Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015254.1 Kokia drynarioides strain JFW-HI SEQ_130299, 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: 1276691
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 890 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:1706 original size:43 final size:43
Alignment explanation
Indices: 1646--1750 Score: 158
Period size: 43 Copynumber: 2.5 Consensus size: 43
1636 AGATGAACTG
* * *
1646 TATAA-TTAATAACATGTCACGATATTAATAAGAGTCAAGTCA
1 TATAATTTAATAACATGTCACCATATTAACAAGAGTCAAGTAA
* *
1688 TATAATTTAGTAACATGTCACCATATTAACACGAGTCAAGTAA
1 TATAATTTAATAACATGTCACCATATTAACAAGAGTCAAGTAA
1731 TATAATTTAATAACATGTCA
1 TATAATTTAATAACATGTCA
1751 ATGAATAACA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
42 5 0.09
43 51 0.91
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.32
Consensus pattern (43 bp):
TATAATTTAATAACATGTCACCATATTAACAAGAGTCAAGTAA
Found at i:2897 original size:18 final size:18
Alignment explanation
Indices: 2869--2927 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
2859 GTTTGAAACA
2869 TAAATTATTTATACTTGGT
1 TAAA-TATTTATACTTGGT
2888 TAAATA-TT-TA-TT-GT
1 TAAATATTTATACTTGGT
*
2902 T-AATAATTTATACTTGAT
1 TAAAT-ATTTATACTTGGT
2920 TAAATATT
1 TAAATATT
2928 AACTGATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
13 3 0.09
14 4 0.12
15 4 0.12
16 4 0.12
17 4 0.12
18 7 0.21
19 7 0.21
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (18 bp):
TAAATATTTATACTTGGT
Found at i:3149 original size:3 final size:3
Alignment explanation
Indices: 3099--3132 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3089 TAAAATTAGA
3099 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3133 ATTTTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3553 original size:21 final size:21
Alignment explanation
Indices: 3528--3567 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3518 TACTTACTAC
*
3528 TACTAGCAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
*
3549 TACTAACAAAATTAAATTA
1 TACTAACAAAATAAAATTA
3568 AATTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (21 bp):
TACTAACAAAATAAAATTACT
Found at i:3567 original size:5 final size:5
Alignment explanation
Indices: 3557--3584 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3547 CTTACTAACA
3557 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
3585 AATAATCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:3895 original size:12 final size:12
Alignment explanation
Indices: 3878--3908 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3868 CTAACAAATT
3878 AAATAAATTTAA
1 AAATAAATTTAA
3890 AAATAAATTTAA
1 AAATAAATTTAA
*
3902 CAATAAA
1 AAATAAA
3909 AACAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
AAATAAATTTAA
Found at i:3960 original size:45 final size:45
Alignment explanation
Indices: 3909--3998 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
3899 TAACAATAAA
3909 AACAAAAAATAAATTTATCTTTCTCTCTTTCTTCTTCTTTTTTTT
1 AACAAAAAATAAATTTATCTTTCTCTCTTTCTTCTTCTTTTTTTT
*
3954 AACAAAAAATAAATTTGTCTTTCTCTCTTTCTTCTTCTTTTTTTT
1 AACAAAAAATAAATTTATCTTTCTCTCTTTCTTCTTCTTTTTTTT
3999 TTTCTTTNNN
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.18, G:0.01, T:0.56
Consensus pattern (45 bp):
AACAAAAAATAAATTTATCTTTCTCTCTTTCTTCTTCTTTTTTTT
Found at i:5186 original size:46 final size:46
Alignment explanation
Indices: 5119--5231 Score: 217
Period size: 46 Copynumber: 2.5 Consensus size: 46
5109 AAAATCAAAA
*
5119 CCATTAAGTTAAAAGGTAAAATTACGTCGTTTTAATAAATGTTTAC
1 CCATTAAGTTAAAAGGCAAAATTACGTCGTTTTAATAAATGTTTAC
5165 CCATTAAGTTAAAAGGCAAAATTACGTCGTTTTAATAAATGTTTAC
1 CCATTAAGTTAAAAGGCAAAATTACGTCGTTTTAATAAATGTTTAC
5211 CCATTAAGTTAAAAGGCAAAA
1 CCATTAAGTTAAAAGGCAAAA
5232 CCATTATATT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (46 bp):
CCATTAAGTTAAAAGGCAAAATTACGTCGTTTTAATAAATGTTTAC
Found at i:5765 original size:18 final size:18
Alignment explanation
Indices: 5732--5766 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5722 GAATTTCAAG
*
5732 TTTGAATCGAATTAAATT
1 TTTGAATCGAAGTAAATT
*
5750 TTTGAATCTAAGTAAAT
1 TTTGAATCGAAGTAAAT
5767 CGAATACCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTGAATCGAAGTAAATT
Found at i:8025 original size:21 final size:20
Alignment explanation
Indices: 8001--8038 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
7991 TAAAAGTACA
8001 TAAAATTCTTAAATTTTTTCT
1 TAAAATTC-TAAATTTTTTCT
8022 TAAAATTCT-AATTTTTT
1 TAAAATTCTAAATTTTTT
8039 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAAATTCTAAATTTTTTCT
Found at i:8047 original size:21 final size:21
Alignment explanation
Indices: 8001--8039 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
7991 TAAAAGTACA
8001 TAAAATTCTTAAATTTTTTCT
1 TAAAATTCTTAAATTTTTTCT
*
8022 TAAAATTC-TAATTTTTTT
1 TAAAATTCTTAAATTTTTT
8040 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (21 bp):
TAAAATTCTTAAATTTTTTCT
Found at i:20870 original size:30 final size:29
Alignment explanation
Indices: 20782--21380 Score: 481
Period size: 30 Copynumber: 20.2 Consensus size: 29
20772 GTAGTTTTGG
* *
20782 GGAAGATTCGGAGTCAAAAATGGGATTTTT
1 GGAAGGTTCGGGGT-AAAAATGGGATTTTT
* * *
20812 GGAA-GTTCAGGGGT-AGAATGGTAATTTT
1 GGAAGGTTC-GGGGTAAAAATGGGATTTTT
* *
20840 GGAAGGTTCGAGATCAAAAATGGGATTTTT
1 GGAAGGTTCGGGGT-AAAAATGGGATTTTT
*
20870 GGAA-GTTCGAGGGT-AAAATGGTAATTTTT
1 GGAAGGTTCG-GGGTAAAAATGG-GATTTTT
*
20899 GGAAGGTTCGGGATAAAAAATGGGACTTTTT
1 GGAAGGTTCGGGGT-AAAAATGGGA-TTTTT
*
20930 GG-AGGTTCGGGGGT-AAAATGGTAATTTTT
1 GGAAGGTTC-GGGGTAAAAATGG-GATTTTT
* * *
20959 GAAAGGTTCGGGGGT-AAAATGGTAATTTTC
1 GGAAGGTTC-GGGGTAAAAATGG-GATTTTT
* *
20989 GAAAGGTTTGGGGTTAAAAATGGGATTTTT
1 GGAAGGTTCGGGG-TAAAAATGGGATTTTT
* * ** *
21019 GGAAGTTTAGGGGT-AAAATGTTAAATTTT
1 GGAAGGTTCGGGGTAAAAATG-GGATTTTT
*
21048 GGAAGGTTTGGGGTTAAAAATGGGATTTTT
1 GGAAGGTTCGGGG-TAAAAATGGGATTTTT
* *
21078 GGAA-GTTTGAGGGT-AAAATGGTAATTTTT
1 GGAAGGTTCG-GGGTAAAAATGG-GATTTTT
*
21107 GGAAGGTTCGGGATAAAAAATGGGACTTTTT
1 GGAAGGTTCGGGGT-AAAAATGGGA-TTTTT
*
21138 GG-AGGTTCGAGGGT-AAAATGGTAATTTTT
1 GGAAGGTTCG-GGGTAAAAATGG-GATTTTT
*
21167 GGAAGGTTTGGGGTTAAAAATGGGATTTTTT
1 GGAAGGTTCGGGG-TAAAAATGGGA-TTTTT
* ** *
21198 GGAAGGTTTGGGGTTTAAATGGTAATTTTT
1 GGAAGGTTCGGGGTAAAAATGG-GATTTTT
* *
21228 GGAAGGTTTGGGGTTAAAATTGGGATTTTT
1 GGAAGGTTCGGGG-TAAAAATGGGATTTTT
* **
21258 GGAAGGTTCGGGGTTAAAATAGTAATTTTT
1 GGAAGGTTCGGGGTAAAAAT-GGGATTTTT
*
21288 GGAAGGTTCGGGGTTAAAAATGAGATTTTT
1 GGAAGGTTCGGGG-TAAAAATGGGATTTTT
*
21318 GGAA-GTTCGGGGGT-AAAATGGTAATTTTT
1 GGAAGGTTC-GGGGTAAAAATGG-GATTTTT
* *
21347 GGAA-GTTCGGTGTTAAAAATGAGATTTTT
1 GGAAGGTTCGG-GGTAAAAATGGGATTTTT
21376 GGAAG
1 GGAAG
21381 TTTAGGGACC
Statistics
Matches: 469, Mismatches: 61, Indels: 78
0.77 0.10 0.13
Matches are distributed among these distances:
28 46 0.10
29 131 0.28
30 206 0.44
31 86 0.18
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.35
Consensus pattern (29 bp):
GGAAGGTTCGGGGTAAAAATGGGATTTTT
Found at i:21032 original size:59 final size:58
Alignment explanation
Indices: 20856--21383 Score: 566
Period size: 60 Copynumber: 8.9 Consensus size: 58
20846 TTCGAGATCA
* * * * *
20856 AAAATGG-GATTTTTGGAA-GTTCGAGGG-T-AAAATGGTAATTTTTGGAAGGTTCGGGAT
1 AAAATGGTAATTTTTGGAAGGTTTG-GGGTTAAAAATGG-GATTTTTGGAA-GTTTGGGGT
* * * * * * *
20913 AAAAAATGGGACTTTTTGG-AGGTTCGGGGGT-AAAATGGTAATTTTTGAAAGGTTCGGGGGT
1 --AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGG-GATTTTTGGAA-GTT-TGGGGT
* *
20974 AAAATGGTAATTTTCGAAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTT-GGGGT
* *
21033 AAAATGTTAAATTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTG-GGGT
* * * * *
21092 AAAATGGTAATTTTTGGAAGGTTCGGGATAAAAAATGGGACTTTTTGGAGGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGA-TTTTTGGAAGTTTG-GGGT
21152 AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTTGGAAGGTTTGGGGTT
1 AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGA-TTTTTGGAA-GTTTGGGG-T
* * *
21213 TAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAATTGGGATTTTTGGAAGGTTCGGGGTT
