Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 58 of 78
Found at i:11643779 original size:24 final size:19
Alignment explanation
Indices: 11643710--11643762 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
11643700 TGAAAAATTA
*
11643710 CTCCCCCTTAATCTAACACTT
1 CTCCCCTTTAA-C-AACACTT
11643731 CTCCCCTTTAACAACACTT
1 CTCCCCTTTAACAACACTT
11643750 CTCCCCTTTAACA
1 CTCCCCTTTAACA
11643763 CTTTTACACT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 20 0.65
20 1 0.03
21 10 0.32
ACGTcount: A:0.25, C:0.43, G:0.00, T:0.32
Consensus pattern (19 bp):
CTCCCCTTTAACAACACTT
Found at i:11645873 original size:16 final size:15
Alignment explanation
Indices: 11645849--11645887 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
11645839 GATTTCGACC
*
11645849 ATATCATATAATGAAT
1 ATATTATATAAT-AAT
11645865 ATATTATATAATAAT
1 ATATTATATAATAAT
11645880 ATA-TATAT
1 ATATTATAT
11645888 TTATACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 6 0.27
16 11 0.50
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
ATATTATATAATAAT
Found at i:11646978 original size:18 final size:18
Alignment explanation
Indices: 11646957--11647001 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
11646947 TTAATTCTAT
* *
11646957 TTATTTATTTACTTTTTA
1 TTATTTATTTACGTTATA
*
11646975 TTATTTAATTACGTTATA
1 TTATTTATTTACGTTATA
*
11646993 TTATATATT
1 TTATTTATT
11647002 CTGTTATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (18 bp):
TTATTTATTTACGTTATA
Found at i:11647018 original size:17 final size:18
Alignment explanation
Indices: 11646972--11647037 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
11646962 TATTTACTTT
*
11646972 TTATTATT-TA-ATTACG
1 TTATTATTATATATTATG
*
11646988 TTA-TATTATATATTCTG
1 TTATTATTATATATTATG
11647005 TTATTATTAT-TATTATG
1 TTATTATTATATATTATG
*
11647022 GTATTATATATATATT
1 TTATTAT-TATATATT
11647038 TCATTCTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 4 0.10
16 5 0.12
17 19 0.46
18 9 0.22
19 4 0.10
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (18 bp):
TTATTATTATATATTATG
Found at i:11647133 original size:4 final size:4
Alignment explanation
Indices: 11647117--11647209 Score: 52
Period size: 4 Copynumber: 23.0 Consensus size: 4
11647107 ATTATCATTC
* *
11647117 TTAT TTA- TCAT TTAT TTAT TTAT TTA- TTATT TTATT TTATT TTAT TTCT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTA-T TTA-T TTAT TTAT
* * *
11647166 TT-T TT-T TTGGT TAAAT TTAT TTAT TTATT TTCT TTAT TT-T TTAT
1 TTAT TTAT TT-AT T-TAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT
11647210 ATCTAACATG
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
3 14 0.19
4 39 0.53
5 20 0.27
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:11657537 original size:1 final size:1
Alignment explanation
Indices: 11657531--11657593 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
11657521 CCTAAGTTGG
* * * * * * *
11657531 AAAAAAAAACAAAAAAACAAAAACAAAAAAACAAAAAAACAAAAAAAACAAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11657594 GAGAAGAACG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11657546 original size:9 final size:8
Alignment explanation
Indices: 11657533--11657593 Score: 90
Period size: 8 Copynumber: 7.6 Consensus size: 8
11657523 TAAGTTGGAA
11657533 AAAAAAAC
1 AAAAAAAC
11657541 AAAAAAAC
1 AAAAAAAC
11657549 --AAAAAC
1 AAAAAAAC
11657555 AAAAAAAC
1 AAAAAAAC
11657563 AAAAAAAC
1 AAAAAAAC
11657571 AAAAAAAAC
1 -AAAAAAAC
11657580 AAAAAAAAC
1 -AAAAAAAC
11657589 AAAAA
1 AAAAA
11657594 GAGAAGAACG
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.12
8 27 0.54
9 17 0.34
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:11657561 original size:22 final size:21
Alignment explanation
Indices: 11657531--11657587 Score: 89
Period size: 22 Copynumber: 2.7 Consensus size: 21
11657521 CCTAAGTTGG
11657531 AAAAAAAAACAAAAAAACAAA
1 AAAAAAAAACAAAAAAACAAA
11657552 AACAAAAAAACAAAAAAACAAA
1 AA-AAAAAAACAAAAAAACAAA
*
11657574 AAAAACAAA-AAAAA
1 AAAAAAAAACAAAAA
11657588 CAAAAAGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 5 0.15
21 8 0.24
22 21 0.62
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAAAAAACAAAAAAACAAA
Found at i:11658611 original size:105 final size:105
Alignment explanation
Indices: 11658429--11659205 Score: 1320
Period size: 105 Copynumber: 7.4 Consensus size: 105
11658419 CAGGTTTTAC
11658429 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
11658494 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
11658534 CCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
11658599 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
11658639 CCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
11658704 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATA
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
11658744 CCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
11658809 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* * *
11658849 TCAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
11658914 GACGAAGGGACCGCTGGTTGTCAACAAACGTTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
11658954 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
11659019 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* * ****
11659059 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTATAAGTTCAACTTCAC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* ** ** * *
11659124 GACGAAGGGGCCGCTGACTGTCAACCGACGATTTCCCAGTT
66 GACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATT
* * *
11659165 CCAGAACCAATTTCAACTTCACAGCGGAGGATATTGGACTC
1 CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
11659206 GGAACAATAT
Statistics
Matches: 644, Mismatches: 27, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 598 0.93
106 46 0.07
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
CCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:11659691 original size:16 final size:15
Alignment explanation
Indices: 11659667--11659705 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
11659657 GATTTTGACC
*
11659667 ATATCATATAATGAAT
1 ATATTATATAAT-AAT
11659683 ATATTATATAATAAT
1 ATATTATATAATAAT
11659698 ATA-TATAT
1 ATATTATAT
11659706 TTATACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 6 0.27
16 11 0.50
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
ATATTATATAATAAT
Found at i:11660797 original size:18 final size:18
Alignment explanation
Indices: 11660776--11660820 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
11660766 TTAATTCTAT
* *
11660776 TTATTTATTTACTTTTTA
1 TTATTTATTTACGTTATA
*
11660794 TTATTTAATTACGTTATA
1 TTATTTATTTACGTTATA
*
11660812 TTATATATT
1 TTATTTATT
11660821 CTGTTATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (18 bp):
TTATTTATTTACGTTATA
Found at i:11660837 original size:17 final size:18
Alignment explanation
Indices: 11660791--11660856 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
11660781 TATTTACTTT
*
11660791 TTATTATT-TA-ATTACG
1 TTATTATTATATATTATG
*
11660807 TTA-TATTATATATTCTG
1 TTATTATTATATATTATG
11660824 TTATTATTAT-TATTATG
1 TTATTATTATATATTATG
*
11660841 GTATTATATATATATT
1 TTATTAT-TATATATT
11660857 TCATTCTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 4 0.10
16 5 0.12
17 19 0.46
18 9 0.22
19 4 0.10
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (18 bp):
TTATTATTATATATTATG
Found at i:11660952 original size:4 final size:4
Alignment explanation
Indices: 11660936--11661028 Score: 52
Period size: 4 Copynumber: 23.0 Consensus size: 4
11660926 ATTATCATTC
* *
11660936 TTAT TTA- TCAT TTAT TTAT TTAT TTA- TTATT TTATT TTATT TTAT TTCT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTA-T TTA-T TTAT TTAT
* * *
11660985 TT-T TT-T TTGGT TAAAT TTAT TTAT TTATT TTCT TTAT TT-T TTAT
1 TTAT TTAT TT-AT T-TAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT
11661029 ATCTAACATG
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
3 14 0.19
4 39 0.53
5 20 0.27
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:11661459 original size:23 final size:22
Alignment explanation
Indices: 11661431--11661512 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
11661421 GCATGGCCTT
11661431 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * **
11661453 CGTGCATCGGTGCACCTT-AATA
1 -GTGCATCGATGCACATTCAAGG
*
11661475 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
11661498 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
11661513 TGTTAAGTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 18 0.39
24 12 0.26
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:11667299 original size:65 final size:64
Alignment explanation
Indices: 11667166--11667373 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 64
11667156 TGCACTAAGA
*
11667166 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATAGCTG
* * *
11667230 GTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-A-CTCTGAGTGCATTGATGCATAG-
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGC-CTGAGTGCATCGATGCATAGC
*
11667292 TAT
63 T-G
* * ** * *
