Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004871.1 Hibiscus syriacus cultivar Beakdansim tig00010980_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: 79231
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1110 original size:19 final size:20
Alignment explanation
Indices: 1086--1135 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1076 TTTTCCCAAT
*
1086 TCGCAATGCGAAT-AGTAAA
1 TCGCAATGCGAATGAGAAAA
* *
1105 TCGCAACGCGAATGGGAAAA
1 TCGCAATGCGAATGAGAAAA
1125 TCGCAATGCGA
1 TCGCAATGCGA
1136 TACTGACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (20 bp):
TCGCAATGCGAATGAGAAAA
Found at i:1147 original size:20 final size:20
Alignment explanation
Indices: 1124--1256 Score: 119
Period size: 20 Copynumber: 6.7 Consensus size: 20
1114 GAATGGGAAA
*
1124 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1144 ATCGCAATGCG-TACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
1163 ATCGCAATGCAATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1184 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1204 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1224 TTCGC-ACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
1243 TTCGCAACGTGATA
1 ATCGCAACGCGATA
1257 ATACATAATC
Statistics
Matches: 95, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
19 38 0.40
20 43 0.45
21 12 0.13
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1160 original size:19 final size:20
Alignment explanation
Indices: 1124--1276 Score: 116
Period size: 20 Copynumber: 7.7 Consensus size: 20
1114 GAATGGGAAA
1124 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1144 ATCGCAATGCG-TACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1163 ATCGCAATGCAATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1184 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
1204 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1224 TTCGC-ACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * * *
1243 TTCGCAACGTGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1263 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1277 TTTCTAAGCG
Statistics
Matches: 109, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
19 40 0.37
20 45 0.41
21 22 0.20
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1463 original size:22 final size:22
Alignment explanation
Indices: 1435--1479 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1425 CACTCTCACA
*
1435 CCCCATCTCTGACAAAATCCGT
1 CCCCATCTCCGACAAAATCCGT
* *
1457 CCCCATCTCCGGCGAAATCCGT
1 CCCCATCTCCGACAAAATCCGT
1479 C
1 C
1480 TATCCCATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.44, G:0.13, T:0.20
Consensus pattern (22 bp):
CCCCATCTCCGACAAAATCCGT
Found at i:1775 original size:20 final size:20
Alignment explanation
Indices: 1752--1792 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1742 GATAGTCAAA
1752 TTCGCGTTGAGATTGTCATT
1 TTCGCGTTGAGATTGTCATT
* * *
1772 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGAGATTGTCATT
1792 T
1 T
1793 CAGAACTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.15, G:0.22, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGAGATTGTCATT
Found at i:3121 original size:17 final size:18
Alignment explanation
Indices: 3096--3139 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
3086 TCCACTTCGG
*
3096 GAGCCATCACCTC-GCCA
1 GAGCCATCACCTCACCCA
*
3113 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3131 GAGCCATCA
1 GAGCCATCA
3140 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.27, C:0.43, G:0.16, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3549 original size:17 final size:17
Alignment explanation
Indices: 3515--3556 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3505 ACTGCTAAAA
3515 TGTTTTT-GTTAGTATT
1 TGTTTTTGGTTAGTATT
* *
3531 TGTTTTTGGTTTGTTTT
1 TGTTTTTGGTTAGTATT
3548 TGTCTTTTG
1 TGT-TTTTG
3557 TTGAAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 7 0.32
17 10 0.45
18 5 0.23
ACGTcount: A:0.05, C:0.02, G:0.21, T:0.71
Consensus pattern (17 bp):
TGTTTTTGGTTAGTATT
Found at i:3682 original size:14 final size:14
Alignment explanation
Indices: 3663--3719 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3653 ATGCGAAATG
3663 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3677 AAAATCGCAATGCGA-
1 AAAATCGCAA--CGAC
3692 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3708 AAAATCGCAACG
1 AAAATCGCAACG
3720 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 21 0.55
15 4 0.11
16 4 0.11
17 9 0.24
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3702 original size:31 final size:33
Alignment explanation
Indices: 3647--3736 Score: 157
Period size: 31 Copynumber: 2.8 Consensus size: 33
3637 GAAAATGGCT
3647 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
3680 ATCGCAATGCG-AATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
3711 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
3737 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
31 26 0.48
32 8 0.15
33 20 0.37
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:3772 original size:14 final size:14
Alignment explanation
Indices: 3753--3810 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3743 TTGTGTTTCA
3753 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3767 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3783 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3799 CGTTGCGATTTT
1 CGTTGCGATTTT
3811 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3794 original size:32 final size:33
Alignment explanation
Indices: 3755--3826 Score: 137
Period size: 32 Copynumber: 2.2 Consensus size: 33
3745 GTGTTTCACG
3755 TTGCGATTTTGTCGTTGCGA-TTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
3787 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
3820 TTGCGAT
1 TTGCGAT
3827 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 20 0.51
33 19 0.49
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
Found at i:3845 original size:20 final size:19
Alignment explanation
Indices: 3811--3866 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
3801 TTGCGATTTT
*
3811 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3830 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
3850 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
3867 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5723 original size:13 final size:14
Alignment explanation
Indices: 5691--5725 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5681 ATTGTTTAAT
5691 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
5705 TGATTTGTAAATG-
1 TGATTTGTAAAAGA
5718 TGATTTGT
1 TGATTTGT
5726 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5954 original size:20 final size:20
Alignment explanation
Indices: 5929--5966 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5919 TCGCATTGCG
*
5929 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
5949 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
5967 TCAAATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:6329 original size:20 final size:20
Alignment explanation
Indices: 6299--6371 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
6289 GATTCTGTAT
*
6299 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6319 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
6339 TATCGCATTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTCAG
6359 TATCGCGTTGCGA
1 TATCGCGTTGCGA
6372 TTTTGTATTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:6524 original size:21 final size:21
Alignment explanation
Indices: 6484--6524 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6474 ACTGTAGACC
