Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008912.1 Hibiscus syriacus cultivar Beakdansim tig00112215_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: 3753803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 18
Found at i:2619749 original size:24 final size:24
Alignment explanation
Indices: 2619721--2619777 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2619711 CCTTCAAGAT
*
2619721 ATTTCTACG-TGTCACTTCAGTGCA
1 ATTTCTACGCGGT-ACTTCAGTGCA
*
2619745 ATTTCTACGCGGTACTTCGGTGCA
1 ATTTCTACGCGGTACTTCAGTGCA
*
2619769 ATTTATACG
1 ATTTCTACG
2619778 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTTCTACGCGGTACTTCAGTGCA
Found at i:2622983 original size:20 final size:21
Alignment explanation
Indices: 2622960--2623040 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
2622950 TTGGTGCAGA
*
2622960 GGGAATCGATACCCCCTTGA-
1 GGGAACCGATACCCCCTTGAG
*
2622980 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTG-AG
* ***
2623003 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATACCCCCTTGAG
*
2623024 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
2623041 GAGATTCTGG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 14 0.28
21 19 0.38
22 1 0.02
23 16 0.32
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCCCTTGAG
Found at i:2623010 original size:23 final size:20
Alignment explanation
Indices: 2622958--2623018 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 20
2622948 TTTTGGTGCA
* *
2622958 GAGGGAATCGATACCCCCTT
1 GAGGGAACCGATTCCCCCTT
2622978 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
2622999 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
2623019 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 16 0.44
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:2628048 original size:21 final size:21
Alignment explanation
Indices: 2628024--2628078 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2628014 TTATGACCTA
*
2628024 TATGGTGAGATTTACAACCCG
1 TATGGTGAGAGTTACAACCCG
** *
2628045 TATGAAGAGAGTTACAACCTG
1 TATGGTGAGAGTTACAACCCG
*
2628066 TCTGGTGAGAGTT
1 TATGGTGAGAGTT
2628079 GCGACATGTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (21 bp):
TATGGTGAGAGTTACAACCCG
Found at i:2628772 original size:26 final size:25
Alignment explanation
Indices: 2628753--2628803 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2628743 AAAGTTGGTT
2628753 GATTGATTCAAAAATGAAAGGATTA
1 GATTGATTCAAAAATGAAAGGATTA
* * *
2628778 TATTGATTTAAAAATGAAAGGCTTA
1 GATTGATTCAAAAATGAAAGGATTA
2628803 G
1 G
2628804 CTATTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (25 bp):
GATTGATTCAAAAATGAAAGGATTA
Found at i:2629154 original size:46 final size:44
Alignment explanation
Indices: 2629054--2629167 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 44
2629044 TTGTCTCCCA
*
2629054 TGTGAACATGATGGTTCAACTATCTTCATAACTTGGCATCCATG
1 TGTGAACATGATGGTTCAACTACCTTCATAACTTGGCATCCATG
* * * *
2629098 T-AG-ACATGATGGTTCGACTACCTTCTTTGAACTTGG-ATTCCTTG
1 TGTGAACATGATGGTTCAACTACCTTC-AT-AACTTGGCA-TCCATG
*
2629142 TGTGAACATGATGTTTCAACTACCTT
1 TGTGAACATGATGGTTCAACTACCTT
2629168 GTATGAACAT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
42 20 0.35
43 3 0.05
44 14 0.25
45 1 0.02
46 19 0.33
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (44 bp):
TGTGAACATGATGGTTCAACTACCTTCATAACTTGGCATCCATG
Found at i:2629175 original size:46 final size:45
Alignment explanation
Indices: 2629054--2629175 Score: 126
Period size: 46 Copynumber: 2.7 Consensus size: 45
2629044 TTGTCTCCCA
* *
2629054 TGTGAACATGATGGTTCAACTATCTTCAT-AACTTGGCATCCATG
1 TGTGAACATGATGGTTCAACTACCTTTATGAACTTGGCATCCATG
* * * *
2629098 T-AG-ACATGATGGTTCGACTACCTTCTTTGAACTTGG-ATTCCTTG
1 TGTGAACATGATGGTTCAACTACCTT-TATGAACTTGGCA-TCCATG
*
2629142 TGTGAACATGATGTTTCAACTACCTTGTATGAAC
1 TGTGAACATGATGGTTCAACTACCTT-TATGAAC
2629176 ATTCATGAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
42 19 0.31
43 3 0.05
44 14 0.23
45 1 0.02
46 25 0.40
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (45 bp):
TGTGAACATGATGGTTCAACTACCTTTATGAACTTGGCATCCATG
Found at i:2644232 original size:2 final size:2
Alignment explanation
Indices: 2644225--2644250 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2644215 TTTGCGAGGC
2644225 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2644251 GGTTTGAGGA
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):
AT
Found at i:2647395 original size:20 final size:20
Alignment explanation
Indices: 2647370--2647407 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2647360 TATGTTTGAG
* *
2647370 TATCGATATTAGATGAACAA
1 TATCGATACTAAATGAACAA
2647390 TATCGATACTAAATGAAC
1 TATCGATACTAAATGAAC
2647408 TAGGATGAAA
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:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (20 bp):
TATCGATACTAAATGAACAA
Found at i:2651950 original size:14 final size:14
Alignment explanation
Indices: 2651931--2651986 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
2651921 CGTTCGTGAA
2651931 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
2651945 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
2651958 --TT-GTTTATGTT
1 CGTTCGATTATGTT
2651969 CGTTCGATTATGTT
1 CGTTCGATTATGTT
2651983 CGTT
1 CGTT
2651987 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:2651965 original size:24 final size:24
Alignment explanation
Indices: 2651938--2652007 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
2651928 GAACGTTCGA
*
2651938 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
2651962 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
2651986 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
2652008 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:2652745 original size:10 final size:10
Alignment explanation
Indices: 2652730--2652804 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
2652720 GGGTCTCCAA
2652730 CGTTTATGTT
1 CGTTTATGTT
2652740 CGTTTATGTT
1 CGTTTATGTT
2652750 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
2652761 ATGTTCGTGTT
1 -CGTTTATGTT
2652772 CGTTTATGTT
1 CGTTTATGTT
2652782 CG----TGTT
1 CGTTTATGTT
2652788 CGTTTATGTT
1 CGTTTATGTT
2652798 CGTTTAT
1 CGTTTAT
2652805 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:2652761 original size:16 final size:16
Alignment explanation
Indices: 2652736--2652800 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
2652726 CCAACGTTTA
2652736 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
2652752 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
2652768 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2652784 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2652800 T
1 T
2652801 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2652891 original size:16 final size:16
Alignment explanation
Indices: 2652870--2652902 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2652860 AAAAAAAATT
2652870 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2652886 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2652902 T
1 T
2652903 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2655200 original size:15 final size:17
Alignment explanation
Indices: 2655182--2655215 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2655172 GTTACATAAG
2655182 AAAAT-TATAAAATATA
1 AAAATCTATAAAATATA
*
2655198 AAAATCTATAATATATA
1 AAAATCTATAAAATATA
2655215 A
1 A
2655216 TCCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATCTATAAAATATA
Found at i:2655416 original size:38 final size:39
Alignment explanation
Indices: 2655323--2655430 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 39
2655313 TGTCAAAAGA
* * ** * * *
2655323 AATAATTTAGATTGTTAGGGCAAAATAATTTAATATATT
1 AATAATTTAGAATGTTACGATAAAATAATTTAAAAAACT
*
2655362 AATAATTTAGAATGTTATGATAAAATAATTTAAAAAACT
1 AATAATTTAGAATGTTACGATAAAATAATTTAAAAAACT
*
2655401 AA-AATTTAGAATGTTACGATGAAATAATTT
1 AATAATTTAGAATGTTACGATAAAATAATTT
2655431 GGGAATTAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 26 0.43
39 34 0.57
ACGTcount: A:0.48, C:0.03, G:0.11, T:0.38
Consensus pattern (39 bp):
AATAATTTAGAATGTTACGATAAAATAATTTAAAAAACT
Found at i:2656932 original size:24 final size:24
Alignment explanation
Indices: 2656905--2656980 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
2656895 TATATCAAAA
*
2656905 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
2656929 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
2656953 AACAGATCAG-AATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
2656977 ATCA
1 ATCA
2656981 GATCAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:2656982 original size:24 final size:24
Alignment explanation
Indices: 2656922--2657037 Score: 164
Period size: 24 Copynumber: 4.8 Consensus size: 24
