Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004593.1 Hibiscus syriacus cultivar Beakdansim tig00010263_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: 1592963
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1415976 original size:21 final size:21
Alignment explanation
Indices: 1415952--1415994 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1415942 CCCAGAATAG
*
1415952 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
*
1415973 AGGGAATCGATACCTCTTCAT
1 AGGGAATCGATACCCCTTCAT
1415994 A
1 A
1415995 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1416058 original size:21 final size:21
Alignment explanation
Indices: 1416032--1416072 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1416022 GTTGAACAGG
1416032 GGGGGAATCGGTACCCCCTGT
1 GGGGGAATCGGTACCCCCTGT
1416053 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
1416073 GACATTCTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.15, C:0.29, G:0.39, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGT
Found at i:1416124 original size:21 final size:21
Alignment explanation
Indices: 1416099--1416177 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
1416089 GCTTTAGACA
*
1416099 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
*
1416120 GGGGGTATCTGTA--CCC---
1 GGGGGAATCTGTACCCCCTGG
*
1416136 -GGGGTATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
1416156 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
1416177 G
1 G
1416178 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 31 0.63
ACGTcount: A:0.13, C:0.28, G:0.39, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:1416139 original size:15 final size:15
Alignment explanation
Indices: 1416121--1416150 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1416111 ACCCCCTGGG
1416121 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1416136 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1416151 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:1416156 original size:36 final size:36
Alignment explanation
Indices: 1416100--1416171 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1416090 CTTTAGACAG
*
1416100 GGGGAATCGGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
* *
1416136 GGGGTATCTGTACCCCCTGGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
1416172 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.21
Consensus pattern (36 bp):
GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
Found at i:1419177 original size:34 final size:32
Alignment explanation
Indices: 1419124--1419189 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 32
1419114 ACCTTACAAC
*
1419124 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1419156 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1419190 CCCCCTTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.23
33 5 0.17
34 18 0.60
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.32
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1419433 original size:20 final size:22
Alignment explanation
Indices: 1419408--1419447 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1419398 AGTCGTATAT
1419408 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1419428 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1419448 TATGCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1419499 original size:21 final size:21
Alignment explanation
Indices: 1419475--1419517 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1419465 CCCAGAATAG
*
1419475 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
*
1419496 AGGGAATCGATACCTCTTCAT
1 AGGGAATCGATACCCCTTCAT
1419517 A
1 A
1419518 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:1419579 original size:21 final size:21
Alignment explanation
Indices: 1419553--1419595 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1419543 CTGTTGAACA
1419553 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
1419574 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
1419595 G
1 G
1419596 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:1419665 original size:15 final size:15
Alignment explanation
Indices: 1419645--1419674 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1419635 CCCCTGGGGG
1419645 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1419660 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
1419675 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:1419696 original size:20 final size:21
Alignment explanation
Indices: 1419621--1419701 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
1419611 GCTTTAGACA
*
1419621 GGGGGAATCGGTACCCCCTGGGG
1 GGGGGAATCTGTACCCCCT--GG
*
1419644 GGGGGTATCTGTA--CCC---
1 GGGGGAATCTGTACCCCCTGG
*
1419660 -GGGGTATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
1419680 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
1419701 G
1 G
1419702 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
21 23 0.47
23 11 0.22
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:1420059 original size:21 final size:21
Alignment explanation
Indices: 1420033--1420309 Score: 96
Period size: 21 Copynumber: 12.6 Consensus size: 21
1420023 GATTTACATA
1420033 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1420054 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* **
1420075 TTCGCGTTGCGATTTTCCAAATTCG
1 TTCGCATTGCGATAGTCC-AA---G
** * * * *
1420100 ACTATCGCAACGCGA-ACTTCGAC
1 --T-TCGCATTGCGATAGTCCAAG
* *
1420123 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
1420144 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
1420165 TTTGCATTGCGATAATCGAAG
1 TTCGCATTGCGATAGTCCAAG
* ** *
1420186 TTCGCGTTGCGATTTTCCAAA
1 TTCGCATTGCGATAGTCCAAG
* * * * * *
1420207 TTCGACTATCGCAACGCAAACTTCGAC
1 TTCG-C-ATTG---CG-ATAGTCCAAG
* * *
1420234 TATCGCATTGTGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
1420255 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1420276 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
1420297 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
1420310 TTTCCAAATT
Statistics
Matches: 187, Mismatches: 48, Indels: 42
0.68 0.17 0.15
Matches are distributed among these distances:
20 25 0.13
21 126 0.67
22 6 0.03
23 3 0.02
25 1 0.01
26 6 0.03
27 9 0.05
28 11 0.06
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1420187 original size:111 final size:111
Alignment explanation
Indices: 1419993--1420399 Score: 733
Period size: 111 Copynumber: 3.7 Consensus size: 111
1419983 GTTTCCAGAT
*
1419993 TCGCAACGCGAACATCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1420058 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
*
1420104 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTTG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
*
1420169 CATTGCGATAATCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
* *
1420215 TCGCAACGCAAACTTCGACTATCGCATTGTGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
*
1420280 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTAGACTA
66 CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
*
1420326 TCGCAACGTGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
**
1420391 TGTTGCGAT
66 CATTGCGAT
1420400 TTTCCAAATT
Statistics
Matches: 283, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 283 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (111 bp):
TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
CATTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
Found at i:1420307 original size:42 final size:42
Alignment explanation
Indices: 1420255--1420464 Score: 153
Period size: 42 Copynumber: 4.9 Consensus size: 42
1420245 GATTTACATA
* * *
1420255 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATTCGCATTGCGATAGTCGAAG
* * * * * *
1420297 TTCGCGTTGCGATTTTCCAAATTAGACTATCGCAACGTGAACTTCG-AC
1 TTCGCGTTGCGATATTCCAAATTCG-C-ATTGCGA--T--A-GTCGAAG
* * * *
1420345 TATCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCCAAG
1 T-TCGCGTTGCGATATTCCAAATTCGCATTGCGATAGTCGAAG
* *
1420387 TTCGTGTTGCGATTTTCCAAATTCG--TTGCGATAGTCGAAG
1 TTCGCGTTGCGATATTCCAAATTCGCATTGCGATAGTCGAAG
1420427 TTCGCGTTGCGATTTATTCCAAATTCG--TTGCGATAGTC
1 TTCGCGTTGCGA--TATTCCAAATTCGCATTGCGATAGTC
1420465 CAAAATCGCA
Statistics
Matches: 131, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
40 25 0.19
41 12 0.09
42 55 0.42
43 1 0.01
44 6 0.05
46 6 0.05
47 1 0.01
48 11 0.08
49 14 0.11
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (42 bp):
TTCGCGTTGCGATATTCCAAATTCGCATTGCGATAGTCGAAG
Found at i:1420396 original size:21 final size:19
Alignment explanation
Indices: 1420372--1420468 Score: 86
Period size: 21 Copynumber: 4.8 Consensus size: 19
1420362 CATATTCGCA
*
1420372 TTGCGATAGTCCAAGTTCGTG
1 TTGCGATAGTCCAAATTC--G
**
1420393 TTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAATTCG
* *
1420412 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
*
1420433 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAATTCG
1420454 TTGCGATAGTCCAAA
1 TTGCGATAGTCCAAA
1420469 ATCGCAACGA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
19 22 0.36
21 31 0.51
23 8 0.13
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:1420420 original size:40 final size:42
Alignment explanation
Indices: 1420372--1420467 Score: 160
Period size: 40 Copynumber: 2.3 Consensus size: 42
1420362 CATATTCGCA
*
1420372 TTGCGATAGTCCAAGTTCGTGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1420412 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1420454 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1420468 AATCGCAACG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 25 0.49
41 2 0.04
42 24 0.47
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1422532 original size:2 final size:2
Alignment explanation
Indices: 1422525--1422574 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1422515 CAATATCAAA
1422525 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
1422567 AT AT AT AT
1 AT AT AT AT
1422575 TGAACAAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1425311 original size:27 final size:27
Alignment explanation
Indices: 1425273--1425325 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1425263 AACCCAATCA
*
1425273 AGAAATTGTTGGAAGCTCTCCTAATTT
1 AGAAATTGTTGGAAGCTCCCCTAATTT
*
1425300 AGAATTTGTTGGAAGCTCCCCTAATT
1 AGAAATTGTTGGAAGCTCCCCTAATT
1425326 CTTCCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (27 bp):
AGAAATTGTTGGAAGCTCCCCTAATTT
Found at i:1427748 original size:31 final size:29
Alignment explanation
Indices: 1427710--1427833 Score: 122
Period size: 31 Copynumber: 4.0 Consensus size: 29
1427700 AAATATAGAG
*
1427710 GTTAAATTATTATTTTATCTAAAGTTTAAGA
1 GTTAAATTAATATTTTATCTAAA-TTTAA-A
*
1427741 GTTAAATTAATGTTTTATCTGAAATTTAAAA
1 GTTAAATTAATATTTTATCT-AAATTT-AAA
* * *
1427772 ATTAAATTGATTTTTTATCTAATATTTAAA
1 GTTAAATTAATATTTTATCTAA-ATTTAAA
* *
1427802 GGTTAGATTAATATTTTATCCAAAATTTAAA
1 -GTTAAATTAATATTTTAT-CTAAATTTAAA
1427833 G
1 G
1427834 AATAAATTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
30 6 0.08
31 64 0.82
32 8 0.10
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (29 bp):
GTTAAATTAATATTTTATCTAAATTTAAA
Found at i:1427777 original size:62 final size:63
Alignment explanation
Indices: 1427711--1427841 Score: 164
Period size: 62 Copynumber: 2.1 Consensus size: 63
1427701 AATATAGAGG
* **
1427711 TTAAATT-ATTATTTTATCTAA-AGTTT-AAGAGTTAAATTAATGTTTTATCTGAAATTTAAA-A
1 TTAAATTGATT-TTTTATCTAATA-TTTAAAG-GTTAAATTAATATTTTATCCAAAATTTAAAGA
1427772 A
63 A
*
1427773 TTAAATTGATTTTTTATCTAATATTTAAAGGTTAGATTAATATTTTATCCAAAATTTAAAGAA
1 TTAAATTGATTTTTTATCTAATATTTAAAGGTTAAATTAATATTTTATCCAAAATTTAAAGAA
1427836 -TAAATT
1 TTAAATT
1427842 TAAAATTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
62 52 0.85
63 9 0.15
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (63 bp):
TTAAATTGATTTTTTATCTAATATTTAAAGGTTAAATTAATATTTTATCCAAAATTTAAAGAA
Found at i:1431760 original size:25 final size:26
Alignment explanation
Indices: 1431725--1431776 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
1431715 TATCCTACAT
1431725 TCCCTTTACACCATTACATATGAGAA
1 TCCCTTTACACCATTACATATGAGAA
*
1431751 TCCC-TTACACCATTACATATGGGAA
1 TCCCTTTACACCATTACATATGAGAA
1431776 T
1 T
1431777 AGGCCCAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31
Consensus pattern (26 bp):
TCCCTTTACACCATTACATATGAGAA
Found at i:1432882 original size:15 final size:15
Alignment explanation
Indices: 1432862--1432899 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1432852 CAATTTGATT
1432862 AAAATAATAAATTCA
1 AAAATAATAAATTCA
*
1432877 AAAAT-ATAAATTTA
1 AAAATAATAAATTCA
1432891 AAATATAAT
1 AAA-ATAAT
1432900 TCGTTATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 7 0.35
16 2 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATAATAAATTCA
Found at i:1432895 original size:13 final size:13
Alignment explanation
Indices: 1432860--1432898 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
1432850 AGCAATTTGA
1432860 TTAAAATAATAAAT
1 TTAAAAT-ATAAAT
*
1432874 TCAAAAATATAAAT
1 T-TAAAATATAAAT
1432888 TTAAAATATAA
1 TTAAAATATAA
1432899 TTCGTTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 8 0.36
15 5 0.23
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAAAATATAAAT
Found at i:1439984 original size:2 final size:2
Alignment explanation
Indices: 1439977--1440004 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1439967 AAACAAGTCT
1439977 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1440005 TCACCATAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1447304 original size:172 final size:172
Alignment explanation
Indices: 1447094--1447430 Score: 642
Period size: 173 Copynumber: 2.0 Consensus size: 172
1447084 GGATTGGGCT
1447094 GAAAACTTGTGACAAATACCACTATTTTGCACCTTGTTGTTTACAGAACGGAAAATTTTCAATTA
1 GAAAACTTGTGACAAATACCACTATTTTGCACCTTGTTGTTTACAGAACGGAAAATTTTCAATTA
1447159 GCAC-CCCTGTTTCTCTTGGGAAACGTATTGAATTAGAAACAAAGGATGAATACTAA-TAATATA
66 GCACACCCTGTTTCTCTTGGGAAACGTATTGAATTAGAAACAAAGGATGAATACTAATTAATATA
1447222 AACTGCAACTGTGTTTCTAGTTTCATTTACGTAATCCTATTGG
131 AACTGCAACTGTGTTTCTAG-TTCATTTACGTAATCCTATTGG
1447265 GAAAACTTGTGACAAATAACCACTATTTTGCACCTTGTTGTTTACAGAACGGAAAATTTTCAATT
1 GAAAACTTGTGACAAAT-ACCACTATTTTGCACCTTGTTGTTTACAGAACGGAAAATTTTCAATT
1447330 AGCACACCCTGTTTCTCTTGGGAAACGTATTGAATTAGAAACAAAGGATGAATACTAATTAATAT
65 AGCACACCCTGTTTCTCTTGGGAAACGTATTGAATTAGAAACAAAGGATGAATACTAATTAATAT
1447395 AAACTGCAACTGTGTTTCTAGTTCATTTACGTAATC
130 AAACTGCAACTGTGTTTCTAGTTCATTTACGTAATC
1447431 ATCCTATTGG
Statistics
Matches: 163, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
171 17 0.10
172 52 0.32
173 67 0.41
174 27 0.17
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (172 bp):
GAAAACTTGTGACAAATACCACTATTTTGCACCTTGTTGTTTACAGAACGGAAAATTTTCAATTA
GCACACCCTGTTTCTCTTGGGAAACGTATTGAATTAGAAACAAAGGATGAATACTAATTAATATA
AACTGCAACTGTGTTTCTAGTTCATTTACGTAATCCTATTGG
Found at i:1452910 original size:3 final size:3
Alignment explanation
Indices: 1452902--1452949 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
1452892 CAACGTTACT
* * *
1452902 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATT ATT ATA ATGA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
1452947 ATA
1 ATA
1452950 CAAGATTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1452957 original size:26 final size:23
Alignment explanation
Indices: 1452911--1452961 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
1452901 TATAATAATA
*
1452911 ATAATAATAATAATAAAATTATT
1 ATAATAAAAATAATAAAATTATT
1452934 ATAATGAAAAATAATACAAGATTATT
1 ATAAT-AAAAATAATA-AA-ATTATT
1452960 AT
1 AT
1452962 TATTATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 9 0.38
25 2 0.08
26 8 0.33
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
ATAATAAAAATAATAAAATTATT
Found at i:1457228 original size:59 final size:60
Alignment explanation
Indices: 1457163--1457282 Score: 233
Period size: 59 Copynumber: 2.0 Consensus size: 60
1457153 TTTTATATGT
1457163 ATTTAATTATTGATTTGATATATATCATATTACATAAATT-AAAACGTGACATGTATTAC
1 ATTTAATTATTGATTTGATATATATCATATTACATAAATTAAAAACGTGACATGTATTAC
1457222 ATTTAATTATTGATTTGATATATATCATATTACATAAATTAAAAACGTGACATGTATTAC
1 ATTTAATTATTGATTTGATATATATCATATTACATAAATTAAAAACGTGACATGTATTAC
1457282 A
1 A
1457283 CTATCAATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 40 0.67
60 20 0.33
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (60 bp):
ATTTAATTATTGATTTGATATATATCATATTACATAAATTAAAAACGTGACATGTATTAC
Found at i:1462522 original size:35 final size:34
Alignment explanation
Indices: 1462483--1462562 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 34
1462473 AACTATATAA
*
1462483 TATATATATATATTCAAAAATTAATTTT-TAAAAAG
1 TATAT-TATATATTC-AAAATTAATTTTCTAAAAAC
* * *
1462518 TATATTTATGTTTTCAAAATTCATTTTCTAAAAAC
1 TATA-TTATATATTCAAAATTAATTTTCTAAAAAC
1462553 TATATTATAT
1 TATATTATAT
1462563 GTTTTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
34 16 0.42
35 21 0.55
36 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (34 bp):
TATATTATATATTCAAAATTAATTTTCTAAAAAC
Found at i:1462544 original size:34 final size:36
Alignment explanation
Indices: 1462499--1462591 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 36
1462489 TATATATTCA
*
1462499 AAAATTAATTTT-TAAAAAGTATATT-TATGTTTTC
1 AAAATTAATTTTCTAAAAACTATATTATATGTTTTC
* *
1462533 AAAATTCATTTTCTAAAAACTATATTATATGTTTTT
1 AAAATTAATTTTCTAAAAACTATATTATATGTTTTC
1462569 AAAA--AA-TTTC-AAAAACTATATTA
1 AAAATTAATTTTCTAAAAACTATATTA
1462592 ATATATATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
32 13 0.25
33 4 0.08
34 12 0.23
35 12 0.23
36 12 0.23
