Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008497.1 Hibiscus syriacus cultivar Beakdansim tig00111342_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: 1504768
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 6 of 6
Found at i:1237960 original size:15 final size:17
Alignment explanation
Indices: 1237938--1237970 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1237928 TATATTATTT
*
1237938 AAAAAATAATTCACATG
1 AAAATATAATTCACATG
1237955 AAAATATAATTCACAT
1 AAAATATAATTCACAT
1237971 TATATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAATATAATTCACATG
Found at i:1237966 original size:43 final size:43
Alignment explanation
Indices: 1237918--1238001 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
1237908 ATATGTATCT
1237918 TAATTCAAATTATATTATTTAAAAAATAATTCACATGAAAATA
1 TAATTCAAATTATATTATTTAAAAAATAATTCACATGAAAATA
*
1237961 TAATTCACATTATATTATTTAAAAAATAATTCACATGAAAA
1 TAATTCAAATTATATTATTTAAAAAATAATTCACATGAAAA
1238002 AAAAGTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.37
Consensus pattern (43 bp):
TAATTCAAATTATATTATTTAAAAAATAATTCACATGAAAATA
Found at i:1242363 original size:51 final size:51
Alignment explanation
Indices: 1242303--1242406 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
1242293 CACCGACTAA
1242303 ATTTGATATTTTTAGTGGCAATTCTTAATATCACTTAAAATACATTTTCTT
1 ATTTGATATTTTTAGTGGCAATTCTTAATATCACTTAAAATACATTTTCTT
1242354 ATTTGATATTTTTAGTGGCAATTCTTAATATCACTTAAAATACATTTTCTT
1 ATTTGATATTTTTAGTGGCAATTCTTAATATCACTTAAAATACATTTTCTT
1242405 AT
1 AT
1242407 AGTGCCGATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.49
Consensus pattern (51 bp):
ATTTGATATTTTTAGTGGCAATTCTTAATATCACTTAAAATACATTTTCTT
Found at i:1243001 original size:56 final size:56
Alignment explanation
Indices: 1242915--1243026 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
1242905 CCTCTACCTC
1242915 ACCTAAACCCCATTAATAAGGCCATTCATCCACAACACTACACATATAGTTTCCGA
1 ACCTAAACCCCATTAATAAGGCCATTCATCCACAACACTACACATATAGTTTCCGA
*
1242971 ACCTAAACCCCATTAATAAGGCCATTCATCCACACCACTACACATATAGTTTCCGA
1 ACCTAAACCCCATTAATAAGGCCATTCATCCACAACACTACACATATAGTTTCCGA
1243027 GTAGAAGAAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.23
Consensus pattern (56 bp):
ACCTAAACCCCATTAATAAGGCCATTCATCCACAACACTACACATATAGTTTCCGA
Found at i:1243052 original size:6 final size:6
Alignment explanation
Indices: 1243038--1243100 Score: 108
Period size: 6 Copynumber: 10.3 Consensus size: 6
1243028 TAGAAGAAGG
*
1243038 AGGAGGA AGAAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
1 AGGA-GA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA AGGAGA
1243087 AGGAGA AGGAGA AG
1 AGGAGA AGGAGA AG
1243101 AAGAGAATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
6 51 0.94
7 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
AGGAGA
Found at i:1250610 original size:16 final size:16
Alignment explanation
Indices: 1250589--1250619 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1250579 TAATAAATAA
1250589 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1250605 ACGAACATAAACGAA
1 ACGAACATAAACGAA
1250620 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1250713 original size:16 final size:16
Alignment explanation
Indices: 1250689--1250733 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1250679 TAATAAATAA
1250689 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1250705 ACTAACATAAACGAAC
1 ACGAACATAAACGAAC
1250721 ACGAACATAAACG
1 ACGAACATAAACG
1250734 TTGGAGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.56, C:0.24, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1250985 original size:12 final size:12
Alignment explanation
Indices: 1250968--1251024 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
1250958 GCACGATTGA
1250968 AGCTCGATTCTG
1 AGCTCGATTCTG
**
1250980 AGCTCGATT-AA
1 AGCTCGATTCTG
*
1250991 AGGTCGATTCTG
1 AGCTCGATTCTG
1251003 AGCTCGATTCTG
1 AGCTCGATTCTG
1251015 AGCTCGATTC
1 AGCTCGATTC
1251025 AAGCTCAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 8 0.21
12 30 0.79
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (12 bp):
AGCTCGATTCTG
Found at i:1251030 original size:23 final size:23
Alignment explanation
Indices: 1250932--1251011 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
1250922 AAAAATTTAA
* **
1250932 GAGCTCGATTAAAACTCGAGACT
1 GAGCTCGATTAAAGCTCGATTCT
* * *
1250955 CAAGCACGATTGAAGCTCGATTCT
1 -GAGCTCGATTAAAGCTCGATTCT
*
1250979 GAGCTCGATTAAAGGTCGATTCT
1 GAGCTCGATTAAAGCTCGATTCT
1251002 GAGCTCGATT
1 GAGCTCGATT
1251012 CTGAGCTCGA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
23 29 0.63
24 17 0.37
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (23 bp):
GAGCTCGATTAAAGCTCGATTCT
Found at i:1253913 original size:2 final size:2
Alignment explanation
Indices: 1253908--1253950 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1253898 TAAAGAGAGG
1253908 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
1253950 A
1 A
1253951 GAGAGAGAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1253955 original size:2 final size:2
Alignment explanation
Indices: 1253950--1254013 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1253940 ATATATATAT
1253950 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1253992 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
1254014 TGAATCATGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1255034 original size:21 final size:21
Alignment explanation
Indices: 1254993--1255035 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1254983 TTCAGTTTCG
*
1254993 GTTTGAATCGAGTTAGATTCA
1 GTTTGAATCGAGGTAGATTCA
*
1255014 GTTTGGATCGATGGTAG-TTCA
1 GTTTGAATCGA-GGTAGATTCA
1255035 G
1 G
1255036 GTCTGAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.37
Consensus pattern (21 bp):
GTTTGAATCGAGGTAGATTCA
Found at i:1255699 original size:16 final size:16
Alignment explanation
Indices: 1255670--1255711 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1255660 TATTTATGCG
*
1255670 TATAT-TATACGTATA
1 TATATATATAAGTATA
1255685 TACT-TATATAAGTATA
1 TA-TATATATAAGTATA
1255701 TATATATATAA
1 TATATATATAA
1255712 ACTAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (16 bp):
TATATATATAAGTATA
Found at i:1255858 original size:2 final size:2
Alignment explanation
Indices: 1255847--1256009 Score: 60
Period size: 2 Copynumber: 82.0 Consensus size: 2
1255837 ATAGTTTATT
* * *
1255847 TA TA TA -A TA TA TA TA AA CTA TA TA CTA TA TA TA AA CTA TG T-
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA
* * *
1255888 TA TA TA AA CTA TA TA TA AA T- TA TA TA TA TA CTA TA AA CTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * *
1255930 T- TA TA TA AA CTA TA TA TA TA CT- TA TA GTT TA TA TA TA AA T-
1 TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* *
1255970 TA TA AA CTA TA -A TG TA T- TA TA -A TA TA TA -A TA TA TA -A TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1256008 TA
1 TA
1256010 ATTTTAATTA
Statistics
Matches: 119, Mismatches: 21, Indels: 42
0.65 0.12 0.23
Matches are distributed among these distances:
1 11 0.09
2 96 0.81
3 12 0.10
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1255992 original size:10 final size:10
Alignment explanation
Indices: 1255977--1256037 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
1255967 AATTATAAAC
*
1255977 TATAATGTAT
1 TATAATATAT
1255987 TATAATATAT
1 TATAATATAT
* *
1255997 AAT-ATATAA
1 TATAATATAT
*
1256006 TATAATTTTAAT
1 TATAA-TAT-AT
*
1256018 TATAATGTAT
1 TATAATATAT
1256028 TATAATATAT
1 TATAATATAT
1256038 AATATAAGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 7 0.17
10 23 0.57
11 4 0.10
12 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (10 bp):
TATAATATAT
Found at i:1255997 original size:7 final size:7