** *
6484 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
6505 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
6525 ACGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:6728 original size:16 final size:16
Alignment explanation
Indices: 6698--6763 Score: 84
Period size: 15 Copynumber: 4.3 Consensus size: 16
6688 CTTAAACAAC
6698 TAACTATTC-TTAATA
1 TAACTATTCTTTAATA
6713 TAACTATTCTTTAATA
1 TAACTATTCTTTAATA
***
6729 TAACT-TTAACTAATA
1 TAACTATTCTTTAATA
6744 -AACTATTCTTTAATA
1 TAACTATTCTTTAATA
6759 TAACT
1 TAACT
6764 TAAACTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
14 4 0.10
15 23 0.55
16 15 0.36
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (16 bp):
TAACTATTCTTTAATA
Found at i:6750 original size:30 final size:30
Alignment explanation
Indices: 6708--6803 Score: 126
Period size: 30 Copynumber: 3.2 Consensus size: 30
6698 TAACTATTCT
6708 TAATATAACTATTCTTTAATATAACTTTAAC
1 TAATA-AACTATTCTTTAATATAACTTTAAC
*
6739 TAATAAACTATTCTTTAATATAACTTAAAC
1 TAATAAACTATTCTTTAATATAACTTTAAC
*
6769 TAATAAACGATT-TTTAATTATAA-TTT-AC
1 TAATAAACTATTCTTTAA-TATAACTTTAAC
*
6797 TACTAAA
1 TAATAAA
6804 AATTAATTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
28 8 0.13
29 7 0.12
30 40 0.67
31 5 0.08
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (30 bp):
TAATAAACTATTCTTTAATATAACTTTAAC
Found at i:6914 original size:43 final size:43
Alignment explanation
Indices: 6872--6977 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 43
6862 TTTAACTAAC
*
6872 ACAAACTAATTACA-TATTTTT-TT-ATATATAACTAACGACTA
1 ACAAACTAACTA-ATTATTTTTATTAATATATAACTAACGACTA
* *
6913 ACAAACTAACTAATTATTTTTATTAATATGTAACTATC-A--A
1 ACAAACTAACTAATTATTTTTATTAATATATAACTAACGACTA
* *
6953 ACATACTAATTAAATTATTTTTATT
1 ACAAACTAACT-AATTATTTTTATT
6978 TCTATATGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
40 11 0.20
41 31 0.55
42 3 0.05
43 11 0.20
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.42
Consensus pattern (43 bp):
ACAAACTAACTAATTATTTTTATTAATATATAACTAACGACTA
Found at i:7161 original size:29 final size:27
Alignment explanation
Indices: 7112--7169 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 27
7102 TTTAAATAAT
* *
7112 TATTCTTTTATATACTTAAACTAATAAAC
1 TATTCTTTTATATAATAAAACT--TAAAC
7141 TATT-TTTTATTATAATAAAACTTAAAC
1 TATTCTTTTA-TATAATAAAACTTAAAC
7168 TA
1 TA
7170 CTAATAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 7 0.27
28 5 0.19
29 14 0.54
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTCTTTTATATAATAAAACTTAAAC
Found at i:7233 original size:45 final size:46
Alignment explanation
Indices: 7128--7218 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
7118 TTTATATACT
* * * *
7128 TAAACTAATAAACTATTTTTTATTATAATAAAACTTAAACTACTAA
1 TAAACTAATTAACTAATTTTTATTATAATAAAACTTAAACAACCAA
7174 TAAACTAATTAACTAATTTTTA-TATAATATAAA-TTAAACAACCAA
1 TAAACTAATTAACTAATTTTTATTATAATA-AAACTTAAACAACCAA
7219 AATATAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 17 0.43
46 23 0.57
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (46 bp):
TAAACTAATTAACTAATTTTTATTATAATAAAACTTAAACAACCAA
Found at i:7421 original size:39 final size:38
Alignment explanation
Indices: 7375--7459 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 38
7365 ACAAAAATAA
*
7375 ACTTAAACTAACAAACTAATTAACTAAAATTTTGTTTT
1 ACTTAAACTAACAAACTAATTAACTAAAATATTGTTTT
*
7413 ACCTTAAACTAACTAACTAATTAACTAAAATATTGTTTT
1 A-CTTAAACTAACAAACTAATTAACTAAAATATTGTTTT
7452 ACTTAAAC
1 ACTTAAAC
7460 CATAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 8 0.18
39 36 0.82
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (38 bp):
ACTTAAACTAACAAACTAATTAACTAAAATATTGTTTT
Found at i:7508 original size:9 final size:9
Alignment explanation
Indices: 7476--7513 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
7466 CTAACAAACT
7476 AATAATTTAA
1 AATAA-TTAA
7486 AATAA-TAA
1 AATAATTAA
*
7494 AGTAATTAA
1 AATAATTAA
7503 AATAATTAA
1 AATAATTAA
7512 AA
1 AA
7514 AACTTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:7853 original size:29 final size:29
Alignment explanation
Indices: 7807--7863 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
7797 CAAAGCATGC
* * *
7807 ATGTCGTTGGGATGCCCTGGCGACCTACA
1 ATGTCGCTGGGATACCCTGACGACCTACA
7836 ATGTCGCTGGGATACCCTGACGACCTAC
1 ATGTCGCTGGGATACCCTGACGACCTAC
7864 CCAGAACCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (29 bp):
ATGTCGCTGGGATACCCTGACGACCTACA
Found at i:7977 original size:29 final size:28
Alignment explanation
Indices: 7943--7998 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
7933 CAACAGGTCA
7943 CCCGGATGCCATGGCGACCTCCAAGCTCG
1 CCCGGATGCCATGGCGACCTCC-AGCTCG
7972 CCCGGATGCCATGGCGACCTCCAGCTC
1 CCCGGATGCCATGGCGACCTCCAGCTC
7999 ACTGTAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.16, C:0.43, G:0.27, T:0.14
Consensus pattern (28 bp):
CCCGGATGCCATGGCGACCTCCAGCTCG
Found at i:8998 original size:19 final size:19
Alignment explanation
Indices: 8942--8998 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
8932 CAATTTTTGA
*
8942 AAAATGTGTTGCGATAATT
1 AAAATGTGTTGCGATAGTT
8961 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
8980 AAAATGTGTTGCGAGAGTT
1 AAAATGTGTTGCGATAGTT
8999 TGAAAAACGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.35
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:15293 original size:21 final size:21
Alignment explanation
Indices: 15267--15311 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
15257 GATTTCTGGG
* *
15267 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
15288 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
15309 CAA
1 CAA
15312 ACGAACAAAA
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:16289 original size:31 final size:31
Alignment explanation
Indices: 16168--16277 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
16158 AGGGTCGAGG
16168 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
16199 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
16230 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
16261 GATTACTTAGGTTCTTC
1 GTTTACCTATGTTCTTC
16278 AGAATCTATG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:21464 original size:41 final size:41
Alignment explanation
Indices: 21419--21578 Score: 277
Period size: 41 Copynumber: 3.9 Consensus size: 41
21409 ATTCGCGTTG
21419 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
21460 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
*
21501 TATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
21542 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
21579 AGTCTACAGT
Statistics
Matches: 111, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.01
41 109 0.98
42 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:21612 original size:41 final size:41
Alignment explanation
Indices: 21567--21934 Score: 555
Period size: 41 Copynumber: 9.0 Consensus size: 41
21557 TAGTTGAAAA
21567 TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
* * *
21608 TCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCATT
*
21649 TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCTATT
1 TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
* *
21690 TCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCATT
* *
21731 TCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCATT
21772 TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
* *
21813 TCGCGTTGCGATAGTTGTA-AATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAG-TCTACAGTCGCGTTGCGATTTTCCATT
*
21854 TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCGTT
1 TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
*