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (36 bp):
AAAATTAATTTTCTAAAAACTATATTATATGTTTTC
Found at i:1462603 original size:32 final size:33
Alignment explanation
Indices: 1462542--1462603 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1462532 CAAAATTCAT
* *
1462542 TTTCTAAAAACTATATTATATGTTTTTAAAAAA
1 TTTCTAAAAACTATATTATATGATATTAAAAAA
1462575 TTTC-AAAAACTATATTAATAT-ATATTAAA
1 TTTCTAAAAACTATATT-ATATGATATTAAA
1462604 TAAGTCTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (33 bp):
TTTCTAAAAACTATATTATATGATATTAAAAAA
Found at i:1466329 original size:37 final size:37
Alignment explanation
Indices: 1466259--1466340 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
1466249 AAAATTTTTT
*
1466259 TATATTTTAATTTTGTAAAAAAATTATATAAATATTA
1 TATAATTTAATTTTGTAAAAAAATTATATAAATATTA
* *
1466296 TA-AATTTAATTTTTTTAAAGAAAA-TATATAAATATTT
1 TATAATTTAA-TTTTGTAAA-AAAATTATATAAATATTA
1466333 TATAATTT
1 TATAATTT
1466341 GTAATATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
36 6 0.15
37 24 0.62
38 9 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (37 bp):
TATAATTTAATTTTGTAAAAAAATTATATAAATATTA
Found at i:1470448 original size:188 final size:187
Alignment explanation
Indices: 1470094--1470468 Score: 725
Period size: 189 Copynumber: 2.0 Consensus size: 187
1470084 GCACGCTTAT
1470094 AATACTAAACTTCTAAGTGCAAACTTATGGCAAGCTAGTTGAGGGGGGCGGAGCTTCATCAAAAA
1 AATACTAAACTTCTAAGTGCAAACTTATGGCAAGCTAGTTGAGGGGGGCGGAGCTTCATCAAAAA
1470159 GGAAATCGTGCCGAAATCACAATCAGGTAGCTCATTAGGTTCATCGCTCCAATACCACAAATACT
66 GGAAATCGTGCCGAAATCACAATCAGGTAGCTCATTAGGTTCATCGCTCCAATACCACAAATACT
1470224 CAGTCTTCGATACTGCAATAATCCTCCAACATCATACCGAAATCATTGACGAACATA
131 CAGTCTTCGATACTGCAATAATCCTCCAACATCATACCGAAATCATTGACGAACATA
1470281 AATACTAAACTTCTAAGTGCAAACTTATGGGCAAGCTATGTTGAGGGGGGCGGAGCTTCATCAAA
1 AATACTAAACTTCTAAGTGCAAACTTAT-GGCAAGCTA-GTTGAGGGGGGCGGAGCTTCATCAAA
1470346 AAGGAAATCGTGCCGAAATCACAATCAGGTAGCTCATTAGGTTCATCGCTCCAATACCA-AAATA
64 AAGGAAATCGTGCCGAAATCACAATCAGGTAGCTCATTAGGTTCATCGCTCCAATACCACAAATA
1470410 CTCAGTCTTCGATACTGCAATAATCCTCCAACATCATACCGAAATCATTGACGAACATA
129 CTCAGTCTTCGATACTGCAATAATCCTCCAACATCATACCGAAATCATTGACGAACATA
1470469 TAGTCCCAGC
Statistics
Matches: 186, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
187 28 0.15
188 73 0.39
189 85 0.46
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (187 bp):
AATACTAAACTTCTAAGTGCAAACTTATGGCAAGCTAGTTGAGGGGGGCGGAGCTTCATCAAAAA
GGAAATCGTGCCGAAATCACAATCAGGTAGCTCATTAGGTTCATCGCTCCAATACCACAAATACT
CAGTCTTCGATACTGCAATAATCCTCCAACATCATACCGAAATCATTGACGAACATA
Found at i:1473736 original size:50 final size:50
Alignment explanation
Indices: 1473673--1473778 Score: 178
Period size: 50 Copynumber: 2.1 Consensus size: 50
1473663 TGGTATATCG
*
1473673 TACTTTGTGCCCTCAAAATTTGATAAATATGATA-AATAACTTTGTGGTTA
1 TACTTTGTGCCCTCAAAA-TTGATAAATATGAAATAATAACTTTGTGGTTA
1473723 TACTTTGTGCCCTCAAAATTGATAAATATGAAATAATAACTTTGTGGTTA
1 TACTTTGTGCCCTCAAAATTGATAAATATGAAATAATAACTTTGTGGTTA
*
1473773 AACTTT
1 TACTTT
1473779 ATATATAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
49 14 0.26
50 39 0.74
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (50 bp):
TACTTTGTGCCCTCAAAATTGATAAATATGAAATAATAACTTTGTGGTTA
Found at i:1475515 original size:24 final size:23
Alignment explanation
Indices: 1475474--1475519 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
1475464 AAAAGAATTT
* *
1475474 AAAATATATAATATTTTTTAAATA
1 AAAATATACAATA-ATTTTAAATA
*
1475498 AAAATATACGATAATTTTAAAT
1 AAAATATACAATAATTTTAAAT
1475520 TTTTAAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
AAAATATACAATAATTTTAAATA
Found at i:1476648 original size:17 final size:18
Alignment explanation
Indices: 1476623--1476662 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1476613 TTTTCTAGAA
*
1476623 AAAAAATAAAGATATT-T
1 AAAAAATAAAAATATTCT
*
1476640 AAAATATAAAAATATTCT
1 AAAAAATAAAAATATTCT
1476658 AAAAA
1 AAAAA
1476663 TAGATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAAAATAAAAATATTCT
Found at i:1477000 original size:24 final size:23
Alignment explanation
Indices: 1476965--1477012 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1476955 TTTAACTTTT
* *
1476965 ATTTTTTCATATTTTGATATTTA
1 ATTTTTTAATATTTTGAAATTTA
*
1476988 ATTTTTTGAATATTTTTAAATTTA
1 ATTTTTT-AATATTTTGAAATTTA
1477012 A
1 A
1477013 AATTTGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
ATTTTTTAATATTTTGAAATTTA
Found at i:1479044 original size:14 final size:15
Alignment explanation
Indices: 1478947--1479050 Score: 102
Period size: 15 Copynumber: 6.5 Consensus size: 15
1478937 TAATAAGGTT
1478947 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1478962 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1478977 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
1478992 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
1479011 TTTGATTTATTTTAAAATA
1 ----ATTTATTTTAAAATA
1479030 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1479044 ATTTATT
1 ATTTATT
1479051 AGTATGGATT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
14 12 0.16
15 43 0.57
16 4 0.05
17 2 0.03
19 2 0.03
21 2 0.03
22 4 0.05
23 6 0.08
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1479067 original size:18 final size:18
Alignment explanation
Indices: 1479044--1479091 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1479034 ATTTTAAATA
*
1479044 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1479062 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1479084 ATTTATTA
1 ATTTATTA
1479092 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1479141 original size:32 final size:31
Alignment explanation
Indices: 1479100--1479571 Score: 333
Period size: 32 Copynumber: 16.7 Consensus size: 31
1479090 TATTGTAGTT
1479100 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
* *
1479132 GTATAGATTGATTTACTTT-AA-AA--TA--C
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
1479158 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
1479186 GTATTGATTGATTTATTTT-AA-AA--TA-T-
1 GTA-TGATTGATTTATTTTAAATAATTTATTA
1479212 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
*
1479240 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
* *
1479272 GTATGGATTGATTGA-TTT--AT--TTTA-AA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
* *
1479298 ATATGGATTGATTTA--TT--AT--TGTAGTT-
1 GTAT-GATTGATTTATTTTAAATAATTTA-TTA
1479324 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
1479356 GTATCGATTGATTTATTTT-AA-AA--TA-T-
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
1479382 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
1479410 GTATAGATTGATTTATTTTAAATAATTTATTTA
1 GTAT-GATTGATTTATTTTAAATAATTTA-TTA
*
1479443 -TATGGGTTGATTTATTTT-AA-AA--TA-T-
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
1479468 G--T-ATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
1479496 GTATGGATTGATTTATTTT-AA-AA--TA-T-
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
1479522 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
1479550 GTATAGATTGATTTATTTTAAA
1 GTAT-GATTGATTTATTTTAAA
1479572 ATATGGATTG
Statistics
Matches: 360, Mismatches: 19, Indels: 122
0.72 0.04 0.24
Matches are distributed among these distances:
22 67 0.19
23 10 0.03
24 11 0.03
25 7 0.02
26 41 0.11
27 11 0.03
28 17 0.05
29 2 0.01
30 13 0.04
31 15 0.04
32 163 0.45
33 3 0.01
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.53
Consensus pattern (31 bp):
GTATGATTGATTTATTTTAAATAATTTATTA
Found at i:1479168 original size:54 final size:54
Alignment explanation
Indices: 1479105--1479431 Score: 379
Period size: 54 Copynumber: 5.9 Consensus size: 54
1479095 TAGTTGTATA
* *
1479105 GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTACTTTAAAATACG
1 GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATG
*
1479159 GATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATG
* *
1479213 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATAATT
1 GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAAT-ATG
* ** * * * * * * *** *
1479267 TATTTGTATGGATTGATTGATTTATTT-TAAAATATGGATTGATTTATTATTGTAGTTGTATA
1 GA-TTG-ATTTATT--TTAAATAATTTAT-TAGTATAGATTGATTTA-T-TT-TA-AAATATG
*
1479329 GATTGATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATG
1479383 GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAA
1 GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAA
1479432 TAATTTATTT
Statistics
Matches: 230, Mismatches: 31, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
53 4 0.02
54 150 0.65
55 5 0.02
56 7 0.03
57 2 0.01
58 45 0.20
59 2 0.01
60 7 0.03
61 4 0.02
62 3 0.01
63 1 0.00
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (54 bp):
GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATG
Found at i:1479248 original size:86 final size:87
Alignment explanation