11667295 GTGCATCAATGCATGAAATGCATTCGAT-TTTCAATTTATTCCATG-GTGCATCGATGCATAGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-GCC-TGAGTGCATCGATGCATAG-C
11667358 TG
63 TG
*
11667360 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
11667374 TACTTTGAAA
Statistics
Matches: 120, Mismatches: 14, Indels: 19
0.78 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 45 0.38
65 64 0.53
66 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATAGCTG
Found at i:11667728 original size:36 final size:37
Alignment explanation
Indices: 11667688--11667780 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 37
11667678 AAGTGAGAAA
*
11667688 AAATTTGTTTTGT-GAG-AAATTGTCTCAAACGAGACG
1 AAATTTATTTT-TAGAGAAAATTGTCTCAAACGAGACG
* * *
11667724 AAATTTATTTTTAGCGAAAATTGTCTCTAGCGAGACG
1 AAATTTATTTTTAGAGAAAATTGTCTCAAACGAGACG
* **
11667761 ACACTTTATTTCGAGAGAAA
1 A-AATTTATTTTTAGAGAAA
11667781 CAACATCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 1 0.02
36 12 0.26
37 19 0.41
38 14 0.30
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (37 bp):
AAATTTATTTTTAGAGAAAATTGTCTCAAACGAGACG
Found at i:11668919 original size:6 final size:6
Alignment explanation
Indices: 11668908--11668956 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
11668898 GTTTCTTGTC
*
11668908 TTCTTT TTCTTT GTT-TTT TTCTTT TTCCTTT TTC--T TTCCTT TTCTTT
1 TTCTTT TTCTTT -TTCTTT TTCTTT TT-CTTT TTCTTT TTCTTT TTCTTT
11668955 TT
1 TT
11668957 TTCTCTTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
4 4 0.11
5 2 0.05
6 23 0.62
7 8 0.22
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:11668931 original size:18 final size:17
Alignment explanation
Indices: 11668908--11668958 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
11668898 GTTTCTTGTC
11668908 TTCTTTTTCTTTGTTTTT
1 TTCTTTTTCTTT-TTTTT
* *
11668926 TTCTTTTTCCTTTTTCT
1 TTCTTTTTCTTTTTTTT
*
11668943 TTCCTTTTCTTTTTTT
1 TTCTTTTTCTTTTTTT
11668959 CTCTTTGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (17 bp):
TTCTTTTTCTTTTTTTT
Found at i:11668950 original size:25 final size:26
Alignment explanation
Indices: 11668909--11668964 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
11668899 TTTCTTGTCT
* *
11668909 TCTTTTTCTTT-GTTTTTTTCTTTTTC
1 TCTTTTTCTTTCCTTTTCTT-TTTTTC
11668935 -CTTTTTCTTTCCTTTTCTTTTTTTC
1 TCTTTTTCTTTCCTTTTCTTTTTTTC
11668960 TCTTT
1 TCTTT
11668965 GATTTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (26 bp):
TCTTTTTCTTTCCTTTTCTTTTTTTC
Found at i:11668959 original size:18 final size:18
Alignment explanation
Indices: 11668912--11668960 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
11668902 CTTGTCTTCT
*
11668912 TTTTCTTTGTTTT-TTTCT
1 TTTTCTTT-TTTTCTTTCC
*
11668930 TTTTC-CTTTTTCTTTCC
1 TTTTCTTTTTTTCTTTCC
11668947 TTTTCTTTTTTTCT
1 TTTTCTTTTTTTCT
11668961 CTTTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 10 0.38
18 12 0.46
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTTCTTTCC
Found at i:11668976 original size:15 final size:15
Alignment explanation
Indices: 11668952--11669017 Score: 89
Period size: 15 Copynumber: 4.3 Consensus size: 15
11668942 TTTCCTTTTC
11668952 TTTTTTTCTCTTTGA
1 TTTTTTTCTCTTTGA
11668967 TTTTTTTCTCTTTGCAA
1 TTTTTTTCTCTTTG--A
*
11668984 TTTTTTTTTCTTTGA
1 TTTTTTTCTCTTTGA
*
11668999 TTATTTTCTCTTT-A
1 TTTTTTTCTCTTTGA
11669013 TTTTT
1 TTTTT
11669018 CTCTTTGCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
14 5 0.11
15 26 0.58
17 14 0.31
ACGTcount: A:0.09, C:0.12, G:0.05, T:0.74
Consensus pattern (15 bp):
TTTTTTTCTCTTTGA
Found at i:11669029 original size:32 final size:30
Alignment explanation
Indices: 11668952--11669032 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 30
11668942 TTTCCTTTTC
* *
11668952 TTTTTTTCTCTTTGATTTTTTTCTCTTTGCAA
1 TTTTTTTTTCTTTGATTATTTTCTCTTT--AA
11668984 TTTTTTTTTCTTTGATTATTTTCTCTTT-A
1 TTTTTTTTTCTTTGATTATTTTCTCTTTAA
11669013 TTTTTCTCTTTGCTTTGATT
1 TTTTT-T-TTT-CTTTGATT
11669033 TGATCTTCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
29 6 0.14
30 1 0.02
31 3 0.07
32 34 0.77
ACGTcount: A:0.09, C:0.14, G:0.06, T:0.72
Consensus pattern (30 bp):
TTTTTTTTTCTTTGATTATTTTCTCTTTAA
Found at i:11674502 original size:3 final size:3
Alignment explanation
Indices: 11674494--11674546 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
11674484 AGATGTTAAC
*
11674494 ATA ATA ATA TTA ATA ATA ATA ATA ATA GATA A-A AT- ATA A-A ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA AT-A
11674538 ATA A-A ATA A
1 ATA ATA ATA A
11674547 AAAAGACCCG
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 8 0.19
3 28 0.67
4 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:11674536 original size:16 final size:16
Alignment explanation
Indices: 11674512--11674549 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
11674502 ATTAATAATA
*
11674512 ATAATAATAGATAAAAT
1 ATAA-AATAAATAAAAT
11674529 ATAAAATAAATAAAAT
1 ATAAAATAAATAAAAT
11674545 A-AAAA
1 ATAAAA
11674550 AGACCCGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 12 0.60
17 4 0.20
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
ATAAAATAAATAAAAT
Found at i:11677513 original size:35 final size:34
Alignment explanation
Indices: 11677438--11677692 Score: 124
Period size: 35 Copynumber: 7.3 Consensus size: 34
11677428 TTTTAGATAC
** * *
11677438 GTTTTCAAAATCC-TTTAAAAACCATATATTATAA
1 GTTTTCAAAA-CCATTTAAAAAATATATACTATAT
*
11677472 G-CTTCAAAACCATTTAGAAAAATATATTA-TATAT
1 GTTTTCAAAACCATTTA-AAAAATATA-TACTATAT
* * * *
11677506 GTTTTCAAAACCATTTTTAAAATTATATATTATAC
1 GTTTTCAAAACCA-TTTAAAAAATATATACTATAT
** *
11677541 GTTTTCAAAAGTATCTTAAAAATTATATACTATAT
1 GTTTTCAAAACCAT-TTAAAAAATATATACTATAT
* ** * * * *
11677576 GTTTTAAAAATCGTTTTGAAAACTATTATATTATAC
1 GTTTTCAAAA-CCATTTAAAAAATA-TATACTATAT
* * *
11677612 ATTTTCAAAACTATATTTTAAAAACA-ATATATTATAT
1 GTTTTCAAAAC--CA-TTTAAAAA-ATATATACTATAT
** * * *
11677649 -TTTTCAAAATTATTTTAAAACTATATACTATAC
1 GTTTTCAAAACCATTTAAAAAATATATACTATAT
*
11677682 ATTTTCAAAAC
1 GTTTTCAAAAC
11677693 TCTTTTTTTA
Statistics
Matches: 172, Mismatches: 34, Indels: 30
0.73 0.14 0.13
Matches are distributed among these distances:
32 2 0.01
33 27 0.16
34 27 0.16
35 70 0.41
36 29 0.17
37 9 0.05
38 8 0.05
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (34 bp):
GTTTTCAAAACCATTTAAAAAATATATACTATAT
Found at i:11677548 original size:70 final size:68
Alignment explanation
Indices: 11677438--11677693 Score: 243
Period size: 70 Copynumber: 3.7 Consensus size: 68
11677428 TTTTAGATAC
* * * ** *
11677438 GTTTTCAAAATC-CTTTAAAAACCATATATTATA-AGCTTCAAAACCATTTAGAAAAATATATTA
1 GTTTTCAAAATCATTTTTAAAACTATATATTATACATTTTCAAAACTATTTA-AAAAATATA-TA
11677501 TATAT
64 TATAT
* * * * *
11677506 GTTTTCAAAACCATTTTTAAAATTATATATTATACGTTTTCAAAAGTATCTTAAAAATTATATAC
1 GTTTTCAAAATCATTTTTAAAACTATATATTATACATTTTCAAAACTAT-TTAAAAAATATATA-
11677571 TATAT
64 TATAT
* * *
11677576 GTTTTAAAAATCGTTTTGAAAACTATTATATTATACATTTTCAAAACTATATTTTAAAAACA-AT
1 GTTTTCAAAATCATTTTTAAAACTA-TATATTATACATTTTCAAAAC--TA-TTTAAAAA-ATAT
11677640 ATATTATAT
61 ATA-TATAT
* *
11677649 -TTTTCAAAATTA-TTTTAAAACTATATACTATACATTTTCAAAACT
1 GTTTTCAAAATCATTTTTAAAACTATATATTATACATTTTCAAAACT
11677694 CTTTTTTTAA
Statistics
Matches: 154, Mismatches: 25, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
68 12 0.08
69 19 0.12
70 62 0.40
71 32 0.21
72 9 0.06
73 19 0.12
74 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (68 bp):
GTTTTCAAAATCATTTTTAAAACTATATATTATACATTTTCAAAACTATTTAAAAAATATATATA
TAT
Found at i:11677706 original size:70 final size:73
Alignment explanation
Indices: 11677484--11677726 Score: 221
Period size: 70 Copynumber: 3.4 Consensus size: 73
11677474 TTCAAAACCA
* * * * * * *
11677484 TTTAGAAA-AATATATTATATATGTTTTCAAAACCATTTTTAAAATTA-TATATTATACGTTTTC
1 TTTAAAAACAATATA-T-TATATGTTTTAAAAATCATTTTGAAAACTATTATACTATACATTTTC
*
11677547 AAAA--GTAT
64 AAAACTATAT
* ** * * *
11677555 CTTAAAAATTATATACTATATGTTTTAAAAATCGTTTTGAAAACTATTATATTATACATTTTCAA
1 TTTAAAAACAATATATTATATGTTTTAAAAATCATTTTGAAAACTATTATACTATACATTTTCAA
11677620 AACTATAT
66 AACTATAT
* *
11677628 TTTAAAAACAATATATTATAT-TTTTCAAAATTATTTT-AAAACTA-TATACTATACATTTTCAA
1 TTTAAAAACAATATATTATATGTTTTAAAAATCATTTTGAAAACTATTATACTATACATTTTCAA
* *
11677690 AACTCTTT
66 AACTATAT
*
11677698 TTTTAAAACTATATATTATTATATGTTTT
1 TTTAAAAAC-A-ATA-TATTATATGTTTT
11677727 CGAAACTACG
Statistics
Matches: 142, Mismatches: 22, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
70 56 0.39
71 33 0.23
72 21 0.15
73 28 0.20
74 4 0.03
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.47
Consensus pattern (73 bp):
TTTAAAAACAATATATTATATGTTTTAAAAATCATTTTGAAAACTATTATACTATACATTTTCAA
AACTATAT
Found at i:11690778 original size:35 final size:35
Alignment explanation
Indices: 11690738--11690922 Score: 164
Period size: 35 Copynumber: 5.2 Consensus size: 35
11690728 TATCATACGC
* **
11690738 TTCAAAACCATTTCGAAAAATATATTATATATGTT
1 TTCAAAACTATTTTTAAAAATATATTATATATGTT
*
11690773 TTCAAAACCATTTTTAAAATTATATATTATA-A-GTT
1 TTCAAAACTATTTTTAAAA--ATATATTATATATGTT
* * *
11690808 TTCAAAATTATCTTTAAAACTATA-TACTATATGTT
1 TTCAAAACTATTTTTAAAAATATATTA-TATATGTT
* * *
