Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011389.1 Kokia drynarioides strain JFW-HI SEQ_126371, 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: 134514
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:7329 original size:230 final size:232
Alignment explanation
Indices: 6912--7365 Score: 643
Period size: 230 Copynumber: 2.0 Consensus size: 232
6902 GATCTGGTGC
* * * * *
6912 CATGAGTGTAGTATATTCGTTTGTAAATTTGTATTTTTTACGGTAAAGTTGTTGTAACTTAATGA
1 CATGAGTGTAGTATATTCATTTGTAAACTTGTATTTTTTACGATAAAGTTGTCGCAACTTAATGA
*
6977 AATTAAAATTGAGTTGAGAAATTTATTTAATTGAAAAAATAATTTATTTAATTACATTAATTAAT
66 AATTAAAATTGAGTTGAGAAATTTATTTAATTGAAAAAATAATTTATCTAATTA-ATTAATTAAT
** *
7042 AAATAATATTTATTTTGGGAAATAGAAAACATGTATTGAGTTGGATTAAATTATACAATGTT-AG
130 AAATAATATTTATTTTAAGAAATAGAAAACATGTATTGAGTTGGATTAAATTATACAATATTGAG
*
7106 TTAAAAGTCTAAGAAGCACATATAATTGAGTTTGTAAA
195 TTAAAAGTCTAAGAAACACATATAATTGAGTTTGTAAA
* **
7144 CATGAGTGTAGTATATTCATTTGTAAACTTGTAATTCTTTTATGATAAAGTTGTCGCGTCTTAAT
1 CATGAGTGTAGTATATTCATTTGTAAACTTGT-ATT-TTTTACGATAAAGTTGTCGCAACTTAAT
*
7209 GGAAA-TAAAATTGAGTTGA-AAATTTATTTAATTGGAAAAATTAATTTATCTAATT-A-T-ATT
64 -GAAATTAAAATTGAGTTGAGAAATTTATTTAATT-GAAAAAATAATTTATCTAATTAATTAATT
* * *
7269 AATTAATAATATTTATTTTAAGAAATAGAAATCGTGTATTG-GATTGGATTAAATTATACAATAT
127 AATAAATAATATTTATTTTAAGAAATAGAAAACATGTATTGAG-TTGGATTAAATTATACAATAT
*
7333 TGAGTTAAAAGTTTAAGAAACACATATAATTGA
191 TGAGTTAAAAGTCTAAGAAACACATATAATTGA
7366 ACCCAATACA
Statistics
Matches: 198, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
229 1 0.01
230 60 0.30
231 30 0.15
232 31 0.16
233 17 0.09
234 55 0.28
235 4 0.02
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.41
Consensus pattern (232 bp):
CATGAGTGTAGTATATTCATTTGTAAACTTGTATTTTTTACGATAAAGTTGTCGCAACTTAATGA
AATTAAAATTGAGTTGAGAAATTTATTTAATTGAAAAAATAATTTATCTAATTAATTAATTAATA
AATAATATTTATTTTAAGAAATAGAAAACATGTATTGAGTTGGATTAAATTATACAATATTGAGT
TAAAAGTCTAAGAAACACATATAATTGAGTTTGTAAA
Found at i:9629 original size:21 final size:21
Alignment explanation
Indices: 9587--9627 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9577 TATCTATAAA
9587 AGACTAACCCAAATCTATTTT
1 AGACTAACCCAAATCTATTTT
* *
9608 AGACTCACCCATAT-TATTTT
1 AGACTAACCCAAATCTATTTT
9628 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (21 bp):
AGACTAACCCAAATCTATTTT
Found at i:9676 original size:21 final size:22
Alignment explanation
Indices: 9640--9681 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
9630 ATTTTTTAAA
*
9640 AATATTTATATTATTTTATATT
1 AATATTTATATAATTTTATATT
9662 AATATTTA-ATAATTTTATAT
1 AATATTTATATAATTTTATAT
9682 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AATATTTATATAATTTTATATT
Found at i:15907 original size:60 final size:58
Alignment explanation
Indices: 15843--16177 Score: 216
Period size: 59 Copynumber: 5.6 Consensus size: 58
15833 TACTCGGGGA
*
15843 TAAAATGGTAATTTTGGGAAAATTCAGGGTCAAAAAATGAAAATTTTAGACA-TCCGAGGG
1 TAAAATGGTAATTTTGGGAAAATTCGGGGT--AAAAATGAAAATTTTAGA-AGTCCGAGGG
* * * * * *
15903 TAAAATGGTAATTTTTGGATAGTTCGGGGTTTAAAATGAGATTTTTAGATA-TCC-AGGG
1 TAAAATGGTAATTTTGGGAAAATTCGGGG-TAAAAATGAAAATTTTAGA-AGTCCGAGGG
* * * * * *
15961 ATAAAATGGTATTTTTGGAAAAAATTTGGGGTAAAAATG-GAATTTTAGGAAGTTCGGGGG
1 -TAAAATGGTAATTTTGG-GAAAATTCGGGGTAAAAATGAAAATTTTA-GAAGTCCGAGGG
* * * * * * * *
16021 TAAAATGGTGACTTTT-AGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGG
1 TAAAATGGT-AATTTTGGGAAAATTCGGGGT-AAAAATGAAAATTTTAGAAGTCCGAGGG
* * * * * * *
16080 TAAAATGGTAATTTTTGGAAAAGAAATCGAGGTAAAAAATGAAATTTTTGGAAGTTCGGGGG
1 TAAAATGGTAA-TTTTGG-GAA-AATTCGGGGT-AAAAATGAAAATTTTAGAAGTCCGAGGG
* *
16142 T-AAATGGTAATTTT-GGAAAGTTTGAGGGTAAAAATG
1 TAAAATGGTAATTTTGGGAAAATTCG-GGGTAAAAATG
16178 TAATATTGGA
Statistics
Matches: 222, Mismatches: 39, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
57 10 0.05
58 27 0.12
59 86 0.39
60 50 0.23
61 12 0.05
62 37 0.17
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (58 bp):
TAAAATGGTAATTTTGGGAAAATTCGGGGTAAAAATGAAAATTTTAGAAGTCCGAGGG
Found at i:15932 original size:29 final size:29
Alignment explanation
Indices: 15900--16333 Score: 183
Period size: 29 Copynumber: 14.8 Consensus size: 29
15890 AGACATCCGA
*
15900 GGGTAAAATGGTAATTTTTGGATAGTTCG
1 GGGTAAAATGGTAATTTTTGGAAAGTTCG
* * *
15929 GGGTTTAAAAT-G-AGATTTTTAGATA-TCCAG
1 GGG--TAAAATGGTA-ATTTTTGGAAAGTTC-G
* * *
15959 GGATAAAATGGT-ATTTTTGGAAAAAATTTG
1 GGGTAAAATGGTAATTTTTGG--AAAGTTCG
*
15989 GGGTAAAAATGG-AATTTTAGG-AAGTTCGG
1 GGGT-AAAATGGTAATTTTTGGAAAGTTC-G
* * * **
16018 GGGTAAAATGGTGACTTTTAGAAAAATCG
1 GGGTAAAATGGTAATTTTTGGAAAGTTCG
*
16047 AGGTCAAAAATGG-AATTTTTGG-AAGTTCG
1 GGGT--AAAATGGTAATTTTTGGAAAGTTCG
*
16076 AGGGTAAAATGGTAATTTTTGGAAAAGAAATCG
1 -GGGTAAAATGGTAATTTTTGG-AAAG--TTCG
* *
16109 AGGTAAAAAAT-GAAATTTTTGG-AAGTTCGG
1 GGGT--AAAATGGTAATTTTTGGAAAGTTC-G
*
16139 GGGT-AAATGGTAA-TTTTGGAAAGTTTG
1 GGGTAAAATGGTAATTTTTGGAAAGTTCG
* **
16166 AGGGTAAAAAT-GTAA-TATTGGAAAGTTTAA
1 -GGGT-AAAATGGTAATTTTTGGAAAG-TTCG
* * **
16196 GGGTAAAATTGTAATTTTTGTAAAGTTTAA
1 GGGTAAAATGGTAATTTTTGGAAAG-TTCG
*
16226 GGG-AAAATGG-AA-TTTTGGAAAATTC-
1 GGGTAAAATGGTAATTTTTGGAAAGTTCG
* *
16251 AGGTAAAAAT-ATAATTTTTGTG-AAGTTCG
1 GGGT-AAAATGGTAATTTTTG-GAAAGTTCG
* * *
16280 GGGTAAAAATGG-AATTTTAGAAAAGTTCAA
1 GGGT-AAAATGGTAATTTTTGGAAAGTTC-G
* *
16310 GGGTCAAAAT-ATGATTTTTGGAAA
1 GGGT-AAAATGGTAATTTTTGGAAA
16334 ATTTAGGGAC
Statistics
Matches: 309, Mismatches: 53, Indels: 85
0.69 0.12 0.19
Matches are distributed among these distances:
25 2 0.01
26 2 0.01
27 26 0.08
28 60 0.19
29 87 0.28
30 77 0.25
31 34 0.11
32 3 0.01
33 13 0.04
34 5 0.02
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTCG
Found at i:15966 original size:59 final size:60
Alignment explanation
Indices: 15816--15982 Score: 189
Period size: 60 Copynumber: 2.8 Consensus size: 60
15806 CAATCAGTCG
* * *
15816 AAAATGAGATTTTTGGATA-CTCGGGGATAAAATGGTAATTTTGGGAAAATTCAGGGTCAA
1 AAAATGAGATTTTTAGATATC-CAGGGATAAAATGGTAATTTTTGGAAAATTCAGGGTCAA
* * * * * * **
15876 AAAATGAAAATTTTAGACATCCGAGGG-TAAAATGGTAATTTTTGGATAGTTCGGGGT-TT
1 AAAATGAGATTTTTAGATATCC-AGGGATAAAATGGTAATTTTTGGAAAATTCAGGGTCAA
