Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014437.1 Kokia drynarioides strain JFW-HI SEQ_129475, 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: 154711
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 67 characters in sequence are not A, C, G, or T
Found at i:276 original size:6 final size:6
Alignment explanation
Indices: 262--325 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
252 ATTTGGAAAA
* *
262 TAAATT TAAACT TAAA-T TAAATT TAAATT CGAAA-- TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT TAAATT
*
308 T-AATA TAAATT TAAATT T
1 TAAATT TAAATT TAAATT T
326 CTAAACAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
4 3 0.06
5 9 0.19
6 33 0.69
7 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:302 original size:34 final size:35
Alignment explanation
Indices: 248--357 Score: 125
Period size: 35 Copynumber: 3.1 Consensus size: 35
238 TATAATAATC
*
248 TTAAATTTGGAAAATAAATTTAAACTTAAATTAAAT
1 TTAAATTTCG-AAATAAATTTAAACTTAAATTAAAT
*
284 TTAAA-TTCGAAATAAATTTAAA-TTTAATATAAAT
1 TTAAATTTCGAAATAAATTTAAACTTAAAT-TAAAT
* * ** *
318 TTAAATTTCTAAACAAATTTATTCTTAAAATAAAT
1 TTAAATTTCGAAATAAATTTAAACTTAAATTAAAT
353 TTAAA
1 TTAAA
358 GAGAGTTTGG
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
33 5 0.08
34 23 0.37
35 26 0.41
36 9 0.14
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (35 bp):
TTAAATTTCGAAATAAATTTAAACTTAAATTAAAT
Found at i:325 original size:17 final size:16
Alignment explanation
Indices: 230--357 Score: 98
Period size: 17 Copynumber: 7.4 Consensus size: 16
220 CCTTATTTAT
230 TTTAAATTTATAAT-AA
1 TTTAAATTTA-AATAAA
246 TCTTAAATTTGGAAAATAAA
1 T-TTAAATTT---AAATAAA
*
266 TTTAAACTTAAATTAAA
1 TTTAAATTTAAA-TAAA
*
283 TTTAAATTCGAAATAAA
1 TTTAAATT-TAAATAAA
300 TTTAAATTTAATATAAA
1 TTTAAATTTAA-ATAAA
*
317 TTTAAATTTCTAAACAAA
1 TTTAAA-TT-TAAATAAA
*
335 TTT-ATTCTTAAAATAAA
1 TTTAAAT-TT-AAATAAA
352 TTTAAA
1 TTTAAA
358 GAGAGTTTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
16 8 0.09
17 53 0.58
18 13 0.14
19 13 0.14
20 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:3430 original size:11 final size:11
Alignment explanation
Indices: 3416--3492 Score: 70
Period size: 11 Copynumber: 6.9 Consensus size: 11
3406 TGCCCTTTTT
*
3416 AATTTATTTTA
1 AATTTAATTTA
3427 AATTTATATTT-
1 AATTTA-ATTTA
*
3438 ATTTTAAATTTA
1 AATTT-AATTTA
*
3450 AA-TTAATCTA
1 AATTTAATTTA
3460 AATTTAAATTT-
1 AATTT-AATTTA
3471 AATTTAAATTTA
1 AATTT-AATTTA
3483 AATTTAATTT
1 AATTTAATTT
3493 CAAAATTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 7 0.13
11 34 0.62
12 14 0.25
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:3439 original size:17 final size:16
Alignment explanation
Indices: 3413--3492 Score: 97
Period size: 17 Copynumber: 4.8 Consensus size: 16
3403 CCCTGCCCTT
*
3413 TTTAATTTATTTTAAA
1 TTTAATTTAATTTAAA
*
3429 TTTATATTTATTTTAAA
1 TTTA-ATTTAATTTAAA
* *
3446 TTTAAATTAATCTAAA
1 TTTAATTTAATTTAAA
3462 TTTAAATTTAATTTAAA
1 TTT-AATTTAATTTAAA
3479 TTTAAATTTAATTT
1 TTT-AATTTAATTT
3493 CAAAATTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
16 16 0.28
17 41 0.72
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAATTTAATTTAAA
Found at i:3503 original size:6 final size:6
Alignment explanation
Indices: 3423--3502 Score: 80
Period size: 6 Copynumber: 14.0 Consensus size: 6
3413 TTTAATTTAT
* * *
3423 TTTAAA TTTATA TTT-AT TTTAAA TTTAAA -TT-AA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
3468 TTT-AA TTTAAA TTTAAA TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
3503 AAAGTCTAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
4 2 0.03
5 16 0.26
6 39 0.64
7 4 0.07
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:3606 original size:26 final size:26
Alignment explanation
Indices: 3527--3606 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
3517 AACAATGTTC
3527 AATTACAAATGGCCCAAGTCAGCCCA
1 AATTACAAATGGCCCAAGTCAGCCCA
* * ** *
3553 AA-TAC--ATGACCCAAATGCCATACTA
1 AATTACAAATGGCCC-AA-GTCAGCCCA
3578 AATTACAAATGGCCCAAGTCAGCCCA
1 AATTACAAATGGCCCAAGTCAGCCCA
3604 AAT
1 AAT
3607 GCCCTAAACC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
23 6 0.15
24 2 0.05
25 10 0.26
26 13 0.33
27 2 0.05
28 6 0.15
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.17
Consensus pattern (26 bp):
AATTACAAATGGCCCAAGTCAGCCCA
Found at i:6258 original size:205 final size:205
Alignment explanation
Indices: 5860--6587 Score: 961
Period size: 205 Copynumber: 3.6 Consensus size: 205
5850 GATTATTCAT
* * *
5860 AAACAAGCGACGCAGTCATCTTCCTGATGAGATACT----A-AAGACCAGGTCGAACCCACGCTC
1 AAACAAGAGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
* * * *
5920 GGTATGAGCAAAACTTCGAATCCCAGCTTCCTGGTGAGATACTGAG-A--A-G-C--A--ATAAA
66 GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATTAA
*
5976 ATGGTTAGCTTCCTGATGAGAT-CTTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGA
131 ACGGTTAGCTTCCTGATGAGATAC-TGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGA
* *
6040 GAAACGAATTG
195 GAAGCGGATTG
* *
6051 AAACAAGAGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGAACAAGTCAAACCCACGCTC
1 AAACAAGAGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
6116 GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATTAA
66 GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATTAA
* *
6181 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCCAATTCGTTCTCTTGATGAGATACAGAG
131 ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAG
6246 AAGCGGATTG
196 AAGCGGATTG
* * * *
6256 AAACAA-ACGACGCGGTCATCTTCCTGACGAGATACTGAGAAGAAGACCAAGTCAAACTCATGCT
1 AAACAAGA-GACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCT
* ** *
6320 CGGTATGAGCAAAGCTTCGAATCCCAACTTCCTGGTGAGACACTAAGAAGCAGGTCGAAGCAATA
65 CGGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATTA
*
6385 AACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCTTTCTCCTGATGAGATACAGA
130 AACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGA
6450 GAAGCGGATTG
195 GAAGCGGATTG
* * * * *
6461 AAACAAGAGATGCGGTCATCTTCCTGATGAGATACTAAGAAGACGACCAAATCAAACCCACGCTC
1 AAACAAGAGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
* * * * * ***
6526 GAAGCAAGTG-AAATCTTCGAACCCCAGCTTCCTGACAAGACACCGAGAAGTC-GGTCGAAGCA
66 G--GTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAG-CAGGTCGAAGCA
6588 AGTAATAAAA
Statistics
Matches: 472, Mismatches: 45, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
191 34 0.07
195 1 0.00
196 63 0.13
197 1 0.00
199 1 0.00
200 1 0.00
201 1 0.00
203 1 0.00
204 1 0.00
205 319 0.68
206 44 0.09
207 5 0.01
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (205 bp):
AAACAAGAGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATTAA
ACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACAGAG
AAGCGGATTG
Found at i:6678 original size:211 final size:204
Alignment explanation
Indices: 5860--6722 Score: 883
Period size: 205 Copynumber: 4.2 Consensus size: 204
5850 GATTATTCAT
* * * * *
5860 AAACAAGCGACGCAGTCATCTTCCTGATGAGATACT----A-AAGACCAGGTCGAACCCACGCTC
1 AAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
* * *
5920 GGTATGAGCAAAACTTCGAATCCCAGCTTCCTGGTGAGATACTGAG-A--A-G-C--A--AT-A-
66 GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATAAT
* *
5974 AAATGGTTAGCTTCCTGATGAGAT-CTTGAGAAGTGAACCAAATTCGTTCTCCTGATGAGATACA
131 AAACGGTTAGCTTCCTGATGAGATAC-TGAGAAGTGAACCAAACTC--T-TCCTGATGAGATACA
* *
6038 GAGAAACGAATTG
192 GAGAAGCGGATTG
* *
6051 AAACAAGAGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGAACAAGTCAAACCCACGCTC
1 AAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
6116 GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCAT--T
66 GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATAAT
* *
6179 AAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCCAATTCGTTCTCTTGATGAGATACAG
131 AAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAACTC-TTC-C-TGATGAGATACAG
6244 AGAAGCGGATTG
193 AGAAGCGGATTG
* * * *
6256 AAACAA-ACGACGCGGTCATCTTCCTGACGAGATACTGAGAAGAAGACCAAGTCAAACTCATGCT
1 AAACAAGA-GATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCT
* **
6320 CGGTATGAGCAAAGCTTCGAATCCCAACTTCCTGGTGAGACACTAAGAAGCAGGTCGAAGC--AA
65 CGGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATAA
*
6383 TAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCTTTCTCCTGATGAGATACA
130 TAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAA--CTCT-TCCTGATGAGATACA
6448 GAGAAGCGGATTG
192 GAGAAGCGGATTG
* * *
6461 AAACAAGAGATGCGGTCATCTTCCTGATGAGATACTAAGAAGACGACCAAATCAAACCCACGCTC
1 AAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
* * * * * ***
6526 GAAGCAAGTG-AAATCTTCGAACCCCAGCTTCCTGACAAGACACCGAGAAGTC-GGTCGAAGCAA
66 G--GTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAG-CAGGTCGAAGC-A
* * * * * * * *
6589 GTAATAAAAAGGTTCGCTTCCTGATGAAATACAGGGAAATGAACCAGAACCATCTTCCTAATGAA
127 -TAAT-AAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCA-AA-C-TCTTCCTGATGAG
* * **
6654 ATGCAGAGAAGTGGATCA
187 ATACAGAGAAGCGGATTG
* ** * * * * *
6672 AAACAAGTGATATGGTCGTCTTCTTGATAAAATACTGAGAAGAAGGCCAAG
1 AAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAG
6723 CTAATGGAAC
Statistics
Matches: 569, Mismatches: 68, Indels: 50
0.83 0.10 0.07
Matches are distributed among these distances:
191 34 0.06
195 1 0.00
196 63 0.11
197 1 0.00
199 1 0.00
200 1 0.00
201 1 0.00
203 3 0.01
204 3 0.01
205 304 0.53
206 45 0.08
207 8 0.01
210 3 0.01
211 97 0.17
212 4 0.01
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (204 bp):
AAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTC
GGTATGAGCAAAGCTTCGAATCCCAGCTTCCTGGTGAGACACCGAGAAGCAGGTCGAAGCATAAT
AAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAACTCTTCCTGATGAGATACAGAGA
AGCGGATTG
Found at i:7051 original size:11 final size:11
Alignment explanation
Indices: 7037--7113 Score: 70
Period size: 11 Copynumber: 6.9 Consensus size: 11
7027 CCCCCTTTTT
*
7037 AATTTATTTTA
1 AATTTAATTTA
7048 AATTTATATTT-
1 AATTTA-ATTTA
*
7059 ATTTTAAATTTA
1 AATTT-AATTTA
*
7071 AA-TTAATCTA
1 AATTTAATTTA
7081 AATTTAAATTT-
1 AATTT-AATTTA
7092 AATTTAAATTTA
1 AATTT-AATTTA
7104 AATTTAATTT
1 AATTTAATTT
7114 CAAAATTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 7 0.13
11 34 0.62
12 14 0.25
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:7060 original size:17 final size:16
Alignment explanation
Indices: 7034--7113 Score: 97
Period size: 17 Copynumber: 4.8 Consensus size: 16
7024 GCCCCCCCTT
*
7034 TTTAATTTATTTTAAA
1 TTTAATTTAATTTAAA
*
7050 TTTATATTTATTTTAAA
1 TTTA-ATTTAATTTAAA
* *
7067 TTTAAATTAATCTAAA
1 TTTAATTTAATTTAAA
7083 TTTAAATTTAATTTAAA
1 TTT-AATTTAATTTAAA
7100 TTTAAATTTAATTT
1 TTT-AATTTAATTT
7114 CAAAATTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
16 16 0.28
17 41 0.72
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAATTTAATTTAAA
Found at i:7124 original size:6 final size:6
Alignment explanation
Indices: 7044--7123 Score: 80
Period size: 6 Copynumber: 14.0 Consensus size: 6
7034 TTTAATTTAT
* * *
7044 TTTAAA TTTATA TTT-AT TTTAAA TTTAAA -TT-AA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
7089 TTT-AA TTTAAA TTTAAA TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
7124 AAAGTCTAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
4 2 0.03
5 16 0.26
6 39 0.64
7 4 0.07
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:7227 original size:26 final size:26
Alignment explanation
Indices: 7148--7227 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
7138 AACAATGTTC
7148 AATTACAAATGGCCCAAGTCAGCCCA
1 AATTACAAATGGCCCAAGTCAGCCCA
* * ** *
7174 AA-TAC--ATGACCCAAATGCCATACTA
1 AATTACAAATGGCCC-AA-GTCAGCCCA
7199 AATTACAAATGGCCCAAGTCAGCCCA
1 AATTACAAATGGCCCAAGTCAGCCCA
7225 AAT
1 AAT
7228 GCCCTAAACC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
23 6 0.15
24 2 0.05
25 10 0.26
26 13 0.33
27 2 0.05
28 6 0.15
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.17
Consensus pattern (26 bp):
AATTACAAATGGCCCAAGTCAGCCCA
Found at i:7893 original size:24 final size:22
Alignment explanation
Indices: 7841--7894 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
7831 TTTCTTAATA
*
7841 ATTAATAATAATAATAAATGTT
1 ATTAATAATAATAATAAATATT
*
7863 -TTGATAATAATAATAATGATATT
1 ATTAATAATAATAATAA--ATATT
7886 ATTAATAAT
1 ATTAATAAT
7895 TATTAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 15 0.58
23 4 0.15
24 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (22 bp):
ATTAATAATAATAATAAATATT
Found at i:8967 original size:30 final size:29
Alignment explanation
Indices: 8900--9236 Score: 324
Period size: 29 Copynumber: 11.5 Consensus size: 29
8890 AGAGGTCCCT
*
8900 AAACTATCCAAAAATTCCATTTTTACCCTC-
1 AAACT-TCCAAAAATCCCATTTTTACCC-CA
*
8930 GAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
*
8960 AAACTTCCAAAAAATTCCATTTTTACCCTC-
1 AAACTTCC-AAAAATCCCATTTTTACCC-CA
* * * * * **
8990 GAATTTCTAAAAATCTCATTTTTA-ACTT
1 AAACTTCCAAAAATCCCATTTTTACCCCA
*
9018 AAACTTCCAAAAATCCCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTACCCCA
*
9047 AAACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
* *
9077 AAACTACCAAAAATTCCA-TTTTACCCTC-
1 AAACTTCCAAAAATCCCATTTTTACCC-CA
* * * *
9105 GAACTTTCAAAAATCTCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTACCCCA
*
9134 AAACTTCTAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
** *
9164 AAACTTCCAAAAATTTCATTTTTACCCCC
1 AAACTTCCAAAAATCCCATTTTTACCCCA
* * * *
9193 GAGCTTCCAAAAATCTCATTTTTGACCCTA
1 AAACTTCCAAAAATCCCATTTTT-ACCCCA
9223 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
9237 TATCATTTTA
Statistics
Matches: 252, Mismatches: 43, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
28 38 0.15
29 114 0.45
30 85 0.34
31 15 0.06
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCA
Found at i:9089 original size:87 final size:89
Alignment explanation
Indices: 8900--9236 Score: 402
Period size: 87 Copynumber: 3.8 Consensus size: 89
8890 AGAGGTCCCT
*
8900 AAACTATCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
1 AAACTA-CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCTAAACT
*
8965 TCCAAAAAATTCCATTTTT-ACCCTC-
65 TCC-AAAAATCCCATTTTTGA-CCTCA
* * * * * **
8990 GAATTTCTAAAAA-TCTCATTTTTA-ACTTAAACTTCCAAAAATCCCATTTTT-ACCCCTAAACT
1 AAACTACCAAAAATTC-CATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCTAAACT
9052 TCCAAAAATCCCATTTTTGACCTCA
65 TCCAAAAATCCCATTTTTGACCTCA
* *
9077 AAACTACCAAAAATTCCA-TTTTACCCTCGAACTTTCAAAAATCTCATTTTT-ACCCCTAAACTT
1 AAACTACCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCTAAACTT
* *
9140 CTAAAAATCCCATTTTTGACCCCA
66 CCAAAAATCCCATTTTTGACCTCA
* * * * * *
9164 AAACTTCCAAAAATTTCATTTTTACCCCCGAGCTTCCAAAAATCTCATTTTTGA-CCCTAAAACT
1 AAACTACCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCT-AAACT
9228 TCCAAAAAT
65 TCCAAAAAT
9237 TATCATTTTA
Statistics
Matches: 213, Mismatches: 26, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
86 23 0.11
87 97 0.46
88 62 0.29
89 28 0.13
90 3 0.01
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (89 bp):
AAACTACCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCCTAAACTT
CCAAAAATCCCATTTTTGACCTCA
Found at i:9184 original size:59 final size:58
Alignment explanation
Indices: 8896--9251 Score: 371
Period size: 59 Copynumber: 6.1 Consensus size: 58
8886 CCTCAGAGGT
* * *
8896 CCCTAAACTATCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAAC
1 CCCTAAACT-TCCAAAAATCCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTT-AC
* * * * *
8956 CCCAAAACTTCCAAAAAATTCCATTTTTACCCTCGAATTTCTAAAAATCTCATTTTTA-
1 CCCTAAACTTCC-AAAAATCCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTTAC
* * *
9014 ACTTAAACTTCCAAAAATCCCATTTTTACCC-CTAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATCCCATTTTTACCCTC-AAACTTCCAAAAATCTCATTTTT-AC
* * * * * *
9073 CTCAAAACTACCAAAAATTCCA-TTTTACCCTCGAACTTTCAAAAATCTCATTTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTTAC
* *
9130 CCCTAAACTTCTAAAAATCCCATTTTTGACCC-CAAAACTTCCAAAAATTTCATTTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTT-ACCCTC-AAACTTCCAAAAATCTCATTTTTAC
** * * * *
9189 CCCCGAGCTTCCAAAAATCTCATTTTTGACCCTAAAACTTCCAAAAATTATCA-TTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTT-ACCCTCAAACTTCCAAAAA-TCTCATTTTTAC
9248 CCCT
1 CCCT
9252 GGATGTCCGA
Statistics
Matches: 249, Mismatches: 37, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
56 1 0.00
57 56 0.22
58 43 0.17
59 96 0.39
60 53 0.21
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.33
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATCCCATTTTTACCCTCAAACTTCCAAAAATCTCATTTTTAC
Found at i:17978 original size:16 final size:18
Alignment explanation
Indices: 17957--17990 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
17947 AACAATATGA
17957 TTAGATTA-ATTT-AAAT
1 TTAGATTATATTTGAAAT
17973 TTAGATTATATTTGAAAT
1 TTAGATTATATTTGAAAT
17991 AGATTAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
TTAGATTATATTTGAAAT
Found at i:20691 original size:15 final size:15
Alignment explanation
Indices: 20671--20700 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20661 AGTGCTCATG
20671 TTTTAAAATATATAT
1 TTTTAAAATATATAT
*
20686 TTTTAATATATATAT
1 TTTTAAAATATATAT
20701 AAATTTTTAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTAAAATATATAT
Found at i:21157 original size:39 final size:36
Alignment explanation
Indices: 21072--21172 Score: 105
Period size: 39 Copynumber: 2.7 Consensus size: 36
21062 ATATATTTCA
* * * *
21072 ATTTTCCGTATGATTTGTTTTAGTATAAGTTGAGAT
1 ATTTTCCGTATGATTTATTTAAGTATAAATTGAAAT
21108 ATATTT-CGTATGATTTATCTCTCAAGTATAAATTGAAAT
1 AT-TTTCCGTATGATTTAT-T-T-AAGTATAAATTGAAAT
* *
21147 ATTTTCCGTATGAATTATTTTAGTAT
1 ATTTTCCGTATGATTTATTTAAGTAT
21173 TGAGAGATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
36 18 0.33
37 5 0.09
38 5 0.09
39 26 0.48
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (36 bp):
ATTTTCCGTATGATTTATTTAAGTATAAATTGAAAT
Found at i:21264 original size:21 final size:22
Alignment explanation
Indices: 21226--21270 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
21216 CATTATCTCT
* *
21226 CAAGTATCGATCTGTTTCA-TA
1 CAAGTATCGATATATTTCAGTA
*
21247 CAAGTATTGATATATTTCAGTA
1 CAAGTATCGATATATTTCAGTA
21269 CA
1 CA
21271 CCAATGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
CAAGTATCGATATATTTCAGTA
Found at i:29114 original size:15 final size:16
Alignment explanation
Indices: 29079--29114 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
29069 CAACGTAATT
29079 TTTTTCAAATGGCTAA
1 TTTTTCAAATGGCTAA
*
29095 TTTTT-AAATGGTTAA
1 TTTTTCAAATGGCTAA
29110 TTTTT
1 TTTTT
29115 TTTTTCTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (16 bp):
TTTTTCAAATGGCTAA
Found at i:29114 original size:16 final size:17
Alignment explanation
Indices: 29078--29115 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
29068 TCAACGTAAT
29078 TTTTTTCAAATGGCTAA
1 TTTTTTCAAATGGCTAA
*
29095 -TTTTT-AAATGGTTAA
1 TTTTTTCAAATGGCTAA
29110 TTTTTT
1 TTTTTT
29116 TTTTCTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (17 bp):
TTTTTTCAAATGGCTAA
Found at i:30801 original size:9 final size:9
Alignment explanation
Indices: 30786--30820 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
30776 TAAATTATCT
30786 TATTATTAA
1 TATTATTAA
* *
30795 CATTATTAT
1 TATTATTAA
30804 TATTATTAA
1 TATTATTAA
30813 TATTATTA
1 TATTATTA
30821 TAACTTGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (9 bp):
TATTATTAA
Found at i:34829 original size:21 final size:21
Alignment explanation
Indices: 34800--34840 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
34790 TTAAGGGTAG
34800 CCAAGAATTTCATGAAGTTGA
1 CCAAGAATTTCATGAAGTTGA
* *
34821 CCAATAATTTCTTGAAGTTG
1 CCAAGAATTTCATGAAGTTG
34841 GCCAGGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (21 bp):
CCAAGAATTTCATGAAGTTGA
Found at i:35327 original size:56 final size:56