11690843 TTCAAAATTATTTTAAAAACTATATATTATAT-TTTT
1 TTCAAAACTATTTTTAAAA--ATATATTATATATGTT
*
11690879 TTCAAAACTATTTTTAAAAA-ACTATATATTATATATT
1 TTCAAAACTATTTTTAAAAATA-TAT-TA-TATATGTT
11690916 TTCAAAA
1 TTCAAAA
11690923 AAAAAATAAG
Statistics
Matches: 125, Mismatches: 13, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
32 2 0.02
33 7 0.06
34 5 0.04
35 58 0.46
36 24 0.19
37 27 0.22
38 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (35 bp):
TTCAAAACTATTTTTAAAAATATATTATATATGTT
Found at i:11690812 original size:70 final size:71
Alignment explanation
Indices: 11690738--11690922 Score: 189
Period size: 70 Copynumber: 2.6 Consensus size: 71
11690728 TATCATACGC
* * * *
11690738 TTCAAAACCATTTCGAAAAATATATTA-TATATGTTTTCAAAACCATTTTTAAAATTATATATTA
1 TTCAAAACTATTT-TAAAAATATATTACTATATGTTTTCAAAACCATTTTAAAAACTATATATTA
11690802 TA-AGTT
65 TATAGTT
* * **
11690808 TTCAAAATTATCTTTAAAACTATA-TACTATATGTTTTCAAAATTATTTTAAAAACTATATATTA
1 TTCAAAACTAT-TTTAAAAATATATTACTATATGTTTTCAAAACCATTTTAAAAACTATATATTA
**
11690872 TATTTTT
65 TATAGTT
* *
11690879 TTCAAAACTATTTTTAAAAA-ACTATATATTATATATTTTCAAAA
1 TTCAAAACTA-TTTTAAAAATA-TAT-TACTATATGTTTTCAAAA
11690923 AAAAAATAAG
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
69 2 0.02
70 53 0.56
71 22 0.23
72 1 0.01
73 16 0.17
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (71 bp):
TTCAAAACTATTTTAAAAATATATTACTATATGTTTTCAAAACCATTTTAAAAACTATATATTAT
ATAGTT
Found at i:11691678 original size:15 final size:15
Alignment explanation
Indices: 11691660--11691688 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11691650 CTCAGCCACT
11691660 CTTGGTTCAGCTCCC
1 CTTGGTTCAGCTCCC
11691675 CTTGGTTCAGCTCC
1 CTTGGTTCAGCTCC
11691689 AACAGTGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.38, G:0.21, T:0.34
Consensus pattern (15 bp):
CTTGGTTCAGCTCCC
Found at i:11695877 original size:39 final size:39
Alignment explanation
Indices: 11695802--11695877 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
11695792 AAATGAATAC
*
11695802 GACATTGCTGGTCAAACACAATTGAATATTGGTGATTAT
1 GACATTGCTGGTCAAACACAATTGAATATAGGTGATTAT
* * *
11695841 GACATTGTTGGTCAAATACAATTGAATATAGTTGATT
1 GACATTGCTGGTCAAACACAATTGAATATAGGTGATT
11695878 TCTTTACCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (39 bp):
GACATTGCTGGTCAAACACAATTGAATATAGGTGATTAT
Found at i:11699190 original size:284 final size:287
Alignment explanation
Indices: 11698620--11699191 Score: 823
Period size: 287 Copynumber: 2.0 Consensus size: 287
11698610 CTACTTGAGA
* * * * *
11698620 CATCAATTAATACATGCCCTATACGTACTTGGCTCCCCAGGCATTGGAATACCTCCTCATTTTCT
1 CATCAAATAATACATACCCCATACGTACTTGGCTCCCCAAGCATTGGAATACCTCATCATTTTCT
* * *
11698685 CTCATTTTGTTGGTTTATTGATGTGGCATTTCCTTTGAAATCCTCAGAATCAACAACACCATCTC
66 ATCATTTTGTTGGATTATTGA-GTGGCATTTCCTGTGAAATCCTCAGAATCAACAACACCATCTC
* **
11698750 TGGCATCTGGATGCAATCATCGTGTATTTGTTAACCAAGATTTTACTCATCAAACTTCTTTCCTT
130 TAGCATCTGGATGCAATCATCGTGTATTTGTTAACCAAGATTTTACTCATCAAACTTAATTCCTT
* *
11698815 ATTCTTCTTTAGGTCAAGTTCACTCATCTTGTCTTCAAAACTCATTAAAATCCAAAATCACTCAT
195 ATTCTTCTTTAGGTCAAGTTCACTCATCATGTCTTCAAAACTCATTAAAATCCAAAATAACTCAT
11698880 CATCATCAAATATCATTAAAGATGGCAC
260 CATCATCAAATATCATTAAAGATGGCAC
* * *
11698908 CATCAAATAATACATACCCCATGCGTACTTGGCTCCCTAAGCATTGGAATGCCTCATCATTTTCC
1 CATCAAATAATACATACCCCATACGTACTTGGCTCCCCAAGCATTGGAATACCTCATCATTTT-C
* * **
11698973 TATCATTTTGTT-GATTATTGCA-TGGCATTTCCTGTGAAATCGTCATAATCAACTGCATCC-TC
65 TATCATTTTGTTGGATTATTG-AGTGGCATTTCCTGTGAAATCCTCAGAATCAACAACA-CCATC
* * * *
11699035 TCTAGTATCTGGATGCAGTGATTGTGTATTTGTTAACCAAGATTTTACTCATCAAACTTAATTCC
128 TCTAGCATCTGGATGCAATCATCGTGTATTTGTTAACCAAGATTTTACTCATCAAACTTAATTCC
* * *
11699100 TTCTTC-TC-TT-GGTCAAGTTCACTCATCATGTCTTCACAACTCATTAAAATCCAAAATAACTT
193 TTATTCTTCTTTAGGTCAAGTTCACTCATCATGTCTTCAAAACTCATTAAAATCCAAAATAACTC
11699162 ATCATCATCAAATATCATTAAAGATGGCAC
258 ATCATCATCAAATATCATTAAAGATGGCAC
11699192 TATTAAAGTT
Statistics
Matches: 254, Mismatches: 27, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
284 78 0.31
285 2 0.01
286 2 0.01
287 95 0.37
288 64 0.25
289 13 0.05
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (287 bp):
CATCAAATAATACATACCCCATACGTACTTGGCTCCCCAAGCATTGGAATACCTCATCATTTTCT
ATCATTTTGTTGGATTATTGAGTGGCATTTCCTGTGAAATCCTCAGAATCAACAACACCATCTCT
AGCATCTGGATGCAATCATCGTGTATTTGTTAACCAAGATTTTACTCATCAAACTTAATTCCTTA
TTCTTCTTTAGGTCAAGTTCACTCATCATGTCTTCAAAACTCATTAAAATCCAAAATAACTCATC
ATCATCAAATATCATTAAAGATGGCAC
Found at i:11702917 original size:7 final size:7
Alignment explanation
Indices: 11702885--11702909 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11702875 AACATACGCA
11702885 ACACTCC
1 ACACTCC
11702892 ACACTCC
1 ACACTCC
11702899 ACACTCC
1 ACACTCC
11702906 ACAC
1 ACAC
11702910 ACTCCACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.56, G:0.00, T:0.12
Consensus pattern (7 bp):
ACACTCC
Found at i:11706987 original size:21 final size:21
Alignment explanation
Indices: 11706933--11707006 Score: 94
Period size: 21 Copynumber: 3.3 Consensus size: 21
11706923 ACTGTTACCA
*
11706933 GAGTTGTTAGTAGCAGTTAGGCTT
1 GAGTTGTTAGT---AGTAAGGCTT
11706957 GAGTTTGTTAGTAGTAAGGCTT
1 GAG-TTGTTAGTAGTAAGGCTT
11706979 GAGTTGTTAGTAGTAAGGCTT
1 GAGTTGTTAGTAGTAAGGCTT
*
11707000 TAGTTGT
1 GAGTTGT
11707007 GAGCTATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
21 24 0.51
22 12 0.26
24 3 0.06
25 8 0.17
ACGTcount: A:0.22, C:0.05, G:0.32, T:0.41
Consensus pattern (21 bp):
GAGTTGTTAGTAGTAAGGCTT
Found at i:11716644 original size:18 final size:19
Alignment explanation
Indices: 11716621--11716657 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11716611 GGTCAGGCTT
11716621 GCCCA-CCCAGTTAGGTTC
1 GCCCACCCCAGTTAGGTTC
*
11716639 GCCCACCCCGGTTAGGTTC
1 GCCCACCCCAGTTAGGTTC
11716658 CTTGCTAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.14, C:0.41, G:0.24, T:0.22
Consensus pattern (19 bp):
GCCCACCCCAGTTAGGTTC
Found at i:11716731 original size:3 final size:3
Alignment explanation
Indices: 11716723--11716748 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11716713 ATGGGAAATA
11716723 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
11716749 ATTAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11716906 original size:35 final size:35
Alignment explanation
Indices: 11716831--11717120 Score: 263
Period size: 35 Copynumber: 8.3 Consensus size: 35
11716821 TTTTCGATAC
* *
11716831 GTTTTCAAAATCC--TTTAAAAACCATATATTATAC
1 GTTTTCAAAA-CCATTTTAAAAACTATATATTATAT
* *
11716865 G-CTTCAAAACCATTTCGAAAAA-TATAT-TATATAT
1 GTTTTCAAAACCATTT-TAAAAACTATATAT-TATAT
* *
11716899 GTTTTCAAAACCATTTT-AAAATTATATATTATAC
1 GTTTTCAAAACCATTTTAAAAACTATATATTATAT
** *
11716933 GTTTTCAAAATTATCTTAAAAACTATATATTATAT
1 GTTTTCAAAACCATTTTAAAAACTATATATTATAT
*
11716968 GTTTTCATAACCATTTTAAAAACTATATATTATAT
1 GTTTTCAAAACCATTTTAAAAACTATATATTATAT
* * * ** *
11717003 ATTTTCATAACCATTTTATAAACTATATAGAATAC
1 GTTTTCAAAACCATTTTAAAAACTATATATTATAT
* *
11717038 ATTTTCAAAACTACTTTTTAAAAACTATATATTATAT
1 GTTTTCAAAAC--CATTTTAAAAACTATATATTATAT
* **
11717075 ATTTT-AAAA-TTTTTTAAGAAAACTATATATTATAT
1 GTTTTCAAAACCATTTT-A-AAAACTATATATTATAT
11717110 GTTTTCGAAAA
1 GTTTTC-AAAA
11717121 TACGACCTCA
Statistics
Matches: 213, Mismatches: 29, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
32 2 0.01
33 17 0.08
34 36 0.17
35 126 0.59
36 4 0.02
37 28 0.13
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.43
Consensus pattern (35 bp):
GTTTTCAAAACCATTTTAAAAACTATATATTATAT
Found at i:11718765 original size:3 final size:3
Alignment explanation
Indices: 11718757--11718804 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
11718747 CGATTCGTTA
*
11718757 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT AAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
11718802 TAT
1 TAT
11718805 AAATTTACAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:11718773 original size:14 final size:14
Alignment explanation
Indices: 11718754--11718804 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
11718744 ACCCGATTCG
11718754 TTATATTATTATTA
1 TTATATTATTATTA
11718768 TTATATTATTATTA
1 TTATATTATTATTA
*
11718782 -T-TATTATTATAA
1 TTATATTATTATTA
11718794 TTA-ATTATTAT
1 TTATATTATTAT
11718805 AAATTTACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
12 10 0.29
13 10 0.29
14 14 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATATTATTATTA
Found at i:11719975 original size:2 final size:2
Alignment explanation
Indices: 11719968--11719998 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
11719958 ATCACTACCG
11719968 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11719999 ATCAATATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11731480 original size:36 final size:36
Alignment explanation
Indices: 11731440--11731574 Score: 173
Period size: 36 Copynumber: 3.7 Consensus size: 36
11731430 TTCTCAATTT
11731440 AATCAAGCCTTCACAAAAGAGTAGTGGAACAATGCA
1 AATCAAGCCTTCACAAAAGAGTAGTGGAACAATGCA
* * *
11731476 AATCAGGCCTTCATAAAAGAGTAGTGGAGCAATGCA
1 AATCAAGCCTTCACAAAAGAGTAGTGGAACAATGCA
* *
11731512 AATCAAGCCTTCACAAAAGAGTAAT-GAAGCAATGTA
