Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018914.1 Corchorus olitorius cultivar O-4 contig18947, 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: 123749
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2522 original size:19 final size:18
Alignment explanation
Indices: 2489--2524 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2479 AAAGCTCCAT
2489 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
2507 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
2525 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:3003 original size:30 final size:30
Alignment explanation
Indices: 2969--3028 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2959 CAATTCTTGC
* *
2969 TCTTCAAATTATTCTTCAAT-GGTCTTCAAA
1 TCTTCAAA-TAGTCTTCAATAAGTCTTCAAA
2999 TCTTCAAATAGTCTTCAATAAGTCTTCAAA
1 TCTTCAAATAGTCTTCAATAAGTCTTCAAA
3029 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (30 bp):
TCTTCAAATAGTCTTCAATAAGTCTTCAAA
Found at i:3014 original size:19 final size:18
Alignment explanation
Indices: 2981--3016 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2971 TTCAAATTAT
*
2981 TCTTCAATGGTCTTCAAA
1 TCTTCAATAGTCTTCAAA
2999 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGTCTTCAA
3017 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAA
Found at i:3015 original size:11 final size:10
Alignment explanation
Indices: 2981--3027 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
2971 TTCAAATTAT
*
2981 TCTTCAATGG
1 TCTTCAATAG
2991 TCTTCAA-A-
1 TCTTCAATAG
2999 TCTTCAAATAG
1 TCTTC-AATAG
3010 TCTTCAATAAG
1 TCTTCAAT-AG
3021 TCTTCAA
1 TCTTCAA
3028 ACACGAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 5 0.16
9 2 0.06
10 11 0.34
11 14 0.44
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (10 bp):
TCTTCAATAG
Found at i:3344 original size:17 final size:17
Alignment explanation
Indices: 3319--3353 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3309 TGCATTATGT
3319 TAATATACCAACAAGAA
1 TAATATACCAACAAGAA
*
3336 TAATGTACCAACAAGAA
1 TAATATACCAACAAGAA
3353 T
1 T
3354 GCACTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (17 bp):
TAATATACCAACAAGAA
Found at i:4190 original size:27 final size:27
Alignment explanation
Indices: 4159--4230 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
4149 CGACCTGAGG
* **
4159 CGAAGTGGGAGGAACCACTGTTGGGGT
1 CGAAGTGGGAGGATCCACTACTGGGGT
4186 CGAAGTGGGAGGATCCACTACTGGGGT
1 CGAAGTGGGAGGATCCACTACTGGGGT
4213 CGAAGTGGGAGGATCCAC
1 CGAAGTGGGAGGATCCAC
4231 CGTGGCAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.24, C:0.18, G:0.42, T:0.17
Consensus pattern (27 bp):
CGAAGTGGGAGGATCCACTACTGGGGT
Found at i:10282 original size:164 final size:163
Alignment explanation
Indices: 9829--10346 Score: 797
Period size: 163 Copynumber: 3.2 Consensus size: 163
9819 GGGAATTTTT
* * * * *
9829 TCCCTCCATATATTACAATTGCGGCGTTTTC-TTTCCTAGACGCCACTAATTAGCGGCGTCTAAT
1 TCCCTCCATATATTAAAATGGCGGCG-TTTCATTTTCTAGACGCCACTACTTAGCGGCGTCTGAT
** * *
9893 GAGAAAACACCGCTATATATTATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTA-GGGTGAGGGA
65 GTCAAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTAGGGGGGAGGGA
*
9957 ATTTTTCCCTCCAAAAAAAAAGGAAAAAAATTCTC
130 ATTTTTCCCTCCAAAAAAAAGGGAAAAAAA-TCTC
*
9992 TCCCTCCATATATTAAAATGGCAGCGTTTCATTTTCTAGACGCCACTACTTAGCGGCGTCTGATG
1 TCCCTCCATATATTAAAATGGCGGCGTTTCATTTTCTAGACGCCACTACTTAGCGGCGTCTGATG
* *
10057 TCAAAATGCCGCTATATATTATAGGCATAGAGTTGGAAACTTTCTTTGTTTTAGGGGGGAGGGAA
66 TCAAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTAGGGGGGAGGGAA
*
10122 TTATTCCCTCCAAAAAAAAGGGAAAAAAATCTC
131 TTTTTCCCTCCAAAAAAAAGGGAAAAAAATCTC
*
10155 TCCCTCCATAAATTAAAATGGCGGCGTTTCATTTTCTAGACGCCACTACTTAGCGGCGTCTGATG
1 TCCCTCCATATATTAAAATGGCGGCGTTTCATTTTCTAGACGCCACTACTTAGCGGCGTCTGATG
* * *
10220 TCAAAACGCCGCTATAAATTATAGGTGTAAAGTTGGAAACTTTCTTTGTTTTATGGGGGGAGGGA
66 TCAAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTA-GGGGGGAGGGA
**
10285 ATTTTTCCCTCCAAAAAAAGAGAAAAAAAAATCTC
130 ATTTTTCCCTCCAAAAAAA-AGGGAAAAAAATCTC
*
10320 TCCCTCCATATATTAATATGGCGGCGT
1 TCCCTCCATATATTAAAATGGCGGCGT
10347 CTTTCTATCG
Statistics
Matches: 325, Mismatches: 26, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
162 4 0.01
163 217 0.67
164 66 0.20
165 38 0.12
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (163 bp):
TCCCTCCATATATTAAAATGGCGGCGTTTCATTTTCTAGACGCCACTACTTAGCGGCGTCTGATG
TCAAAACGCCGCTATATATTATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTAGGGGGGAGGGAA
TTTTTCCCTCCAAAAAAAAGGGAAAAAAATCTC
Found at i:11551 original size:11 final size:12
Alignment explanation
Indices: 11535--11566 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
11525 GAAGTTCGTG
11535 TTTGAAGACT-A
1 TTTGAAGACTAA
11546 TTTGAAGA-TAA
1 TTTGAAGACTAA
11557 TTTGAAGACT
1 TTTGAAGACT
11567 CGAAGACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Found at i:11820 original size:11 final size:12
Alignment explanation
Indices: 11804--11835 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
11794 GAAGTTCGTG
11804 TTTGAAGACT-A
1 TTTGAAGACTAA
11815 TTTGAAGA-TAA
1 TTTGAAGACTAA
11826 TTTGAAGACT
1 TTTGAAGACT
11836 CGAAGACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Found at i:11822 original size:269 final size:270