21895 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 TCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTCCA
21935 AATTCGTTGT
Statistics
Matches: 301, Mismatches: 19, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
40 5 0.02
41 277 0.92
42 19 0.06
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
Found at i:21731 original size:185 final size:185
Alignment explanation
Indices: 21419--21763 Score: 681
Period size: 185 Copynumber: 1.9 Consensus size: 185
21409 ATTCGCGTTG
21419 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
21484 GTCGCGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCG
66 GTCGCGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCG
21549 CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
131 CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
*
21604 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTCTACA
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
21669 GTCGCGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCG
66 GTCGCGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCG
21734 CGTTGCGATAGTTGAAAATCGCGTTGCGAT
131 CGTTGCGATAGTTGAAAATCGCGTTGCGAT
21764 TTTCCATTTC
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 159 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.37
Consensus pattern (185 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACA
GTCGCGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCG
CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTC
Found at i:21799 original size:185 final size:184
Alignment explanation
Indices: 21423--21804 Score: 651
Period size: 185 Copynumber: 2.1 Consensus size: 184
21413 GCGTTGCATT
21423 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCG
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCG
21488 CGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
66 CGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
* * *
21553 GCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATT
131 GCGATAGTTGAAAATCGCGTTGCGATA-TCTACAGTCGCGTTGCGATTCTACATG
*
21608 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTCTACAGTCG
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCG
21673 CGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
66 CGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
* * *
21738 GCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTCTACA-G
131 GCGATAGTTGAAAATCGCGTTGCGATATCTACA-GTCGCGTTGCGAT--TCTACATG
21793 TCGCGTTGCGAT
1 TCGCGTTGCGAT
21805 TTTCCATTTC
Statistics
Matches: 187, Mismatches: 7, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
183 4 0.02
184 12 0.06
185 167 0.89
186 4 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (184 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCG
CGTTGCGATTTTCTATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTT
GCGATAGTTGAAAATCGCGTTGCGATATCTACAGTCGCGTTGCGATTCTACATG
Found at i:22051 original size:5 final size:5
Alignment explanation
Indices: 22032--22070 Score: 69
Period size: 5 Copynumber: 7.6 Consensus size: 5
22022 CGTATTACCA
22032 CGACC CGACC ACGACC CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC -CGACC CGACC CGACC CGACC CGACC CGA
22071 GACGAGACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.23, C:0.56, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:22567 original size:6 final size:6
Alignment explanation
Indices: 22558--22594 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
22548 CCGTCTCGTC
22558 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
22595 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:22718 original size:21 final size:21
Alignment explanation
Indices: 22654--22718 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
22644 TCTTTTTTTT
*
22654 AACTATCGCAACGCGAAATGG
1 AACTATCGCAACGCGAAATGC
* * ** *
22675 AA-AAACGCAACGCGATCTCC
1 AACTATCGCAACGCGAAATGC
*
22695 AACTATCGCAATGCGAAATGC
1 AACTATCGCAACGCGAAATGC
22716 AAC
1 AAC
22719 GTGAATTTGC
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.40, C:0.28, G:0.18, T:0.14
Consensus pattern (21 bp):
AACTATCGCAACGCGAAATGC
Found at i:23975 original size:112 final size:112
Alignment explanation
Indices: 23766--24227 Score: 780
Period size: 112 Copynumber: 4.1 Consensus size: 112
23756 TGTCGGTTTC
* *
23766 TGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
* **
23831 GTATATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAAG
66 GTCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAAG
*
23878 TGTCGATACTTTATAAAAATGTATCGATCCATAAAAATATAACAGGTAAAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
* *
23943 GTCTATAAATGACAAAACAGATAAAACACTACCGGATATATTGAAAG
66 GTCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAAG
* * *
23990 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACCAAATCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
* *
24055 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAG
66 GTCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAAG
24102 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
* * *
24167 GTCTATAAATGATAAAACAGGTAAAGCACTACCGGATATGTTGATAG
66 GTCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAAG
24214 TGTCGATACTTTAT
1 TGTCGATACTTTAT
24228 TATAAGTATC
Statistics
Matches: 326, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 326 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAAG
Found at i:24406 original size:182 final size:182
Alignment explanation
Indices: 24098--24553 Score: 747
Period size: 182 Copynumber: 2.5 Consensus size: 182
24088 GAATATATTG
* *
24098 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGACAAA
** * *
24163 ACCGGTCTATAAATGATAAAA-CAGGTAAAGCACTACCGGATATGTTGATAGTGTCGATACTTTA
66 ACCGGTCTCGAAATGACAAAACCA-GTAAAGCACTACCGGATATGTTGAAAGTGTCGATACTTTA
*
24227 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCG-CTAAT
130 TTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTC-AAT
* *
24280 AAAGTGTCGATACTTTATAAAAATGTATCGATCTATAACAATATAACAGTTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGACAAA
*
24345 ACCGGTCTCGAAATGACAAAACCAGTAAAG-AGCTACCGGATATGTTGAAAGTGTTGATACTTTA
66 ACCGGTCTCGAAATGACAAAACCAGTAAAGCA-CTACCGGATATGTTGAAAGTGTCGATACTTTA
24409 TTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAAT
130 TTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAAT
* *
24462 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACAGAAAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGACAAA
*
24527 ATCGGTCTCGAAATGACAAAACCAGTA
66 ACCGGTCTCGAAATGACAAAACCAGTA
24554 GTAAAAAAGT
Statistics
Matches: 257, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
181 1 0.00
182 253 0.98
183 3 0.01
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGATAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCAGTAAAGCACTACCGGATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAAT
Found at i:24828 original size:23 final size:23
Alignment explanation
Indices: 24799--24846 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
24789 AAATATGTCA
*
24799 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
24822 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
24845 AT
1 AT
24847 TGTACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:25330 original size:18 final size:17
Alignment explanation
Indices: 25294--25337 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
25284 ATAAATCTAA
* * *
25294 ATAATAATTATTAATAT
1 ATAATAAATAATAAAAT
25311 ATTAATAAATAATAAAAT
1 A-TAATAAATAATAAAAT
25329 ATAATAAAT
1 ATAATAAAT
25338 TAACTAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATAAATAATAAAAT
Found at i:25333 original size:25 final size:25
Alignment explanation