1 AATCAAGCCTTCACAAAAGAGTAGTGGAA-CAATGCA
** *
11731548 AATTTAGCCTTAACAAAAAGAGTAGTG
1 AATCAAGCCTTCAC-AAAAGAGTAGTG
11731575 AAGCAAGATC
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 2 0.02
36 72 0.86
37 10 0.12
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (36 bp):
AATCAAGCCTTCACAAAAGAGTAGTGGAACAATGCA
Found at i:11731783 original size:3 final size:3
Alignment explanation
Indices: 11731761--11731807 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
11731751 TTCATTATAA
* *
11731761 TAT TAA TAT TAC TA- TAT TAT TAT TAT TAT TAT TAT TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
11731806 TA
1 TA
11731808 CAATTTTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:11732994 original size:2 final size:2
Alignment explanation
Indices: 11732987--11733063 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
11732977 ATCACTATCG
11732987 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
11733029 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 T
11733064 CAGATTTAGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11740624 original size:9 final size:9
Alignment explanation
Indices: 11740610--11740634 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11740600 TCCATCTCCT
11740610 CAACCATGA
1 CAACCATGA
11740619 CAACCATGA
1 CAACCATGA
11740628 CAACCAT
1 CAACCAT
11740635 CAACTTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.36, G:0.08, T:0.12
Consensus pattern (9 bp):
CAACCATGA
Found at i:11741686 original size:21 final size:21
Alignment explanation
Indices: 11741660--11741699 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11741650 ACTTGCAAAA
*
11741660 ATCAAGCTTACAACTTTTAAC
1 ATCAAGCTTACAAATTTTAAC
11741681 ATCAAGCTTACAAATTTTA
1 ATCAAGCTTACAAATTTTA
11741700 GTCTGTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (21 bp):
ATCAAGCTTACAAATTTTAAC
Found at i:11744506 original size:28 final size:28
Alignment explanation
Indices: 11744475--11744530 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
11744465 TCTATTTTTT
*
11744475 TTTTCAAAAACTCTTGTTTCTCAACATG
1 TTTTCAAAAACTATTGTTTCTCAACATG
11744503 TTTTCAAAAACTATTGTTTCTCAACATG
1 TTTTCAAAAACTATTGTTTCTCAACATG
11744531 GTATCAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (28 bp):
TTTTCAAAAACTATTGTTTCTCAACATG
Found at i:11744537 original size:28 final size:28
Alignment explanation
Indices: 11744478--11744537 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
11744468 ATTTTTTTTT
* * *
11744478 TCAAAAACTCTTGTTTCTCAACATGTTT
1 TCAAAAACTATTGTTTCTCAACATGGTA
11744506 TCAAAAACTATTGTTTCTCAACATGGTA
1 TCAAAAACTATTGTTTCTCAACATGGTA
11744534 TCAA
1 TCAA
11744538 TCACAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.38
Consensus pattern (28 bp):
TCAAAAACTATTGTTTCTCAACATGGTA
Found at i:11746637 original size:25 final size:23
Alignment explanation
Indices: 11746604--11746670 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 23
11746594 CGTTGTGTTA
*
11746604 GAGTTGTTAGTAGCAGTTAGGCTT
1 GAGTTGTTAGTAG-AGTAAGGCTT
11746628 GAGTTTGTTAG--GAGTAAGGCTT
1 GAG-TTGTTAGTAGAGTAAGGCTT
*
11746650 GAGTTATTAGT--AGTAAGGCTT
1 GAGTTGTTAGTAGAGTAAGGCTT
11746671 TAATTATGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 16 0.41
22 12 0.31
23 1 0.03
24 3 0.08
25 7 0.18
ACGTcount: A:0.24, C:0.06, G:0.33, T:0.37
Consensus pattern (23 bp):
GAGTTGTTAGTAGAGTAAGGCTT
Found at i:11746664 original size:21 final size:22
Alignment explanation
Indices: 11746622--11746670 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
11746612 AGTAGCAGTT
*
11746622 AGGCTTGAGTTTGTTAGGAGTA
1 AGGCTTGAGTTTATTAGGAGTA
*
11746644 AGGCTTGAG-TTATTAGTAGTA
1 AGGCTTGAGTTTATTAGGAGTA
11746665 AGGCTT
1 AGGCTT
11746671 TAATTATGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.24, C:0.06, G:0.33, T:0.37
Consensus pattern (22 bp):
AGGCTTGAGTTTATTAGGAGTA
Found at i:11746677 original size:21 final size:21
Alignment explanation
Indices: 11746635--11746677 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11746625 CTTGAGTTTG
*
11746635 TTAGGAGTAAGGCTTGAGTTA
1 TTAGGAGTAAGGCTTGAATTA
* *
11746656 TTAGTAGTAAGGCTTTAATTA
1 TTAGGAGTAAGGCTTGAATTA
11746677 T
1 T
11746678 GAGCTATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.05, G:0.26, T:0.40
Consensus pattern (21 bp):
TTAGGAGTAAGGCTTGAATTA
Found at i:11754298 original size:15 final size:16
Alignment explanation
Indices: 11754278--11754308 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11754268 TTATCCAAAT
11754278 TTTGA-TATTAAATGC
1 TTTGATTATTAAATGC
11754293 TTTGATTATTAAATGC
1 TTTGATTATTAAATGC
11754309 AATTGGCGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (16 bp):
TTTGATTATTAAATGC
Found at i:11756085 original size:26 final size:24
Alignment explanation
Indices: 11756022--11756091 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 24
11756012 GAATTTTTTT
* * *
11756022 TTAAGAAGGTTTAAGGTTTTTTTG
1 TTAAAAAGGTTTAGGGTTTTTCTG
**
11756046 TTAAAAATAATTTAGGCGTTTCTTCTG
1 TTAAAAA-GGTTTAGG-GTTT-TTCTG
11756073 TTAAAAAGGTTTAGGGTTT
1 TTAAAAAGGTTTAGGGTTT
11756092 AGTATATATG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
24 6 0.17
25 9 0.25
26 10 0.28
27 11 0.31
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (24 bp):
TTAAAAAGGTTTAGGGTTTTTCTG
Found at i:11756319 original size:29 final size:28
Alignment explanation
Indices: 11756286--11756350 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
11756276 TCTCTGATTA
**
11756286 TATGTGTTTAGTATGTATGTTTTACTAAT
1 TATGTGTTTAGTATACATG-TTTACTAAT
*
11756315 TATGTGTTTAGTATACATGTTTACTGAT
1 TATGTGTTTAGTATACATGTTTACTAAT
*
11756343 TATATGTT
1 TATGTGTT
11756351 GTGAATAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.25, C:0.05, G:0.17, T:0.54
Consensus pattern (28 bp):
TATGTGTTTAGTATACATGTTTACTAAT
Found at i:11756350 original size:28 final size:28
Alignment explanation
Indices: 11756279--11756374 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
11756269 ACATGTGTCT
**
11756279 CTGATTATATGTGTTTAGTATGTATGTTTTA
1 CTGATTATA--TGTTTAGTATACATG-TTTA
* *
11756310 CTAATTATGTGTTTAGTATACATGTTTA
1 CTGATTATATGTTTAGTATACATGTTTA
* *
11756338 CTGATTATATGTTGT-GAATAGATGTTT-
1 CTGATTATATGTT-TAGTATACATGTTTA
11756365 CTGATTATAT
1 CTGATTATAT
11756375 ATTTGTTAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
27 10 0.18
28 25 0.45
29 14 0.25
31 7 0.12
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (28 bp):
CTGATTATATGTTTAGTATACATGTTTA
Found at i:11756447 original size:16 final size:16
Alignment explanation
Indices: 11756426--11756479 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
11756416 TATGCTGTGA
11756426 ATATATGTTTCTGATT
1 ATATATGTTTCTGATT
*
11756442 ATATA--TTTGTGA--
1 ATATATGTTTCTGATT
**
11756454 ATATATACTTCTGATT
1 ATATATGTTTCTGATT
11756470 ATATATGTTT
1 ATATATGTTT
11756480 ATTGATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 5 0.17
14 11 0.38
16 13 0.45
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.54
Consensus pattern (16 bp):
ATATATGTTTCTGATT
Found at i:11756452 original size:28 final size:28
Alignment explanation
Indices: 11756406--11756475 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
11756396 TTATTTTTGT
* *
11756406 TTTCTGATTATAT-GCTGTGAATATATG
1 TTTCTGATTATATATCTGTGAATATATA
*
11756433 TTTCTGATTATATATTTGTGAATATATA
1 TTTCTGATTATATATCTGTGAATATATA
*
11756461 CTTCTGATTATATAT
1 TTTCTGATTATATAT
11756476 GTTTATTGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 13 0.34
28 25 0.66
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (28 bp):
TTTCTGATTATATATCTGTGAATATATA
Found at i:11756458 original size:14 final size:14
Alignment explanation
Indices: 11756423--11756475 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
11756413 TTATATGCTG
*
11756423 TGAATATATGTTTC
1 TGAATATATATTTC
* *
11756437 TGATTATATATTTG
1 TGAATATATATTTC
*
11756451 TGAATATATACTTC
1 TGAATATATATTTC
*
11756465 TGATTATATAT
1 TGAATATATAT
11756476 GTTTATTGAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.51
Consensus pattern (14 bp):
TGAATATATATTTC
Found at i:11756540 original size:26 final size:26
Alignment explanation
Indices: 11756511--11756565 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
11756501 TTCTTCATAT
*
11756511 TATGTTTACTAATCATATATGAATAA
1 TATGTTTACTAATCATATACGAATAA
* * *
11756537 TATGTTTCCTAATTATATCCGAATAA
1 TATGTTTACTAATCATATACGAATAA
11756563 TAT
1 TAT
11756566 ACGTTGATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (26 bp):
TATGTTTACTAATCATATACGAATAA
Found at i:11773966 original size:8 final size:8
Alignment explanation
Indices: 11773922--11773969 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
11773912 TCGTAATTGC
11773922 TTTATTA-
1 TTTATTAT
11773929 TTTATTAT
1 TTTATTAT
**
11773937 TTTAAGAT
1 TTTATTAT
*
11773945 TTTATCAT
1 TTTATTAT
*
11773953 TATATTAT
1 TTTATTAT
11773961 TTTATTAT
1 TTTATTAT
11773969 T
1 T
11773970 GTTGAGTTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
7 7 0.21
8 26 0.79
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (8 bp):
TTTATTAT
Found at i:11774132 original size:29 final size:26
Alignment explanation
