Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011837.1 Kokia drynarioides strain JFW-HI SEQ_126833, 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: 78873
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:74 original size:16 final size:16
Alignment explanation
Indices: 53--152 Score: 69
Period size: 16 Copynumber: 5.9 Consensus size: 16
43 ATAAGTAACA
*
53 TTAATAGTAATAATAG
1 TTAATAATAATAATAG
*
69 TTAATAATAATAATAA
1 TTAATAATAATAATAG
*
85 TAACTATTTAATAAATAATA-
1 T---TA-ATAAT-AATAATAG
* *
105 ATAATAATAATAACTAT
1 TTAATAATAATAA-TAG
122 TTAATAAATAATAATA-
1 TTAAT-AATAATAATAG
*
138 ATAATAATAATAATA
1 TTAATAATAATAATA
153 ATAAATAGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
15 15 0.22
16 25 0.36
17 8 0.12
18 8 0.12
19 2 0.03
20 4 0.06
21 7 0.10
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
TTAATAATAATAATAG
Found at i:76 original size:3 final size:3
Alignment explanation
Indices: 54--156 Score: 107
Period size: 3 Copynumber: 32.0 Consensus size: 3
44 TAAGTAACAT
* * *
54 TAA TAG TAA TAA TAGT TAA TAA TAA TAA TAA TAA CTATT TAA TAAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA -TA-A TAA T-AA TAA
*
103 TAA TAA TAA TAA TAA CTATT TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA
151 TAA TAA
1 TAA TAA
157 ATAGTAGTAA
Statistics
Matches: 85, Mismatches: 8, Indels: 14
0.79 0.07 0.13
Matches are distributed among these distances:
3 69 0.81
4 16 0.19
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:97 original size:30 final size:30
Alignment explanation
Indices: 70--195 Score: 165
Period size: 30 Copynumber: 4.4 Consensus size: 30
60 TAATAATAGT
70 TAATAATAATAATAATAACTATTTAATAAA
1 TAATAATAATAATAATAACTATTTAATAAA
100 TAATAATAATAATAATAACTATTTAATAAA
1 TAATAATAATAATAATAACTATTTAATAAA
*
130 TAATAATAATAATAATAA-TA-ATAATAAA
1 TAATAATAATAATAATAACTATTTAATAAA
* * *
158 TAGTAGTAAT-A-AATAGC-A-TTAATAAA
1 TAATAATAATAATAATAACTATTTAATAAA
*
184 TATTAATAATAA
1 TAATAATAATAA
196 AATGAATAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.23
27 2 0.02
28 15 0.17
29 2 0.02
30 48 0.55
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (30 bp):
TAATAATAATAATAATAACTATTTAATAAA
Found at i:97 original size:33 final size:31
Alignment explanation
Indices: 60--147 Score: 144
Period size: 30 Copynumber: 2.8 Consensus size: 31
50 ACATTAATAG
60 TAATAATAGTTAATAATAATAATAATAACTATT
1 TAATAATA--TAATAATAATAATAATAACTATT
93 TAATAA-ATAATAATAATAATAATAACTATT
1 TAATAATATAATAATAATAATAATAACTATT
123 TAATAA-ATAATAATAATAATAATAA
1 TAATAATATAATAATAATAATAATAA
148 TAATAATAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
30 48 0.87
32 1 0.02
33 6 0.11
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (31 bp):
TAATAATATAATAATAATAATAATAACTATT
Found at i:1414 original size:59 final size:57
Alignment explanation
Indices: 1315--1661 Score: 303
Period size: 59 Copynumber: 5.9 Consensus size: 57
1305 AGAGACCTCG
**
1315 AAACTTCCAAAAATTCCATTTTTTACCCTCGAACTTTTGAAAA-TCTCATTTTTGACCCAA
1 AAACTTCCAAAAATTCCA-TTTTTACCCTCGAACTTTCAAAAATTC-CATTTTT-ACCC-A
* **
1375 AAACTTCTAAAAATTCCATTTTTACCCTCGAACTTTTGAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATTCCATTTTT-A-CCCA
* * * *
