Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011080.1 Kokia drynarioides strain JFW-HI SEQ_126053, 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: 146168
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:59 original size:12 final size:12
Alignment explanation
Indices: 44--73 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34 TCATTATTAA
44 ATGTTATTATTG
1 ATGTTATTATTG
*
56 ATGTCATTATTG
1 ATGTTATTATTG
68 ATGTTA
1 ATGTTA
74 GCGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.53
Consensus pattern (12 bp):
ATGTTATTATTG
Found at i:830 original size:23 final size:23
Alignment explanation
Indices: 787--844 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
777 TTTGTAAGTA
*
787 AATTTAAATTAAAGATTAATTTC
1 AATTTAAATTAAAGATAAATTTC
*
810 AATTTAAATTTAA-ATCAAATTT-
1 AATTTAAATTAAAGAT-AAATTTC
**
832 AAAATAAATTAAA
1 AATTTAAATTAAA
845 AAGGGCCCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 12 0.41
23 17 0.59
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (23 bp):
AATTTAAATTAAAGATAAATTTC
Found at i:2984 original size:41 final size:41
Alignment explanation
Indices: 2912--3196 Score: 281
Period size: 41 Copynumber: 7.0 Consensus size: 41
2902 AATTAACGAT
* * *
2912 GCTTATGGGAAAGCGCCGCTAGTA-CTCTGACCTTTAGCGAC
1 GCTTATGGAAAAGCGCCGCTAATACCT-TGACCTTTAGCGGC
* * * *
2953 GGTGATGGAAAAGCGCCACTAATACCTTGACCTTTTGCGGC
1 GCTTATGGAAAAGCGCCGCTAATACCTTGACCTTTAGCGGC
* * * * **
2994 GCTTATGGGAAAGC-CCTACTAATACCCTGACCTTTTGCGAT
1 GCTTATGGAAAAGCGCC-GCTAATACCTTGACCTTTAGCGGC
*
3035 GCTTAT-GAGAAAGCGCCGCTAATACCCTGACCTTTAGCGGC
1 GCTTATGGA-AAAGCGCCGCTAATACCTTGACCTTTAGCGGC
* * * *
3076 GCTTATGAAAAAGCTCCGCGAATTCCTTGACCTTTAGCGGC
1 GCTTATGGAAAAGCGCCGCTAATACCTTGACCTTTAGCGGC
* * * *
3117 ACTTAT-GAGAAAGCGCCGCGAATGCCCTGACCTTTAGCGGC
1 GCTTATGGA-AAAGCGCCGCTAATACCTTGACCTTTAGCGGC
* * *
3158 GCTTATGGGAAAGCACCGCTAATGCCTTGACCTTTAGCG
1 GCTTATGGAAAAGCGCCGCTAATACCTTGACCTTTAGCG
3197 TTGCTAATGC
Statistics
Matches: 204, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.02
41 194 0.95
42 6 0.03
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.25
Consensus pattern (41 bp):
GCTTATGGAAAAGCGCCGCTAATACCTTGACCTTTAGCGGC
Found at i:3050 original size:82 final size:82
Alignment explanation
Indices: 2912--3196 Score: 331
Period size: 82 Copynumber: 3.5 Consensus size: 82
2902 AATTAACGAT
* * * * *
2912 GCTTATGGGAAAGCGCCGCTAGTACTCTGACCTTTAGCGACGGTGATG-GAAAAGCGCCACTAAT
1 GCTTATGGGAAAGCGCCGCTAATACCCTGACCTTTAGCGACGCTTATGAG-AAAGCGCCGCTAAT
* *
2976 ACCTTGACCTTTTGCGGC
65 ACCCTGACCTTTAGCGGC
* * *
2994 GCTTATGGGAAAGC-CCTACTAATACCCTGACCTTTTGCGATGCTTATGAGAAAGCGCCGCTAAT
1 GCTTATGGGAAAGCGCC-GCTAATACCCTGACCTTTAGCGACGCTTATGAGAAAGCGCCGCTAAT
3058 ACCCTGACCTTTAGCGGC
65 ACCCTGACCTTTAGCGGC
** * * * * * * * *
3076 GCTTATGAAAAAGCTCCGCGAATTCCTTGACCTTTAGCGGCACTTATGAGAAAGCGCCGCGAATG
1 GCTTATGGGAAAGCGCCGCTAATACCCTGACCTTTAGCGACGCTTATGAGAAAGCGCCGCTAATA
3141 CCCTGACCTTTAGCGGC
66 CCCTGACCTTTAGCGGC
* * *
3158 GCTTATGGGAAAGCACCGCTAATGCCTTGACCTTTAGCG
1 GCTTATGGGAAAGCGCCGCTAATACCCTGACCTTTAGCG
3197 TTGCTAATGC
Statistics
Matches: 173, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
81 2 0.01
82 168 0.97
83 3 0.02
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.25
Consensus pattern (82 bp):
GCTTATGGGAAAGCGCCGCTAATACCCTGACCTTTAGCGACGCTTATGAGAAAGCGCCGCTAATA
CCCTGACCTTTAGCGGC
Found at i:3129 original size:123 final size:123
Alignment explanation
Indices: 2908--3196 Score: 355
Period size: 123 Copynumber: 2.3 Consensus size: 123
2898 AATAAATTAA
* * * * *
2908 CGATGCTTATGGGAAAGCGCCGCTAGTACTCTGACCTTTAGCGACGGTGATGGAAAAGCGCCACT
1 CGATGCTTATGGGAAAGCGCCGCTAATACCCTGACCTTTAGCGACGCTGATGAAAAAGCGCCACG
* * * * *
2973 AATACCTTGACCTTTTGCGGCGCTTATGGGAAAGC-CCTACTAATACCCTGACCTTTTG
66 AATACCTTGACCTTTAGCGGCACTTATGAGAAAGCGCC-ACGAATACCCTGACCTTTAG
* * * * *
3031 CGATGCTTATGAGAAAGCGCCGCTAATACCCTGACCTTTAGCGGCGCTTATGAAAAAGCTCCGCG
1 CGATGCTTATGGGAAAGCGCCGCTAATACCCTGACCTTTAGCGACGCTGATGAAAAAGCGCCACG
* * *
3096 AATTCCTTGACCTTTAGCGGCACTTATGAGAAAGCGCCGCGAATGCCCTGACCTTTAG
66 AATACCTTGACCTTTAGCGGCACTTATGAGAAAGCGCCACGAATACCCTGACCTTTAG
** * * *
3154 CGGCGCTTATGGGAAAGCACCGCTAATGCCTTGACCTTTAGCG
1 CGATGCTTATGGGAAAGCGCCGCTAATACCCTGACCTTTAGCG
3197 TTGCTAATGC
Statistics
Matches: 141, Mismatches: 24, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
123 139 0.99
124 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.25
Consensus pattern (123 bp):
CGATGCTTATGGGAAAGCGCCGCTAATACCCTGACCTTTAGCGACGCTGATGAAAAAGCGCCACG
AATACCTTGACCTTTAGCGGCACTTATGAGAAAGCGCCACGAATACCCTGACCTTTAG
Found at i:3207 original size:24 final size:24
Alignment explanation
Indices: 3175--3220 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3165 GGAAAGCACC
*
3175 GCTAATGCCTTGACCTTTAGCGTT
1 GCTAATGCCCTGACCTTTAGCGTT
3199 GCTAATGCCCTGACCTTTAGCG
1 GCTAATGCCCTGACCTTTAGCG
3221 ACGCTTATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (24 bp):
GCTAATGCCCTGACCTTTAGCGTT
Found at i:3242 original size:65 final size:65
Alignment explanation
Indices: 3137--3261 Score: 180
Period size: 65 Copynumber: 1.9 Consensus size: 65
3127 AAGCGCCGCG
* * *
3137 AATGCCCTGACCTTTAGCGGCGCTTATGGGAAAGCACCGCTAATGCCT-TGACCTTTAGCGTTGC
1 AATGCCCTGACCTTTAGCGACGCTTATAGGAAAGCACCGCTAAT-ACTATGACCTTTAGCGTTGC
3201 T
65 T
* **
3202 AATGCCCTGACCTTTAGCGACGCTTATAGGATAGTGCCGCTAATACTATGACCTTTAGCG
1 AATGCCCTGACCTTTAGCGACGCTTATAGGAAAGCACCGCTAATACTATGACCTTTAGCG
3262 GCGCTTTGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 2 0.04