Indices: 25291--25340 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
25281 AAAATAAATC
* *
25291 TAAATAATAATTATTAATATATTAA
1 TAAATAATAAATATTAATAAATTAA
25316 TAAATAATAAA-ATATAATAAATTAA
1 TAAATAATAAATAT-TAATAAATTAA
25341 CTAATCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAATAATAAATATTAATAAATTAA
Found at i:25373 original size:44 final size:41
Alignment explanation
Indices: 25312--25396 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 41
25302 TATTAATATA
25312 TTAATAAATAATAAAATATAATAAATTAACTAATCTATTATTTT
1 TTAATAAATAATAAAATATAATAAATTAA-TAA--TATTATTTT
* *
25356 TTAATAAATAATAAAATATTATTAATTAATAATATTATTTT
1 TTAATAAATAATAAAATATAATAAATTAATAATATTATTTT
25397 AATACCAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
41 9 0.23
43 3 0.08
44 27 0.69
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (41 bp):
TTAATAAATAATAAAATATAATAAATTAATAATATTATTTT
Found at i:25398 original size:18 final size:18
Alignment explanation
Indices: 25350--25400 Score: 50
Period size: 21 Copynumber: 2.7 Consensus size: 18
25340 ACTAATCTAT
25350 TATT-TTTTAATAAATAA
1 TATTATTTTAATAAATAA
* *
25367 TAAAATATTATTAATTAATAA
1 T--ATTATT-TTAATAAATAA
25388 TATTATTTTAATA
1 TATTATTTTAATA
25401 CCAAAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
17 1 0.04
18 5 0.19
19 7 0.27
20 2 0.08
21 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTATTTTAATAAATAA
Found at i:31689 original size:23 final size:23
Alignment explanation
Indices: 31663--31706 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
31653 ACCGGTCATA
31663 ACCCAACCCGACCCGTTGACCCG
1 ACCCAACCCGACCCGTTGACCCG
*
31686 ACCCGACCCGACCCGTTGACC
1 ACCCAACCCGACCCGTTGACC
31707 GTTGACCGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.52, G:0.18, T:0.09
Consensus pattern (23 bp):
ACCCAACCCGACCCGTTGACCCG
Found at i:34283 original size:24 final size:24
Alignment explanation
Indices: 34165--34280 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
34155 TTCGATTTGA
34165 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
34189 ATTCTGATATGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
34213 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
34237 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
*
34261 AGTT-TGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
34281 CTGATTTATG
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 1 0.01
24 78 0.95
25 3 0.04
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:36238 original size:23 final size:22
Alignment explanation
Indices: 36212--36286 Score: 102
Period size: 23 Copynumber: 3.5 Consensus size: 22
36202 ATAGGTAAAA
36212 ATATGATGTAATAGGTAGCGCTT
1 ATAT-ATGTAATAGGTAGCGCTT
36235 ATATAATGTAATAGGTAGCG-TT
1 ATAT-ATGTAATAGGTAGCGCTT
*
36257 -TATATGTAATAGGTAGTGCTT
1 ATATATGTAATAGGTAGCGCTT
36278 ATAT-TGTAA
1 ATATATGTAA
36287 AGTATCTATC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
20 14 0.29
21 10 0.21
22 5 0.10
23 19 0.40
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (22 bp):
ATATATGTAATAGGTAGCGCTT
Found at i:36265 original size:20 final size:20
Alignment explanation
Indices: 36217--36286 Score: 86
Period size: 20 Copynumber: 3.3 Consensus size: 20
36207 TAAAAATATG
36217 ATGTAATAGGTAGCGCTTATAT
1 ATGTAATAGGTAGCG-TT-TAT
36239 AATGTAATAGGTAGCGTTTAT
1 -ATGTAATAGGTAGCGTTTAT
* *
36260 ATGTAATAGGTAGTGCTTAT
1 ATGTAATAGGTAGCGTTTAT
36280 ATTGTAA
1 A-TGTAA
36287 AGTATCTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.43
21 8 0.18
22 2 0.05
23 15 0.34
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.39
Consensus pattern (20 bp):
ATGTAATAGGTAGCGTTTAT
Found at i:36720 original size:20 final size:20
Alignment explanation
Indices: 36695--36764 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 20
36685 GTAAAATATG
36695 ATGTAATAGGTAGCGCTTAT
1 ATGTAATAGGTAGCGCTTAT
* *
36715 ATGTAATAGGTAACGTTTATAT
1 ATGTAATAGGTAGCG-CT-TAT
*
36737 AATGTAATAGGTAGTGCTTAT
1 -ATGTAATAGGTAGCGCTTAT
36758 ATTGTAA
1 A-TGTAA
36765 AGTATCTATC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
20 15 0.37
21 9 0.22
22 4 0.10
23 13 0.32
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (20 bp):
ATGTAATAGGTAGCGCTTAT
Found at i:36757 original size:23 final size:22
Alignment explanation
Indices: 36690--36764 Score: 84
Period size: 23 Copynumber: 3.5 Consensus size: 22
36680 AATAGGTAAA
36690 ATATGATGTAATAGGTAGCGC-T
1 ATAT-ATGTAATAGGTAGCGCTT
* *
36712 -TATATGTAATAGGTAACGTTT
1 ATATATGTAATAGGTAGCGCTT
*
36733 ATATAATGTAATAGGTAGTGCTT
1 ATAT-ATGTAATAGGTAGCGCTT
36756 ATAT-TGTAA
1 ATATATGTAA
36765 AGTATCTATC
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 14 0.31
21 9 0.20
22 3 0.07
23 19 0.42
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (22 bp):
ATATATGTAATAGGTAGCGCTT
Found at i:37001 original size:481 final size:477
Alignment explanation
Indices: 35799--37161 Score: 2303
Period size: 477 Copynumber: 2.8 Consensus size: 477
35789 ATTTTACCTG
* *
35799 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACCGTAGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
*
35864 AATTTAAGGTTATCTTTTGAGTAAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
*
35929 TTATTTTTACATTACGGTATATTATTATTAAATTAAAAATAATAAAC--ATATA-TACATATTTA
131 TTATTTTTACATTACGGTATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTA
*
35991 TTATTATCTTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATC-AAACA
196 TTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACA
*
36055 ATCAAATAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACAC
261 ATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACAC
* *
36120 TGTTAAAAAAATTAAAACATAAATTACATAACTTTAAAAAAAAATATCGATCATTTTTAT-AAAA
326 TATT--AAAAATTGAAACATAAATTACATAACTTT--AAAAAAATATCGATCATTTTTATAAAAA
36184 GTATGAACACTTTCAATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAG
387 GTATG-ACACTTTCAATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAG
*
36249 GTAGCGTTTATATGTAATAGGTAGTGC
451 GTAACGTTTATATGTAATAGGTAGTGC
36276 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
* **
36341 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGTATCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
** *
36406 TTATTTTTATGTTACGGTATATTATCATTAAATTAAAAACAATAAACATATATATTACATATTTA
131 TTATTTTTACATTACGGTATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTA
36471 TTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACA
196 TTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACA
* *
36536 ATCAAATAATGTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACAC
261 ATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACAC
*
36601 TATTAAAAATTGAAACATAAATTACATAACTTTAAAAAAGTATCGATCATTTTTATAAAAAGTAT
326 TATTAAAAATTGAAACATAAATTACATAACTTTAAAAAAATATCGATCATTTTTATAAAAAGTAT
36666 AGACACTTTCATATAATAGGT-AAAATATGATGTAATAGGTAGCGC-T-TAT-ATGTAATAGGTA
391 -GACACTTTCA-ATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTA
36727 ACGTTTATATAATGTAATAGGTAGTGC
454 ACG-TT-TAT-ATGTAATAGGTAGTGC
36754 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
1 TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
36819 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
66 AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
36884 TTATTTTTTACATTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
131 TTA-TTTTTACATTACGG--TATATTATTATTAAATTAAAAACAATAAACATATATATTACATAT
*
36949 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAA
193 TTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAA
*
37014 ACAATCAAATAATTTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAA
258 ACAATCAAATAA-TTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAA
* * *