1434 AAACTTCCAAAAATTCCATTTTTACCC-CCAACTTCCAAAAATCCCATTTTTTTACCTTA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATTCCA--TTTTTACC-CA
* *
1493 AAACTTCCAAAAATTCCATTTTGA-CCT-GAAACTTTCAAAAATTCCATTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCTCG-AACTTTCAAAAATTCCATTTTTACCCA
* * * * *
1549 GAACTTTCAAAAATTCCATTTTTTACCC-CAAAACTCTT-AAAAATTCCAATTTTACCCCC
1 AAACTTCCAAAAATTCCA-TTTTTACCCTC-GAACT-TTCAAAAATTCCATTTTTA-CCCA
* * * * *
1608 AAACTTCCAAAAAAATCCCATTTTAACCCCCGAAC-CTCTAAAAATTCCAATTTT
1 AAACTTCC--AAAAATTCCATTTTTACCCTCGAACTTTC-AAAAATTCCATTTTT
1662 GCCCCTGGAT
Statistics
Matches: 243, Mismatches: 26, Indels: 36
0.80 0.09 0.12
Matches are distributed among these distances:
56 16 0.07
57 13 0.05
58 40 0.16
59 111 0.46
60 53 0.22
61 10 0.04
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATTCCATTTTTACCCA
Found at i:1601 original size:87 final size:87
Alignment explanation
Indices: 1376--1661 Score: 285
Period size: 87 Copynumber: 3.3 Consensus size: 87
1366 TTGACCCAAA
* * * *
1376 AACTTCTAAAAATTCCA-TTTTTACCCTC-GAACTTTTGAAAATTCCATTTTTAACCCCAAAACT
1 AACTTCCAAAAATTCCATTTTTTACCC-CAAAAC-TTTAAAAATTCCAATTTTAACCCCAAAACT
1439 TCCAAAAATTCCATTTTTACCCCC
64 TCCAAAAATTCCATTTTTACCCCC
* ** * * **
1463 AACTTCCAAAAATCCCATTTTTTTACCTTAAAACTTCCAAAAATTCC-ATTTTGA-CCTGAAACT
1 AACTTCCAAAAATTCCA-TTTTTTACCCCAAAACTT-TAAAAATTCCAATTTTAACCCCAAAACT
* *
1526 TTCAAAAATTCCATTTTTACCCCG
64 TCCAAAAATTCCATTTTTACCCCC
* *
1550 AACTTTCAAAAATTCCATTTTTTACCCCAAAACTCTTAAAAATTCCAATTTT-ACCCCCAAACTT
1 AACTTCCAAAAATTCCATTTTTTACCCCAAAACT-TTAAAAATTCCAATTTTAACCCCAAAACTT
* *
1614 CCAAAAAAATCCCATTTTAACCCCC
65 CC--AAAAATTCCATTTTTACCCCC
* * *
1639 GAACCTCTAAAAATTCCAATTTT
1 -AACTTCCAAAAATTCCATTTTT
1662 GCCCCTGGAT
Statistics
Matches: 161, Mismatches: 28, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
86 25 0.16
87 74 0.46
88 7 0.04
89 37 0.23
90 18 0.11
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTTTACCCCAAAACTTTAAAAATTCCAATTTTAACCCCAAAACTTC
CAAAAATTCCATTTTTACCCCC
Found at i:1621 original size:30 final size:29
Alignment explanation
Indices: 1315--1666 Score: 273
Period size: 30 Copynumber: 12.0 Consensus size: 29
1305 AGAGACCTCG
*
1315 AAACTTCCAAAAATTCCATTTTTTACCCTC
1 AAACTTCCAAAAATTCCA-TTTTTACCCCC
* *** **
1345 GAACTTTTGAAAA-TCTCATTTTTGACCCAA
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCC
* *
1375 AAACTTCTAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *** *
1404 GAACTTTTGAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
1434 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* ***
1463 -AACTTCCAAAAATCCCATTTTTTTACCTTA
1 AAACTTCCAAAAATTCCA--TTTTTACCCCC
* **
1493 AAACTTCCAAAAATTCCATTTTGA-CCTG
1 AAACTTCCAAAAATTCCATTTTTACCCCC
*
1521 AAACTTTCAAAAATTCCATTTTTA-CCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
1549 GAACTTTCAAAAATTCCATTTTTTACCCCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCCC
* *
1579 AAAC-TCTTAAAAATTCCAATTTTACCCCC
1 AAACTTC-CAAAAATTCCATTTTTACCCCC
* *
1608 AAACTTCCAAAAAAATCCCATTTTAACCCCC
1 AAACTTCC--AAAAATTCCATTTTTACCCCC
* * * * *
1639 GAACCTCTAAAAATTCCAATTTTGCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
1667 TGGATATCTA
Statistics
Matches: 258, Mismatches: 51, Indels: 27
0.77 0.15 0.08