1 AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAA-GTTTGGGG-T
* * * *
21273 AAAATAGTAATTTTTGGAAGGTTCGGGGTTAAAAATGAGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTT-TGGGGT
* * *
21332 AAAATGGTAATTTTTGGAA-GTTCGGTGTTAAAAATGAGATTTTTGGAAGTTT
1 AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTT
21384 AGGGACCTCC
Statistics
Matches: 414, Mismatches: 43, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
58 32 0.08
59 142 0.34
60 186 0.45
61 54 0.13
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGT
Found at i:22107 original size:28 final size:25
Alignment explanation
Indices: 22060--22112 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 25
22050 TAACCCAGAT
*
22060 CTTCAAAAAAAACTCTTTTTTATTC
1 CTTCAAAAAAAACTATTTTTTATTC
22085 CTTCAAAAAAAAATCTATCTTTTTATTC
1 CTTC-AAAAAAAA-CTAT-TTTTTATTC
22113 TCAAATCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 8 0.33
27 3 0.12
28 9 0.38
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (25 bp):
CTTCAAAAAAAACTATTTTTTATTC
Found at i:22443 original size:14 final size:15
Alignment explanation
Indices: 22400--22443 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
22390 TTTTATTCTC
22400 ATTTAATACTTATATT
1 ATTTAATAC-TATATT
22416 ATTTAATACT-TATT
1 ATTTAATACTATATT
22430 ATTTAATA-TATATT
1 ATTTAATACTATATT
22444 TATTACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.04
14 16 0.59
15 1 0.04
16 9 0.33
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTAATACTATATT
Found at i:23086 original size:15 final size:15
Alignment explanation
Indices: 23068--23123 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
23058 TTTTGGGTAG
23068 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
23083 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
*
23098 TTTGTTATTGGGCCA
1 TTTGTAATTGGGCCA
23113 TTTGTAATTGG
1 TTTGTAATTGG
23124 ACTTTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.46
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:23177 original size:17 final size:17
Alignment explanation
Indices: 23155--23236 Score: 61
Period size: 17 Copynumber: 5.2 Consensus size: 17
23145 TTGGATTTTC
*
23155 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
23172 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
23189 TAAA-TT---TTTAAAA
1 TAAATTTAAATTTCAAA
*
23202 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
* *
23218 TAAA-TTCAATTTCCAA
1 TAAATTTAAATTTCAAA
23234 TAA
1 TAA
23237 GTCCAGACAA
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
13 10 0.18
14 2 0.04
15 7 0.13
16 14 0.25
17 16 0.29
18 6 0.11
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:23204 original size:30 final size:29
Alignment explanation
Indices: 23164--23223 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
23154 CTAAATTTAA
* *
23164 TTTTATAATAAATTTAAATTTCAAATAAAT
1 TTTTAAAATAAACTTAAATTT-AAATAAAT
23194 TTTTAAAATAAACTTAAATTTAAATAAAT
1 TTTTAAAATAAACTTAAATTTAAATAAAT
23223 T
1 T
23224 CAATTTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTTAAAATAAACTTAAATTTAAATAAAT
Found at i:25012 original size:22 final size:22
Alignment explanation
Indices: 24978--25051 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
24968 ATCACACTAG
* *
24978 TAGGCATCGAAGTGCTGAGCAA
1 TAGGCACCAAAGTGCTGAGCAA
*
25000 TAGGCACCAAAGTGTTGAGCAA
1 TAGGCACCAAAGTGCTGAGCAA
*
25022 TAGGCACCAAAGTGC-GAATCAA
1 TAGGCACCAAAGTGCTG-AGCAA
25044 TAGGCACC
1 TAGGCACC
25052 GTAACGCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 1 0.02
22 45 0.98
ACGTcount: A:0.35, C:0.22, G:0.27, T:0.16
Consensus pattern (22 bp):
TAGGCACCAAAGTGCTGAGCAA
Found at i:25758 original size:28 final size:28
Alignment explanation
Indices: 25705--25758 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
25695 ATAATATATC
* *
25705 AAATACACTTAAAAACATTTACACAAAA
1 AAATACACTTAAAAACATTAAAACAAAA
*
25733 AAATGCACTTAAAAACATTAAAACAA
1 AAATACACTTAAAAACATTAAAACAA
25759 TCATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.61, C:0.17, G:0.02, T:0.20
Consensus pattern (28 bp):
AAATACACTTAAAAACATTAAAACAAAA
Found at i:25945 original size:20 final size:20
Alignment explanation
Indices: 25910--25972 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
25900 AAAAACGCAT
25910 AAAAATAAT-ACTCAAACAAC
1 AAAAATAATAAC-CAAACAAC
25930 AAAAATAATAACCAAAACAAC
1 AAAAATAATAACC-AAACAAC
*
25951 AGCAAAATAACAA--AAACAAC
1 A--AAAATAATAACCAAACAAC
25971 AA
1 AA
25973 CAACAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 1 0.03
20 18 0.47
21 10 0.26
23 9 0.24
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.10
Consensus pattern (20 bp):
AAAAATAATAACCAAACAAC
Found at i:25951 original size:3 final size:3
Alignment explanation
Indices: 25945--26016 Score: 55
Period size: 3 Copynumber: 25.7 Consensus size: 3
25935 TAATAACCAA
* * * *
25945 AAC AAC AGC AA- AAT AAC AAA AAC AAC AAC AAC AA- AA- AAC AA- AAT
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* *
25989 AAC AAC AAA AAC AGC AAC AA- AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
26017 AAATAAAAGC
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 10 0.18
3 45 0.82
ACGTcount: A:0.72, C:0.22, G:0.03, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:25987 original size:41 final size:39
Alignment explanation
Indices: 25923--26019 Score: 97
Period size: 41 Copynumber: 2.5 Consensus size: 39
25913 AATAATACTC
* * * * *
25923 AAACAACAAAAATAATAACCAAAACAACAGCAAAATAACAA
1 AAACAACAACAACAAAAAACAAAACAACAAC-AAA-AACAA
* *
25964 AAACAACAACAACAAAAAACAAAATAACAACAAAAACAG
1 AAACAACAACAACAAAAAACAAAACAACAACAAAAACAA
*
26003 CAACAA-AACAACAAAAA
1 AAACAACAACAACAAAAA
26020 TAAAAGCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 11 0.23
39 9 0.19
40 3 0.06
41 25 0.52
ACGTcount: A:0.73, C:0.21, G:0.02, T:0.04
Consensus pattern (39 bp):
AAACAACAACAACAAAAAACAAAACAACAACAAAAACAA
Found at i:25989 original size:30 final size:31
Alignment explanation
Indices: 25924--26031 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 31
25914 ATAATACTCA
* *
25924 AACAACAAAAATAATAACCAAAACAACAGCAAAAT
1 AACAACAAAAACAACAA-CAAAAC-A-A-CAAAAT
25959 AACAA-AAACAACAACAACAAAA-AACAAAAT
1 AACAACAAA-AACAACAACAAAACAACAAAAT
*
25989 AACAACAAAAACAGCAACAAAACAACAAAAAT
1 AACAACAAAAACAACAACAAAACAAC-AAAAT
26021 AA-AAGCAAAAA
1 AACAA-CAAAAA
26032 TAGTACCAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
30 23 0.35
31 9 0.14
32 14 0.22
34 8 0.12
35 11 0.17
ACGTcount: A:0.73, C:0.19, G:0.03, T:0.05
Consensus pattern (31 bp):
AACAACAAAAACAACAACAAAACAACAAAAT
Found at i:29721 original size:21 final size:21
Alignment explanation
Indices: 29697--29736 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29687 TATTATAAAC
29697 ATTAAATCAAATAAATTAATA
1 ATTAAATCAAATAAATTAATA
* * *
29718 ATTAATTCAACTTAATTAA
1 ATTAAATCAAATAAATTAA
29737 CAAGCAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAAATCAAATAAATTAATA
Found at i:31710 original size:6 final size:6
Alignment explanation
Indices: 31699--31772 Score: 139
Period size: 6 Copynumber: 12.3 Consensus size: 6
31689 ACCATGGATA
31699 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
*
31747 GTATAT GTGTAT GTATAT GTATAT GT
1 GTATAT GTATAT GTATAT GTATAT GT
31773 TCTCCATTCC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:34474 original size:33 final size:33
Alignment explanation
Indices: 34432--34501 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
34422 CTTTTCTTAG
34432 CTTAGTGTTAGTAACCACTGAGAGAGGATTTTA
1 CTTAGTGTTAGTAACCACTGAGAGAGGATTTTA
34465 CTTAGTGTTAGTAACCACTGAGAGAGGATTTTA
1 CTTAGTGTTAGTAACCACTGAGAGAGGATTTTA
34498 CTTA
1 CTTA
34502 CTTTTCTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (33 bp):
CTTAGTGTTAGTAACCACTGAGAGAGGATTTTA
Found at i:38847 original size:21 final size:21
Alignment explanation
Indices: 38823--38871 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
38813 AGACCCTTAA
* *
38823 AGATGAGTTAAAGAAGCTGTC
1 AGATGAATGAAAGAAGCTGTC
**
38844 AGATGAATGCGAGAAGCTGTC
1 AGATGAATGAAAGAAGCTGTC
38865 AGATGAA
1 AGATGAA
38872 AATAGTTCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.31, T:0.20