Alignment explanation
Indices: 1255987--1256043 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
1255977 TATAATGTAT
1255987 TATAATA
1 TATAATA
1255994 TATAATA
1 TATAATA
1256001 TAT-A-A
1 TATAATA
1256006 TATAAT-
1 TATAATA
*
1256012 TTTAAT-
1 TATAATA
1256018 TATAATGTA
1 TATAA--TA
1256027 TTATAATA
1 -TATAATA
1256035 TATAATA
1 TATAATA
1256042 TA
1 TA
1256044 AGTATAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
5 4 0.10
6 11 0.26
7 19 0.45
8 3 0.07
10 5 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (7 bp):
TATAATA
Found at i:1256005 original size:31 final size:32
Alignment explanation
Indices: 1255960--1256044 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 32
1255950 CTTATAGTTT
1255960 ATATATAA-ATTATAAACTATAA-TGT-ATTATA
1 ATATATAATA-TATAAA-TATAATTGTAATTATA
*
1255991 ATATATAATATAT-AATATAATTTTAATTATA
1 ATATATAATATATAAATATAATTGTAATTATA
1256022 ATGTATTATAATATAT-AATATAA
1 A--TA-TATAATATATAAATATAA
1256045 GTATAAAATA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
29 5 0.11
30 4 0.09
31 18 0.38
32 1 0.02
33 2 0.04
34 17 0.36
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (32 bp):
ATATATAATATATAAATATAATTGTAATTATA
Found at i:1256443 original size:102 final size:102
Alignment explanation
Indices: 1256337--1256560 Score: 247
Period size: 102 Copynumber: 2.2 Consensus size: 102
1256327 AATCTTTTCA
* ** *
1256337 TTTTTTCGATCAAACCACAAAAA-TGAATTGTGTTATTCAGTTGCTCATTCC-TAAAAAGTCC-A
1 TTTTTTCGATCAAAACACAAAAACCCAATTGTGTTATTCAGTTGCTCA-TCCTTAAAAA-CCCTA
*
1256399 TTCGATCCAAAATAAACACAATTCTTCATTCCTTTTGTG
64 TTCAATCCAAAATAAACACAATTCTTCATTCCTTTTGTG
* * * * *
1256438 TTTTTTGGATCAAAACACAAAAACCCATTTGTGTTCTTCATTTGTTCATCCTTAAAAACCCTATT
1 TTTTTTCGATCAAAACACAAAAACCCAATTGTGTTATTCAGTTGCTCATCCTTAAAAACCCTATT
** ** ** *
1256503 CAATCCAAAATAAACACAAACCTTCCGTCGATTTCTG
66 CAATCCAAAATAAACACAATTCTTCATTCCTTTTGTG
*
1256540 TTTTTTGGATCAAAACACAAA
1 TTTTTTCGATCAAAACACAAA
1256561 CCCTAACCTT
Statistics
Matches: 103, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
101 26 0.25
102 77 0.75
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (102 bp):
TTTTTTCGATCAAAACACAAAAACCCAATTGTGTTATTCAGTTGCTCATCCTTAAAAACCCTATT
CAATCCAAAATAAACACAATTCTTCATTCCTTTTGTG
Found at i:1256737 original size:193 final size:193
Alignment explanation
Indices: 1256398--1256755 Score: 458
Period size: 193 Copynumber: 1.9 Consensus size: 193
1256388 TAAAAAGTCC
* * * *
1256398 ATTCGATCCAAAATAAACACAATTCTTCATTCCTTTTGTGTTTTTTGGATCAAAACACAAAAACC
1 ATTCGATCCAAAATAAACACAAATCTTCATTCCATTTCTGTTTTTTCGATCAAAACACAAAAACC
* * * * * *
1256463 CATTTGTGTTCTTCATTTGTTCATCCTTAAAAACCCTATTCAATCCAAAATAAACACAAACCTTC
66 CAATTCTGTTATTCATTTATTCATCCCTAAAAACCCTATCCAATCCAAAATAAACACAAACCTTC
*
1256528 CGTCGATTTCTGTTTTT-TGGATCAAAACACAAACCCTAACCTTATTCTTCCCTAAATAACAT
131 CGTCGATTTCTGTTTTTCTCGATCAAAACACAAACCCTAACCTTATTCTTCCCTAAATAACAT
* * *
1256590 ATTCGATCCAAAATAAACACAAATCTTCCTTCGATTTCTGTTTTTCTCGATC-AAA-ACATAAAC
1 ATTCGATCCAAAATAAACACAAATCTTCATTCCATTTCTGTTTTT-TCGATCAAAACACAAAAAC
*
1256653 CCTAATTCTAGTTATTCATTTATT-ATTCCCTAAATAACCC-ATCCGATCCAAAATAAACACAAA
65 CC-AATTCT-GTTATTCATTTATTCA-TCCCTAAA-AACCCTATCCAATCCAAAATAAACACAAA
* * *
1256716 TCTTCCTTCTG-TTTTTGTTTTTCTCGATCAAAACACAAAC
126 CCTTCCGTC-GATTTCTGTTTTTCTCGATCAAAACACAAAC
1256756 TGTTAGGATT
Statistics
Matches: 141, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
191 9 0.06
192 48 0.34
193 62 0.44
194 22 0.16
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (193 bp):
ATTCGATCCAAAATAAACACAAATCTTCATTCCATTTCTGTTTTTTCGATCAAAACACAAAAACC
CAATTCTGTTATTCATTTATTCATCCCTAAAAACCCTATCCAATCCAAAATAAACACAAACCTTC
CGTCGATTTCTGTTTTTCTCGATCAAAACACAAACCCTAACCTTATTCTTCCCTAAATAACAT
Found at i:1256748 original size:103 final size:103
Alignment explanation
Indices: 1256569--1256755 Score: 304
Period size: 103 Copynumber: 1.8 Consensus size: 103
1256559 AACCCTAACC
* * *
1256569 TTATTCTTCCCTAAATAACATATTCGATCCAAAATAAACACAAATCTTCCTTCGATTTCTGTTTT
1 TTATTATTCCCTAAATAACACATCCGATCCAAAATAAACACAAATCTTCCTTCGATTTCTGTTTT
*
1256634 TCTCGATCAAAACATAAACCCTAATTCTAGTTATTCAT
66 TCTCGATCAAAACACAAACCCTAATTCTAGTTATTCAT
* *
1256672 TTATTATTCCCTAAATAACCCATCCGATCCAAAATAAACACAAATCTTCCTTCTG-TTTTTGTTT
1 TTATTATTCCCTAAATAACACATCCGATCCAAAATAAACACAAATCTTCCTTC-GATTTCTGTTT
1256736 TTCTCGATCAAAACACAAAC
65 TTCTCGATCAAAACACAAAC
1256756 TGTTAGGATT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 76 0.99
104 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (103 bp):
TTATTATTCCCTAAATAACACATCCGATCCAAAATAAACACAAATCTTCCTTCGATTTCTGTTTT
TCTCGATCAAAACACAAACCCTAATTCTAGTTATTCAT
Found at i:1257045 original size:34 final size:32
Alignment explanation
Indices: 1256992--1257061 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1256982 ACCTTACAAC
*
1256992 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
* *
1257024 TCCCTAGCTTTTACACGGGCTAAGCTATAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1257058 TCCC
1 TCCC
1257062 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1257371 original size:21 final size:21
Alignment explanation
Indices: 1257345--1257386 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1257335 CCAGAATGGG
*
1257345 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1257366 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1257387 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1257518 original size:19 final size:19
Alignment explanation
Indices: 1257494--1257560 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1257484 AGCCTCGGGG
*
1257494 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
*
1257513 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
1257532 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
1257551 TTACTATTCA
1 TTACTGTTCA
1257561 TAAAAACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:1257657 original size:29 final size:31
Alignment explanation
Indices: 1257625--1257684 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1257615 AAATTTTGAA
*
1257625 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1257654 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1257685 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1260231 original size:15 final size:15
Alignment explanation
Indices: 1260203--1260242 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1260193 TTTCCAGGTA
1260203 TATTATTCTA-TTTTT
1 TATT-TTCTATTTTTT
1260218 TATTTTCTATTTTTT
1 TATTTTCTATTTTTT
1260233 TATTTT-TATT
1 TATTTTCTATT
1260243 AAATATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (15 bp):
TATTTTCTATTTTTT
Found at i:1260420 original size:14 final size:15
Alignment explanation
Indices: 1260401--1260430 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1260391 TTATTTTCGG
1260401 TTTATA-TTCTATTT
1 TTTATATTTCTATTT
1260415 TTTATATTTCTATTT
1 TTTATATTTCTATTT
1260430 T
1 T
1260431 ATAGACCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATATTTCTATTT
Found at i:1260630 original size:21 final size:20
Alignment explanation
Indices: 1260606--1260668 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
1260596 ATTATATTGA
1260606 TTTATGTTTTTTATGTTTATG
1 TTTATGTTTTTTAT-TTTATG
* * *
1260627 TTTATGTTTTATATTCTATT
1 TTTATGTTTTTTATTTTATG
1260647 TTGTAT-TTTTTTATTTT-TG
1 TT-TATGTTTTTTATTTTATG
1260666 TTT
1 TTT
1260669 TATATTTGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 1 0.03
19 3 0.09
20 15 0.43
21 16 0.46
ACGTcount: A:0.14, C:0.02, G:0.10, T:0.75
Consensus pattern (20 bp):
TTTATGTTTTTTATTTTATG
Found at i:1260668 original size:33 final size:33
Alignment explanation
Indices: 1260586--1260707 Score: 104
Period size: 33 Copynumber: 3.5 Consensus size: 33
1260576 TGTAAATCTC
* * *
1260586 TTATTTTTGTATTATATTGATTTATGTTTTTTATGT