Alignment explanation
Indices: 11341--11875 Score: 1018
Period size: 269 Copynumber: 2.0 Consensus size: 270
11331 TTTTTATGGC
*
11341 TATTTTACTATGTTTTTGGATCCATTTATGCTTAAATATATGCTATTTTGATAATATTTGTGTTT
1 TATTTTACTATGTTTTTGGATCCATTTATGCTTAAATATATGCTATTTTGATAATATTTGTATTT
*
11406 TGAGTCTTTAAGTGATGTGAAATTGAGAAATTGTTATTTTGTCACTATTTTTAGAGCTATTTTGA
66 TGAGTCTTTAAGTGATGTGAAATTGAGAAATTGTTATTTTGCCACTATTTTTAGAGCTATTTTGA
11471 TGACTTTTTACAAAGATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGT
131 TGACTTTTTACAAAGATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGT
*
11536 TTGAAGACTATTTGAAGATAATTTGAAGACTCGAAGACTATTGAAGAATTATTTCAAGAGCAAGA
196 TTGAAGACTATTTGAAGATAATTTGAAGACTCGAAGACTATTGAAAAATTATTTCAAGAGCAAGA
11601 ATTGAACAAT
261 ATTGAACAAT
11611 TATTTTACTATGTTTTTGGATCCATTTATGCTTAAATATATGCTATTTTGATAATATTTGTATTT
1 TATTTTACTATGTTTTTGGATCCATTTATGCTTAAATATATGCTATTTTGATAATATTTGTATTT
*
11676 TGAGTCTTTAAGTGATGTGAAATTGAGAAATTGTTATTTT-CCACTATTTTTGGAGCTATTTTGA
66 TGAGTCTTTAAGTGATGTGAAATTGAGAAATTGTTATTTTGCCACTATTTTTAGAGCTATTTTGA
*
11740 TGACTTTTTACACAGATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGT
131 TGACTTTTTACAAAGATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGT
11805 TTGAAGACTATTTGAAGATAATTTGAAGACTCGAAGACTATTGAAAAATTATTTCAAGAGCAAGA
196 TTGAAGACTATTTGAAGATAATTTGAAGACTCGAAGACTATTGAAAAATTATTTCAAGAGCAAGA
11870 ATTGAA
261 ATTGAA
11876 GATTGGAGCT
Statistics
Matches: 260, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
269 156 0.60
270 104 0.40
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (270 bp):
TATTTTACTATGTTTTTGGATCCATTTATGCTTAAATATATGCTATTTTGATAATATTTGTATTT
TGAGTCTTTAAGTGATGTGAAATTGAGAAATTGTTATTTTGCCACTATTTTTAGAGCTATTTTGA
TGACTTTTTACAAAGATTTGAGCAAAGCAATTTTGAGCATAGATTTGGAGATTCGAAGTTCGTGT
TTGAAGACTATTTGAAGATAATTTGAAGACTCGAAGACTATTGAAAAATTATTTCAAGAGCAAGA
ATTGAACAAT
Found at i:13253 original size:15 final size:15
Alignment explanation
Indices: 13222--13263 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
13212 TTACTTTGCT
*
13222 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-TTTTAA
13238 TTGTTTTCTTTTTAA
1 TTGTTTTCTTTTTAA
13253 TTGTTCTTCTT
1 TTGTT-TTCTT
13264 AACCCTCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.69
Consensus pattern (15 bp):
TTGTTTTCTTTTTAA
Found at i:17504 original size:29 final size:29
Alignment explanation
Indices: 17472--17527 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
17462 TCATGCATAT
17472 TGATCATAATTTTAATGTCATAATTTTCA
1 TGATCATAATTTTAATGTCATAATTTTCA
17501 TGATCATAATTTTAATGTCATAATTTT
1 TGATCATAATTTTAATGTCATAATTTT
17528 TTCGAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (29 bp):
TGATCATAATTTTAATGTCATAATTTTCA
Found at i:17528 original size:15 final size:14
Alignment explanation
Indices: 17475--17527 Score: 88
Period size: 14 Copynumber: 3.7 Consensus size: 14
17465 TGCATATTGA
17475 TCATAATTTTAATG
1 TCATAATTTTAATG
*
17489 TCATAATTTTCATG
1 TCATAATTTTAATG
17503 ATCATAATTTTAATG
1 -TCATAATTTTAATG
17518 TCATAATTTT
1 TCATAATTTT
17528 TTCGAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (14 bp):
TCATAATTTTAATG
Found at i:18774 original size:11 final size:11
Alignment explanation
Indices: 18758--18787 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
18748 GAAGTTCGTG
18758 TTTGAAGATAA
1 TTTGAAGATAA
18769 TTTGAAGATAA
1 TTTGAAGATAA
18780 TTTGAAGA
1 TTTGAAGA
18788 CTCGAGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:20216 original size:15 final size:15
Alignment explanation
Indices: 20185--20226 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
20175 TTACTTTGTT
*
20185 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-TTTTAA
20201 TTGTTTTCTTTTTAA
1 TTGTTTTCTTTTTAA
20216 TTGTTCTTCTT
1 TTGTT-TTCTT
20227 AACCCTCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.69
Consensus pattern (15 bp):
TTGTTTTCTTTTTAA
Found at i:25384 original size:40 final size:40
Alignment explanation
Indices: 25248--25474 Score: 196
Period size: 41 Copynumber: 5.6 Consensus size: 40
25238 CCAATTTCTG
**
25248 AAATCAGGGATTAAATTGCATCAAGA-AATAAATAGA-ATCCT
1 AAATCAGGGACCAAATTGCATCAA-ACAA-AAATA-ATATCCT
* * *
25289 AAAGCAGGGACCAAATTGCATTCAATCATGAAATAA-AT-CT
1 AAATCAGGGACCAAATTGCA-TCAAACA-AAAATAATATCCT
* *
25329 GAAATCAAGTACCAAATTGCATCAAACAAAAATAATATCCT
1 -AAATCAGGGACCAAATTGCATCAAACAAAAATAATATCCT
* * * *
25370 AAATCAGGGACCAAATTGAATTCAATCATGAAATAAATAT--G
1 AAATCAGGGACCAAATTGCA-TCAAACA-AAAAT-AATATCCT
* * *
25411 AAATCAAGTACCAAAATGCATCAAACAAAAATAATATCCT
1 AAATCAGGGACCAAATTGCATCAAACAAAAATAATATCCT
*
25451 AAATCAGGGACCAAATTGAATCAA
1 AAATCAGGGACCAAATTGCATCAA
25475 TTAATAAATA
Statistics
Matches: 148, Mismatches: 27, Indels: 23
0.75 0.14 0.12
Matches are distributed among these distances:
38 5 0.03
39 10 0.07
40 53 0.36
41 61 0.41
42 14 0.09
43 5 0.03
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (40 bp):
AAATCAGGGACCAAATTGCATCAAACAAAAATAATATCCT
Found at i:25393 original size:81 final size:81
Alignment explanation
Indices: 25260--25475 Score: 348
Period size: 81 Copynumber: 2.7 Consensus size: 81
25250 ATCAGGGATT
* *
25260 AAATTGCATCAAGA-AATAAATAGA-ATCCTAAAGCAGGGACCAAATTGCATTCAATCATGAAAT
1 AAATTGCATCAA-ACAA-AAATA-ATATCCTAAATCAGGGACCAAATTGAATTCAATCATGAAAT