15935 AAAATGAGATTTTTAGATATCCAGGGATAAAATGGT-ATTTTTGGAAAA
1 AAAATGAGATTTTTAGATATCCAGGGATAAAATGGTAATTTTTGGAAAA
15983 AATTTGGGGT
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
58 14 0.16
59 28 0.32
60 42 0.48
61 4 0.05
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (60 bp):
AAAATGAGATTTTTAGATATCCAGGGATAAAATGGTAATTTTTGGAAAATTCAGGGTCAA
Found at i:16126 original size:33 final size:32
Alignment explanation
Indices: 16041--16132 Score: 86
Period size: 33 Copynumber: 2.9 Consensus size: 32
16031 ACTTTTAGAA
*
16041 AAATCGAGGTCAAAAATGGAATTTTTGG--AAG
1 AAATCGAGGT-AAAAATGAAATTTTTGGAAAAG
* *
16072 --TTCGAGGGT-AAAATGGTAATTTTTGGAAAAG
1 AAATCGA-GGTAAAAAT-GAAATTTTTGGAAAAG
16103 AAATCGAGGTAAAAAATGAAATTTTTGGAA
1 AAATCGAGGT-AAAAATGAAATTTTTGGAA
16133 GTTCGGGGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
28 5 0.10
29 14 0.29
30 3 0.06
31 3 0.06
32 3 0.06
33 16 0.33
34 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.28
Consensus pattern (32 bp):
AAATCGAGGTAAAAATGAAATTTTTGGAAAAG
Found at i:16200 original size:57 final size:57
Alignment explanation
Indices: 16139--16246 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 57
16129 GGAAGTTCGG
* *
16139 GGGT-AAATGGTAA-TTTTGGAAAGTTTGAGGGTAAAAATGTAATATTGGAAAGTTTAA
1 GGGTAAAATGGTAATTTTTGGAAAGTTTAAGGG--AAAATGGAATATTGGAAAGTTTAA
* * *
16196 GGGTAAAATTGTAATTTTTGTAAAGTTTAAGGGAAAATGGAATTTTGGAAA
1 GGGTAAAATGGTAATTTTTGGAAAGTTTAAGGGAAAATGGAATATTGGAAA
16247 ATTCAGGTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
57 20 0.45
58 8 0.18
59 16 0.36
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTTAAGGGAAAATGGAATATTGGAAAGTTTAA
Found at i:16200 original size:119 final size:119
Alignment explanation
Indices: 15957--16215 Score: 303
Period size: 119 Copynumber: 2.2 Consensus size: 119
15947 TTAGATATCC
* * * *
15957 AGGGATAAAATGGT-ATTTTTGGAAAAAATTTGGGGTAAAAATGGAATTTTAGGAAGTTCGGGGG
1 AGGG-TAAAATGGTAATTTTTGGAAAAAAATCGAGGTAAAAATGAAATTTTAGGAAGTTCGGGGG
* * *
16021 TAAAATGGTGACTTTTAGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCG
65 TAAAATGGTGAATTTTAGAAAAATCGAGGTCAAAAATGGAATTATTGGAAGTTCA
*
16076 AGGGTAAAATGGTAATTTTTGGAAAAGAAATCGAGGTAAAAAATGAAATTTTTGGAAGTTCGGGG
1 AGGGTAAAATGGTAATTTTTGGAAAA-AAATCGAGGT-AAAAATGAAATTTTAGGAAGTTCGGGG
* ** * * *
16141 GT-AAATGGT-AATTTTGGAAAGTTTGAGGGT-AAAAATGTAA-TATTGGAAAGTTTA
64 GTAAAATGGTGAATTTTAGAAAAATCGA-GGTCAAAAATGGAATTATTGG-AAGTTCA
*
16195 AGGGTAAAATTGTAATTTTTG
1 AGGGTAAAATGGTAATTTTTG
16216 TAAAGTTTAA
Statistics
Matches: 120, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
118 14 0.12
119 62 0.52
120 17 0.14
121 27 0.22
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.32
Consensus pattern (119 bp):
AGGGTAAAATGGTAATTTTTGGAAAAAAATCGAGGTAAAAATGAAATTTTAGGAAGTTCGGGGGT
AAAATGGTGAATTTTAGAAAAATCGAGGTCAAAAATGGAATTATTGGAAGTTCA
Found at i:22261 original size:60 final size:61
Alignment explanation
Indices: 22174--22351 Score: 189
Period size: 59 Copynumber: 3.0 Consensus size: 61
22164 ACTCGAGGGT
* *
22174 AAAATGGTAA-TTTTAGACACTCG-GGGTAAAATGGTAATTTTGGGAAAGTTCGAGGGTTAA
1 AAAATGG-AATTTTTAGACAATCGAGGGTAAAATGGTAATTTTAGGAAAGTTCGAGGGTTAA
* *
22234 AAAAT-GAATTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTC-AGGGCTT--
1 AAAATGGAATTTTTAGACAATCGAGGGTAAAATGGTAATTTTAGGAAAGTTCGAGGG-TTAA
* *
22292 AAAATGGGATTTTTAGA-AATC-ATGGTCAAAAATGG-AATTTTAGG-AAGTTCGAGGG-TAA
1 AAAATGGAATTTTTAGACAATCGAGGGT--AAAATGGTAATTTTAGGAAAGTTCGAGGGTTAA
22350 AA
1 AA
22352 TGGTGACTTT
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
56 1 0.01
57 10 0.10
58 24 0.23
59 34 0.33
60 34 0.33
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (61 bp):
AAAATGGAATTTTTAGACAATCGAGGGTAAAATGGTAATTTTAGGAAAGTTCGAGGGTTAA
Found at i:22371 original size:59 final size:58
Alignment explanation
Indices: 22261--22598 Score: 213
Period size: 59 Copynumber: 5.6 Consensus size: 58
22251 ATTCGAGGGT
* * * *
22261 AAAATGGTAATTTTTGGAAAG-TTCAGGGCTTAAAATGG-GA-TTTT-TAGAAATCATGGTCA
1 AAAATGG-AATTTTTGG-AAGTTTGAGGG--TAAAATGGTGACTTTTGGAAAAATCA-GGTTA
* * ***
22320 AAAATGGAATTTTAGGAAGTTCGAGGGTAAAATGGTGACTTTTGGAAAAATCGAGACCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTGACTTTTGGAAAAATC-AGGTTA
* * * * * *
22379 AAATTGGAATTTTTGGGAGTTTG-GTGGTAAAATGCTAATTTTTTGGAAAAAAAAATCGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTGAG-GGTAAAATGGTGA-CTTTTGG----AAAAATC-AGGTTA
* * * * **
22443 AAAATGGAATTTTTGGAA-TTTTAGGGGTAAATTGGTGACTTTTAGAATAATTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTGA-GGGTAAAATGGTGACTTTTGGAA-AAATCAGGTTA
* * * *
22502 AAAATGAAATTTTT-GAGAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAAAATCGAGGTTA
1 AAAATGGAATTTTTGGA-AGTTTGAGGGTAAAATGGTGACTTTTGG--AAAAATC-AGGTTA
* *
22563 AAAATTGAATTTTTGGAAGTTTAAGGGTAAAATGGT
1 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGT
22599 AATTTTGTAA
Statistics
Matches: 217, Mismatches: 42, Indels: 38
0.73 0.14 0.13
Matches are distributed among these distances:
56 8 0.04
57 5 0.02
58 20 0.09
59 85 0.39
60 16 0.07
61 36 0.17
62 2 0.01
63 8 0.04
64 36 0.17
65 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGTAAAATGGTGACTTTTGGAAAAATCAGGTTA
Found at i:22603 original size:29 final size:29
Alignment explanation
Indices: 22561--22785 Score: 172
Period size: 30 Copynumber: 7.7 Consensus size: 29
22551 AAATCGAGGT
22561 TAAAAAT-TGAATTTTTGGAAGTTTAAGGG
1 TAAAAATGT-AATTTTTGGAAGTTTAAGGG
* * *
22590 T-AAAATGGTAA-TTTTGTAAAGTTTGAGGA
1 TAAAAAT-GTAATTTTTG-GAAGTTTAAGGG
*
22619 TAAAAATGTAA-TTTTGGAAAGTTTAGGGG
1 TAAAAATGTAATTTTTGG-AAGTTTAAGGG
*
22648 TAAAAATGTAATTTTTATGAAGTTTAAGGG
1 TAAAAATGTAATTTTT-GGAAGTTTAAGGG
** * *
22678 GGAAAATGGAA-TTTTGGAAAGTTTAAGAG
1 TAAAAATGTAATTTTTGG-AAGTTTAAGGG
* *
22707 TAAAAATGAAATTTTTGTGAAGTTTAGGGG
1 TAAAAATGTAATTTTTG-GAAGTTTAAGGG
* * * * *
22737 CAAAAATGGAATTTTAGAAAATTTCAAGGG
1 TAAAAATGTAATTTTTGGAAGTTT-AAGGG
* * *
22767 TCAAAATATGATTTTTGGA
1 TAAAAATGTAATTTTTGGA
22786 CAATTTAGGG
Statistics
Matches: 153, Mismatches: 32, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
28 11 0.07
29 68 0.44
30 72 0.47
31 2 0.01
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (29 bp):