Indices: 11774097--11774170 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 26
11774087 TAATTATGTT
11774097 ATATTTTATAAATTTAAAAAAAATTA
1 ATATTTTATAAATTTAAAAAAAATTA
* *
11774123 ATAATCTTT-TACAATTTTAATAATAATTA
1 AT-AT-TTTATA-AA-TTTAAAAAAAATTA
11774152 ATATTTTATAACATTTAAA
1 ATATTTTATAA-ATTTAAA
11774171 TGATTTCCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
26 2 0.05
27 13 0.33
28 10 0.26
29 14 0.36
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTTTATAAATTTAAAAAAAATTA
Found at i:11781536 original size:28 final size:27
Alignment explanation
Indices: 11781496--11781555 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
11781486 TTATTTTATA
*
11781496 TTTTAGAAATTTAA-AAAAATTAATCAT
1 TTTTACAAATTTAATAAAAATTAAT-AT
* *
11781523 CTTTTACAATTTTAATAATAATTAATAT
1 -TTTTACAAATTTAATAAAAATTAATAT
11781551 TTTTA
1 TTTTA
11781556 TTACATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.18
28 14 0.50
29 9 0.32
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTTACAAATTTAATAAAAATTAATAT
Found at i:11781687 original size:20 final size:19
Alignment explanation
Indices: 11781657--11781720 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
11781647 CTTTTTATAA
11781657 TTTTATTAAAATATAATAT
1 TTTTATTAAAATATAATAT
*
11781676 TTTTATTTAAAATTTAGA-AT
1 TTTTA-TTAAAATATA-ATAT
* *
11781696 TTTCATAAAAATATAATAT
1 TTTTATTAAAATATAATAT
11781715 TTTTAT
1 TTTTAT
11781721 AATTTTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.54
20 15 0.41
21 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTATTAAAATATAATAT
Found at i:11782083 original size:13 final size:13
Alignment explanation
Indices: 11782065--11782089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11782055 AACTTGAATC
11782065 TCATTATTTTTTG
1 TCATTATTTTTTG
11782078 TCATTATTTTTT
1 TCATTATTTTTT
11782090 CTATCATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
TCATTATTTTTTG
Found at i:11785173 original size:17 final size:16
Alignment explanation
Indices: 11785151--11785182 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11785141 CTCAATCAGT
11785151 TTAATTTAATAAAAAAA
1 TTAATTTAA-AAAAAAA
11785168 TTAATTTAAAAAAAA
1 TTAATTTAAAAAAAA
11785183 GAATCAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAATTTAAAAAAAAA
Found at i:11794863 original size:24 final size:24
Alignment explanation
Indices: 11794817--11794863 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
11794807 ATACCTGACC
* * *
11794817 TGGATTCTTTTATGATTTTTTATA
1 TGGATTCTGTTATGATATCTTATA
11794841 TGGATTCTGTTATGATATCTTAT
1 TGGATTCTGTTATGATATCTTAT
11794864 CTGAATTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.57
Consensus pattern (24 bp):
TGGATTCTGTTATGATATCTTATA
Found at i:11794881 original size:48 final size:48
Alignment explanation
Indices: 11794783--11794889 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
11794773 ATTTTATCTA
* * * *
11794783 ATTTTTTATTTGAATTCTGTTTTGATACCTGACCTGGATTCTTTTATG
1 ATTTTTTATATGAATTCTGTTATGATACCTGACCTGAATTATTTTATG
* * * *
11794831 ATTTTTTATATGGATTCTGTTATGATATCTTATCTGAATTATGTTT-TG
1 ATTTTTTATATGAATTCTGTTATGATACCTGACCTGAATTAT-TTTATG
*
11794879 ATTTTTGATAT
1 ATTTTTTATAT
11794890 ATCCGTTTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
48 46 0.94
49 3 0.06
ACGTcount: A:0.21, C:0.08, G:0.14, T:0.56
Consensus pattern (48 bp):
ATTTTTTATATGAATTCTGTTATGATACCTGACCTGAATTATTTTATG
Found at i:11797463 original size:36 final size:37
Alignment explanation
Indices: 11797423--11797515 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 37
11797413 AGTTTTCAAC
*
11797423 TTTTTAATATTTTTATAATTTT-ATTA-ATATATAATA
1 TTTTTAATATTTTTATAATTTTCA-TACAAATATAATA
** ** *
11797459 TTTTTTTTAAATTTAAAATTTTCATACAAATATAATA
1 TTTTTAATATTTTTATAATTTTCATACAAATATAATA
11797496 -TTTTAATATTTTTATAATTT
1 TTTTTAATATTTTTATAATTT
11797516 AATTTTTAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
36 34 0.77
37 10 0.23
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (37 bp):
TTTTTAATATTTTTATAATTTTCATACAAATATAATA
Found at i:11799723 original size:25 final size:24
Alignment explanation
Indices: 11799695--11799742 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
11799685 AATTTTAAAT
11799695 TTTATAAATTTGTGTAATTTGTTTG
1 TTTATAAATTTGTGT-ATTTGTTTG
* * *
11799720 TTTATTATTTTGTGTCTTTGTTT
1 TTTATAAATTTGTGTATTTGTTT
11799743 TGTCTTATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.67
Consensus pattern (24 bp):
TTTATAAATTTGTGTATTTGTTTG
Found at i:11799744 original size:25 final size:26
Alignment explanation
Indices: 11799703--11799751 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
11799693 ATTTTATAAA
11799703 TTTGTGTAATTTGTTTGT-TTATTAT
1 TTTGTGTAATTTGTTTGTCTTATTAT
*
11799728 TTTGTGT-CTTTGTTTTGTCTTATT
1 TTTGTGTAATTTG-TTTGTCTTATT
11799752 CATAACATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 12 0.57
26 5 0.24
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.69
Consensus pattern (26 bp):
TTTGTGTAATTTGTTTGTCTTATTAT
Found at i:11800704 original size:25 final size:24
Alignment explanation
Indices: 11800658--11800704 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
11800648 TTATTAATTC
**
11800658 TTTATATTTTTAAATATTTATAAA
1 TTTATATTTTTAAATAAATATAAA
*
11800682 TTTATTTTTTTAAAATAAATATA
1 TTTATATTTTT-AAATAAATATA
11800705 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTATATTTTTAAATAAATATAAA
Found at i:11804641 original size:28 final size:27
Alignment explanation
Indices: 11804601--11804660 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
11804591 TTATGTTATA
*
11804601 TTTTAGAAATTTAA-AAAAATTAATCAT
1 TTTTACAAATTTAATAAAAATTAAT-AT
* *
11804628 CTTTTACAATTTTAATAATAATTAATAT
1 -TTTTACAAATTTAATAAAAATTAATAT
11804656 TTTTA
1 TTTTA
11804661 TTACATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.18
28 14 0.50
29 9 0.32
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (27 bp):
TTTTACAAATTTAATAAAAATTAATAT
Found at i:11806082 original size:18 final size:18
Alignment explanation
Indices: 11806059--11806096 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
11806049 TTTTAAGATT
11806059 TTATATTCGATTTAAATA
1 TTATATTCGATTTAAATA
*
11806077 TTATATTCGATTTAATTA
1 TTATATTCGATTTAAATA
11806095 TT
1 TT
11806097 CAAATATTAT
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:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATATTCGATTTAAATA
Found at i:11806485 original size:44 final size:44
Alignment explanation
Indices: 11806435--11806518 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
11806425 CCACGATCGG
** * *
11806435 TATCGATACTACTTTACATAGTAGTATTGATACTCACTGGACGA
1 TATCGATACTACACTACAAAGTAGTATCGATACTCACTGGACGA
*
11806479 TATCGATACTACACTACAAAGTAGTATCGATACTCCCTGG
1 TATCGATACTACACTACAAAGTAGTATCGATACTCACTGG
11806519 CCAATATTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (44 bp):
TATCGATACTACACTACAAAGTAGTATCGATACTCACTGGACGA
Found at i:11806531 original size:44 final size:44
Alignment explanation
Indices: 11806435--11806531 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
11806425 CCACGATCGG
** * * *
11806435 TATCGATACTACTTTACATAGTAGTATTGATACTCACTGGACGA
1 TATCGATACTACACTACAAAGTAGTATCGATACTCACTGGACAA
* *
11806479 TATCGATACTACACTACAAAGTAGTATCGATACTCCCTGGCCAA
1 TATCGATACTACACTACAAAGTAGTATCGATACTCACTGGACAA
*
11806523 TATTGATAC
1 TATCGATAC
11806532 CGTTGGATTG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (44 bp):
TATCGATACTACACTACAAAGTAGTATCGATACTCACTGGACAA
Found at i:11812346 original size:21 final size:21
Alignment explanation
Indices: 11812320--11812392 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
11812310 TACTAGCATA
*
11812320 GTATCGATACTGCTTCAATAG
1 GTATCGATACTTCTTCAATAG
* * *
11812341 GTATCGATACTTTTTTTAACA-
1 GTATCGATAC-TTCTTCAATAG
* *
11812362 GTACCGATACTTCTTCAATGG
1 GTATCGATACTTCTTCAATAG
11812383 GTATCGATAC
1 GTATCGATAC
11812393 CCTAGTATCT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 6 0.15
21 28 0.70
22 6 0.15
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (21 bp):
GTATCGATACTTCTTCAATAG
Found at i:11814511 original size:13 final size:13
Alignment explanation
Indices: 11814493--11814517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11814483 TCCCTATTGC
11814493 ATATTGATTATGA
1 ATATTGATTATGA
11814506 ATATTGATTATG
1 ATATTGATTATG
11814518 TTGACTAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
ATATTGATTATGA
Found at i:11815344 original size:22 final size:24
Alignment explanation
Indices: 11815300--11815344 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
11815290 TATTTGAATT
* *
11815300 TATAATAGGAAGTACTAATACCCC
1 TATAATAGGAAGTACCAAAACCCC
11815324 TATAA-AGG-AGTACCAAAACCC
1 TATAATAGGAAGTACCAAAACCC
11815345 ATAAGCTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 3 0.16
24 5 0.26
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.20
Consensus pattern (24 bp):
TATAATAGGAAGTACCAAAACCCC
Found at i:11816973 original size:23 final size:22
Alignment explanation
Indices: 11816928--11816974 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
11816918 ATAAATATTT
**
11816928 TATTTTAAATAATTTACCTTTA