*
25323 AAATCTGAAATCAAGTACC
63 AAATATGAAATCAAGTACC
25342 AAATTGCATCAAACAAAAATAATATCCTAAATCAGGGACCAAATTGAATTCAATCATGAAATAAA
1 AAATTGCATCAAACAAAAATAATATCCTAAATCAGGGACCAAATTGAATTCAATCATGAAATAAA
25407 TATGAAATCAAGTACC
66 TATGAAATCAAGTACC
*
25423 AAAATGCATCAAACAAAAATAATATCCTAAATCAGGGACCAAATTGAA-TCAAT
1 AAATTGCATCAAACAAAAATAATATCCTAAATCAGGGACCAAATTGAATTCAAT
25476 TAATAAATAA
Statistics
Matches: 128, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
80 6 0.05
81 108 0.84
82 14 0.11
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (81 bp):
AAATTGCATCAAACAAAAATAATATCCTAAATCAGGGACCAAATTGAATTCAATCATGAAATAAA
TATGAAATCAAGTACC
Found at i:28515 original size:11 final size:11
Alignment explanation
Indices: 28499--28524 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28489 AAATAATTTC
28499 TTTTCTTCTAG
1 TTTTCTTCTAG
28510 TTTTCTTCTAG
1 TTTTCTTCTAG
28521 TTTT
1 TTTT
28525 TAGACAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:29315 original size:15 final size:15
Alignment explanation
Indices: 29295--29325 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29285 TGTAATCTAA
*
29295 TTTAATTGTTTTCTG
1 TTTAATTGCTTTCTG
29310 TTTAATTGCTTTCTG
1 TTTAATTGCTTTCTG
29325 T
1 T
29326 CAATCTCTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.13, T:0.65
Consensus pattern (15 bp):
TTTAATTGCTTTCTG
Found at i:30072 original size:39 final size:39
Alignment explanation
Indices: 30010--30101 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
30000 TTCTGAAATT
*
30010 AACTGAT-AAGCAATGATCCTAAATCA-GAATCGAAACAA
1 AACTGATAAAGCAATAATCCTAAATCATG-ATCGAAACAA
* * * *
30048 AACTGATAAAGCGATAATCCTAAATCATGATTGAAATAT
1 AACTGATAAAGCAATAATCCTAAATCATGATCGAAACAA
30087 AACTGATAAAGCAAT
1 AACTGATAAAGCAAT
30102 GATCAAGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 7 0.15
39 38 0.83
40 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (39 bp):
AACTGATAAAGCAATAATCCTAAATCATGATCGAAACAA
Found at i:30254 original size:30 final size:30
Alignment explanation
Indices: 30193--31742 Score: 2030
Period size: 30 Copynumber: 51.0 Consensus size: 30
30183 TTAACGGATG
*
30193 AAGCAAT-AGTCCTAAACCATGATTAAAAATA
1 AAGCAATGA-TCCTAAACCAGGATT-AAAATA
*
30224 AAGCAATGATCCTAAACCATGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
30254 AAGCAATGATCCTAAACCAGGATTAATATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
30284 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* ** * *
30314 AAACGCTGATCCTAAACCGGGATTAAAACA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
30344 AAGCAATGATCCTAACCCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
30374 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
30404 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
30434 AAGCAATGATCCTAAACCAGGATTAAAACA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
30464 AAGCAATGATCCTAAACAAGGATTAAAAT-
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
30493 AAGCAATGATCCTAAACCAGGACTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* * *
30523 AAACAATAATCCTAAACCAGGATTAAGATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
30553 AAGTAATAATCCTAAACCAGGATTAAAAT-
1 AAGCAATGATCCTAAACCAGGATTAAAATA
30582 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
30612 AAGCGATGATCATAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
30642 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
30672 AAGCGATGATCCTAAACCAGGATTAAAACA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* * *
30702 AAGCAATGATCCTAACCCAGGGTTAAAA-C
1 AAGCAATGATCCTAAACCAGGATTAAAATA
30731 AAGCAATGATCCT-AACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
30760 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
30790 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
30820 AACCAATGA-CTCTAAACTAGGATTAAAATA
1 AAGCAATGATC-CTAAACCAGGATTAAAATA
*
30850 AACCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
30880 AAGCAATGA-CTATAAACCAGGATTAAAATA
1 AAGCAATGATC-CTAAACCAGGATTAAAATA
*
30910 AAGGAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
30940 AAGTAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
30970 AAGCAATGATCCTAAACCAGGATTAAAACA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
31000 AAGCAATTAT-CTAAACCAGGATTAAAAT-
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
31028 AAGCAATGATCCTAAACAAGGACTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* * *
31058 AAGCAATAATCCTAAACCATGATTAAGATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
31088 AAGCAATAATCCTAAACCAGGATTAAAATAAACTGATA
1 AAGCAATGATCCTAAACCAGGA-T----TAAA---ATA
* *
31126 AAGCAATAATCCCAAACCAGGATTAAAATAAACTAATA
1 AAGCAATGATCCTAAACCAGGA-T----T-AA--AATA
* * *
31164 AAGCAATGATCTTAAATCAACATTGAAATAAACTGATA
1 AAGCAATGATCCTAAA-C--CA--GGATTAAA---ATA
* * * * *
31202 AAGCAATGATCCTACATCGGGATTAACGGATG
1 AAGCAATGATCCTAAACCAGGATTAA--AATA
* * *
31234 AAGCAATGGTCCTAAATCATGATTAAAAATA
1 AAGCAATGATCCTAAACCAGGATT-AAAATA
*
31265 AAGCAATGATCCT-AACTCAAGATTAAAATA
1 AAGCAATGATCCTAAAC-CAGGATTAAAATA
**
31295 AATAAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* * *
31325 CAGCAATGATCCTAAACCAAGATTACAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
31355 AAGCAATGATCCTAAACCAGGATTAAAACA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