TAAAAATGTAATTTTTGGAAGTTTAAGGG
Found at i:22654 original size:120 final size:121
Alignment explanation
Indices: 22319--22663 Score: 337
Period size: 123 Copynumber: 2.9 Consensus size: 121
22309 AATCATGGTC
* ** * * * * * *
22319 AAAAATGGAATTTTAGGAAGTTCGAGGGTAAAATGGTGACTTTTGGAAAAATCGA-GACCAAAAT
1 AAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGTGAATTTTAGAATAATTGAGGA-TAAAAA
* * * *
22383 TGGAATTTTTGG-GAGTTT-GGTGGTAAAATGCTAATTTTTTGGAAAAAAAAATCGGGGTT
65 T-GAAATTTTGGAAAGTTTAGG-GGTAAAATGGTAA-TTTTTGG-AAAAAAAATCGAGGTT
* * * * * *
22442 AAAAATGGAATTTTTGGAATTTTAGGGGTAAATTGGTGACTTTTAGAATAATTGGGGTTAAAAAT
1 AAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGTGAATTTTAGAATAATTGAGGATAAAAAT
* * *
22507 GAAATTTTTGAGAGTTTGGGGGTAAAATGGTAATTTTTGG-AAAAAAATCGAGGTT
66 GAAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAAAAATCGAGGTT
* *
22562 AAAAATTGAATTTTTGGAAGTTTAAGGGTAAAATGGT-AATTTT-GTAA-AGTTTGAGGATAAAA
1 AAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGTGAATTTTAG-AATA-ATTGAGGATAAAA
*
22624 ATGTAATTTTGGAAAGTTTAGGGGTAAAAAT-GTAATTTTT
64 ATGAAATTTTGGAAAGTTTAGGGGT-AAAATGGTAATTTTT
22664 ATGAAGTTTA
Statistics
Matches: 187, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
118 2 0.01
119 47 0.25
120 52 0.28
122 15 0.08
123 68 0.36
124 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.35
Consensus pattern (121 bp):
AAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGTGAATTTTAGAATAATTGAGGATAAAAAT
GAAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGAAAAAAAATCGAGGTT
Found at i:22673 original size:30 final size:29
Alignment explanation
Indices: 22436--22751 Score: 161
Period size: 29 Copynumber: 10.7 Consensus size: 29
22426 AAAAAAAATC
* *
22436 GGGGTTAAAAATGGAATTTTTGGAATTTTA
1 GGGG-TAAAAATGTAATTTTTGGAAGTTTA
* * * *
22466 GGGGT-AAATTGGTGACTTTTAGAA-TAATT-
1 GGGGTAAAAAT-GTAATTTTTGGAAGT--TTA
* *
22495 GGGGTTAAAAATGAAATTTTT-GAGAGTTTG
1 GGGG-TAAAAATGTAATTTTTGGA-AGTTTA
*** *
22525 GGGGT-AAAATGGTAATTTTTGGAAAAAAATC
1 GGGGTAAAAAT-GTAATTTTTGG--AAGTTTA
*
22556 GAGGTTAAAAAT-TGAATTTTTGGAAGTTTA
1 G-GGGTAAAAATGT-AATTTTTGGAAGTTTA
* *
22586 AGGGT-AAAATGGTAA-TTTTGTAAAGTTT-
1 GGGGTAAAAAT-GTAATTTTTG-GAAGTTTA
*
22614 GAGGATAAAAATGTAA-TTTTGGAAAGTTTA
1 G-GGGTAAAAATGTAATTTTTGG-AAGTTTA
*
22644 GGGGTAAAAATGTAATTTTTATGAAGTTTAA
1 GGGGTAAAAATGTAATTTTT-GGAAGTTT-A
* *
22675 GGGG-GAAAATGGAA-TTTTGGAAAGTTTA
1 GGGGTAAAAATGTAATTTTTGG-AAGTTTA
* * *
22703 AGAGTAAAAATGAAATTTTTGTGAAGTTTA
1 GGGGTAAAAATGTAATTTTTG-GAAGTTTA
* *
22733 GGGGCAAAAATGGAATTTT
1 GGGGTAAAAATGTAATTTT
22752 AGAAAATTTC
Statistics
Matches: 219, Mismatches: 38, Indels: 58
0.70 0.12 0.18
Matches are distributed among these distances:
28 24 0.11
29 87 0.40
30 74 0.34
31 16 0.07
32 13 0.06
33 5 0.02
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTA
Found at i:22691 original size:59 final size:58
Alignment explanation
Indices: 22562--22782 Score: 225
Period size: 59 Copynumber: 3.8 Consensus size: 58
22552 AATCGAGGTT
* **
22562 AAAAATTGAATTTTTGG-AAGTTTAAGGGT-AAAATGGTAATTTTGTA--AAGTTTGAGGAT
1 AAAAATGGAA-TTTTGGAAAGTTTAAGGGTAAAAAT-GTAATTTT-TATGAAGTTT-AGGGG
* *
22620 AAAAATGTAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTATGAAGTTTAAGGGG
1 AAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTATGAAGTTT-AGGGG
* * * *
22679 GAAAATGGAATTTTGGAAAGTTTAAGAGTAAAAATGAAATTTTTGTGAAGTTTAGGGG
1 AAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTATGAAGTTTAGGGG
* * * * *
22737 CAAAAATGGAATTTTAGAAAATTTCAAGGGTCAAAATATGATTTTT
1 -AAAAATGGAATTTTGGAAAGTTT-AAGGGTAAAAATGTAATTTTT
22783 GGACAATTTA
Statistics
Matches: 137, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
57 8 0.06
58 32 0.23
59 81 0.59
60 16 0.12
ACGTcount: A:0.40, C:0.01, G:0.24, T:0.35
Consensus pattern (58 bp):
AAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTATGAAGTTTAGGGG
Found at i:23833 original size:28 final size:28
Alignment explanation
Indices: 23776--23878 Score: 73
Period size: 28 Copynumber: 3.5 Consensus size: 28
23766 CAGATTTTAT
*
23776 TTAATATTAATATTAATTATTAATATTG
1 TTAATATTAATATTAATTATTAATAATG
** *
23804 TTAATATTTTTATTAA-TATTTATTAATG
1 TTAATATTAATATTAATTA-TTAATAATG
* * *
23832 TTATTTATTACCATTATTTATTATTAATAATA
1 TTA-ATATTA--A-TATTAATTATTAATAATG
* *
23864 TTATTATTATTATTA
1 TTAATATTAATATTA
23879 CTACTTATTA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
27 2 0.04
28 28 0.49
29 4 0.07
31 6 0.11
32 15 0.26
33 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TTAATATTAATATTAATTATTAATAATG
Found at i:23857 original size:3 final size:3
Alignment explanation
Indices: 23780--23888 Score: 56
Period size: 3 Copynumber: 34.7 Consensus size: 3
23770 TTTTATTTAA
* * * * * *
23780 TAT TAA TAT TAAT TAT TAA TAT TGT TAA TAT TTT TAT TAA TATT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* * * * * *
23827 TAA TGT TATT TAT TAC CAT TATT TAT TAT TAA TAA TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
*
23874 TAT TAC TACT TAT TA
1 TAT TAT TA-T TAT TA
23889 AATACGTTTT
Statistics
Matches: 77, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
3 64 0.83
4 13 0.17
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:24618 original size:17 final size:17
Alignment explanation
Indices: 24596--24667 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
24586 CATTTCAAAT
*
24596 TTTAAATTTAAAATAAA
1 TTTAAACTTAAAATAAA
24613 TTTAAACTT--AATAAA
1 TTTAAACTTAAAATAAA
*
24628 TTTAAATTTAAAAT-AA
1 TTTAAACTTAAAATAAA
*
24644 TTCTAAACTTAGAATAAA
1 TT-TAAACTTAAAATAAA
24662 TTTAAA
1 TTTAAA
24668 ATAAAGATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
15 14 0.30
16 4 0.09
17 25 0.53
18 4 0.09
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:24633 original size:32 final size:33
Alignment explanation
Indices: 24596--24667 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 33
24586 CATTTCAAAT
24596 TTTAAATTTAAAATAAATT-TAAACTT-AATAAA
1 TTTAAATTTAAAAT-AATTCTAAACTTAAATAAA
24628 TTTAAATTTAAAATAATTCTAAACTTAGAATAAA
1 TTTAAATTTAAAATAATTCTAAACTTA-AATAAA
24662 TTTAAA
1 TTTAAA
24668 ATAAAGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
31 4 0.11
32 21 0.57
34 12 0.32