Matches are distributed among these distances:
28 59 0.23
29 77 0.30
30 81 0.31
31 41 0.16
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:13866 original size:204 final size:203
Alignment explanation
Indices: 13308--13951 Score: 859
Period size: 199 Copynumber: 3.2 Consensus size: 203
13298 AGCGATGCGA
* * * *
13308 TCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACACTCGATGTGAGCAAATCT
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT-AAACCCACGCGCGA--TGAACAAATCT
*
13373 TCGAACCCCAGTTTCCTGATGAAATACTGAGAAGCAGGTCGAAGTAAT-AGAACGGTTAGCTTCC
63 TCGAACCCCAGCTTCCTGATGAAATACTGAGAAGCAGGTCGAAGTAATAAG-ACGGTTAGCTTCC
* *
13437 TGATGAGATACTGAGAGGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAGGATTGAAA
127 TGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGAGGATTGAAA
13502 CAAACGACGCGG
192 CAAACGACGCGG
* *
13514 TTATCTTCCTGATGAGATACTGAGAAGAAGACC----AAACCCACGCGCAATGAACAAATCTTCG
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATAAACCCACGCGCGATGAACAAATCTTCG
* * *
13575 AACCCCAGCTTCCTGTTGAAATACTGAGAAGCAGGTCGAAGTAATAAAACGGTTAGCTTCCTAAT
66 AACCCCAGCTTCCTGATGAAATACTGAGAAGCAGGTCGAAGTAATAAGACGGTTAGCTTCCTGAT
* *
13640 GAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGCGAAGCGGATTGAAACAAA
131 GAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGAGGATTGAAACAAA
13705 CGACGCGG
196 CGACGCGG
* * *
13713 TCATCTTCCTGATGAGATGCTGAGAAAAAGACCAAATGAAACCCATGCGCGATGAACAAATCTTC
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT-AAACCCACGCGCGATGAACAAATCTTC
* * *
13778 GAACCCCAGCTTCCTAATGAAATACTGAGAAGAAGGTCGAAGTAATAAGACGATTAGCTTCCTGA
65 GAACCCCAGCTTCCTGATGAAATACTGAGAAGCAGGTCGAAGTAATAAGACGGTTAGCTTCCTGA
* * * * * * * * **
13843 TGAAATACGGGGAAGTAAACCAAAATT-ATCTTCCTAATGAAACACAGAGAAGTGGATCAAAACA
130 TGAGATACTGAGAAGTGAACC-AAATTCATCTTCCTGATGAGATACAGAGAAGAGGATTGAAACA
** ***
13907 AGTGATATGG
194 AACGACGCGG
* *
13917 TCATCTTCCGGATGAGATACTGAGAAGAAGGCCAA
1 TCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
13952 GTCAATGAAA
Statistics
Matches: 386, Mismatches: 45, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
199 171 0.44
200 1 0.00
201 11 0.03
204 167 0.43
205 5 0.01
206 31 0.08
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (203 bp):
TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATAAACCCACGCGCGATGAACAAATCTTCG
AACCCCAGCTTCCTGATGAAATACTGAGAAGCAGGTCGAAGTAATAAGACGGTTAGCTTCCTGAT
GAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGAGGATTGAAACAAA
CGACGCGG
Found at i:14324 original size:6 final size:6
Alignment explanation
Indices: 14313--14378 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
14303 TCAAATTTAT
** **
14313 TTTAAA TTTAAA TTTATCT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
14361 TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
14379 GGATTTAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
5 7 0.15
6 36 0.77
7 4 0.09
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:14327 original size:17 final size:17
Alignment explanation
Indices: 14305--14378 Score: 94
Period size: 17 Copynumber: 4.2 Consensus size: 17
14295 AAATTGATTC
14305 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
14322 AAATTTATCTTTTAAATTT
1 AAATTTA--TTTTAAATTT
**
14341 AAATTTGCTTTAAATTT