1 TATTTTAAATAATTTACAATTA
*
11816950 TATTTTAAAGTAATTTATAATTA
1 TATTTTAAA-TAATTTACAATTA
11816973 TA
1 TA
11816975 CATTGAGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TATTTTAAATAATTTACAATTA
Found at i:11818122 original size:24 final size:24
Alignment explanation
Indices: 11818072--11818128 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
11818062 TTATTAATTC
**
11818072 TTTATATTTTTAAATATTTATAAA
1 TTTATATTTTTAAATAAATATAAA
*
11818096 TTTAT-TTTTTAAATAAATATATTA
1 TTTATATTTTTAAATAAATATA-AA
11818120 TTTATATTT
1 TTTATATTT
11818129 CTTTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.50
24 11 0.39
25 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTATATTTTTAAATAAATATAAA
Found at i:11821975 original size:15 final size:17
Alignment explanation
Indices: 11821955--11821988 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
11821945 CTCATTAGAA
11821955 ATTTTATA-TTTT-TAT
1 ATTTTATACTTTTCTAT
11821970 ATTTTATACTTTTCTAT
1 ATTTTATACTTTTCTAT
11821987 AT
1 AT
11821989 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATACTTTTCTAT
Found at i:11822282 original size:19 final size:19
Alignment explanation
Indices: 11822260--11822298 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
11822250 ATTTTTATTT
*
11822260 AAAATTTAAAATTTTCATA
1 AAAATATAAAATTTTCATA
* *
11822279 AAAATATAATATTTTTATA
1 AAAATATAAAATTTTCATA
11822298 A
1 A
11822299 TTTAATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATATAAAATTTTCATA
Found at i:11825554 original size:27 final size:27
Alignment explanation
Indices: 11825524--11825607 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 27
11825514 ATTTTATCTT
11825524 TTTATTAATTCTTTATTTTTTTAAATA
1 TTTATTAATTCTTTATTTTTTTAAATA
*
11825551 TTTATAAATT-TATT-TTTTTTAAATAAATA
1 TTTATTAATTCT-TTATTTTTT---TAAATA
11825580 TATTATTTATATTTCTTTATTTTTTTAA
1 T-TTA-TTA-A-TTCTTTATTTTTTTAA
11825608 CTTTTATGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
26 7 0.16
27 11 0.24
29 7 0.16
30 3 0.07
31 5 0.11
32 1 0.02
33 4 0.09
34 7 0.16
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTATTAATTCTTTATTTTTTTAAATA
Found at i:11825581 original size:25 final size:24
Alignment explanation
Indices: 11825535--11825581 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
11825525 TTATTAATTC
**
11825535 TTTATTTTTTTAAATATTTATAAA
1 TTTATTTTTTTAAATAAATATAAA
11825559 TTTATTTTTTTTAAATAAATATA
1 TTTA-TTTTTTTAAATAAATATA
11825582 TTATTTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTATTTTTTTAAATAAATATAAA
Found at i:11826172 original size:13 final size:13
Alignment explanation
Indices: 11826154--11826185 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
11826144 TACATCAATA
11826154 GAGAAAATAAGAG
1 GAGAAAATAAGAG
11826167 GAGAAAATAAGAG
1 GAGAAAATAAGAG
11826180 GAGAAA
1 GAGAAA
11826186 TAGACAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.06
Consensus pattern (13 bp):
GAGAAAATAAGAG
Found at i:11828224 original size:24 final size:24
Alignment explanation
Indices: 11828192--11828249 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
11828182 ATTTGAACTA
*
11828192 TGTTTTGATTGCTGACCTAGATTC
1 TGTTATGATTGCTGACCTAGATTC
* ** * *
11828216 TTTTATGATTTTTGATCTGGATTC
1 TGTTATGATTGCTGACCTAGATTC
11828240 TGTTATGATT
1 TGTTATGATT
11828250 TTTTATATGG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.17, C:0.10, G:0.19, T:0.53
Consensus pattern (24 bp):
TGTTATGATTGCTGACCTAGATTC
Found at i:11828250 original size:24 final size:24
Alignment explanation
Indices: 11828211--11828305 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
11828201 TGCTGACCTA
* *
11828211 GATTCTTTTATGATTTTTGATCTG
1 GATTCTGTTATGATTTTTGATATG
*
11828235 GATTCTGTTATGATTTTTTATATG
1 GATTCTGTTATGATTTTTGATATG
* * *
11828259 GATTATGTTATGATATCTGATATG
1 GATTCTGTTATGATTTTTGATATG
* * * *
11828283 AATTATGTTTTAATTTTTGATAT
1 GATTCTGTTATGATTTTTGATAT
11828306 ATCTATTTAC
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.56
Consensus pattern (24 bp):
GATTCTGTTATGATTTTTGATATG
Found at i:11828613 original size:156 final size:156
Alignment explanation
Indices: 11828322--11828618 Score: 413
Period size: 156 Copynumber: 1.9 Consensus size: 156
11828312 TTACGGATGG
*
11828322 AAAATGTTTTATTTGGGGGTATTGTTAGAGGAAGTATACTTGCAGGCTCCTCGACTTTGTGCTCA
1 AAAATGTTTTATTTGGGGGTATTGTTAGAGGAAGTATACTTGCAGGCTCATCGACTTTGTGCTCA
* * * *
11828387 AGGCCTTTCCTGATGTGACGGTGGGTGTATGGTTCTGGGGAACGTACACATTATGATGTGTTGGG
66 AGGCCTTACCTGATGTGACGGTGGGTGTATAGTTCTGGGGAACCTACACATTATGATGTGTTCGG
11828452 CTGGAGGGATTGCTATAGTTTCTGAT
131 CTGGAGGGATTGCTATAGTTTCTGAT
* * *
11828478 AAAATGTTTTATTTGGGGGTATTGTTGGATGAAGTAT-TTTCGCAGGCTCATC-AGCTTTGTGCG
1 AAAATGTTTTATTTGGGGGTATTGTTAGAGGAAGTATACTT-GCAGGCTCATCGA-CTTTGTGC-
* * * *
11828541 T-AGGGCCTTACTTGATGTG-CAGGTGGGTGTATAGTTCTGGGGATCCTACACATTCTGATGTGT
63 TCAAGGCCTTACCTGATGTGAC-GGTGGGTGTATAGTTCTGGGGAACCTACACATTATGATGTGT
*
11828604 TCGGTTGGAGGGATT
127 TCGGCTGGAGGGATT
11828619 ACAATGGTTT
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
155 4 0.03
156 119 0.96
157 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.36
Consensus pattern (156 bp):
AAAATGTTTTATTTGGGGGTATTGTTAGAGGAAGTATACTTGCAGGCTCATCGACTTTGTGCTCA
AGGCCTTACCTGATGTGACGGTGGGTGTATAGTTCTGGGGAACCTACACATTATGATGTGTTCGG
CTGGAGGGATTGCTATAGTTTCTGAT
Found at i:11834354 original size:20 final size:21
Alignment explanation
Indices: 11834308--11834367 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
11834298 TGTGGGGGGG
*
11834308 GGGGGAATTGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTT-AAA
11834331 GGGGGAATCGGTTCCCTT-AA
1 GGGGGAATCGGTTCCCTTAAA
*
11834351 GGGGGAATCGATTCCCT
1 GGGGGAATCGGTTCCCT
11834368 CTGCACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 18 0.51
22 5 0.14
23 12 0.34
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTTAAA
Found at i:11843183 original size:17 final size:17
Alignment explanation
Indices: 11843159--11843207 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
11843149 AGCCACCCGA
11843159 GCCGTTGAGTCGTTGACC
1 GCCGTTGA-TCGTTGACC
*
11843177 G-CGTTGATTGTTGACC
1 GCCGTTGATCGTTGACC
*
11843193 GCCGTTGACCGTTGA
1 GCCGTTGATCGTTGA
11843208 TCGCTGACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 9 0.33
17 17 0.63
18 1 0.04
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (17 bp):
GCCGTTGATCGTTGACC
Found at i:11848878 original size:24 final size:24
Alignment explanation
Indices: 11848851--11848909 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
11848841 GGTTCTGTAA
* *
11848851 TGATTTTTGATCTGGATTCTGTTC
1 TGATTTTTGATCTGAATTATGTTC
* * *
11848875 TGATATCTGATCTGAATTATGTTT
1 TGATTTTTGATCTGAATTATGTTC
11848899 TGATTTTTGAT
1 TGATTTTTGAT
11848910 ATATTCGTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (24 bp):
TGATTTTTGATCTGAATTATGTTC
Found at i:11849226 original size:156 final size:156
Alignment explanation
Indices: 11848928--11849235 Score: 467
Period size: 156 Copynumber: 2.0 Consensus size: 156
11848918 TTATAGACGG
* *
11848928 AAATTTTTATTTGGGGGGTATTGTTGGAGGAAGTATACTTGCAGGCTCCTCGGCTTTGTGCTCAG
1 AAATTTTTATTTGGGGGGTATTATTGGAGGAAGTATACTTACAGGCTCCTCGGCTTTGTGCTCAG
* * *
11848993 GGCCTTACCTGATGTGACGGCGGGTGTATGGTTCTTGGGAACCTACACATTATGATGTGTTGGGC
66 GGCCTTACCTGATGTGACGGCGGGTGTATAGTTCTGGGGAACCTACACATTATGATGTGTTCGGC
11849058 TGGAGGGATTACTATGGTTTTTGATA
131 TGGAGGGATTACTATGGTTTTTGATA
* * **
11849084 AAATGTTTTATTT-TGGGGTATTATTGGAGGAAGTGTTTTTACAGGCTCCTCGGCTTTGTGCTCA
1 AAAT-TTTTATTTGGGGGGTATTATTGGAGGAAGTATACTTACAGGCTCCTCGGCTTTGTGCTCA
* * *
11849148 GGGCCTTACTTGATGTG-CAGGTGGGTGTATAGTTCTGGGGAACCTACACATTCTGATGTGTTCG
65 GGGCCTTACCTGATGTGAC-GGCGGGTGTATAGTTCTGGGGAACCTACACATTATGATGTGTTCG
*
11849212 GTTGGAGGGATTACTATGGTTTTT
129 GCTGGAGGGATTACTATGGTTTTT
11849236 TGAAAAAAGA
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
155 1 0.01
156 128 0.93
157 8 0.06
ACGTcount: A:0.18, C:0.14, G:0.31, T:0.37
Consensus pattern (156 bp):
AAATTTTTATTTGGGGGGTATTATTGGAGGAAGTATACTTACAGGCTCCTCGGCTTTGTGCTCAG
GGCCTTACCTGATGTGACGGCGGGTGTATAGTTCTGGGGAACCTACACATTATGATGTGTTCGGC
TGGAGGGATTACTATGGTTTTTGATA
Found at i:11852254 original size:24 final size:24
Alignment explanation
Indices: 11852227--11852294 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
11852217 TTCGATTTGA
*
11852227 ATTCTGTTTTGATACCTGATATGG
1 ATTCTGTTTTGATATCTGATATGG
*
11852251 ATTCT-TTTATGATTTCTGATATGG
1 ATTCTGTTT-TGATATCTGATATGG
* *
11852275 ATTTTGTTATGATATCTGAT
1 ATTCTGTTTTGATATCTGAT
11852295 TTGAATTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 3 0.08
24 32 0.86
25 2 0.05
ACGTcount: A:0.22, C:0.09, G:0.18, T:0.51
Consensus pattern (24 bp):
ATTCTGTTTTGATATCTGATATGG
Found at i:11855936 original size:24 final size:24
Alignment explanation
Indices: 11855909--11855979 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
11855899 ACCTGACCTT
11855909 GATTCTGTTATGATTTTTGATATG
1 GATTCTGTTATGATTTTTGATATG
* *
11855933 GATTCTGTTATGATATCTT-ATCTG
1 GATTCTGTTATGAT-TTTTGATATG
* * *
11855957 AATTATGTTTTGATTTTTGATAT
1 GATTCTGTTATGATTTTTGATAT
11855980 ATCCGTTTAC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 3 0.08