37079 ACATTATTAAAATTTTGAAACATAAATTACATAACTTTAAAAAAATATCGATCCTTTTTATAAAA
322 ACACTATTAAAA-ATTGAAACATAAATTACATAACTTTAAAAAAATATCGATCATTTTTAT-AAA
37144 AAGTATGGACACTTTCAA
385 AAGTAT-GACACTTTCAA
37162 CATATTATAA
Statistics
Matches: 837, Mismatches: 33, Indels: 26
0.93 0.04 0.03
Matches are distributed among these distances:
475 14 0.02
476 5 0.01
477 193 0.23
478 187 0.22
479 55 0.07
480 68 0.08
481 190 0.23
482 60 0.07
483 46 0.05
484 19 0.02
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (477 bp):
TTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATT
AATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGAT
TTATTTTTACATTACGGTATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTA
TTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACA
ATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACAC
TATTAAAAATTGAAACATAAATTACATAACTTTAAAAAAATATCGATCATTTTTATAAAAAGTAT
GACACTTTCAATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAAC
GTTTATATGTAATAGGTAGTGC
Found at i:37887 original size:11 final size:11
Alignment explanation
Indices: 37871--37914 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
37861 GTCAGATTCC
37871 TTAAAAATATT
1 TTAAAAATATT
37882 TTAAAAAAATATT
1 TT--AAAAATATT
37895 TTAAAAATATT
1 TTAAAAATATT
*
37906 TGAAAAATA
1 TTAAAAATA
37915 AAACTATAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:37891 original size:13 final size:13
Alignment explanation
Indices: 37873--37901 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
37863 CAGATTCCTT
37873 AAAAATATTTTAA
1 AAAAATATTTTAA
37886 AAAAATATTTTAA
1 AAAAATATTTTAA
37899 AAA
1 AAA
37902 TATTTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAAATATTTTAA
Found at i:40309 original size:29 final size:31
Alignment explanation
Indices: 40256--40332 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 31
40246 TTTCAAACCC
* *
40256 CTGTTTTTGCT-GTTTGATACTTTAAA-TTT
1 CTGTTTTTGCTATTTTAATACTTTAAACTTT
40285 CTGTTTTTGCTATTTTAATAC-TTAAAGCTTT
1 CTGTTTTTGCTATTTTAATACTTTAAA-CTTT
*
40316 -TGTTTTTCTCTATTTTA
1 CTGTTTTT-GCTATTTTA
40333 GTCTTTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 16 0.39
30 14 0.34
31 11 0.27
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.60
Consensus pattern (31 bp):
CTGTTTTTGCTATTTTAATACTTTAAACTTT
Found at i:43271 original size:8 final size:7
Alignment explanation
Indices: 43245--43335 Score: 70
Period size: 6 Copynumber: 13.6 Consensus size: 7
43235 AGATCAACAT
43245 TTTTGCA
1 TTTTGCA
*
43252 -TCTGCA
1 TTTTGCA
43258 -TTTGCA
1 TTTTGCA
43264 TCTTTGCA
1 T-TTTGCA
43272 TTTTGCA
1 TTTTGCA
*
43279 -TCTGCA
1 TTTTGCA
43285 -TTTGCA
1 TTTTGCA
43291 TATTTGCA
1 T-TTTGCA
43299 TTTTGCA
1 TTTTGCA
* *
43306 -TCTACA
1 TTTTGCA
43312 -TTTGCA
1 TTTTGCA
43318 TCTTTGCA
1 T-TTTGCA
43326 TTTT-CA
1 TTTTGCA
43332 TTTT
1 TTTT
43336 ATTTTTAAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
6 34 0.49
7 15 0.21
8 21 0.30
ACGTcount: A:0.16, C:0.20, G:0.12, T:0.52
Consensus pattern (7 bp):
TTTTGCA
Found at i:43281 original size:27 final size:27
Alignment explanation
Indices: 43245--43329 Score: 152
Period size: 27 Copynumber: 3.1 Consensus size: 27
43235 AGATCAACAT
43245 TTTTGCATCTGCATTTGCATCTTTGCA
1 TTTTGCATCTGCATTTGCATCTTTGCA
*
43272 TTTTGCATCTGCATTTGCATATTTGCA
1 TTTTGCATCTGCATTTGCATCTTTGCA
*
43299 TTTTGCATCTACATTTGCATCTTTGCA
1 TTTTGCATCTGCATTTGCATCTTTGCA
43326 TTTT
1 TTTT
43330 CATTTTATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.16, C:0.20, G:0.13, T:0.51
Consensus pattern (27 bp):
TTTTGCATCTGCATTTGCATCTTTGCA
Found at i:45778 original size:16 final size:15
Alignment explanation
Indices: 45757--45801 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
45747 GACATTTTGT
*
45757 AAAAAAAAAGAAGCA
1 AAAAAAAAAAAAGCA
45772 AAAAAAAACAAAAGCA
1 AAAAAAAA-AAAAGCA
45788 AAAAAAAAACAAAG
1 AAAAAAAAA-AAAG
45802 ATCAGATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGCA
Found at i:45797 original size:17 final size:16
Alignment explanation
Indices: 45757--45800 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
45747 GACATTTTGT
*
45757 AAAAAAAA-AGAAGCA
1 AAAAAAAACAAAAGCA
45772 AAAAAAAACAAAAGCAA
1 AAAAAAAACAAAAGC-A
45789 AAAAAAAACAAA
1 AAAAAAAACAAA
45801 GATCAGATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 8 0.31
16 5 0.19
17 13 0.50
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAGCA
Found at i:47537 original size:24 final size:23
Alignment explanation
Indices: 47502--47574 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 23
47492 AGAGAGGGGC
47502 AATA-TTTTCAAAACTTTTGACTA
1 AATATTTTTCAAAACTTTTGA-TA
*
47525 AATATTTTTCAAAACTCTT-ATA
1 AATATTTTTCAAAACTTTTGATA
*
47547 ATTGATATTTTCAAAACTTTTGA-A
1 AAT-AT-TTTTCAAAACTTTTGATA
47571 AATA
1 AATA
47575 AAAGAAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
22 4 0.10
23 8 0.19
24 29 0.69
25 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (23 bp):
AATATTTTTCAAAACTTTTGATA
Found at i:47793 original size:33 final size:32
Alignment explanation
Indices: 47691--47807 Score: 198
Period size: 32 Copynumber: 3.6 Consensus size: 32
47681 AAGCAATAGA
*
47691 GGGCATCTTTGAAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
47723 GGGCATCTTTAGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
47755 TGGCATCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
47788 GGGCATCTTTGGAGATTCAA
1 GGGCATCTTTGGAGATTCAA
47808 TATCGAATAT
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 52 0.66
33 27 0.34
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:47825 original size:65 final size:63
Alignment explanation
Indices: 47685--47825 Score: 192
Period size: 65 Copynumber: 2.2 Consensus size: 63
47675 GTGCTGAAGC
*
47685 AATAGAGGGCATCTTTGAAGATTCAACATCAAATGTTGGGGCATCTTTAGAGATTCAACATCA
1 AATATAGGGCATCTTTGAAGATTCAACATCAAATGTTGGGGCATCTTTAGAGATTCAACATCA
* * * * * *
47748 AATGTTGTGGCATCTTTGGAGATTCAACATCAAAATGTTGGGGCATCTTTGGAGATTCAATATCG
1 AATATAG-GGCATCTTTGAAGATTCAACATC-AAATGTTGGGGCATCTTTAGAGATTCAACATCA
47813 AATATAAGGGCAT
1 AATAT-AGGGCAT
47826 TCGATATCCT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 4 0.06
64 22 0.33
65 39 0.59
66 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (63 bp):
AATATAGGGCATCTTTGAAGATTCAACATCAAATGTTGGGGCATCTTTAGAGATTCAACATCA
Found at i:47973 original size:34 final size:34
Alignment explanation
Indices: 47933--48037 Score: 165
Period size: 34 Copynumber: 3.1 Consensus size: 34
47923 AAAAAAATTT
47933 TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
1 TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
* *
47967 TTTTGTCTCACTTGAGACACTTTCTCAAAACAAA
1 TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
* *
48001 TTTCGTCTCACTTGAGATAATTTCTTTAAAACAAA
1 TTTTGTCTCACTTGAGATAATTTC-TCAAAACAAA
48036 TT
1 TT
48038 CCGTCTCGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
34 53 0.83
35 11 0.17
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (34 bp):
TTTTGTCTCACTTGAGATAATTTCTCAAAACAAA
Found at i:48043 original size:35 final size:34
Alignment explanation
Indices: 47937--48058 Score: 163
Period size: 34 Copynumber: 3.6 Consensus size: 34
47927 AAATTTTTTT
* *
47937 GTCTCACTTGAGATAATTTCTCAAAACAAATTTT
1 GTCTCACTTGAGACAATTTCTCAAAACAAATTTC
*
47971 GTCTCACTTGAGACACTTTCTCAAAACAAATTTC
1 GTCTCACTTGAGACAATTTCTCAAAACAAATTTC
* * *
48005 GTCTCACTTGAGATAATTTCTTTAAAACAAATTCC
1 GTCTCACTTGAGACAATTTC-TCAAAACAAATTTC
**
48040 GTCTCGTTTGAGACAATTT
1 GTCTCACTTGAGACAATTT
48059 TTCTCTGAGA
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
34 49 0.64
35 28 0.36
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (34 bp):
GTCTCACTTGAGACAATTTCTCAAAACAAATTTC
Found at i:48323 original size:77 final size:77