2656912 CATAAATCAG
* *
2656922 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* *
2656946 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
2656970 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
2656994 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
2657018 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
2657038 TCGAATCGAA
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 5 0.06
24 77 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:2659620 original size:21 final size:20
Alignment explanation
Indices: 2659584--2659632 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2659574 TCGGTCAATA
*
2659584 GTCAACGGTCAACGGGTTGG
1 GTCAACGGTCAACGGGTCGG
*
2659604 GTCAACAGGTCATCGGGTCGG
1 GTCAAC-GGTCAACGGGTCGG
*
2659625 GTAAACGG
1 GTCAACGG
2659633 GTCGGTCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.22, C:0.20, G:0.39, T:0.18
Consensus pattern (20 bp):
GTCAACGGTCAACGGGTCGG
Found at i:2659635 original size:21 final size:21
Alignment explanation
Indices: 2659590--2659648 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
2659580 AATAGTCAAC
* * *
2659590 GGTCAACGGGTTGGGTCAACA
1 GGTCATCGGGTCGGGTAAACA
*
2659611 GGTCATCGGGTCGGGTAAACG
1 GGTCATCGGGTCGGGTAAACA
*
2659632 GGTCGGTCGGGTCGGGT
1 GGTC-ATCGGGTCGGGT
2659649 TATGACCGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.15, C:0.19, G:0.46, T:0.20
Consensus pattern (21 bp):
GGTCATCGGGTCGGGTAAACA
Found at i:2663478 original size:85 final size:85
Alignment explanation
Indices: 2663306--2663496 Score: 217
Period size: 85 Copynumber: 2.2 Consensus size: 85
2663296 ATGAACTTTT
* * * * *
2663306 GATGACACGCAATTGTGTGTCATAAATCTATGACGCGAATTTATGACGCTCATTGCGCGTCATTG
1 GATGACACACATTTGTGTGTCATAAATCTATGACGAGAATGTATGACACTCATTGCGCGTCATTG
* * * *
2663371 AAGCCCCCGTCATAAATGAA
66 AAGCACACGACATAAATAAA
* * *
2663391 GATGACACACATTTGTGTGTCATAAATTTATGAC-ATACATGTATGACACTCATTGCGTGTCATT
1 GATGACACACATTTGTGTGTCATAAATCTATGACGAGA-ATGTATGACACTCATTGCGCGTCATT
2663455 GAAGCACACGACATTAAA-AAA
65 GAAGCACACGACA-TAAATAAA
*
2663476 GATGAGACACATTCT-TGTGTC
1 GATGACACACATT-TGTGTGTC
2663497 GTGATTGTAT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
84 1 0.01
85 84 0.93
86 5 0.06
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (85 bp):
GATGACACACATTTGTGTGTCATAAATCTATGACGAGAATGTATGACACTCATTGCGCGTCATTG
AAGCACACGACATAAATAAA
Found at i:2665006 original size:2 final size:2
Alignment explanation
Indices: 2664994--2665066 Score: 137
Period size: 2 Copynumber: 36.0 Consensus size: 2
2664984 TATTTGGTGC
2664994 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2665037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2665067 GTGTGTGTGT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 68 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2665071 original size:2 final size:2
Alignment explanation
Indices: 2665066--2665090 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2665056 TATATATATA
2665066 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2665091 TCGCCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2670057 original size:24 final size:25
Alignment explanation
Indices: 2670016--2670063 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2670006 AGACTTGTAT
* *
2670016 TTTTAGTATTTACTTATTTATTTTG
1 TTTTAGTAGTTACCTATTTATTTTG
2670041 TTTT-GTAGTTACCTATTTATTTT
1 TTTTAGTAGTTACCTATTTATTTT
2670064 TGTAGTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.67
Consensus pattern (25 bp):
TTTTAGTAGTTACCTATTTATTTTG
Found at i:2690929 original size:2 final size:2
Alignment explanation
Indices: 2690922--2690971 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2690912 GCACATAGTT
2690922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2690964 TA TA TA TA
1 TA TA TA TA
2690972 GAAATAATAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2691971 original size:38 final size:39
Alignment explanation
Indices: 2691929--2692017 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
2691919 TAAAAAATAG
*
2691929 TTTAGAATGTTAAGGTGAAAT-TTTTAAGAAATTAAG-AA
1 TTTAGAATGTTAAGGTGAAATAATTTAAGAAATT-AGTAA
* *
2691967 TTTAGAATTTTATGGTGAAATAATTTAAGAAATTAGTAA
1 TTTAGAATGTTAAGGTGAAATAATTTAAGAAATTAGTAA
*
2692006 TTTAAAATGTTA
1 TTTAGAATGTTA
2692018 GAGTGAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
38 21 0.48
39 23 0.52
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (39 bp):
TTTAGAATGTTAAGGTGAAATAATTTAAGAAATTAGTAA
Found at i:2692024 original size:39 final size:39
Alignment explanation
Indices: 2691929--2692029 Score: 111
Period size: 39 Copynumber: 2.6 Consensus size: 39
2691919 TAAAAAATAG
*
2691929 TTTAGAATGTTA-AGGTGAAAT-TTTTAAGAAATTAAGAA
1 TTTAGAATGTTAGA-GTGAAATAATTTAAGAAATTAAGAA
*
2691967 TTTAGAATTTTATG-GTGAAATAATTTAAGAAATT-AGTAA
1 TTTAGAATGTTA-GAGTGAAATAATTTAAGAAATTAAG-AA
*
2692006 TTTAAAATGTTAGAGTGAATATAA
1 TTTAGAATGTTAGAGTGAA-ATAA
2692030 AAACTTAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
38 21 0.40
39 28 0.53
40 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.39
Consensus pattern (39 bp):
TTTAGAATGTTAGAGTGAAATAATTTAAGAAATTAAGAA
Found at i:2696843 original size:21 final size:21
Alignment explanation
Indices: 2696818--2696861 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2696808 TAAAAAATTG
2696818 TGTTTT-AGAGTTTTAATTGAA
1 TGTTTTAAG-GTTTTAATTGAA
*
2696839 TGTTTTAAGGTTTTGATTGAA
1 TGTTTTAAGGTTTTAATTGAA
2696860 TG
1 TG
2696862 GTTAAATCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (21 bp):
TGTTTTAAGGTTTTAATTGAA
Found at i:2703961 original size:29 final size:29
Alignment explanation
Indices: 2703901--2703961 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
2703891 AAGAAATTAC
* **
2703901 TTCGTTCCAGTTTGGTGTCTAACGTTTAT
1 TTCGTTCCAGTTTGGTGCCTAAAATTTAT
* *
2703930 TTCGTTCTAGTTTGGTGCCTAAAATTTCT
1 TTCGTTCCAGTTTGGTGCCTAAAATTTAT
2703959 TTC
1 TTC
2703962 TCTATCTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.49
Consensus pattern (29 bp):
TTCGTTCCAGTTTGGTGCCTAAAATTTAT
Found at i:2706335 original size:18 final size:18
Alignment explanation
Indices: 2706293--2706335 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2706283 TACTGAAATA
* *
2706293 AATGAAAATTTTGAATTT
1 AATGAAAATATTGAATTG
* *
2706311 AACGAAAATATTGGATTG
1 AATGAAAATATTGAATTG
2706329 AATGAAA
1 AATGAAA
2706336 GGACTAAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (18 bp):
AATGAAAATATTGAATTG
Found at i:2706613 original size:26 final size:27
Alignment explanation
Indices: 2706559--2706628 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
2706549 TCGAATTGCG
* *
2706559 AAATAACTAAAATAACCTCCGATATTC
1 AAATAACTAAAATAACCTCCGAGACTC
* *
2706586 AAATAACTAAAAT-ACCTCTGAGCCTC
1 AAATAACTAAAATAACCTCCGAGACTC
* *
2706612 AAAAAGATTAAAATAAC
1 AAATA-ACTAAAATAAC
2706629 TTGACATTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 13 0.37
27 20 0.57
28 2 0.06
ACGTcount: A:0.51, C:0.20, G:0.06, T:0.23
Consensus pattern (27 bp):
AAATAACTAAAATAACCTCCGAGACTC
Found at i:2708817 original size:29 final size:29
Alignment explanation
Indices: 2708775--2708830 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2708765 GGGTGTTACA
*
2708775 GTTAGACACCAAACTGGAACAAAATAAAT
1 GTTAGACACCAAACTAGAACAAAATAAAT
2708804 GTTAGACACCAAACTAGAACAAAATAA
1 GTTAGACACCAAACTAGAACAAAATAA
2708831 TTTCTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.18, G:0.12, T:0.16
Consensus pattern (29 bp):
GTTAGACACCAAACTAGAACAAAATAAAT
Found at i:2715588 original size:2 final size:2
Alignment explanation
Indices: 2715583--2715612 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2715573 ACGCGCGCAC
2715583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2715613 GGGTTAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2716667 original size:15 final size:15
Alignment explanation
Indices: 2716647--2716697 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
2716637 TGCCCCGCAT
*
2716647 CCGCCCCGCATCCAC
1 CCGCCCCGCATCCGC
*
2716662 CCGCCCCGCATCTGC
1 CCGCCCCGCATCCGC
* *
2716677 CCACCCCACATCCGC
1 CCGCCCCGCATCCGC
2716692 CCGCCC
1 CCGCCC
2716698 AGTTAAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.12, C:0.67, G:0.14, T:0.08
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:2723519 original size:3 final size:3
Alignment explanation
Indices: 2723511--2723581 Score: 108
Period size: 3 Copynumber: 23.0 Consensus size: 3
2723501 TTTTTTCATC
2723511 TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA
2723558 TT- TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA
2723582 AATTAAATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.03
3 53 0.83
4 9 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2723536 original size:13 final size:12