Indices: 1479158--1479517 Score: 542
Period size: 86 Copynumber: 4.2 Consensus size: 87
1479148 TTTAAAATAC
1479158 GGATTGATTTATTTTAAATAATTTA-TTAGTATTGATTGATTTATTTTAAAATATGGATTGATTT
1 GGATTGATTTATTTTAAATAATTTATTTAGTATTGATTGATTTATTTTAAAATATGGATTGATTT
1479222 ATTTTAAATAATTTATTAGTAT
66 ATTTTAAATAATTTATTAGTAT
*
1479244 GGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTTATTTTAAAATATGGATTGA
1 GGATTGATTTATTTTAAATAATTTA-TT-TA-GTATTGATTGATTTATTTTAAAATATGGATTGA
*
1479309 TTTA--TT--AT--TGTAGTT-GTAT
63 TTTATTTTAAATAATTTA-TTAGTAT
* *
1479328 AGATTGATTTATTTTAAATAATTTA-TTAGTATCGATTGATTTATTTTAAAATATGGATTGATTT
1 GGATTGATTTATTTTAAATAATTTATTTAGTATTGATTGATTTATTTTAAAATATGGATTGATTT
1479392 ATTTTAAATAATTTATTAGTAT
66 ATTTTAAATAATTTATTAGTAT
* * * *
1479414 AGATTGATTTATTTTAAATAATTTATTTA-TATGGGTTGATTTATTTTAAAATATGTATTGATTT
1 GGATTGATTTATTTTAAATAATTTATTTAGTATTGATTGATTTATTTTAAAATATGGATTGATTT
1479478 ATTTTAAATAATTTATTAGTAT
66 ATTTTAAATAATTTATTAGTAT
1479500 GGATTGATTTATTTTAAA
1 GGATTGATTTATTTTAAA
1479518 ATATGGATTG
Statistics
Matches: 251, Mismatches: 10, Indels: 26
0.87 0.03 0.09
Matches are distributed among these distances:
80 35 0.14
81 2 0.01
82 3 0.01
84 33 0.13
85 4 0.02
86 130 0.52
87 3 0.01
88 3 0.01
89 2 0.01
90 36 0.14
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (87 bp):
GGATTGATTTATTTTAAATAATTTATTTAGTATTGATTGATTTATTTTAAAATATGGATTGATTT
ATTTTAAATAATTTATTAGTAT
Found at i:1479314 original size:224 final size:218
Alignment explanation
Indices: 1479030--1479683 Score: 848
Period size: 224 Copynumber: 3.0 Consensus size: 218
1479020 TTTTAAAATA
1479030 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1479095 TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTACTTTAAAATACGG
66 TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTACTTTAAAATA-GG
*
1479160 ATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGGATTGATTTATT
130 ATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATAT-GATTGATTTATT
*
1479225 TTAAATAATTTATTAGTATGGATTG
194 TTAAATAATTTATTAATATGGATTG
*
1479250 ATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTTATTTTAAAATATGGATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTAT-G---GATTGATTTATTTTAAAATATGGATTGATTTATT
* *
1479315 ATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAAAT
62 ATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTACTTTAAAAT
*
1479380 ATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT-AAATA--ATTTATTT
127 A-GGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGATTGATTT
* * * * *
1479442 ATATGGGTTGATTTATTT-TAAAATATGTATTG
191 AT-T---TTAAATAATTTAT-TAATATGGATTG
1479474 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
* ** ** *
1479539 ATAATTTA-TTAGTATAGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATT-ATTGTAGTTG
62 AT--TGTAGTT-GTATAGATTGATTTATTTTAAATA-ATTTATTAGTATAGATTGATT-TACTT-
*
1479599 T---ATA-GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGAT
121 TAAAATAGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATAT-GAT
1479660 TGATTTATTTTAAATAATTTATTA
185 TGATTTATTTTAAATAATTTATTA
1479684 TTTTAGTTGT
Statistics
Matches: 385, Mismatches: 25, Indels: 48
0.84 0.05 0.10
Matches are distributed among these distances:
220 120 0.31
221 8 0.02
222 5 0.01
223 11 0.03
224 206 0.54
225 5 0.01
226 30 0.08
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (218 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTACTTTAAAATAGGA
TTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGATTGATTTATTTT
AAATAATTTATTAATATGGATTG
Found at i:1479359 original size:170 final size:166
Alignment explanation
Indices: 1479159--1479480 Score: 572
Period size: 170 Copynumber: 1.9 Consensus size: 166
1479149 TTAAAATACG
*
1479159 GATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAAATATGGATTGATTTAT
* *
1479224 TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTGATT
66 TTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTATATGG---G-TTGATT
1479289 TATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATA
127 TATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATA
1479329 GATTGATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAAATATGGATTGATTTAT
1 GATTGATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAAATATGGATTGATTTAT
1479394 TTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTATATGGGTTGATTTATT
66 TTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTATATGGGTTGATTTATT
*
1479459 TTAAAATATGTATTGATTTATT
131 TTAAAATATGGATTGATTTATT
1479481 TTAAATAATT
Statistics
Matches: 148, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
166 31 0.21
167 1 0.01
170 116 0.78
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (166 bp):
GATTGATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAAATATGGATTGATTTAT
TTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTATATGGGTTGATTTATT
TTAAAATATGGATTGATTTATTATTGTAGTTGTATA
Found at i:1479407 original size:14 final size:14
Alignment explanation
Indices: 1479388--1479441 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1479378 ATATGGATTG
1479388 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1479402 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
1479420 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1479434 ATTTATTT
1 ATTTATTT
1479442 ATATGGGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1479467 original size:22 final size:22
Alignment explanation
Indices: 1479442--1479485 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1479432 TAATTTATTT
*
1479442 ATATGGGTTGATTTATTTTAAA
1 ATATGGATTGATTTATTTTAAA
*
1479464 ATATGTATTGATTTATTTTAAA
1 ATATGGATTGATTTATTTTAAA
1479486 TAATTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
ATATGGATTGATTTATTTTAAA
Found at i:1479474 original size:54 final size:54
Alignment explanation
Indices: 1479415--1479588 Score: 305
Period size: 54 Copynumber: 3.2 Consensus size: 54
1479405 TATTAGTATA
*
1479415 GATTGATTTATTTTAAATAATTTATTTA-TATGGGTTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATG
*
1479469 TATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
*
1479523 GATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1479577 GATTGATTTATT
1 GATTGATTTATT
1479589 ATTGTAGTTG
Statistics
Matches: 115, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
53 3 0.03
54 112 0.97
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
Found at i:1479513 original size:22 final size:22
Alignment explanation
Indices: 1479497--1479539 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1479487 AATTTATTAG
1479497 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1479519 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1479540 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1479670 original size:54 final size:54
Alignment explanation
Indices: 1479325--1479683 Score: 221
Period size: 54 Copynumber: 6.6 Consensus size: 54
1479315 ATTGTAGTTG
* *
1479325 TATAGATTGATTTATTTTAAATAATTTATTAGTATCGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAAA
* * *
1479379 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT--AA
1 TATAGATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAAA
* * * * * *
1479431 -ATA-ATTTATTTATATGGGTTGATTTATTT-TAAAATATGTATTGATTTATTTTAAATAA
1 TATAGATTGATTTAT-T---TTAAATAATTTAT-TAATATGGATTGATTTATTTT-AA-AA
* * *
1479489 TTTATTAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTTTAAATAA
1 --TA-TAG-ATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTT-AA-AA
* * * ***
1479543 TTTATTAGTATAGATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTATTGTAGTTG
1 --TA-TAG-ATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTA-T-TT-TA-AAA
*
1479599 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAAA
1479653 TATAGATTGATTTATTTTAAATAATTTATTA
1 TATAGATTGATTTATTTTAAATAATTTATTA
1479684 TTTTAGTTGT
Statistics
Matches: 252, Mismatches: 27, Indels: 52
0.76 0.08 0.16
Matches are distributed among these distances:
50 9 0.04
51 3 0.01
52 9 0.04
53 7 0.03
54 175 0.69
55 8 0.03
56 5 0.02
57 7 0.03
58 17 0.07
59 2 0.01
61 1 0.00
62 3 0.01
64 6 0.02
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
TATAGATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTTAAAA
Found at i:1489239 original size:14 final size:14
Alignment explanation
Indices: 1489220--1489249 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1489210 TTCCAACACA
1489220 TTATCTCGTGGATT
1 TTATCTCGTGGATT
*
1489234 TTATCTTGTGGATT
1 TTATCTCGTGGATT
1489248 TT
1 TT
1489250 GCCTACTTAA
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:0.13, C:0.10, G:0.20, T:0.57
Consensus pattern (14 bp):
TTATCTCGTGGATT
Found at i:1490505 original size:7 final size:7
Alignment explanation
Indices: 1490493--1490750 Score: 140
Period size: 7 Copynumber: 35.3 Consensus size: 7
1490483 TGATTATATC