Consensus pattern (21 bp):
AGATGAATGAAAGAAGCTGTC
Found at i:40395 original size:47 final size:47
Alignment explanation
Indices: 40302--40394 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 47
40292 AGTTTTCAAG
*
40302 GGGTCTAAATTTTTTTTTTATTATCAAATTTTAGGGGATCTAAAAAA
1 GGGTCTAAATTTTTTTTTTATTACCAAATTTTAGGGGATCTAAAAAA
40349 GGGTCTAAATTTTTTTTTT-TTACCAAATTTTAGGGGATCTAAAAAA
1 GGGTCTAAATTTTTTTTTTATTACCAAATTTTAGGGGATCTAAAAAA
40395 AACTTTCTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 26 0.58
47 19 0.42
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (47 bp):
GGGTCTAAATTTTTTTTTTATTACCAAATTTTAGGGGATCTAAAAAA
Found at i:43986 original size:17 final size:17
Alignment explanation
Indices: 43964--43996 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43954 CTGAGAGAGT
43964 TTTGGT-TTTGTCTTGTG
1 TTTGGTGTTTGT-TTGTG
43981 TTTGGTGTTTGTTTGT
1 TTTGGTGTTTGTTTGT
43997 TTGTTTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.00, C:0.03, G:0.30, T:0.67
Consensus pattern (17 bp):
TTTGGTGTTTGTTTGTG
Found at i:49491 original size:18 final size:18
Alignment explanation
Indices: 49457--49508 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
49447 ACAAAATAAT
*
49457 TCAAAATAATTTTTAAAAA
1 TCAAAAT-ATTTATAAAAA
49476 TCAAAATATTTATAAAAAA
1 TCAAAATATTTAT-AAAAA
* *
49495 TTAAAAAATTTATA
1 TCAAAATATTTATA
49509 TTTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (18 bp):
TCAAAATATTTATAAAAA
Found at i:49509 original size:25 final size:26
Alignment explanation
Indices: 49481--49533 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
49471 AAAAATCAAA
49481 ATATTTATAAAAAA-T-TAAAAAATTT
1 ATATTTA-AAAAAAGTATAAAAAATTT
49506 ATATTTAAAAAAATGTATAAAAAATTT
1 ATATTTAAAAAAA-GTATAAAAAATTT
49533 A
1 A
49534 AAAATTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 6 0.24
25 7 0.28
26 1 0.04
27 11 0.44
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
ATATTTAAAAAAAGTATAAAAAATTT
Found at i:49547 original size:30 final size:27
Alignment explanation
Indices: 49483--49569 Score: 79
Period size: 30 Copynumber: 3.1 Consensus size: 27
49473 AAATCAAAAT
* *
49483 ATTTATAAAAA-AT-TAAAAAATTTAT
1 ATTTAAAAAAATATATAAAAAATTTAA
*
49508 ATTTAAAAAAATGTATAAAAAATTTAAAA
1 ATTTAAAAAAATATATAAAAAATTT--AA
* *
49537 ATTCTAAAAAAATATGTAAAAAAGTTCAA
1 ATT-TAAAAAAATATATAAAAAA-TTTAA
49566 ATTT
1 ATTT
49570 TAGAAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
25 10 0.20
26 1 0.02
27 10 0.20
28 1 0.02
29 9 0.18
30 17 0.34
31 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (27 bp):
ATTTAAAAAAATATATAAAAAATTTAA
Found at i:53071 original size:2 final size:2
Alignment explanation
Indices: 53064--53088 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53054 CTTTCGTTAA
53064 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
53089 GTTTTAGAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53556 original size:31 final size:31
Alignment explanation
Indices: 53519--53582 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
53509 TCTTGGGTTA
53519 TTTTATTTACATAATATAAAAATTAAATTAT
1 TTTTATTTACATAATATAAAAATTAAATTAT
* * ** *
53550 TTTTATTTATATAATTTTTATATTAAATTAT
1 TTTTATTTACATAATATAAAAATTAAATTAT
53581 TT
1 TT
53583 CATTGAACGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTTATTTACATAATATAAAAATTAAATTAT
Found at i:54793 original size:22 final size:21
Alignment explanation
Indices: 54768--54808 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
54758 AATTCATAAA
54768 TTTA-ATTTCATTAATATAATAT
1 TTTATATTTC-TTAA-ATAATAT
54790 TTTATATTTCTTAAATAAT
1 TTTATATTTCTTAAATAAT
54809 TTTGGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTATATTTCTTAAATAATAT
Found at i:55232 original size:26 final size:27
Alignment explanation
Indices: 55203--55256 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
55193 TTAATTTTAT
55203 TTAAAATTAAAAATATTA-AA-ATTAAA
1 TTAAAATTAAAAA-ATTATAATATTAAA
55229 TTAAAATTAAAAAATTATAATATTAAA
1 TTAAAATTAAAAAATTATAATATTAAA
55256 T
1 T
55257 ATTTAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 4 0.15
26 15 0.58
27 7 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
TTAAAATTAAAAAATTATAATATTAAA
Found at i:55241 original size:27 final size:26
Alignment explanation
Indices: 55203--55256 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
55193 TTAATTTTAT
55203 TTAAAATTAAAAA-TATTAAAATTAAA
1 TTAAAATTAAAAATTA-TAAAATTAAA
*
55229 TTAAAATTAAAAAATTATAATATTAAA
1 TTAAAATT-AAAAATTATAAAATTAAA
55256 T
1 T
55257 ATTTAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 15 0.60
28 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TTAAAATTAAAAATTATAAAATTAAA
Found at i:55242 original size:19 final size:20
Alignment explanation
Indices: 55206--55245 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
55196 ATTTTATTTA
*
55206 AAATTAAAAATATTAAAATT
1 AAATTAAAAATATAAAAATT
*
55226 AAATTAAAATTA-AAAAATT
1 AAATTAAAAATATAAAAATT
55245 A
1 A
55246 TAATATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTAAAAATATAAAAATT
Found at i:55502 original size:29 final size:30
Alignment explanation
Indices: 55451--55511 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
55441 AAAATAACTT
*
55451 TTTTATAAAGTTCTAAAATATATAGTTAAAA
1 TTTTATAAAGTTCTAAAATATATA-TAAAAA
55482 TTTTA-AAAG-TC-AAAATAATATATAAAAA
1 TTTTATAAAGTTCTAAAAT-ATATATAAAAA
55510 TT
1 TT
55512 AAAAAATGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 12 0.43
29 7 0.25
30 4 0.14
31 5 0.18
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.39
Consensus pattern (30 bp):
TTTTATAAAGTTCTAAAATATATATAAAAA
Found at i:63101 original size:142 final size:142
Alignment explanation
Indices: 62845--63129 Score: 534
Period size: 142 Copynumber: 2.0 Consensus size: 142
62835 AAACTTGCGT
*
62845 GCTGGCAATAAGCTCCTCTTAACTGGAACACCTCTGCAGAACAATTTGGCAGAGCTATGGTCACT
1 GCTGGCAATAAGCTCCTCTTAACTGGAACACCTCTGCAGAACAATTTGGCAGAGATATGGTCACT
62910 GTTAAATTTCATTTTGCCTGATATTTTTCAATCTCATGAAGAATTTGAGTCATGGTATGTTGCTT
66 GTTAAATTTCATTTTGCCTGATATTTTTCAATCTCATGAAGAATTTGAGTCATGGTATGTTGCTT
62975 AATCTTTTCTTA
131 AATCTTTTCTTA
* * *
62987 GCTGGCAATAAGCTCCTCTTAACTGGAACACCTCTGCAGAACAATTTGGCAGTGATATGGTTATT
1 GCTGGCAATAAGCTCCTCTTAACTGGAACACCTCTGCAGAACAATTTGGCAGAGATATGGTCACT
63052 GTTAAATTTCATTTTGCCTGATATTTTTCAATCTCATGAAGAATTTGAGTCATGGTATGTTGCTT
66 GTTAAATTTCATTTTGCCTGATATTTTTCAATCTCATGAAGAATTTGAGTCATGGTATGTTGCTT
63117 AATCTTTTCTTA
131 AATCTTTTCTTA
63129 G
1 G
63130 TCGACTCTGG
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 139 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (142 bp):
GCTGGCAATAAGCTCCTCTTAACTGGAACACCTCTGCAGAACAATTTGGCAGAGATATGGTCACT
GTTAAATTTCATTTTGCCTGATATTTTTCAATCTCATGAAGAATTTGAGTCATGGTATGTTGCTT
AATCTTTTCTTA
Found at i:70468 original size:16 final size:17
Alignment explanation
Indices: 70441--70478 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
70431 AATATTCTGT
*
70441 ATATATTATATATGTAA
1 ATATATTATATACGTAA
*
70458 ATATATT-TATACGTTA
1 ATATATTATATACGTAA
70474 ATATA
1 ATATA
70479 AATTTTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (17 bp):
ATATATTATATACGTAA
Found at i:76634 original size:157 final size:157
Alignment explanation
Indices: 76342--76641 Score: 471
Period size: 157 Copynumber: 1.9 Consensus size: 157
76332 CAGTATTAAT
* * *
76342 TTGACAGGTGTATTTGAGTTGAGAACAGCTTTCTGTTATTGAGAAACCTAGTGATATCCGTATTA
1 TTGACAGGTGTATTTGAATTAAGAACAGCTTTCTGTTATTGAGAAACCTAGTCATATCCGTATTA
*
76407 ATAGTTTTATAATGTTTGGACTTTTAGGCTATTGAGTTTTATTTAAATATGAACCTTAGTTACTT
66 ATAGTTTTATAATGTTTGGACTTTTAGGCTATTGAGTTTTATTTAAATATGAACCTTAGTCACTT
*
76472 CAAAGAAAAAGGTGGGTTCAGAATTTA
131 AAAAGAAAAAGGTGGGTTCAGAATTTA
* * *
76499 TTGACAGGTGTATTTGAATTAAGAACAGCTTTTTGTTATT-AGCAATCTAG-CATAATCCGTACT
1 TTGACAGGTGTATTTGAATTAAGAACAGCTTTCTGTTATTGAGAAACCTAGTCAT-ATCCGTA-T
*
76562 T-ATAGTTTTATAATGTTTGGACTTTTAGGCTATTGAGTTTTATTTAGAATATGAACCTTTGTCA
64 TAATAGTTTTATAATGTTTGGACTTTTAGGCTATTGAGTTTTATTTA-AATATGAACCTTAGTCA
76626 CTTAAAAGAAAAAGGT
128 CTTAAAAGAAAAAGGT
76642 TGTTTAGGCG
Statistics