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (33 bp):
TTTAAATTTAAAATAATTCTAAACTTAAATAAA
Found at i:32979 original size:98 final size:98
Alignment explanation
Indices: 32808--33003 Score: 293
Period size: 98 Copynumber: 2.0 Consensus size: 98
32798 TTTGTAGTTG
* *
32808 CATCTGGCTATGTGCCTATAATTGATCAAGGTGCAAATGTACCTACAAATTCTGATTAGAATTCT
1 CATCTGGCTATGTGCCTACAATTGATCAAGGTGCAAATGTACCTACAAATTCTGATTAAAATTCT
32873 GCTATTGATTGTTGTTGTAACTCCCTTGTCTAT
66 GCTATTGATTGTTGTTGTAACTCCCTTGTCTAT
* * * *** *
32906 CATCTGGCTATGTGGCTGCAATTGATCAAGGTGCGAATGTACCTGTGAATTTTGATTAAAATTCT
1 CATCTGGCTATGTGCCTACAATTGATCAAGGTGCAAATGTACCTACAAATTCTGATTAAAATTCT
* *
32971 GTTGTTGATTGTTGTTGTAACTCCCTTGTCTAT
66 GCTATTGATTGTTGTTGTAACTCCCTTGTCTAT
33004 AACTCCAGGA
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (98 bp):
CATCTGGCTATGTGCCTACAATTGATCAAGGTGCAAATGTACCTACAAATTCTGATTAAAATTCT
GCTATTGATTGTTGTTGTAACTCCCTTGTCTAT
Found at i:39733 original size:33 final size:33
Alignment explanation
Indices: 39691--39754 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
39681 TTTGAATTTG
*
39691 AATTCTAAAAAAATCAATAAATTTAACCCTTAA
1 AATTCTAAAAAAATCAATAAATATAACCCTTAA
* * *
39724 AATTTTAAAAAAATTAATAAATATAATCCTT
1 AATTCTAAAAAAATCAATAAATATAACCCTT
39755 GAATTACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (33 bp):
AATTCTAAAAAAATCAATAAATATAACCCTTAA
Found at i:40826 original size:28 final size:27
Alignment explanation
Indices: 40774--40827 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40764 GGTTTTCTCT
40774 TGTTTTCTGTCATCCTCTCTTTTCCCG
1 TGTTTTCTGTCATCCTCTCTTTTCCCG
* * *
40801 TGTTTTCTTTCCTCTTCTTCTTTTCCC
1 TGTTTTCTGTCATCCTC-TCTTTTCCC
40828 ATCTCCTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.02, C:0.33, G:0.07, T:0.57
Consensus pattern (27 bp):
TGTTTTCTGTCATCCTCTCTTTTCCCG
Found at i:41536 original size:29 final size:30
Alignment explanation
Indices: 41504--41564 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
41494 CATAAATTGA
41504 CAAAATACAACCATTAA-TAAAGT-GTCCAT
1 CAAAATACAACCATTAATTAAA-TCGTCCAT
41533 CAAAATACAACCATTAATTAAATCGTCCAT
1 CAAAATACAACCATTAATTAAATCGTCCAT
41563 CA
1 CA
41565 TCGAAATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.48, C:0.23, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAAATACAACCATTAATTAAATCGTCCAT
Found at i:44282 original size:20 final size:20
Alignment explanation
Indices: 44245--44282 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44235 TGTTCTTTTT
* *
44245 CCTTTATATTTTTTACCAAG
1 CCTTTATATTTCTCACCAAG
44265 CCTTTATATTTCTCACCA
1 CCTTTATATTTCTCACCA
44283 CTTTATCCTT
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:0.24, C:0.26, G:0.03, T:0.47
Consensus pattern (20 bp):
CCTTTATATTTCTCACCAAG
Found at i:44578 original size:27 final size:27
Alignment explanation
Indices: 44540--44615 Score: 152
Period size: 27 Copynumber: 2.8 Consensus size: 27
44530 GTATCATTAA
44540 CAACATCAGGTGTGTCAACCTTGTGTT
1 CAACATCAGGTGTGTCAACCTTGTGTT
44567 CAACATCAGGTGTGTCAACCTTGTGTT
1 CAACATCAGGTGTGTCAACCTTGTGTT
44594 CAACATCAGGTGTGTCAACCTT
1 CAACATCAGGTGTGTCAACCTT
44616 CTTTATCTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (27 bp):
CAACATCAGGTGTGTCAACCTTGTGTT
Found at i:49086 original size:21 final size:20
Alignment explanation
Indices: 49028--49094 Score: 109
Period size: 20 Copynumber: 3.3 Consensus size: 20
49018 TAGGAGGCAT
49028 TTTGAATGGTTTT-CCCTTAC
1 TTTG-ATGGTTTTCCCCTTAC
49048 TTTGATGGTTTTCCCCTTAC
1 TTTGATGGTTTTCCCCTTAC
49068 TTTGATGGTTTTCCCCCTTAC
1 TTTGATGGTTTT-CCCCTTAC
49089 TTTGAT
1 TTTGAT
49095 TCAATGTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.18
20 23 0.51
21 14 0.31
ACGTcount: A:0.12, C:0.22, G:0.15, T:0.51
Consensus pattern (20 bp):
TTTGATGGTTTTCCCCTTAC
Found at i:53911 original size:24 final size:23
Alignment explanation
Indices: 53859--53904 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
53849 TGCGTAATAT
*
53859 ACATACATAAACATTAATAAACA
1 ACATACATAAACAATAATAAACA
*
53882 ATCATACACTTAACAATAATAAA
1 A-CATACA-TAAACAATAATAAA
53905 ACACATAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 6 0.32
25 12 0.63
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (23 bp):
ACATACATAAACAATAATAAACA
Found at i:53994 original size:37 final size:37
Alignment explanation
Indices: 53907--54108 Score: 179
Period size: 37 Copynumber: 5.5 Consensus size: 37
53897 ATAATAAAAC
* * *
53907 ACATAACA-ACCATACAATTATACATACATAATAGTACATA
1 ACATAACATA-CATACAAATATACAAACATAACAGT--A-A
* * *
53947 ACATAACATACATATAAATATACAAACATGATAGTAA
1 ACATAACATACATACAAATATACAAACATAACAGTAA
* *
53984 ACATAACATACATACAAATATCCTAACATAACAGT-A
1 ACATAACATACATACAAATATACAAACATAACAGTAA
* * **
54020 AC-CAAC--ACATAACAAACATACAATTAT-ACA-T--
1 ACATAACATACAT-ACAAATATACAAACATAACAGTAA
54051 ACATAACATACATACAAATATACAAACATAACAGTAA
1 ACATAACATACATACAAATATACAAACATAACAGTAA
54088 ACATAACATACATACATAATA
1 ACATAACATACATACA-AATA
54109 GCACATAACA
Statistics
Matches: 133, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
31 2 0.02
32 4 0.03
33 20 0.15
34 18 0.14
35 4 0.03
36 3 0.02
37 47 0.35
38 5 0.04
40 29 0.22
41 1 0.01
ACGTcount: A:0.55, C:0.20, G:0.02, T:0.22
Consensus pattern (37 bp):
ACATAACATACATACAAATATACAAACATAACAGTAA
Found at i:54014 original size:67 final size:67
Alignment explanation
Indices: 53942--54097 Score: 167
Period size: 67 Copynumber: 2.3 Consensus size: 67
53932 ACATAATAGT
*
53942 ACATAACA-TAACATACATATAA-ATATACAAAC-ATGATAGTAAACATAACATACATACAAATA
1 ACATAACAGTAACATACATATAACA-A-ACAAACAATGATA-CAAACATAACATACATACAAATA
* *
54004 TCCTA
63 TACAA
* * * *
54009 ACATAACAGTAACCA-ACACATAACAAACATACAATTATACATACATAACATACATACAAATATA
1 ACATAACAGTAA-CATACATATAACAAACAAACAATGATACAAACATAACATACATACAAATATA
54073 CAA
65 CAA
54076 ACATAACAGTAAACATAACATA
1 ACATAACAGT-AACAT-ACATA
54098 CATACATAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
67 49 0.66
68 18 0.24
69 7 0.09
ACGTcount: A:0.56, C:0.20, G:0.03, T:0.21
Consensus pattern (67 bp):
ACATAACAGTAACATACATATAACAAACAAACAATGATACAAACATAACATACATACAAATATAC
AA
Found at i:54098 original size:25 final size:25
Alignment explanation
Indices: 54026--54136 Score: 91