1 TTATTTTTGTTTTATATTTATTT-TG-TATTT-TGT
1260622 TTATGTTTATGTTTTATATTCTATTTTGTATTTT-T
1 TTAT-TTT-TGTTTTATATT-TATTTTGTATTTTGT
* *
1260657 TTATTTTTGTTTTATATTTGGTTTTATATTTTGT
1 TTATTTTTGTTTTATATTT-ATTTTGTATTTTGT
* *
1260691 TT-TTATTGTTTTTTATT
1 TTATTTTTGTTTTATATT
1260708 GCTGTTTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
32 1 0.01
33 34 0.46
34 6 0.08
35 5 0.07
36 5 0.07
37 7 0.09
38 12 0.16
39 4 0.05
ACGTcount: A:0.16, C:0.01, G:0.10, T:0.73
Consensus pattern (33 bp):
TTATTTTTGTTTTATATTTATTTTGTATTTTGT
Found at i:1260680 original size:12 final size:12
Alignment explanation
Indices: 1260621--1260706 Score: 74
Period size: 12 Copynumber: 7.4 Consensus size: 12
1260611 GTTTTTTATG
*
1260621 TTTATGTTTATGT
1 TTTATATTT-TGT
* *
1260634 TTTATATTCTAT
1 TTTATATTTTGT
*
1260646 TTTGTA-TTT-T
1 TTTATATTTTGT
1260656 TTTAT-TTTTGT
1 TTTATATTTTGT
*
1260667 TTTATATTTGGT
1 TTTATATTTTGT
1260679 TTTATATTTTGT
1 TTTATATTTTGT
1260691 TTT-TATTGTT-T
1 TTTATATT-TTGT
1260702 TTTAT
1 TTTAT
1260707 TGCTGTTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
10 8 0.13
11 16 0.27
12 29 0.48
13 7 0.12
ACGTcount: A:0.15, C:0.01, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTATATTTTGT
Found at i:1260704 original size:23 final size:22
Alignment explanation
Indices: 1260652--1260727 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
1260642 CTATTTTGTA
1260652 TTTTTTTATTTTTGTTTTATAT
1 TTTTTTTATTTTTGTTTTATAT
*
1260674 TTGGTTTTATATTTTGTTTT-TAT
1 TT-TTTTTAT-TTTTGTTTTATAT
** *
1260697 TGTTTTTTATTGCTGTTTTTTAT
1 T-TTTTTTATTTTTGTTTTATAT
1260720 TTTATTTT
1 TTT-TTTT
1260728 CTGTTATAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
22 11 0.24
23 24 0.53
24 10 0.22
ACGTcount: A:0.12, C:0.01, G:0.09, T:0.78
Consensus pattern (22 bp):
TTTTTTTATTTTTGTTTTATAT
Found at i:1260706 original size:46 final size:45
Alignment explanation
Indices: 1260632--1260721 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 45
1260622 TTATGTTTAT
**
1260632 GTTTTATATTCTATTTTGTATTTTTTTATTTTTGTTTTATATTTG
1 GTTTTATATTCTATTTTGTATTTTTTTATTGCTGTTTTATATTTG
* * *
1260677 GTTTTATATTTTGTTTT-TATTGTTTTTTATTGCTGTTTTTTATTT
1 GTTTTATATTCTATTTTGTA-T-TTTTTTATTGCTGTTTTATATTT
1260722 TATTTTCTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
44 2 0.05
45 16 0.42
46 20 0.53
ACGTcount: A:0.13, C:0.02, G:0.10, T:0.74
Consensus pattern (45 bp):
GTTTTATATTCTATTTTGTATTTTTTTATTGCTGTTTTATATTTG
Found at i:1263141 original size:9 final size:9
Alignment explanation
Indices: 1263129--1263180 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
1263119 ATATATAAAA
1263129 AGTAAATTT
1 AGTAAATTT
**
1263138 AGTAAAATAA
1 AGT-AAATTT
1263148 AGTAAATTT
1 AGTAAATTT
**
1263157 AGTAATATAA
1 AGTAA-ATTT
1263167 AGTAAATTT
1 AGTAAATTT
1263176 AGTAA
1 AGTAA
1263181 TAATATTATC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
9 19 0.58
10 14 0.42
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (9 bp):
AGTAAATTT
Found at i:1263151 original size:19 final size:19
Alignment explanation
Indices: 1263127--1263185 Score: 100
Period size: 19 Copynumber: 3.1 Consensus size: 19
1263117 ATATATATAA
1263127 AAAGTAAATTTAGTAAAAT
1 AAAGTAAATTTAGTAAAAT
*
1263146 AAAGTAAATTTAGTAATAT
1 AAAGTAAATTTAGTAAAAT
1263165 AAAGTAAATTTAGTAATAAT
1 AAAGTAAATTTAGTAA-AAT
1263185 A
1 A
1263186 TTATCTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
19 34 0.92
20 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (19 bp):
AAAGTAAATTTAGTAAAAT
Found at i:1265620 original size:25 final size:25
Alignment explanation
Indices: 1265592--1265651 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
1265582 CTGCTCTGAA
*
1265592 TATTTATATTATCAATGAAATTTAT
1 TATTTATATTATAAATGAAATTTAT
*
1265617 TATTTATATGATAAATGAAATTTAT
1 TATTTATATTATAAATGAAATTTAT
*
1265642 TATGTATATT
1 TATTTATATT
1265652 TGTTGAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (25 bp):
TATTTATATTATAAATGAAATTTAT
Found at i:1271207 original size:2 final size:2
Alignment explanation
Indices: 1271200--1271232 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1271190 ATTTGAGCAA
1271200 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1271233 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1271237 original size:2 final size:2
Alignment explanation
Indices: 1271232--1271271 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1271222 TCTCTCTCTC
1271232 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1271272 AATTGCAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1282819 original size:16 final size:17
Alignment explanation
Indices: 1282793--1282825 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1282783 ATCATTATAT
1282793 TACTAATAAAAATAACA
1 TACTAATAAAAATAACA
1282810 TACT-ATAAAAATAACA
1 TACTAATAAAAATAACA
1282826 ACCAGATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
TACTAATAAAAATAACA
Found at i:1285662 original size:17 final size:17
Alignment explanation
Indices: 1285640--1285674 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1285630 GCTTGGCCTG
1285640 GGCCTGTTTAAAAACCT
1 GGCCTGTTTAAAAACCT
*
1285657 GGCCTGTTTAAAAGCCT
1 GGCCTGTTTAAAAACCT
1285674 G
1 G
1285675 TTTAGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (17 bp):
GGCCTGTTTAAAAACCT
Found at i:1285682 original size:17 final size:17
Alignment explanation
Indices: 1285662--1285695 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1285652 AACCTGGCCT
*
1285662 GTTTAAAAGCCTGTTTA
1 GTTTAAAAACCTGTTTA
1285679 GTTTAAAAACCTGTTTA
1 GTTTAAAAACCTGTTTA
1285696 AAAGTGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (17 bp):
GTTTAAAAACCTGTTTA
Found at i:1288126 original size:20 final size:18
Alignment explanation
Indices: 1288090--1288124 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1288080 AAGGGGCATC
1288090 GGGGAATCAAACACACAT
1 GGGGAATCAAACACACAT
*
1288108 GGGGAATCAAATACACA
1 GGGGAATCAAACACACA
1288125 CACTTATATA
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:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (18 bp):
GGGGAATCAAACACACAT
Found at i:1288134 original size:2 final size:2
Alignment explanation
Indices: 1288129--1288160 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1288119 TACACACACT
*
1288129 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1288161 ATTATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1288415 original size:2 final size:2
Alignment explanation
Indices: 1288408--1288437 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1288398 CTATAATTTA
1288408 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
1288438 TATTTGGTTT
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:1298416 original size:9 final size:9
Alignment explanation
Indices: 1298404--1298433 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1298394 GAAAATCGAA
1298404 AAAAACCGG
1 AAAAACCGG
1298413 AAAAACCGAG
1 AAAAACCG-G
1298423 AAAAACCGG
1 AAAAACCGG
1298432 AA
1 AA
1298434 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAACCGG
Found at i:1298722 original size:14 final size:14
Alignment explanation
Indices: 1298703--1298730 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1298693 AAGTGAAAGA
1298703 ATAGTTATATAATT
1 ATAGTTATATAATT
1298717 ATAGTTATATAATT
1 ATAGTTATATAATT
1298731 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:1299642 original size:20 final size:19
Alignment explanation
Indices: 1299600--1299636 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1299590 GAGGTTTTTT
1299600 TATA-ATTTTTTAAAAATA
1 TATATATTTTTTAAAAATA
1299618 TATATATTTTTTATAAAAT
1 TATATATTTTTTA-AAAAT
1299637 TAATATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATATTTTTTAAAAATA
Found at i:1304165 original size:43 final size:42
Alignment explanation