Matches: 131, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
155 2 0.02
156 60 0.46
157 69 0.53
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (157 bp):
TTGACAGGTGTATTTGAATTAAGAACAGCTTTCTGTTATTGAGAAACCTAGTCATATCCGTATTA
ATAGTTTTATAATGTTTGGACTTTTAGGCTATTGAGTTTTATTTAAATATGAACCTTAGTCACTT
AAAAGAAAAAGGTGGGTTCAGAATTTA
Found at i:83735 original size:23 final size:24
Alignment explanation
Indices: 83698--83753 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
83688 ATATATATAT
**
83698 ATATATAACTATATTTTAAATATTAA
1 ATATATAAC-ATATTACAAAT-TTAA
83724 A-ATATAAC-TATTACAAATTTAA
1 ATATATAACATATTACAAATTTAA
83746 ATATATAA
1 ATATATAA
83754 TTTACATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 14 0.52
25 7 0.26
26 1 0.04
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATATAACATATTACAAATTTAA
Found at i:83749 original size:21 final size:20
Alignment explanation
Indices: 83723--83775 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
83713 TTAAATATTA
*
83723 AAATATAACTATTACAAATTT
1 AAATATAAAT-TTACAAATTT
*
83744 AAATATATAATTTACATATTT
1 AAATATA-AATTTACAAATTT
83765 AAA-ATAAATTT
1 AAATATAAATTT
83776 CAATAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 5 0.17
20 3 0.10
21 19 0.66
22 2 0.07
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATAAATTTACAAATTT
Found at i:84543 original size:17 final size:17
Alignment explanation
Indices: 84523--84556 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
84513 TAATTAATGA
*
84523 GATAAAAATATTATTTT
1 GATAAAAATATAATTTT
*
84540 GATAAATATATAATTTT
1 GATAAAAATATAATTTT
84557 TTATATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
GATAAAAATATAATTTT
Found at i:87667 original size:19 final size:20
Alignment explanation
Indices: 87622--87667 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
87612 AAAGAACATG
87622 AAATTAT-TAAAAAAATTAA
1 AAATTATATAAAAAAATTAA
*
87641 AAATTATATAAAAATA-TAA
1 AAATTATATAAAAAAATTAA
87660 AAATTATA
1 AAATTATA
87668 GAAACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTATATAAAAAAATTAA
Found at i:93007 original size:95 final size:94
Alignment explanation
Indices: 92866--93053 Score: 270
Period size: 95 Copynumber: 2.0 Consensus size: 94
92856 TTTAATAACT
* * * *
92866 AATAAATTAATTTAAATAACTTTATTAAATATGATTGATTGGATTTAGT-GTTTTTATGGTAAAT
1 AATAAATTAATTTAAACAACTTTATTAAATATGATTGATTGAATTTAATAGTTTTTATGATAAAT
* *
92930 GTTTTTTCTTTAAATGATTGATTGAATAAAC
66 -ATTTTT-TTTAAATGATTGATCGAATAAAC
* * *
92961 AATAAATTAATTTAGACAATTTTATTAAATATGATTGATTGAATTTAATATTTTTTATGATAAAT
1 AATAAATTAATTTAAACAACTTTATTAAATATGATTGATTGAATTTAATAGTTTTTATGATAAAT
93026 ATTTTTTTTAAATGATTGATCGAATAAA
66 ATTTTTTTTAAATGATTGATCGAATAAA
93054 AAAAAAACTT
Statistics
Matches: 83, Mismatches: 9, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
94 21 0.25
95 49 0.59
96 13 0.16
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (94 bp):
AATAAATTAATTTAAACAACTTTATTAAATATGATTGATTGAATTTAATAGTTTTTATGATAAAT
ATTTTTTTTAAATGATTGATCGAATAAAC
Found at i:105506 original size:28 final size:25
Alignment explanation
Indices: 105475--105543 Score: 59
Period size: 27 Copynumber: 2.6 Consensus size: 25
105465 TTGATATAAT
105475 AAATTAATTAAATATTAATTTAATTTAA
1 AAATT-ATTAAATATTAATTT--TTTAA
* *
105503 AAA-TATTAAAAAATTTATTTTTTAAA
1 AAATTATT-AAATATTAATTTTTT-AA
105529 AATATTATTAAATAT
1 AA-ATTATTAAATAT
105544 AAATATGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
25 3 0.09
26 7 0.21
27 17 0.50
28 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATTATTAAATATTAATTTTTTAA
Found at i:108205 original size:43 final size:45
Alignment explanation
Indices: 108122--108207 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 45
108112 AGATTTTGTA
*
108122 TAAAAAAAAAAAAGCAAATATGATTAGAACATATAATAAAATAGTT
1 TAAAAAAAAAAAAG-AAATATGATTAGAAAATATAATAAAATAGTT
108168 TAAAAAAAAAAAAG-AAT-TGATT-GAAAA-ATAAATTAAAATA
1 TAAAAAAAAAAAAGAAATATGATTAGAAAATAT-AA-TAAAATA
108208 TTAACCCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
41 2 0.05
42 6 0.16
43 12 0.32
44 3 0.08
46 14 0.38
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.23
Consensus pattern (45 bp):
TAAAAAAAAAAAAGAAATATGATTAGAAAATATAATAAAATAGTT
Found at i:109704 original size:65 final size:66
Alignment explanation
Indices: 109598--109726 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 66
109588 ATAAAACTTC
*
109598 TCAGCCTTGAATCCACCCTTCAACCTGCAATCTAAAGTTTAGTTAT-CAAGAGCCAAATTCCTGT
1 TCAGCCTTGAATCCACCCTTCAACCTGCAATCTAAAGTTTAGTCATCCAAGAGCCAAATTCCTGT
109662 T
66 T
* * *
109663 TCAGCCTTTAATCCACCCTTCAACCTGCAATCTAAATTTTAGTCATCCAAGAGCTAAATTCCTG
1 TCAGCCTTGAATCCACCCTTCAACCTGCAATCTAAAGTTTAGTCATCCAAGAGCCAAATTCCTG
109727 CACCAAGTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
65 43 0.73
66 16 0.27
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (66 bp):
TCAGCCTTGAATCCACCCTTCAACCTGCAATCTAAAGTTTAGTCATCCAAGAGCCAAATTCCTGT
T
Found at i:113337 original size:13 final size:14
Alignment explanation
Indices: 113289--113338 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
113279 ACTTAATCAA
*
113289 AATTAATTTTTTTC
1 AATTAAATTTTTTC
113303 AAATT-AATTTTTTC
1 -AATTAAATTTTTTC
**
113317 AAGAAAATTTTTT-
1 AATTAAATTTTTTC
113330 AATTAAATT
1 AATTAAATT
113339 CTCTAGTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 9 0.31
14 16 0.55
15 4 0.14
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (14 bp):
AATTAAATTTTTTC
Found at i:114579 original size:61 final size:61
Alignment explanation
Indices: 114484--114606 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
114474 TAATAGTTAG
114484 GACCCAAACCTTCCTGCATATTGAGGTGCCAACATAAAGCTTTAATCACTTGTTTCTTCAA
1 GACCCAAACCTTCCTGCATATTGAGGTGCCAACATAAAGCTTTAATCACTTGTTTCTTCAA
*
114545 GACCCAAACCTTCCTGCATATTGAGGTGCCAACATAGAGCTTTAATCACTTGTTTCTTCAA
1 GACCCAAACCTTCCTGCATATTGAGGTGCCAACATAAAGCTTTAATCACTTGTTTCTTCAA
114606 G
1 G
114607 TTGTTATCAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (61 bp):
GACCCAAACCTTCCTGCATATTGAGGTGCCAACATAAAGCTTTAATCACTTGTTTCTTCAA
Found at i:120511 original size:20 final size:21
Alignment explanation
Indices: 120478--120525 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
120468 TAAAAAACGA
120478 TTGAATCAATTTTTCT-ATTT
1 TTGAATCAATTTTTCTAATTT
*
120498 TTGAAT-AATTTTTTTTAATTT
1 TTGAATCAA-TTTTTCTAATTT
120519 TATGAAT
1 T-TGAAT
120526 TTTAATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 12 0.50
21 5 0.21
22 5 0.21
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (21 bp):
TTGAATCAATTTTTCTAATTT
Found at i:126562 original size:4 final size:4
Alignment explanation
Indices: 126553--126578 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
126543 ATAAGGTAAT
126553 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
126579 CACCCTTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:134781 original size:15 final size:15
Alignment explanation
Indices: 134763--134800 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
134753 CAAAAAAATT
134763 ATAAAAAATAAAAAA
1 ATAAAAAATAAAAAA
* *
134778 ATAAAAAATATATAA
1 ATAAAAAATAAAAAA
134793 A-AAAAAAT
1 ATAAAAAAT
134801 TATAAGATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
ATAAAAAATAAAAAA
Found at i:135078 original size:90 final size:89
Alignment explanation
Indices: 134969--135142 Score: 217
Period size: 90 Copynumber: 1.9 Consensus size: 89
134959 TTGAGGGCCT
* * * * *
134969 TTTTGATGTATTTTGAAAGTTCAAGTACCCAATTAAGTGTAAAATAAAA-GTAGAGGCTTAATTG
1 TTTTGATGCATTTTGAAAGTTCAAGTACCCAAGTAAGTGCAAAATAAAAGGAAGA-ACTTAATT-
135033 CTTTTTTTGAAAAAAATTGAAGACCTA
64 -TTTTTTTGAAAAAAATTGAAGACCTA
* * * *
135060 TTTT-ATGCATTTTGAAAGTTCAAGTATCCAAGTGAGTGCCAAATAAACGGAAGAACTTAATTTT
1 TTTTGATGCATTTTGAAAGTTCAAGTACCCAAGTAAGTGCAAAATAAAAGGAAGAACTTAATTTT
*
135124 TTTTTGAAAAAATTTGAAG
66 TTTTTGAAAAAAATTGAAG
135143 GCTTTTTATA
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
88 20 0.28
90 44 0.61
91 8 0.11
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (89 bp):
TTTTGATGCATTTTGAAAGTTCAAGTACCCAAGTAAGTGCAAAATAAAAGGAAGAACTTAATTTT
TTTTTGAAAAAAATTGAAGACCTA