31385 AAGTAATGATCCTAAACCAAGATTAAAAT-
1 AAGCAATGATCCTAAACCAGGATTAAAATA
31414 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
31444 AAGCAATGA-CTCTAAACCAAGATTAAAATA
1 AAGCAATGATC-CTAAACCAGGATTAAAATA
*
31474 AAGCAATGATCCTAAAACAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
31504 AAGCAATGA-CTGTAAACCATGATTAAAATA
1 AAGCAATGATC-CTAAACCAGGATTAAAATA
31534 AAGCAATGATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
31564 AAGCAATGATCCTAAATCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
31594 AAGCAATGATCCTAAACCAGGATTAAAACA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
31624 AAGCAATTATCCTAAACCAGGATTAAAAT-
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
31653 AAGCAATGATCCTAAACAAGGACTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* ** *
31683 AAGCAATAATCCTAAACCAGTTTTAAGATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
31713 AAGCAATAATCCTAAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
31743 TACTGATAAA
Statistics
Matches: 1349, Mismatches: 129, Indels: 83
0.86 0.08 0.05
Matches are distributed among these distances:
28 21 0.02
29 170 0.13
30 998 0.74
31 50 0.04
32 23 0.02
33 7 0.01
35 5 0.00
37 2 0.00
38 65 0.05
39 3 0.00
41 3 0.00
43 2 0.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (30 bp):
AAGCAATGATCCTAAACCAGGATTAAAATA
Found at i:31096 original size:38 final size:38
Alignment explanation
Indices: 31085--31215 Score: 172
Period size: 38 Copynumber: 3.4 Consensus size: 38
31075 CATGATTAAG
*
31085 ATAAAGCAATAATCCTAAACCAGGATTAAAATAAACTG
1 ATAAAGCAATAATCCTAAACCAGGATTAAAATAAACTA
*
31123 ATAAAGCAATAATCCCAAACCAGGATTAAAATAAACTA
1 ATAAAGCAATAATCCTAAACCAGGATTAAAATAAACTA
* * * ** * *
31161 ATAAAGCAATGATCTTAAATCAACATTGAAATAAACTG
1 ATAAAGCAATAATCCTAAACCAGGATTAAAATAAACTA
*
31199 ATAAAGCAATGATCCTA
1 ATAAAGCAATAATCCTA
31216 CATCGGGATT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 82 1.00
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (38 bp):
ATAAAGCAATAATCCTAAACCAGGATTAAAATAAACTA
Found at i:31751 original size:38 final size:38
Alignment explanation
Indices: 31709--31880 Score: 254
Period size: 38 Copynumber: 4.5 Consensus size: 38
31699 CCAGTTTTAA
* *
31709 GATAAAGCAATAATCCTAAACCAGGATTAAAATATACT
1 GATAAAGCAATGATCCTAAACCAGGATTAAAATAAACT
*
31747 GATAAAGCAATGATCCTAAACCATGATTAAAATAAACT
1 GATAAAGCAATGATCCTAAACCAGGATTAAAATAAACT
* * * *
31785 AATAAAGCAATGATCTTAAATCAGGATTGAAATAAACT
1 GATAAAGCAATGATCCTAAACCAGGATTAAAATAAACT
* *
31823 GATAAAGCAATGATCCTAAACCAGGATTTATATAAACT
1 GATAAAGCAATGATCCTAAACCAGGATTAAAATAAACT
*
31861 AATAAAGCAATGATCCTAAA
1 GATAAAGCAATGATCCTAAA
31881 TGAGGATCGA
Statistics
Matches: 120, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 120 1.00
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (38 bp):
GATAAAGCAATGATCCTAAACCAGGATTAAAATAAACT
Found at i:32246 original size:163 final size:163
Alignment explanation
Indices: 32029--32356 Score: 424
Period size: 163 Copynumber: 2.0 Consensus size: 163
32019 GATTTTAAAC
* * * *
32029 TTAAACATGAATGTTTTATGAAAAGCTCGATAAAATGAAATGATACCCGGAGGTTTTATCAAATG
1 TTAAACACGAATGTTTGATGAAAAACTCGATAAAATGAAATGATACCCGGAGGTTTTACCAAATG
* * * * *
32094 CCCGAAGGACTTATCATAATTAGTACCTGGAGGTTTCTGAAATCGTGCCCGGAGGTCTCATCAAT
66 CCCGAAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAATCGTGCCCGGAGGACTCACCAAT
* *
32159 GCAAACTTTAAATTGAAACCTTAACCAAGGATT
131 GCAAACTCTAAATAGAAACCTTAACCAAGGATT
* * * * * *
32192 TTAAACACGAAT-TGTTGATGAAAAACTTGATGAAATGAAATGGTACCTGGAGGTTTTACCGATT
1 TTAAACACGAATGT-TTGATGAAAAACTCGATAAAATGAAATGATACCCGGAGGTTTTACCAAAT
* * * *
32256 GCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAA
65 GCCCGAAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAATCGTGCCCGGAGGACTCACCAA
* * *
32321 TGCAAACTCTGAATAGAGACCTTGACCAAGGATT
130 TGCAAACTCTAAATAGAAACCTTAACCAAGGATT
32355 TT
1 TT
32357 TAACTTAAAT
Statistics
Matches: 140, Mismatches: 24, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
162 1 0.01
163 139 0.99
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (163 bp):
TTAAACACGAATGTTTGATGAAAAACTCGATAAAATGAAATGATACCCGGAGGTTTTACCAAATG
CCCGAAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAATCGTGCCCGGAGGACTCACCAAT
GCAAACTCTAAATAGAAACCTTAACCAAGGATT
Found at i:33848 original size:12 final size:12
Alignment explanation
Indices: 33831--33862 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
33821 AATCAATTCT
33831 TTTTCTTTTATG
1 TTTTCTTTTATG
33843 TTTTCTTTTATG
1 TTTTCTTTTATG
33855 TTTT-TTTT
1 TTTTCTTTT
33863 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTATG
Found at i:33863 original size:12 final size:12
Alignment explanation
Indices: 33830--33873 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
33820 CAATCAATTC
33830 TTTTTCTTTTATG
1 TTTTT-TTTTATG
*
33843 TTTTCTTTTATG
1 TTTTTTTTTATG
33855 TTTTTTTTTTAT-
1 -TTTTTTTTTATG
33867 TTTTTTT
1 TTTTTTT
33874 GAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.25
12 7 0.25
13 14 0.50
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTATG
Found at i:33869 original size:10 final size:10
Alignment explanation
Indices: 33856--33918 Score: 67
Period size: 10 Copynumber: 6.3 Consensus size: 10
33846 TCTTTTATGT
*
33856 TTTTTTTTTA
1 TTTTTTTTGA