Period size: 25 Copynumber: 4.3 Consensus size: 25
54016 AGTAACCAAC
* **
54026 ACATAACAAACATACAATTATACAT
1 ACATAACATACATACAAACATACAT
* *
54051 ACATAACATACATACAAATATACAA
1 ACATAACATACATACAAACATACAT
54076 ACATAACAGTA-A-ACATAACATACAT
1 ACATAACA-TACATACA-AACATACAT
* * *
54101 ACATAATAGCACATAACAAACATAATAT
1 ACATAACA-TACAT-ACAAACAT-ACAT
54129 ACATAACA
1 ACATAACA
54137 ATTTAAAAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
24 3 0.04
25 47 0.66
26 3 0.04
27 5 0.07
28 13 0.18
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.21
Consensus pattern (25 bp):
ACATAACATACATACAAACATACAT
Found at i:54122 original size:32 final size:34
Alignment explanation
Indices: 53946--54133 Score: 122
Period size: 37 Copynumber: 5.4 Consensus size: 34
53936 AATAGTACAT
* **
53946 AACATAACATACATATAAATATACAAACATGATAGTA
1 AACATAACATACATACAAATATAC-AACAT-A-ACAA
* *
53983 AACATAACATACATACAAATATCCTAACATAACAGT
1 AACATAACATACATACAAATATAC-AACATAACA-A
* * *
54019 AAC-CAAC--ACATAACAAACATACAA-TTATAC-A
1 AACATAACATACAT-ACAAATATACAACATA-ACAA
*
54050 TACATAACATACATACAAATATACAAACATAACAGTA
1 AACATAACATACATACAAATATAC-AACATAACA--A
*
54087 AACATAACATACATACATAATA-GC-ACATAAC-A
1 AACATAACATACATACA-AATATACAACATAACAA
*
54119 AACATAATATACATA
1 AACATAACATACATA
54134 ACAATTTAAA
Statistics
Matches: 121, Mismatches: 18, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
31 2 0.02
32 20 0.17
33 17 0.14
34 16 0.13
35 13 0.11
36 4 0.03
37 45 0.37
38 4 0.03
ACGTcount: A:0.56, C:0.20, G:0.03, T:0.21
Consensus pattern (34 bp):
AACATAACATACATACAAATATACAACATAACAA
Found at i:54125 original size:19 final size:18
Alignment explanation
Indices: 54024--54137 Score: 59
Period size: 21 Copynumber: 5.6 Consensus size: 18
54014 ACAGTAACCA
54024 ACACATAACAAACATACAATT
1 ACACATAACAAACAT--AA-T
*
54045 ATACAT-ACATAACATACAT
1 ACACATAACA-AACATA-AT
*
54064 ACAAATATACAAACATAACAGT
1 ACACATA-ACAAACAT-A-A-T
*
54086 AAACATAACATACATACATAAT
1 ACACATAAC--A-A-ACATAAT
54108 AGCACATAACAAACATAAT
1 A-CACATAACAAACATAAT
*
54127 ATACATAACAA
1 ACACATAACAA
54138 TTTAAAAACT
Statistics
Matches: 75, Mismatches: 7, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
18 9 0.12
19 14 0.19
20 10 0.13
21 19 0.25
22 8 0.11
23 9 0.12
24 2 0.03
25 4 0.05
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (18 bp):
ACACATAACAAACATAAT
Found at i:57995 original size:22 final size:22
Alignment explanation
Indices: 57968--58011 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
57958 TAAGTTTAAG
57968 ATTTAGAATCAATTTTGATACC
1 ATTTAGAATCAATTTTGATACC
57990 ATTTAGAATCAATTTTGATACC
1 ATTTAGAATCAATTTTGATACC
58012 TCTGCATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
ATTTAGAATCAATTTTGATACC
Found at i:58724 original size:25 final size:25
Alignment explanation
Indices: 58655--58744 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
58645 TAATACTTTT
*
58655 TAAATTTTATAAAAATATAAAA-TTA
1 TAAA-TTTATAAAAAAATAAAATTTA
* * * *
58680 -AAGTTTTATGAAATACTAAAATTTA
1 TAA-ATTTATAAAAAAATAAAATTTA
*
58705 TAAATTTATAAAAAAATAAAATATA
1 TAAATTTATAAAAAAATAAAATTTA
*
58730 TAAAATTACTAAAAA
1 TAAATTTA-TAAAAA
58745 GCACAAGTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
24 15 0.30
25 27 0.54
26 8 0.16
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
TAAATTTATAAAAAAATAAAATTTA
Found at i:59468 original size:20 final size:21
Alignment explanation
Indices: 59440--59483 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
59430 TATGATACTC
*
59440 AAAATATGA-TTTGA-CATAAA
1 AAAAAATGACTTTGAGCA-AAA
59460 AAAAAATGACTTTGAGCAAAA
1 AAAAAATGACTTTGAGCAAAA
59481 AAA
1 AAA
59484 TCGATGTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 11 0.52
22 2 0.10
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (21 bp):
AAAAAATGACTTTGAGCAAAA
Found at i:60121 original size:121 final size:118
Alignment explanation
Indices: 59944--60281 Score: 306
Period size: 121 Copynumber: 2.8 Consensus size: 118
59934 AGAAAAACTT
* * * * * * **
59944 GGGTATTTATAGGGAAAACAAATTTATCT-TTTT-AGTTTCTTTTATTATTATTTTTTTAGAATT
1 GGGTTTTTATAAGAAAAACAATTTTATCTCTTTTAATTTTC-TTTATTTTTCCTTTTTTAGAATT
* * * * * * *
60007 AGTTTTAGTTTTTCT-AGTAAAAGGAAAAAATGGGATTTTGCAGAGGAATTGTTT
65 AATTTTAGTTTTTCTAAATAAAAGGAAAAAATGGAATATTACAGA-AAATTGTTC
* * * *
60061 GGGTTTTTTTTTTTAGGAAAACCATTTTTATC-CTTTTAATTTTCTTTATTTTTTCCTTTTTTAG
1 GGG----TTTTTATAAGAAAAACAATTTTATCTCTTTTAATTTTCTTTA-TTTTTCCTTTTTTAG
* * *
60125 ATTTAATTTTAGTTTTTTCTCAATAAAAGAGAAAAATATGGAATATTATAGAAAATTGTTC
61 AATTAATTTTAG-TTTTTCTAAATAAAAG-GAAAAA-ATGGAATATTACAGAAAATTGTTC
* * * *
60186 GGGTTTTTATAAGAAAAACAATTTTATCTTTTTTAATTTTTTTTATTTTTCCTTTTCTAAAATTA
1 GGGTTTTTATAAGAAAAACAATTTTATCTCTTTTAATTTTCTTTATTTTTCCTTTTTTAGAATTA
*
60251 ATTTTTAGTTTTTCTAAATAAAAAGAAAAAA
66 A-TTTTAGTTTTTCTAAATAAAAGGAAAAAA
60282 GAAAAAAAAA
Statistics
Matches: 178, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
117 3 0.02
119 1 0.01
120 6 0.03
121 80 0.45
122 47 0.26
123 7 0.04
124 7 0.04
125 16 0.09
126 11 0.06
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (118 bp):
GGGTTTTTATAAGAAAAACAATTTTATCTCTTTTAATTTTCTTTATTTTTCCTTTTTTAGAATTA
ATTTTAGTTTTTCTAAATAAAAGGAAAAAATGGAATATTACAGAAAATTGTTC
Found at i:64775 original size:3 final size:3
Alignment explanation
Indices: 64767--64809 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
64757 TTTTATAACA
64767 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
64810 TTGAAGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:65452 original size:14 final size:14
Alignment explanation
Indices: 65432--65478 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
65422 CCTTAAACTC
65432 GAGGTTCAAAGTTT
1 GAGGTTCAAAGTTT
*
65446 AAGGTTC-AAGATTT
1 GAGGTTCAAAG-TTT
65460 GA-GTTCAAAGTTT
1 GAGGTTCAAAGTTT
65473 GAGGTT
1 GAGGTT
65479 TTGAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.30, C:0.06, G:0.28, T:0.36
Consensus pattern (14 bp):
GAGGTTCAAAGTTT
Found at i:67677 original size:27 final size:27
Alignment explanation
Indices: 67613--67677 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
67603 ATAAGAAAAC
67613 TAATTA-ATAATAATTTTTTTGAAATAT