Found at i:135317 original size:21 final size:23
Alignment explanation
Indices: 135265--135313 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
135255 TTTCAGACTT
* *
135265 AATATTTCATACAAATTCTCCTA
1 AATATTTTATACAAACTCTCCTA
135288 AATATTTTATACAAACTCTCCTA
1 AATATTTTATACAAACTCTCCTA
135311 AAT
1 AAT
135314 TTTAATTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (23 bp):
AATATTTTATACAAACTCTCCTA
Found at i:136706 original size:39 final size:39
Alignment explanation
Indices: 136639--136715 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
136629 TCAAAGCCTC
136639 AAACTTAGCCATAACATCTCCACCCATGATCTTATCACT
1 AAACTTAGCCATAACATCTCCACCCATGATCTTATCACT
* * ** *
136678 AAACTTAGCCATAAGATCTTCATTCATGATCTTTTCAC
1 AAACTTAGCCATAACATCTCCACCCATGATCTTATCAC
136716 CAGATGCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (39 bp):
AAACTTAGCCATAACATCTCCACCCATGATCTTATCACT
Found at i:139176 original size:23 final size:22
Alignment explanation
Indices: 139150--139200 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
139140 CATTTTATGT
139150 TTATATATTATAT-ACATAAATAA
1 TTATAT-TTATATAACATAAA-AA
*
139173 TTATATTTATCTAACATAAAAA
1 TTATATTTATATAACATAAAAA
139195 -TATATT
1 TTATATT
139201 AATGTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 6 0.23
22 7 0.27
23 13 0.50
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATATTTATATAACATAAAAA
Found at i:139179 original size:21 final size:20
Alignment explanation
Indices: 139152--139201 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
139142 TTTTATGTTT
139152 ATATATTATAT-ACATAAATA
1 ATATATTATATAACATAAA-A
*
139172 ATTATATTTATCTAACATAAAA
1 A-TATA-TTATATAACATAAAA
139194 ATATATTA
1 ATATATTA
139202 ATGTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.15
21 8 0.31
22 7 0.27
23 7 0.27
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATATTATATAACATAAAA
Found at i:171280 original size:32 final size:32
Alignment explanation
Indices: 171239--171310 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
171229 GGTGCTGTTT
** *
171239 AAATGACAATAAACCCTTCAACGTGGCCGATC
1 AAATGACAATAAAAACTCCAACGTGGCCGATC
* *
171271 AAATGACAATAAAAACTCCAACGTGGCCGGTT
1 AAATGACAATAAAAACTCCAACGTGGCCGATC
171303 AAATGACA
1 AAATGACA
171311 GGTCACCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.18
Consensus pattern (32 bp):
AAATGACAATAAAAACTCCAACGTGGCCGATC
Found at i:172328 original size:47 final size:47
Alignment explanation
Indices: 172274--172368 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
172264 TGCTTTTAGA
*
172274 AGGTTTGATCTATATGTTGAGAAAGCACATCTATTTTGCTCAGAACT
1 AGGTTTGATCTACATGTTGAGAAAGCACATCTATTTTGCTCAGAACT
*
172321 AGGTTTGATCTACGTGTTGAGAAAGCACATCTATTTTGCTCAGAACT
1 AGGTTTGATCTACATGTTGAGAAAGCACATCTATTTTGCTCAGAACT
172368 A
1 A
172369 CTATAACAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (47 bp):
AGGTTTGATCTACATGTTGAGAAAGCACATCTATTTTGCTCAGAACT
Found at i:185886 original size:27 final size:27
Alignment explanation
Indices: 185848--185902 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
185838 TGAAGAGTTT
*
185848 GTTTCTGTCTTCGGAGTCATCTAAAGG
1 GTTTCTGTCTTCAGAGTCATCTAAAGG
185875 GTTTCTGTCTTCAGAGTCATCTAAAGG
1 GTTTCTGTCTTCAGAGTCATCTAAAGG
185902 G
1 G
185903 GTCTATTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (27 bp):
GTTTCTGTCTTCAGAGTCATCTAAAGG
Found at i:186239 original size:61 final size:61
Alignment explanation
Indices: 186124--186327 Score: 212
Period size: 61 Copynumber: 3.3 Consensus size: 61
186114 AAACATCGAA
* * * * * * * * *
186124 AAAGGAACGCCTTTTTAGCAAATCTCT-GAACAGGAAATCCTTTATGGTAGGTATTGTATGT
1 AAAGGAACGCCTTTGTGGCAAATATATAG-ACAAGAAAGCCTTTGTGGCAAGTATTGTATGT
* * *
186185 AAAGGAACGCCTTTGTGGTAAATATATGGACAAGAAAGCCTTTGTGGCGAGTATTGTATGT
1 AAAGGAACGCCTTTGTGGCAAATATATAGACAAGAAAGCCTTTGTGGCAAGTATTGTATGT
* * * * *
186246 AAACGAACGCTTTTGTGGCAAATATCTAGACAGGAAAGCCTTTGTGGCAAGTATTGTATTT
1 AAAGGAACGCCTTTGTGGCAAATATATAGACAAGAAAGCCTTTGTGGCAAGTATTGTATGT
* * *
186307 AAAGGAATGCTTTTATGGCAA
1 AAAGGAACGCCTTTGTGGCAA
186328 TCCCTGTAAA
Statistics
Matches: 120, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
61 119 0.99
62 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (61 bp):
AAAGGAACGCCTTTGTGGCAAATATATAGACAAGAAAGCCTTTGTGGCAAGTATTGTATGT
Found at i:186293 original size:29 final size:29
Alignment explanation
Indices: 186187--186295 Score: 83
Period size: 29 Copynumber: 3.7 Consensus size: 29
186177 TTGTATGTAA
* * *
186187 AGGAACGCCTTTGTGGTAAATATATGGAC
1 AGGAAAGCCTTTGTGGCAAATATATAGAC
* * * * *
186216 AAGAAAGCCTTTGTGGCGAGTATTGTATGTAA
1 AGGAAAGCCTTTGTGGCAAATA-TATA-G-AC
* * * *
186248 ACGAACGCTTTTGTGGCAAATATCTAGAC
1 AGGAAAGCCTTTGTGGCAAATATATAGAC
186277 AGGAAAGCCTTTGTGGCAA
1 AGGAAAGCCTTTGTGGCAA
186296 GTATTGTATT
Statistics
Matches: 59, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
29 34 0.58
30 3 0.05
31 4 0.07
32 18 0.31
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (29 bp):
AGGAAAGCCTTTGTGGCAAATATATAGAC
Found at i:186349 original size:61 final size:61
Alignment explanation
Indices: 186174--186353 Score: 150
Period size: 61 Copynumber: 3.0 Consensus size: 61
186164 TTTATGGTAG
* * * * ** * * *
186174 GTATTGTATGTAAAGGAACGCCTTTGTGGTAAATATATGGACAAG-AAAGCCTTTGTGGCGA
1 GTATTGTATGTAAACGAACGCTTTTATGGCAAATACCTAGA-AAGCAAAACCTTTGTGGCAA
* * * * *
186235 GTATTGTATGTAAACGAACGCTTTTGTGGCAAATATCTAGACAGGAAAGCCTTTGTGGCAA
1 GTATTGTATGTAAACGAACGCTTTTATGGCAAATACCTAGAAAGCAAAACCTTTGTGGCAA
* * * *
186296 GTATTGTATTTAAAGGAATGCTTTTATGGC-AATCCCT-GTAAAGCAAACACCTTTGTGG
1 GTATTGTATGTAAACGAACGCTTTTATGGCAAATACCTAG-AAAGCAAA-ACCTTTGTGG
186354 TGAACTCTAT
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 13 0.13
61 86 0.86
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (61 bp):
GTATTGTATGTAAACGAACGCTTTTATGGCAAATACCTAGAAAGCAAAACCTTTGTGGCAA
Found at i:192213 original size:15 final size:14
Alignment explanation
Indices: 192193--192251 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
192183 CAATAGTAGG
*
192193 TTCTTTCTTTCTTTC
1 TTCTTTCCTTC-TTC
192208 TTCTTTTCCTTCTTC
1 TTC-TTTCCTTCTTC
*
192223 TTC--TCGTTCTTC
1 TTCTTTCCTTCTTC
192235 TTCTTTTCCTTCTTC
1 TTC-TTTCCTTCTTC
192250 TT
1 TT
192252 TCTCCTCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 11 0.30
15 19 0.51
16 7 0.19
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.68
Consensus pattern (14 bp):
TTCTTTCCTTCTTC
Found at i:192215 original size:12 final size:12
Alignment explanation
Indices: 192200--192257 Score: 62
Period size: 12 Copynumber: 4.5 Consensus size: 12
192190 AGGTTCTTTC
*
192200 TTTCTTTCTTCT
1 TTTCCTTCTTCT
192212 TTTCCTTCTTCT
1 TTTCCTTCTTCT
*
192224 TCTCGTTCTTCTTCT
1 T-T--TCCTTCTTCT
192239 TTTCCTTCTTCT
1 TTTCCTTCTTCT
192251 TTCTCCT
1 TT-TCCT
192258 CATTAGACTC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 23 0.59
13 5 0.13
14 1 0.03
15 10 0.26
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.66
Consensus pattern (12 bp):
TTTCCTTCTTCT
Found at i:202069 original size:19 final size:19
Alignment explanation
Indices: 202045--202083 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
202035 TAACAGGTTG
202045 TTTACATGATTGTGCCAGC
1 TTTACATGATTGTGCCAGC
*
202064 TTTACATGATTGTGTCAGC
1 TTTACATGATTGTGCCAGC
202083 T
1 T
202084 CCTCTGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (19 bp):
TTTACATGATTGTGCCAGC
Found at i:212885 original size:3 final size:3
Alignment explanation
Indices: 212877--212904 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
212867 ACAGACCCAA
212877 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
212905 GGGTTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:213562 original size:22 final size:23
Alignment explanation
Indices: 213518--213561 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
213508 GATTTTCATT
*
213518 AAAAAAAAAATTTAGATTTTTTA
1 AAAAAAAAAATATAGATTTTTTA
213541 AAAAATAAAAATAT-GATTTTT
1 AAAAA-AAAAATATAGATTTTT
213562 AGTGATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
AAAAAAAAAATATAGATTTTTTA