1 AAATTTATTTTAAATTT
* *
14358 AAATTTAATTAAAATTT
1 AAATTTATTTTAAATTT
14375 AAAT
1 AAAT
14379 GGATTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
17 34 0.68
19 16 0.32
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:14336 original size:19 final size:19
Alignment explanation
Indices: 14312--14364 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
14302 TTCAAATTTA
*
14312 TTTTAAATTTAAATTTATC
1 TTTTAAATTTAAATTTAGC
14331 TTTTAAATTTAAATTT-GC
1 TTTTAAATTTAAATTTAGC
14349 -TTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
14365 ATTAAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
19 16 0.50
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTAAATTTAAATTTAGC
Found at i:15155 original size:16 final size:16
Alignment explanation
Indices: 15134--15164 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15124 ATAAGTAACA
*
15134 TTAATAGTAATAATAG
1 TTAATAATAATAATAG
15150 TTAATAATAATAATA
1 TTAATAATAATAATA
15165 ACTATTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
TTAATAATAATAATAG
Found at i:15157 original size:13 final size:12
Alignment explanation
Indices: 15141--15249 Score: 51
Period size: 12 Copynumber: 8.5 Consensus size: 12
15131 ACATTAATAG
15141 TAATAATAGTTAA
1 TAATAATA-TTAA
*
15154 TAATAATAATAA
1 TAATAATATTAA
* *
15166 CTATTTAATAAATAA
1 -TA-ATAAT-ATTAA
* *
15181 TATTATTATTAA
1 TAATAATATTAA
15193 TAATAAATAGTTGTAA
1 TAAT-AATA--T-TAA
**
15209 TAAATAGCATTAA
1 T-AATAATATTAA
15222 T-A-AATATTAA
1 TAATAATATTAA
*
15232 TAAAAATATTAA
1 TAATAATATTAA
15244 TAATAA
1 TAATAA
15250 AATGAATAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
10 7 0.09
11 2 0.03
12 23 0.31
13 21 0.28
14 7 0.09
15 6 0.08
16 6 0.08
17 3 0.04
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:15240 original size:12 final size:12
Alignment explanation
Indices: 15223--15261 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
15213 TAGCATTAAT
15223 AAATATTAATAA
1 AAATATTAATAA
15235 AAATATTAATAA
1 AAATATTAATAA
*
15247 TAAA-ATGAATAA
1 -AAATATTAATAA
15259 AAA
1 AAA
15262 AGGGAAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 3 0.12
12 19 0.76
13 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
AAATATTAATAA
Found at i:16411 original size:29 final size:29
Alignment explanation
Indices: 16364--16654 Score: 342
Period size: 29 Copynumber: 9.9 Consensus size: 29
16354 GCCTTGGAGA
*
16364 CCTCGAAACTTCCACAAATTCCATTTTTAC
1 CCTCG-AACTTCCAAAAATTCCATTTTTAC
*
16394 CCTCGAACTTCCAAAAATCCCATTTTTGAC
1 CCTCGAACTTCCAAAAATTCCATTTTT-AC
*
16424 CC-CAAAACTTCCAAAAATTCCATTTTTAC
1 CCTC-GAACTTCCAAAAATTCCATTTTTAC
* *
16453 CCTTGAACTTCCAAAAATTTCATTTTTAAC
1 CCTCGAACTTCCAAAAATTCCATTTTT-AC
*
16483 CC-CGAACTTCCAAAAATTCCAATTTTAC
1 CCTCGAACTTCCAAAAATTCCATTTTTAC
* *
16511 CCTCAAACTTTCAAAAATTCCATTTTTGAC
1 CCTCGAACTTCCAAAAATTCCATTTTT-AC
*
16541 CC-CGAAAC-TCCTAAAATTCCATTTTTAC
1 CCTCG-AACTTCCAAAAATTCCATTTTTAC
* *
16569 CCTCGAACTTTCAAAAATTTCATTTTTGA-
1 CCTCGAACTTCCAAAAATTCCATTTTT-AC
16598 CCTCGAAAC-TCCTAAAAATTCCATTTTTAC
1 CCTCG-AACTTCC-AAAAATTCCATTTTTAC
* *
16628 CCCCGAACCTCCAAAAATTCCATTTTT
1 CCTCGAACTTCCAAAAATTCCATTTTT
16655 GCCCCCGGAT
Statistics
Matches: 225, Mismatches: 22, Indels: 29
0.82 0.08 0.11