65 51 0.96
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.28
Consensus pattern (65 bp):
AATGCCCTGACCTTTAGCGACGCTTATAGGAAAGCACCGCTAATACTATGACCTTTAGCGTTGCT
Found at i:4538 original size:23 final size:21
Alignment explanation
Indices: 4485--4539 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
4475 GTGTCCATCT
4485 TATTTTTTTATAAAAATAATA
1 TATTTTTTTATAAAAATAATA
* *
4506 TACTTATTTATAGAAAATAGATA
1 TATTTTTTTATA-AAAATA-ATA
*
4529 TTTTTTTTTAT
1 TATTTTTTTAT
4540 CATAATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TATTTTTTTATAAAAATAATA
Found at i:5541 original size:28 final size:28
Alignment explanation
Indices: 5510--5599 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
5500 AAAATGAGAT
* *
5510 TTTTGGGTATCCGGGGGCAAAATGGTAA
1 TTTTGGGTATTCGGGGGAAAAATGGTAA
* *
5538 TTTTGGGGAAGTTCGGGGTTAAAAATGG-AA
1 TTTT-GGGTA-TTCGGGG-GAAAAATGGTAA
* * *
5568 TTTTAGGTATTCGAGGGTAAAATGGTAA
1 TTTTGGGTATTCGGGGGAAAAATGGTAA
5596 TTTT
1 TTTT
5600 TGGAAAATCG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
27 7 0.14
28 16 0.33
29 7 0.14
30 12 0.24
31 7 0.14
ACGTcount: A:0.28, C:0.06, G:0.32, T:0.34
Consensus pattern (28 bp):
TTTTGGGTATTCGGGGGAAAAATGGTAA
Found at i:5625 original size:36 final size:37
Alignment explanation
Indices: 5585--5657 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 37
5575 TATTCGAGGG
5585 TAAAATGGTAATTTTTGG-AAAATCGAGGTCAAAAAT
1 TAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAAT
* *
5621 TAAAATGGTAATTTTTGGAAAAATGGAGGTTAAAAAT
1 TAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAAT
5658 GGATTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 18 0.53
37 16 0.47
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (37 bp):
TAAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAAT
Found at i:5703 original size:30 final size:29
Alignment explanation
Indices: 5669--5783 Score: 115
Period size: 30 Copynumber: 3.9 Consensus size: 29
5659 GATTTTTTAG
* * *
5669 AAGTTTAGTGGTAAAAATGTAATTTTCAAA
1 AAGTTTAGAGGTCAAAATATAATTTT-AAA
*
5699 AAG-TTCGAGGTCCAAAATATAATTTTAAA
1 AAGTTTAGAGGT-CAAAATATAATTTTAAA
* *
5728 GAAGTTTAGGGGTCAAAATATAATTTTGGAA
1 -AAGTTTAGAGGTCAAAATATAATTTT-AAA
* *
5759 AAGTTTAAAGGTCAAAATATGATTT
1 AAGTTTAGAGGTCAAAATATAATTT
5784 CTAGACAGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
29 9 0.13
30 54 0.76
31 8 0.11
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (29 bp):
AAGTTTAGAGGTCAAAATATAATTTTAAA
Found at i:5794 original size:60 final size:58
Alignment explanation
Indices: 5663--5798 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 58
5653 AAAATGGATT
* * **
5663 TTTTAGAAGTTTAGTGGTAAAAATGTAATTTTCAAAAAGTTCGAGGTCCAAAATATAA
1 TTTTAGAAGTTTAGGGGTAAAAATATAATTTTCAAAAAGTTAAAGGTCCAAAATATAA
* ** *
5721 TTTTAAAGAAGTTTAGGGGTCAAAATATAATTTTGGAAAAGTTTAAAGGT-CAAAATATGA
1 TTTT--AGAAGTTTAGGGGTAAAAATATAATTTTCAAAAAG-TTAAAGGTCCAAAATATAA
5781 TTTCTAGACAGTTTAGGG
1 TTT-TAGA-AGTTTAGGG
5799 ACCTTCAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
58 4 0.06
59 3 0.05
60 51 0.78
61 7 0.11
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.35
Consensus pattern (58 bp):
TTTTAGAAGTTTAGGGGTAAAAATATAATTTTCAAAAAGTTAAAGGTCCAAAATATAA
Found at i:6862 original size:3 final size:3
Alignment explanation
Indices: 6849--6938 Score: 58
Period size: 3 Copynumber: 30.0 Consensus size: 3
6839 AAATTTCCTT
* * * * *
6849 TTA TT- TTA TTA TTA ATA TTA TTA ATG TCA -TA TTTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * *
6893 TTA TTA ATA TTA ATA CTA ATA TTA TTTA TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
6939 ATAAAGTTAT
Statistics
Matches: 65, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
2 3 0.05
3 57 0.88
4 5 0.08
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:6869 original size:9 final size:9
Alignment explanation
Indices: 6855--6935 Score: 71
Period size: 9 Copynumber: 8.9 Consensus size: 9
6845 CCTTTTATTT
6855 TATTATTAA
1 TATTATTAA
6864 TATTATTAA
1 TATTATTAA
*
6873 TGTCATATT--
1 TAT--TATTAA
*
6882 TATTATTAC
1 TATTATTAA
6891 TATTATTAA
1 TATTATTAA
6900 TATTAATACTAA
1 TATT-AT--TAA
6912 TATTATT--
1 TATTATTAA
6919 TATTATTAA
1 TATTATTAA
6928 TATTATTA
1 TATTATTA
6936 TTAATAAAGT
Statistics
Matches: 60, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
7 11 0.18
9 34 0.57
10 2 0.03
11 6 0.10
12 7 0.12
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.56
Consensus pattern (9 bp):
TATTATTAA
Found at i:6949 original size:15 final size:12
Alignment explanation
Indices: 6854--6941 Score: 72
Period size: 12 Copynumber: 7.0 Consensus size: 12
6844 TCCTTTTATT
6854 TTATTATTAATA
1 TTATTATTAATA
*
6866 TTATTAATGTCATA
1 TTATT-AT-TAATA
6880 TTTATTATTACTATTA
1 -TTATTATTA--A-TA
*
6896 TTAATATTAATA
1 TTATTATTAATA
* *
6908 CTAATATT-AT-
1 TTATTATTAATA
6918 TTATTATTAATA
1 TTATTATTAATA
6930 TTATTATTAATA
1 TTATTATTAATA
6942 AAGTTATTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
10 6 0.10
11 4 0.06
12 26 0.42
13 4 0.06
14 6 0.10
15 14 0.23
16 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:8705 original size:38 final size:37
Alignment explanation
Indices: 8663--8742 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 37
8653 CATAGAATTG
* *
8663 AGTTAAAAAATTTATATCCCTAGAGATTTGAATTTAA
1 AGTTAAAAAAATTATATCCCTAGAGATTTGAACTTAA
*
8700 TAGTTAAAAAAATTATATCCCTTGAGATTTGAACTTAA
1 -AGTTAAAAAAATTATATCCCTAGAGATTTGAACTTAA
8738 AGTTA
1 AGTTA
8743 TCAAAGGGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 5 0.13