33866 TTTTTTTTGA
1 TTTTTTTTGA
*
33876 ATTTTTTTGAA
1 TTTTTTTTG-A
33887 TTTTTTTT-A
1 TTTTTTTTGA
*
33896 TTTTTGATTGA
1 TTTTT-TTTGA
33907 TTTTTTTT-A
1 TTTTTTTTGA
33916 TTT
1 TTT
33919 AATTTCTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
9 10 0.22
10 21 0.47
11 14 0.31
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.79
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:33873 original size:13 final size:13
Alignment explanation
Indices: 33830--33872 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
33820 CAATCAATTC
33830 TTTTTCTTTTA-T
1 TTTTTCTTTTATT
*
33842 GTTTTCTTTTATGT
1 TTTTTCTTTTAT-T
33856 TTTTT-TTTTATT
1 TTTTTCTTTTATT
33868 TTTTT
1 TTTTT
33873 TGAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
13 6 0.22
14 5 0.19
ACGTcount: A:0.07, C:0.05, G:0.05, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTATT
Found at i:33891 original size:30 final size:31
Alignment explanation
Indices: 33857--33914 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
33847 CTTTTATGTT
*
33857 TTTTTTTTATTTTT-TTTGAATTTTTTTGAA
1 TTTTTTTTATTTTTGATTGAATTTTTTTGAA
*
33887 TTTTTTTTATTTTTGATTGATTTTTTTT
1 TTTTTTTTATTTTTGATTGAATTTTTTT
33915 ATTTAATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (31 bp):
TTTTTTTTATTTTTGATTGAATTTTTTTGAA
Found at i:52844 original size:27 final size:27
Alignment explanation
Indices: 52814--52881 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
52804 ATTAGGGTCA
52814 TCCAGGGGCATTTTGGTCATTTGCACG
1 TCCAGGGGCATTTTGGTCATTTGCACG
* *
52841 TCCAGGGGCATTTTTGTCATTTGCATG
1 TCCAGGGGCATTTTGGTCATTTGCACG
*
52868 TCTAGGGGCATTTT
1 TCCAGGGGCATTTT
52882 AGTAATTTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (27 bp):
TCCAGGGGCATTTTGGTCATTTGCACG
Found at i:52889 original size:27 final size:27
Alignment explanation
Indices: 52814--52889 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
52804 ATTAGGGTCA
*
52814 TCCAGGGGCATTTTGGTCATTTGCACG
1 TCCAGGGGCATTTTAGTCATTTGCACG
* *
52841 TCCAGGGGCATTTTTGTCATTTGCATG
1 TCCAGGGGCATTTTAGTCATTTGCACG
* *
52868 TCTAGGGGCATTTTAGTAATTT
1 TCCAGGGGCATTTTAGTCATTT
52890 CAAGCACATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (27 bp):
TCCAGGGGCATTTTAGTCATTTGCACG
Found at i:56588 original size:17 final size:17
Alignment explanation
Indices: 56568--56603 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
56558 TTTACGTGCG
*
56568 GATCAAATAACTGGATA
1 GATCAAATAACTCGATA
56585 GATCAAATAACTCGATA
1 GATCAAATAACTCGATA
56602 GA
1 GA
56604 ATAGATTCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (17 bp):
GATCAAATAACTCGATA
Found at i:57780 original size:50 final size:50
Alignment explanation
Indices: 57704--58055 Score: 532
Period size: 50 Copynumber: 7.1 Consensus size: 50
57694 TCCAGAAGCC
*
57704 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTCTTAAGATT-
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* *
57753 AGATTGGAAGACAGTTCAAAGGATAAGCAGGAGACGGTCCTCTTAAGATTG
1 A-ATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* * *
57804 GATTGGAAGACAGTTCAAAGGATAAGCGGGAGATGATCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
57854 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* * **
57904 AATTGGAAGACAGTTCAAAGGATAAGAC-GAAAACGAACCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAG-CGGGAGACGGTCCTTTTAAGATTG
57954 AATTGGAAGACAGTTCAAAGGA-AAGCGGGAGACGGTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
* * *
58003 AATTGGAAGACAGTTCAAAGGATAAGCGGAATACGGT-TTTTTGAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTT-AAGATTG
58053 AAT
1 AAT
58056 CGGGAGACGA
Statistics
Matches: 277, Mismatches: 20, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
48 1 0.00
49 48 0.17
50 227 0.82
51 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (50 bp):
AATTGGAAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTG
Found at i:58360 original size:27 final size:27
Alignment explanation
Indices: 58285--58352 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
58275 ATTAAGGTCA
58285 TCCAGGGGCATTTTGGTCATTTGCACG
1 TCCAGGGGCATTTTGGTCATTTGCACG
58312 TCCAGGGGCATTTTGGTCATTTGCACG
1 TCCAGGGGCATTTTGGTCATTTGCACG
*
58339 TCTAGGGGCATTTT
1 TCCAGGGGCATTTT
58353 AATCATTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (27 bp):
TCCAGGGGCATTTTGGTCATTTGCACG
Found at i:61391 original size:20 final size:20
Alignment explanation
Indices: 61362--61399 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61352 AAAGTGGTGA
*
61362 TTTTACTAAAAAGTTTAGCT
1 TTTTACTAAAAAGATTAGCT
*
61382 TTTTATTAAAAAGATTAG
1 TTTTACTAAAAAGATTAG
61400 TCCTTGATTG
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:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (20 bp):
TTTTACTAAAAAGATTAGCT
Found at i:62999 original size:30 final size:31
Alignment explanation
Indices: 62925--63013 Score: 153
Period size: 31 Copynumber: 2.9 Consensus size: 31
62915 ACTTTTTCTT
62925 AAGTAAATCCAAAAGAAGATTTTGGAAAATA
1 AAGTAAATCCAAAAGAAGATTTTGGAAAATA
* *
62956 AGGTAATTCCAAAAGAAGATTTTGGAAAATA
1 AAGTAAATCCAAAAGAAGATTTTGGAAAATA
62987 AAG-AAATCCAAAAGAAGATTTTGGAAA
1 AAGTAAATCCAAAAGAAGATTTTGGAAA
63014 TTAATAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
30 23 0.43
31 31 0.57