Alignment explanation
Indices: 48223--48368 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 77
48213 GTTTCATTTG
* * * * * *
48223 AAACAAAGTTGTCTCACTTGAGAC-TGTTTTACTTGAAAGAAGACATTTCATTTGACTCAAGATT
1 AAACAAAGTTGTCTCACTGGAGACATATTTTACTTAAAACAAGACATTTCATTTCACTCAAGATA
48287 GTTTTTTTCTCA
66 GTTTTTTTCTCA
* * * *
48299 AAACAAGATTTGTCTCGCTGGAGACATATTTTATTTAAAACAAGACATTTTATTTCACTCAAGAT
1 AAACAA-AGTTGTCTCACTGGAGACATATTTTACTTAAAACAAGACATTTCATTTCACTCAAGAT
48364 AGTTT
65 AGTTT
48369 CCCTCGAAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
76 6 0.10
77 15 0.26
78 37 0.64
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (77 bp):
AAACAAAGTTGTCTCACTGGAGACATATTTTACTTAAAACAAGACATTTCATTTCACTCAAGATA
GTTTTTTTCTCA
Found at i:48428 original size:36 final size:35
Alignment explanation
Indices: 48381--48472 Score: 166
Period size: 36 Copynumber: 2.6 Consensus size: 35
48371 CTCGAAACAG
48381 AAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGGA
1 AAAAATTTTGTCTCCCTTGAGACAGTTTCCCTT-GA
48417 AAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
1 AAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
48452 AACAAATTTTGTCTCCCTTGA
1 AA-AAATTTTGTCTCCCTTGA
48473 AACAAATTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
35 4 0.07
36 51 0.93
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (35 bp):
AAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
Found at i:48434 original size:21 final size:21
Alignment explanation
Indices: 48408--48493 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
48398 TGAGACAGTT
48408 TCCCTTGGAAA-AAATTTTGTC
1 TCCCTT-GAAACAAATTTTGTC
* *
48429 TCCCTTGAGAC--A-GTT-TC
1 TCCCTTGAAACAAATTTTGTC
48446 -C-CTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
48465 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
48486 TCCCTTGA
1 TCCCTTGA
48494 GACAGTTTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
15 7 0.13
16 1 0.02
17 3 0.06
18 4 0.07
19 3 0.06
20 4 0.07
21 32 0.59
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:48481 original size:57 final size:56
Alignment explanation
Indices: 48408--48529 Score: 208
Period size: 57 Copynumber: 2.1 Consensus size: 56
48398 TGAGACAGTT
48408 TCCCTTGGAAAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
1 TCCCTT-GAAAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
*
48465 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATATTTTGTC
1 TCCCTTGAAA-AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
*
48522 TCTCTTGA
1 TCCCTTGA
48530 GACGGTTTCA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
56 4 0.06
57 58 0.94
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.39
Consensus pattern (56 bp):
TCCCTTGAAAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
Found at i:48489 original size:93 final size:93
Alignment explanation
Indices: 48383--48570 Score: 315
Period size: 93 Copynumber: 2.0 Consensus size: 93
48373 CGAAACAGAA
*
48383 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGGAAA-AAATTTTGTCTCCCTTGAGACAGTTTCC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTT-GAAACAAATTTTGTCTCCCTTGAGACAGTTTCA
48447 CTTGAAACAAATTTTGTCTCCCTTGAAAC
65 CTTGAAACAAATTTTGTCTCCCTTGAAAC
* * *
48476 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACGGTTTCAC
1 AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCAC
*
48541 TTGAAACAAATTTTGTCTCCCTTGAGAC
66 TTGAAACAAATTTTGTCTCCCTTGAAAC
48569 AA
1 AA
48571 TTTCACTTGA
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 4 0.04
93 85 0.96
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (93 bp):
AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCAC
TTGAAACAAATTTTGTCTCCCTTGAAAC
Found at i:48505 original size:36 final size:36
Alignment explanation
Indices: 48468--48623 Score: 195
Period size: 36 Copynumber: 4.2 Consensus size: 36
48458 TTTTGTCTCC
*
48468 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCC
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCA
* * *
48504 CTTGAAACATATTTTGTCTCTCTTGAGACGGTTTCA
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCA
*
48540 CTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCA
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCA
* * * **
48576 CTTGAAACAGAAGATTGTATCTCGCTTGAGATTGTTTCA
1 CTTGAAAC--AA-ATTTTGTCTCCCTTGAGACAGTTTCA
48615 CTTGAAACA
1 CTTGAAACA
48624 GAAGATTTTA
Statistics
Matches: 103, Mismatches: 14, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
36 72 0.70
37 1 0.01
38 2 0.02
39 28 0.27
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCA
Found at i:48615 original size:39 final size:39
Alignment explanation
Indices: 48478--48671 Score: 175
Period size: 39 Copynumber: 5.1 Consensus size: 39
48468 CTTGAAACAA
* * * *
48478 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC---AT
1 ATTTTATCTCGCTTGAGACAGTTTCACTTGAAACAGAAG
* * *
48514 ATTTTGTCTCTCTTGAGACGGTTTCACTTGAAAC--AA-
1 ATTTTATCTCGCTTGAGACAGTTTCACTTGAAACAGAAG
* * *
48550 ATTTTGTCTCCCTTGAGACAATTTCACTTGAAACAGAAG
1 ATTTTATCTCGCTTGAGACAGTTTCACTTGAAACAGAAG
* **
48589 ATTGTATCTCGCTTGAGATTGTTTCACTTGAAACAGAAG
1 ATTTTATCTCGCTTGAGACAGTTTCACTTGAAACAGAAG
* * * * * *
48628 ATTTTAGCTCGCTTGAGATAGTTTCGCTCGAAACACAAT
1 ATTTTATCTCGCTTGAGACAGTTTCACTTGAAACAGAAG
48667 ATTTT
1 ATTTT
48672 TAGAAACTAA
Statistics
Matches: 135, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
36 62 0.46
37 1 0.01
38 2 0.01
39 70 0.52
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (39 bp):
ATTTTATCTCGCTTGAGACAGTTTCACTTGAAACAGAAG
Found at i:48760 original size:43 final size:43
Alignment explanation
Indices: 48693--49033 Score: 348
Period size: 43 Copynumber: 7.6 Consensus size: 43
48683 CCTGATTTTC
* * *
48693 AGGGGTTTCTTGAAGAAAATCTTGAGAGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGAGACCATCGTGATATGT
*
48736 AGGGGTTTCTTGAGGACAAGCTTGA-AGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGA-GACCATCGTGATATGT
*
48779 AGGGGTTCCTTGATGACAAGCTTGA-AGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGA-GACCATCGTGATATGT
*
48822 AGGGG-TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGACAAGCTTGAGAGACCATCGTGATATGT
* *
48865 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGACAAGCTTGAGAGACCATCGTGATATGT
* * *
48908 AGGGGGGGTTCCTTGATGACAAACTTGATTACACACTTGAAGGACCATCGTAATATGT
1 A---GGGGTTTCTTGATGACAAGCTTG-------A---G-A-GACCATCGTGATATGT
*
48966 AGGGG-TTCTTCGATGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTCTT-GATGACAAGCTTGAGAGACCATCGTGATATGT
* * *
49009 AGGGGTTTCTTAATGAAAAACTTGA
1 AGGGGTTTCTTGATGACAAGCTTGA
49034 TGAACACTTA
Statistics
Matches: 255, Mismatches: 22, Indels: 42
0.80 0.07 0.13
Matches are distributed among these distances:
42 3 0.01
43 182 0.71
44 10 0.04
45 1 0.00
46 20 0.08
48 1 0.00
53 1 0.00
54 4 0.02
55 16 0.06
56 1 0.00
58 16 0.06
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (43 bp):
AGGGGTTTCTTGATGACAAGCTTGAGAGACCATCGTGATATGT
Found at i:49080 original size:97 final size:98
Alignment explanation
Indices: 48850--49081 Score: 308
Period size: 101 Copynumber: 2.3 Consensus size: 98
48840 AGCTTGAGAA
* **
48850 ACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGGG
1 ACCATCGTGATATGTAGGGG-TTCTTGATGACAAGCTTGAGAAACCATCGTGATATGTA--GGGG
* * *
48915 GTTCCTTGATGACAAACTTGATTACACACTTGAAGG
63 GTTCCTTAATGAAAAACTTGATGACACACTTGAAGG
*
48951 ACCATCGTAATATGTAGGGGTTCTTCGATGACAAGCTTGAGAAACCATCGTGATATGTA-GGGGT
1 ACCATCGTGATATGTAGGGGTTCTT-GATGACAAGCTTGAGAAACCATCGTGATATGTAGGGGGT
*
49015 TTCTTAATGAAAAACTTGATGA-ACACTT-AAGGG
65 TCCTTAATGAAAAACTTGATGACACACTTGAA-GG
*
49048 ACCATCGTGATATGTAGGGGTTCCTTGGTGACAA
1 ACCATCGTGATATGTAGGGGTT-CTTGATGACAA
49082 TTAAGAAACT
Statistics