38 34 0.87
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (37 bp):
AGTTAAAAAAATTATATCCCTAGAGATTTGAACTTAA
Found at i:9250 original size:27 final size:27
Alignment explanation
Indices: 9220--9275 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
9210 AAATCATTTA
*
9220 TTGATATCTTTAATCCAATAAACAGTG
1 TTGATATCTCTAATCCAATAAACAGTG
9247 TTGATATCTCTAATCCAATAAACAGTG
1 TTGATATCTCTAATCCAATAAACAGTG
9274 TT
1 TT
9276 ATAAACTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (27 bp):
TTGATATCTCTAATCCAATAAACAGTG
Found at i:27630 original size:14 final size:14
Alignment explanation
Indices: 27611--27639 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27601 AGCAGTTGGA
27611 AGCGGAAAAAATAC
1 AGCGGAAAAAATAC
27625 AGCGGAAAAAATAC
1 AGCGGAAAAAATAC
27639 A
1 A
27640 ACTTACTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.21, T:0.07
Consensus pattern (14 bp):
AGCGGAAAAAATAC
Found at i:31843 original size:14 final size:14
Alignment explanation
Indices: 31832--31862 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31822 TTGAAAATAG
*
31832 TTTTTGGAAAATGA
1 TTTTTAGAAAATGA
31846 TTTTTAGAAAATGA
1 TTTTTAGAAAATGA
31860 TTT
1 TTT
31863 ACTTTTCTGG
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:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (14 bp):
TTTTTAGAAAATGA
Found at i:35636 original size:20 final size:22
Alignment explanation
Indices: 35602--35652 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
35592 ATTATTTAAA
35602 AATATTTATATTAATTTGATTT
1 AATATTTATATTAATTTGATTT
*
35624 AATATTTA-A-TAATTTTATTT
1 AATATTTATATTAATTTGATTT
**
35644 TTTATTTAT
1 AATATTTAT
35653 TGAAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 16 0.64
21 1 0.04
22 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
AATATTTATATTAATTTGATTT
Found at i:36379 original size:30 final size:30
Alignment explanation
Indices: 36327--36388 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
36317 AAATAAAATT
** *
36327 ATAAAAATATGTATAATTTTTTTTTAAAAA
1 ATAAAAATATGTATAAAATTTTTTAAAAAA
36357 ATAAAAATATGT-TAGAAATTTTTTAAAAAA
1 ATAAAAATATGTATA-AAATTTTTTAAAAAA
36387 AT
1 AT
36389 GTAAAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (30 bp):
ATAAAAATATGTATAAAATTTTTTAAAAAA
Found at i:55020 original size:23 final size:23
Alignment explanation
Indices: 54994--55038 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
54984 TTATTTGTAA
*
54994 GAAAGACATAGTATCTAAATTTT
1 GAAAAACATAGTATCTAAATTTT
55017 GAAAAACATAGTATCTAAATTT
1 GAAAAACATAGTATCTAAATTT
55039 ATACTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (23 bp):
GAAAAACATAGTATCTAAATTTT
Found at i:66288 original size:2 final size:2
Alignment explanation
Indices: 66281--66306 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
66271 CTTGTTATAT
66281 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
66307 TTCTAATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:69376 original size:10 final size:9
Alignment explanation
Indices: 69363--69502 Score: 51
Period size: 10 Copynumber: 15.3 Consensus size: 9
69353 AAAAATCAAC
*
69363 AAAAGTTAT
1 AAAAATTAT
69372 AAAAATTATT
1 AAAAATTA-T
*
69382 AAATATTAAT
1 AAAAATT-AT
*
69392 AAAAATATTT
1 AAAAAT-TAT
**
69402 AAATTTTATT
1 AAAAATTA-T
69412 AAAAATTA-
1 AAAAATTAT
*
69420 AACAATTAT
1 AAAAATTAT
69429 -AAAA-TAT
1 AAAAATTAT
69436 ATAAAA--AT
1 A-AAAATTAT
*
69444 -AAATTTAT
1 AAAAATTAT
*
69452 AAAATTTTAT
1 AAAA-ATTAT
**
69462 AAAGTCTTA-
1 AAA-AATTAT
69471 AGAAAATTAT
1 A-AAAATTAT
*
69481 AAAAAATAT
1 AAAAATTAT
69490 AAAAATATAT
1 AAAAAT-TAT
69500 AAA
1 AAA
69503 TTTCGTAAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
6 3 0.03
7 3 0.03
8 14 0.14
9 31 0.32
10 45 0.46
11 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAAATTAT
Found at i:69393 original size:20 final size:21
Alignment explanation
Indices: 69370--69419 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
69360 AACAAAAGTT
69370 ATAAAAATTA-TTAAATATTA
1 ATAAAAATTATTTAAATATTA
*
69390 ATAAAAA-TATTTAAATTTTA
1 ATAAAAATTATTTAAATATTA
*
69410 TTAAAAATTA
1 ATAAAAATTA
69420 AACAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAAATTATTTAAATATTA
Found at i:69538 original size:22 final size:22
Alignment explanation
Indices: 69490--69531 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
69480 TAAAAAATAT
69490 AAAAA-TATATAAATTTCGTAA
1 AAAAATTATATAAATTTCGTAA
69511 AAAAATTATA-AAATTATCGTA
1 AAAAATTATATAAATT-TCGTA
69532 TCAAAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (22 bp):
AAAAATTATATAAATTTCGTAA
Found at i:69721 original size:9 final size:9
Alignment explanation
Indices: 69709--69797 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
69699 TTTTTATGTA
69709 TTTTATAATT
1 TTTTATAA-T
*
69719 TTTTATATT
1 TTTTATAAT
*
69728 TTTTACAAT
1 TTTTATAAT
69737 TTTTAT-AT
1 TTTTATAAT
*
69745 TTTTATTATAA
1 TTTTA-TA-AT
* *
69756 TTTAATAAA
1 TTTTATAAT
* *
69765 TTTAAGAAT
1 TTTTATAAT
* *
69774 TTTTTTATT
1 TTTTATAAT
*
69783 TTTTATATT
1 TTTTATAAT
69792 TTTTAT
1 TTTTAT
69798 CACGTGTCAT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
8 7 0.11
9 42 0.67
10 9 0.14
11 5 0.08
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:69722 original size:10 final size:10
Alignment explanation
Indices: 69709--69758 Score: 59
Period size: 9 Copynumber: 5.1 Consensus size: 10
69699 TTTTTATGTA
69709 TTTTATAATT
1 TTTTATAATT
69719 TTTTAT-ATT
1 TTTTATAATT
*
69728 TTTTACAA-T
1 TTTTATAATT
*
69737 TTTTATATTT
1 TTTTATAATT