Found at i:214278 original size:25 final size:25
Alignment explanation
Indices: 214207--214279 Score: 62
Period size: 25 Copynumber: 2.9 Consensus size: 25
214197 ATATTTTTAA
* * *
214207 ATTTATTCATATTTGTATAATT-TTT
1 ATTTATTCTTATTT-CATATTTATTT
*
214232 ATTTATTCTTATTTCATCTTTATTT
1 ATTTATTCTTATTTCATATTTATTT
214257 ATTTAATGTC-TATTT-ATATTTAT
1 ATTT-AT-TCTTATTTCATATTTAT
214280 GTTTTTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 4 0.10
25 27 0.68
26 7 0.17
27 2 0.05
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (25 bp):
ATTTATTCTTATTTCATATTTATTT
Found at i:227269 original size:21 final size:21
Alignment explanation
Indices: 227237--227283 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
227227 GGTTGGTACG
* *
227237 AAGGAAAGAAAGAGGAAGCAC
1 AAGGAAAGAAAGAAGAAACAC
227258 AAGGACAA-AAAGAAGAAACAC
1 AAGGA-AAGAAAGAAGAAACAC
227279 AAGGA
1 AAGGA
227284 GGAAGGAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.62, C:0.11, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGGAAAGAAAGAAGAAACAC
Found at i:229952 original size:35 final size:35
Alignment explanation
Indices: 229906--229976 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
229896 TAGTGGACAT
229906 AGTGCGAAGTATGCTTACTTGCTCTAAACTACCTA
1 AGTGCGAAGTATGCTTACTTGCTCTAAACTACCTA
229941 AGTGCGAAGTATGCTTACTTGCTCTAAACTACCTA
1 AGTGCGAAGTATGCTTACTTGCTCTAAACTACCTA
229976 A
1 A
229977 TTCCTTATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (35 bp):
AGTGCGAAGTATGCTTACTTGCTCTAAACTACCTA
Found at i:234290 original size:20 final size:20
Alignment explanation
Indices: 234253--234290 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
234243 AGCTAAATTC
*
234253 GACGTGCTCATCAGTGGTTT
1 GACGTGCTCATCAATGGTTT
234273 GACGTGCTCGA-CAATGGT
1 GACGTGCTC-ATCAATGGT
234291 GTTACGACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (20 bp):
GACGTGCTCATCAATGGTTT
Found at i:238040 original size:15 final size:15
Alignment explanation
Indices: 238020--238048 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
238010 TTTATATATA
238020 TTTATTTATTATTTG
1 TTTATTTATTATTTG
238035 TTTATTTATTATTT
1 TTTATTTATTATTT
238049 ATTAACATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTATTTATTATTTG
Found at i:242770 original size:15 final size:15
Alignment explanation
Indices: 242750--242780 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
242740 CACTATTTGA
242750 TGAATACTAAACTTT
1 TGAATACTAAACTTT
242765 TGAATACTAAACTTT
1 TGAATACTAAACTTT
242780 T
1 T
242781 ACCTTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (15 bp):
TGAATACTAAACTTT
Found at i:251131 original size:15 final size:14
Alignment explanation
Indices: 251113--251161 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
251103 TTGTGTGATA
251113 TTATTATGTGTTGTG
1 TTATT-TGTGTTGTG
*
251128 TTATTTGTG-TGATT
1 TTATTTGTGTTG-TG
251142 TTAATTTGTGTTGTG
1 TT-ATTTGTGTTGTG
251157 TTATT
1 TTATT
251162 GCATGTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 2 0.07
14 10 0.34
15 15 0.52
16 2 0.07
ACGTcount: A:0.14, C:0.00, G:0.22, T:0.63
Consensus pattern (14 bp):
TTATTTGTGTTGTG
Found at i:251136 original size:29 final size:29
Alignment explanation
Indices: 251103--251161 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
251093 GTTCCACAGC
251103 TTGTGTGATATT-ATTATGTGTTGTGTTAT
1 TTGTGTGATATTAATT-TGTGTTGTGTTAT
*
251132 TTGTGTGATTTTAATTTGTGTTGTGTTAT
1 TTGTGTGATATTAATTTGTGTTGTGTTAT
251161 T
1 T
251162 GCATGTTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.61
Consensus pattern (29 bp):
TTGTGTGATATTAATTTGTGTTGTGTTAT
Found at i:251704 original size:17 final size:17
Alignment explanation
Indices: 251682--251715 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
251672 AGTTATTTAG
251682 TGGTTTTCAAATTATTT
1 TGGTTTTCAAATTATTT
*
251699 TGGTTTTCATATTATTT
1 TGGTTTTCAAATTATTT
251716 GGGAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.62
Consensus pattern (17 bp):
TGGTTTTCAAATTATTT
Found at i:257043 original size:17 final size:17
Alignment explanation
Indices: 257021--257059 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
257011 AGGTGGAGAA
* * *
257021 CTTGTTCGTTGAGAGTT
1 CTTGTTAGTAGAGAATT
257038 CTTGTTAGTAGAGAATT
1 CTTGTTAGTAGAGAATT
257055 CTTGT
1 CTTGT
257060 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTAGTAGAGAATT
Found at i:257260 original size:49 final size:49
Alignment explanation
Indices: 257188--257291 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
257178 GAATAGGTCA
* *
257188 TCTATTTTATTTTAATTAGAATAAGGTGTTTCAGCCTTACTACGTTACT
1 TCTATTTTATTTTAATTAGAATAAAGTGTTTCAACCTTACTACGTTACT
*
257237 TCTATTTTATTTTAATTAGAATAAAGTGTTTCAACCTTACTACGTTTCT
1 TCTATTTTATTTTAATTAGAATAAAGTGTTTCAACCTTACTACGTTACT
*
257286 TTTATT
1 TCTATT
257292 AGTTGTTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (49 bp):
TCTATTTTATTTTAATTAGAATAAAGTGTTTCAACCTTACTACGTTACT
Found at i:257308 original size:49 final size:49
Alignment explanation
Indices: 257188--257322 Score: 166
Period size: 49 Copynumber: 2.8 Consensus size: 49
257178 GAATAGGTCA
* *
257188 TCTATTTTATTTTAATTAGAATAAGGTGTTTCAGCCTTACTACGTTACT
1 TCTATATTATTTTAATTAGAATAAGGTGTTTCAACCTTACTACGTTACT
* * *
257237 TCTATTTTATTTTAATTAGAATAAAGTGTTTCAACCTTACTACGTTTCT
1 TCTATATTATTTTAATTAGAATAAGGTGTTTCAACCTTACTACGTTACT
* * *
257286 T-T-TATTAGTTGTTGATTGGAATAAGGTTTTTCAACCT
1 TCTATATTA-TT-TTAATTAGAATAAGGTGTTTCAACCT
257323 ATAAATAGGC
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
47 4 0.05
48 3 0.04
49 69 0.91
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.48
Consensus pattern (49 bp):
TCTATATTATTTTAATTAGAATAAGGTGTTTCAACCTTACTACGTTACT
Found at i:259819 original size:18 final size:18
Alignment explanation
Indices: 259790--259824 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
259780 CTTGCTCTCC
259790 TTTTATCTTTAT-CTTTT
1 TTTTATCTTTATGCTTTT
259807 TTTTATGCTTTATGCTTT
1 TTTTAT-CTTTATGCTTT
259825 ACGCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTATCTTTATGCTTTT
Found at i:261783 original size:4 final size:5
Alignment explanation
Indices: 261757--261785 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
261747 CATAGATACG
261757 ATTTT ATTTT ATTTT ATTTT A-TTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
261786 TCGTATTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:261786 original size:15 final size:15
Alignment explanation
Indices: 261757--261785 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
261747 CATAGATACG
261757 ATTTTATTTTATTTT
1 ATTTTATTTTATTTT
261772 ATTTTA-TTTATTTT
1 ATTTTATTTTATTTT
261786 TCGTATTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTATTTTATTTT
Found at i:262718 original size:79 final size:78
Alignment explanation
Indices: 262587--262742 Score: 240
Period size: 79 Copynumber: 2.0 Consensus size: 78
262577 CAATGAGTCA
* * *
262587 TGTCTCTTCATTAGAATCTGATGTAGTTGAAAAGGCATGACATTTCTCCTTAATGAAGATTTATT
1 TGTCTCTTCATTAGAATCTGATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGACTTA-T
*
262652 GTATCCTTAATGTG
65 GTAACCTTAATGTG
* **
262666 TGTCTCTTCATTAGGATCTGATGTAGCTAAAAAGGCATGGTATTTCTCCTTAATGAAGACTTATG
1 TGTCTCTTCATTAGAATCTGATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGACTTATG
262731 TAACCTTAATGT
66 TAACCTTAATGT
262743 TTTTATTGGT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 13 0.19
79 57 0.81
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (78 bp):
TGTCTCTTCATTAGAATCTGATGTAGCTAAAAAGGCATGACATTTCTCCTTAATGAAGACTTATG
TAACCTTAATGTG
Found at i:263113 original size:48 final size:48
Alignment explanation
Indices: 262997--263114 Score: 182
Period size: 48 Copynumber: 2.5 Consensus size: 48
262987 AAAACACTCA
* *
262997 TAACAAACAAAACATTTAATAATGCAGATTACTAAACAAAGATGCATT
1 TAACAAACAAAACACTTAATGATGCAGATTACTAAACAAAGATGCATT
* * *
263045 TAACAAACAAGACACTTAATGATGTAGATTATTAAACAAAGATGCATT
1 TAACAAACAAAACACTTAATGATGCAGATTACTAAACAAAGATGCATT
*
263093 TAATAAACAAAACACTTAATGA
1 TAACAAACAAAACACTTAATGA
263115 AGCATAATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (48 bp):
TAACAAACAAAACACTTAATGATGCAGATTACTAAACAAAGATGCATT
