25 0.43
48 33 0.57
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (47 bp):
TGCCCCGCGCTATATAAAATTATGTAGTAAAGGTATGTCACGGTACA
Found at i:740834 original size:51 final size:51
Alignment explanation
Indices: 740758--740886 Score: 170
Period size: 51 Copynumber: 2.5 Consensus size: 51
740748 TCCTACGTGG
* * * *
740758 CGTATAGCGCGCTGCAGGGGCCGCGCTATA-CCCACGTGTATGCCAGATCAC
1 CGTATAGCGCGGTGCAGGGGACGCGCTATACCCCACGTG-ACGCCAAATCAC
* * *
740809 CGTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGACGCGCTATACCCCACGTGACGCCAAATCAC
*
740860 CGTATAGCGCGGTGCAGAGGACGCGCT
1 CGTATAGCGCGGTGCAGGGGACGCGCT
740887 TTACTGCTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 61 0.88
52 8 0.12
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.16
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGACGCGCTATACCCCACGTGACGCCAAATCAC
Found at i:741174 original size:3 final size:3
Alignment explanation
Indices: 741168--741233 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
741158 ATCCATTTTT
741168 TTA TTA TTGA -TA TTA TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
**
741213 TTA TTA TTA AAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
741234 CAAACAGGCC
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 3 0.05
3 48 0.87
4 4 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:742820 original size:20 final size:19
Alignment explanation
Indices: 742795--742836 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
742785 CTATTTTATA
742795 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
742815 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
742834 AAT
1 AAT
742837 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:742838 original size:119 final size:117
Alignment explanation
Indices: 742691--742927 Score: 289
Period size: 120 Copynumber: 2.0 Consensus size: 117
742681 ATTTTAATCC
* * * *
742691 TGTTTTAATATATATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCT
1 TGTTTTAATATATATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC-
*
742754 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
65 ATTTTCTGATATTTTTAAATAAATAAATATCCTA-TTTATAAATT-TATATAAAT
* * * * ** *
742809 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAATAGCTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATATATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* **
742874 CTTTTCTGATATTTTTAAATAAATAAATATTTTATTTATAAATTTATATAAAT
65 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAAT
742927 T
1 T
742928 AATAAATTTA
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 17 0.17
119 29 0.29
120 34 0.34
121 21 0.21
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (117 bp):
TGTTTTAATATATATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAAT
Found at i:748179 original size:3 final size:3
Alignment explanation
Indices: 748171--748197 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
748161 GAATTGGGTT
748171 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
748198 CTTTATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:749705 original size:8 final size:7
Alignment explanation
Indices: 749681--749722 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
749671 TTTTCATACA
749681 TGCA-TT
1 TGCATTT
749687 TGCATTT
1 TGCATTT
749694 TGCATCTT
1 TGCAT-TT
749702 TGCATTT
1 TGCATTT
* *
749709 TTCATTG
1 TGCATTT
749716 TGCATTT
1 TGCATTT
749723 ATAATTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:749705 original size:15 final size:14
Alignment explanation
Indices: 749681--749722 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
749671 TTTTCATACA
749681 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
749694 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
749709 TTCATTGTGCATTT
1 TGCATTTTGCATTT
749723 ATAATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:749798 original size:12 final size:12
Alignment explanation
Indices: 749781--749835 Score: 65
Period size: 12 Copynumber: 4.3 Consensus size: 12
749771 ACATTCACAT
749781 ATTTACATTTGC
1 ATTTACATTTGC
749793 ATTTACATTTGC
1 ATTTACATTTGC
* *
749805 ATTTTTTACGTTTGT
1 A---TTTACATTTGC
749820 ATTTACATTTGC
1 ATTTACATTTGC
749832 ATTT
1 ATTT