69747 TTATTATAATT
1 TT-TTATAATT
69758 T
1 T
69759 AATAAATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 15 0.45
10 10 0.30
11 8 0.24
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTATAATT
Found at i:69722 original size:19 final size:18
Alignment explanation
Indices: 69698--69758 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
69688 TAAAGAGTCT
*
69698 TTTTTTATGTATTTTATAA
1 TTTTTTAT-TTTTTTATAA
*
69717 TTTTTTATATTTTTTACAA
1 TTTTTTAT-TTTTTTATAA
69736 TTTTTATATTTTTATTATAA
1 TTTTT-TATTTTT-TTATAA
69756 TTT
1 TTT
69759 AATAAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 25 0.69
20 11 0.31
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTTTATTTTTTTATAA
Found at i:69730 original size:18 final size:19
Alignment explanation
Indices: 69698--69750 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
69688 TAAAGAGTCT
*
69698 TTTTTTATGTATTTTATA-A
1 TTTTTTATAT-TTTTATACA
69717 TTTTTTATATTTTT-TACA
1 TTTTTTATATTTTTATACA
*
69735 ATTTTTATATTTTTAT
1 TTTTTTATATTTTTAT
69751 TATAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 18 0.60
19 10 0.33
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTTTATATTTTTATACA
Found at i:72960 original size:28 final size:28
Alignment explanation
Indices: 72939--73007 Score: 138
Period size: 28 Copynumber: 2.5 Consensus size: 28
72929 AAATCAATAA
72939 AAAAATATAAAAACTATTAAATTTTAAT
1 AAAAATATAAAAACTATTAAATTTTAAT
72967 AAAAATATAAAAACTATTAAATTTTAAT
1 AAAAATATAAAAACTATTAAATTTTAAT
72995 AAAAATATAAAAA
1 AAAAATATAAAAA
73008 ATTAAAAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAAATATAAAAACTATTAAATTTTAAT
Found at i:73016 original size:28 final size:26
Alignment explanation
Indices: 72935--73034 Score: 103
Period size: 28 Copynumber: 3.6 Consensus size: 26
72925 ATAAAAATCA
72935 ATAAAAAAATATAAAAACTATTAAATT
1 ATAAAAAAATATAAAAAC-ATTAAATT
*
72962 TTAATAAAAATATAAAAACTATTAAATT
1 ATAA-AAAAATATAAAAAC-ATTAAATT
*
72990 TTAATAAAAATATAAAAA-ATTAAAAATT
1 ATAA-AAAAATATAAAAACATT--AAATT
*
73018 AGAAAAAAATTATAAAA
1 ATAAAAAAA-TATAAAA
73035 TGCATAAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
26 3 0.05
27 8 0.12
28 55 0.83
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (26 bp):
ATAAAAAAATATAAAAACATTAAATT
Found at i:73316 original size:90 final size:91
Alignment explanation
Indices: 73155--73327 Score: 224
Period size: 90 Copynumber: 1.9 Consensus size: 91
73145 TGTAAATGGT
* * *
73155 TTAATTGCTTTTTTTGAAAAAATTTGGGGGCTTTTTTTTATGCATTTTGAAAGTTCAAATACCTA
1 TTAATTGCTTTTTTTGAAAAAATTTGAGGGCTTTTTATAATGCATTTTGAAAGTTCAAATACCTA
* *
73220 ATTGAGTGCAAAACAAAAGCAAGGTC
66 AGTGAGTACAAAACAAAAGCAAGGTC
* * * * *
73246 TTAATTGCTTTTTTTGATAGAGTTTGAGGG-TTTTTATAATGCATTTTGAAAGTTCAAGTA-TTC
1 TTAATTGCTTTTTTTGAAAAAATTTGAGGGCTTTTTATAATGCATTTTGAAAGTTCAAATACCT-
*
73309 AAGTGAGTACAAAATAAAA
65 AAGTGAGTACAAAACAAAA
73328 ATTAAAACTC
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
89 1 0.01
90 43 0.61
91 26 0.37
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (91 bp):
TTAATTGCTTTTTTTGAAAAAATTTGAGGGCTTTTTATAATGCATTTTGAAAGTTCAAATACCTA
AGTGAGTACAAAACAAAAGCAAGGTC
Found at i:80222 original size:23 final size:23
Alignment explanation
Indices: 80196--80252 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
80186 TTAAACTCAA
*
80196 AACTCAAATTACT-TATTCGAGTT
1 AACTCAAATTACTCGATTCGA-TT
* *
80219 AACTCAAGTAACTCGATTCGATT
1 AACTCAAATTACTCGATTCGATT
80242 AACTCGAAATT
1 AACTC-AAATT
80253 TAGATTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (23 bp):
AACTCAAATTACTCGATTCGATT
Found at i:87448 original size:26 final size:25
Alignment explanation
Indices: 87362--87448 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 25
87352 CTATTTTTTT
* *
87362 TATTTTAAAAATATAAAAGTTTAAAATTA
1 TATTTT-AAAATA-AAAA-TATAAAA-AA
87391 TATATTTAAAATAAAAATATAAAAAA
1 TAT-TTTAAAATAAAAATATAAAAAA
87417 CT-TTTTAAAATTCAAAAA-ATAAAAAA
1 -TATTTTAAAA-T-AAAAATATAAAAAA
87443 TATTTT
1 TATTTT
87449 TTACAAAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
25 8 0.16
26 15 0.29
27 12 0.24
28 4 0.08
29 9 0.18
30 3 0.06
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (25 bp):
TATTTTAAAATAAAAATATAAAAAA
Found at i:98632 original size:96 final size:96
Alignment explanation
Indices: 98456--98642 Score: 229
Period size: 96 Copynumber: 1.9 Consensus size: 96
98446 GGGAAAAAGA
** * ** *
98456 TATTCGATTATCTCAATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCAGAATT
1 TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACCAAATATTTCAGAATC
*
98521 GAAGATAAGGAAACATTGCCTCGATTAAGGG
66 GAAGATAAAGAAACATTGCCTCGATTAAGGG
* *
98552 TATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAAAT-TTTC-GAAA
1 TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGAC-CAAATATTTCAG-AA
98615 CTCGAA-ATAAA-AGAACATTGCCTCGATT
64 -TCGAAGATAAAGA-AACATTGCCTCGATT
98643 TTAAAGTTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
95 2 0.03
96 69 0.88
97 7 0.09
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (96 bp):
TATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACCAAATATTTCAGAATC
GAAGATAAAGAAACATTGCCTCGATTAAGGG
Found at i:99067 original size:30 final size:29
Alignment explanation
Indices: 99024--99139 Score: 139
Period size: 29 Copynumber: 3.9 Consensus size: 29
99014 ATCTGGGGGC
*
99024 AAAATGGTTATTTTTGAATGTTTCGA-GGTCA
1 AAAATGG-AATTTTTGAATGTTT-GAGGGT-A
99055 AAAATGGAATTTTTGGAA-GTTTGAGGGTA
1 AAAATGGAATTTTT-GAATGTTTGAGGGTA
* *
99084 AAAATGGAATTTTTAAAAGTTTGAGGGTA