Found at i:268184 original size:79 final size:78
Alignment explanation
Indices: 268053--268210 Score: 255
Period size: 79 Copynumber: 2.0 Consensus size: 78
268043 CAATGAATCA
*
268053 TGTCTCTTCATTAGAATCTGATGTAGTTGAAAAAGCATGATATTTCTCCTTAATGAAGACTTATT
1 TGTCTCTTCATTAGAATCTGATGTAGCTGAAAAAGCATGATATTTCTCCTTAATGAAGACTTA-T
*
268118 GTATCCTTAATGTG
65 GTAACCTTAATGTG
* *
268132 TGTCTCTTCATTAGGATCTGATGTAGCTGAAAAGGCAT-AGTATTTCTCCTTAATGAAGACTTAT
1 TGTCTCTTCATTAGAATCTGATGTAGCTGAAAAAGCATGA-TATTTCTCCTTAATGAAGACTTAT
268196 GTAACCTTAATGTG
65 GTAACCTTAATGTG
268210 T
1 T
268211 TTATTGGTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
78 16 0.22
79 58 0.78
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (78 bp):
TGTCTCTTCATTAGAATCTGATGTAGCTGAAAAAGCATGATATTTCTCCTTAATGAAGACTTATG
TAACCTTAATGTG
Found at i:268575 original size:48 final size:48
Alignment explanation
Indices: 268459--268576 Score: 164
Period size: 48 Copynumber: 2.5 Consensus size: 48
268449 CTTAAAACAC
* * * *
268459 TAACAAACAATACATTTAATAATGCAGATTACTAAATAAAGATGCATT
1 TAACAAACAAAACACTTAATGATGCAGATTACTAAACAAAGATGCATT
* * *
268507 TAACAAACAAAACACTTAATGATGTAGATTATTAAACAAAGTTGCATT
1 TAACAAACAAAACACTTAATGATGCAGATTACTAAACAAAGATGCATT
*
268555 TAACAAACAAAACAGTTAATGA
1 TAACAAACAAAACACTTAATGA
268577 AGCATAATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (48 bp):
TAACAAACAAAACACTTAATGATGCAGATTACTAAACAAAGATGCATT
Found at i:272069 original size:22 final size:23
Alignment explanation
Indices: 272044--272087 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
272034 AAATAGTCAA
*
272044 AATTACCAGTGTAA-TAAAAGTT
1 AATTACCAGTGCAACTAAAAGTT
**
272066 AATTGTCAGTGCAACTAAAAGT
1 AATTACCAGTGCAACTAAAAGT
272088 AAATCAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (23 bp):
AATTACCAGTGCAACTAAAAGTT
Found at i:277356 original size:13 final size:13
Alignment explanation
Indices: 277324--277365 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
277314 TTAGCAAACA
277324 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
*
277337 TTCTTTTC-TCTT
1 TTTTTTTCTTCTT
*
277349 TTATTTTTTTTCTT
1 TT-TTTTTCTTCTT
277363 TTT
1 TTT
277366 CTCAATTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 6 0.25
13 12 0.50
14 6 0.25
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:277378 original size:29 final size:29
Alignment explanation
Indices: 277324--277379 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
277314 TTAGCAAACA
*
277324 TTTTTTTCTTCTTTTCTTTTCTCTTTTAT
1 TTTTTTTCTTCTTTTCATTTCTCTTTTAT
277353 TTTTTTTCTT-TTTCTCAATTTC-CTTTT
1 TTTTTTTCTTCTTT-TC-ATTTCTCTTTT
277380 CTAAGTGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.12
29 17 0.71
30 4 0.17
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTTTTCTTCTTTTCATTTCTCTTTTAT
Found at i:278010 original size:16 final size:17
Alignment explanation
Indices: 277978--278011 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
277968 GTGACAAAAT
*
277978 AAAATGCATAGACACTA
1 AAAATGCATAGAAACTA
277995 AAAATGCATA-AAACTA
1 AAAATGCATAGAAACTA
278011 A
1 A
278012 CTAAAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.59, C:0.15, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAATGCATAGAAACTA
Found at i:278435 original size:21 final size:21
Alignment explanation
Indices: 278409--278453 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
278399 CGGCAGTTCT
278409 TTCTCTTTATT-TTCTCTT-TCC
1 TTCTCTTT-TTCTTCT-TTATCC
278430 TTCTCTTTTTCTTCTTTATCC
1 TTCTCTTTTTCTTCTTTATCC
278451 TTC
1 TTC
278454 AACTGATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (21 bp):
TTCTCTTTTTCTTCTTTATCC
Found at i:280312 original size:20 final size:21
Alignment explanation
Indices: 280287--280325 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
280277 GCAAGGAATT
280287 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
280307 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
280326 TATCAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:288215 original size:15 final size:16
Alignment explanation
Indices: 288197--288226 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
288187 AAATTGAAAA
288197 GAAACAAATA-AAAGT
1 GAAACAAATACAAAGT
288212 GAAACAAATACAAAG
1 GAAACAAATACAAAG
288227 AAATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.10, G:0.13, T:0.10
Consensus pattern (16 bp):
GAAACAAATACAAAGT
Found at i:293854 original size:15 final size:15
Alignment explanation
Indices: 293834--293863 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
293824 AAGAATTCTG
*
293834 AAAAAAGTTAACAAA
1 AAAAAAGTAAACAAA
293849 AAAAAAGTAAACAAA
1 AAAAAAGTAAACAAA
293864 TTAGTAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAAAAGTAAACAAA
Found at i:297704 original size:23 final size:23
Alignment explanation
Indices: 297677--298122 Score: 615
Period size: 23 Copynumber: 19.3 Consensus size: 23
297667 ATCTTAATTC
*
297677 TTTAAGCACAAATCACTTTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
297700 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
297723 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
297746 TTTAATCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
297769 TTTTAGCACAAAAGCATATTAATA
1 TTTAAGCAC-AAATCACATTAATA
*
297793 TTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
297816 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
297839 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
297862 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
297885 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
297908 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
297931 GTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
297954 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
297977 CTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* **
298000 TTTAATC-CTAAATCATTTTAATA
1 TTTAAGCAC-AAATCACATTAATA
*
298023 TTTAAGTACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
** *
298046 TTTAAATATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
298069 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
298092 TTTAAGTACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
298115 TTTAAGCA
1 TTTAAGCA
298123 TGGATATAAG
Statistics
Matches: 369, Mismatches: 51, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
22 1 0.00
23 348 0.94
24 20 0.05
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:299272 original size:27 final size:30
Alignment explanation
Indices: 299204--299273 Score: 74
Period size: 32 Copynumber: 2.4 Consensus size: 30
299194 TTAACTCACT
299204 AATTGGTACCTAAATTATGCTATTTTTTCCCA
1 AATTGGTACCTAAATTA--CTATTTTTTCCCA
** *
299236 TCTTGATACCTAAATTA-T-TTTTTT-CCA
1 AATTGGTACCTAAATTACTATTTTTTCCCA
299263 AATTGGTACCT
1 AATTGGTACCT
299274 CCGTTAGTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
27 11 0.34
28 6 0.19
29 1 0.03
32 14 0.44
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.46
Consensus pattern (30 bp):
AATTGGTACCTAAATTACTATTTTTTCCCA
Found at i:299800 original size:30 final size:30
Alignment explanation
Indices: 299766--299837 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
299756 TTAGATACTC
* *
299766 ATTTTTTCGAAAAATGAGAGAAATATGCCA
1 ATTTTATCGAAAAATGAGAGAAATAGGCCA
** * * *
299796 ATTTTAAAGAAAAATTAGGGAATTAGGCCA
1 ATTTTATCGAAAAATGAGAGAAATAGGCCA
299826 ATTTTATCGAAA
1 ATTTTATCGAAA
299838 TTTAGGGAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (30 bp):
ATTTTATCGAAAAATGAGAGAAATAGGCCA
Found at i:301188 original size:30 final size:30
Alignment explanation
Indices: 301092--301193 Score: 100
Period size: 32 Copynumber: 3.4 Consensus size: 30
301082 GTTTTAGTTT
* * *
301092 CTTTAAAAGTTGGTACAAAA-ATTTTGGAC
1 CTTTAAAAGTTGATAAAAAATATTTTTGAC
* * *
301121 CTTTAAAAGTT-AAAACAAAATTTTTTTTGGGC
1 CTTTAAAAGTTGATAA-AAAA-TATTTTT-GAC
*
301153 CTTTAAAAGTTGATAAAAAATATTTTTGTC
1 CTTTAAAAGTTGATAAAAAATATTTTTGAC
301183 CTTTAAAAGTT
1 CTTTAAAAGTT
301194 AAATTTTTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
28 1 0.02
29 15 0.25
30 13 0.22
31 10 0.17