Alignment explanation
Indices: 35266--35371 Score: 149
Period size: 56 Copynumber: 1.9 Consensus size: 56
35256 TTTCCAAATA
* * *
35266 CCCAAAAATATTTTTTCGAGTGTACCATCCCATGGCTGAGACCCATTTTTGCAGGT
1 CCCAAAAATATTTTTACGAGTGTACCATCCCATGACTGAGACCCACTTTTGCAGGT
* * * *
35322 CCCAAAAATATTTTTAGGTGTTTACCATCCCATGATTGAGACCCACTTTT
1 CCCAAAAATATTTTTACGAGTGTACCATCCCATGACTGAGACCCACTTTT
35372 AATCCTAGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 43 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (56 bp):
CCCAAAAATATTTTTACGAGTGTACCATCCCATGACTGAGACCCACTTTTGCAGGT
Found at i:35732 original size:18 final size:18
Alignment explanation
Indices: 35709--35745 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
35699 AATAAAGCTT
35709 GTTGATGATAATGATTTA
1 GTTGATGATAATGATTTA
35727 GTTGATGATAATGATTTA
1 GTTGATGATAATGATTTA
35745 G
1 G
35746 GGACAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.43
Consensus pattern (18 bp):
GTTGATGATAATGATTTA
Found at i:48612 original size:41 final size:41
Alignment explanation
Indices: 48562--48758 Score: 225
Period size: 41 Copynumber: 4.8 Consensus size: 41
48552 AACCATATTA
* * * *
48562 TCATTCTCATCACGAGACACGAGTCTTCCTTAATCAAAATT
1 TCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAGTC
* * *
48603 TCATTCTCATTTCGAGACATGAGTCTTCCTTATTCATAGTC
1 TCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAGTC
* *
48644 TCATTCTCATCTCGAGACATGAGTCTTCCTTATTCATAGTC
1 TCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAGTC
* * **
48685 TCATTCTTATCTCGAGATATGAGTCTTCCATTTATAT-AATTTC
1 TCATTCTCATCTCGAGACATGAGTCTTCC--TTA-ATCAAAGTC
* *
48728 TCATGCTCAACTCGAGACATGAGTCTTCCTT
1 TCATTCTCATCTCGAGACATGAGTCTTCCTT
48759 TTTATACACC
Statistics
Matches: 135, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
41 103 0.76
43 31 0.23
44 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.39
Consensus pattern (41 bp):
TCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAGTC
Found at i:48742 original size:43 final size:43
Alignment explanation
Indices: 48531--48764 Score: 216
Period size: 41 Copynumber: 5.6 Consensus size: 43
48521 TTACGCTTTA
* * ** * *
48531 TCGAGTCATAAGTCTTCCTTTA-ACCATATTATCATTCTCATC
1 TCGAGACATGAGTCTTCCTTTATATAATAGTCTCATTCTCATC
* * * * *
48573 ACGAGACACGAGTCTTCC-TTA-ATCAA-AATTTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTTATAT-AATAGTCTCATTCTCATC
*
48614 TCGAGACATGAGTCTTCC-TTAT-TCATAGTCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTTATATAATAGTCTCATTCTCATC
* *
48655 TCGAGACATGAGTCTTCC-TTAT-TCATAGTCTCATTCTTATC
1 TCGAGACATGAGTCTTCCTTTATATAATAGTCTCATTCTCATC
* * * *
48696 TCGAGATATGAGTCTTCCATTTATATAAT-TTCTCATGCTCAAC
1 TCGAGACATGAGTCTTCC-TTTATATAATAGTCTCATTCTCATC
*
48739 TCGAGACATGAGTCTTCCTTTTTATA
1 TCGAGACATGAGTCTTCCTTTATATA
48765 CACCAAGTAT
Statistics
Matches: 162, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.01
41 105 0.65
42 22 0.14
43 31 0.19
44 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (43 bp):
TCGAGACATGAGTCTTCCTTTATATAATAGTCTCATTCTCATC
Found at i:49599 original size:22 final size:21
Alignment explanation
Indices: 49552--49599 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
49542 GACTTTCATA
*
49552 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
49573 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
49595 ATTAA
1 ATTAA
49600 TCAATATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:54174 original size:21 final size:21
Alignment explanation
Indices: 54150--54227 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
54140 CCTGCAACTT
54150 CTACCGATACAAGTATTCTAA
1 CTACCGATACAAGTATTCTAA
* * *
54171 CTACCAATACAAATATGCTCAGTA
1 CTACCGATACAAGTATTCT-A--A
* ** * *
54195 CTACCGAAACTTGAATTTTAA
1 CTACCGATACAAGTATTCTAA
54216 CTACCGATACAA
1 CTACCGATACAA
54228 ATATGCTTAG
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
21 26 0.65
22 1 0.03
23 1 0.03
24 12 0.30
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTATTCTAA
Found at i:54852 original size:41 final size:41
Alignment explanation
Indices: 54775--55033 Score: 306
Period size: 41 Copynumber: 6.2 Consensus size: 41
54765 TCAAGTCATA
** * *
54775 AGTCTTCCTTTAACCATATTCTAATTCTCATCTCGAGACATG
1 AGTCTTCC-TTATTCATAGTCTCATTCTCATCTCGAGACATG
* * * *
54817 AGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGACATG
1 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCGAGACATG
54858 AGTCTTCCTTATTCATAGTCTCATTCTCATCT-GAAGACATG
1 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCG-AGACATG
* *
54899 AGTATGCCTTATTCATAGTCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCGAGACATG
*
54940 AGTCTTTCTTATTCATAGTCTCATTCTCATCTCGAGACATG
1 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCGAGACATG
* * * * * *
54981 AGTCTTCCATTTATATAAT-TTCTCATGCTCAACACAAGACATG
1 AGTCTTCC--TTAT-TCATAGTCTCATTCTCATCTCGAGACATG
55024 AGTCTTCCTT
1 AGTCTTCCTT
55034 TTTATACACC
Statistics
Matches: 191, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.01
41 147 0.77
42 9 0.05
43 31 0.16
44 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (41 bp):
AGTCTTCCTTATTCATAGTCTCATTCTCATCTCGAGACATG
Found at i:55882 original size:22 final size:21
Alignment explanation
Indices: 55835--55887 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
55825 GACTTTCATA
*
55835 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
55856 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
55878 ATTAA-TTAAT
1 ATTAACTTAAT
55888 ATTTGTCATG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 5 0.19
21 4 0.15
22 17 0.65
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:56192 original size:11 final size:11
Alignment explanation
Indices: 56176--56288 Score: 51
Period size: 11 Copynumber: 10.6 Consensus size: 11
56166 ATTTCGATTT
56176 TTTTTTAAATA
1 TTTTTTAAATA
56187 TTTTTT---TA
1 TTTTTTAAATA
**
56195 TTTTCCAAATA
1 TTTTTTAAATA
56206 TTTTTT--ATA
1 TTTTTTAAATA
*
56215 -TTTTCAAAT-
1 TTTTTTAAATA
*
56224 TTTTTAAAATTA
1 TTTTTTAAA-TA
*
56236 TATTTTCAAAATA
1 T-TTTT-TAAATA
*
56249 TTTTTTACATA
1 TTTTTTAAATA
** *
56260 TACTTTACATA
1 TTTTTTAAATA
**
56271 TTTTCGAAATA
1 TTTTTTAAATA
56282 TTTTTTA
1 TTTTTTA
56289 GTTTTCTAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
8 10 0.13
9 3 0.04
10 9 0.12
11 37 0.49
12 5 0.07
13 7 0.09
14 4 0.05
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:56204 original size:19 final size:19
Alignment explanation
Indices: 56177--56255 Score: 79
Period size: 19 Copynumber: 3.9 Consensus size: 19
56167 TTTCGATTTT
*
56177 TTTTTAAATATTTTTT-TA
1 TTTTCAAATATTTTTTATA
56195 TTTTCCAAATATTTTTTATA
1 TTTT-CAAATATTTTTTATA