1 AAAATGGAATTTTTGAATGTTTGAGGGTA
99113 AAAATGGAATTTTTGAATAGTTT-AGGG
1 AAAATGGAATTTTTGAAT-GTTTGAGGG
99140 ACCTCGAAGG
Statistics
Matches: 77, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
28 2 0.03
29 48 0.62
30 17 0.22
31 10 0.13
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGAATGTTTGAGGGTA
Found at i:99096 original size:59 final size:58
Alignment explanation
Indices: 98934--99127 Score: 193
Period size: 59 Copynumber: 3.3 Consensus size: 58
98924 GAAAACTTGG
* * * *
98934 GGTCAAAATTGGAATTTTTAGACA-TTAAGGGTAAAAGGGTAA-TTTTGAGAGTTTCGA
1 GGTCAAAAATGGAATTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGA-AGTTTCGA
* * * * * *
98991 GGTCGAAAATGGAGTTTTTGGACATCTGGGGGCAAAATGGTTATTTTTGAATGTTTCGA
1 GGTCAAAAATGGAATTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAA-GTTTCGA
*
99050 GGTCAAAAATGGAATTTTTGGA-AGTTTGAGGGTAAAAATGG-AATTTTTAAAAGTTT-GA
1 GGTCAAAAATGGAATTTTTGGACA-TTTGAGGGT-AAAATGGTAATTTTT-GAAGTTTCGA
99108 GGGT-AAAAATGGAATTTTTG
1 -GGTCAAAAATGGAATTTTTG
99128 AATAGTTTAG
Statistics
Matches: 113, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
57 20 0.18
58 32 0.28
59 52 0.46
60 9 0.08
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (58 bp):
GGTCAAAAATGGAATTTTTGGACATTTGAGGGTAAAATGGTAATTTTTGAAGTTTCGA
Found at i:100174 original size:3 final size:3
Alignment explanation
Indices: 100166--100200 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
100156 AATTTGTTAT
100166 TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA T
100201 ACTTACGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:100897 original size:19 final size:19
Alignment explanation
Indices: 100857--100900 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
100847 TGGACTTTGA
* *
100857 TTTAATTTTTATTTTGGCT
1 TTTAATTTTAATTTTAGCT
*
100876 TTTAATTTTAATATTTAGTT
1 TTTAATTTTAAT-TTTAGCT
100896 TTTAA
1 TTTAA
100901 ATCCATTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (19 bp):
TTTAATTTTAATTTTAGCT
Found at i:100928 original size:6 final size:6
Alignment explanation
Indices: 100917--100978 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
100907 TCAAATTTGA
**
100917 TTAAAT TTAAAT TTAAA- GCAAAT TTAAAT TTAAGA- -TAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT
* *
100962 TTAAAA ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAA
100979 CTAATTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
4 1 0.02
5 11 0.26
6 30 0.70
7 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:100941 original size:17 final size:18
Alignment explanation
Indices: 100919--100978 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 18
100909 AAATTTGATT
100919 AAATTTAAATTTAAAG-C
1 AAATTTAAATTTAAAGAC
*
100936 AAATTTAAATTT-AAGAT
1 AAATTTAAATTTAAAGAC
* *
100953 AAATTT-AATTTAAAAAT
1 AAATTTAAATTTAAAGAC
100970 AAATTTAAA
1 AAATTTAAA
100979 CTAATTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
16 8 0.21
17 28 0.74
18 2 0.05
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATTTAAATTTAAAGAC
Found at i:101529 original size:47 final size:48
Alignment explanation
Indices: 101430--101542 Score: 147
Period size: 47 Copynumber: 2.4 Consensus size: 48
101420 TTTTGGTTCA
* * * * * *
101430 CTTCTCCGTATTTCATCGGGAAGCTAACCGTTTTATTACTTTGACTTG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATCACTTCGACCTG
*
101478 CTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATCGCTTCGACCTG
1 CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATCACTTCGACCTG
*
101525 CTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCA
101543 AGAAACTAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
47 31 0.54
48 26 0.46
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.38
Consensus pattern (48 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTATCACTTCGACCTG
Found at i:101687 original size:118 final size:119
Alignment explanation
Indices: 101478--101737 Score: 450
Period size: 118 Copynumber: 2.2 Consensus size: 119
101468 CTTTGACTTG
101478 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
101543 AGAAACTAGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTTGACTTGGTCTT
66 AGAAACTAGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTTGACTTGGTCTT
* *
101597 CTTCTCAGTATCTCATCAGGAAGCTAACC-TTTATTGCTTCGACCTGTTTCTCAGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
* * * *
101661 GGAAGCTAGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTT
66 AGAAACTAGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTTGACTTGGTCTT
*
101715 CTTCTCAGTATCTCATTAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
101738 ATGACCGCGT
Statistics
Matches: 134, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
118 105 0.78
119 29 0.22
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (119 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATCGCTTCGACCTGCTTCTCAGTGTCTCATCA
AGAAACTAGGGTTCGAAGATTTGCTCACATCAAGCGTGGGTTTGACTTGGTCTT
Found at i:101970 original size:72 final size:72
Alignment explanation
Indices: 101848--102007 Score: 257
Period size: 72 Copynumber: 2.2 Consensus size: 72
101838 CTTCGACCTA
* * *
101848 CTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCAAATCGAGTGTAGGTTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCAAATCGAGCGTAGGTTTGATT
101913 TGGTCTT
66 TGGTCTT
* * *
101920 CTTCTTAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCATATCGAGCGTAGGTTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCAAATCGAGCGTAGGTTTGATT
101985 TGGTCTT
66 TGGTCTT
*
101992 TTTCTCAGTATCTCAT