Alignment explanation
Indices: 2723511--2723581 Score: 108
Period size: 13 Copynumber: 5.8 Consensus size: 12
2723501 TTTTTTCATC
2723511 TTATTATTATTA
1 TTATTATTATTA
2723523 TTATTATATATTA
1 TTATTAT-TATTA
2723536 TTATTATATATTA
1 TTATTAT-TATTA
2723549 TTATTATTATT-
1 TTATTATTATTA
2723560 TTATTATTATTA
1 TTATTATTATTA
2723572 TTTATTATTA
1 -TTATTATTA
2723582 AATTAAATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.20
12 11 0.20
13 34 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATTATTATTA
Found at i:2725075 original size:2 final size:2
Alignment explanation
Indices: 2725068--2725137 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
2725058 ATATCCTTCT
2725068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2725110 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
2725138 CTTCATTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2728096 original size:20 final size:19
Alignment explanation
Indices: 2728071--2728156 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 19
2728061 GAGTAACACC
*
2728071 TTTTCATATATGCATTTGCA
1 TTTTCATATTTGCATTT-CA
2728091 TTTTCAT-TTTGCA-TTCA
1 TTTTCATATTTGCATTTCA
*
2728108 TACTTTTATATTTGCATTTTCA
1 T--TTTCATATTTGCA-TTTCA
* *
2728130 TTTTTATATTTTCATTTACA
1 TTTTCATATTTGCATTT-CA
2728150 TTTTCAT
1 TTTTCAT
2728157 TTTATATTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
17 3 0.05
18 2 0.04
19 13 0.23
20 33 0.59
22 5 0.09
ACGTcount: A:0.22, C:0.14, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTCATATTTGCATTTCA
Found at i:2728146 original size:26 final size:25
Alignment explanation
Indices: 2728117--2728165 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
2728107 ATACTTTTAT
*
2728117 ATTTGCATTTTCATTTTTATATTTTC
1 ATTTACATTTTCA-TTTTATATTTTC
2728143 ATTTACATTTTCATTTTATATTT
1 ATTTACATTTTCATTTTATATTT
2728166 GCATCTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTACATTTTCATTTTATATTTTC
Found at i:2728147 original size:12 final size:13
Alignment explanation
Indices: 2728123--2728165 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
2728113 TTATATTTGC
2728123 ATTTTCATTTTTAT
1 ATTTTCA-TTTTAT
*
2728137 ATTTTCA-TTTAC
1 ATTTTCATTTTAT
2728149 ATTTTCATTTTAT
1 ATTTTCATTTTAT
2728162 ATTT
1 ATTT
2728166 GCATCTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 11 0.42
13 8 0.31
14 7 0.27
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTCATTTTAT
Found at i:2730422 original size:72 final size:73
Alignment explanation
Indices: 2730294--2730438 Score: 229
Period size: 72 Copynumber: 2.0 Consensus size: 73
2730284 ATACAATAAA
*
2730294 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAAGCCCCGGCTTTATGGAAAATATTCAGCTAG
1 GCTTGAGTTATCCCCCTAAAGCAATTGATTAATAAGCCCCGGCTTTATGGAAAATATTCAGCTAG
*
2730359 TCTATTAT
66 CCTATTAT
* * * *
2730367 GCTTGAGTTATCTCCCTAGAGCAATTGATTAAT-AGCCCTGGCTTTATGGATAATATTCAGCTAG
1 GCTTGAGTTATCCCCCTAAAGCAATTGATTAATAAGCCCCGGCTTTATGGAAAATATTCAGCTAG
2730431 CCTATTAT
66 CCTATTAT
2730439 ACTATTATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
72 36 0.55
73 30 0.45
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (73 bp):
GCTTGAGTTATCCCCCTAAAGCAATTGATTAATAAGCCCCGGCTTTATGGAAAATATTCAGCTAG
CCTATTAT
Found at i:2734009 original size:22 final size:22
Alignment explanation
Indices: 2733983--2734059 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
2733973 AGAATCATTC
*
2733983 TTCAAATATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2734005 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
2734027 TTAAAAGATTATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
2734049 TTCAAAGATGA
1 TTCAAAGATGA
2734060 AAACTTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:2734899 original size:45 final size:45
Alignment explanation
Indices: 2734830--2734933 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
2734820 GGGAGCTTTT
* * * **
2734830 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAAACCTACAATGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCCATAAAACCTACAATGCA
* *
2734875 TGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCCATAAAACCTACAATGCA
2734920 TGATGTTTTCAAAA
1 TGATGTTTTCAAAA
2734934 AGCCTTCGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCAGGTCATCCATAAAACCTACAATGCA
Found at i:2734946 original size:121 final size:121
Alignment explanation
Indices: 2734732--2735490 Score: 1218
Period size: 121 Copynumber: 6.3 Consensus size: 121
2734722 CTATTTCTAA
** *
2734732 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCATGTCATCCATAAGACCTACAATG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
2734797 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
* * *
2734853 CATCTGTAAAACCTACAATGCATGATGTTTTCAAAACCTTCAGGTCATCCATAAGACCTACAGTG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
* * *
2734918 CATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTTATATTTTCAAAGACTTCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
*
2734974 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTATAGTG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
*
2735039 CAGGATGTTTTCAAAAAGTCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
*
2735095 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATACGACCTACAGTG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
* * *
2735160 CAAGATGTTTTCAAAAATCCTTCGGGAGGTTTTTGATATTTTCAAAGCCTTCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
* * *
2735216 CATCTGTAAGACCTACAGTGCATGATATTTTCAAAACCTTCGGGCCATCCATAAGATCTACAGTG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
** * *
2735281 CAGGAAATTTTCAAAAAGCCTTCGGGAG-TGTTTTGATGTTTCCAAAGCCTTCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCT-TTTTGATATTTTCAAAGCCTTCGGGT
* * *
2735337 CATCTGTAAAACCTACAGTGCATGATGTTTTCAAAACCTTCGGTTTATCCATAAGACCTACAGTG
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
* * *
2735402 CAGGATGTTTTCAAAAAGCCTTCTGGAGCTTTTTGATA-TTT-AAAACCTCCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
* *
2735456 CATCTGTAAGACTTACAGTGCAGGATGTTTTCAAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAA
2735491 TGAGATTTTA
Statistics
Matches: 589, Mismatches: 47, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
119 43 0.07
120 3 0.01
121 542 0.92
122 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (121 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTG
CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
Found at i:2735020 original size:45 final size:44
Alignment explanation
Indices: 2734956--2735054 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 44
2734946 CTTTTTTATA
** *
2734956 TTTTCAAAGACTTCGGGTCATCTGTAAGACCTACAGTGCATGATG
1 TTTTCAAA-ACTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
*
2735001 TTTTCAAAACCTTCGGGTCATCCATAAGACCTATAGTGCAGGATG
1 TTTTCAAAA-CTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
2735046 TTTTCAAAA
1 TTTTCAAAA
2735055 AGTCTTCGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 1 0.02
45 48 0.98
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (44 bp):
TTTTCAAAACTTCGGGTCATCCATAAGACCTACAGTGCAGGATG
Found at i:2735141 original size:45 final size:45
Alignment explanation
Indices: 2735072--2735185 Score: 156
Period size: 45 Copynumber: 2.5 Consensus size: 45
2735062 GGGAGCTTTT
* * **
2735072 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
*
2735117 TGATGTTTTCAAAACCTTCGGGTCATCCATACGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
*
2735162 AGATGTTTTCAAAAATCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
2735186 AGGTTTTTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 49 0.80
46 4 0.07
47 8 0.13
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
Found at i:2735204 original size:76 final size:74
Alignment explanation
Indices: 2735117--2735259 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 74
2735107 CTACAGTGCA
* * *
2735117 TGATGTTTTCAAAACCTTCGGGTCATCCATACGACCTACAGTGCAAGATGTTTTCAAAAATCCTT
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATATTTTC-AAAA-CCTT
2735182 CGGGAGGTTTT
64 CGGGAGGTTTT
* ** *
2735193 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATATTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATATTTTCAAAACCTTCG
2735258 GG
66 GG
2735260 CCATCCATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 8 0.13
75 4 0.07
76 48 0.80
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (74 bp):
TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATATTTTCAAAACCTTCG
GGAGGTTTT
Found at i:2735257 original size:45 final size:45
Alignment explanation
Indices: 2735193--2735306 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
2735183 GGGAGGTTTT
* * **
2735193 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATATTTTCAAAACCTTCGGGCCATCCATAAGACCTACAGTGCA