749836 TTACATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 26 0.72
15 10 0.28
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:749818 original size:27 final size:27
Alignment explanation
Indices: 749782--749841 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
749772 CATTCACATA
749782 TTTACATTTGCATTTACATTTGCATTT
1 TTTACATTTGCATTTACATTTGCATTT
* *
749809 TTTACGTTTGTATTTACATTTGCA-TT
1 TTTACATTTGCATTTACATTTGCATTT
749835 TTTACAT
1 TTTACAT
749842 AATTACATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.22, C:0.13, G:0.08, T:0.57
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:751461 original size:2 final size:2
Alignment explanation
Indices: 751454--751481 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
751444 ATCCTTTTAA
751454 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
751482 CATTTGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:751802 original size:14 final size:14
Alignment explanation
Indices: 751783--751846 Score: 74
Period size: 15 Copynumber: 4.4 Consensus size: 14
751773 GCAAAGAAAG
751783 AAGAAGAAGAAAAA
1 AAGAAGAAGAAAAA
751797 AAGAAGAAGAAAAAA
1 AAGAAGAAG-AAAAA
* * *
751812 AATAAAAATAAAAA
1 AAGAAGAAGAAAAA
*
751826 AAGAAAAAAGAAAAA
1 AAG-AAGAAGAAAAA
751841 AAGAAG
1 AAGAAG
751847 GAAAATTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
14 18 0.43
15 24 0.57
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (14 bp):
AAGAAGAAGAAAAA
Found at i:751825 original size:7 final size:7
Alignment explanation
Indices: 751775--751841 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
751765 CTCATCCAGC
751775 AAAGAAA
1 AAAGAAA
*
751782 GAAG-AA
1 AAAGAAA
*
751788 GAAGAAAA
1 AAAG-AAA
751796 AAAGAAGA
1 AAAGAA-A
751804 AGAA-AAA
1 A-AAGAAA
*
751811 AAATAAA
1 AAAGAAA
751818 AATA-AAA
1 AA-AGAAA
751825 AAAGAAA
1 AAAGAAA
751832 AAAGAAA
1 AAAGAAA
751839 AAA
1 AAA
751842 AGAAGGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
6 9 0.18
7 30 0.59
8 10 0.20
9 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:754322 original size:114 final size:114
Alignment explanation
Indices: 754121--754344 Score: 367
Period size: 114 Copynumber: 2.0 Consensus size: 114
754111 GTGCTACGTT
*
754121 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTTTAGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
754186 GTTTGATATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTG
66 GTTCGATAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTG
*
754235 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
* * * *
754300 GTTCGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GTTCGATAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAA
754345 CTGCATGATC
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
GTTCGATAGGAACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTG
Found at i:757024 original size:22 final size:22
Alignment explanation
Indices: 756998--757077 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
756988 TACATCTACA
756998 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
757020 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAGATTCT
* * *
757042 TTTTTTAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
757064 CTTTTCGAAGATGA
1 CTCTTCAAAGATGA
757078 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:758474 original size:113 final size:113
Alignment explanation
Indices: 757823--758461 Score: 1107
Period size: 113 Copynumber: 5.7 Consensus size: 113
757813 TTCCAGAAGG
* *
757823 GTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
757888 ACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAA
*
757936 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
*
758001 ACCTTTTGCTCAAATCCATCACTCGATGGATCATCTTTTCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAA
758049 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
*
758114 ACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAA
*
758162 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGACCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* *
758227 ACCTTTTGCTCAAATCCATCACTCGATGAATCAGCTTTTCCAGAGATA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAA
**
758275 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