1 CTTCTCAGTATCTCAT
102008 TAGAAAGATG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 80 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (72 bp):
CTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCAAATCGAGCGTAGGTTTGATT
TGGTCTT
Found at i:109428 original size:256 final size:256
Alignment explanation
Indices: 108973--109482 Score: 795
Period size: 256 Copynumber: 2.0 Consensus size: 256
108963 GATCGTATTA
* * * *
108973 CTTTAAGAAAGCTTGTGTCAAATCTTTCCATGAATAGATTTTTGATCGGCTCAATTGATTGTACC
1 CTTTAAGAAAGCTTGTGCCAAATCTTCCCATGAATAGATTTTTGATCGGCTCAATTGAATGCACC
* *
109038 ATCGGACTGCCGACCCGGCCACGCTGTCTTGAAAGCAATGAATTAACAATTAGTCATTATGCACG
66 ATCGAACTGCCGAACCGGCCACGCTGTCTTGAAAGCAATGAATTAACAATTAGTCATTATGCACG
* * *
109103 TGCCCCGCTATCTTCCTGTAGAACATGGTTAAGTGGGCTTCAGGGCAACTCGTCCCGCTATATTT
131 TGCCCCGCCATCTTCCTGCAGAACATGGTTAAGTGGGCTTCAAGGCAACTCGTCCCGCTATATTT
* * *
109168 TTCAAATTCTAGAACCTTGAATTTGGGAGGGTGAACCAGATCCGAAACTAGACTTAACTTG
196 TTCAAATTCTAGAACCTTGAATTTGGGAGAGAGAACCAGATCCGAAACCAGACTTAACTTG
*
109229 CTTTAAGAAAGCTTGTGCCAAATCTTCCCATGAATGGATTTTTGATCGGCTCAATTGAATGCACC
1 CTTTAAGAAAGCTTGTGCCAAATCTTCCCATGAATAGATTTTTGATCGGCTCAATTGAATGCACC
* * * * * *
109294 ATCTAACTGCTGAATCGGCCAGGCTTTCTTGAAAGCAATGAATTAATAATTAGTCATTATGCACG
66 ATCGAACTGCCGAACCGGCCACGCTGTCTTGAAAGCAATGAATTAACAATTAGTCATTATGCACG
* * *
109359 TGCCCCGCCATCTTCCTGCAGAACATGGTTAGGTGGGCTTCAAGGCAACTCGTGCCGTTATATTT
131 TGCCCCGCCATCTTCCTGCAGAACATGGTTAAGTGGGCTTCAAGGCAACTCGTCCCGCTATATTT
* * *
109424 TTCAAATTCTGGAACCTTGAATTTGGGAGAGAGAACCAGATTCGGAACCAGACTTAACT
196 TTCAAATTCTAGAACCTTGAATTTGGGAGAGAGAACCAGATCCGAAACCAGACTTAACT
109483 CTTTGGCATC
Statistics
Matches: 229, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
256 229 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (256 bp):
CTTTAAGAAAGCTTGTGCCAAATCTTCCCATGAATAGATTTTTGATCGGCTCAATTGAATGCACC
ATCGAACTGCCGAACCGGCCACGCTGTCTTGAAAGCAATGAATTAACAATTAGTCATTATGCACG
TGCCCCGCCATCTTCCTGCAGAACATGGTTAAGTGGGCTTCAAGGCAACTCGTCCCGCTATATTT
TTCAAATTCTAGAACCTTGAATTTGGGAGAGAGAACCAGATCCGAAACCAGACTTAACTTG
Found at i:111576 original size:29 final size:29
Alignment explanation
Indices: 111519--111691 Score: 188
Period size: 30 Copynumber: 5.9 Consensus size: 29
111509 AAATTTTTAG
111519 GGTTAAAAAT-AGAATTTTTGGAAGTTTCGA
1 GGTTAAAAATGA-AATTTTTGGAAG-TTCGA
*
111549 GGTTAAAAATGAAATTTTTGGAAGTTCGT
1 GGTTAAAAATGAAATTTTTGGAAGTTCGA
* *
111578 GG-TAAAAATGAAATTTTTCGAAGTTTGA
1 GGTTAAAAATGAAATTTTTGGAAGTTCGA
* * * **
111606 GGGTAAAAATGAATTTTTTGGAAATTTTA
1 GGTTAAAAATGAAATTTTTGGAAGTTCGA
* *
111635 GGGTCAAAAATGAAATTATTGGAAGTTCGA
1 -GGTTAAAAATGAAATTTTTGGAAGTTCGA
* *
111665 GGGTAAAAATGGAATTTTTGGATAGTT
1 GGTTAAAAATGAAATTTTTGGA-AGTT
111692 TAAGGACCTT
Statistics
Matches: 120, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
28 25 0.21
29 46 0.38
30 48 0.40
31 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
GGTTAAAAATGAAATTTTTGGAAGTTCGA
Found at i:111646 original size:30 final size:29
Alignment explanation
Indices: 111489--111686 Score: 170
Period size: 30 Copynumber: 6.8 Consensus size: 29
111479 ACAGGTTCGG
**
111489 GGGTAAAAATGAAA-TTTTAAAAATTTTTA
1 GGGTAAAAATGAAATTTTTGGAAA-TTTTA
* *
111518 GGGTTAAAAAT-AGAATTTTTGGAAGTTTCGA
1 GGG-TAAAAATGA-AATTTTTGGAAATTT-TA
* * *
111549 GGTTAAAAATGAAATTTTTGG-AA-GTTC
1 GGGTAAAAATGAAATTTTTGGAAATTTTA
* * *
111576 GTGGTAAAAATGAAATTTTTCGAAGTTTGA
1 G-GGTAAAAATGAAATTTTTGGAAATTTTA
*
111606 GGGTAAAAATGAATTTTTTGGAAATTTTA
1 GGGTAAAAATGAAATTTTTGGAAATTTTA
* * **
111635 GGGTCAAAAATGAAATTATTGGAAGTTCGA
1 GGGT-AAAAATGAAATTTTTGGAAATTTTA
*
111665 GGGTAAAAATGGAATTTTTGGA
1 GGGTAAAAATGAAATTTTTGGA
111687 TAGTTTAAGG
Statistics
Matches: 134, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.01
28 19 0.14
29 50 0.37
30 54 0.40
31 10 0.07
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGAAATTTTTGGAAATTTTA
Found at i:111684 original size:59 final size:57
Alignment explanation
Indices: 111483--111686 Score: 216
Period size: 59 Copynumber: 3.5 Consensus size: 57
111473 GTCGGGACAG
* * **
111483 GTTCGGGGGTAAAAATGAAATTTTAAAAATTTTTAGGGTTAAAAAT-AGAATTTTTGGAA
1 GTTCGAGGGTAAAAATGAATTTTTGGAAA-TTTTAGGG-TAAAAATGA-AATTTTTGGAA
* * * *
111542 GTTTCGAGGTTAAAAATGAAATTTTTGG-AA-GTTCGTGGTAAAAATGAAATTTTTCGAA
1 G-TTCGAGGGTAAAAATG-AATTTTTGGAAATTTTAG-GGTAAAAATGAAATTTTTGGAA
* *
111600 GTTTGAGGGTAAAAATGAATTTTTTGGAAATTTTAGGGTCAAAAATGAAATTATTGGAA
1 GTTCGAGGGTAAAAATGAA-TTTTTGGAAATTTTAGGGT-AAAAATGAAATTTTTGGAA
111659 GTTCGAGGGTAAAAATGGAATTTTTGGA
1 GTTCGAGGGTAAAAAT-GAATTTTTGGA
111687 TAGTTTAAGG
Statistics
Matches: 121, Mismatches: 15, Indels: 18
0.79 0.10 0.12
Matches are distributed among these distances:
56 2 0.02
57 21 0.17
58 26 0.21
59 47 0.39
60 19 0.16
61 6 0.05
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (57 bp):
GTTCGAGGGTAAAAATGAATTTTTGGAAATTTTAGGGTAAAAATGAAATTTTTGGAA
Found at i:116150 original size:21 final size:23
Alignment explanation
Indices: 116111--116152 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
116101 ATACTTCTTG
*
116111 TTATAAAAAAATATTATTATAGA
1 TTATAAAAAAATATAATTATAGA
116134 TTAT-AAAAAATA-AATTATA
1 TTATAAAAAAATATAATTATA
116153 ATTTTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TTATAAAAAAATATAATTATAGA
Found at i:118029 original size:25 final size:25
Alignment explanation
Indices: 118001--118053 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
117991 ATTATTTTGG
** *
118001 TTTGTTCATGACTTCGTGTTTTTAT
1 TTTGTTCACAACTTCGTGGTTTTAT