1490493 ATATTAT
1 ATATTAT
1490500 ATATTAT
1 ATATTAT
1490507 -T-TTAT
1 ATATTAT
* *
1490512 ACAGTAT
1 ATATTAT
1490519 ATATTAT
1 ATATTAT
*
1490526 ATAGTATGGT
1 ATA-T-T-AT
1490536 ATATTAT
1 ATATTAT
*
1490543 ATAGCATAT
1 ATA--TTAT
1490552 ATATTAT
1 ATATTAT
1490559 AATATTTAT
1 -ATA-TTAT
1490568 ATAGTATACT
1 ATA-T-TA-T
*
1490578 TTATTAT
1 ATATTAT
1490585 ATATTATGTT
1 ATATTA---T
1490595 ATATTAT
1 ATATTAT
**
1490602 ATAGCAT
1 ATATTAT
1490609 ATATTGTAT
1 ATA-T-TAT
1490618 AATATT-T
1 -ATATTAT
*
1490625 ATATTAC
1 ATATTAT
1490632 ATATTAT
1 ATATTAT
*
1490639 ATAGTATT
1 ATATTA-T
1490647 ATATTAT
1 ATATTAT
1490654 ATATTAT
1 ATATTAT
1490661 A-A-TAGT
1 ATATTA-T
1490667 ATATTAT
1 ATATTAT
1490674 ATATTAT
1 ATATTAT
1490681 ATA-TAT
1 ATATTAT
*
1490687 -TATAAT
1 ATATTAT
1490693 ATATGTAT
1 ATAT-TAT
*
1490701 TTATTAT
1 ATATTAT
1490708 -TATTAT
1 ATATTAT
1490714 A-A-TAT
1 ATATTAT
1490719 AGTATTATT
1 A-TATTA-T
*
1490728 ATATCAT
1 ATATTAT
*
1490735 ATATCAT
1 ATATTAT
1490742 ATATTAT
1 ATATTAT
1490749 AT
1 AT
1490751 TCTTTTATAT
Statistics
Matches: 197, Mismatches: 24, Indels: 60
0.70 0.09 0.21
Matches are distributed among these distances:
5 12 0.06
6 21 0.11
7 96 0.49
8 31 0.16
9 20 0.10
10 17 0.09
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (7 bp):
ATATTAT
Found at i:1490559 original size:5 final size:5
Alignment explanation
Indices: 1490551--1490767 Score: 80
Period size: 5 Copynumber: 42.6 Consensus size: 5
1490541 ATATAGCATA
* *
1490551 TATAT TATAA TAT-T TATAT AGTATACT T-TAT TATATAT TATGT TATAT
1 TATAT TATAT TATAT TATAT --TATA-T TATAT TA--TAT TATAT TATAT
* * *
1490599 TATA- TAGCA- TATAT TGTAT AATATT TATAT TACATAT TATA- TAGTAT
1 TATAT TA-TAT TATAT TATAT TATA-T TATAT T--ATAT TATAT TA-TAT
* * *
1490646 TATAT TATA- TATTAT AATAG TATAT TATA- TATTAT ATATAT TATAA
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TA-TAT -TATAT TATAT
* * * *
1490692 TATA- TGTAT T-TAT TATTAT TATAA TATAG TATTAT TATAT CATA- TATCA-
1 TATAT TATAT TATAT TA-TAT TATAT TATAT TA-TAT TATAT TATAT TAT-AT
* *
1490741 TATAT TATAT TCTTT TATAT T-TAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
1490768 TTTTAGGTCC
Statistics
Matches: 161, Mismatches: 25, Indels: 52
0.68 0.11 0.22
Matches are distributed among these distances:
4 28 0.17
5 96 0.60
6 20 0.12
7 16 0.10
8 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (5 bp):
TATAT
Found at i:1490586 original size:17 final size:17
Alignment explanation
Indices: 1490564--1490605 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1490554 ATTATAATAT
1490564 TTATATAGTATACTT-TA
1 TTATATAGTAT-CTTATA
* *
1490581 TTATATATTATGTTATA
1 TTATATAGTATCTTATA
1490598 TTATATAG
1 TTATATAG
1490606 CATATATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (17 bp):
TTATATAGTATCTTATA
Found at i:1490657 original size:59 final size:57
Alignment explanation
Indices: 1490535--1490714 Score: 164
Period size: 59 Copynumber: 3.2 Consensus size: 57
1490525 TATAGTATGG
*
1490535 TATATTATATAGCATATATATTATAATATTTATA-TAGTATACTTTATTATA-TATTAT-GT-
1 TATATTATATAGCATATAT-TTATAATATTTATATTA--ATA--TTA-TATAGTATTATATTA
1490594 TATATTATATAGCATATATTGTATAATATTTATATTACATATTATATAGTATTATATTA
1 TATATTATATAGCATATATT-TATAATATTTATATTA-ATATTATATAGTATTATATTA
* * *
1490653 TATATTATAATAG--TATATTATATATTATATATATT-ATAATATAT-GTATT-TATTA
1 TATATTAT-ATAGCATATATT-TATAATATTTATATTAATATTATATAGTATTATATTA
1490707 T-TATTATA
1 TATATTATA
1490715 ATATAGTATT
Statistics
Matches: 109, Mismatches: 6, Indels: 19
0.81 0.04 0.14
Matches are distributed among these distances:
52 1 0.01
53 6 0.06
54 6 0.06
55 5 0.05
56 12 0.11
57 9 0.08
58 21 0.19
59 43 0.39
60 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (57 bp):
TATATTATATAGCATATATTTATAATATTTATATTAATATTATATAGTATTATATTA
Found at i:1490681 original size:54 final size:53
Alignment explanation
Indices: 1490639--1490750 Score: 113
Period size: 53 Copynumber: 2.0 Consensus size: 53
1490629 TACATATTAT
* *
1490639 ATAGTATTATATTATATATTATAATAGTATATTATATATTATATATATTATAAT
1 ATAGTATTATATTATATATTATAATAGTATATTATATATTATAT-TAATATTAT
*
1490693 ATATGTATT-TATTAT-TATTATAATA-TAGTATTATTATATCATATATCATATATTAT
1 ATA-GTATTATATTATATATTATAATAGTA-TATTA-TATAT--TATATTA-ATATTAT
1490749 AT
1 AT
1490751 TCTTTTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
52 2 0.04
53 15 0.31
54 14 0.29
55 6 0.12
56 12 0.24
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (53 bp):
ATAGTATTATATTATATATTATAATAGTATATTATATATTATATTAATATTAT
Found at i:1492661 original size:2 final size:2
Alignment explanation
Indices: 1492654--1492696 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1492644 ATCTTATCTC
*
1492654 AT AT AT AT AT AT AT GT 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
1492696 A
1 A
1492697 ATTGACACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1496118 original size:245 final size:245
Alignment explanation
Indices: 1495654--1496390 Score: 1399
Period size: 245 Copynumber: 3.0 Consensus size: 245
1495644 GTTGTTATTA
*
1495654 TTATGATTTTTATTTACTACA-ATTATTCCCTTTATAAAATAATATTAATTCTTATTATTAATTC
1 TTATGATTATTATTTACTA-AGATTATTCCCTTTATAAAATAATATTAATTCTTATTATTAATTC
*
1495718 TAACTTTTAATTTTTTCATTATTAATGATAATTTTTTCAAACTAAACGATGAATAAATATTAAAA
65 TAACTTTTAATTTTTTCGTTATTAATGATAATTTTTTCAAACTAAACGATGAATAAATATTAAAA
1495783 ATAATAAAAGTATGAAGGATTTATAAAAAAATATAATGTCAATTTTACATTATATGTAACTTTTA
130 ATAATAAAAGTATGAAGGATTTATAAAAAAATATAATGTCAATTTTACATTATATGTAACTTTTA
1495848 CTATAAATTCAATCATCATTTTTTAAGAAAAAAAGTCAAAAGTTTTCATTT
195 CTATAAATTCAATCATCATTTTTTAAGAAAAAAAGTCAAAAGTTTTCATTT
1495899 TTATGATTATTATTTACTAAGATTATTCCCTTTATAAAATAATATTAATTCTTATTATTAATTCT
1 TTATGATTATTATTTACTAAGATTATTCCCTTTATAAAATAATATTAATTCTTATTATTAATTCT
1495964 AACTTTTAATTTTTTCGTTATTAATGATAATTTTTTTCAAACTAAACGATGAATAAATATTAAAA
66 AACTTTTAATTTTTTCGTTATTAATGATAA-TTTTTTCAAACTAAACGATGAATAAATATTAAAA
1496029 ATAATAAAAGTATGAAGGATTTATAAAAAAATATAATGTCAATTTTACATTATATGTAACTTTTA
130 ATAATAAAAGTATGAAGGATTTATAAAAAAATATAATGTCAATTTTACATTATATGTAACTTTTA
1496094 CTATAAATTCAATCATCA-TTTTTAAGAAAAAAAGTCAAAAGTTTTCATTT
195 CTATAAATTCAATCATCATTTTTTAAGAAAAAAAGTCAAAAGTTTTCATTT
1496144 TTATGATTATTATTTACTAAGATTATTCCCTTTATAAAATAATATTAATTCTTATTATTAATTCT
1 TTATGATTATTATTTACTAAGATTATTCCCTTTATAAAATAATATTAATTCTTATTATTAATTCT
1496209 AACTTTTAATTTTTTCGTTATTAATGATAATTTTTTCAAACTAAACGATGAATAAATATTAAAAA
66 AACTTTTAATTTTTTCGTTATTAATGATAATTTTTTCAAACTAAACGATGAATAAATATTAAAAA
1496274 TAATAAAAGTATGAAGGATTTATAAAAAAAAATATAATGTCAATTTTACATTATATGTAACTTTT
131 TAATAAAAGTATGAAGGATTTAT--AAAAAAATATAATGTCAATTTTACATTATATGTAACTTTT
1496339 ACTATAAATTCAATCATCATTTTTTAAGAAAAAAAGTCAAAAGTTTTC-TTT
194 ACTATAAATTCAATCATCATTTTTTAAGAAAAAAAGTCAAAAGTTTTCATTT
1496390 T
1 T
1496391 ATAAAAATGT
Statistics
Matches: 485, Mismatches: 2, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
244 59 0.12
245 218 0.45
246 180 0.37
247 28 0.06
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (245 bp):
TTATGATTATTATTTACTAAGATTATTCCCTTTATAAAATAATATTAATTCTTATTATTAATTCT
AACTTTTAATTTTTTCGTTATTAATGATAATTTTTTCAAACTAAACGATGAATAAATATTAAAAA
TAATAAAAGTATGAAGGATTTATAAAAAAATATAATGTCAATTTTACATTATATGTAACTTTTAC
TATAAATTCAATCATCATTTTTTAAGAAAAAAAGTCAAAAGTTTTCATTT
Found at i:1496826 original size:5 final size:5
Alignment explanation
Indices: 1496818--1496843 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1496808 CAGTAATATG
1496818 AATTA AATTA AATTA AATTA AATTA A
1 AATTA AATTA AATTA AATTA AATTA A
1496844 TAAACATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:1498846 original size:6 final size:6
Alignment explanation
Indices: 1498835--1498861 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1498825 AAGTATATGG
1498835 ATTAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATT
1498862 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:1501285 original size:7 final size:7
Alignment explanation
Indices: 1501273--1501302 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1501263 TATTTAAGAT
1501273 CATTATG
1 CATTATG
1501280 CATTATG
1 CATTATG
1501287 CATTATG
1 CATTATG
1501294 CATTATG
1 CATTATG
1501301 CA
1 CA
1501303 AGCCACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (7 bp):
CATTATG
Found at i:1510697 original size:6 final size:6
Alignment explanation
Indices: 1510670--1510762 Score: 96
Period size: 6 Copynumber: 15.5 Consensus size: 6
1510660 CCAAGCAAGT
* * * * *
1510670 GCACCA GCTCCG GCACCA GCACCG GCACCA GCACCA GCACCA GCTCCG
1 GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA
* * * * *
1510718 GCACCA GCACCA GCTCCG GCACCA GCACCG GCACCT GCTCCA GCA
1 GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA GCACCA GCA
1510763 ACAGTTTCTT
Statistics
Matches: 68, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.23, C:0.49, G:0.23, T:0.05
Consensus pattern (6 bp):
GCACCA