1 TAATTATAT-ATAATTTTTTTGAAATAT
67640 TAATT-TAATATAATTTTTTT--AATACT
1 TAATTAT-ATATAATTTTTTTGAAATA-T
67666 ATAATTATATAT
1 -TAATTATATAT
67678 GTATAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
25 4 0.12
26 1 0.03
27 25 0.76
28 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TAATTATATATAATTTTTTTGAAATAT
Found at i:74034 original size:15 final size:15
Alignment explanation
Indices: 73997--74037 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
73987 ATTTCTTTGA
73997 TTTCACAATTTGAAGC
1 TTTCACAATTT-AAGC
74013 --T-ACAATTTAAGC
1 TTTCACAATTTAAGC
74025 TTTCACAATTTAA
1 TTTCACAATTTAA
74038 AGCCACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 2 0.09
15 9 0.41
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (15 bp):
TTTCACAATTTAAGC
Found at i:77248 original size:29 final size:30
Alignment explanation
Indices: 77207--77265 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
77197 TATAATTTTA
*
77207 ACCCCACTGTTTTCAT-TTTAT-TTAATTTG
1 ACCCCAATGTTTT-ATGTTTATATTAATTTG
* *
77236 ACCCCAATTTTTTATGTTTATATTATTTTG
1 ACCCCAATGTTTTATGTTTATATTAATTTG
77266 TTAATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.54
Consensus pattern (30 bp):
ACCCCAATGTTTTATGTTTATATTAATTTG
Found at i:77351 original size:21 final size:21
Alignment explanation
Indices: 77325--77373 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
77315 TTGTTATTTA
77325 TTTTTATTAAATTT-ATATATT
1 TTTTTATTAAATTTAAT-TATT
*
77346 TTTTTATTTAATTTAATTATT
1 TTTTTATTAAATTTAATTATT
*
77367 TATTTAT
1 TTTTTAT
77374 GTGTTATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTATTAAATTTAATTATT
Found at i:77577 original size:22 final size:22
Alignment explanation
Indices: 77549--77592 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
77539 TATGTTGTTA
77549 ATTGCTACTAATTGTAATCATT
1 ATTGCTACTAATTGTAATCATT
77571 ATTGCTACTAATTGTAATCATT
1 ATTGCTACTAATTGTAATCATT
77593 TAATTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
ATTGCTACTAATTGTAATCATT
Found at i:80185 original size:3 final size:3
Alignment explanation
Indices: 80177--80208 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
80167 TTCAAAGCAA
80177 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
80209 ATACTTGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:80291 original size:10 final size:9
Alignment explanation
Indices: 80250--80308 Score: 59
Period size: 9 Copynumber: 6.4 Consensus size: 9
80240 TTAGATCCCA
*
80250 AAATTTTTA
1 AAATTTTTT
80259 AAATTTATTT
1 AAATTT-TTT
80269 --ATTTTTT
1 AAATTTTTT
*
80276 ATATTTTTT
1 AAATTTTTT
80285 AGAATTTTTAT
1 A-AATTTTT-T
80296 AAATTTTTT
1 AAATTTTTT
80305 AAAT
1 AAAT
80309 ATAAATTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 19 0.44
10 15 0.35
11 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
AAATTTTTT
Found at i:80337 original size:19 final size:20
Alignment explanation
Indices: 80299--80365 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 20
80289 TTTTTATAAA
80299 TTTTTTAAATATAAATTTTGGAT
1 TTTTTTAAAT-T--ATTTTGGAT
80322 TTTTTTAAA-TATTTT-GAT
1 TTTTTTAAATTATTTTGGAT
* *
80340 TTTTTAAAATTATTTTGAAT
1 TTTTTTAAATTATTTTGGAT
80360 TTTTTT
1 TTTTTT
80366 TTGTAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 11 0.28
19 11 0.28
20 7 0.18
21 1 0.03
23 9 0.23
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (20 bp):
TTTTTTAAATTATTTTGGAT
Found at i:81586 original size:21 final size:20
Alignment explanation
Indices: 81561--81636 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
81551 AAAAATAGAA
81561 ATTTTGAAATTTTTTATAAAT
1 ATTTTGAAATTTTTTA-AAAT
**
81582 ATTTTGAAA-TTTAAAAAAT
1 ATTTTGAAATTTTTTAAAAT
*
81601 TTATTTG-AATTTTTTAAAAT
1 AT-TTTGAAATTTTTTAAAAT
*
81621 AATTTGAAATTATTTT
1 ATTTTGAAATT-TTTT
81637 TGTAATTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 11 0.25
20 20 0.45
21 13 0.30
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTGAAATTTTTTAAAAT
Found at i:96380 original size:67 final size:67
Alignment explanation
Indices: 96267--96398 Score: 246
Period size: 67 Copynumber: 2.0 Consensus size: 67
96257 CATTACACGT
*
96267 GCAATCAGCCTAACATACTAGCTAAAAGAGTGAACGAGACTCAGTTCAAACACCAAATCAGAGCT
1 GCAACCAGCCTAACATACTAGCTAAAAGAGTGAACGAGACTCAGTTCAAACACCAAATCAGAGCT
96332 TA
66 TA
*
96334 GCAACCAGCCTAACATATTAGCTAAAAGAGTGAACGAGACTCAGTTCAAACACCAAATCAGAGCT
1 GCAACCAGCCTAACATACTAGCTAAAAGAGTGAACGAGACTCAGTTCAAACACCAAATCAGAGCT
96399 CAGTGTTTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17
Consensus pattern (67 bp):
GCAACCAGCCTAACATACTAGCTAAAAGAGTGAACGAGACTCAGTTCAAACACCAAATCAGAGCT
TA
Found at i:104571 original size:53 final size:53
Alignment explanation
Indices: 104483--104728 Score: 303
Period size: 53 Copynumber: 4.6 Consensus size: 53
104473 TTCACATTTG
* * * *
104483 ATAACTCGCGATGACACAGAGTCATTGGACCTTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACATAGAGTCATCGGACCTTTAATCCGAAATAGGATTCAT
** * *
104536 ATAACTCACGATGACATAGAGTCATCGGATATTTAATCCAAAATAAGATTCAT
1 ATAACTCACGATGACATAGAGTCATCGGACCTTTAATCCGAAATAGGATTCAT
* * * *
104589 ATAACTCACGATGACATAAAGTCATTGGACCTTTAATCTGAAATAGGATTTAT
1 ATAACTCACGATGACATAGAGTCATCGGACCTTTAATCCGAAATAGGATTCAT
* * * *
104642 ATATCTCACGATGACATAGAGTCATCGAACCTTTAATTCGGAATAGGATTCAT
1 ATAACTCACGATGACATAGAGTCATCGGACCTTTAATCCGAAATAGGATTCAT
* * * * *
104695 ATAACGCACAATGACACACAGTCATCAGACCTTT
1 ATAACTCACGATGACATAGAGTCATCGGACCTTT
104729 TTGCATTTAC
Statistics
Matches: 162, Mismatches: 31, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 162 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACATAGAGTCATCGGACCTTTAATCCGAAATAGGATTCAT
Found at i:106428 original size:17 final size:17
Alignment explanation
Indices: 106370--106439 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
106360 ACCCCTTTTT
*
106370 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
* *
106387 AA-TTAATCTAAATTTG
1 AATTTAATTTAAATTTA
106403 AATTTAATTTAAATTTA
1 AATTTAATTTAAATTTA
*
106420 AATTTAATTTCAAAATTA
1 AATTTAATTT-AAATTTA
106438 AA
1 AA
106440 AAAGTCCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 13 0.29
17 24 0.53
18 8 0.18
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:106440 original size:6 final size:6