Matches are distributed among these distances:
28 11 0.05
29 148 0.66
30 66 0.29
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.34
Consensus pattern (29 bp):
CCTCGAACTTCCAAAAATTCCATTTTTAC
Found at i:16520 original size:58 final size:59
Alignment explanation
Indices: 16362--16661 Score: 417
Period size: 58 Copynumber: 5.1 Consensus size: 59
16352 TTGCCTTGGA
* * *
16362 GACCTCGAAACTTCCACAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTT
1 GACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT
* * *
16421 GACCCCAAAACTTCCAAAAATTCCATTTTTACCCTTGAACTTCCAAAAATTTCATTTTT
1 GACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT
* * * *
16480 AACCCCG-AACTTCCAAAAATTCCAATTTTACCCTCAAACTTTCAAAAATTCCATTTTT
1 GACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT
* * *
16538 GACCCCGAAAC-TCCTAAAATTCCATTTTTACCCTCGAACTTTCAAAAATTTCATTTTT
1 GACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT
* * *
16596 GACCTCGAAAC-TCCTAAAAATTCCATTTTTACCCCCGAACCTCCAAAAATTCCATTTTT
1 GACCCCGAAACTTCC-AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT
*
16655 GCCCCCG
1 GACCCCG
16662 GATGTCTAAA
Statistics
Matches: 213, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
58 108 0.51
59 105 0.49
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.33
Consensus pattern (59 bp):
GACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT
Found at i:16673 original size:88 final size:87
Alignment explanation
Indices: 16374--16704 Score: 355
Period size: 88 Copynumber: 3.8 Consensus size: 87
16364 CCTCGAAACT
* * * * * *
16374 TCCACAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAA
1 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAAC-TCTAAA
** *
16439 AATTCCATTTTTACCCTTGAACT
65 AATTCCATTTTTACCCCCGAACC
* * * *
16462 TCCAAAAATTTCATTTTTAACCCCGAACTTCCAAAAATTCCAATTTT-ACCCTC-AAACTTTCAA
1 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGA-CCTCGAAACTCT-AA
*
16525 AAATTCCATTTTTGA-CCCCGAAAC
64 AAATTCCATTTTT-ACCCCCGAACC
* * * *
16549 TCCTAAAATTCCATTTTTACCCTCGAACTTTCAAAAATTTCATTTTTGACCTCGAAACTCCTAAA
1 TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACT-CTAAA
16614 AATTCCATTTTTACCCCCGAACC
65 AATTCCATTTTTACCCCCGAACC
* * * * ** *
16637 TCCAAAAATTCCATTTTTGCCCCCGGA-TGTCTAAAAACTCCATTTTCAACCTCGAAACTCTCAA
1 TCCAAAAATTCCATTTTTACCCCCGAACT-TCCAAAAATTCCATTTTTGACCTCGAAACTCTAAA
16701 AATT
65 AATT
16705 ACTCTTTTAA
Statistics
Matches: 202, Mismatches: 33, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
86 1 0.00
87 79 0.39
88 121 0.60
89 1 0.00
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (87 bp):
TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTCTAAAA
ATTCCATTTTTACCCCCGAACC
Found at i:16704 original size:58 final size:60
Alignment explanation
Indices: 16362--16702 Score: 357
Period size: 58 Copynumber: 5.8 Consensus size: 60
16352 TTGCCTTGGA
* * *
16362 GACCTCGAAACTTCC-ACAAATTCCATTTTTACCCTCG-AACT-TCCAAAAATCCCATTTTT
1 GACCCCGAAAC-TCCTAAAAATTCCATTTTTACCCTCGAAACTCT-CAAAAATTCCATTTTT
* * *
16421 GACCCCAAAACTTCC-AAAAATTCCATTTTTACCCTTG-AACT-TCCAAAAATTTCATTTTT
1 GACCCCGAAAC-TCCTAAAAATTCCATTTTTACCCTCGAAACTCT-CAAAAATTCCATTTTT
* * *
16480 AACCCCG-AACTTCC-AAAAATTCCAATTTTACCCTC-AAACTTTCAAAAATTCCATTTTT