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (31 bp):
AAGTAAATCCAAAAGAAGATTTTGGAAAATA
Found at i:65269 original size:17 final size:17
Alignment explanation
Indices: 65247--65282 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
65237 GCGAATCTAT
*
65247 TCTATCGAGTTATTTGA
1 TCTATCCAGTTATTTGA
65264 TCTATCCAGTTATTTGA
1 TCTATCCAGTTATTTGA
65281 TC
1 TC
65283 CGCACGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (17 bp):
TCTATCCAGTTATTTGA
Found at i:69264 original size:21 final size:21
Alignment explanation
Indices: 69238--69310 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
69228 TCTAACTATC
69238 TTGCATATTTAAGTTTCTTGT
1 TTGCATATTTAAGTTTCTTGT
* * *
69259 TTGCATA-TTAGGATTGTGTGT
1 TTGCATATTTAAGTTTCT-TGT
* *
69280 TT--AGATTTAATTTTCTTGT
1 TTGCATATTTAAGTTTCTTGT
*
69299 TTGCATGTTTAA
1 TTGCATATTTAA
69311 TTTTGTGTCT
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
19 7 0.18
20 13 0.34
21 18 0.47
ACGTcount: A:0.21, C:0.07, G:0.18, T:0.55
Consensus pattern (21 bp):
TTGCATATTTAAGTTTCTTGT
Found at i:69644 original size:20 final size:19
Alignment explanation
Indices: 69616--69657 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
69606 TGGAGGAGTG
*
69616 ATTTAGAAAATCTAAAAAAA
1 ATTTAGAAAAT-AAAAAAAA
*
69636 ATTTTGAAAATAAAAAAAA
1 ATTTAGAAAATAAAAAAAA
69655 ATT
1 ATT
69658 GTTTTTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
ATTTAGAAAATAAAAAAAA
Found at i:73506 original size:18 final size:19
Alignment explanation
Indices: 73483--73518 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
73473 AGTCTAAGGC
73483 TTAAGTACCTTAA-TTTAT
1 TTAAGTACCTTAAGTTTAT
*
73501 TTAAGTAGCTTAAGTTTA
1 TTAAGTACCTTAAGTTTA
73519 AATTGTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.47
Consensus pattern (19 bp):
TTAAGTACCTTAAGTTTAT
Found at i:74957 original size:17 final size:17
Alignment explanation
Indices: 74935--74972 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
74925 AAAGCAAACT
74935 AAAGAAAACAATAGTTA
1 AAAGAAAACAATAGTTA
74952 AAAGAAAACAATAGTTA
1 AAAGAAAACAATAGTTA
74969 AAAG
1 AAAG
74973 GTATACTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.13, T:0.16
Consensus pattern (17 bp):
AAAGAAAACAATAGTTA
Found at i:76117 original size:20 final size:20
Alignment explanation
Indices: 76092--76142 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
76082 AATTGGCATT
*
76092 GGCATAGGGTTGGACCGCAC
1 GGCATAGGGCTGGACCGCAC
76112 GGCATAGGGCTGGACCGCAC
1 GGCATAGGGCTGGACCGCAC
76132 GGCATAGGGCT
1 GGCATAGGGCT
76143 TTGACTCCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.41, T:0.14
Consensus pattern (20 bp):
GGCATAGGGCTGGACCGCAC
Found at i:76618 original size:21 final size:23
Alignment explanation
Indices: 76563--76620 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 23
76553 TCGACCAGAA
76563 GTTATCAAAATTTC-GTAGTGTG
1 GTTATCAAAATTTCAGTAGTGTG
76585 GTTATCAAAATTTCAG-AGTGTG
1 GTTATCAAAATTTCAGTAGTGTG
76607 GTTATC-AAATTTCA
1 GTTATCAAAATTTCA
76621 TAGGAGGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.23
22 26 0.74
23 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (23 bp):
GTTATCAAAATTTCAGTAGTGTG
Found at i:79449 original size:24 final size:24
Alignment explanation
Indices: 79421--79468 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
79411 TATTGAAGTC
79421 AAGGATCACCATGGTATATTGCTT
1 AAGGATCACCATGGTATATTGCTT
79445 AAGGATCACCATGGTATATTGCTT
1 AAGGATCACCATGGTATATTGCTT
79469 GCTGAAATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (24 bp):
AAGGATCACCATGGTATATTGCTT
Found at i:82897 original size:17 final size:17
Alignment explanation
Indices: 82875--82910 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
82865 TGATTTGTAA
82875 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
82892 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
82909 AG
1 AG
82911 CTCTTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:87476 original size:18 final size:18
Alignment explanation
Indices: 87455--87502 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
87445 TGTTCCACTA
87455 CCGCAGAATGTTGCATTG
1 CCGCAGAATGTTGCATTG
*
87473 CCGCAGAATGTTGCATTT
1 CCGCAGAATGTTGCATTG
*
87491 CCGCAGGATGTT
1 CCGCAGAATGTT
87503 CCGCTGCCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (18 bp):
CCGCAGAATGTTGCATTG
Found at i:89306 original size:17 final size:17
Alignment explanation
Indices: 89284--89319 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
89274 TGATTTGTAA
89284 AGTTTGTTACACCAGAT
1 AGTTTGTTACACCAGAT
* *
89301 AGTTTGTTATACTAGAT
1 AGTTTGTTACACCAGAT
89318 AG
1 AG
89320 CTCTTTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (17 bp):
AGTTTGTTACACCAGAT
Found at i:89596 original size:31 final size:31
Alignment explanation
Indices: 89560--89621 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
89550 CACAAGAGAA
* *
89560 CTCTTGATTCATGAATATTTACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
89591 CTCTTGATTCATGAATAATCACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
89622 TAATAACTTT
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:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (31 bp):
CTCTTGATTCATGAATAATCACAATATTCAT
Found at i:92759 original size:31 final size:31
Alignment explanation