Indices: 1304108--1304233 Score: 162
Period size: 43 Copynumber: 2.9 Consensus size: 42
1304098 CGGATACCGT
* * *
1304108 AAAACGCCGTTATAGATTTTGATCTTTTGCGGCGTTTGTTCCA
1 AAAACGTCGTTATAGATCTTGA-CTTTTGCGGCATTTGTTCCA
* *
1304151 AAAACGTCGGTATAGATCTTGACATTTTGCGGCATTTGTTCTA
1 AAAACGTCGTTATAGATCTTGAC-TTTTGCGGCATTTGTTCCA
* *
1304194 AAAACGTTGTTATAGATCTTGACTTTTTGCAGCATTTGTT
1 AAAACGTCGTTATAGATCTTGAC-TTTTGCGGCATTTGTT
1304234 TAAAAAATAT
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 1 0.01
43 72 0.99
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (42 bp):
AAAACGTCGTTATAGATCTTGACTTTTGCGGCATTTGTTCCA
Found at i:1305415 original size:6 final size:6
Alignment explanation
Indices: 1305404--1305429 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1305394 AACAATTAAC
1305404 CTAAAA CTAAAA CTAAAA CTAAAA CT
1 CTAAAA CTAAAA CTAAAA CTAAAA CT
1305430 GGGTAAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (6 bp):
CTAAAA
Found at i:1309667 original size:2 final size:2
Alignment explanation
Indices: 1309656--1309707 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
1309646 AAAACCACAA
*
1309656 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AC 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
1309697 AT AT AT A- AT AT
1 AT AT AT AT AT AT
1309708 TTGAAAGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1311072 original size:36 final size:36
Alignment explanation
Indices: 1311031--1311103 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
1311021 TAATATATTT
1311031 TAATATCTAAACTTTAATTTT-TTTTAAAACTATACC
1 TAATAT-TAAACTTTAATTTTATTTTAAAACTATACC
* * * * *
1311067 TAATATTTAATTTTCATTTTATTTTAATACTCTACC
1 TAATATTAAACTTTAATTTTATTTTAAAACTATACC
1311103 T
1 T
1311104 TTAAAAACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 11 0.35
36 20 0.65
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (36 bp):
TAATATTAAACTTTAATTTTATTTTAAAACTATACC
Found at i:1313820 original size:2 final size:2
Alignment explanation
Indices: 1313808--1313838 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1313798 GTAGTAAAAC
*
1313808 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1313839 GTGTGTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1314347 original size:22 final size:22
Alignment explanation
Indices: 1314319--1314368 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1314309 GAGAGTCGGA
1314319 GACATGTATGTATCCGACAGGC
1 GACATGTATGTATCCGACAGGC
*
1314341 GACATGTATGTCTCCGACAGGC
1 GACATGTATGTATCCGACAGGC
1314363 GACATG
1 GACATG
1314369 GTTATATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (22 bp):
GACATGTATGTATCCGACAGGC
Found at i:1315953 original size:2 final size:2
Alignment explanation
Indices: 1315843--1315939 Score: 194
Period size: 2 Copynumber: 48.5 Consensus size: 2
1315833 GAATGGACTC
1315843 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
1315885 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
1315927 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1315940 GGATAAAGTA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 95 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1316404 original size:59 final size:60
Alignment explanation
Indices: 1316294--1316406 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 60
1316284 ATCGATTATC
*
1316294 ATTTTATAATTTTTAATAATTTAAACACTTAACAAAATAACATCCTATAATTAAGATATT
1 ATTTTATAACTTTTAATAATTTAAACACTTAACAAAATAACATCCTATAATTAAGATATT
* * * *
1316354 ATTTTATAACTTTTAATAA-TTAAATACTTAATAAAATAATATCTTATAATTAA
1 ATTTTATAACTTTTAATAATTTAAACACTTAACAAAATAACATCCTATAATTAA
1316407 TACGATTTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 30 0.62
60 18 0.38
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAATTTAAACACTTAACAAAATAACATCCTATAATTAAGATATT
Found at i:1325187 original size:2 final size:2
Alignment explanation
Indices: 1325180--1325246 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1325170 TATACTAAAT
1325180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1325222 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
1325247 GATTTTAGGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1326775 original size:24 final size:24
Alignment explanation
Indices: 1326747--1326799 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1326737 AAATTCGAAA
*
1326747 GGAAATGTTGTATGTAAA-TTGTGT
1 GGAAATGGTGTATGTAAACTT-TGT
1326771 GGAAATGGTGTATGTAAACTTTGT
1 GGAAATGGTGTATGTAAACTTTGT
1326795 GGAAA
1 GGAAA
1326800 AGTTACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (24 bp):
GGAAATGGTGTATGTAAACTTTGT
Found at i:1334791 original size:2 final size:2
Alignment explanation
Indices: 1334784--1334813 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1334774 TATAGTGTTG
1334784 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
1334814 GTCATTTTTT
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:1338618 original size:2 final size:2
Alignment explanation
Indices: 1338611--1338644 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1338601 AAGGTGTATG
1338611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1338645 ATTAATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1341771 original size:15 final size:15
Alignment explanation
Indices: 1341729--1341778 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1341719 GTCGTCGTCG
* *
1341729 TCATCTCCGTCACCT
1 TCATCTTCGTCATCT
* * *
1341744 TCACCGTCTTCATCT
1 TCATCTTCGTCATCT
1341759 TCATCTTCGTCATCT
1 TCATCTTCGTCATCT
1341774 TCATC
1 TCATC
1341779 CTCTTCCTCG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.14, C:0.40, G:0.06, T:0.40
Consensus pattern (15 bp):
TCATCTTCGTCATCT
Found at i:1341858 original size:9 final size:9
Alignment explanation
Indices: 1341841--1341898 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
1341831 ATAACCTGCA
*
1341841 CTTCATCGT
1 CTTCGTCGT
1341850 CTTCGTCGT
1 CTTCGTCGT
*
1341859 CCTC-TC--
1 CTTCGTCGT
1341865 CTTCGTCGT
1 CTTCGTCGT
*
1341874 CTTCCTC-T
1 CTTCGTCGT
1341882 CCTTCGTCGT
1 -CTTCGTCGT
1341892 CTTCGTC
1 CTTCGTC
1341899 ATCCTCTCCG
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
6 3 0.08
7 2 0.05
8 3 0.08
9 30 0.77
10 1 0.03
ACGTcount: A:0.02, C:0.41, G:0.14, T:0.43
Consensus pattern (9 bp):
CTTCGTCGT
Found at i:1341873 original size:24 final size:22
Alignment explanation
Indices: 1341841--1341929 Score: 69
Period size: 24 Copynumber: 4.0 Consensus size: 22
1341831 ATAACCTGCA
1341841 CTTCATCGTCTTCGTCGTCCTCTC
1 CTTCATCGT-TTCGTC-TCCTCTC
*
1341865 CTTCGTCG--TC-T-TCCTCTC
1 CTTCATCGTTTCGTCTCCTCTC
*
1341883 CTTCGTCGTCTTCGTCATCCTCTC
1 CTTCATCGT-TTCGTC-TCCTCTC
*
1341907 CGTCATCGTTGTCGTCTTCCTCT
1 CTTCATCGTT-TCGTC-TCCTCT
1341930 TCGCCGCCGT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
18 15 0.28
20 1 0.02
21 4 0.07
22 1 0.02
23 1 0.02
24 32 0.59
ACGTcount: A:0.03, C:0.40, G:0.13, T:0.43
Consensus pattern (22 bp):
CTTCATCGTTTCGTCTCCTCTC
Found at i:1341879 original size:18 final size:18
Alignment explanation
Indices: 1341852--1341895 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1341842 TTCATCGTCT
*
1341852 TCGTCGTCCTCTCCTTCG
1 TCGTCTTCCTCTCCTTCG
1341870 TCGTCTTCCTCTCCTTCG
1 TCGTCTTCCTCTCCTTCG
1341888 TCGTCTTC
1 TCGTCTTC
1341896 GTCATCCTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.00, C:0.43, G:0.14, T:0.43
Consensus pattern (18 bp):
TCGTCTTCCTCTCCTTCG
Found at i:1347137 original size:25 final size:25
Alignment explanation
Indices: 1347089--1347137 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1347079 AAATTTATAA
*
1347089 AATTTTAGAGAAAATAAACTTAAAG
1 AATTTTAGAGAAAATAAACATAAAG
*
1347114 AATTTTATAGAAAAATAAA-ATAAA
1 AATTTTAGAG-AAAATAAACATAAA
1347138 TTACCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (25 bp):
AATTTTAGAGAAAATAAACATAAAG