24 32 0.84
25 3 0.08
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.55
Consensus pattern (24 bp):
GATTCTGTTATGATTTTTGATATG
Found at i:11855947 original size:48 final size:48
Alignment explanation
Indices: 11855871--11855979 Score: 112
Period size: 48 Copynumber: 2.3 Consensus size: 48
11855861 ATGTTTTATC
* * * *
11855871 TGATTTTCGATTTGAATTATGTTTTGATACCTGACCTTG-ATTCTGTTA
1 TGATTTTTGATATGAATTATGTTATGATACCTGACC-TGAATTATGTTA
* * * * * *
11855919 TGATTTTTGATATGGATTCTGTTATGATATCTTATCTGAATTATGTTT
1 TGATTTTTGATATGAATTATGTTATGATACCTGACCTGAATTATGTTA
11855967 TGATTTTTGATAT
1 TGATTTTTGATAT
11855980 ATCCGTTTAC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 2 0.04
48 48 0.96
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.53
Consensus pattern (48 bp):
TGATTTTTGATATGAATTATGTTATGATACCTGACCTGAATTATGTTA
Found at i:11856304 original size:155 final size:156
Alignment explanation
Indices: 11855996--11856304 Score: 417
Period size: 155 Copynumber: 2.0 Consensus size: 156
11855986 TTACGGACGA
* * * *
11855996 AAAATATTTTATTTGGGGGGTATTGTTGGAGGAAGTATACTTGTAGGCTCCTCGGCTTTGTGCTC
1 AAAATATTTTACTT-GGGGGTATTATTGGAGGAAATATACTTGCAGGCTCCTCGGCTTTGTGCTC
* * * *
11856061 AGGACTTAACTTGATGTGATGGTGGGTGTTTGGTTCTGGGGAACCTACACATTATGATGTGTTGG
65 AGGACTTAACTTGATGTGATAGTGGGTGTATGGTTCTAGGGAACCTACACATTATGATGTGTTCG
* * * *
11856126 GTTGGAGGGATTATTATGGTTTTTGAT
130 GTTAGAGGGATTACTACGATTTTTGAT
**
11856153 AAAATATTTTACTT-GGGGTATTATTGGAGGAAATATTTTTGCAGGCTCCTCGGCTTTGTGCTCA
1 AAAATATTTTACTTGGGGGTATTATTGGAGGAAATATACTTGCAGGCTCCTCGGCTTTGTGCTCA
* *
11856217 GGGACTT-ACTTGATTTGCA-AGTGGGTGTATGGTTCTAGGGAACCTACACATTTTGATGTGTTC
66 -GGACTTAACTTGATGTG-ATAGTGGGTGTATGGTTCTAGGGAACCTACACATTATGATGTGTTC
*
11856280 GGTTAGAGGGTTTACTACGATTTTT
129 GGTTAGAGGGATTACTACGATTTTT
11856305 CAAAAAAATG
Statistics
Matches: 133, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
155 113 0.85
156 7 0.05
157 13 0.10
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (156 bp):
AAAATATTTTACTTGGGGGTATTATTGGAGGAAATATACTTGCAGGCTCCTCGGCTTTGTGCTCA
GGACTTAACTTGATGTGATAGTGGGTGTATGGTTCTAGGGAACCTACACATTATGATGTGTTCGG
TTAGAGGGATTACTACGATTTTTGAT
Found at i:11858273 original size:15 final size:17
Alignment explanation
Indices: 11858253--11858284 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
11858243 CAATAAAAAA
11858253 TTTATA-TTTT-TATAT
1 TTTATACTTTTCTATAT
11858268 TTTATACTTTTCTATAT
1 TTTATACTTTTCTATAT
11858285 ATTTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATACTTTTCTATAT
Found at i:11865640 original size:15 final size:17
Alignment explanation
Indices: 11865620--11865653 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
11865610 CTCATTAGAA
11865620 ATTTTATA-TTTT-TAT
1 ATTTTATACTTTTCTAT
11865635 ATTTTATACTTTTCTAT
1 ATTTTATACTTTTCTAT
11865652 AT
1 AT
11865654 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATACTTTTCTAT
Found at i:11865924 original size:20 final size:19
Alignment explanation
Indices: 11865896--11865959 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
11865886 CTTTTTATAA
*
11865896 TTTTATTAATATATAATAT
1 TTTTATTAAAATATAATAT
* *
11865915 TTTTATTTAAAATTTAAAAT
1 TTTTA-TTAAAATATAATAT
* *
11865935 TTTCATAAAAATATAATAT
1 TTTTATTAAAATATAATAT
11865954 TTTTAT
1 TTTTAT
11865960 AATTTTATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 21 0.58
20 15 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTATTAAAATATAATAT
Found at i:11867682 original size:11 final size:10
Alignment explanation
Indices: 11867659--11867688 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
11867649 TGTCGTGACA
11867659 TTAATTTTAT
1 TTAATTTTAT
11867669 TTAATTTATAT
1 TTAATTT-TAT
11867680 TTAATTTTA
1 TTAATTTTA
11867689 ATCAATAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTAATTTTAT
Found at i:11868966 original size:21 final size:21
Alignment explanation
Indices: 11868942--11868988 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
11868932 AAGTACTTGA
11868942 AGAATAATTTATTAATTTGTC
1 AGAATAATTTATTAATTTGTC
11868963 AGAATAATTTATTAATTTGTC
1 AGAATAATTTATTAATTTGTC
11868984 AGAAT
1 AGAAT
11868989 TATTCGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (21 bp):
AGAATAATTTATTAATTTGTC
Found at i:11874551 original size:20 final size:18
Alignment explanation
Indices: 11874515--11874557 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
11874505 CATCTCTTTT
11874515 CTTATTTTATTTCCATTA
1 CTTATTTTATTTCCATTA
*
11874533 CTTATTTTACTTATCCATTT
1 CTTATTTTA-TT-TCCATTA
11874553 CTTAT
1 CTTAT
11874558 ACCATTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (18 bp):
CTTATTTTATTTCCATTA
Found at i:11884500 original size:182 final size:181
Alignment explanation
Indices: 11884193--11884530 Score: 545
Period size: 182 Copynumber: 1.9 Consensus size: 181
11884183 CTTTTTTTCA
*
11884193 AAATCGGTATCTATTAACCAGTTACATTGTATATTGAAGTCAGTTTTATCAAATTTTAACCTTTT
1 AAATCGGTATCTATTAACCAGTTACATTGTATATTGAACTCAGTTTTATCAAATTTTAACCTTTT
*
11884258 ATATCATTATATATCGATACAATTTTTTAGGTATCGATACTTCTTACGTGCATGTAGTTTTAAGA
66 ATAACATTATATATCGATACAATTTTTTAGGTATCGATACTTCTTACGTGCATGTAGTTTTAAGA
*
11884323 AGCATACTGAATGAAAAAGTATCGATACTTTATATAAACTTATGTTACCATT
131 AGCATACTGAA-CAAAAAGTATCGATACTTTATATAAACTTATGTTACCATT
* * * *
11884375 AAATCGGTATCTATTGACCGGTTACATTGTATATTGAAACTGA-TTTTATCAATTTTTAACCTTT
1 AAATCGGTATCTATTAACCAGTTACATTGTATATTG-AACTCAGTTTTATCAAATTTTAACCTTT
* *
11884439 TATAACATTATATATCGATAC-ATTTTTATAGGTATCGATACTTCTTATGTGTATGTAGTTTTAA
65 TATAACATTATATATCGATACAATTTTT-TAGGTATCGATACTTCTTACGTGCATGTAGTTTTAA
*
11884503 GAAGCATACTGGACAAAAAGTATCGATA
129 GAAGCATACTGAACAAAAAGTATCGATA
11884531 AATATTAAAA
Statistics
Matches: 144, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
181 20 0.14
182 120 0.83
183 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (181 bp):
AAATCGGTATCTATTAACCAGTTACATTGTATATTGAACTCAGTTTTATCAAATTTTAACCTTTT
ATAACATTATATATCGATACAATTTTTTAGGTATCGATACTTCTTACGTGCATGTAGTTTTAAGA
AGCATACTGAACAAAAAGTATCGATACTTTATATAAACTTATGTTACCATT
Found at i:11892033 original size:6 final size:6
Alignment explanation
Indices: 11892022--11892054 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
11892012 GGAGTGTCCC
11892022 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT- TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
11892055 CAAGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTA
Found at i:11905228 original size:175 final size:176
Alignment explanation
Indices: 11904948--11905453 Score: 619
Period size: 175 Copynumber: 2.9 Consensus size: 176
11904938 TATTTTTACC
* * * *
11904948 TGTTATATTATTACGTATCGATACATGTTTATAAAGTATCAATACTTTATAGGCGTTATTATTGC
1 TGTTATACTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGCGTTATTACTGC
* *
11905013 TTTTCTTTTAAATTCCAAAAGTATTGATACTTATTTGAATGAAATTGATACATTCAACATATCCA
66 TTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGAAATCGATACATTCAACATATCCA
*
11905078 ATAGTGATTTACCAGTTTTGTCATAATGAAACCAGTTTTGTCA-AAA
131 ATAGCGATTTACCAGTTTTGTCATAATGAAA-CAGTTTTGTCATAAA
* * *
11905124 T-TT-TACCTGTTTATGTATCGATACATGTTTATAAAGAATCGATACTTTATAGGAGTTATTA-T
1 TGTTATA-CTG-TTACGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGCGTTATTACT
*
11905186 GCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGAATCGATACATTCAACATATC
64 GCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGAAATCGATACATTCAACATATC
* * *
11905251 CAGTAGCGCTTTACCAGTTTTGTCATAATGAAACGGTTTTGTCATTTTTTAAA
129 CAATAGCGATTTACCAGTTTTGTCATAATGAAACAGTTTTGTCA-----TAAA
* *
11905304 TGTTATATTGTTACGTATCGATATC-TGTTTATAAAGTATCGATACTTTATAGGCGCTATTACTG
1 TGTTATACTGTTACGTATCGATA-CATGTTTATAAAGTATCGATACTTTATAGGCGTTATTACTG
* *
11905368 CCTTTCTTTTAAATTCC---A--A---A-ACTTATTTGAATGGAATC-ATACATTCAACATATCC
65 CTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGAAATCGATACATTCAACATATCC
** * * *
11905423 CGTAGCGCTTTACCGGTTTTGTCATATTGAA
130 AATAGCGATTTACCAGTTTTGTCATAATGAA
11905454 CCCGATTTTC
Statistics
Matches: 296, Mismatches: 22, Indels: 29
0.85 0.06 0.08
Matches are distributed among these distances:
171 45 0.15
172 18 0.06
173 1 0.00
174 12 0.04
175 96 0.32
176 49 0.17
178 1 0.00
180 49 0.17
181 23 0.08
182 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (176 bp):
TGTTATACTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGCGTTATTACTGC
TTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGAAATCGATACATTCAACATATCCA
ATAGCGATTTACCAGTTTTGTCATAATGAAACAGTTTTGTCATAAA
Found at i:11905510 original size:20 final size:21
Alignment explanation
Indices: 11905481--11905521 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
11905471 TTTACCTTAT
*
11905481 ATATTGTAAT-GTATTGATAC
1 ATATTGTAATGGTATCGATAC
*
11905501 ATATTTTAATGGTATCGATAC
1 ATATTGTAATGGTATCGATAC
11905522 GTACAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (21 bp):
ATATTGTAATGGTATCGATAC
Found at i:11906137 original size:16 final size:16
Alignment explanation
Indices: 11906102--11906145 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
11906092 TTTAAAGAAA
* * *
11906102 AATAAAATAAGTACTT
1 AATAAAATAAATAATC
11906118 AATAAAATAAATAATC