1 GACCCCGAAAC-TCCTAAAAATTCCATTTTTACCCTCGAAACTCTCAAAAATTCCATTTTT
* *
16538 GACCCCGAAACTCCT-AAAATTCCATTTTTACCCTCG-AACTTTCAAAAATTTCATTTTT
1 GACCCCGAAACTCCTAAAAATTCCATTTTTACCCTCGAAACTCTCAAAAATTCCATTTTT
* * *
16596 GACCTCGAAACTCCTAAAAATTCCATTTTTACCCCCGAACCTC-CAAAAATTCCATTTTT
1 GACCCCGAAACTCCTAAAAATTCCATTTTTACCCTCGAAACTCTCAAAAATTCCATTTTT
* * ** * * *
16655 GCCCCCGGATGT-CTAAAAACTCCATTTTCAACCTCGAAACTCTCAAAA
1 GACCCCGAAACTCCTAAAAATTCCATTTTTACCCTCGAAACTCTCAAAA
16703 TTACTCTTTT
Statistics
Matches: 245, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
58 133 0.54
59 109 0.44
60 3 0.01
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (60 bp):
GACCCCGAAACTCCTAAAAATTCCATTTTTACCCTCGAAACTCTCAAAAATTCCATTTTT
Found at i:29596 original size:3 final size:3
Alignment explanation
Indices: 29588--29627 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
29578 AATAAGATAC
29588 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29628 GTGGTGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:32290 original size:29 final size:29
Alignment explanation
Indices: 32206--32431 Score: 180
Period size: 29 Copynumber: 7.7 Consensus size: 29
32196 CTAAATTGTC
*
32206 CAAAAATTCCA-TTTTACCCTTGAACTTT
1 CAAAAATTCCATTTTTACCCTCGAACTTT
* *
32234 CAAAAATCCCATTTTTGATCC-CGAAACTTT
1 CAAAAATTCCATTTTT-ACCCTCG-AACTTT
* *
32264 CAAAAATTCTATTTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTT
32293 CAAAAA-TCTCATTTTTGA-CCTCGAAC-TT
1 CAAAAATTC-CATTTTT-ACCCTCGAACTTT
* * *
32321 CTAAAAATTCCATTTTTACCCCCAAACTTC
1 C-AAAAATTCCATTTTTACCCTCGAACTTT
* *
32351 CAAAAA-TCTCATTTTTGA-CCTTGAAATTT
1 CAAAAATTC-CATTTTT-ACCCTCGAACTTT
*
32380 CTAAAAAATTCCATTTTTACCCCCGAAC-TT
1 C--AAAAATTCCATTTTTACCCTCGAACTTT
**
32410 CTAAAAACCCCATTTTTGACCC
1 C-AAAAATTCCATTTTT-ACCC
32432 CAAAACTTCC
Statistics
Matches: 158, Mismatches: 23, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
28 17 0.11
29 83 0.53
30 39 0.25
31 17 0.11
32 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCTCGAACTTT
Found at i:32297 original size:59 final size:59
Alignment explanation
Indices: 32206--32484 Score: 298
Period size: 58 Copynumber: 4.7 Consensus size: 59
32196 CTAAATTGTC
** *
32206 CAAAAATTCCA-TTTTACCCTTGAACTTTCAAAAATCCCATTTTTGATCC-CGAAACTTT
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTCGAAACTTT
* * *
32264 CAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCG-AAC-TT
1 CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTT
* * *
32321 CTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCTCATTTTTGACCTTGAAA-TTT
1 C-AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTT
* * * * *
32380 CTAAAAAATTCCATTTTTACCCCCGAACTTCTAAAAACCCCATTTTTGACCCCAAAACTTC
1 C--AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTT
* *** * *
32441 CCAAAATTTTGTTTTTACTCCCGAACTTCCAAAAAATACCATTT
1 CAAAAATTCCATTTTTACCCCCGAACTTCC-AAAAATCCCATTT
32485 ACCCTCGAAT
Statistics
Matches: 188, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
57 3 0.02
58 62 0.33
59 62 0.33
60 58 0.31
61 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
CAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTT
Found at i:33583 original size:24 final size:24
Alignment explanation