Found at i:1353627 original size:39 final size:39
Alignment explanation
Indices: 1353520--1353629 Score: 150
Period size: 39 Copynumber: 2.8 Consensus size: 39
1353510 CATGGATAAA
* * *
1353520 TTACATCATTCATCACTTAATTATCTTCTAACTCCTATT
1 TTACATCATTCACCACTCAATTATCTTCTCACTCCTATT
* *
1353559 TTGCATCATTCACCA-TGCAATTATCTTCTCACTCTTATT
1 TTACATCATTCACCACT-CAATTATCTTCTCACTCCTATT
*
1353598 TTACATCATTTACCACTCAATTATCTTCTCAC
1 TTACATCATTCACCACTCAATTATCTTCTCAC
1353630 CGAATATTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.02
39 60 0.97
40 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (39 bp):
TTACATCATTCACCACTCAATTATCTTCTCACTCCTATT
Found at i:1355060 original size:18 final size:18
Alignment explanation
Indices: 1355037--1355074 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1355027 AACCTTGTGA
1355037 CATGTCACCATCTTTAAG
1 CATGTCACCATCTTTAAG
*
1355055 CATGTCTCCATCTTTAAG
1 CATGTCACCATCTTTAAG
1355073 CA
1 CA
1355075 ACATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (18 bp):
CATGTCACCATCTTTAAG
Found at i:1357091 original size:15 final size:16
Alignment explanation
Indices: 1357055--1357093 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1357045 AGAGTCTCTA
*
1357055 AATCATTCAGTATTTG
1 AATCATTCAGCATTTG
*
1357071 AATCATTCAGCGTTT-
1 AATCATTCAGCATTTG
1357086 AATCATTC
1 AATCATTC
1357094 TGAAATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (16 bp):
AATCATTCAGCATTTG
Found at i:1361023 original size:19 final size:20
Alignment explanation
Indices: 1360999--1361049 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1360989 TCCCAAAAAA
*
1360999 TTTCGATACTTTTCA-AGAG
1 TTTCGATACTTTTCATAAAG
*
1361018 TTTCGAAACTTTTCATAAAG
1 TTTCGATACTTTTCATAAAG
1361038 TTTCGATACTTT
1 TTTCGATACTTT
1361050 GGCTCCAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (20 bp):
TTTCGATACTTTTCATAAAG
Found at i:1364951 original size:17 final size:17
Alignment explanation
Indices: 1364929--1364968 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1364919 CCGTGTCCCG
*
1364929 ACCCGGATGTTACGGGT
1 ACCCGGATGTTACAGGT
* *
1364946 ACCCGGATTTTGCAGGT
1 ACCCGGATGTTACAGGT
1364963 ACCCGG
1 ACCCGG
1364969 TAATCGGGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.23
Consensus pattern (17 bp):
ACCCGGATGTTACAGGT
Found at i:1365138 original size:16 final size:15
Alignment explanation
Indices: 1365112--1365147 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1365102 CAAAATACAA
1365112 AATATAATAATTCAT
1 AATATAATAATTCAT
1365127 AATATAAATAATTCAT
1 AATAT-AATAATTCAT
*
1365143 TATAT
1 AATAT
1365148 TTTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAATAATTCAT
Found at i:1375687 original size:20 final size:20
Alignment explanation
Indices: 1375664--1375746 Score: 73
Period size: 19 Copynumber: 4.2 Consensus size: 20
1375654 AATTCGTGTT
*
1375664 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
*
1375684 GCGAAAGTCAAATTTGCAAC
1 GCGAAAGTCAAATTCGCAAC
* **
1375704 -TGAATTTCAAATTCGCAA-
1 GCGAAAGTCAAATTCGCAAC
* *
1375722 -CTAAATTTCAAATTCGCAAC
1 GCGAAA-GTCAAATTCGCAAC
1375742 GCGAA
1 GCGAA
1375747 TTTAATTTTG
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.04
19 27 0.54
20 18 0.36
21 3 0.06
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:1375715 original size:19 final size:19
Alignment explanation
Indices: 1375671--1375741 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
1375661 GTTGCGATAG
* **
1375671 TCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAAC-TGAATT
*
1375691 TCAAATTTGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
1375710 TCAAATTCGCAACTAAATT
1 TCAAATTCGCAACTGAATT
1375729 TCAAATTCGCAAC
1 TCAAATTCGCAAC
1375742 GCGAATTTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
19 33 0.73
20 12 0.27
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:1376680 original size:24 final size:24
Alignment explanation
Indices: 1376653--1376706 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1376643 GTATTCAAAA
1376653 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
1376677 TTTGATTTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1376701 TTTGAT
1 TTTGAT
1376707 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1378991 original size:18 final size:18
Alignment explanation
Indices: 1378968--1379003 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1378958 AGGTAAAAGG
*
1378968 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1378986 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1379004 CAGCCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1379314 original size:20 final size:20
Alignment explanation
Indices: 1379289--1379358 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
1379279 ATGTTTCGAT
1379289 CAACGCGAAAGTCAAATTTG
1 CAACGCGAAAGTCAAATTTG
1379309 CAACGCGAAAGTCAAATTTG
1 CAACGCGAAAGTCAAATTTG
*
1379329 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTTG
1379349 CAACGCGAAA
1 CAACGCGAAA
1379359 TAAGCGTTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTTG
Found at i:1379390 original size:20 final size:20
Alignment explanation
Indices: 1379362--1379403 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1379352 CGCGAAATAA
*
1379362 GCGTTGCGAATTTGACTATC
1 GCGTAGCGAATTTGACTATC
1379382 GCGTAGCGAATTTGACTATC
1 GCGTAGCGAATTTGACTATC
1379402 GC
1 GC
1379404 AACGCTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (20 bp):
GCGTAGCGAATTTGACTATC
Found at i:1379522 original size:25 final size:25
Alignment explanation
Indices: 1379494--1379543 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1379484 AAATCAATTA
* *
1379494 AACATTATTGTGGGTACATTATTTG
1 AACATTATTATGGCTACATTATTTG
*
1379519 AACATTGTTATGGCTACATTATTTG
1 AACATTATTATGGCTACATTATTTG
1379544 GAAAAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (25 bp):
AACATTATTATGGCTACATTATTTG
Found at i:1381715 original size:2 final size:2
Alignment explanation
Indices: 1381704--1381743 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1381694 TATGTTATTT
1381704 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1381744 TAGTGAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1382223 original size:21 final size:21
Alignment explanation
Indices: 1382158--1382234 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
1382148 AAACGATGAC
* *
1382158 AGGGGCCTCTTCAACGGTAGG
1 AGGGGCCTCTTGAACGATAGG
* * *
1382179 AAGGGCTTCTTCG-ATGAT-GAG
1 AGGGGCCTCTT-GAACGATAG-G
1382200 AGGGGCCTCTTGAACGATAGG
1 AGGGGCCTCTTGAACGATAGG
*
1382221 AGGCGCCTCTTGAA
1 AGGGGCCTCTTGAA
1382235 TGATGATAGG
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 2 0.05
21 40 0.93
22 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATAGG
Found at i:1382238 original size:42 final size:42
Alignment explanation
Indices: 1382152--1382240 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
1382142 CCACTTAAAC
* *
1382152 GATGACAGGGGCCTCTTCAACGGTAGGAAGGGCTTCTTCGAT
1 GATGACAGGGGCCTCTTCAACGATAGGAAGGGCCTCTTCGAT
* *
1382194 GATGAGAGGGGCCTCTTGAACGATAGG-AGGCGCCTCTT-GAAT
1 GATGACAGGGGCCTCTTCAACGATAGGAAGG-GCCTCTTCG-AT
1382236 GATGA
1 GATGA
1382241 TAGGTGCATC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.10
42 37 0.90
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTCAACGATAGGAAGGGCCTCTTCGAT
Found at i:1384873 original size:20 final size:20
Alignment explanation
Indices: 1384848--1384952 Score: 117
Period size: 20 Copynumber: 5.2 Consensus size: 20
1384838 GCGTAAAAAT
1384848 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1384868 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1384888 ATTTGACTTAT-GTGTTGCG-
1 ATTTGACTT-TCGCGTTGCGA
*
1384907 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
* *
1384928 ATTTGACTATCGCGTTGCAA
1 ATTTGACTTTCGCGTTGCGA