*
56215 TTTTCAAATTTTTTAAAATTATA
1 TTTTCAAATATTTT----TTATA
56238 TTTTCAAAATATTTTTTA
1 TTTTC-AAATATTTTTTA
56256 CATATACTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 4 0.08
19 20 0.39
20 9 0.18
23 10 0.20
24 8 0.16
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTCAAATATTTTTTATA
Found at i:56400 original size:21 final size:22
Alignment explanation
Indices: 56351--56397 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
56341 TCCATATATA
*
56351 TTTTATATTTTTAAATTATTTT
1 TTTTACATTTTTAAATTATTTT
56373 TTTTACATTTTTGAAA-TATTTT
1 TTTTACATTTTT-AAATTATTTT
56395 TTT
1 TTT
56398 ACAAATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTACATTTTTAAATTATTTT
Found at i:57342 original size:30 final size:31
Alignment explanation
Indices: 57302--57364 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
57292 AATTTTTATT
57302 TTTTCGTTTAT-TTTATAAATTTAATTTGTAA
1 TTTTCGTTTATATTT-TAAATTTAATTTGTAA
57333 TTTT-GTTTATATTTTAAATTTAATTTGTAA
1 TTTTCGTTTATATTTTAAATTTAATTTGTAA
57363 TT
1 TT
57365 ATTATTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 24 0.77
31 7 0.23
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (31 bp):
TTTTCGTTTATATTTTAAATTTAATTTGTAA
Found at i:57407 original size:22 final size:21
Alignment explanation
Indices: 57360--57408 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
57350 ATTTAATTTG
*
57360 TAATTA-TTATTTTTTCAATA
1 TAATTATTTAATTTTTCAATA
57380 T-A-TATTTAATTTTTCAATAA
1 TAATTATTTAATTTTTCAAT-A
57400 TAATTATTT
1 TAATTATTT
57409 CCCCACATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 3 0.12
21 1 0.04
22 5 0.21
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTATTTAATTTTTCAATA
Found at i:58278 original size:61 final size:61
Alignment explanation
Indices: 58159--58341 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 61
58149 GGGTTGGTCG
* * *
58159 ACACCCAAAAAATATA--TTTTTTCTATCTGAAAAAGGAGGTGTCGATCATGGCTTGGCAA
1 ACACCCAAAAAATATATTTTTTTTATATCTGAAAAAGGAGGTGTAGACCATGGCTTGGCAA
*
58218 ACACCCAAAAAATATATTTTTTTTATATCT-AATAAA-GAGTGTGTTAG-CCATTGCTTGGCAA
1 ACACCCAAAAAATATATTTTTTTTATATCTGAA-AAAGGAG-GTG-TAGACCATGGCTTGGCAA
* *
58279 ACACCC--AAAA-ATA--TTTTTT-TATCTGAAAAAGGGGGTGTCGACCATGGCTTGGCAA
1 ACACCCAAAAAATATATTTTTTTTATATCTGAAAAAGGAGGTGTAGACCATGGCTTGGCAA
*
58334 ATACCCAA
1 ACACCCAA
58342 GTTTTTTTAT
Statistics
Matches: 106, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
54 2 0.02
55 29 0.27
56 10 0.09
58 3 0.03
59 20 0.19
60 5 0.05
61 35 0.33
62 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (61 bp):
ACACCCAAAAAATATATTTTTTTTATATCTGAAAAAGGAGGTGTAGACCATGGCTTGGCAA
Found at i:58372 original size:53 final size:54
Alignment explanation
Indices: 58172--58406 Score: 176
Period size: 61 Copynumber: 4.2 Consensus size: 54
58162 CCCAAAAAAT
*
58172 ATATTTTTTCTATCTGAAAAAG-GAGGTGTCGATCATGGCTTGGCAAACACCCAAAAAA
1 ATATTTTTT-TATCTGAAAAAGAG-GGTGTCGACCATGGCTTGGCAAACACCC---AAA
* * *
58230 TATATTTTTTTTATATCT-AATAAAGAGTGTGT-TAGCCATTGCTTGGCAAACACCCAAAA
1 -ATA--TTTTTT-TATCTGAA-AAAGAGGGTGTCGA-CCATGGCTTGGCAAACACCC-AAA
* *
58289 ATATTTTTTTATCTGAAAAAGGGGGTGTCGACCATGGCTTGGCAAATACCC-AA
1 ATATTTTTTTATCTGAAAAAGAGGGTGTCGACCATGGCTTGGCAAACACCCAAA
* * * * * *
58342 GT-TTTTTTATATCTGGAAAAA-AGGGTGTCGACTATTGCATGGTATACACCCAAA
1 ATATTTTTT-TATCT-GAAAAAGAGGGTGTCGACCATGGCTTGGCAAACACCCAAA
*
58396 AAATTTATTTT
1 ATATTT-TTTT
58407 TTATTAATAT
Statistics
Matches: 144, Mismatches: 20, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
52 6 0.04
53 31 0.22
54 8 0.06
55 36 0.25
56 12 0.08
58 3 0.02
59 7 0.05
60 3 0.02
61 37 0.26
62 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (54 bp):
ATATTTTTTTATCTGAAAAAGAGGGTGTCGACCATGGCTTGGCAAACACCCAAA
Found at i:59321 original size:20 final size:20
Alignment explanation
Indices: 59284--59322 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
59274 TAATGCCACC
59284 ATTTTTGTCAAATCATTTATT
1 ATTTTTGTCAAA-CATTTATT
59305 ATTTTTGTCTAAA-ATTTA
1 ATTTTTGTC-AAACATTTA
59323 AATTTAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 9 0.53
22 3 0.18
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTTTTGTCAAACATTTATT
Found at i:59353 original size:25 final size:26
Alignment explanation
Indices: 59324--59375 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
59314 TAAAATTTAA
* *
59324 ATTTAAAACATTATTATT-TAAATAT
1 ATTTAAAAAATAATTATTATAAATAT
59349 ATTTAAAAAATAATTATTAATAAATAT
1 ATTTAAAAAATAATTATT-ATAAATAT
59376 GGTGGTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 16 0.70
27 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTTAAAAAATAATTATTATAAATAT
Found at i:59393 original size:122 final size:132
Alignment explanation
Indices: 59245--59569 Score: 418
Period size: 138 Copynumber: 2.5 Consensus size: 132
59235 GAGGTTAAAA
* ** *
59245 AATAAATATGATGGTGGAGCCGTTTAATATAATGCCACCATTTTTGTCAAATCATTTATTATTTT
1 AATAAATATGATGGTGGAGCCATTTAATATGGTGCCACCACTTTTGTCAAATCATTTATTATTTT
* *
59310 TGTCTAAAATTTAAATTT-AAAACAT-TATTATTT-AA-A-T-A-T-A-TTT-AAAAAATAATTA
66 TATCTAAAATTTAAATTTAAAAAAATATATTATTTAAATATTAATTAAGTTTCAAAAAATAATTA
59365 TT
131 TT
* * * *
59367 AATAAATATGGTGGTGAAACCATTTAATAGGGTGCCACCACTTTTGTCAAATCATTTATTATTTT
1 AATAAATATGATGGTGGAGCCATTTAATATGGTGCCACCACTTTTGTCAAATCATTTATTA-TTT
59432 TTATCTAAAATTTAAATTTAAAAAAATATATTATTTAAATATGTTAGATTTAAGGTTTCAAAAAA
65 TTATCTAAAATTTAAATTTAAAAAAATATATTATTTAAATA--TTA-A-TTAA-GTTTCAAAAAA
59497 TAATTATT
125 TAATTATT
* *
59505 AATAAATATGATGGTGGAGCCATTTAATATGGTGCCACCACTTTTGTTAAATGATTTATTATTTT
1 AATAAATATGATGGTGGAGCCATTTAATATGGTGCCACCACTTTTGTCAAATCATTTATTATTTT
59570 AAATTTATCT
Statistics
Matches: 171, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
122 53 0.31
123 21 0.12
124 6 0.04
125 8 0.05
126 2 0.01
127 1 0.01
130 1 0.01
132 1 0.01
134 1 0.01
135 1 0.01
137 7 0.04
138 69 0.40
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (132 bp):
AATAAATATGATGGTGGAGCCATTTAATATGGTGCCACCACTTTTGTCAAATCATTTATTATTTT
TATCTAAAATTTAAATTTAAAAAAATATATTATTTAAATATTAATTAAGTTTCAAAAAATAATTA
TT
Found at i:64312 original size:11 final size:11
Alignment explanation
Indices: 64296--64324 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
64286 GATATGAGTA
64296 TGAATTGTTGT
1 TGAATTGTTGT
64307 TGAATTGTTGT
1 TGAATTGTTGT
64318 TGAATTG
1 TGAATTG
64325 GTTAATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (11 bp):
TGAATTGTTGT
Found at i:68259 original size:20 final size:20
Alignment explanation
Indices: 68218--68262 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
68208 CATGATTTGT
**
68218 ATTAAGATTAAATAGGCTTA
1 ATTAAGATTAAATAGGAATA
68238 ATTAAGATTAAA-AGAGAATA