Matches: 118, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
96 2 0.02
97 36 0.31
98 26 0.22
100 5 0.04
101 49 0.42
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (98 bp):
ACCATCGTGATATGTAGGGGTTCTTGATGACAAGCTTGAGAAACCATCGTGATATGTAGGGGGTT
CCTTAATGAAAAACTTGATGACACACTTGAAGG
Found at i:49200 original size:90 final size:91
Alignment explanation
Indices: 49083--49401 Score: 502
Period size: 90 Copynumber: 3.5 Consensus size: 91
49073 TGGTGACAAT
*
49083 TAAGAAACTGAGCCTTCGGGGGTTTCTTGA-TTTTTATGTCCTTCGGGCCATCCATAAGACCTTC
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
*
49147 AGTGCAGAATGTTTTCAAATGAGATC
66 AGTGCAGGATGTTTTCAAATGAGATC
* *
49173 TAAGAAACTAAGTCTTCGGGGGTTTCTTGATTTTTTAAGTCCTTCGGGCCATTCCATAAGACCTT
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTTAAGTCCTTCGGGCCA-TCCATAAGACCTT
* * *
49238 TAGTGCAGGATGTTTTTAAATGAAATC
65 CAGTGCAGGATGTTTTCAAATGAGATC
* * *
49265 TAAGAAACTCAGCCTTCGGGAGTTTCTTGA-TTTTTAAGTCCTTCGGGTCATCCATAAGACCTTC
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
49329 AGTGCAGGATGTTTTCAAATGAGATC
66 AGTGCAGGATGTTTTCAAATGAGATC
*
49355 TAAGAAATTGAGCCTTC--GGGTTTCTTGATTTTTTAAGTCCTTCGGGC
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTTAAGTCCTTCGGGC
49402 AGAATGTTTT
Statistics
Matches: 208, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
88 10 0.05
89 17 0.08
90 80 0.38
91 38 0.18
92 63 0.30
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (91 bp):
TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTTAAGTCCTTCGGGCCATCCATAAGACCTTC
AGTGCAGGATGTTTTCAAATGAGATC
Found at i:50943 original size:18 final size:18
Alignment explanation
Indices: 50904--50943 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
50894 TTTCCTCCTT
*
50904 TAAATTATTAATTTGAAG
1 TAAATTATTAATTTCAAG
50922 TAAATTAATTAATTTCAA-
1 TAAATT-ATTAATTTCAAG
50940 TAAA
1 TAAA
50944 AGGATCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (18 bp):
TAAATTATTAATTTCAAG
Found at i:51353 original size:14 final size:14
Alignment explanation
Indices: 51336--51366 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
51326 AAATAATGTC
*
51336 AAAAAAAATAAAAT
1 AAAAAAAAGAAAAT
51350 AAAAAAAAGAAAAT
1 AAAAAAAAGAAAAT
51364 AAA
1 AAA
51367 TTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (14 bp):
AAAAAAAAGAAAAT
Found at i:51364 original size:19 final size:18
Alignment explanation
Indices: 51336--51371 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
51326 AAATAATGTC
51336 AAAAAAAATAAAATAAAA
1 AAAAAAAATAAAATAAAA
*
51354 AAAAGAAAATAAATTAAA
1 AAAA-AAAATAAAATAAA
51372 TTAAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAAAAATAAAATAAAA
Found at i:52682 original size:20 final size:20
Alignment explanation
Indices: 52638--52689 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
52628 CAAACTGAAA
**
52638 AAATAAAAATAAAAAGGAAT
1 AAATAAAAATAAAAACAAAT
* *
52658 TAATAAAAATATAAACAAAT
1 AAATAAAAATAAAAACAAAT
*
52678 AAATAATAATAA
1 AAATAAAAATAA
52690 TAATAATAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (20 bp):
AAATAAAAATAAAAACAAAT
Found at i:52847 original size:110 final size:103
Alignment explanation
Indices: 52718--53091 Score: 350
Period size: 110 Copynumber: 3.5 Consensus size: 103
52708 AAAGAAATTT
*
52718 AAAACTATATATTGTATATAATTTTTTAAAAAGTTTTC-AAACTATATATTATAAACTTTTCAAA
1 AAAACTATATA-T-TATAT-ATTTTTCAAAAAGTTTTCAAAACTATATATTATAAA-TTTTCAAA
* *
52782 ACGTTTTAAAAAAATCATATATTATATACATTTTCAAAATGCTTTTTT
62 ATGTTTT--AAAAA-CATATATTATATA-ATTTTCAAAATG--TTTTA
* * * * *
52830 AAAACTATATATTATATAAATTTTT-AAAATGATTTCAAAACAATATATTATAAGTTTCCAAAAT
1 AAAACTATATATTATAT--ATTTTTCAAAAAGTTTTCAAAACTATATATTATAAATTTTCAAAAT
*
52894 GTTTTAAAAAC-TATA-TATGT--TTTT-AAAATGTTTTA
64 GTTTTAAAAACATATATTATATAATTTTCAAAATGTTTTA
* * *
52929 AAAACTATATATTATATA-TTTTCAAAATATTTTTAAAAACTATATATTATATAATTTTTAAAAT
1 AAAACTATATATTATATATTTTTCAAAA-AGTTTTCAAAACTATATATTATA-AA-TTTTCAAA-
*
52993 ATTTTTTAAAAACTATATATTATATATATAGTTTCAAAATGTTTTA
62 ATGTTTTAAAAAC-ATATATTATATA-AT--TTTCAAAATGTTTTA
* * *
53039 AAAACTATATATTATATATGTTTTCAAAATGCTTTCAAAAACTATACATTATA
1 AAAACTATATATTATATAT-TTTTCAAAAAGTTTTC-AAAACTATATATTATA
53092 TATATGTTAA
Statistics
Matches: 220, Mismatches: 23, Indels: 38
0.78 0.08 0.14
Matches are distributed among these distances:
96 4 0.02
97 5 0.02
98 18 0.08
99 22 0.10
100 6 0.03
101 18 0.08
102 4 0.02
103 4 0.02
104 4 0.02
105 4 0.02
106 4 0.02
107 2 0.01
108 5 0.02
109 3 0.01
110 56 0.25
111 26 0.12
112 35 0.16
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (103 bp):
AAAACTATATATTATATATTTTTCAAAAAGTTTTCAAAACTATATATTATAAATTTTCAAAATGT
TTTAAAAACATATATTATATAATTTTCAAAATGTTTTA
Found at i:52909 original size:63 final size:63
Alignment explanation
Indices: 52842--53049 Score: 204
Period size: 63 Copynumber: 3.1 Consensus size: 63
52832 AACTATATAT
*
52842 TATATAAATTTTTAAAATGATTTCAAAACAATATATTATA-AGTTTCCAAAATGTTTTAAAAAC
1 TATATAAATTTTTAAAATGATTTAAAAACAATATATTATATAGTTT-CAAAATGTTTTAAAAAC
** * * * *
52905 TATATATGTTTTTAAAATGTTTTAAAAACTATATATTATATATTTTCAAAATATTTTTAAAAAC
1 TATATAAATTTTTAAAATGATTTAAAAACAATATATTATATAGTTTCAAAAT-GTTTTAAAAAC
52969 TATATATTATATAATTTTTAAAAT-ATTTTTTAAAAACTATATATTATATATATAGTTTCAAAAT
1 ----TA-TATA-AATTTTTAAAATGA---TTTAAAAAC-A-ATA-TAT-TATATAGTTTCAAAAT
53033 GTTTTAAAAAC
53 GTTTTAAAAAC
53044 TATATA
1 TATATA
53050 TTATATATGT
Statistics
Matches: 117, Mismatches: 13, Indels: 23
0.76 0.08 0.15
Matches are distributed among these distances:
63 41 0.35
64 14 0.12
68 2 0.02
69 4 0.03
70 14 0.12
71 2 0.02
72 9 0.08
74 3 0.03
75 13 0.11
76 15 0.13
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (63 bp):
TATATAAATTTTTAAAATGATTTAAAAACAATATATTATATAGTTTCAAAATGTTTTAAAAAC
Found at i:52999 original size:37 final size:38
Alignment explanation
Indices: 52924--53135 Score: 197
Period size: 37 Copynumber: 5.7 Consensus size: 38
52914 TTTTAAAATG
*
52924 TTTTAAAAACTATATATTATAT-AT-TTTCAAAATA-T
1 TTTTAAAAACTATATATTATATAATATTTTAAAATATT
52959 TTTTAAAAACTATATATTATATAAT-TTTTAAAATATT
1 TTTTAAAAACTATATATTATATAATATTTTAAAATATT
* * *
52996 TTTTAAAAACTATATATTATATATATAGTTTCAAA-ATG
1 TTTTAAAAACTATATATTATATA-ATATTTTAAAATATT
* **
53034 TTTTAAAAACTATATATTATAT-ATGTTTTCAAAAT-GC
1 TTTTAAAAACTATATATTATATAATATTTT-AAAATATT
* * * * *
53071 TTTCAAAAACTATACATTATAT-ATATGTTAAAAAATC
1 TTTTAAAAACTATATATTATATAATATTTTAAAATATT
* ** *
53108 ATTTGCAAACTATATAATATATATATAT
1 TTTTAAAAACTATATATTATATA-ATAT
53136 ATATATATAT
Statistics
Matches: 147, Mismatches: 21, Indels: 14
0.81 0.12 0.08
Matches are distributed among these distances:
35 22 0.15
36 20 0.14
37 69 0.47
38 26 0.18
39 10 0.07
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (38 bp):
TTTTAAAAACTATATATTATATAATATTTTAAAATATT
Found at i:53093 original size:112 final size:111
Alignment explanation
Indices: 52905--53134 Score: 304
Period size: 112 Copynumber: 2.1 Consensus size: 111
52895 TTTTAAAAAC
* * *
52905 TATATAT-GTTTTTAAAATGTTTTAAAAACTATATATTATATATTTTCAAAATATTTTTAAAAAC
1 TATATATAGTTTTCAAAATGTTTTAAAAACTATATATTATATATTTTCAAAATACTTTCAAAAAC
* * * ** *
52969 TATATATTATATA-ATTTTTAAAATATTTTTTAAAAACTATATATTA
66 TATACATTATATATA-TGTTAAAAAATCATTTAAAAACTATATAATA
*
53015 TATATATAG-TTTCAAAATGTTTTAAAAACTATATATTATATATGTTTTCAAAATGCTTTCAAAA
1 TATATATAGTTTTCAAAATGTTTTAAAAACTATATATTATATA--TTTTCAAAATACTTTCAAAA
**
53079 ACTATACATTATATATATGTTAAAAAATCATTTGCAAACTATATAATA
64 ACTATACATTATATATATGTTAAAAAATCATTTAAAAACTATATAATA
53127 TATATATA
1 TATATATA
53135 TATATATATA
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
110 39 0.38
111 1 0.01
112 63 0.61
113 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (111 bp):
TATATATAGTTTTCAAAATGTTTTAAAAACTATATATTATATATTTTCAAAATACTTTCAAAAAC