1384948 ATTTG
1 ATTTG
1384953 GAAAATCGCA
Statistics
Matches: 71, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.03
19 5 0.07
20 57 0.80
21 5 0.07
22 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:1384893 original size:40 final size:42
Alignment explanation
Indices: 1384848--1385033 Score: 131
Period size: 40 Copynumber: 4.6 Consensus size: 42
1384838 GCGTAAAAAT
*
1384848 ATTTGACTTTCGCGTTGCGAATTTGAC-TA-TCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGAATTTGACAAATTCGCGTTGCGA
*
1384888 ATTTGACTTAT-GTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTT-TCGCGTTGCGAATTTGACAAATTCGCGTTGCGA
* * ***
1384928 ATTTGACTATCGCGTTGCAAATTTGGA-AAA-TCGCAACGCGA
1 ATTTGACTTTCGCGTTGCGAATTT-GACAAATTCGCGTTGCGA
*** ** * *
1384969 ATTTGGAAAATCGCAATGCGAAATTG--TAATTCGCGTTGCGA
1 ATTT-GACTTTCGCGTTGCGAATTTGACAAATTCGCGTTGCGA
**
1385010 ATTTGA-GATCGCGTTGCGAATTTG
1 ATTTGACTTTCGCGTTGCGAATTTG
1385034 TTGGTCATTT
Statistics
Matches: 115, Mismatches: 22, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
38 2 0.02
39 20 0.17
40 45 0.39
41 30 0.26
42 17 0.15
43 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (42 bp):
ATTTGACTTTCGCGTTGCGAATTTGACAAATTCGCGTTGCGA
Found at i:1384971 original size:21 final size:21
Alignment explanation
Indices: 1384947--1384990 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1384937 TCGCGTTGCA
1384947 AATTTGGAAAATCGCAACGCG
1 AATTTGGAAAATCGCAACGCG
*
1384968 AATTTGGAAAATCGCAATGCG
1 AATTTGGAAAATCGCAACGCG
1384989 AA
1 AA
1384991 ATTGTAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (21 bp):
AATTTGGAAAATCGCAACGCG
Found at i:1385008 original size:20 final size:20
Alignment explanation
Indices: 1384985--1385034 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
1384975 AAAATCGCAA
*
1384985 TGCGAAATTGTA-ATTCGCGT
1 TGCGAATTTGTAGA-TCGCGT
1385005 TGCGAATTTG-AGATCGCGT
1 TGCGAATTTGTAGATCGCGT
1385024 TGCGAATTTGT
1 TGCGAATTTGT
1385035 TGGTCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (20 bp):
TGCGAATTTGTAGATCGCGT
Found at i:1406953 original size:2 final size:2
Alignment explanation
Indices: 1406946--1406982 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1406936 ATTAACAATA
1406946 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1406983 AACTTGCAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1417101 original size:23 final size:23
Alignment explanation
Indices: 1417075--1417122 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1417065 ATAAAGTACA
* *
1417075 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAAGTAGCGCTTAT
**
1417098 ATAATGTAATAAGTAGCGCTTAT
1 ATAACATAATAAGTAGCGCTTAT
1417121 AT
1 AT
1417123 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAAGTAGCGCTTAT
Found at i:1417628 original size:23 final size:23
Alignment explanation
Indices: 1417598--1417670 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1417588 ATACTTTACA
*
1417598 ATATAAACATTACCTATTACATT
1 ATATAAACACTACCTATTACATT
*
1417621 ATATAAACGCTACCTATTACATT
1 ATATAAACACTACCTATTACATT
*** *
1417644 ATATAAGTGCTACCTATTACATC
1 ATATAAACACTACCTATTACATT
1417667 ATAT
1 ATAT
1417671 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (23 bp):
ATATAAACACTACCTATTACATT
Found at i:1419337 original size:33 final size:33
Alignment explanation
Indices: 1419300--1419365 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1419290 CATCTTAATA
* *
1419300 TCACCTCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1419333 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1419366 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1419424 original size:21 final size:21
Alignment explanation
Indices: 1419411--1419463 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1419401 CTCAAATGTA
1419411 TCTTCGACTCTCTCAAGTTTC
1 TCTTCGACTCTCTCAAGTTTC
*
1419432 TCTTCGACTCTATCAAGTTTC
1 TCTTCGACTCTCTCAAGTTTC
1419453 TCTTCGACTCT
1 TCTTCGACTCT
1419464 TGATTGTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.32, G:0.09, T:0.43
Consensus pattern (21 bp):
TCTTCGACTCTCTCAAGTTTC
Found at i:1421709 original size:20 final size:20
Alignment explanation
Indices: 1421677--1421733 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1421667 ATCCGGTATC
*
1421677 ATTT-TACCGGTTTTATCAT
1 ATTTATACCTGTTTTATCAT
1421696 -TTTGATACCTGTTTTATCAT
1 ATTT-ATACCTGTTTTATCAT
* *
1421716 ATTTTTACCTGTTATATC
1 ATTTATACCTGTTTTATC
1421734 GTTGTGGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (20 bp):
ATTTATACCTGTTTTATCAT
Found at i:1422101 original size:182 final size:180
Alignment explanation
Indices: 1421645--1422116 Score: 676
Period size: 180 Copynumber: 2.6 Consensus size: 180
1421635 CGTACTTACG
* * * * ** *
1421645 AAAGTATCGACACTTTCAATAAATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCTGTTT
1 AAAGTACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1421710 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTAAAGTATCGACACATTATA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
*
1421775 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* * * * *
1421825 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACGGGTTTTATCATTTTGATACCGATTT
1 AAAGTACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1421890 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGTCACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTT-AAAGTATCGACACATTAT
** *
1421955 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* **
1422007 AAAGTACCGACACTTTAAATGTATCCGGTAGA-GCTTTACCGGTTTTATCATTTCAATACCGGTT
1 AAAGTACCGACACTTTAAATATATCCGGTA-ACGCTTTACCGGTTTTATCATTTTGATACCGGTT
* * *
1422071 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1422117 AATTTGGATC
Statistics
Matches: 264, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
180 103 0.39
181 62 0.23
182 98 0.37
183 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1427590 original size:24 final size:24
Alignment explanation
Indices: 1427563--1427662 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
1427553 GATATCAAAA
*
1427563 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
1427587 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
1427611 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
1427635 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
1427659 ATCA
1 ATCA
1427663 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:1427662 original size:48 final size:48
Alignment explanation
Indices: 1427556--1427664 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
1427546 AAACGGAGAT
* * * * *
1427556 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1427604 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1427652 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1427665 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1430210 original size:13 final size:13
Alignment explanation
Indices: 1430192--1430219 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1430182 CAACGGCCAA
1430192 CGAGTCAACGGGT
1 CGAGTCAACGGGT
1430205 CGAGTCAACGGGT
1 CGAGTCAACGGGT
1430218 CG
1 CG
1430220 GGTCGGGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.25, G:0.39, T:0.14
Consensus pattern (13 bp):
CGAGTCAACGGGT
Found at i:1431097 original size:39 final size:38
Alignment explanation
Indices: 1431050--1431123 Score: 130
Period size: 39 Copynumber: 1.9 Consensus size: 38
1431040 TACCTAATAT
*
1431050 TTAATTTTTATTTCATTTTAACACCTATTATTAAAAAC
1 TTAATTTTTATTTCATTTTAACACCCATTATTAAAAAC
1431088 TTAACTTTTTATTTCATTTTAACACCCATTATTAAA
1 TTAA-TTTTTATTTCATTTTAACACCCATTATTAAA
1431124 CACTAACACG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (38 bp):
TTAATTTTTATTTCATTTTAACACCCATTATTAAAAAC
Found at i:1431396 original size:24 final size:24
Alignment explanation