Found at i:1510703 original size:18 final size:18
Alignment explanation
Indices: 1510670--1510746 Score: 127
Period size: 18 Copynumber: 4.3 Consensus size: 18
1510660 CCAAGCAAGT
1510670 GCACCAGCTCCGGCACCA
1 GCACCAGCTCCGGCACCA
* * *
1510688 GCACCGGCACCAGCACCA
1 GCACCAGCTCCGGCACCA
1510706 GCACCAGCTCCGGCACCA
1 GCACCAGCTCCGGCACCA
1510724 GCACCAGCTCCGGCACCA
1 GCACCAGCTCCGGCACCA
1510742 GCACC
1 GCACC
1510747 GGCACCTGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.23, C:0.51, G:0.22, T:0.04
Consensus pattern (18 bp):
GCACCAGCTCCGGCACCA
Found at i:1510760 original size:18 final size:18
Alignment explanation
Indices: 1510670--1510762 Score: 114
Period size: 18 Copynumber: 5.2 Consensus size: 18
1510660 CCAAGCAAGT
*
1510670 GCACCAGCTCCGGCACCA
1 GCACCAGCACCGGCACCA
* *
1510688 GCACCGGCACCAGCACCA
1 GCACCAGCACCGGCACCA
*
1510706 GCACCAGCTCCGGCACCA
1 GCACCAGCACCGGCACCA
*
1510724 GCACCAGCTCCGGCACCA
1 GCACCAGCACCGGCACCA
* * *
1510742 GCACCGGCACCTGCTCCA
1 GCACCAGCACCGGCACCA
1510760 GCA
1 GCA
1510763 ACAGTTTCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.23, C:0.49, G:0.23, T:0.05
Consensus pattern (18 bp):
GCACCAGCACCGGCACCA
Found at i:1514883 original size:184 final size:183
Alignment explanation
Indices: 1514565--1514934 Score: 632
Period size: 184 Copynumber: 2.0 Consensus size: 183
1514555 AACCGAAATT
* * * *
1514565 AAATTTTAAATATATTATATATAACATATGGGTTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATAAATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
*
1514630 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
* *
1514695 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTAAATTAAA
*
1514749 AAATATTATATATATTATAAATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATAAATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* * *
1514814 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
1514879 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAAATTAAA
1514932 AAA
1 AAA
1514935 AGTAATTTTT
Statistics
Matches: 175, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
183 15 0.09
184 160 0.91
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (183 bp):
AAATATTAAATATATTATAAATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTAAATTAAA
Found at i:1514912 original size:20 final size:21
Alignment explanation
Indices: 1514887--1514930 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1514877 TTTTATTTTA
*
1514887 TAATTATATA-TTATTTAAAT
1 TAATTATAAACTTATTTAAAT
*
1514907 TAATTATAAACTTTTTTAAAT
1 TAATTATAAACTTATTTAAAT
1514928 TAA
1 TAA
1514931 AAAAAGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATTATAAACTTATTTAAAT
Found at i:1520452 original size:21 final size:21
Alignment explanation
Indices: 1520408--1520452 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1520398 TGATTCTGGG
* * *
1520408 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
1520429 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1520450 CAA
1 CAA
1520453 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1521614 original size:32 final size:32
Alignment explanation
Indices: 1521573--1521669 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
1521563 GAGTCGAGGG
1521573 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
1521605 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* * *
1521636 TATACCTATGTTTTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
1521668 TT
1 TT
1521670 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:1521645 original size:31 final size:31
Alignment explanation
Indices: 1521572--1521672 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
1521562 AGAGTCGAGG
* *
1521572 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTTTAAGGAACATATGGACA
*
1521603 GTTTTACCTATGTCTTT--CGAGACATATGGACA
1 G-TTTACCTATGT-TTTAAGGA-ACATATGGACA
*
1521635 GTATACCTATGTTTTAAGGAACATATGGACA
1 GTTTACCTATGTTTTAAGGAACATATGGACA
1521666 GTTTACC
1 GTTTACC
1521673 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
30 3 0.05
31 30 0.50
32 25 0.42
33 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTTTAAGGAACATATGGACA
Found at i:1521704 original size:30 final size:30
Alignment explanation
Indices: 1521660--1521753 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
1521650 AAGGAACATA
1521660 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
1521691 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
1521721 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1521750 TGGA
1 TGGA
1521754 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1526396 original size:32 final size:32
Alignment explanation
Indices: 1526355--1526451 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
1526345 GAGTCGAGGG
1526355 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
1526387 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* * * *
1526418 TATATCTATGTTCTAAGGAATATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
1526450 TT
1 TT
1526452 ACCGAGGATC
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
31 24 0.45
32 29 0.55
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:1526486 original size:30 final size:30
Alignment explanation
Indices: 1526442--1526535 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
1526432 AAGGAATATA
1526442 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
1526473 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
1526503 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1526532 TGGA
1 TGGA
1526536 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1529688 original size:19 final size:19
Alignment explanation
Indices: 1529664--1529703 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1529654 ACACATGTAC
1529664 ATAAGTCACAACAGAACAT
1 ATAAGTCACAACAGAACAT
1529683 ATAAGTCACAACAGAACAT
1 ATAAGTCACAACAGAACAT
1529702 AT
1 AT
1529704 GTCGTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.20, G:0.10, T:0.17
Consensus pattern (19 bp):
ATAAGTCACAACAGAACAT
Found at i:1532160 original size:10 final size:10
Alignment explanation
Indices: 1532131--1532169 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1532121 AACCAAAAAA
1532131 CCCGGTTTTT
1 CCCGGTTTTT
* *
1532141 CCTGGGTTTT
1 CCCGGTTTTT
1532151 CCCGGTTTTT
1 CCCGGTTTTT
*
1532161 ACCGGTTTT
1 CCCGGTTTT
1532170 CAGCCGGTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.03, C:0.26, G:0.23, T:0.49
Consensus pattern (10 bp):
CCCGGTTTTT
Found at i:1537084 original size:20 final size:20
Alignment explanation
Indices: 1537059--1537133 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
1537049 ACGAAATACA
1537059 AATCGCAACGCGATCT-CCAG
1 AATCGCAACGCGAT-TACCAG
**
1537079 AATCGCAAATC-AGTTACCAG
1 AATCGCAACGCGA-TTACCAG
**
1537099 AATCGCAACGCGATTATTAAG
1 AATCGCAACGCGATTA-CCAG
*
1537120 AATCGCAATGCGAT
1 AATCGCAACGCGAT
1537134 AGTACAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 26 0.59
21 16 0.36
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGATTACCAG
Found at i:1537174 original size:21 final size:21
Alignment explanation
Indices: 1537059--1537174 Score: 69
Period size: 21 Copynumber: 5.6 Consensus size: 21
1537049 ACGAAATACA
*
1537059 AATCGCAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
1537079 AATCGCAAATC-AGTTACCAG
1 AATCGCAACGCGATTTTCCAG
*
1537099 AATCGCAACGCGATTATT-AAG
1 AATCGCAACGCGATT-TTCCAG
* ** *
1537120 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
** *
1537140 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTTTCCAG
1537162 AATCGCAACGCGA
1 AATCGCAACGCGA
1537175 ACATATAAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
19 1 0.01
20 26 0.37
21 41 0.58
22 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:1537224 original size:40 final size:39
Alignment explanation
Indices: 1537180--1537356 Score: 212
Period size: 40 Copynumber: 4.4 Consensus size: 39
1537170 CGCGAACATA
* * *
1537180 TAAATCGCAACGCGATTC-TGACTATCGCAACGAGTATCCG
1 TAAATCGCAACGCGATACGT-A-AATCGCAACGCGTATCCG
* *
1537220 TAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTG
1 TAAATCGCAACGCG-ATACGTAAATCGCAACGCGTATCCG
* *
1537260 TAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCG-ATACGTAAATCGCAACGCGTATCCG
* *
1537300 TAAATCGCAACGACAATACGTAAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-CGATACGT-AAATCGCAACGCGTATCCG
1537341 TAAATCGCAACGCGAT
1 TAAATCGCAACGCGAT
1537357 TTTTAATCGT
Statistics
Matches: 121, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
40 87 0.72
41 33 0.27
42 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (39 bp):
TAAATCGCAACGCGATACGTAAATCGCAACGCGTATCCG
Found at i:1537226 original size:20 final size:20
Alignment explanation
Indices: 1537203--1537352 Score: 183
Period size: 20 Copynumber: 7.5 Consensus size: 20
1537193 GATTCTGACT
1537203 ATCGCAACGAGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