1 ATTAAGATTAAATAG-GAATA
68258 ATTAA
1 ATTAA
68263 ATCTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.31
Consensus pattern (20 bp):
ATTAAGATTAAATAGGAATA
Found at i:72008 original size:22 final size:21
Alignment explanation
Indices: 71983--72030 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
71973 CAAATATTGA
*
71983 TTAATAATAGGATAAATTAAGG
1 TTAATAAGAGGATAAATTAA-G
* * *
72005 TTAAAAAGATGATTAATTAAG
1 TTAATAAGAGGATAAATTAAG
72026 TTAAT
1 TTAAT
72031 TATGAAAGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (21 bp):
TTAATAAGAGGATAAATTAAG
Found at i:72925 original size:41 final size:41
Alignment explanation
Indices: 72880--73020 Score: 174
Period size: 41 Copynumber: 3.4 Consensus size: 41
72870 TATATAAATG
* *
72880 GAAGACTCATGTCTCGAAATAAGAATGAGATTATGAATAAA
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAAA
* *
72921 GAAGACTCATGTCTCAAAATGAGAATGAGATTTTGATTAAA
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAAA
* * * * *
72962 AAAGACACATGTCTCGAGATGAGAATGAGAATATGGTTAAA
1 GAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAAA
* *
73003 GGAAGACTTATGACTCGA
1 -GAAGACTCATGTCTCGA
73021 TAGAGCATAA
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 71 0.85
42 13 0.15
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.25
Consensus pattern (41 bp):
GAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTAAA
Found at i:73602 original size:27 final size:27
Alignment explanation
Indices: 73572--73647 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 27
73562 CGGTAGTTGA
73572 ATTTCAAGTTTCCGTAGTACTAAGCAT
1 ATTTCAAGTTTCCGTAGTACTAAGCAT
* *
73599 ATTT---GTATCGGTAGT--T--G-A-
1 ATTTCAAGTTTCCGTAGTACTAAGCAT
73617 ATTTCAAGTTTCCGTAGTACTAAGCAT
1 ATTTCAAGTTTCCGTAGTACTAAGCAT
73644 ATTT
1 ATTT
73648 GTATCGGTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 1 0.03
21 9 0.25
22 1 0.03
23 1 0.03
24 9 0.25
25 1 0.03
26 1 0.03
27 8 0.22
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (27 bp):
ATTTCAAGTTTCCGTAGTACTAAGCAT
Found at i:73620 original size:45 final size:45
Alignment explanation
Indices: 73556--73664 Score: 209
Period size: 45 Copynumber: 2.4 Consensus size: 45
73546 CTGACTTGAG
73556 TTGTATCGGTAGTTGAATTTCAAGTTTCCGTAGTACTAAGCATAT
1 TTGTATCGGTAGTTGAATTTCAAGTTTCCGTAGTACTAAGCATAT
73601 TTGTATCGGTAGTTGAATTTCAAGTTTCCGTAGTACTAAGCATAT
1 TTGTATCGGTAGTTGAATTTCAAGTTTCCGTAGTACTAAGCATAT
73646 TTGTATCGGTAGTTAGAAT
1 TTGTATCGGTAGTT-GAAT
73665 ACTTGTATCG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 59 0.94
46 4 0.06
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (45 bp):
TTGTATCGGTAGTTGAATTTCAAGTTTCCGTAGTACTAAGCATAT
Found at i:81602 original size:137 final size:136
Alignment explanation
Indices: 81384--81682 Score: 417
Period size: 137 Copynumber: 2.2 Consensus size: 136
81374 TGATGCCACC
81384 CTTTTGTCAAATCA-TTTATTATTTTTACTTAAATTTTAAATTTTAAAAAATTATTATTAAATAT
1 CTTTTGTCAAATCATTTTATTATTTTTACTTAAATTTTAAATTTTAAAAAATTATTATTAAATAT
* * *
81448 GTCAAATTTAGAGTTTCAAAAAATAATTATTAATAAATATGATAGTGAAACCATTTAATATGACG
66 GTCAAATTTAAAATTTCAAAAAATAATTATTAATAAATATGATAGTGAAACCATTTAATATGACA
*
81513 TCATTA
131 TCATCA
* * * *
81519 TTTTTATCAAATCATTATTATTATTTTTTCTTAAA-TTTAAA-TTTAAAAACCTTATTATTCAAA
1 CTTTTGTCAAATCATT-TTATTATTTTTACTTAAATTTTAAATTTTAAAAA-ATTATTATT-AAA
* * **
81582 TATGTTAAGTTTAAAATTTCAAAAAATAATTATTAATAAATATGATAGTGAAGTCATTTAATATG
63 TATGTCAAATTTAAAATTTCAAAAAATAATTATTAATAAATATGATAGTGAAACCATTTAATATG
*
81647 GCATCATCA
128 ACATCATCA
*
81656 CTTTTGTCAAATCA-TTTATTTTTTTTA
1 CTTTTGTCAAATCATTTTATTATTTTTA
81683 AATTATCTGG
Statistics
Matches: 143, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
135 30 0.21
136 16 0.11
137 97 0.68
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (136 bp):
CTTTTGTCAAATCATTTTATTATTTTTACTTAAATTTTAAATTTTAAAAAATTATTATTAAATAT
GTCAAATTTAAAATTTCAAAAAATAATTATTAATAAATATGATAGTGAAACCATTTAATATGACA
TCATCA
Found at i:85116 original size:21 final size:21
Alignment explanation
Indices: 85072--85116 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
85062 ACGATACCTG
* *
85072 CAAAAAGAAAGAGAAACAAGA
1 CAAAAAGAAAGAAAAACAAAA
* *
85093 CAAAACGAAAGAAAAAGAAAA
1 CAAAAAGAAAGAAAAACAAAA
85114 CAA
1 CAA
85117 TTTCTTTATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.73, C:0.11, G:0.16, T:0.00
Consensus pattern (21 bp):
CAAAAAGAAAGAAAAACAAAA
Found at i:86062 original size:30 final size:30
Alignment explanation
Indices: 86026--86085 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
86016 TCCATGTGGT
* * *
86026 CCCCGTACTTTCCAAGGTTTTTGATTTGAG
1 CCCCGTACTTTCCAAAGTTTCTAATTTGAG
86056 CCCCGTACTTTCCAAAGTTTCTAATTTGAG
1 CCCCGTACTTTCCAAAGTTTCTAATTTGAG
86086 TCTCGTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (30 bp):
CCCCGTACTTTCCAAAGTTTCTAATTTGAG
Found at i:86205 original size:16 final size:16
Alignment explanation
Indices: 86184--86218 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
86174 CCCCTTCATC
*
86184 TTTAATTCATTTTTAA
1 TTTAATCCATTTTTAA
86200 TTTAATCCATTTTTAA
1 TTTAATCCATTTTTAA
86216 TTT
1 TTT
86219 CTTTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAATCCATTTTTAA
Found at i:86657 original size:109 final size:110
Alignment explanation
Indices: 86521--86739 Score: 332
Period size: 109 Copynumber: 2.0 Consensus size: 110
86511 AAAAAAAGGT
* *
86521 AATGTTCTTTTATTTAGGAAATTCGAGAAGTTGTGCTCAAACGTATTGAGTATAATTTTTT-CTT
1 AATGTTATTTTATTTAGGAAATTCGAGAAGTTGTGCTCAAACGTACTGAGTATAATTTTTTCCTT
* *
86585 TGAACCTAAATAATCGAGTATTCTATTTAAAATCAATAAATGTTC
66 TGAACCTAAATAATCGAGTATCCTATTTAAAATCAATAAAGGTTC
* * * *
86630 AATGTTATTTTATTTAGGGAATTCGAGAAGTTGTGCTTAAACGTACTGGGTATGATTTTTTCCTT
1 AATGTTATTTTATTTAGGAAATTCGAGAAGTTGTGCTCAAACGTACTGAGTATAATTTTTTCCTT
* * *
86695 TTAACTTAAATAATCGAGTATCCTATTTTAAATCAATAAAGGTTC
66 TGAACCTAAATAATCGAGTATCCTATTTAAAATCAATAAAGGTTC
86740 GTTATTTCGA
Statistics
Matches: 98, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
109 55 0.56
110 43 0.44
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (110 bp):
AATGTTATTTTATTTAGGAAATTCGAGAAGTTGTGCTCAAACGTACTGAGTATAATTTTTTCCTT
TGAACCTAAATAATCGAGTATCCTATTTAAAATCAATAAAGGTTC
Found at i:86905 original size:18 final size:18
Alignment explanation
Indices: 86879--86913 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
86869 ACATTTAAGG
*
86879 ATCGCATTTTAAATTTTA
1 ATCGAATTTTAAATTTTA
*
86897 ATCGAATTTTCAATTTT
1 ATCGAATTTTAAATTTT
86914 TCAACAATCA
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:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (18 bp):
ATCGAATTTTAAATTTTA
Found at i:87199 original size:26 final size:27