Alignment explanation
Indices: 106377--106439 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
106367 TTTAATTTAT
* *
106377 TTTAAA TTTAAA -TT-AA TCTAAA TTTGAA TTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
106422 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
106440 AAAGTCCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
4 2 0.04
5 13 0.27
6 29 0.60
7 4 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:108342 original size:30 final size:30
Alignment explanation
Indices: 108275--108585 Score: 361
Period size: 30 Copynumber: 10.5 Consensus size: 30
108265 GGAGGTCCCT
108275 AAACTGTCCAAAAATTCCATTTTT-ACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTGACCC-CG
108306 -AACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* *
108335 AAACTTCCAAAAATTCCATTTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* *
108365 AAACTTCCAAAAA-TCCTATTCTTGACCCCA
1 AAACTTCCAAAAATTCC-ATTTTTGACCCCG
*
108395 AAACTTCCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
* * ***
108424 AAACATCCAAAAATGCCATTTTTGACCTTA
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
108454 AAACTTCCAAAAATTCCA-TTTT-ACCCCCG
1 AAACTTCCAAAAATTCCATTTTTGA-CCCCG
* *
108483 -AACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
108512 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCC-CG
* * **
108542 -AGCTTCCAAAAATCCCATTTTTGACCTTG
1 AAACTTCCAAAAATTCCATTTTTGACCCCG
*
108571 AAACTTCGAAAAATT
1 AAACTTCCAAAAATT
108586 ATCATTTTAC
Statistics
Matches: 240, Mismatches: 28, Indels: 25
0.82 0.10 0.09
Matches are distributed among these distances:
28 17 0.07
29 87 0.36
30 133 0.55
31 3 0.01
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCG
Found at i:108449 original size:59 final size:59
Alignment explanation
Indices: 108275--108600 Score: 449
Period size: 59 Copynumber: 5.5 Consensus size: 59
108265 GGAGGTCCCT
* * *
108275 AAACTGTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
* * * * *
108335 AAACTTCCAAAAATTCCATTTTTTACCCCCAAACTTCCAAAAATCCTATTCTTGACCCCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
* * * **
108395 AAACTTCCAAAAATTCCATTTTTACCCCCAAACATCCAAAAATGCCATTTTTGACCTTA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
108454 AAACTTCCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
* * *
108512 AAACTTCCAAAAATTCCATTTTTACCCTCGAGCTTCCAAAAATCCCATTTTTGACCTTG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
* *
108571 AAACTTCGAAAAATTATCA-TTTTACCCCCG
1 AAACTTCCAAAAATT-CCATTTTTACCCCCG
108601 GATGTCCGAA
Statistics
Matches: 240, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
58 53 0.22
59 127 0.53
60 60 0.25
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
Found at i:108653 original size:117 final size:116
Alignment explanation
Indices: 108275--108600 Score: 422
Period size: 117 Copynumber: 2.8 Consensus size: 116
108265 GGAGGTCCCT
* **
108275 AAACTGTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCCGAAACT
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTTGAAACT
* * * *
108340 TCCAAAAATTCCAT-TTTTTACCCCCAAACTTCCAAAAATCCTATTCTTGACCCCA
65 TCCAAAAATT--ATCATTTTACCCCCGAACTTCCAAAAATCCTATTC--GACCTCG
* * * * *
108395 AAACTTCCAAAAATTCCATTTTTACCCCCAAACATCCAAAAATGCCATTTTTGACCTTAAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTTGAAACTT
* * *
108460 CCAAAAATT-CCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
66 CCAAAAATTATCATTTTACCCCCGAACTTCCAAAAAT-CC-TATTCGACCTCG
*
108512 AAACTTCCAAAAATTCCATTTTTACCCTCGAGCTTCCAAAAATCCCATTTTTGACCTTGAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTTGAAACTT
*
108577 CGAAAAATTATCATTTTACCCCCG
66 CCAAAAATTATCATTTTACCCCCG
108601 GATGTCCGAA
Statistics
Matches: 180, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
117 95 0.53
118 15 0.08
119 65 0.36
120 5 0.03
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (116 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTTGAAACTT
CCAAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCTATTCGACCTCG
Found at i:120920 original size:205 final size:205
Alignment explanation
Indices: 120525--121136 Score: 970
Period size: 205 Copynumber: 3.0 Consensus size: 205
120515 ACAAACAAGT
* * * *
120525 GACGCAGTTATCTTCCTGATGAGATACT-----GAAGACCAGGTCGAACCCACGCTCGGTATGAG
1 GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAG
* * * *
120585 CAAAGCTTCGAATCCCAGCTCCCTGGTGAGATACTAAGAAGC-AGATCGAAGCAATAAAACGGTT
66 CAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACTGAGAAGCAAG-TCGAAGC-ATTAAACGGTT
*
120649 AGCTTCCTGATGAGAT-CTTGAGAAGTGAACGAAATTCGTTCTCCTGATGAGATACAGAGAAGCG
129 AGCTTCCTGATGAGATAC-TGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAGAAGCG
120713 GATTGAAACAAGA-
193 GATTGAAACAA-AC
* *
120726 GATGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAG
1 GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAG
*
120791 CAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAAGTCGAAGCATTAAACGGTTAG
66 CAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACTGAGAAGCAAGTCGAAGCATTAAACGGTTAG
120856 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAGAAGCGGAT
131 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAGAAGCGGAT
120921 TGAAACAAAC
196 TGAAACAAAC
* * *
120931 GACGCGGTCATCTTCCTGACGAGATACTGAGAAGAAGACCAAGTCAAACTCACACTCGGTATGAG
1 GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAG
* * *
120996 CAAAGCTTCGAATCCCAGCTTCCTGGTGAGACATTGAGAAGCAGGTCGAAGCAATAAACGGTTAG
66 CAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACTGAGAAGCAAGTCGAAGCATTAAACGGTTAG
121061 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAGAAGCGGAT
131 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAGAAGCGGAT
121126 TGAAACAAAC
196 TGAAACAAAC
121136 G
1 G
121137 NNNNNNNNNN
Statistics
Matches: 382, Mismatches: 21, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
201 24 0.06
204 1 0.00
205 279 0.73
206 76 0.20
207 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (205 bp):
GACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAG
CAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACTGAGAAGCAAGTCGAAGCATTAAACGGTTAG