1537223 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* *
1537243 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGTATCCGTAA
* *
1537263 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* *
1537283 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
1537303 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
1537324 ATCGCAACGTGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
1537344 ATCGCAACG
1 ATCGCAACG
1537353 CGATTTTTAA
Statistics
Matches: 106, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
20 90 0.85
21 16 0.15
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:1537244 original size:60 final size:60
Alignment explanation
Indices: 1537162--1537355 Score: 214
Period size: 60 Copynumber: 3.2 Consensus size: 60
1537152 GATTTTCCAT
* ** *
1537162 AATCGCAACGCGAACATATAAATCGCAACGCGATTCTG-ACTATCGCAACGAGTATCCGTA
1 AATCGCAACGCGAATACGTAAATCGCAACGCGATTCTGTA-AATCGCAACGAGTATCCGTA
* * *
1537222 AATCGCAACGAGAATACGTAAATCGCAACGCG-TATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTAAATCGCAACGCGAT-TCTGTAAATCGCAACGAGTATCCGTA
* * * * * *
1537282 AATCGCAATGCGTATCCGTAAATCGCAACGACAATAC-GTAAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGTAAATCGCAACG-CGATTCTGT-AAATCGCAACGAGTATCCGTA
1537343 AATCGCAACGCGA
1 AATCGCAACGCGA
1537356 TTTTTAATCG
Statistics
Matches: 111, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
59 1 0.01
60 77 0.69
61 32 0.29
62 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATACGTAAATCGCAACGCGATTCTGTAAATCGCAACGAGTATCCGTA
Found at i:1537971 original size:21 final size:21
Alignment explanation
Indices: 1537911--1537989 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
1537901 TTCTAAACTT
1537911 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
1537931 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
** *
1537951 ACTATCGTAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
1537972 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
1537990 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 29 0.58
21 21 0.42
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1538012 original size:19 final size:19
Alignment explanation
Indices: 1537911--1538032 Score: 83
Period size: 20 Copynumber: 6.5 Consensus size: 19
1537901 TTCTAAACTT
**
1537911 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
1537931 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** * *
1537951 ACTATCGTAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
1537972 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
1537986 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
1538005 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
1538024 AAAATCGCA
1 AAAATCGCA
1538033 TTGCGATTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 15
0.74 0.13 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 26 0.32
20 27 0.33
21 12 0.15
22 1 0.01
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1538050 original size:19 final size:19
Alignment explanation
Indices: 1538028--1538140 Score: 92
Period size: 20 Copynumber: 6.1 Consensus size: 19
1538018 GAAACCAAAA
*
1538028 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1538047 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1538061 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
**
1538080 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* **
1538099 TCCGTGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
1538119 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1538139 TC
1 TC
1538141 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
19 28 0.37
20 31 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1539125 original size:14 final size:14
Alignment explanation
Indices: 1539106--1539141 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1539096 ATTGTTTAAT
1539106 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1539120 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1539134 TGATTTGT
1 TGATTTGT
1539142 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1539345 original size:33 final size:33
Alignment explanation
Indices: 1539303--1539502 Score: 231
Period size: 33 Copynumber: 5.8 Consensus size: 33
1539293 ACTAAATTCG
* * * *
1539303 CGTTGCGATTTTTATTTCGCTTTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1539336 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1539369 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* * *
1539408 CGTTGCGATTTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1539441 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1539474 CGTTGCGATTTTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
1539503 AGACATTAAA
Statistics
Matches: 143, Mismatches: 15, Indels: 17
0.82 0.09 0.10
Matches are distributed among these distances:
33 100 0.70
34 12 0.08
35 2 0.01
37 1 0.01
38 2 0.01
39 26 0.18
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1539415 original size:20 final size:19
Alignment explanation
Indices: 1539369--1539435 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
1539359 GCAATTCTCT
**
1539369 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
1539388 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
* *
1539408 CGTTGCGAT-TTTAGTTTCG
1 CGTTGCGATAGTCA-TTTCG
1539427 CGTTGCGAT
1 CGTTGCGAT
1539436 TTTGTCGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 27 0.68
20 13 0.32
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1539444 original size:105 final size:106
Alignment explanation
Indices: 1539301--1539509 Score: 323
Period size: 105 Copynumber: 2.0 Consensus size: 106
1539291 AAACTAAATT
* *
1539301 CGCGTTGCGATTTTTATTTCGCTTTGTGATTCCCTCGTTGCGATTTTCATTTCGCATTGCAATTC
1 CGCGTTGCGATTTTTATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCAATTC
*
1539366 TCTCGTTGCGATTTTCATTT-CGCATTGCGATAGTCATTTC
66 TCTCGTTGCGATTTTCATTTCCGCATTGCGATAGACATTTC
*** *
1539406 CGCGTTGCGA-TTTTAGTTTCGCGTTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 CGCGTTGCGATTTTTA-TTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCAATT
*
1539470 CTCTCGTTGCGATTTTCATTTCCGCGTTGCGATAGACATT
65 CTCTCGTTGCGATTTTCATTTCCGCATTGCGATAGACATT
1539510 AAAATGATTG
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
104 5 0.05
105 73 0.78
106 16 0.17
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (106 bp):
CGCGTTGCGATTTTTATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCAATTC
TCTCGTTGCGATTTTCATTTCCGCATTGCGATAGACATTTC
Found at i:1539548 original size:20 final size:20
Alignment explanation
Indices: 1539475--1539548 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
1539465 CGATTCTCTC
** *
1539475 GTTGCGATTTTCATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* ****
1539495 GTTGCGATAGACATTAAAAT
1 GTTGCGATAGTCATTTCCGT
1539515 GATTGCGA-ACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
1539536 GTTGCGATAGTCA
1 GTTGCGATAGTCA
1539549 AATGAATGTC
Statistics
Matches: 38, Mismatches: 13, Indels: 6
0.67 0.23 0.11
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:1542086 original size:24 final size:24
Alignment explanation
Indices: 1542035--1542086 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1542025 ATCCAAGTAT
** *
1542035 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
1542059 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
1542083 TGAC
1 TGAC
1542087 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:1542950 original size:20 final size:20
Alignment explanation
Indices: 1542927--1542988 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1542917 CGATAGTCAG
*
1542927 AATCTCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
* * **
1542947 AATCGCGTTGTGATTTTCCA
1 AATCGCGTTGCGATTTACGT
1542967 AATTCGCGTTGCGATTTACGT
1 AA-TCGCGTTGCGATTTACGT
1542988 A
1 A
1542989 TTCGTATTAC
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
AATCGCGTTGCGATTTACGT
Found at i:1543024 original size:21 final size:21
Alignment explanation
Indices: 1542998--1543042 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1542988 ATTCGTATTA
1542998 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* * *
1543019 CGAATTTGGGAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
1543040 CGA
1 CGA
1543043 TAATTAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:1549887 original size:2 final size:2
Alignment explanation
Indices: 1549876--1549907 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1549866 AAATTTATTA
1549876 AT AT -T 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 A
1549908 ATAATTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1551655 original size:29 final size:30
Alignment explanation
Indices: 1551609--1551674 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
1551599 TCATTAATTA
*
1551609 TTATTTTTAACAACAATTAATAATGTGTAT