* * ** * *
758340 ACTTTTTGTTTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAA
66 ACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAA
* * *
758388 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAAAAGAGCTTGTTCG
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
758453 ACCTTTTGC
66 ACCTTTTGC
758462 ATGACTCTAT
Statistics
Matches: 498, Mismatches: 28, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 498 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (113 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCA
ACCTTTTGCTCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAA
Found at i:758806 original size:3 final size:3
Alignment explanation
Indices: 758800--758859 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
758790 ACCCATTTTT
758800 TTA TTA TTGA -TA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
**
758845 TTA AAA TTA TTA TTA
1 TTA TTA TTA TTA TTA
758860 CAAATAGGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 3 0.06
3 42 0.86
4 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:760453 original size:20 final size:19
Alignment explanation
Indices: 760428--760469 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
760418 CTATTTTATA
760428 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
760448 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
760467 AAT
1 AAT
760470 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:760465 original size:119 final size:117
Alignment explanation
Indices: 760324--760560 Score: 298
Period size: 120 Copynumber: 2.0 Consensus size: 117
760314 ATTTTAATCA
* ** * *
760324 TGTTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCT
1 TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAACAGTCTTAAAACAACTAGAAGTCT
*
760387 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
66 -TTTTCTGATATTTTTAAATAAATAAATATCCTA-TTTATAAATT-TATATAAAT
* * * ** *
760442 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAATAACTGTCTTAAGGCACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAACAGTCTTAAAACAACTAGAAGTC
**
760507 TTTTTCTGATATTTTTAAATAAATAAATATTTTATTTATAAATTTATATAAAT
65 TTTTTCTGATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAAT
760560 T
1 T
760561 AATAAATTTA
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
118 17 0.17
119 30 0.29
120 34 0.33
121 21 0.21
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (117 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAACAGTCTTAAAACAACTAGAAGTCT
TTTTCTGATATTTTTAAATAAATAAATATCCTATTTATAAATTTATATAAAT
Found at i:767136 original size:60 final size:58
Alignment explanation
Indices: 767025--767136 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 58
767015 TTGAATGTTT
* * * **
767025 TAATTTCATCCCTAAATTGTGACTCATTTCAAATTAGTCCTTAAACTTTTGAACATTC
1 TAATTCCATCCCTAAACTATGACTCATTTCAAATTAGTCCCCAAACTTTTGAACATTC
*
767083 TAATTCCATCCCTAAACTATGATCCTC-TTTCTAAATTTGTCCCCAAACTTTTGA
1 TAATTCCATCCCTAAACTATGA--CTCATTTC-AAATTAGTCCCCAAACTTTTGA
767137 GTCTTCCAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 19 0.42
59 4 0.09
60 22 0.49
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.40
Consensus pattern (58 bp):
TAATTCCATCCCTAAACTATGACTCATTTCAAATTAGTCCCCAAACTTTTGAACATTC
Found at i:767644 original size:25 final size:24
Alignment explanation
Indices: 767594--767643 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
767584 ATAATTTAAT
*
767594 AATATATTCTTAAGATAAGAATAA
1 AATATATTATTAAGATAAGAATAA
*
767618 AATATATTTATTAAGTTAAG-ATAA
1 AATATA-TTATTAAGATAAGAATAA
767642 AA
1 AA
767644 AAATAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (24 bp):
AATATATTATTAAGATAAGAATAA
Found at i:767654 original size:19 final size:20
Alignment explanation
Indices: 767630--767669 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
767620 TATATTTATT
767630 AAGTTAAGA-TAAAAAAATA
1 AAGTTAAGAGTAAAAAAATA
767649 AAGTTAAGATGTAAAAAAATA
1 AAGTTAAGA-GTAAAAAAATA
767670 TTATTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
21 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (20 bp):
AAGTTAAGAGTAAAAAAATA
Found at i:768756 original size:2 final size:2
Alignment explanation
Indices: 768751--768780 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