Indices: 92723--92784 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
92713 CACAAGAGAA
* *
92723 CTCTTGATTCATGAATATTTACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
92754 CTCTTGATTCATGAATAATCACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
92785 TAATAACTTT
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:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (31 bp):
CTCTTGATTCATGAATAATCACAATATTCAT
Found at i:95864 original size:13 final size:13
Alignment explanation
Indices: 95846--95872 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
95836 AAACAACTGA
95846 AAAGCACTTCTGG
1 AAAGCACTTCTGG
95859 AAAGCACTTCTGG
1 AAAGCACTTCTGG
95872 A
1 A
95873 TTTTCCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:101355 original size:31 final size:31
Alignment explanation
Indices: 101313--101394 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
101303 GGTAATTTTC
* *
101313 TCAGATTATTCGGGTTTCGGCTCATGTAGAT
1 TCAGATCATTCGGGTTTCGGCTCATCTAGAT
*
101344 TCAGATCATTCGGGTTTCGGCTCATCTGGAT
1 TCAGATCATTCGGGTTTCGGCTCATCTAGAT
* * *
101375 TCAGGTCATCCGGGTCTCGG
1 TCAGATCATTCGGGTTTCGG
101395 GTCTACTGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.16, C:0.22, G:0.28, T:0.34
Consensus pattern (31 bp):
TCAGATCATTCGGGTTTCGGCTCATCTAGAT
Found at i:101426 original size:31 final size:31
Alignment explanation
Indices: 101369--101427 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
101359 TTCGGCTCAT
*
101369 CTGGATTCAGGTCATCCGGGTCTCGGGTCTA
1 CTGGATTCAGGTCATCCAGGTCTCGGGTCTA
* *
101400 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATCCAGGTCTCGGGT
101428 TTTGGCCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.14, C:0.20, G:0.36, T:0.31
Consensus pattern (31 bp):
CTGGATTCAGGTCATCCAGGTCTCGGGTCTA
Found at i:104460 original size:21 final size:21
Alignment explanation
Indices: 104434--104577 Score: 89
Period size: 22 Copynumber: 6.7 Consensus size: 21
104424 TCTCACAGGG
*
104434 AGGTTATCAAAAATCATAGTA
1 AGGTTATCAAAATTCATAGTA
* *
104455 AGGTTA-CAAATTTTCATAGGA
1 AGGTTATCAAA-ATTCATAGTA
* *
104476 AGGTTTATTAAAATTTCATAGTT
1 AGG-TTATCAAAA-TTCATAGTA
**
104499 AGGTTATCAGAGTTTCATA-TGA
1 AGGTTATCA-AAATTCATAGT-A
* *
104521 AGTTTATCACAATTTCATAGGTA
1 AGGTTATCA-AAATTCATA-GTA
*
104544 A--TTATCAAAACTTCATAGTG
1 AGGTTATCAAAA-TTCATAGTA
*
104564 TGGTTATCAAAATT
1 AGGTTATCAAAATT
104578 TAATAGGGTA
Statistics
Matches: 95, Mismatches: 17, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
20 8 0.08
21 31 0.33
22 39 0.41
23 16 0.17
24 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
AGGTTATCAAAATTCATAGTA
Found at i:104526 original size:44 final size:44
Alignment explanation
Indices: 104437--104540 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 44
104427 CACAGGGAGG
* *
104437 TTATCAAAA-ATCATAGTAAGGTTACAAATTTTCATAGGAAGGT
1 TTATCAAAATTTCATAGTAAGGTTACAAAGTTTCATAGGAAGGT
* * * *
104480 TTATTAAAATTTCATAGTTAGGTTATCAGAGTTTCATATGAA-GT
1 TTATCAAAATTTCATAGTAAGGTTA-CAAAGTTTCATAGGAAGGT
*
104524 TTATCACAATTTCATAG
1 TTATCAAAATTTCATAG
104541 GTAATTATCA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 8 0.16
44 30 0.59
45 13 0.25
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTAAGGTTACAAAGTTTCATAGGAAGGT
Found at i:104573 original size:22 final size:22
Alignment explanation
Indices: 104480--104604 Score: 103
Period size: 22 Copynumber: 5.7 Consensus size: 22
104470 ATAGGAAGGT
* *
104480 TTATTAAAATTTCATA-GTTAGG
1 TTATCAAAATTTCATAGGGTA-G
* * * *
104502 TTATCAGAGTTTCATA-TGAAG
1 TTATCAAAATTTCATAGGGTAG
* *
104523 TTTATCACAATTTCATA-GGTAA
1 -TTATCAAAATTTCATAGGGTAG
* * *
104545 TTATCAAAACTTCATAGTGTGG
1 TTATCAAAATTTCATAGGGTAG
*
104567 TTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATAGGGTAG
104589 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
104605 AAAATATTCA
Statistics
Matches: 80, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
21 15 0.19
22 65 0.81
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGTAG
Found at i:104820 original size:6 final size:6
Alignment explanation
Indices: 104809--104833 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
104799 TATCATATCA
104809 ATTGTT ATTGTT ATTGTT ATTGTT A
1 ATTGTT ATTGTT ATTGTT ATTGTT A
104834 ATTTTGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (6 bp):
ATTGTT
Found at i:105709 original size:21 final size:21
Alignment explanation
Indices: 105685--105727 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
105675 TTGTAACTCT
105685 ACAATTAAAATTTCAATAACA
1 ACAATTAAAATTTCAATAACA
** *
105706 ACAATTTTAATTTTAATAACA
1 ACAATTAAAATTTCAATAACA
105727 A
1 A
105728 TAAAAAGCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
ACAATTAAAATTTCAATAACA
Found at i:108941 original size:19 final size:19
Alignment explanation
Indices: 108919--108969 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
108909 TATTTTAAAA
* *
108919 AATTGAATATAAC-TTCAAG
1 AATTAAATATAACGTT-AAC
*
108938 AATTAAATCTAACGTTAAC
1 AATTAAATATAACGTTAAC
108957 AATTAAATATAAC
1 AATTAAATATAAC
108970 AAGCAGGGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (19 bp):
AATTAAATATAACGTTAAC
Found at i:112351 original size:19 final size:18
Alignment explanation
Indices: 112327--112377 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