Alignment explanation
Indices: 87162--87212 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
87152 TTTCGACAGT
87162 TTTATTTAATTTGTTTGTTA-TTTATTA
1 TTTATTTAATTT-TTTGTTACTTTATTA
*
87189 TTTA-TTAATTTTTTTTTACTTTAT
1 TTTATTTAATTTTTTGTTACTTTAT
87213 CTTAGTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 12 0.55
27 4 0.18
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (27 bp):
TTTATTTAATTTTTTGTTACTTTATTA
Found at i:89687 original size:31 final size:31
Alignment explanation
Indices: 89652--89713 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
89642 TGTATCAAAT
89652 TTAATTGGTTCATGTAACAAAAAAAAAAAAA
1 TTAATTGGTTCATGTAACAAAAAAAAAAAAA
* *
89683 TTAATTGGTTCATGTAACCAAAAAGAAAAAA
1 TTAATTGGTTCATGTAACAAAAAAAAAAAAA
89714 GAGTTAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (31 bp):
TTAATTGGTTCATGTAACAAAAAAAAAAAAA
Found at i:90352 original size:26 final size:24
Alignment explanation
Indices: 90298--90357 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
90288 TATTTAGATA
*
90298 ATTTAAAATTGAATATTATATTAT
1 ATTTAAAATTGAATATTAAATTAT
*
90322 TTTTAAAATTGATAATATTTAAATT-T
1 ATTTAAAATTG--AATA-TTAAATTAT
*
90348 ATTTATAATT
1 ATTTAAAATT
90358 TTATATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 10 0.34
26 13 0.45
27 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
ATTTAAAATTGAATATTAAATTAT
Found at i:90605 original size:20 final size:19
Alignment explanation
Indices: 90582--90632 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
90572 TTTTATATTT
*
90582 AAAATATAAAAATATTAAAG
1 AAAATATAAAAAT-TTAAAA
90602 AAAATA-AATATAATTTAAAA
1 AAAATATAA-A-AATTTAAAA
90622 AAAAT-TAAAAA
1 AAAATATAAAAA
90633 GTAAGAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 3 0.11
20 19 0.70
21 3 0.11
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAATATAAAAATTTAAAA
Found at i:92718 original size:21 final size:22
Alignment explanation
Indices: 92693--92733 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
92683 ATTAAGGTTG
92693 AAAAATAGATT-GTTGAAAAAA
1 AAAAATAGATTCGTTGAAAAAA
* *
92714 AAAAATTGATTCGTTTAAAA
1 AAAAATAGATTCGTTGAAAA
92734 TATAAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.29
Consensus pattern (22 bp):
AAAAATAGATTCGTTGAAAAAA
Found at i:102460 original size:13 final size:14
Alignment explanation
Indices: 102430--102467 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
102420 TGTTTCATTG
* *
102430 AAAATAGTTTTCGA
1 AAAATAATTTTTGA
102444 AAAATAATTTTTGA
1 AAAATAATTTTTGA
102458 AAAATAATTT
1 AAAATAATTT
102468 ATTTTTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (14 bp):
AAAATAATTTTTGA
Found at i:102952 original size:18 final size:17
Alignment explanation
Indices: 102931--102967 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
102921 TATTATTAAT
102931 ATATTTATAATTATAAAA
1 ATATTTATAATTA-AAAA
*
102949 ATATTTATTATTAAAAA
1 ATATTTATAATTAAAAA
102966 AT
1 AT
102968 TAATATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTTATAATTAAAAA
Found at i:102964 original size:15 final size:15
Alignment explanation
Indices: 102913--102964 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
102903 TTTATACTAC
*
102913 AAAACATTTATTATT
1 AAAATATTTATTATT
* *
102928 AATATATTTATAATTATA
1 AAAATA-TT-T-ATTATT
102946 AAAATATTTATTATT
1 AAAATATTTATTATT
102961 AAAA
1 AAAA
102965 AATTAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 13 0.45
16 3 0.10
17 3 0.10
18 10 0.34
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:103080 original size:30 final size:29
Alignment explanation
Indices: 103002--103082 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 29
102992 TGTGAAGAAT
103002 ATTAT-TTAAATT-TATTATTAAAATATAA
1 ATTATATT-AATTATATTATTAAAATATAA
* *
103030 TTTAATATTAAATA-ATTTATTAAAATAATAA
1 ATT-ATATTAATTATA-TTATTAAAAT-ATAA
103061 ATTATATTAATTATATTATTAA
1 ATTATATTAATTATATTATTAA
103083 TTTATTACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
28 2 0.05
29 6 0.14
30 28 0.65
31 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTATATTAATTATATTATTAAAATATAA
Found at i:103951 original size:26 final size:26
Alignment explanation
Indices: 103921--104005 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 26
103911 GTTATTAAAT
103921 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAGATTATTATTAAATATAA
* *
103947 TTTAATAA-A-TA--ATTTAATCAT-T
1 TTTAATAAGATTATTATTAAAT-ATAA
* * *
103969 TTTAACATGATTATTATTAAATACAA
1 TTTAATAAGATTATTATTAAATATAA
103995 TTTAATAAGAT
1 TTTAATAAGAT
104006 AGTATACAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
22 12 0.27
23 3 0.07
24 4 0.09
25 2 0.05
26 23 0.52
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (26 bp):
TTTAATAAGATTATTATTAAATATAA
Found at i:105501 original size:40 final size:40
Alignment explanation
Indices: 105455--105575 Score: 172
Period size: 40 Copynumber: 3.0 Consensus size: 40
105445 CATTATAAAT
105455 TTAACATATTGTACTGTTATA-AGTTTATGGAACATTAACA
1 TTAACATATTGTACTGTTATAGA-TTTATGGAACATTAACA
* *
105495 TTAACATACTGTACTGTTATAGATTTATGAAACATTAACA
1 TTAACATATTGTACTGTTATAGATTTATGGAACATTAACA
* * * *
105535 CTAACATATTGTACTGTTACAGACTAATGGAACATTAACA
1 TTAACATATTGTACTGTTATAGATTTATGGAACATTAACA
105575 T
1 T
105576 AGCTTGAGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 70 0.99
41 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (40 bp):
TTAACATATTGTACTGTTATAGATTTATGGAACATTAACA
Found at i:111445 original size:22 final size:21
Alignment explanation
Indices: 111420--111462 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
111410 TAAACGAAGT
*
111420 ACAATATTATTTAACTACATAA
1 ACAATATAATTTAACTA-ATAA
*
111442 ACAATATAATTTACCTAATAA
1 ACAATATAATTTAACTAATAA
111463 TTACATGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (21 bp):
ACAATATAATTTAACTAATAA
Found at i:113394 original size:36 final size:36
Alignment explanation
Indices: 113352--113429 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
113342 ATTCACATCA
* *
113352 GTCACATGGCATGAAGAACATGCCCACATATTCTCT
1 GTCACATGGCATGAAGAACATACCCACATATTCACT
*
113388 GTCACATGGCATGAAGAACATACTCACATATTCACT
1 GTCACATGGCATGAAGAACATACCCACATATTCACT
*
113424 TTCACA
1 GTCACA
113430 ACAGTCACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (36 bp):
GTCACATGGCATGAAGAACATACCCACATATTCACT
Found at i:115014 original size:20 final size:22
Alignment explanation
Indices: 114974--115019 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
114964 ATTGACTAAG
114974 CCTATCTTCGATTTTACTTG-A
1 CCTATCTTCGATTTTACTTGAA
114995 CCTAT-TTC-ATTTTCACTTGAA
1 CCTATCTTCGATTTT-ACTTGAA
115016 CCTA
1 CCTA