118026 TTTGTTCACAACTTCGTGGTTTTAT
1 TTTGTTCACAACTTCGTGGTTTTAT
118051 TTT
1 TTT
118054 ATCCATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.58
Consensus pattern (25 bp):
TTTGTTCACAACTTCGTGGTTTTAT
Found at i:118587 original size:9 final size:8
Alignment explanation
Indices: 118566--118607 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
118556 AATTAATTTT
118566 AAAAATAA
1 AAAAATAA
118574 AAAAATAA
1 AAAAATAA
*
118582 AGAAAATTA
1 A-AAAATAA
118591 AAAAA-AA
1 AAAAATAA
*
118598 AAAAACAA
1 AAAAATAA
118606 AA
1 AA
118608 CGGTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 6 0.20
8 17 0.57
9 7 0.23
ACGTcount: A:0.86, C:0.02, G:0.02, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:119467 original size:21 final size:21
Alignment explanation
Indices: 119430--119470 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
119420 TTCATTTAAA
119430 AAAAATAATTTAATTAACTTTG
1 AAAAATAA-TTAATTAACTTTG
119452 AAAAATAA-TAATTTAACTT
1 AAAAATAATTAA-TTAACTT
119471 GTAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 7 0.39
22 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATAATTAATTAACTTTG
Found at i:125247 original size:23 final size:23
Alignment explanation
Indices: 125206--125262 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
125196 ACTGGTTAAT
125206 AGTTTCAATTTACAATTCA-TATC
1 AGTTTCAA-TTACAATTCACTATC
* *
125229 AGTTTCAATTCCAATTTCACTTTC
1 AGTTTCAATTACAA-TTCACTATC
*
125253 ACTTTCAATT
1 AGTTTCAATT
125263 TTGATCACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.17
23 12 0.41
24 12 0.41
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.46
Consensus pattern (23 bp):
AGTTTCAATTACAATTCACTATC
Found at i:127952 original size:26 final size:26
Alignment explanation
Indices: 127923--127974 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
127913 CCAATACATG
127923 GGATCTTTAGGCTCAACAATTGGGTT
1 GGATCTTTAGGCTCAACAATTGGGTT
*
127949 GGATCTTTAGGCTCAACGATTGGGTT
1 GGATCTTTAGGCTCAACAATTGGGTT
127975 TTCTCCAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (26 bp):
GGATCTTTAGGCTCAACAATTGGGTT
Found at i:128687 original size:16 final size:16
Alignment explanation
Indices: 128664--128699 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
128654 AAGGAGGAAA
128664 AAGAAAAAGAAAAACAG
1 AAGAAAAAGAAAAA-AG
128681 AAGAAAAAGAAAAAAG
1 AAGAAAAAGAAAAAAG
128697 AAG
1 AAG
128700 TATAAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAAAAG
Found at i:131197 original size:3 final size:3
Alignment explanation
Indices: 131189--131225 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
131179 CCTTCATTCA
131189 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
131226 CCATGTCCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:140439 original size:17 final size:17
Alignment explanation
Indices: 140429--140489 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
140419 TTTAGATTTT
140429 AATTTATTTTAAGTTTA
1 AATTTATTTTAAGTTTA
* *
140446 AATTTATTGTAAATTTA
1 AATTTATTTTAAGTTTA
** * **
140463 AGCTTAGTTGGAGTTTA
1 AATTTATTTTAAGTTTA
140480 AATTTATTTT
1 AATTTATTTT
140490 GAAATAAAAA
Statistics
Matches: 31, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAGTTTA
Found at i:141162 original size:3 final size:3
Alignment explanation
Indices: 141154--141192 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
141144 AAACGATTAG
141154 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
141193 AGGGGAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:142502 original size:116 final size:116
Alignment explanation
Indices: 142312--142829 Score: 495
Period size: 116 Copynumber: 4.5 Consensus size: 116
142302 CACCCAAAAT
* * * * **
142312 TTTCGAAAATTACA-TTTTAACCCCTAAACTTT-CAAAAATTA-TATTTTGACCTTAAACTTTCC
1 TTTCGAAAATTCCATTTTTGA-CCCTAAACTTTCCAAAAATTACCATTTTAACCCCAAA-TTTCC
* *
142374 AAAAATTACATTTTTACCCTCAAAC-TTCCAAAAAATACCATTTTACCCTCAAA
64 AAAAATTTCATTTTTA-CCTCAAACTTTCCAAAAATTACCATTTTACCCTCAAA
* * * * * * *
142427 TTTCCAAAATTCCATTTTTAACCTTGAACTTTCCAAAAATTACTATTTTAACCTCAAATTTTCAA
1 TTTCGAAAATTCCATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTAACCCCAAATTTCCAA
* * *
142492 AGATTTCATTTTTAACC-CTAAACTTTTCAAAAATTACCATTTTACCCTTAAA
66 AAATTTCATTTTT-ACCTC-AAACTTTCCAAAAATTACCATTTTACCCTCAAA
* * ** *
142544 TTTCTTAAAATTCCATTTTTGACTCT-AACTTTCTTAAAATTACCATTTTACCCCCAAATTTCCA
1 TTTC-GAAAATTCCATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTAACCCCAAATTTCCA
* * *
142608 AAAATTTCATTTTTAACTCGGAACTTTCC-AAAATTACCATTTTACCCTTAAA
65 AAAATTTCATTTTTACCTC-AAACTTTCCAAAAATTACCATTTTACCCTCAAA
* * * *
142660 TTTTTGAAAATTTCATTTTTGACCCTAAACTTTCCAAAAATTACCA-TTTACCCCCAAATTT-AA
1 -TTTCGAAAATTCCATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTAACCCCAAATTTCCA
* * *
142723 AAAAATCCATTTTTTTACC-CAAAC-TTCTCGAAAATTACCATTTTACCCTCAAA
65 AAAATTTCA--TTTTTACCTCAAACTTTC-CAAAAATTACCATTTTACCCTCAAA
* * * * *
142776 TTTCTAAAAATTCCATTTTTGCCCCT-GAGTTTCCAAAAATTACCGTTTT-ACCCC
1 TTTC-GAAAATTCCATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTAACCCC
142830 TCGAGCATCC
Statistics
Matches: 340, Mismatches: 47, Indels: 32
0.81 0.11 0.08
Matches are distributed among these distances:
114 3 0.01
115 57 0.17
116 140 0.41
117 123 0.36
118 17 0.05
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.39
Consensus pattern (116 bp):
TTTCGAAAATTCCATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTAACCCCAAATTTCCAA
AAATTTCATTTTTACCTCAAACTTTCCAAAAATTACCATTTTACCCTCAAA
Found at i:142766 original size:29 final size:28