*
2735238 TGATATTTTCAAAACCTTCGGGCCATCCATAAGATCTACAGTGCA
1 TGATATTTTCAAAACCTTCGGGCCATCCATAAGACCTACAGTGCA
* *
2735283 GGAAATTTTCAAAAAGCCTTCGGG
1 TGATATTTTC-AAAA-CCTTCGGG
2735307 AGTGTTTTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 48 0.80
46 4 0.07
47 8 0.13
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (45 bp):
TGATATTTTCAAAACCTTCGGGCCATCCATAAGACCTACAGTGCA
Found at i:2735378 original size:45 final size:45
Alignment explanation
Indices: 2735314--2735417 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
2735304 GGGAGTGTTT
* * **
2735314 TGATGTTTCCAAAGCCTTCGGGTCATCTGTAAAACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCA
* * *
2735359 TGATGTTTTCAAAACCTTCGGTTTATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCA
*
2735404 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
2735418 AGCCTTCTGG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCA
Found at i:2735719 original size:3 final size:3
Alignment explanation
Indices: 2735711--2735768 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
2735701 TTTTTTCATC
*
2735711 TTA TTA TTA TATA TTA TTA TTA TTTA TTA TTA TTA TTA ATA -TA TTA
1 TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
2735757 TTA TTA TTA TTA
1 TTA TTA TTA TTA
2735769 AATTAAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2735739 original size:20 final size:20
Alignment explanation
Indices: 2735712--2735769 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
2735702 TTTTTCATCT
*
2735712 TATTATTATATATTATTATTA
1 TATTATTAT-TATTATTAATA
2735733 T-TTATTATTATTATTAATA
1 TATTATTATTATTATTAATA
2735752 TATTATTATTATTATTAA
1 TATTATTATTATTATTAA
2735770 ATTAAATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 11 0.31
20 23 0.66
21 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATTATTATTATTAATA
Found at i:2736519 original size:15 final size:15
Alignment explanation
Indices: 2736499--2736534 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
2736489 GCCGAAGCAA
2736499 GGCGGCAGCACGGTG
1 GGCGGCAGCACGGTG
2736514 GGCGGCAGCACGGTG
1 GGCGGCAGCACGGTG
2736529 GGCGGC
1 GGCGGC
2736535 CGGTGATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.28, G:0.56, T:0.06
Consensus pattern (15 bp):
GGCGGCAGCACGGTG
Found at i:2737334 original size:2 final size:2
Alignment explanation
Indices: 2737322--2737360 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2737312 ATATCCTGCT
*
2737322 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2737361 TTACTTCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2739424 original size:13 final size:12
Alignment explanation
Indices: 2739406--2739449 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
2739396 TGTCAAGCAA
2739406 TTAAAAATATCTT
1 TTAAAAATAT-TT
*
2739419 TTAAAATTATTT
1 TTAAAAATATTT
2739431 TATAAAAATTATTT
1 T-TAAAAA-TATTT
2739445 TTAAA
1 TTAAA
2739450 GGATAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 18 0.67
14 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAAAAATATTT
Found at i:2739440 original size:14 final size:13
Alignment explanation
Indices: 2739406--2739449 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
2739396 TGTCAAGCAA
2739406 TTAAAAA-TATCTT
1 TTAAAAATTAT-TT
2739419 TT-AAAATTATTT
1 TTAAAAATTATTT
2739431 TATAAAAATTATTT
1 T-TAAAAATTATTT
2739445 TTAAA
1 TTAAA
2739450 GGATAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.25
13 10 0.36
14 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAAAAATTATTT
Found at i:2747736 original size:47 final size:48
Alignment explanation
Indices: 2747632--2747783 Score: 261
Period size: 48 Copynumber: 3.2 Consensus size: 48
2747622 TCGACATACT
* *
2747632 TTTTTGTATGATGGTTATTGATCGATTTTGTTTAATACATATGTTGCA
1 TTTTCGTATGATGGTTATTGATCGATTTTGTTTAATGCATATGTTGCA
*
2747680 TTTTTGTATGATGGTTATTGATCGATTTT-TTTAATGCATATGTTGCA
1 TTTTCGTATGATGGTTATTGATCGATTTTGTTTAATGCATATGTTGCA
*
2747727 TTTTCGTATGATGGTTATCGATCGATTTTGTTTAATGCATATGTTGCA
1 TTTTCGTATGATGGTTATTGATCGATTTTGTTTAATGCATATGTTGCA
2747775 TTTTCGTAT
1 TTTTCGTAT
2747784 CAGTACTATG
Statistics
Matches: 100, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
47 44 0.44
48 56 0.56
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.52
Consensus pattern (48 bp):
TTTTCGTATGATGGTTATTGATCGATTTTGTTTAATGCATATGTTGCA
Found at i:2750474 original size:2 final size:2
Alignment explanation
Indices: 2750467--2750517 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
2750457 TGATATTACC
* **
2750467 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA GG TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2750508 TA TA TA TA TA
1 TA TA TA TA TA
2750518 CTTTTATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2750474 original size:18 final size:18
Alignment explanation
Indices: 2750453--2750517 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
2750443 ATTATTTTCC
*
2750453 TATATGATAT-TACCTATA
1 TATAT-ATATATACATATA
2750471 TATATATATATACATATA
1 TATATATATATACATATA
2750489 TATATATATAGGTA-ATATA
1 TATATATATA--TACATATA
2750508 TATATATATA
1 TATATATATA
2750518 CTTTTATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
17 4 0.09
18 22 0.51
19 15 0.35
20 2 0.05
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATATATATACATATA
Found at i:2750794 original size:4 final size:4
Alignment explanation
Indices: 2750780--2750881 Score: 52
Period size: 4 Copynumber: 26.0 Consensus size: 4
2750770 ATTTTTTCCC
* * *
2750780 TTAT CTTAT TTAT TTAG TTAT CTAT TTAT TTA- TT-T TTCT TTA- TT-T
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * **
2750825 TTCT TTAT CT-T TGAT TTAT TTACT CATAT TTGT TTAT TTAT TTAT CCAT
1 TTAT TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT
2750874 TTAT TTAT
1 TTAT TTAT
2750882 GTATATTGTC
Statistics
Matches: 72, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
3 9 0.12
4 55 0.76
5 6 0.08
6 2 0.03
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:2750823 original size:10 final size:10
Alignment explanation
Indices: 2750808--2750832 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2750798 TATCTATTTA
2750808 TTTATTTTTC
1 TTTATTTTTC
2750818 TTTATTTTTC
1 TTTATTTTTC
2750828 TTTAT
1 TTTAT
2750833 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:2763297 original size:105 final size:105
Alignment explanation
Indices: 2763115--2763781 Score: 1190
Period size: 105 Copynumber: 6.3 Consensus size: 105
2763105 AGGTTTTACC
*
2763115 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
2763180 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
2763220 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2763285 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
2763325 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
2763390 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
2763430 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
2763495 AAGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
2763535 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
2763600 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
2763640 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
2763705 ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * *
2763746 CGGAGCCAATTTCAACTTCATAGCGAAAGATATTGG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
2763782 CCTCGAAACA
Statistics
Matches: 539, Mismatches: 22, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 497 0.92
106 42 0.08
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:2765527 original size:2 final size:2
Alignment explanation
Indices: 2765520--2765545 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2765510 TTATTTTCTA
2765520 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2765546 CGTATTTTAT
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):
AT
Found at i:2765656 original size:2 final size:2
Alignment explanation
Indices: 2765649--2765701 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
2765639 TGATATTACC
* **
2765649 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA GG TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2765690 TA TA TA TA TA TA
1 TA TA TA TA TA TA
2765702 CTTTTATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2765978 original size:4 final size:4
Alignment explanation
Indices: 2765964--2766065 Score: 52
Period size: 4 Copynumber: 26.0 Consensus size: 4
2765954 ATTTTTTCCC
* * *
2765964 TTAT CTTAT TTAT TTAG TTAT CTAT TTAT TTA- TT-T TTCT TTA- TT-T
1 TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * **
2766009 TTCT TTAT CT-T TGAT TTAT TTACT CATAT TTGT TTAT TTAT TTAT CCAT
1 TTAT TTAT TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT TTAT TTAT TTAT
2766058 TTAT TTAT
1 TTAT TTAT
2766066 GTATATTGTC