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAAAC
Found at i:129318 original size:17 final size:17
Alignment explanation
Indices: 129260--129329 Score: 97
Period size: 17 Copynumber: 4.1 Consensus size: 17
129250 CCCCCTTTTT
*
129260 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
*
129277 AA-TTAATCTAAATTTA
1 AATTTAATTTAAATTTA
129293 AATTTAATTTAAATTTA
1 AATTTAATTTAAATTTA
*
129310 AATTTAATTTCAAAATTA
1 AATTTAATTT-AAATTTA
129328 AA
1 AA
129330 AAAGTCCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
16 14 0.30
17 25 0.53
18 8 0.17
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:129319 original size:11 final size:11
Alignment explanation
Indices: 129260--129316 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
129250 CCCCCTTTTT
*
129260 AATTTATTTTA
1 AATTTAATTTA
*
129271 AATTTAAATT-
1 AATTTAATTTA
*
129281 AATCTAAATTTA
1 AAT-TTAATTTA
129293 AATTTAATTTA
1 AATTTAATTTA
129304 AATTTAAATTTA
1 AATTT-AATTTA
129316 A
1 A
129317 TTTCAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
10 3 0.08
11 25 0.66
12 10 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:129330 original size:6 final size:6
Alignment explanation
Indices: 129267--129329 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
129257 TTTAATTTAT
*
129267 TTTAAA TTTAAA -TT-AA TCTAAA TTTAAA TTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
129312 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
129330 AAAGTCCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 2 0.04
5 13 0.27
6 30 0.61
7 4 0.08
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:130485 original size:59 final size:59
Alignment explanation
Indices: 130379--130757 Score: 475
Period size: 59 Copynumber: 6.4 Consensus size: 59
130369 ACTCGAAGGT
* *
130379 CCCTAAACTGTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTAC
1 CCCTGAACT-TCCAAAAATCACATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTAC
* * * *
130439 CCCTGAACTTCCAAAAATCATATTTTTAACCTTAAAACTTCTAAAAATTCCA-TTTTAC
1 CCCTGAACTTCCAAAAATCACATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTAC
** * * *
130497 CCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCTATTTTTAC
1 CCCTGAACTTCCAAAAATCACATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTAC
* * *
130556 CCCCGAACTTCCAAAAATCCCATTTTTAACC-CTAAAACTTCCAAAAATTCCATTTTTAC
1 CCCTGAACTTCCAAAAATCACATTTTTGACCTC-AAAACTTCCAAAAATTCCATTTTTAC
* *
130615 CCCTGAACTTCGAAAAATCTCATTTTTGACC-CAAAACTTCCAAAAAGTT-CATTTTTAC
1 CCCTGAACTTCCAAAAATCACATTTTTGACCTCAAAACTTCCAAAAA-TTCCATTTTTAC
* * *
130673 CCC-GAACTTGCAAAAATC-CAATTTTGACC-CTAAAACTTCCAACAATTCCATTTTTAC
1 CCCTGAACTTCCAAAAATCACATTTTTGACCTC-AAAACTTCCAAAAATTCCATTTTTAC
*
130730 CCCTGAAACTTCCAAAAATTATCATTTT
1 CCCTG-AACTTCCAAAAATCA-CATTTT
130758 ACCCCCGGAT
Statistics
Matches: 280, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
56 13 0.05
57 38 0.14
58 77 0.28
59 139 0.50
60 8 0.03
61 5 0.02
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.32
Consensus pattern (59 bp):
CCCTGAACTTCCAAAAATCACATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTAC
Found at i:130595 original size:117 final size:117
Alignment explanation
Indices: 130383--130748 Score: 524
Period size: 117 Copynumber: 3.1 Consensus size: 117
130373 GAAGGTCCCT
*
130383 AAACTGTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCCATTTTTACCCCTGAACT
1 AAACT-TCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATT-CATTTTTACCCCCGAACT
** * *
130448 TCCAAAAATCATATTTTTAACCTTAAAACTTCTAAAAATTCCA-TTTTACCCCC
64 TCCAAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCCC
*
130501 AAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCTATTTTTACCCCCGAACTT
1 AAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTC-ATTTTTACCCCCGAACTT
*
130566 CCAAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCCT
65 CCAAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCCC
* * *
130619 GAACTTCGAAAAATCTCATTTTTGACC-CAAAACTTCCAAAAAGTTCATTTTTA-CCCCGAACTT
1 AAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAA-TTCATTTTTACCCCCGAACTT
* * * * *
130682 GCAAAAAT-CCAATTTTGACCCTAAAACTTCCAACAATTCCATTTTTACCCCTG
65 CCAAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCC-C
130735 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
130749 TATCATTTTA
Statistics
Matches: 226, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
115 40 0.18
116 30 0.13
117 115 0.51
118 41 0.18
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (117 bp):
AAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTCATTTTTACCCCCGAACTTC
CAAAAATCCCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:130758 original size:30 final size:30
Alignment explanation
Indices: 130379--130762 Score: 354
Period size: 29 Copynumber: 13.1 Consensus size: 30
130369 ACTCGAAGGT
*
130379 CCCT-AAACTGTCCAAAAATCCCATTTTTGAC
1 CCCTGAAACT-TCCAAAAATTCCATTTTT-AC
* *
130410 CTC-AAAACTTCCAAAAATTCCATTTTTAC
1 CCCTGAAACTTCCAAAAATTCCATTTTTAC
* *
130439 CCCTG-AACTTCCAAAAA-TCATATTTTTAA
1 CCCTGAAACTTCCAAAAATTC-CATTTTTAC
* * *
130468 CCTTAAAACTTCTAAAAATTCCA-TTTTAC
1 CCCTGAAACTTCCAAAAATTCCATTTTTAC
* *
130497 CCC-CAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTGAAACTTCCAAAAATTCCATTTTT-AC
* *
130527 CTC-GAAACTTCCAAAAATTCTATTTTTAC
1 CCCTGAAACTTCCAAAAATTCCATTTTTAC
* * *
130556 CCCCG-AACTTCCAAAAATCCCATTTTTAA
1 CCCTGAAACTTCCAAAAATTCCATTTTTAC
*
130585 CCCTAAAACTTCCAAAAATTCCATTTTTAC
1 CCCTGAAACTTCCAAAAATTCCATTTTTAC
*
130615 CCCTG-AACTTCGAAAAA-TCTCATTTTTGA-
1 CCCTGAAACTTCCAAAAATTC-CATTTTT-AC
*
130644 CCC-AAAACTTCCAAAAAGTT-CATTTTTAC
1 CCCTGAAACTTCCAAAAA-TTCCATTTTTAC
* *
130673 CCC-G-AACTTGCAAAAA-TCCAATTTTGA-
1 CCCTGAAACTTCCAAAAATTCC-ATTTTTAC
* *
130700 CCCTAAAACTTCCAACAATTCCATTTTTAC
1 CCCTGAAACTTCCAAAAATTCCATTTTTAC
*
130730 CCCTGAAACTTCCAAAAATTATCA-TTTTAC
1 CCCTGAAACTTCCAAAAATT-CCATTTTTAC
130760 CCC
1 CCC
130763 CGGATGTCCG
Statistics
Matches: 290, Mismatches: 41, Indels: 45
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 38 0.13
29 123 0.42
30 112 0.39
31 12 0.04
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (30 bp):
CCCTGAAACTTCCAAAAATTCCATTTTTAC
Done.