Alignment explanation
Indices: 142292--142795 Score: 211
Period size: 29 Copynumber: 17.3 Consensus size: 28
142282 CTATCCAAAA
* *
142292 ACCATATTTTCACCCAAAATTTTCGAAAATT
1 ACCAT-TTTT-ACCC-AAACTTTCAAAAATT
*
142323 A-CATTTTAACCCCTAAACTTTCAAAAATT
1 ACCATTTTTA-CCC-AAACTTTCAAAAATT
* * *
142352 A-TATTTTGACCTTAAACTTTCCAAAAATT
1 ACCATTTTTACC-CAAACTTT-CAAAAATT
* *
142381 A-CATTTTTACCCTCAAACTTCCAAAAAAT
1 ACCATTTTTA-CC-CAAACTTTCAAAAATT
*
142410 ACCA-TTTTACCCTCAAA-TTTCCAAAATT
1 ACCATTTTTA-CC-CAAACTTTCAAAAATT
**
142438 -CCATTTTTAACCTTGAACTTTCCAAAAATT
1 ACCATTTTT-ACC-CAAACTTT-CAAAAATT
* * * *
142468 ACTATTTTAACCTCAAATTTTCAAAGATT
1 ACCATTTTTACC-CAAACTTTCAAAAATT
*
142497 -TCATTTTTAACCCTAAACTTTTCAAAAATT
1 ACCATTTTT-ACCC-AAAC-TTTCAAAAATT
*
142527 ACCA-TTTTACCCTTAAA-TTTCTTAAAATT
1 ACCATTTTTACCC--AAACTTTC-AAAAATT
* * *
142556 -CCATTTTTGACTCTAACTTTCTTAAAATT
1 ACCATTTTT-ACCCAAACTTTC-AAAAATT
142585 ACCA-TTTTACCCCCAAA-TTTCCAAAAATT
1 ACCATTTTTA--CCCAAACTTT-CAAAAATT
* ** *
142614 -TCATTTTTAACTCGGAACTTTCCAAAATT
1 ACCATTTTT-AC-CCAAACTTTCAAAAATT
* **
142643 ACCA-TTTTACCCTTAAATTTTTGAAAATT
1 ACCATTTTTACCC--AAACTTTCAAAAATT
*
142672 -TCATTTTTGACCCTAAACTTTCCAAAAATT
1 ACCATTTTT-ACCC-AAACTTT-CAAAAATT
*** * *
142702 ACCATTTACCCCCAAA-TTTAAAAAAAT
1 ACCATTTTTACCCAAACTTTCAAAAATT
*
142729 -CCATTTTTTTACCCAAACTTCTCGAAAATT
1 ACCA--TTTTTACCCAAACTT-TCAAAAATT
142759 ACCA-TTTTACCCTCAAA-TTTCTAAAAATT
1 ACCATTTTTA-CC-CAAACTTTC-AAAAATT
142788 -CCATTTTT
1 ACCATTTTT
142796 GCCCCTGAGT
Statistics
Matches: 367, Mismatches: 63, Indels: 88
0.71 0.12 0.17
Matches are distributed among these distances:
26 3 0.01
27 10 0.03
28 72 0.20
29 177 0.48
30 88 0.24
31 17 0.05
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (28 bp):
ACCATTTTTACCCAAACTTTCAAAAATT
Found at i:142795 original size:58 final size:57
Alignment explanation
Indices: 142317--142828 Score: 435
Period size: 58 Copynumber: 8.8 Consensus size: 57
142307 AAAATTTTCG
* * * *
142317 AAAATTACA-TTTTAACCCCTAAACTTTCAAAAATTA-TATTTTGA-CCTTAAACTTTCCA
1 AAAATTCCATTTTTAA-CCC-AAACTTTCAAAAATTACCATTTT-ACCCTCAAA-TTTCTA
* * * * *
142375 AAAATTACATTTTTACCCTCAAACTTCCAAAAAATACCATTTTACCCTCAAATTTC-C
1 AAAATTCCATTTTTAACC-CAAACTTTCAAAAATTACCATTTTACCCTCAAATTTCTA
** * *
142432 AAAATTCCATTTTTAACCTTGAACTTTCCAAAAATTACTATTTTAACCTCAAATTT-TCA
1 AAAATTCCATTTTTAACC-CAAACTTT-CAAAAATTACCATTTTACCCTCAAATTTCT-A
* * * *
142491 AAGATTTCATTTTTAACCCTAAACTTTTCAAAAATTACCATTTTACCCTTAAATTTCTT
1 AAAATTCCATTTTTAACCC-AAAC-TTTCAAAAATTACCATTTTACCCTCAAATTTCTA
* * * * * *
142550 AAAATTCCATTTTTGACTCTAACTTTCTTAAAATTACCATTTTACCCCCAAATTTCCA
1 AAAATTCCATTTTTAACCCAAACTTTC-AAAAATTACCATTTTACCCTCAAATTTCTA
* ** * * * *
142608 AAAATTTCATTTTTAACTCGGAACTTTCCAAAATTACCATTTTACCCTTAAATTTTTG
1 AAAATTCCATTTTTAAC-CCAAACTTTCAAAAATTACCATTTTACCCTCAAATTTCTA
* * * *
142666 AAAATTTCATTTTTGACCCTAAACTTTCCAAAAATTACCA-TTTACCCCCAAATTT-AA
1 AAAATTCCATTTTTAACCC-AAACTTT-CAAAAATTACCATTTTACCCTCAAATTTCTA
* * *
142723 AAAAATCCATTTTTTTACCCAAACTTCTCGAAAATTACCATTTTACCCTCAAATTTCTA
1 AAAATTCCA-TTTTTAACCCAAACTT-TCAAAAATTACCATTTTACCCTCAAATTTCTA
** ** * *
142782 AAAATTCCATTTTTGCCCCTGAGTTTCCAAAAATTACCGTTTTACCC
1 AAAATTCCATTTTTAACCCAAACTTT-CAAAAATTACCATTTTACCC
142829 CTCGAGCATC
Statistics
Matches: 369, Mismatches: 66, Indels: 38
0.78 0.14 0.08
Matches are distributed among these distances:
57 52 0.14
58 210 0.57
59 103 0.28
60 4 0.01
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (57 bp):
AAAATTCCATTTTTAACCCAAACTTTCAAAAATTACCATTTTACCCTCAAATTTCTA
Found at i:142854 original size:116 final size:115
Alignment explanation
Indices: 142369--142829 Score: 500
Period size: 116 Copynumber: 4.0 Consensus size: 115
142359 GACCTTAAAC
* *
142369 TTTCCAAAAATTACA-TTTTTACCCTCAAACTTC-CAAAAAATACCATTTTACCCTCAAATTTC-
1 TTTCC-AAAATTTCATTTTTTA-CC-CAAACTTCTCAAAAATTACCATTTTACCCTCAAATTTCT
* * * * * *
142431 CAAAATTCCATTTTTAACCTTGAACTTTCCAAAAATTACTATTTTAACCTCAAA
63 AAAAATTCCATTTTTGACCCT-AACTTTCCAAAAATTACCATTTTACCCCCAAA
* * * * *
142485 TTTTCAAAGATTTCATTTTTAACCCTAAACTTTTCAAAAATTACCATTTTACCCTTAAATTTCTT
1 TTTCCAAA-ATTTCATTTTTTACCC-AAACTTCTCAAAAATTACCATTTTACCCTCAAATTTCTA
* **
142550 AAAATTCCATTTTTGACTCTAACTTTCTTAAAATTACCATTTTACCCCCAAA
64 AAAATTCCATTTTTGACCCTAACTTTCCAAAAATTACCATTTTACCCCCAAA
* ** * * * *
142602 TTTCCAAAAATTTCATTTTTAACTCGGAACTT-TCCAAAATTACCATTTTACCCTTAAATTTTTG
1 TTTCC-AAAATTTCATTTTTTAC-CCAAACTTCTCAAAAATTACCATTTTACCCTCAAATTTCTA
*
142666 AAAATTTCATTTTTGACCCTAAACTTTCCAAAAATTACCA-TTTACCCCCAAA
64 AAAATTCCATTTTTGACCCT-AACTTTCCAAAAATTACCATTTTACCCCCAAA
** * * *
142718 TTTAAAAAAATCCATTTTTTTACCCAAACTTCTCGAAAATTACCATTTTACCCTCAAATTTCTAA
1 TTTCCAAAATTTCA-TTTTTTACCCAAACTTCTCAAAAATTACCATTTTACCCTCAAATTTCTAA
* * * *
142783 AAATTCCATTTTTGCCCCTGAGTTTCCAAAAATTACCGTTTTACCCC
65 AAATTCCATTTTTGACCCTAACTTTCCAAAAATTACCATTTTACCCC
142830 TCGAGCATCC
Statistics
Matches: 293, Mismatches: 41, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
115 33 0.11
116 140 0.48
117 99 0.34
118 21 0.07
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (115 bp):
TTTCCAAAATTTCATTTTTTACCCAAACTTCTCAAAAATTACCATTTTACCCTCAAATTTCTAAA
AATTCCATTTTTGACCCTAACTTTCCAAAAATTACCATTTTACCCCCAAA
Found at i:144245 original size:2 final size:2
Alignment explanation
Indices: 144240--144265 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
144230 CATTATAAAT
144240 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
144266 AAGGATAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.