32 17 0.29
33 3 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (30 bp):
CTTTAAAAGTTGATAAAAAATATTTTTGAC
Found at i:301190 original size:55 final size:55
Alignment explanation
Indices: 301130--301233 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 55
301120 CCTTTAAAAG
*
301130 TTAAAA-CAAAATTTTTTTTGGGCCT-TTAAAAGTT-GATAAAAAATATTTTTGTCCT
1 TTAAAAGCAAAA--TTTTTTGGGCCTCTTAAAAATTAGA-AAAAAATATTTTTGTCCT
** *
301185 TTAAAAGTTAAATTTTTTGGGCCTCTTAAAAATTAGAAAACAATATTTT
1 TTAAAAGCAAAATTTTTTGGGCCTCTTAAAAATTAGAAAAAAATATTTT
301234 GGACCTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
54 12 0.29
55 25 0.60
56 5 0.12
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (55 bp):
TTAAAAGCAAAATTTTTTGGGCCTCTTAAAAATTAGAAAAAAATATTTTTGTCCT
Found at i:303791 original size:29 final size:33
Alignment explanation
Indices: 303722--303804 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 33
303712 TTTTTTAAAA
**
303722 ATTTTAAAATTTTAAATTAATAAAAATAAAATTAT
1 ATTTTAATCTTTTAAA--AATAAAAATAAAATTAT
303757 ATTTT-ATCTTTTAAAAATAAAAA-AAAATT-T
1 ATTTTAATCTTTTAAAAATAAAAATAAAATTAT
*
303787 A-TTTAATTTTTTAAAAAT
1 ATTTTAATCTTTTAAAAAT
303805 TGTTAGTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 3 0.07
30 14 0.32
31 6 0.14
32 8 0.18
34 8 0.18
35 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (33 bp):
ATTTTAATCTTTTAAAAATAAAAATAAAATTAT
Found at i:303799 original size:30 final size:32
Alignment explanation
Indices: 303731--303804 Score: 98
Period size: 30 Copynumber: 2.3 Consensus size: 32
303721 AATTTTAAAA
*
303731 TTTTAAATTAATAAAAATAAAATTATATTTTATC
1 TTTTAAA--AATAAAAATAAAATTATATTTAATC
*
303765 TTTTAAAAATAAAAA-AAAATT-TATTTAATT
1 TTTTAAAAATAAAAATAAAATTATATTTAATC
303795 TTTTAAAAAT
1 TTTTAAAAAT
303805 TGTTAGTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 17 0.45
31 6 0.16
32 8 0.21
34 7 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (32 bp):
TTTTAAAAATAAAAATAAAATTATATTTAATC
Found at i:310012 original size:3 final size:3
Alignment explanation
Indices: 310004--310039 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
309994 CTACTTCTTT
*
310004 ATC ATC ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
310040 GTTATTGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:310050 original size:3 final size:3
Alignment explanation
Indices: 310044--310081 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
310034 ATCATCGTTA
*
310044 TTG TTG TTG TTG CTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
310082 ATTTTAACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.32, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:310344 original size:31 final size:30
Alignment explanation
Indices: 310299--310377 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
310289 AATGTGTATG
*
310299 ATTGAATCAAAATTAAAGATTCATATATACA
1 ATTGAA-CCAAATTAAAGATTCATATATACA
* * *
310330 TTTGAACCACAATTAAAAATTCATGTATACA
1 ATTGAACCA-AATTAAAGATTCATATATACA
* *
310361 ATTGTACTAAATTAAAG
1 ATTGAACCAAATTAAAG
310378 TTTGTGTATC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 9 0.23
31 30 0.77
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (30 bp):
ATTGAACCAAATTAAAGATTCATATATACA
Found at i:310688 original size:18 final size:18
Alignment explanation
Indices: 310655--310689 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
310645 TAAATTATTT
310655 TTTATAAAATTAAAAATA
1 TTTATAAAATTAAAAATA
310673 TTTA-AAAATTATAAAAT
1 TTTATAAAATTA-AAAAT
310690 CTTATTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTATAAAATTAAAAATA
Found at i:312520 original size:52 final size:52
Alignment explanation
Indices: 312447--312592 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 52
312437 AAGCCGTAAG
* * *
312447 TTAAGAGGTCCGATGACTCTGTCTCATCGTGAGCATATGAATCCTTTACGGA
1 TTAAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCATTACGGA
* * *
312499 TTAAGAGGTCCGATGAATCTGTGTCATCATGAGTATATGAATTCATTACGGA
1 TTAAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCATTACGGA
* * * *
312551 TTATGAGGTTCGATGGCTATGTGTCATCGTGAGTATATGAAT
1 TTAAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAAT
312593 GGAGAGAAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 82 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (52 bp):
TTAAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCATTACGGA
Found at i:315363 original size:18 final size:16
Alignment explanation
Indices: 315330--315372 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
315320 TCAAACTTAA
*
315330 AATAAATATCATAATT
1 AATAATTATCATAATT
315346 AATAATTATCATTGAATT
1 AATAATTATCA-T-AATT
*
315364 AATTATTAT
1 AATAATTAT
315373 TATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 10 0.43
17 1 0.04
18 12 0.52
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (16 bp):
AATAATTATCATAATT
Found at i:321568 original size:29 final size:30
Alignment explanation
Indices: 321535--321608 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 30
321525 GCAAAATATG
321535 GAATAATTTATTCAATTTAAAAT-CAATAA
1 GAATAATTTATTCAATTTAAAATCCAATAA
* *
321564 GAATAATTTATTTAATTTAAAATCCATTAA
1 GAATAATTTATTCAATTTAAAATCCAATAA
321594 -AATAATTTATTCAAT
1 GAATAATTTATTCAAT
321609 CACTCAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 36 0.88
30 5 0.12
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (30 bp):
GAATAATTTATTCAATTTAAAATCCAATAA
Found at i:329127 original size:12 final size:12
Alignment explanation
Indices: 329110--329134 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
329100 TATGAAGTAT
329110 ACGTGAATTGTC
1 ACGTGAATTGTC
329122 ACGTGAATTGTC
1 ACGTGAATTGTC
329134 A
1 A
329135 TATTTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (12 bp):
ACGTGAATTGTC
Found at i:330570 original size:17 final size:17
Alignment explanation
Indices: 330549--330584 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
330539 AATTTTTTTA
*
330549 AAAAATATTATAAATTAT
1 AAAAAT-TTAAAAATTAT
330567 AAAAATTTAAAAATTAT
1 AAAAATTTAAAAATTAT
330584 A
1 A
330585 TATATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATTTAAAAATTAT
Found at i:330588 original size:2 final size:2
Alignment explanation
Indices: 330581--330618 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
330571 ATTTAAAAAT
330581 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
330619 AATTTAACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:341028 original size:24 final size:23
Alignment explanation
Indices: 341001--341074 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 23
340991 CAAATCAGGC
*
341001 AAAAGAAAGAAAAAAAGAAACGGA
1 AAAAGAGAGAAAAAAAGAAA-GGA
*
341025 AAAAGAGAGAAAAAAAAAAAAGGAA
1 AAAAGAGAG-AAAAAAAGAAAGG-A
* *
341050 AAAAGAGAGAGAAAAAGGAAGGA
1 AAAAGAGAGAAAAAAAGAAAGGA
341073 AA
1 AA
341075 TATTTTTCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
23 3 0.07
24 20 0.47
25 20 0.47
ACGTcount: A:0.74, C:0.01, G:0.24, T:0.00
Consensus pattern (23 bp):
AAAAGAGAGAAAAAAAGAAAGGA
Found at i:350301 original size:3 final size:3
Alignment explanation
Indices: 350293--350328 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
350283 CTCTATTTAT
350293 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
350329 GGTAAATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:353320 original size:6 final size:6
Alignment explanation
Indices: 353309--353341 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
353299 TCTATCCCCA
353309 GCATGG GCATGG GCATGG GCATGG GCATGG GCA
1 GCATGG GCATGG GCATGG GCATGG GCATGG GCA
353342 GAGCAACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.48, T:0.15
Consensus pattern (6 bp):
GCATGG
Found at i:360056 original size:28 final size:29
Alignment explanation
Indices: 359993--360049 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
359983 TATTGGTTAC
* * *
359993 TAAAA-AATAATTTATTTAAATTATAAAA
1 TAAAATAATTATTTAATTAAATTACAAAA
360021 TAAAATAATTATTTAATT-AATTACAAAA
1 TAAAATAATTATTTAATTAAATTACAAAA
360049 T
1 T
360050 TATATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAATAATTATTTAATTAAATTACAAAA
Done.