TATACATTATATATATGTTAAAAAATCATTTAAAAACTATATAATA
Found at i:53123 original size:2 final size:2
Alignment explanation
Indices: 53118--53160 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
53108 ATTTGCAAAC
53118 TA TA TA -A 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
53159 TA
1 TA
53161 AATAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53908 original size:84 final size:84
Alignment explanation
Indices: 53704--54874 Score: 1610
Period size: 84 Copynumber: 13.9 Consensus size: 84
53694 TTCTTGACAT
* * * * * * *
53704 ATAACCCTTCTTGCCTTGAGCTATACTGTAAATTTGATTTGCCTCTGAGTTAAATGTAATCGAAC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * ** *
53769 TCAAAGTTC-TTTCATGACAG
64 TCGAAGGTCTTTTGTTGGCAG
* *
53789 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
53854 GAAGGTCTTTTGTTGACAG
66 GAAGGTCTTTTGTTGGCAG
* * * * * * *
53873 ATAACCCTT-TTCACCTTAAGCTATGTTACAAATGATGTGCATTTGAGCTGAGTGTAATTGAAAT
1 ATAACCCTTCTT-GCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACT
53937 CGAAGGTCTTTTGTTGGCAG
65 CGAAGGTCTTTTGTTGGCAG
* * * *
53957 ATAACCCTTCTTGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTAAGTGCAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
54022 GAAGGTATTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* *
54041 ATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
54106 GAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * * * *
54125 ATAACCCTTCTTGCCTTGAGCTATGCTACAAATAATGTGCCTTTGAGCTGAATATTATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
54190 GAAGGGCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* *
54209 ATAACCCTTCTTGCCTTGGGCTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * *
54274 GAAGATCTTTTATTGGTAG
66 GAAGGTCTTTTGTTGGCAG
* * * *
54293 ATAACCCTTCTTGCCTTGAGCTATTCTACAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTT
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
54358 GAAGGTCTTTTGTTGGAAG
66 GAAGGTCTTTTGTTGGCAG
* * *
54377 ATAGCCCTTCTTGCCTTGAGTTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * *
54442 TAAGGTCTTTTGGTGGTAG
66 GAAGGTCTTTTGTTGGCAG
* * * *
54461 ATATCCCTTCTTGCCTTGAGCTATGCTACAAATGACGTGCCTTTGAACTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
54526 GAAAGTCTTTTTTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * *
54545 ATAACCCTTCTTGCCTTGAGCTATACTGCAAATGATATGCCTTTGACCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* * *
54610 GAAGGACTTTTGATGGAAG
66 GAAGGTCTTTTGTTGGCAG
* ** *
54629 ATAGCCCTTCTTTTCTTGAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
54694 AAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* *
54713 ATAACCCTTCTTGCCTTGAGCTAT-ATGCAAATGATGTGCCTTTGGGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
54777 GAAGGTCTTTTGTTGGCAG
66 GAAGGTCTTTTGTTGGCAG
* * * * * *
54796 ATAATCATTCTTTCCTTGAGCTATACTGCAAATGATGTTCCTTTGAGCTGAGTATAATCGAACTC
1 ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
54861 GAAGGTCTTTTGTT
66 GAAGGTCTTTTGTT
54875 AAAAGTGCTT
Statistics
Matches: 960, Mismatches: 122, Indels: 9
0.88 0.11 0.01
Matches are distributed among these distances:
83 110 0.11
84 820 0.85
85 30 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (84 bp):
ATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTTGTTGGCAG
Found at i:58436 original size:15 final size:15
Alignment explanation
Indices: 58416--58475 Score: 75
Period size: 15 Copynumber: 3.8 Consensus size: 15
58406 TGAATGATGC
*
58416 AAATGATAAAAATAA
1 AAATGAAAAAAATAA
58431 AAATGAAAAAAATAA
1 AAATGAAAAAAATAA
*
58446 AAATGAAAGAAAACAAA
1 AAATGAAA-AAAA-TAA
58463 AAATGAAAGAAAA
1 AAATGAAA-AAAA
58476 AAGTTAGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
15 22 0.54
16 4 0.10
17 15 0.37
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.12
Consensus pattern (15 bp):
AAATGAAAAAAATAA
Found at i:58464 original size:17 final size:16
Alignment explanation
Indices: 58423--58477 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
58413 TGCAAATGAT
58423 AAAAATAAAAATGAAA-
1 AAAAA-AAAAATGAAAG
*
58439 AAAATAAAAATGAAAG
1 AAAAAAAAAATGAAAG
58455 AAAACAAAAAATGAAAG
1 AAAA-AAAAAATGAAAG
58472 AAAAAA
1 AAAAAA
58478 GTTAGTGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 10 0.29
16 10 0.29
17 15 0.43
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAAAAAATGAAAG
Found at i:61085 original size:20 final size:20
Alignment explanation
Indices: 61049--61086 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61039 ATCCTATTCC
**
61049 CTGGTAATCTTTTATTCTCA
1 CTGGTAATCTTACATTCTCA
61069 CTGGTAATCTTACATTCT
1 CTGGTAATCTTACATTCT
61087 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (20 bp):
CTGGTAATCTTACATTCTCA
Found at i:63648 original size:15 final size:15
Alignment explanation
Indices: 63628--63682 Score: 74
Period size: 15 Copynumber: 3.5 Consensus size: 15
63618 TGAATGATGC
*
63628 AAATGATAAAAATAA
1 AAATGAAAAAAATAA
63643 AAATGAAAAAAATAA
1 AAATGAAAAAAATAA
*
63658 AAATGAAAGAAAACAAA
1 AAATGAAA-AAAA-TAA
63675 AAATGAAA
1 AAATGAAA
63683 GGAAAAAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 22 0.61
16 4 0.11
17 10 0.28
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (15 bp):
AAATGAAAAAAATAA
Found at i:63676 original size:17 final size:16
Alignment explanation
Indices: 63635--63689 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
63625 TGCAAATGAT
63635 AAAAATAAAAATGAAA-
1 AAAAA-AAAAATGAAAG
*
63651 AAAATAAAAATGAAAG
1 AAAAAAAAAATGAAAG
63667 AAAACAAAAAATGAAAGG
1 AAAA-AAAAAATGAAA-G
63685 AAAAA
1 AAAAA
63690 GTTAGTGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 10 0.29
16 8 0.24
17 11 0.32
18 5 0.15
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (16 bp):
AAAAAAAAAATGAAAG
Found at i:67270 original size:30 final size:30
Alignment explanation
Indices: 67196--67284 Score: 133
Period size: 30 Copynumber: 3.0 Consensus size: 30
67186 GGCAGCAACA
* * *
67196 TTTTCTTCTTCCTCCTCATTTCTTCCTTCT
1 TTTTCTCCTTCCTCTTTATTTCTTCCTTCT
67226 TTTTCTCCTTCCTCTTTATTTCTTCCTTCT
1 TTTTCTCCTTCCTCTTTATTTCTTCCTTCT
* *
67256 TTTTCTCCTTCCTCTTTCTTCCTTCCTTC
1 TTTTCTCCTTCCTCTTTATTTCTTCCTTC
67285 ATTCCTTCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTTCTCCTTCCTCTTTATTTCTTCCTTCT
Found at i:73347 original size:3 final size:3
Alignment explanation
Indices: 73316--73375 Score: 57
Period size: 3 Copynumber: 18.3 Consensus size: 3
73306 CATATTTGTG
* *
73316 AGA AGA ATGA AGGA AGGA ACA AGGA AGA AGA AGA AGG AGA AGA AGGA
1 AGA AGA A-GA A-GA A-GA AGA A-GA AGA AGA AGA AGA AGA AGA A-GA
73363 AGA AGA AGA AGA A
1 AGA AGA AGA AGA A
73376 ATTGTTGCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
3 34 0.69
4 15 0.31
ACGTcount: A:0.60, C:0.02, G:0.37, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:73361 original size:22 final size:24
Alignment explanation
Indices: 73316--73373 Score: 84
Period size: 22 Copynumber: 2.5 Consensus size: 24
73306 CATATTTGTG
73316 AGAAGAATGAAGGAAGGAACAAGGA
1 AGAAGAA-GAAGGAAGGAACAAGGA
*
73341 AGAAGAAGAAGG-A-GAAGAAGGA
1 AGAAGAAGAAGGAAGGAACAAGGA
73363 AGAAGAAGAAG
1 AGAAGAAGAAG
73374 AAATTGTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 19 0.59
23 1 0.03
24 5 0.16
25 7 0.22
ACGTcount: A:0.59, C:0.02, G:0.38, T:0.02
Consensus pattern (24 bp):
AGAAGAAGAAGGAAGGAACAAGGA
Found at i:75115 original size:23 final size:23
Alignment explanation
Indices: 75072--75116 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
75062 TAATATTTTA
*
75072 TTTTAAATAATTTACTTTTATAT
1 TTTTAAATAATTTACTATTATAT
*
75095 TTTTAACTAATTTA-TAATTATA
1 TTTTAAATAATTTACT-ATTATA
75117 CGTTCAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAAATAATTTACTATTATAT
Done.