768741 ATTATATAAG
768751 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
768781 TTCTTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:771421 original size:43 final size:43
Alignment explanation
Indices: 771304--771588 Score: 374
Period size: 43 Copynumber: 6.7 Consensus size: 43
771294 AAAAACACTA
* * *
771304 CTATAAATCTCAACCTTTTGCGGCGTTTGTTACAAAAGCGCCG
1 CTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * *
771347 CTATAGATCT-GACCTTTTGCGGCATTTGTTCCAAAAACACCG
1 CTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* *
771389 CTATAAATCTCGATCTTTAGCGGCGTTTGTTCCAAAAACGCCG
1 CTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * * *
771432 TTATAGATCTCGACCTTTTGCGGCGTTTATTCCAAAAACACCG
1 CTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * *
771475 CTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAATAACGCTG
1 CTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* *
771518 CTATAAATCTTGACCTTTTGCGGCGTTTGTTCCAAAAATGCCG
1 CTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
* * * *
771561 CTATATATCTCAACTTTTTGCGGTGTTT
1 CTATAAATCTCGACCTTTTGCGGCGTTT
771589 TTTGTTCTCA
Statistics
Matches: 209, Mismatches: 32, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 36 0.17
43 173 0.83
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (43 bp):
CTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCG
Found at i:776444 original size:13 final size:13
Alignment explanation
Indices: 776426--776452 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
776416 TGAGTTCGTA
776426 TAGGATGAGAGTT
1 TAGGATGAGAGTT
776439 TAGGATGAGAGTT
1 TAGGATGAGAGTT
776452 T
1 T
776453 CCTGGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (13 bp):
TAGGATGAGAGTT
Found at i:779505 original size:72 final size:71
Alignment explanation
Indices: 779389--779523 Score: 180
Period size: 72 Copynumber: 1.9 Consensus size: 71
779379 GAGTTGGACA
* * * * *
779389 GTGCTCGACTCGTGATCGTTAAAAAATTTGTTGCTCGACACGACTCGTTGTTCATTAAGCTCGTT
1 GTGCTCGACCCGTGATCGTAAAAAAATTTGCTGCTCAACACGACTCGTTGCTCATTAAGCTCGTT
779454 AAAATT
66 AAAATT
* * * *
779460 GTGCTCGACCCGTGCTCGTGAAAAAAATTTGCTGCTCAACTCGACTTGTTGCTCGTTAAGCTCG
1 GTGCTCGACCCGTGATCGT-AAAAAAATTTGCTGCTCAACACGACTCGTTGCTCATTAAGCTCG
779524 ACTCGTTGCT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
71 17 0.31
72 37 0.69
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (71 bp):
GTGCTCGACCCGTGATCGTAAAAAAATTTGCTGCTCAACACGACTCGTTGCTCATTAAGCTCGTT
AAAATT
Found at i:779524 original size:21 final size:21
Alignment explanation
Indices: 779499--779543 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
779489 TGCTGCTCAA
*
779499 CTCGACTTGTTGCTCGTTAAG
1 CTCGACTCGTTGCTCGTTAAG
779520 CTCGACTCGTTGCTCGTTAAG
1 CTCGACTCGTTGCTCGTTAAG
779541 CTC
1 CTC
779544 ACTAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.29, G:0.22, T:0.36
Consensus pattern (21 bp):
CTCGACTCGTTGCTCGTTAAG
Found at i:784801 original size:16 final size:16
Alignment explanation
Indices: 784780--784810 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
784770 TACAAAATCT
784780 AATAATTCATAATATA
1 AATAATTCATAATATA
*
784796 AATAATTCATTATAT
1 AATAATTCATAATAT
784811 TATTATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:787776 original size:3 final size:3
Alignment explanation
Indices: 787768--787802 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
787758 AGCATAAAGA
787768 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
787803 AAAAGAACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:797627 original size:40 final size:41
Alignment explanation
Indices: 797534--797632 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 41
797524 ATACCAAATT
* * * *
797534 CAGAAAACAATCTCTTAGTGAGCCCCAGATACAGAAAGAGTT
1 CAGAAAACCAGCTCTTAGTGAGCCCCAGACACAG-AAGAGTC
*
797576 CAGAAAACCAGCTCTTAGTGAGTCCCAGACACAG-AGAGTC
1 CAGAAAACCAGCTCTTAGTGAGCCCCAGACACAGAAGAGTC
* * *
797616 CAGGAAGCCAGCACTTA
1 CAGAAAACCAGCTCTTA
797633 ACAAGACCCA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 19 0.39
42 30 0.61
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.16
Consensus pattern (41 bp):
CAGAAAACCAGCTCTTAGTGAGCCCCAGACACAGAAGAGTC
Done.