Statistics
Matches: 72, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
3 9 0.12
4 55 0.76
5 6 0.08
6 2 0.03
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:2766007 original size:10 final size:10
Alignment explanation
Indices: 2765992--2766016 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2765982 TATCTATTTA
2765992 TTTATTTTTC
1 TTTATTTTTC
2766002 TTTATTTTTC
1 TTTATTTTTC
2766012 TTTAT
1 TTTAT
2766017 CTTTGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:2768892 original size:18 final size:20
Alignment explanation
Indices: 2768855--2768896 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
2768845 ACTAGACTTC
2768855 ACTTT-AGATTTTATTATAT
1 ACTTTAAGATTTTATTATAT
2768874 ACTTTAAGA-TTTA-TATAT
1 ACTTTAAGATTTTATTATAT
2768892 A-TTTA
1 ACTTTA
2768897 TATGTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.18
18 6 0.27
19 9 0.41
20 3 0.14
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
ACTTTAAGATTTTATTATAT
Found at i:2770299 original size:30 final size:30
Alignment explanation
Indices: 2770265--2770324 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
2770255 AAAAAACTAG
*
2770265 TTTATCGCATTCCTTTCAAACTCAATTTGT
1 TTTATCACATTCCTTTCAAACTCAATTTGT
*
2770295 TTTATCACATTCCTTTCTAACTCAATTTGT
1 TTTATCACATTCCTTTCAAACTCAATTTGT
2770325 GGCTTTCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.48
Consensus pattern (30 bp):
TTTATCACATTCCTTTCAAACTCAATTTGT
Found at i:2773252 original size:44 final size:43
Alignment explanation
Indices: 2773171--2773253 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
2773161 ATATTAGTTA
* **
2773171 CATGTTCTAAAATCTTTTACTGCAATTGGTTAGATATTTACAT
1 CATGTTCTAAAATCTTTTACTACAATTCATTAGATATTTACAT
*
2773214 CATGTTCTAAATATCTTTTAGTACAATTCATT-GTATATTT
1 CATGTTCTAAA-ATCTTTTACTACAATTCATTAG-ATATTT
2773254 GATGTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 12 0.35
44 22 0.65
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (43 bp):
CATGTTCTAAAATCTTTTACTACAATTCATTAGATATTTACAT
Found at i:2779355 original size:6 final size:6
Alignment explanation
Indices: 2779350--2779420 Score: 124
Period size: 6 Copynumber: 11.8 Consensus size: 6
2779340 AGGAAAAGGA
* *
2779350 AGAGGA AGAGGA AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT
1 AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT AGAGGT
2779398 AGAGGT AGAGGT AGAGGT AGAGG
1 AGAGGT AGAGGT AGAGGT AGAGG
2779421 AATAAATCAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.13
Consensus pattern (6 bp):
AGAGGT
Found at i:2779361 original size:18 final size:18
Alignment explanation
Indices: 2779338--2779378 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2779328 GATATCTTAG
2779338 AGAGGAAAAGGAAGAGGA
1 AGAGGAAAAGGAAGAGGA
* * *
2779356 AGAGGAAGAGGTAGAGGT
1 AGAGGAAAAGGAAGAGGA
2779374 AGAGG
1 AGAGG
2779379 TAGAGGTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.49, T:0.05
Consensus pattern (18 bp):
AGAGGAAAAGGAAGAGGA
Found at i:2783703 original size:23 final size:23
Alignment explanation
Indices: 2783677--2783769 Score: 125
Period size: 23 Copynumber: 4.1 Consensus size: 23
2783667 GGTTCTACGC
*
2783677 GGTCCTTCGGGATAATTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
*
2783700 GGTCCTTCGGGACATTTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
* * *
2783723 GGTCATTCGAGACAATACTATGT
1 GGTCCTTCGGGACAATTCTATGT
*
2783746 GGTCCTTCCGGAC-ATTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
2783768 GG
1 GG
2783770 CACTTTGATG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
22 10 0.17
23 50 0.83
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.35
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTATGT
Found at i:2785081 original size:104 final size:103
Alignment explanation
Indices: 2784832--2785073 Score: 297
Period size: 104 Copynumber: 2.3 Consensus size: 103
2784822 CGTTTGCTGA
* * * *
2784832 AGATGACATTGTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAT
1 AGATGACATTGTTCCTTCTCATTGAGGAAGTC-AGTCAATCTGGAGATAATCTGGTATTGAAGAT
* *
2784897 GACACTGCTTATCCATGTTAAAGAGTTATGGTCGCTTTC
65 GACACTGCTCATCCATGTTAAAGAGTTATGCTCGCTTTC
* * * * *
2784936 AGAAGACATTGTTTCTTCTTATTGAGAAAGTCTAGTCAATCTGGAGATAATCTGTTATTGAAGAT
1 AGATGACATTGTTCCTTCTCATTGAGGAAGTC-AGTCAATCTGGAGATAATCTGGTATTGAAGAT
* **
2785001 GACACTGGTCATCCATGTTGGAGAGTTATGACT-GCTTTC
65 GACACTGCTCATCCATGTTAAAGAGTTATG-CTCGCTTTC
* * *
2785040 ATATGACATTATTCCTTCTCATTAAGGAAGTCAG
1 AGATGACATTGTTCCTTCTCATTGAGGAAGTCAG
2785074 ATTAATCTAG
Statistics
Matches: 115, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
103 2 0.02
104 112 0.97
105 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (103 bp):
AGATGACATTGTTCCTTCTCATTGAGGAAGTCAGTCAATCTGGAGATAATCTGGTATTGAAGATG
ACACTGCTCATCCATGTTAAAGAGTTATGCTCGCTTTC
Found at i:2785828 original size:36 final size:36
Alignment explanation
Indices: 2785788--2785856 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
2785778 GCATTTCAAG
2785788 GGAAAATC-ATCTCAAGCGAGAT-AATATTTGTTTTTA
1 GGAAAA-CAATCTCAAGCGAGATCAAT-TTTGTTTTTA
*
2785824 GGAAAACAATCTCAAGTGAGATCAATTTTGTTT
1 GGAAAACAATCTCAAGCGAGATCAATTTTGTTT
2785857 CAAGTGAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 1 0.03
36 26 0.87
37 3 0.10
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (36 bp):
GGAAAACAATCTCAAGCGAGATCAATTTTGTTTTTA
Found at i:2785868 original size:36 final size:36
Alignment explanation
Indices: 2785781--2785865 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 36
2785771 AAAATTTGCA
2785781 TTTCAAGGGAAAATC-ATCTCAAGCGAGATAATATTTG
1 TTTCAA-GGAAAA-CAATCTCAAGCGAGATAATATTTG
** *
2785818 TTTTTAGGAAAACAATCTCAAGTGAGATCAAT-TTTG
1 TTTCAAGGAAAACAATCTCAAGCGAGAT-AATATTTG
2785854 TTTCAAGTGAAA
1 TTTCAAG-GAAA
2785866 CAACTCTGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
35 1 0.03
36 28 0.70
37 11 0.28
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.33
Consensus pattern (36 bp):
TTTCAAGGAAAACAATCTCAAGCGAGATAATATTTG
Found at i:2785980 original size:67 final size:67
Alignment explanation
Indices: 2785884--2786331 Score: 506
Period size: 67 Copynumber: 6.9 Consensus size: 67
2785874 AAATTTGGGC
* * * * *
2785884 TTCAAGGGAAAGTGTCTAAAGCGAGACGAAACTTTGTTTCGAGGGAAAAAATCTCAAAGGTTTAT
1 TTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
*
2785949 AT
66 GT
* *
2785951 TTCAAGAGAAACTATCTCAAACGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
1 TTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
2786016 GT
66 GT
* ** * **
2786018 TTCAAGATAATTTGTCTCAAGTGAGGTGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
1 TTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
2786083 GT
66 GT
* * * * * *
2786085 TTCTAGAGAAACTTTCTCAAGTGAGAC-AAAATTTATTTCAAGAGAAACAATCTCAAAGGTTTAT
1 TTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
2786149 GT
66 GT
*
2786151 TTCAAGAGAAACTGTCTCAAGCGAGATGAAACTTTG-TTCTGAGAGAAACAATCTCAAAGGTTTA
1 TTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTC-GAGAGAAACAATCTCAAAGGTTTA
2786215 TGT
65 TGT
* * * * *
2786218 TTCAAGAAAAACTGTCTCAAGTGAGAC-AAAATTTGTTTC-A-AG--A-GA---CAAATGTTTAT
1 TTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
2786274 GT
66 GT
** * * * * *
2786276 TTCAAGAGAATTTTTCTCAAGCGAGA-GAAAATTTGTTTCAAGATAAACTATCTCAA
1 TTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAA
2786332 GGGAGACAAA
Statistics
Matches: 323, Mismatches: 46, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
58 45 0.14
59 1 0.00
60 1 0.00
61 1 0.00
62 2 0.01
63 1 0.00
64 2 0.01
65 1 0.00
66 72 0.22
67 197 0.61
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (67 bp):
TTCAAGAGAAACTGTCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
GT
Found at i:2786019 original size:30 final size:30
Alignment explanation
Indices: 2785985--2786162 Score: 92
Period size: 30 Copynumber: 5.5 Consensus size: 30
2785975 GACGAAACTT
*
2785985 TGTTTCGAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
* ****
2786015 TGTTTCAAGATAATTTGTCTCAAGTGAGGTGAAACTT-
1 TGTTTCAAGAGAAACAATCTCAA---AGGT-----TTA
*
2786052 TGTTTCGAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
* ** *
2786082 TGTTTCTAGAGAAACTTTCTCAAGTGAGACAAAATTTA
1 TGTTTCAAGAGAAACAATCTCAA---AG-----GTTTA
2786120 --TTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
2786148 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
2786163 TGTCTCAAGC
Statistics
Matches: 109, Mismatches: 20, Indels: 38
0.65 0.12 0.23
Matches are distributed among these distances:
28 4 0.04
29 2 0.02
30 50 0.46
33 8 0.07
34 4 0.04
36 18 0.17
37 17 0.16
38 6 0.06
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:2786186 original size:133 final size:133
Alignment explanation
Indices: 2785827--2786331 Score: 568