1 TTATTTTTAACAACAATTAATAATGTATAT
* * * *
1551639 TTATTTTTAATAA-AATTATTATTTTATAT
1 TTATTTTTAACAACAATTAATAATGTATAT
1551668 TTATTTT
1 TTATTTT
1551675 ATATTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (30 bp):
TTATTTTTAACAACAATTAATAATGTATAT
Found at i:1552760 original size:2 final size:2
Alignment explanation
Indices: 1552753--1552779 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1552743 ACTCAACAGG
1552753 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 T
1552780 TCTCGTTCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1552965 original size:21 final size:21
Alignment explanation
Indices: 1552941--1552984 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1552931 ATATATAATA
*
1552941 CTGAATATTTTTTATTTATTT
1 CTGAATAATTTTTATTTATTT
1552962 CTGAATAATTTTTATTTATTT
1 CTGAATAATTTTTATTTATTT
1552983 CT
1 CT
1552985 TACCACCTCT
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:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (21 bp):
CTGAATAATTTTTATTTATTT
Found at i:1555125 original size:23 final size:23
Alignment explanation
Indices: 1555070--1555143 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
1555060 TAAACGGGCA
* *
1555070 TTAAATGAACATGCTCAAGAAAA
1 TTAAATAAACATGCTCAAGAAAG
* ** *
1555093 TCAAGCAAACATGCTCATGAAAG
1 TTAAATAAACATGCTCAAGAAAG
* *
1555116 TTAAATAAACATGTTCAAGAACG
1 TTAAATAAACATGCTCAAGAAAG
1555139 TTAAA
1 TTAAA
1555144 CGAGTATGTT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.23
Consensus pattern (23 bp):
TTAAATAAACATGCTCAAGAAAG
Found at i:1555175 original size:23 final size:23
Alignment explanation
Indices: 1555100--1555179 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 23
1555090 AAATCAAGCA
* * * *
1555100 AACATGCTCATGAAAGTTAAATA
1 AACATGTTCACGAACGTTAAATG
* *
1555123 AACATGTTCAAGAACGTTAAACG
1 AACATGTTCACGAACGTTAAATG
**
1555146 AGTATGTTCACGAACGTTAAATG
1 AACATGTTCACGAACGTTAAATG
1555169 AACATGTTCAC
1 AACATGTTCAC
1555180 AAACACTAAG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (23 bp):
AACATGTTCACGAACGTTAAATG
Found at i:1557755 original size:7 final size:7
Alignment explanation
Indices: 1557745--1557789 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
1557735 TTTCCATCAT
1557745 TTTCTTC
1 TTTCTTC
*
1557752 TTTCTTAT
1 TTTCTT-C
1557760 TCTTCTTC
1 T-TTCTTC
1557768 TTTCTTC
1 TTTCTTC
1557775 TTTCTTC
1 TTTCTTC
*
1557782 TTTTTTC
1 TTTCTTC
1557789 T
1 T
1557790 CTCCCTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 26 0.79
8 2 0.06
9 5 0.15
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTCTTC
Found at i:1557756 original size:23 final size:22
Alignment explanation
Indices: 1557722--1557780 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
1557712 GACTCCTATA
*
1557722 ATTTT-TT-TTTCTTTTTCCATC
1 ATTTTCTTCTTTCTTATT-CATC
*
1557743 ATTTTCTTCTTTCTTATTCTTC
1 ATTTTCTTCTTTCTTATTCATC
*
1557765 TTCTTTCTTCTTTCTT
1 AT-TTTCTTCTTTCTT
1557781 CTTTTTTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 5 0.16
22 6 0.19
23 21 0.66
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTTCTTCTTTCTTATTCATC
Found at i:1558905 original size:2 final size:2
Alignment explanation
Indices: 1558898--1558923 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1558888 ATTGAATCAC
1558898 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
1558924 AGTTACTCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1566203 original size:17 final size:17
Alignment explanation
Indices: 1566181--1566215 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1566171 ATCAACTTAG
* *
1566181 AGCAATTCTTTATCATA
1 AGCAATTCGTCATCATA
1566198 AGCAATTCGTCATCATA
1 AGCAATTCGTCATCATA
1566215 A
1 A
1566216 AGATGTTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (17 bp):
AGCAATTCGTCATCATA
Found at i:1580249 original size:32 final size:31
Alignment explanation
Indices: 1580203--1580316 Score: 131
Period size: 32 Copynumber: 3.6 Consensus size: 31
1580193 TTATCTTAGA
* **
1580203 GCCTCAGAGCCTACCCAATAGTGTACCTTGGG
1 GCCTCAGAGCCTACCCAA-GGAATACCTTGGG
*
1580235 GCCTAAGAGCCTACCCAAGGGAATA-CTTGGG
1 GCCTCAGAGCCTACCCAA-GGAATACCTTGGG
* * *
1580266 GACTTAGAGCCTAGCCAAGGAAATACCTTGGG
1 GCCTCAGAGCCTACCCAAGG-AATACCTTGGG
1580298 GCCTCAGAGCCTACCCAAG
1 GCCTCAGAGCCTACCCAAG
1580317 CGCCACCTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
30 2 0.03
31 25 0.36
32 42 0.61
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (31 bp):
GCCTCAGAGCCTACCCAAGGAATACCTTGGG
Found at i:1580275 original size:31 final size:32
Alignment explanation
Indices: 1580226--1580316 Score: 130
Period size: 31 Copynumber: 2.9 Consensus size: 32
1580216 CCCAATAGTG
*
1580226 TACCTTGGGGCCTAAGAGCCTACCCAAGGGAA
1 TACCTTGGGGCCTAAGAGCCTACCCAAGGAAA
* * *
1580258 TA-CTTGGGGACTTAGAGCCTAGCCAAGGAAA
1 TACCTTGGGGCCTAAGAGCCTACCCAAGGAAA
*
1580289 TACCTTGGGGCCTCAGAGCCTACCCAAG
1 TACCTTGGGGCCTAAGAGCCTACCCAAG
1580317 CGCCACCTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 27 0.53
32 24 0.47
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (32 bp):
TACCTTGGGGCCTAAGAGCCTACCCAAGGAAA
Found at i:1583680 original size:64 final size:64
Alignment explanation
Indices: 1583570--1583703 Score: 159
Period size: 64 Copynumber: 2.1 Consensus size: 64
1583560 TTCAATGTGT
*
1583570 ATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGTGTATCGATGCACAAG-TAGTGC
1 ATCGATGCACCCCTTTAAAATAAAAACATCGAATGCCATCAGTGTATCGATGCA-AAGATAGTGC
* * * *
1583634 ATCGATGCACCCCCTTT-AAATATAAACATCGAATAG-GATTTA-TGTATCGATGCATAGATAGT
1 ATCGATGCA-CCCCTTTAAAATAAAAACATCGAAT-GCCA-TCAGTGTATCGATGCAAAGATAGT
1583696 GC
63 GC
1583698 ATCGAT
1 ATCGAT
1583704 ACATGGTGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
63 2 0.03
64 50 0.82
65 9 0.15
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (64 bp):
ATCGATGCACCCCTTTAAAATAAAAACATCGAATGCCATCAGTGTATCGATGCAAAGATAGTGC
Found at i:1584377 original size:23 final size:22
Alignment explanation
Indices: 1584326--1584380 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
1584316 ATAATCTTAT
*
1584326 ATGGCACTATGGTGCAATTTTAC
1 ATGGCACT-TGGTGCAATTCTAC
*
1584349 ACGGCACTTCGGTGCAATTCTAC
1 ATGGCACTT-GGTGCAATTCTAC
*
1584372 GTGGCACTT
1 ATGGCACTT
1584381 TGATGTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (22 bp):
ATGGCACTTGGTGCAATTCTAC
Found at i:1585735 original size:21 final size:21
Alignment explanation
Indices: 1585709--1585752 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1585699 ATTTCTGGGA
* *
1585709 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
1585730 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
1585751 AA
1 AA
1585753 ACGACAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:1586466 original size:31 final size:31
Alignment explanation
Indices: 1586428--1586581 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
1586418 GGGTCGAGGG
1586428 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1586459 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1586490 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1586521 TTACCTAAGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1586552 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1586582 GTCCTTCGGG
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1586841 original size:2 final size:2
Alignment explanation
Indices: 1586834--1586876 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1586824 AGAAGATAAT
1586834 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
1586876 T
1 T
1586877 GAAAGGTGCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1590416 original size:21 final size:21
Alignment explanation
Indices: 1590390--1590434 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1590380 GATTTATGGG
* *
1590390 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1590411 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1590432 CAA
1 CAA
1590435 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1590504 original size:23 final size:22
Alignment explanation
Indices: 1590460--1590504 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1590450 AATGCCAGAG
*
1590460 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
1590482 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1590505 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:1591138 original size:31 final size:31
Alignment explanation
Indices: 1591100--1591253 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
1591090 GGGTCGAGGG
1591100 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1591131 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1591162 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1591193 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1591224 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1591254 GTCCTTCGGA
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Done.