115020 AAGCTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 8 0.35
21 10 0.43
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.46
Consensus pattern (22 bp):
CCTATCTTCGATTTTACTTGAA
Found at i:118489 original size:24 final size:24
Alignment explanation
Indices: 118452--118528 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
118442 TGAGAAATAA
* *
118452 TATTTCAGTCAAACTCTGTTTATT
1 TATTTCAATTAAACTCTGTTTATT
118476 TCA-TTCAATTAAACTCTGTTTATT
1 T-ATTTCAATTAAACTCTGTTTATT
* *
118500 TATTTTAATTAAACTCTATTTATT
1 TATTTCAATTAAACTCTGTTTATT
118524 TATTT
1 TATTT
118529 GAGTCAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.02
24 45 0.96
25 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.55
Consensus pattern (24 bp):
TATTTCAATTAAACTCTGTTTATT
Found at i:120410 original size:24 final size:24
Alignment explanation
Indices: 120382--120443 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
120372 AGAAATAATC
120382 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
120406 TTTCAATTAAA-TCTGTTTATTTT
1 TTTCAGTTAAACTCTGTTTATTTG
* *
120429 TTTTAGTCAAACTCT
1 TTTCAGTTAAACTCT
120444 TATTAGTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.24, C:0.13, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:134234 original size:12 final size:12
Alignment explanation
Indices: 134217--134279 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
134207 GGGTATTGAG
134217 GAAGAGAAAGAA
1 GAAGAGAAAGAA
134229 GAAGAGAAAG-A
1 GAAGAGAAAGAA
* *
134240 GGAGAAAAAGGAA
1 GAAGAGAAA-GAA
134253 GAAG-GAAAAGAA
1 GAAGAG-AAAGAA
*
134265 TG-AGAGAAGGAA
1 -GAAGAGAAAGAA
134277 GAA
1 GAA
134280 ATTTTTGCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
11 9 0.22
12 22 0.55
13 9 0.22
ACGTcount: A:0.62, C:0.00, G:0.37, T:0.02
Consensus pattern (12 bp):
GAAGAGAAAGAA
Found at i:137420 original size:52 final size:52
Alignment explanation
Indices: 137337--137622 Score: 396
Period size: 52 Copynumber: 5.5 Consensus size: 52
137327 TAAATGAAAA
*
137337 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* *
137389 AGGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCTTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* *
137441 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* * * *
137493 AGGTCCGATGGC--TGTGTCATCATGAATATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* ** *** *
137543 AGGTCTGATGGTTATGTGTCATCGTGAGTATATGAATCCTTTACAAATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* *
137595 AGGTCTGATGACTATGTGTCATTGTGAG
1 AGGTCCGATGACTATGTGTCATCGTGAG
137623 CGTATAGATT
Statistics
Matches: 209, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
50 44 0.21
52 165 0.79
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
Found at i:137575 original size:102 final size:103
Alignment explanation
Indices: 137343--137616 Score: 415
Period size: 102 Copynumber: 2.7 Consensus size: 103
137333 AAAAAGGTTC
*
137343 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTCCGATGGCTATGTGT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTATGAGGTCCGATGGC-ATGTGT
* * * *
137408 CATCGTGAGTATATGAATCTTTTATGGATTATGAGGTCT
65 CATCATGAATATATGAATCCTTTACGGATTATGAGGTCT
137447 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTATGAGGTCCGATGGC-TGTGTC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTATGAGGTCCGATGGCATGTGTC
137511 ATCATGAATATATGAATCCTTTACGGATTATGAGGTCT
66 ATCATGAATATATGAATCCTTTACGGATTATGAGGTCT
** ** * * *
137549 GATGGTTATGTGTCATCGTGAGTATATGAATCCTTTACAAATTAAGAGGTCTGATGACTATGTGT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTATGAGGTCCGATGGC-ATGTGT
137614 CAT
65 CAT
137617 TGTGAGCGTA
Statistics
Matches: 156, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
102 91 0.58
104 65 0.42
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTATGAGGTCCGATGGCATGTGTC
ATCATGAATATATGAATCCTTTACGGATTATGAGGTCT
Found at i:138625 original size:14 final size:15
Alignment explanation
Indices: 138600--138628 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
138590 GAGATGAAAA
138600 TATAATATGAACAGT
1 TATAATATGAACAGT
138615 TATAA-ATGAACAGT
1 TATAATATGAACAGT
138629 AAGACATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (15 bp):
TATAATATGAACAGT
Found at i:142778 original size:52 final size:52
Alignment explanation
Indices: 142706--142943 Score: 288
Period size: 52 Copynumber: 4.6 Consensus size: 52
142696 TAAATGAAAA
* *
142706 AGGTCCGATGACTATATGTCATCGTGAGTATATGAAT-CTTGTACGGATTATG
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTT-TACGGATTATG
*
142758 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTTTG
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * **
142810 AGGTCCGAAGGTTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT-
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
142861 AGG-TCTGATGGCTATGTGTCATCGTGAGCATAT-AGATCATTTTACGGATT-TA
1 AGGTTC-GATGACTATGTGTCATCGTGAGTATATGA-ATC-CTTTACGGATTATG
* *
142913 AGGTTCGATGACTTTGTGTCATCATGAGTAT
1 AGGTTCGATGACTATGTGTCATCGTGAGTAT
142944 TAATTGGGAA
Statistics
Matches: 163, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
50 2 0.01
51 31 0.19
52 125 0.77
53 5 0.03
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (52 bp):
AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:150471 original size:19 final size:20
Alignment explanation
Indices: 150435--150472 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
150425 AAATATATTA
* *
150435 AAATTTTTATTTTGACATCT
1 AAATTTTTATATTAACATCT
150455 AAATTTTTA-ATTAACATC
1 AAATTTTTATATTAACATC
150473 AGTTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATTTTTATATTAACATCT
Found at i:153992 original size:17 final size:17
Alignment explanation
Indices: 153965--154017 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
153955 GCTCCTTTTT
*
153965 AATTTATTTTAAATTTA
1 AATTAATTTTAAATTTA
*
153982 GATTAATTTTAAATTTA
1 AATTAATTTTAAATTTA
*
153999 AATTAATTTTAAAATTA
1 AATTAATTTTAAATTTA
154016 AA
1 AA
154018 AAAGTTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATTAATTTTAAATTTA
Found at i:154081 original size:37 final size:35
Alignment explanation
Indices: 154039--154117 Score: 122
Period size: 37 Copynumber: 2.2 Consensus size: 35
154029 AAAATGTCCA
154039 AATTACAAAGGGTCCAAAGACTAGCCCAATTACACCC
1 AATTACAAAGGGTCCAAAGACTAGCCCAA-T-CACCC
* *
154076 AATTACAAAGTGTCCAAAGACTAGCCCAATGACCC
1 AATTACAAAGGGTCCAAAGACTAGCCCAATCACCC
154111 AATTACA
1 AATTACA
154118 CCCAACACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 11 0.28
36 1 0.03
37 28 0.70
ACGTcount: A:0.42, C:0.28, G:0.13, T:0.18
Consensus pattern (35 bp):
AATTACAAAGGGTCCAAAGACTAGCCCAATCACCC
Done.