Period size: 133 Copynumber: 3.9 Consensus size: 133
2785817 GTTTTTAGGA
* * * * ** *
2785827 AAACAATCTCAAGTGAGATC-AATTTTGTTTCAAGTGAAACAACTCTGAAA--TTTGGGCTTCAA
1 AAACTATCTCAAGTGAGA-CAAAATTTGTTTCAAGAGAAACAA-TCTCAAAGGTTTATGTTTCAA
* * * * * * *
2785889 GGGAAAGTGTCTAAAGCGAGACGAAACTTTGTTTCGAGGGAAAAAATCTCAAAGGTTTATATTTC
64 GAGAAATTGTCTCAAGCGAGATGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTC
2785954 AAGAG
129 AAGAG
** * *
2785959 AAACTATCTCAAACGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAG
1 AAACTATCTCAAGTGAGAC-AAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAG
* * * * *
2786024 ATAATTTGTCTCAAGTGAGGTGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCT
65 AGAAATTGTCTCAAGCGAGATGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCA
2786089 AGAG
130 AGAG
* *
2786093 AAACTTTCTCAAGTGAGACAAAATTTATTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGA
1 AAACTATCTCAAGTGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGA
*
2786158 GAAACTGTCTCAAGCGAGATGAAACTTTG-TTCTGAGAGAAACAATCTCAAAGGTTTATGTTTCA
66 GAAATTGTCTCAAGCGAGATGAAACTTTGTTTC-GAGAGAAACAATCTCAAAGGTTTATGTTTCA
*
2786222 AGAA
130 AGAG
* *
2786226 AAACTGTCTCAAGTGAGACAAAATTTGTTTCAAGAG-----A---CAAATGTTTATGTTTCAAGA
1 AAACTATCTCAAGTGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGA
* * * * * *
2786283 GAATTTTTCTCAAGCGAGA-GAAAATTTGTTTCAAGATAAACTATCTCAA
66 GAAATTGTCTCAAGCGAGATGAAACTTTGTTTCGAGAGAAACAATCTCAA
2786332 GGGAGACAAA
Statistics
Matches: 322, Mismatches: 45, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
124 22 0.07
125 38 0.12
128 1 0.00
131 1 0.00
132 24 0.07
133 153 0.48
134 83 0.26
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (133 bp):
AAACTATCTCAAGTGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGA
GAAATTGTCTCAAGCGAGATGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAA
GAG
Found at i:2786307 original size:58 final size:58
Alignment explanation
Indices: 2786205--2786318 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 58
2786195 GAAACAATCT
*
2786205 CAAAGGTTTATGTTTCAAGAAAAACTGTCTCAAGTGAGACAAAATTTGTTTCAAGAGA
1 CAAAGGTTTATGTTTCAAGAAAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGA
* * ** * *
2786263 CAAATGTTTATGTTTCAAGAGAATTTTTCTCAAGCGAGAGAAAATTTGTTTCAAGA
1 CAAAGGTTTATGTTTCAAGAAAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGA
2786319 TAAACTATCT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (58 bp):
CAAAGGTTTATGTTTCAAGAAAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGA
Found at i:2788742 original size:9 final size:8
Alignment explanation
Indices: 2788730--2788771 Score: 57
Period size: 9 Copynumber: 4.9 Consensus size: 8
2788720 ACTTGATATG
2788730 TTTTCTTT
1 TTTTCTTT
2788738 ATTTTCCTTT
1 -TTTT-CTTT
2788748 TTTTCTTAT
1 TTTTCTT-T
2788757 TTTTCTTT
1 TTTTCTTT
2788765 TTTTCTT
1 TTTTCTT
2788772 CTTCTTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 11 0.35
9 16 0.52
10 4 0.13
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCTTT
Found at i:2788753 original size:18 final size:18
Alignment explanation
Indices: 2788730--2788771 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
2788720 ACTTGATATG
2788730 TTTTCTTTATTTTCCTTT
1 TTTTCTTTATTTTCCTTT
*
2788748 TTTTC-TTATTTTTCTTT
1 TTTTCTTTATTTTCCTTT
2788765 TTTTCTT
1 TTTTCTT
2788772 CTTCTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCTTTATTTTCCTTT
Found at i:2788773 original size:20 final size:20
Alignment explanation
Indices: 2788745--2788785 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2788735 TTTATTTTCC
2788745 TTTTTTTCTTATTTTT-CTT
1 TTTTTTTCTTATTTTTGCTT
*
2788764 TTTTTCTTCTTCTTTTTGCTT
1 TTTTT-TTCTTATTTTTGCTT
2788785 T
1 T
2788786 GTGTTCTCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTTTCTTATTTTTGCTT
Found at i:2796932 original size:17 final size:17
Alignment explanation
Indices: 2796910--2796943 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2796900 TTATCTTATC
2796910 TTTATTTTGAATTCAAA
1 TTTATTTTGAATTCAAA
2796927 TTTATTTTGAATTCAAA
1 TTTATTTTGAATTCAAA
2796944 ATTAAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTATTTTGAATTCAAA
Found at i:2796968 original size:14 final size:14
Alignment explanation
Indices: 2796946--2796976 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2796936 AATTCAAAAT
*
2796946 TAAAGATAATTAAA
1 TAAAAATAATTAAA
2796960 TAAAAATAATTAAA
1 TAAAAATAATTAAA
2796974 TAA
1 TAA
2796977 TAAAAGACTT
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:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
TAAAAATAATTAAA
Found at i:2797329 original size:31 final size:31
Alignment explanation
Indices: 2797294--2797366 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
2797284 CATGTTGAAA
*
2797294 TATCATGTCAGCATTTAGATATTTATAAATG
1 TATCATGTCAGCATTTAAATATTTATAAATG
*
2797325 TATCATGTCAACATTTAAATATTTATAAATG
1 TATCATGTCAGCATTTAAATATTTATAAATG
2797356 TATCATGTCAG
1 TATCATGTCAG
2797367 AAAATAACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (31 bp):
TATCATGTCAGCATTTAAATATTTATAAATG
Found at i:2802367 original size:53 final size:53
Alignment explanation
Indices: 2802292--2802450 Score: 282
Period size: 53 Copynumber: 3.0 Consensus size: 53
2802282 ATTTACATTT
* *
2802292 ATCTACAGGTAAATTTCACTTATAATATATGACCTTTAATATTTCATTTCCATA
1 ATCTACAGGT-AATTTCACTTATAGTCTATGACCTTTAATATTTCATTTCCATA
2802346 ATCTACAGGTAATTTCACTTATAGTCTATGACCTTTAATATTTCATTTCCATA
1 ATCTACAGGTAATTTCACTTATAGTCTATGACCTTTAATATTTCATTTCCATA
*
2802399 GTCTACAGGTAATTTCACTTATAGTCTATGACCTTTAATATTTCATTTCCAT
1 ATCTACAGGTAATTTCACTTATAGTCTATGACCTTTAATATTTCATTTCCAT
2802451 CAGTAGCTTT
Statistics
Matches: 102, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
53 92 0.90
54 10 0.10
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (53 bp):
ATCTACAGGTAATTTCACTTATAGTCTATGACCTTTAATATTTCATTTCCATA
Found at i:2802415 original size:25 final size:25
Alignment explanation
Indices: 2802332--2802415 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 25
2802322 GACCTTTAAT
*
2802332 ATTTCATTTCCATAATCTACAGGTA
1 ATTTCATTTCCATAGTCTACAGGTA
* ***
2802357 ATTTCACTT--ATAGTCTATGACCTTTAA
1 ATTTCATTTCCATAGTC--T-ACAGGT-A
2802384 TATTTCATTTCCATAGTCTACAGGTA
1 -ATTTCATTTCCATAGTCTACAGGTA
2802410 ATTTCA
1 ATTTCA
2802416 CTTATAGTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
23 5 0.12
25 15 0.35
26 4 0.09
27 4 0.09
28 9 0.21
30 6 0.14
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (25 bp):
ATTTCATTTCCATAGTCTACAGGTA
Found at i:2808339 original size:18 final size:18
Alignment explanation
Indices: 2808316--2808355 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2808306 TAAGCATGAA
*
2808316 AATGTAATTTATATTTAC
1 AATGTAATCTATATTTAC
*
2808334 AATGTAATCTGTATTTAC
1 AATGTAATCTATATTTAC
2808352 AATG
1 AATG
2808356 CATCAGATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (18 bp):
AATGTAATCTATATTTAC
Found at i:2809847 original size:14 final size:15
Alignment explanation
Indices: 2809830--2809866 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2809820 TTAATTTAAA
2809830 TAAAAATAATT-TAT
1 TAAAAATAATTATAT
2809844 TAAAAAT-ATTATAT
1 TAAAAATAATTATAT
*
2809858 TTAAAATAA
1 TAAAAATAA
2809867 AATAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAAATAATTATAT
Found at i:2812838 original size:15 final size:14
Alignment explanation
Indices: 2812784--2812840 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 14
2812774 TTCGGGTATT
*
2812784 CGGGTACCCGACATA
1 CGGGTACCCGA-AAA
2812799 CGGGTACCCGCAAAA
1 CGGGTACCCG-AAAA
*
2812814 TTCAGGTACCCGAAAA
1 --CGGGTACCCGAAAA
2812830 CCGGGTACCCG
1 -CGGGTACCCG
2812841 GATCATCCGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 21 0.60
16 5 0.14
17 9 0.26
ACGTcount: A:0.28, C:0.33, G:0.26, T:0.12
Consensus pattern (14 bp):
CGGGTACCCGAAAA
Found at i:2814543 original size:34 final size:34
Alignment explanation
Indices: 2814495--2814607 Score: 95
Period size: 34 Copynumber: 3.3 Consensus size: 34
2814485 AAAGCTTTAG
* * *
2814495 AAAAATTCAATGACCGTTACTATACTTTACCCTT
1 AAAAGTTCAGTGACCGTTACTATGCTTTACCCTT
** * *
2814529 AAAAGTTCAGTGACCG-TACTAATGC-AAATGCCTG
1 AAAAGTTCAGTGACCGTTACT-ATGCTTTA-CCCTT
* * **
2814563 AAAAGTTCAGTGATCATTACTATGCTTTATTCTT
1 AAAAGTTCAGTGACCGTTACTATGCTTTACCCTT
2814597 AAAAGTTCAGT
1 AAAAGTTCAGT
2814608 CAAGATATAT
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
33 5 0.08
34 51 0.84
35 5 0.08
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.34
Consensus pattern (34 bp):
AAAAGTTCAGTGACCGTTACTATGCTTTACCCTT
Found at i:2817973 original size:4 final size:4
Alignment explanation
Indices: 2817964--2817994 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2817954 TCTATATTAC