1 AATAAAATAAATAATC
11906134 AATAAAAATAAA
1 AAT-AAAATAAA
11906146 AATAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (16 bp):
AATAAAATAAATAATC
Found at i:11906143 original size:22 final size:21
Alignment explanation
Indices: 11906118--11906175 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
11906108 ATAAGTACTT
11906118 AATAAAATAAATAATCAATAAA
1 AATAAAATAAATAAT-AATAAA
*
11906140 AATAAAAATAAA-AATATTAAA
1 AAT-AAAATAAATAATAATAAA
*
11906161 AATGAAATGAAATAA
1 AATAAAAT-AAATAA
11906176 AATGAAATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 4 0.13
21 11 0.35
22 8 0.26
23 8 0.26
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (21 bp):
AATAAAATAAATAATAATAAA
Found at i:11906270 original size:15 final size:16
Alignment explanation
Indices: 11906250--11906290 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
11906240 CAGATTACAA
11906250 GTTCTTCCAATTC-AT
1 GTTCTTCCAATTCAAT
11906265 GTTCTTCCAATTCAAT
1 GTTCTTCCAATTCAAT
11906281 -TTCTT-CAATT
1 GTTCTTCCAATT
11906291 AAACCAACTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.20
15 18 0.72
16 2 0.08
ACGTcount: A:0.22, C:0.24, G:0.05, T:0.49
Consensus pattern (16 bp):
GTTCTTCCAATTCAAT
Found at i:11927611 original size:18 final size:18
Alignment explanation
Indices: 11927588--11927625 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
11927578 ATTTCTTTAA
11927588 ATTATTTTATTATT-TTTT
1 ATTATTTTATT-TTATTTT
11927606 ATTATTTTATTTTATTTT
1 ATTATTTTATTTTATTTT
11927624 AT
1 AT
11927626 ATCCTTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTATTTTATTTTATTTT
Found at i:11929093 original size:20 final size:22
Alignment explanation
Indices: 11929068--11929117 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
11929058 AATTCCTTTG
11929068 TTGCATTTACA-TTTTGTAT-T
1 TTGCATTTACATTTTTGTATCT
** *
11929088 TTGCATTCCCATTTTTTTATCT
1 TTGCATTTACATTTTTGTATCT
11929110 TTGCATTT
1 TTGCATTT
11929118 GCATGAGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.38
21 7 0.29
22 8 0.33
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (22 bp):
TTGCATTTACATTTTTGTATCT
Found at i:11930505 original size:18 final size:19
Alignment explanation
Indices: 11930484--11930567 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 19
11930474 AAAAAGTCAT
*
11930484 AAAAATAGAAAAAAGAAA-
1 AAAAAAAGAAAAAAGAAAG
*
11930502 AAAAAAAGAAAAATGAAAG
1 AAAAAAAGAAAAAAGAAAG
11930521 AAAAAACAGAAGAAAA-AACAG
1 AAAAAA-AGAA-AAAAGAA-AG
*
11930542 AAGAAAAAGGATAAAAGAAA-
1 AA-AAAAA-GAAAAAAGAAAG
11930562 AAAAAA
1 AAAAAA
11930568 GAATAAATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
18 16 0.29
19 10 0.18
20 8 0.15
21 13 0.24
22 8 0.15
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (19 bp):
AAAAAAAGAAAAAAGAAAG
Found at i:11930506 original size:11 final size:11
Alignment explanation
Indices: 11930492--11930567 Score: 71
Period size: 11 Copynumber: 6.5 Consensus size: 11
11930482 ATAAAAATAG
11930492 AAAAAAGAAAA
1 AAAAAAGAAAA
11930503 AAAAAAGAAAA
1 AAAAAAGAAAA
**
11930514 ATGAAAGAAAA
1 AAAAAAGAAAA
*
11930525 AACAGAAGAAAA
1 AA-AAAAGAAAA
*
11930537 AACAGAAGAAAA
1 AA-AAAAGAAAA
11930549 AGGATAAAAGAAAA
1 A--A-AAAAGAAAA
11930563 AAAAA
1 AAAAA
11930568 GAATAAATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
11 24 0.44
12 21 0.38
14 10 0.18
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:11930507 original size:12 final size:12
Alignment explanation
Indices: 11930492--11930567 Score: 57
Period size: 12 Copynumber: 6.3 Consensus size: 12
11930482 ATAAAAATAG
11930492 AAAAAAG-AAAA
1 AAAAAAGAAAAA
11930503 AAAAAAG-AAAA
1 AAAAAAGAAAAA
**
11930514 ATGAAAGAAAAA
1 AAAAAAGAAAAA
* *
11930526 ACAGAAGAAAAA
1 AAAAAAGAAAAA
* *
11930538 ACAGAAGAAAAA
1 AAAAAAGAAAAA
*
11930550 GGATAAAAGAAAAA
1 --AAAAAAGAAAAA
11930564 AAAA
1 AAAA
11930568 GAATAAATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
11 16 0.30
12 28 0.52
14 10 0.19
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:11930545 original size:24 final size:22
Alignment explanation
Indices: 11930495--11930570 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 22
11930485 AAAATAGAAA
**
11930495 AAAGAAAAAAAAAAGAAAAATG
1 AAAGAAAAAAAAAAGAAAAAAC
*
11930517 AAAGAAAAAACAGAAGAAAAAAC
1 AAAGAAAAAA-AAAAGAAAAAAC
11930540 AGAAGAAAAAGGATAAAAGAAAAAA-
1 A-AAGAAAAA--A-AAAAGAAAAAAC
11930565 AAAGAA
1 AAAGAA
11930571 TAAATAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.22
23 10 0.22
24 13 0.29
25 1 0.02
26 11 0.24
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (22 bp):
AAAGAAAAAAAAAAGAAAAAAC
Found at i:11932859 original size:41 final size:41
Alignment explanation
Indices: 11932773--11932859 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 41
11932763 GGACCATCAT
* * *
11932773 TAAGTCTTTCGAGCATGATACTTATATCCTTCGGGTCATCTA
1 TAAGTCTTTCGAGCAAGATAC-TATATCCTTCGGCTCATCCA
*
11932815 TAAGTCTTTCGAGCAAGATGA-TATGTCCTTCAGGCT-ATCCA
1 TAAGTCTTTCGAGCAAGAT-ACTATATCCTTC-GGCTCATCCA
11932856 TAAG
1 TAAG
11932860 ACCTTCAGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
41 17 0.44
42 21 0.54
43 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (41 bp):
TAAGTCTTTCGAGCAAGATACTATATCCTTCGGCTCATCCA
Found at i:11933155 original size:18 final size:18
Alignment explanation
Indices: 11933128--11933165 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
11933118 CCAGGAAAAT
*
11933128 AATGATGACTGCTCTAGC
1 AATGAAGACTGCTCTAGC
*
11933146 AATGAAGACTGCTCTTGC
1 AATGAAGACTGCTCTAGC
11933164 AA
1 AA
11933166 AAAATTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (18 bp):
AATGAAGACTGCTCTAGC
Found at i:11933939 original size:135 final size:136
Alignment explanation
Indices: 11933695--11934176 Score: 616
Period size: 135 Copynumber: 3.6 Consensus size: 136
11933685 ACCAATCAAT
* * * *
11933695 ATTTCCAATGGAGAGTTCAAAATGAGAAGAACTCATCCGACAGAGGGAGAATAAGTTCATAATGA
1 ATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAATGA
* * * *
11933760 GAAGAACTTGTTCGA-CTATCACTCGATTCACGACATTTCGAATCAATGATACCTCGCTTGAGGA
66 GAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCAAATCAGTGACACCTCACTTGAGGA
11933824 ATTGAC
131 ATTGAC
11933830 ATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAA-AAGTTCATAATGA
1 ATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAATGA
* * * * * *
11933894 GAATAGCTTGTTCGACCTATCACTCGATTCATGACATTTCTAATCAGTGACGCCTCACTTGAGAA
66 GAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCAAATCAGTGACACCTCACTTGAGGA
11933959 ATTGAC
131 ATTGAC
* *
11933965 ATTTCAAATGGAGAGTTCATAATGAGAAGAACTAATCCTACAGA-AGGAGAAGAAGTTCATAATG
1 ATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGA-GAGAAGAAGTTCATAATG
* * * * * ** **
11934029 AGAAGAGA-TTATTCGACCTATCGCTCAATTCACAATATTTCAAATCAGCAACACCTCACTCAAG
65 AGAAGA-ACTTGTTCGACCTATCACTCGATTCACGACATTTCAAATCAGTGACACCTCACTTGAG
* **
11934093 GGATCAAC
129 GAATTGAC
* * *
11934101 ATTTTC-AGTGGAGAGTTCATAATGAGAAGAACTCATCCGATA-AGGGAGAAGAAGTTCATAATG
1 A-TTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAATG
11934164 AGAAGAACTTGTT
65 AGAAGAACTTGTT
11934177 TAACCTTAGC
Statistics
Matches: 302, Mismatches: 38, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
134 28 0.09
135 172 0.57
136 98 0.32
137 4 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (136 bp):
ATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGAGAGAAGAAGTTCATAATGA
GAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCAAATCAGTGACACCTCACTTGAGGA
ATTGAC
Found at i:11934290 original size:42 final size:43
Alignment explanation
Indices: 11934192--11934306 Score: 171
Period size: 42 Copynumber: 2.7 Consensus size: 43
11934182 TTAGCTTCTT
* * *
11934192 TCCATCGCATAAGGAGTTGGATCAACATCATCGTTTTTGCTCA
1 TCCATCACATAAGGAGTTGGATCAGCATCATCGTTTTTCCTCA
*
11934235 TCTATCACATAAGGAGTTGGAT-ATGCATCATCG-TTTTCCTCA
1 TCCATCACATAAGGAGTTGGATCA-GCATCATCGTTTTTCCTCA
11934277 TCCATCACATAAGGAGTTGGATCAGCATCA
1 TCCATCACATAAGGAGTTGGATCAGCATCA
11934307 CATTGGATCA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
42 36 0.55
43 29 0.45
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (43 bp):
TCCATCACATAAGGAGTTGGATCAGCATCATCGTTTTTCCTCA
Found at i:11935901 original size:20 final size:20
Alignment explanation
Indices: 11935864--11935917 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
11935854 CTTGTACTTA
*
11935864 ATTTATTT-TT-TATTTTAT
1 ATTTATTTATTGTTTTTTAT
* *
11935882 GTTTTTTTATTGTTTTTTAT
1 ATTTATTTATTGTTTTTTAT
*
11935902 ATTTATTTGTTGTTTT
1 ATTTATTTATTGTTTT
11935918 AATTATTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
18 6 0.21
19 2 0.07
20 20 0.71
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (20 bp):
ATTTATTTATTGTTTTTTAT
Found at i:11938647 original size:21 final size:21
Alignment explanation
Indices: 11938621--11938677 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
11938611 TTTGTTGAGT
*
11938621 AGTATCGATATTGATTCAATC
1 AGTATCGATACTGATTCAATC
*
11938642 AGTATCGATAGTGATTCAATC
1 AGTATCGATACTGATTCAATC
*
11938663 AGTATCAATACTGAT
1 AGTATCGATACTGAT
11938678 GAGGTAATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (21 bp):
AGTATCGATACTGATTCAATC
Done.