Indices: 1431369--1431417 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1431359 GTATGCCTCA
*
1431369 AGTATGCATATAGT-GTACAAATAC
1 AGTATACATATA-TCGTACAAATAC
*
1431393 AGTATACATATATCGTACGAATAC
1 AGTATACATATATCGTACAAATAC
1431417 A
1 A
1431418 CAAATTGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (24 bp):
AGTATACATATATCGTACAAATAC
Found at i:1441010 original size:93 final size:93
Alignment explanation
Indices: 1440900--1441093 Score: 327
Period size: 93 Copynumber: 2.1 Consensus size: 93
1440890 TTAAAAAAAA
* * *
1440900 TAAGTTTTAATGATCAAAATAGGAGTGA-AAAGATAGTTGAGTGATGAATGGTGTAATTTACTCA
1 TAAGTTTTAATGATCAAAATAAGAGTGAGAAA-ATAATTGAGTGATGAATGGTGTAATTTACCCA
1440964 TAAAAAGGTATCATGTGCAAATCACCCGT
65 TAAAAAGGTATCATGTGCAAATCACCCGT
*
1440993 TAAGTTTTAGTGATCAAAATAAGAGTGAGAAAATAATTGAGTGATGAATGGTGTAATTTACCCAT
1 TAAGTTTTAATGATCAAAATAAGAGTGAGAAAATAATTGAGTGATGAATGGTGTAATTTACCCAT
*
1441058 AAAAATGTATCATGTGCAAATCACCCGT
66 AAAAAGGTATCATGTGCAAATCACCCGT
1441086 TAAGTTTT
1 TAAGTTTT
1441094 TAACGACGAG
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
93 92 0.97
94 3 0.03
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (93 bp):
TAAGTTTTAATGATCAAAATAAGAGTGAGAAAATAATTGAGTGATGAATGGTGTAATTTACCCAT
AAAAAGGTATCATGTGCAAATCACCCGT
Found at i:1441765 original size:22 final size:22
Alignment explanation
Indices: 1441734--1441826 Score: 168
Period size: 22 Copynumber: 4.2 Consensus size: 22
1441724 CGACGGTGCA
1441734 AGCAGTGACCGGCGAGATTAGG
1 AGCAGTGACCGGCGAGATTAGG
*
1441756 AGCAGAGACCGGCGAGATTAGG
1 AGCAGTGACCGGCGAGATTAGG
*
1441778 AGCAGCGACCGGCGAGATTAGG
1 AGCAGTGACCGGCGAGATTAGG
1441800 AGCAGTGACCGGCGAGATTAGG
1 AGCAGTGACCGGCGAGATTAGG
1441822 AGCAG
1 AGCAG
1441827 CGACAGACCT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 68 1.00
ACGTcount: A:0.29, C:0.19, G:0.41, T:0.11
Consensus pattern (22 bp):
AGCAGTGACCGGCGAGATTAGG
Found at i:1443954 original size:24 final size:24
Alignment explanation
Indices: 1443925--1443980 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
1443915 TGGAAGCCTT
1443925 TGTTGATGCTGATTGGACGAGTAA
1 TGTTGATGCTGATTGGACGAGTAA
1443949 TGTTGATGCTGATTGGACGAGTAA
1 TGTTGATGCTGATTGGACGAGTAA
1443973 TGTTGATG
1 TGTTGATG
1443981 ATCGACGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.07, G:0.34, T:0.36
Consensus pattern (24 bp):
TGTTGATGCTGATTGGACGAGTAA
Found at i:1446681 original size:58 final size:60
Alignment explanation
Indices: 1446616--1446727 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1446606 TGATCTTTCG
* * ** *
1446616 ATTATAAAATATTATTTT-TTTA-TTTTTTTATTATTAAAAATTATAAAATAATTATTTA
1 ATTATAAAATATTATTTTATTAAGTCTTTCAAATATTAAAAATTATAAAATAATTATTTA
* *
1446674 ATTATAAAATGTTATTTTATTAAGTCTTTCAAATATTAAAAGTTATAAAATAAT
1 ATTATAAAATATTATTTTATTAAGTCTTTCAAATATTAAAAATTATAAAATAAT
1446728 CATCTAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 17 0.38
59 3 0.07
60 25 0.56
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (60 bp):
ATTATAAAATATTATTTTATTAAGTCTTTCAAATATTAAAAATTATAAAATAATTATTTA
Found at i:1448928 original size:2 final size:2
Alignment explanation
Indices: 1448923--1448956 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1448913 AAAAAGGGGA
1448923 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
1448957 GAACAACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1456558 original size:21 final size:21
Alignment explanation
Indices: 1456532--1456594 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1456522 ACCATTAAGG
*
1456532 TGTTGATGTGGTAATTTATGA
1 TGTTGATGTGGTAATTTACGA
** *
1456553 TGTTGATGTGGTGGTCTACGA
1 TGTTGATGTGGTAATTTACGA
*
1456574 TGTTGATGTGATAATTTACGA
1 TGTTGATGTGGTAATTTACGA
1456595 CGTGATGGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.05, G:0.30, T:0.43
Consensus pattern (21 bp):
TGTTGATGTGGTAATTTACGA
Found at i:1464037 original size:14 final size:14
Alignment explanation
Indices: 1464018--1464047 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1464008 TATAATTATC
*
1464018 AATAATGTATTTTT
1 AATAATGTAATTTT
1464032 AATAATGTAATTTT
1 AATAATGTAATTTT
1464046 AA
1 AA
1464048 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:1464386 original size:52 final size:52
Alignment explanation
Indices: 1464321--1464477 Score: 269
Period size: 52 Copynumber: 3.0 Consensus size: 52
1464311 AAATATATAT
* *
1464321 TATTATTATTATTAGTCATTTCATTACTAAAGAAACCATCACTTCAAAAAAA
1 TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTCAAAAAAA
1464373 TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTCAAAAAAAA
1 TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTC-AAAAAAA
* *
1464426 TATTATTATTATTAGTCATTTTATCATTAAAGAAACAATCACTTCAAAAAAA
1 TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTCAAAAAAA
1464478 ATATAAATTT
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
52 50 0.50
53 50 0.50
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (52 bp):
TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTCAAAAAAA
Found at i:1464446 original size:53 final size:53
Alignment explanation
Indices: 1464321--1464481 Score: 279
Period size: 53 Copynumber: 3.1 Consensus size: 53
1464311 AAATATATAT
* *
1464321 TATTATTATTATTAGTCATTTCATTACTAAAGAAACCATCACTTC-AAAAAAA
1 TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTCAAAAAAAA
1464373 TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTCAAAAAAAA
1 TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTCAAAAAAAA
* *
1464426 TATTATTATTATTAGTCATTTTATCATTAAAGAAACAATCACTTCAAAAAAAA
1 TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTCAAAAAAAA
1464479 TAT
1 TAT
1464482 AAATTTATTT
Statistics
Matches: 104, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 43 0.41
53 61 0.59
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.37
Consensus pattern (53 bp):
TATTATTATTATTAGTCATTTCATCACTAAAGAAACAATCACTTCAAAAAAAA
Found at i:1465587 original size:51 final size:51
Alignment explanation
Indices: 1465531--1465635 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 51
1465521 AAATAAATTT
*
1465531 ATATTTTTTTTTGAAGTGATTGTTTCTTTAATGATAAAATGACTAATAATA
1 ATATTTTTTTTTGAAGTGATTGTTTCTTGAATGATAAAATGACTAATAATA
* * *
1465582 ATATTTTTTTTTGAAGTGATTGTTTCTTGAGTGATGAAATGGCTAATAATA
1 ATATTTTTTTTTGAAGTGATTGTTTCTTGAATGATAAAATGACTAATAATA
1465633 ATA
1 ATA
1465636 ATAATATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (51 bp):
ATATTTTTTTTTGAAGTGATTGTTTCTTGAATGATAAAATGACTAATAATA
Found at i:1467211 original size:36 final size:37
Alignment explanation
Indices: 1467164--1467239 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 37
1467154 ATGGCGAAAA
1467164 CAAACACATAGGACCCATAGCATTCTTCCCTCGAC-G
1 CAAACACATAGGACCCATAGCATTCTTCCCTCGACAG
*
1467200 CAAACACATAGGACCCATAGCATTCTTCCCTGGACAG
1 CAAACACATAGGACCCATAGCATTCTTCCCTCGACAG
1467237 CAA
1 CAA
1467240 CCGCGCGTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 34 0.89
37 4 0.11
ACGTcount: A:0.33, C:0.34, G:0.14, T:0.18
Consensus pattern (37 bp):
CAAACACATAGGACCCATAGCATTCTTCCCTCGACAG
Found at i:1470575 original size:16 final size:16
Alignment explanation
Indices: 1470525--1470568 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
1470515 GGCCATTAAG
1470525 AGATTTTGAGATAGTA
1 AGATTTTGAGATAGTA
1470541 AGATTTTGAGATAGTA
1 AGATTTTGAGATAGTA
1470557 AGATTTTGAGAT
1 AGATTTTGAGAT
1470569 TTGAAGAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (16 bp):
AGATTTTGAGATAGTA
Found at i:1481024 original size:180 final size:181
Alignment explanation
Indices: 1480716--1481066 Score: 508
Period size: 180 Copynumber: 1.9 Consensus size: 181
1480706 GCCGGAGATA
* *
1480716 CGGAAACGGTGGATTCAACCCTGGTTATCACGGACACGGGAGATTTAACAAGAAGCCCATTCAGA
1 CGGAAACGGCGGATTCAACCCTAGTTATCACGGACACGGGAGATTTAACAAGAAGCCCATTCAGA
* *