2817964 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2817995 GAGAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2819891 original size:20 final size:20
Alignment explanation
Indices: 2819862--2819911 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2819852 GGCAATTAAT
*
2819862 CGGCTGAAAACCGGTAGAAC
1 CGGCTAAAAACCGGTAGAAC
*
2819882 TGGCTAAAAACCGGTAGAAC
1 CGGCTAAAAACCGGTAGAAC
2819902 CGGCTGAAAA
1 CGGCT-AAAA
2819912 TTGAACAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (20 bp):
CGGCTAAAAACCGGTAGAAC
Found at i:2820726 original size:13 final size:14
Alignment explanation
Indices: 2820695--2820745 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
2820685 ATCAGAACAA
*
2820695 AAAGAGAAAAAAAGC
1 AAAGAGAAAATAA-C
2820710 AAAGAGAAAATAA-
1 AAAGAGAAAATAAC
2820723 AAAGAGAAAA-AAC
1 AAAGAGAAAATAAC
2820736 AAAG-GAAAAT
1 AAAGAGAAAAT
2820746 TGAAGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
15 12 0.36
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAGAAAATAAC
Found at i:2820732 original size:26 final size:26
Alignment explanation
Indices: 2820693--2820745 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
2820683 CAATCAGAAC
2820693 AAAAAGAGAAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAAA-CAAAG-GAAAAT
2820721 AAAAAGAG-AAAAAACAAAGGAAAAT
1 AAAAAGAGAAAAAAACAAAGGAAAAT
2820746 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 6 0.24
28 8 0.32
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (26 bp):
AAAAAGAGAAAAAAACAAAGGAAAAT
Found at i:2821901 original size:32 final size:31
Alignment explanation
Indices: 2821865--2821980 Score: 117
Period size: 32 Copynumber: 3.6 Consensus size: 31
2821855 GGAACAATGA
*
2821865 GGGCATCTTTGAAGATTCAATATCAAATGTTG
1 GGGCATCTTTG-AGATTCAACATCAAATGTTG
*
2821897 GGGCATTTTTTGAGATTTC-ACATCAAATGTTG
1 GGGCA-TCTTTGAGA-TTCAACATCAAATGTTG
* * * *
2821929 GGGAATCTTTTTAGATTCAACATCGAATATTG
1 GGGCATC-TTTGAGATTCAACATCAAATGTTG
*
2821961 GGGCATCTTTGGGAATTCAA
1 GGGCATCTTTGAG-ATTCAA
2821981 TATCCTTATA
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
31 8 0.12
32 53 0.77
33 8 0.12
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.36
Consensus pattern (31 bp):
GGGCATCTTTGAGATTCAACATCAAATGTTG
Found at i:2823232 original size:37 final size:36
Alignment explanation
Indices: 2823179--2823290 Score: 161
Period size: 37 Copynumber: 3.1 Consensus size: 36
2823169 TTTCCAAGTT
2823179 TTATCTCTCTTGAGACAGTTTCCCTTGAAATAAAATC
1 TTATCTCTCTTGAGACAGTTTCCCTTGAAA-AAAATC
* * *
2823216 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
1 TTATCTCTCTTGAGACAGTTTCCCTTGAAAAAAATC
* *
2823252 TTATCTATCTTGGGACAGTTTCCCTTGAAACAAAATC
1 TTATCTCTCTTGAGACAGTTTCCCTTGAAA-AAAATC
2823289 TT
1 TT
2823291 TGAATATCTT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
36 31 0.47
37 35 0.53
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (36 bp):
TTATCTCTCTTGAGACAGTTTCCCTTGAAAAAAATC
Found at i:2823270 original size:36 final size:36
Alignment explanation
Indices: 2823177--2823285 Score: 164
Period size: 36 Copynumber: 3.0 Consensus size: 36
2823167 AGTTTCCAAG
*
2823177 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAATAAAA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAA-CAAA
* *
2823214 TCTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
2823250 TTTTATCTATCTTGGGACAGTTTCCCTTGAAACAAA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
2823286 ATCTTTGAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
36 35 0.54
37 30 0.46
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:2823366 original size:37 final size:36
Alignment explanation
Indices: 2823305--2823421 Score: 164
Period size: 36 Copynumber: 3.2 Consensus size: 36
2823295 TATCTTTTCC
* *
2823305 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
*
2823341 TT-AGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
2823378 TTGAAACAAATTTTGTCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
2823414 TTGAAACA
1 TTGAAACA
2823422 CAAAAAAAAC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
35 1 0.01
36 39 0.54
37 31 0.43
38 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.40
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:2823382 original size:102 final size:102
Alignment explanation
Indices: 2823201--2823387 Score: 236
Period size: 102 Copynumber: 1.8 Consensus size: 102
2823191 AGACAGTTTC
* *
2823201 CCTTGAAATAAAATCTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTATCTTGGG
1 CCTTGAAATAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTATCTTGAG
2823266 ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
66 ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
* * * * * *
2823303 CCTTGAAA-CAAAT-TTCGTCTCCCTTGAGACAGTTT-CTTTTAGAACTAAGTTTTGTCTCTCTT
1 CCTTGAAATAAAATCTT-GTCTCCCTTGAGACAGTTTCCCTTGA-AAC-AAATTTTATCTATCTT
**
2823365 GAGACAGTTTCTTTTGAAACAAA
63 GAGACAGTTTCCCTTGAAACAAA
2823388 TTTTGTCCCT
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
100 6 0.08
101 25 0.35
102 41 0.57
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (102 bp):
CCTTGAAATAAAATCTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTATCTTGAG
ACAGTTTCCCTTGAAACAAAATCTTTGAATATCTTTT
Found at i:2823459 original size:30 final size:29
Alignment explanation
Indices: 2823423--2823483 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
2823413 CTTGAAACAC
* *
2823423 AAAAAAAACCCTCGAAATTGTTTCTCTTG
1 AAAAAAAAACCTCGAAAATGTTTCTCTTG
* *
2823452 AAAAAAAAACTTTGAAAATGTTTCTCTTG
1 AAAAAAAAACCTCGAAAATGTTTCTCTTG
2823481 AAA
1 AAA
2823484 CATAAAGCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (29 bp):
AAAAAAAAACCTCGAAAATGTTTCTCTTG
Found at i:2823631 original size:83 final size:83
Alignment explanation
Indices: 2823487--2823740 Score: 332
Period size: 83 Copynumber: 3.0 Consensus size: 83
2823477 CTTGAAACAT
* * * *
2823487 AAAG-CCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGATTACACTCAAC-TCCAAGGCACATCATTTGCAGCATAACTCAAGGCA
2823551 AGAAGGGTTATCTGTCAAC
65 AGAAGGGTTATCTGTCAAC
* *
2823570 AAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAACTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAA
* * *
2823635 GAAGGGATATCAGTCATC
66 GAAGGGTTATCTGTCAAC
* * * *
2823653 AAAGACCTTCGAGTTCGATTACATTCAACT-CAGAGGCAAATCAAATTTACAGCATAGCTCAAGG
1 AAAGACCTTCGAGTTCGATTACACTCAACTCCA-AGGCACATC--ATTTGCAGCATAACTCAAGG
*
2823717 CAAGAAGGGTTATCTGCCAAC
63 CAAGAAGGGTTATCTGTCAAC
2823738 AAA
1 AAA
2823741 ATTGTCTAGT
Statistics
Matches: 148, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
82 2 0.01
83 87 0.59
84 21 0.14
85 38 0.26
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (83 bp):
AAAGACCTTCGAGTTCGATTACACTCAACTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAA
GAAGGGTTATCTGTCAAC
Found at i:2824278 original size:37 final size:37
Alignment explanation
Indices: 2824228--2824339 Score: 161
Period size: 37 Copynumber: 3.0 Consensus size: 37
2824218 GATTCAACGT
*
2824228 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
**
2824265 TAGAGTTTTACTAGGATTCAATTTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* * * *
2824302 TAAAGTTCTAATATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
2824339 T
1 T
2824340 TCATAAGCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:2824302 original size:21 final size:21
Alignment explanation
Indices: 2824276--2824342 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
2824266 AGAGTTTTAC
*
2824276 TAGGATTCAATTTCCTAAAAA
1 TAGGATTCAAATTCCTAAAAA
2824297 TAGGA-T-AAAGTT-CT---AA
1 TAGGATTCAAA-TTCCTAAAAA
* *
2824313 TATGATTCAAACTCCTAAAAA
1 TAGGATTCAAATTCCTAAAAA
2824334 TAGGATTCA
1 TAGGATTCA
2824343 TAAGCATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
16 6 0.17
17 2 0.06
18 5 0.14
19 4 0.11
20 3 0.09
21 15 0.43
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (21 bp):
TAGGATTCAAATTCCTAAAAA
Found at i:2824883 original size:2 final size:2
Alignment explanation
Indices: 2824878--2825020 Score: 129
Period size: 2 Copynumber: 74.5 Consensus size: 2
2824868 TTTTTTAGAT
2824878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2824920 TA TA TA TA TA TA TT TA CTT TT TA T- TA TA TG T- TT TA T- TA -A
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
2824959 TT TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TT TA TG T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2824999 TA TT TA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2825021 TATTTTTACT
Statistics
Matches: 119, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
1 7 0.06
2 111 0.93
3 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (2 bp):
TA
Found at i:2825010 original size:29 final size:28
Alignment explanation
Indices: 2824977--2825058 Score: 77
Period size: 29 Copynumber: 3.0 Consensus size: 28
2824967 TATATATATA