112317 AGTATAGATG
112327 AATATAACATTAAGAATTA
1 AATATAACATTAA-AATTA
*
112346 AATATAACTTTATAAATTA
1 AATATAACATTA-AAATTA
*
112365 AATATAACGTTAA
1 AATATAACATTAA
112378 TATGATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 1 0.03
19 27 0.93
20 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (18 bp):
AATATAACATTAAAATTA
Found at i:112726 original size:31 final size:32
Alignment explanation
Indices: 112674--112737 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
112664 TCTAACATAA
112674 TTAAATTGCTGGAAAAAAAAACATAATTTCTTT
1 TTAAATTGCTGG-AAAAAAAACATAATTTCTTT
112707 TTAAATTGCTGG-AAAAAAACATAATTTCTTT
1 TTAAATTGCTGGAAAAAAAACATAATTTCTTT
112738 CGAAAGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 19 0.61
33 12 0.39
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (32 bp):
TTAAATTGCTGGAAAAAAAACATAATTTCTTT
Found at i:113326 original size:155 final size:155
Alignment explanation
Indices: 113044--113353 Score: 620
Period size: 155 Copynumber: 2.0 Consensus size: 155
113034 TAAGTCAAAG
113044 CATCCAATTACTGAAACGTAACCGCGTCTACAAAAGTAGATTTTTTCATATACAACATTTTATTG
1 CATCCAATTACTGAAACGTAACCGCGTCTACAAAAGTAGATTTTTTCATATACAACATTTTATTG
113109 TATATATGTTTCAATTTACTTCTTTATATTTTCTAACTTGACCAAAATTTTCGTTGAAGGCATTG
66 TATATATGTTTCAATTTACTTCTTTATATTTTCTAACTTGACCAAAATTTTCGTTGAAGGCATTG
113174 AAATTACTCGAGTGAGTGCGACATA
131 AAATTACTCGAGTGAGTGCGACATA
113199 CATCCAATTACTGAAACGTAACCGCGTCTACAAAAGTAGATTTTTTCATATACAACATTTTATTG
1 CATCCAATTACTGAAACGTAACCGCGTCTACAAAAGTAGATTTTTTCATATACAACATTTTATTG
113264 TATATATGTTTCAATTTACTTCTTTATATTTTCTAACTTGACCAAAATTTTCGTTGAAGGCATTG
66 TATATATGTTTCAATTTACTTCTTTATATTTTCTAACTTGACCAAAATTTTCGTTGAAGGCATTG
113329 AAATTACTCGAGTGAGTGCGACATA
131 AAATTACTCGAGTGAGTGCGACATA
113354 TAATTGTCCA
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 155 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (155 bp):
CATCCAATTACTGAAACGTAACCGCGTCTACAAAAGTAGATTTTTTCATATACAACATTTTATTG
TATATATGTTTCAATTTACTTCTTTATATTTTCTAACTTGACCAAAATTTTCGTTGAAGGCATTG
AAATTACTCGAGTGAGTGCGACATA
Found at i:116752 original size:30 final size:30
Alignment explanation
Indices: 116714--117243 Score: 637
Period size: 30 Copynumber: 17.7 Consensus size: 30
116704 AATCTCCAAA
*
116714 TGACACCAGAAGTTGTCATGATCTTGTAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* **
116744 TGATACCAGAAGTTGTCATGATCTTTTTAAAT
1 TGACACCAGAAGTTGTCATGATC--TTGCAAT
* * * *
116776 TGATACCATAAGTTGTCATGATCATGTAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
116806 TGACACTAGAAGTTGTCATGGTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
116836 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
116866 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
116896 TGACACTAGAAGTTGTCATGCT-TTCGCAAT
1 TGACACCAGAAGTTGTCATGATCTT-GCAAT
* *
116926 TGACACCAGAAGTTGTCATGCTCTCGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
116956 TGACACCAGAAGTTGTCATGCTCTCGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
116986 TGACACCAGAAGTTGTCATGCTCTCGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
117016 TGACACCAGAAGTTGTCATGCTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
117046 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
**
117076 TGACACCAGAAGTTGTCATGATCTTATAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
117106 TGACACCAGAAGTTGTCAATGGTCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTGCAAT
* * *
117137 TG--ACCAGAAATTGTCATGATAAATTTCCAAT
1 TGACACCAGAAGTTGTCATGAT---CTTGCAAT
* *** * *
117168 AGACATTTGAAGATGTCAT-A-ATT-CAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
117195 TGACACCAGAAGTTGTCAT-A-ATT-CAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
117222 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
117244 TTTACCTTTC
Statistics
Matches: 447, Mismatches: 41, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
27 45 0.10
28 7 0.02
29 14 0.03
30 322 0.72
31 21 0.05
32 28 0.06
33 10 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:117206 original size:27 final size:27
Alignment explanation
Indices: 117176--117240 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
117166 ATAGACATTT
*
117176 GAAGATGTCATAATTCAATTGACACCA
1 GAAGTTGTCATAATTCAATTGACACCA
117203 GAAGTTGTCATAATTCAATTGACACCA
1 GAAGTTGTCATAATTCAATTGACACCA
117230 GAAGTTGTCAT
1 GAAGTTGTCAT
117241 GATTTTACCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (27 bp):
GAAGTTGTCATAATTCAATTGACACCA
Found at i:122108 original size:15 final size:16
Alignment explanation
Indices: 122077--122110 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
122067 CTTCTCAAAA
122077 GAACTTCTTCTAAACC
1 GAACTTCTTCTAAACC
*
122093 GAACTTTTTC-AAACC
1 GAACTTCTTCTAAACC
122108 GAA
1 GAA
122111 ACCTCAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.29
Consensus pattern (16 bp):
GAACTTCTTCTAAACC
Found at i:122272 original size:19 final size:19
Alignment explanation
Indices: 122248--122286 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
122238 TGCACTTAAC
122248 ATAGCCTATATAAAATTGT
1 ATAGCCTATATAAAATTGT
122267 ATAGCCTATATAAAATTGT
1 ATAGCCTATATAAAATTGT
122286 A
1 A
122287 AGCAGAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (19 bp):
ATAGCCTATATAAAATTGT
Done.