1480781 AGAAGCGGGTCGGGTCGGATCAAGCAGTTTCGAAAAGATCTAGCTCCAACGACAAGCTGAAGGTG
66 AGAAGCGGATCGGGTCGGATCAAGCAGTCTCGAAAAGATCTAGCTCCAACGACAAGCTGAAGGTG
*
1480846 GTGAGG-AACAATGTTGGGATAGAGAAGGTTACGATTTTTAGGCGAGGCTG
131 GTGAGGAAACAATGTTGGAATAGAGAAGGTTACGATTTTTAGGCGAGGCTG
* * * * *
1480896 CGGAAACGGCGGATTTAGCCCTAGTTATCATGGGA-ACGGTAGATTTAACAAGAAGCCCGTTCAG
1 CGGAAACGGCGGATTCAACCCTAGTTATCA-CGGACACGGGAGATTTAACAAGAAGCCCATTCAG
* * * * * * *
1480960 ATGAAGCGGATCGGTTCGGATCATGCCGTCTCGAAGAGATCTAGCTCCAACGATAAGTTGAAGGT
65 AAGAAGCGGATCGGGTCGGATCAAGCAGTCTCGAAAAGATCTAGCTCCAACGACAAGCTGAAGGT
1481025 GGTGAGGAACAACAATGTTGGAATAGAGAAGGTTACGATTTT
130 GGTGAGG-A-AACAATGTTGGAATAGAGAAGGTTACGATTTT
1481067 GAGGGAAGAC
Statistics
Matches: 150, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
180 116 0.77
181 3 0.02
183 31 0.21
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (181 bp):
CGGAAACGGCGGATTCAACCCTAGTTATCACGGACACGGGAGATTTAACAAGAAGCCCATTCAGA
AGAAGCGGATCGGGTCGGATCAAGCAGTCTCGAAAAGATCTAGCTCCAACGACAAGCTGAAGGTG
GTGAGGAAACAATGTTGGAATAGAGAAGGTTACGATTTTTAGGCGAGGCTG
Found at i:1489253 original size:5 final size:5
Alignment explanation
Indices: 1489243--1489267 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1489233 CCCCCCCTAG
1489243 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
1489268 ACTCGTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1489687 original size:31 final size:30
Alignment explanation
Indices: 1489652--1489709 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1489642 GGTAATAAAA
*
1489652 TGAAACAAAAACAAAATTTTAGATATTATTT
1 TGAAA-AAAAACAAAAGTTTAGATATTATTT
** *
1489683 TGAAAAAAATTATAAGTTTAGATATTA
1 TGAAAAAAAACAAAAGTTTAGATATTA
1489710 AAACGGATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (30 bp):
TGAAAAAAAACAAAAGTTTAGATATTATTT
Found at i:1490931 original size:2 final size:2
Alignment explanation
Indices: 1490924--1490960 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1490914 CTTAAAAAGA
1490924 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1490961 CGGCAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1491359 original size:63 final size:62
Alignment explanation
Indices: 1491278--1491405 Score: 193
Period size: 62 Copynumber: 2.0 Consensus size: 62
1491268 TTTCGATTCG
** * * *
1491278 TTATATTAAAGTCGATCAATAGTTTTATATATAAATAGATATAGTAACCATACGATCATAATT
1 TTATATTAAACCCAATCAATAATTTTATATAT-AATAGATATAGTAACCATACAATCATAATT
*
1491341 TTATATTAAACCCAATCAATAATTTTATATATAATAGATATAGTAACCCTACAATCATAATT
1 TTATATTAAACCCAATCAATAATTTTATATATAATAGATATAGTAACCATACAATCATAATT
1491403 TTA
1 TTA
1491406 ATTGAAATGG
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 31 0.53
63 28 0.47
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (62 bp):
TTATATTAAACCCAATCAATAATTTTATATATAATAGATATAGTAACCATACAATCATAATT
Found at i:1491611 original size:60 final size:60
Alignment explanation
Indices: 1491427--1491611 Score: 194
Period size: 60 Copynumber: 3.1 Consensus size: 60
1491417 TTGCATATTT
* * * * * * *
1491427 GGATGAAATTGAAAGATTTAAAAGTTTAGGGACCAATTTAGAATGTGATTCATAGTTTAG
1 GGATAAAATTTAAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAG
* * * * * *
1491487 GAATAAAATTTGAATGTTCAAAAGTTTAAGGATTAATTTAGAATTAGAGTCATAGTTT-G
1 GGATAAAATTTAAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAG
* * *
1491546 AGGATAAAA-TTAAACTATTTAAAAGTTTAAGGACTAATTTAAAATGAAAGTCATAATTTAG
1 -GGATAAAATTTAAA-TATTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAG
1491607 GGATA
1 GGATA
1491612 TATGATACAA
Statistics
Matches: 100, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
59 5 0.05
60 94 0.94
61 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (60 bp):
GGATAAAATTTAAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTAG
Found at i:1492892 original size:60 final size:59
Alignment explanation
Indices: 1492794--1492952 Score: 167
Period size: 60 Copynumber: 2.7 Consensus size: 59
1492784 TTAAAAGATG
* * * *
1492794 TAAAAGTTTAGGGA-TCAATTTAGAATGAGATTCATAGTTTAAGGATAAAACTCGAATGT
1 TAAAAGTTTAAGGACT-AATTTAGAATTAGATTCATAGTTTAAGAATAAAACTCGAATAT
* * ** * * *
1492853 TCAAAAGTTTAAGGACTAATTTAGAATTAGATTCGTAGTTTGAGAATTGAATTGGACTAT
1 T-AAAAGTTTAAGGACTAATTTAGAATTAGATTCATAGTTTAAGAATAAAACTCGAATAT
* * *
1492913 TAAAAGTTTAAGGACTAATTTAAAATTAAAGTCATAGTTT
1 TAAAAGTTTAAGGACTAATTTAGAATTAGATTCATAGTTT
1492953 GAGGGTGAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
59 36 0.43
60 46 0.55
61 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (59 bp):
TAAAAGTTTAAGGACTAATTTAGAATTAGATTCATAGTTTAAGAATAAAACTCGAATAT
Found at i:1492965 original size:59 final size:59
Alignment explanation
Indices: 1492855--1492972 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 59
1492845 TCGAATGTTC
* * * * *
1492855 AAAAGTTTAAGGACTAATTTAGAATTAGATTCGTAGTTTGAGAATTGAATTGGACTATT
1 AAAAGTTTAAGGACTAATTTAAAATTAAAGTCATAGTTTGAGAAGTGAATTGGACTATT
* *
1492914 AAAAGTTTAAGGACTAATTTAAAATTAAAGTCATAGTTTGAG-GGTGAAATTGTACTATT
1 AAAAGTTTAAGGACTAATTTAAAATTAAAGTCATAGTTTGAGAAGTG-AATTGGACTATT
1492973 TTGTTATTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 2 0.04
59 49 0.96
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.36
Consensus pattern (59 bp):
AAAAGTTTAAGGACTAATTTAAAATTAAAGTCATAGTTTGAGAAGTGAATTGGACTATT
Found at i:1494316 original size:13 final size:13
Alignment explanation
Indices: 1494298--1494323 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1494288 CTAACTTAAA
1494298 AAATAAATTCAAT
1 AAATAAATTCAAT
1494311 AAATAAATTCAAT
1 AAATAAATTCAAT
1494324 GTGGCACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATAAATTCAAT
Found at i:1500514 original size:62 final size:62
Alignment explanation
Indices: 1500444--1500569 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
1500434 TATTATATAT
1500444 TATATTTGATTTCTAAACTATCATCATTCTAAATTAATCTCTAAACTATAACCTCAGACAAG
1 TATATTTGATTTCTAAACTATCATCATTCTAAATTAATCTCTAAACTATAACCTCAGACAAG
**
1500506 TATATTTGATTTCTAAACTATCATCATTCTAAATTAATCTCTAAACTATAACCTTTGACAAG
1 TATATTTGATTTCTAAACTATCATCATTCTAAATTAATCTCTAAACTATAACCTCAGACAAG
1500568 TA
1 TA
1500570 GGGATGGATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (62 bp):
TATATTTGATTTCTAAACTATCATCATTCTAAATTAATCTCTAAACTATAACCTCAGACAAG
Found at i:1502123 original size:18 final size:19
Alignment explanation
Indices: 1502100--1502137 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1502090 AGGTTCACGC
1502100 CCTTCGTTTCC-GGTTCAT
1 CCTTCGTTTCCGGGTTCAT
1502118 CCTTCGTTTCCGGGTTCAT
1 CCTTCGTTTCCGGGTTCAT
1502137 C
1 C
1502138 TCACGGCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.05, C:0.34, G:0.18, T:0.42
Consensus pattern (19 bp):
CCTTCGTTTCCGGGTTCAT
Found at i:1502874 original size:20 final size:21
Alignment explanation
Indices: 1502849--1502890 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
1502839 TGAGCCGTGA
1502849 GATGAACCCGG-AAACGAAGG
1 GATGAACCCGGAAAACGAAGG
1502869 GATGAACCCGGAAAACGAAGG
1 GATGAACCCGGAAAACGAAGG
1502890 G
1 G
1502891 CGTGAACCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.19, G:0.36, T:0.05
Consensus pattern (21 bp):
GATGAACCCGGAAAACGAAGG
Found at i:1504540 original size:28 final size:28
Alignment explanation
Indices: 1504445--1504540 Score: 104
Period size: 28 Copynumber: 3.4 Consensus size: 28
1504435 GTCAAAGGTT
1504445 ATAGTTTAGAGATTAATTTAGAATGATG
1 ATAGTTTAGAGATTAATTTAGAATGATG
* * ** *
1504473 ATAGTTTAGAAATCAAATACTT-GTCTGAGG
1 ATAGTTTAGAGAT-TAAT--TTAGAATGATG
*
1504503 TTAGTTTAGAGATTAATTTAGAATGATG
1 ATAGTTTAGAGATTAATTTAGAATGATG
1504531 ATAGTTTAGA
1 ATAGTTTAGA
1504541 ATCAAATATA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
27 2 0.04
28 26 0.50
29 6 0.12
30 16 0.31
31 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.39
Consensus pattern (28 bp):
ATAGTTTAGAGATTAATTTAGAATGATG
Done.