2824977 TATATATATTATTTTTATGTTTTA-TTTAT
1 TATATATATTATTTTTAT-TTTTACTTT-T
*
2825006 TATATATA-TATATATTATTTTTACTTTT
1 TATATATATTAT-TTTTATTTTTACTTTT
*
2825034 T-TAT-TATTA-TTTTATTTATA-TTTT
1 TATATATATTATTTTTATTTTTACTTTT
2825058 T
1 T
2825059 CTTCTTTTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
24 5 0.11
25 9 0.19
26 2 0.04
27 5 0.11
28 10 0.21
29 16 0.34
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (28 bp):
TATATATATTATTTTTATTTTTACTTTT
Found at i:2825010 original size:35 final size:35
Alignment explanation
Indices: 2824971--2825043 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
2824961 TATATATATA
2824971 TATATATATATATATTATTTTTA-TGTTTTATTTAT
1 TATATATATATATATTATTTTTACTGTTTTA-TTAT
*
2825006 TATATATATATATATTATTTTTACTTTTTTATTAT
1 TATATATATATATATTATTTTTACTGTTTTATTAT
2825041 TAT
1 TAT
2825044 TTTATTTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 30 0.83
36 6 0.17
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (35 bp):
TATATATATATATATTATTTTTACTGTTTTATTAT
Found at i:2825055 original size:6 final size:6
Alignment explanation
Indices: 2824857--2825056 Score: 73
Period size: 6 Copynumber: 34.2 Consensus size: 6
2824847 TACTTTAGTA
* * * * * *
2824857 TATATT TTTATT T-T-TT TAGATT ATATATA TATATA TATATA TATATA
1 TATATT TATATT TATATT TATATT -TATATT TATATT TATATT TATATT
* * * *
2824904 TATATA TATATA TATATA TATATA TATATT TACT-TT T-TA-T TATATGT
1 TATATT TATATT TATATT TATATT TATATT TA-TATT TATATT TATAT-T
* * * * * *
2824951 TTTA-T TA-ATT TATATA TATATA TATATA TATATAT TATTTT TATGTT
1 TATATT TATATT TATATT TATATT TATATT TATAT-T TATATT TATATT
* * * *
2824998 T-TATT TAT-TA TATATA TATATAT TATTTT TACT-TT TTTA-T TATTATT
1 TATATT TATATT TATATT TATAT-T TATATT TA-TATT TATATT TA-TATT
2825045 T-TATT TATATT T
1 TATATT TATATT T
2825057 TTCTTCTTTT
Statistics
Matches: 158, Mismatches: 17, Indels: 38
0.74 0.08 0.18
Matches are distributed among these distances:
4 7 0.04
5 24 0.15
6 107 0.68
7 20 0.13
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:2825067 original size:32 final size:32
Alignment explanation
Indices: 2824981--2825112 Score: 94
Period size: 35 Copynumber: 4.0 Consensus size: 32
2824971 TATATATATA
* * * *
2824981 TATATTATTTTTATGTTTTATTTATTATATATATA
1 TATATT-TTTTTCT-TTTTACTTATTAT-TTTATT
2825016 TATATTATTTTTACTTTTTTA-TTATTATTTTATT
1 TATATT-TTTTT-C-TTTTTACTTATTATTTTATT
2825050 TATATTTTTCTTCTTTTT-C-T-TTATTTT-TT
1 TATATTTTT-TTCTTTTTACTTATTATTTTATT
*
2825079 TATATTTTTTTATTTATTTTACTTATTATTTTAT
1 TATA-TTTTTT-TCT-TTTTACTTATTATTTTAT
2825113 CTTTGCTTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
29 7 0.09
30 14 0.17
31 5 0.06
32 6 0.07
33 5 0.06
34 19 0.23
35 20 0.24
36 5 0.06
37 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.73
Consensus pattern (32 bp):
TATATTTTTTTCTTTTTACTTATTATTTTATT
Found at i:2825079 original size:52 final size:57
Alignment explanation
Indices: 2825018--2825139 Score: 141
Period size: 52 Copynumber: 2.2 Consensus size: 57
2825008 TATATATATA
*
2825018 TATTATTTTTACT-TTTTTATTA-TTATTTTATTTA-TATTTT-TC-TT-CTTTTTCTT
1 TATTATTTTTA-TATTTTT-TTATTTATTTTACTTATTATTTTATCTTTGCTTTTTCTT
*
2825071 TATT-TTTTTATATTTTTTTATTTATTTTACTTATTATTTTATCTTTGCTTTTTCTA
1 TATTATTTTTATATTTTTTTATTTATTTTACTTATTATTTTATCTTTGCTTTTTCTT
*
2825127 TCTTATCTTTTAT
1 TATTAT-TTTTAT
2825140 TTAATTTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
51 4 0.07
52 22 0.38
53 10 0.17
54 2 0.03
55 2 0.03
56 11 0.19
57 1 0.02
58 6 0.10
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (57 bp):
TATTATTTTTATATTTTTTTATTTATTTTACTTATTATTTTATCTTTGCTTTTTCTT
Found at i:2825105 original size:31 final size:30
Alignment explanation
Indices: 2825016--2825112 Score: 83
Period size: 31 Copynumber: 3.1 Consensus size: 30
2825006 TATATATATA
2825016 TATATTATTTTTACTTTTTTATTA-TTATTTTATT
1 TATATT-TTTTTA--TTTTT-TTACTTATTTT-TT
* *
2825050 TATATTTTTCT-TCTTTTT-CTTTATTTTTT
1 TATATTTTTTTATTTTTTTAC-TTATTTTTT
*
2825079 TATATTTTTTTATTTATTTTACTTATTATTT
1 TATATTTTTTTATTT-TTTTACTTATTTTTT
2825110 TAT
1 TAT
2825113 CTTTGCTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
29 14 0.26
30 13 0.25
31 15 0.28
32 1 0.02
33 4 0.08
34 6 0.11
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (30 bp):
TATATTTTTTTATTTTTTTACTTATTTTTT
Found at i:2825160 original size:18 final size:18
Alignment explanation
Indices: 2825139--2825187 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2825129 TTATCTTTTA
*
2825139 TTTAATTTTTTTCTTCAT
1 TTTAATTTTTTTATTCAT
* *
2825157 TTTAATTTATTTATTTAT
1 TTTAATTTTTTTATTCAT
*
2825175 TTCTTATTTTTTT
1 TT-TAATTTTTTT
2825188 TATCTAACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTAATTTTTTTATTCAT
Found at i:2825186 original size:27 final size:27
Alignment explanation
Indices: 2825135--2825184 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2825125 TATCTTATCT
*
2825135 TTTATTTAATTTTTTTCTTCATTTTAA
1 TTTATTTAATTTATTTCTTCATTTTAA
2825162 TTTATTT-ATTTATTTCTT-ATTTT
1 TTTATTTAATTTATTTCTTCATTTT
2825185 TTTTATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 10 0.45
27 7 0.32
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTATTTAATTTATTTCTTCATTTTAA
Found at i:2827625 original size:22 final size:24
Alignment explanation
Indices: 2827600--2827644 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
2827590 ATGATGATTT
*
2827600 ATATGTTGATGAA-ATGT-TTTAA
1 ATATATTGATGAATATGTGTTTAA
*
2827622 ATATATTTATGAATATGTGTTTA
1 ATATATTGATGAATATGTGTTTA
2827645 GTTCAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (24 bp):
ATATATTGATGAATATGTGTTTAA
Found at i:2827644 original size:24 final size:24
Alignment explanation
Indices: 2827599--2827644 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
2827589 TATGATGATT
2827599 TATATGTTGATGAAATGTTTTAAA
1 TATATGTTGATGAAATGTTTTAAA
2827623 TATAT-TT-ATGAATATGTGTTTA
1 TATATGTTGATGAA-ATGT-TTTA
2827645 GTTCAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (24 bp):
TATATGTTGATGAAATGTTTTAAA
Found at i:2829221 original size:34 final size:34
Alignment explanation
Indices: 2829178--2829243 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
2829168 ACAATCACAC
* *
2829178 CATTTAATACTTCAAACTAAATAAAACCTCAAAG
1 CATTTAATACTTCAAACTAAACAAAACATCAAAG
**
2829212 CATTTAATACTTTGAACTAAACAAAACATCAA
1 CATTTAATACTTCAAACTAAACAAAACATCAA
2829244 TATGACAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.50, C:0.20, G:0.03, T:0.27
Consensus pattern (34 bp):
CATTTAATACTTCAAACTAAACAAAACATCAAAG
Found at i:2829346 original size:2 final size:2
Alignment explanation
Indices: 2829339--2829378 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2829329 ACTTGAAATA
2829339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2829379 TATTTCAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2829955 original size:15 final size:17
Alignment explanation
Indices: 2829937--2829969 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2829927 AAAAAATATT
2829937 TATAAAA-AA-TTAAAA
1 TATAAAATAATTTAAAA
2829952 TATAAAATAATTTAAAA
1 TATAAAATAATTTAAAA
2829969 T
1 T
2829970 TTTTAGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAAAATAATTTAAAA
Found at i:2832608 original size:40 final size:41
Alignment explanation
Indices: 2832547--2832636 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 41
2832537 AATCCTTAAA
* * *
2832547 TTAATTTTTTTAATAATTTAAT-TTTGTAGTA-ATTTTATAT
1 TTAATTTATTGAATAATTTAATAATTGT-GTATATTTTATAT
*
2832587 TTAATTTATTGAAT-ATCTTAATAATTGTTTATATTTTATAT
1 TTAATTTATTGAATAAT-TTAATAATTGTGTATATTTTATAT
2832628 TTAAATTTA
1 TT-AATTTA
2832637 AATAAACTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
39 2 0.05
40 19 0.45
41 15 0.36
42 6 0.14
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (41 bp):
TTAATTTATTGAATAATTTAATAATTGTGTATATTTTATAT
Found at i:2835041 original size:26 final size:26
Alignment explanation
Indices: 2834999--2835048 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2834989 ATTGGCTTAT
*
2834999 TTAATATTTTTAAATAAAAATATATA
1 TTAATATTTTAAAATAAAAATATATA
2835025 TTAA-ATTTTAAATATAAAAATATA
1 TTAATATTTTAAA-ATAAAAATATA
2835049 AAAAATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAATATTTTAAAATAAAAATATATA
Found at i:2835060 original size:10 final size:9
Alignment explanation
Indices: 2835034--2835086 Score: 53
Period size: 10 Copynumber: 6.2 Consensus size: 9
2835024 ATTAAATTTT
2835034 AAATAT-AA
1 AAATATAAA
2835042 AAATATAAA
1 AAATATAAA
2835051 AAATACTAAA
1 AAATA-TAAA
2835061 AAAT-T---
1 AAATATAAA
2835066 AAATATAAA
1 AAATATAAA
2835075 AAATACTAAA
1 AAATA-TAAA
2835085 AA
1 AA
2835087 TAAAAATTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
8 7 0.18
9 12 0.32
10 14 0.37
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATATAAA
Done.