Indices: 33549--33597 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
33539 TGATGTGGAA
* *
33549 CCAATAGAAAATGAAGATCCAACT
1 CCAATAAAAAATGAAAATCCAACT
33573 CCAATAAAAAATGAAAATCCAACT
1 CCAATAAAAAATGAAAATCCAACT
33597 C
1 C
33598 TGTGTATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.22, G:0.08, T:0.16
Consensus pattern (24 bp):
CCAATAAAAAATGAAAATCCAACT
Found at i:38013 original size:21 final size:21
Alignment explanation
Indices: 37988--38027 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
37978 TACTTACTAC
37988 TACTAACAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
38009 TACTAACAAAATAAAATTA
1 TACTAACAAAATAAAATTA
38028 AATTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
TACTAACAAAATAAAATTACT
Found at i:38109 original size:12 final size:12
Alignment explanation
Indices: 38080--38121 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
38070 TTTACTCAAC
38080 TAAATAAAAAAAT
1 TAAAT-AAAAAAT
*
38093 TAAATAACAAAT
1 TAAATAAAAAAT
*
38105 CAAATAAAAAAT
1 TAAATAAAAAAT
38117 TAAAT
1 TAAAT
38122 TAAACAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:38140 original size:24 final size:24
Alignment explanation
Indices: 38085--38148 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
38075 TCAACTAAAT
38085 AAAAAAATTAAA-T-AACAAATCAA
1 AAAAAAATTAAATTAAACAAA-CAA
38108 ATAAAAAATTAAATTAAACAAA-AA
1 A-AAAAAATTAAATTAAACAAACAA
*
38132 AAAACAAA-TAACTTAAA
1 AAAA-AAATTAAATTAAA
38149 ATAATAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 12 0.33
24 17 0.47
25 1 0.03
26 6 0.17
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (24 bp):
AAAAAAATTAAATTAAACAAACAA
Found at i:38955 original size:18 final size:17
Alignment explanation
Indices: 38928--38967 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
38918 TATTTAAAAC
38928 TATATAATAATAAACAAA
1 TATATAATAAT-AACAAA
* *
38946 TATATGATAATAACTAA
1 TATATAATAATAACAAA
38963 TATAT
1 TATAT
38968 TATGTAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (17 bp):
TATATAATAATAACAAA
Found at i:46522 original size:29 final size:29
Alignment explanation
Indices: 46483--46632 Score: 86
Period size: 29 Copynumber: 5.1 Consensus size: 29
46473 AAAATTGAAC
* *
46483 TTTTGGAAAATTTAAGGTCGAAAAT-GTGAT
1 TTTTGG-AAATTTAAGGGC-AAAATGGTAAT
*
46513 TTTTGGAAATTTGAGGGCAAAATGGTAAT
1 TTTTGGAAATTTAAGGGCAAAATGGTAAT
*** ** * *
46542 TTTTGGATGCTCGAGGGAAAAATGGTGAT
1 TTTTGGAAATTTAAGGGCAAAATGGTAAT
* * * **
46571 TTTAGAAAAGTTCGGGGTCAAAATGGTAAT
1 TTTTGGAAATTTAAGGG-CAAAATGGTAAT
** ** *
46601 TTTTGGATGTTCGAGGGTAAAATGGTAAT
1 TTTTGGAAATTTAAGGGCAAAATGGTAAT
46630 TTT
1 TTT
46633 AATGTTCGGG
Statistics
Matches: 90, Mismatches: 28, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
28 5 0.06
29 60 0.67
30 25 0.28
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (29 bp):
TTTTGGAAATTTAAGGGCAAAATGGTAAT
Found at i:46645 original size:27 final size:29
Alignment explanation
Indices: 46531--46708 Score: 123
Period size: 29 Copynumber: 6.1 Consensus size: 29
46521 ATTTGAGGGC
* * * *
46531 AAAATGGTAATTTTTGGATGCTCGAGGGA
1 AAAATGGTAATTTTTGAATGTTCGGGGGT
* * *
46560 AAAATGGTGATTTTAGAAAAGTTC-GGGGT
1 AAAATGGTAATTTTTG-AATGTTCGGGGGT
* *
46589 CAAAATGGTAATTTTTGGATGTTCGAGGGT
1 -AAAATGGTAATTTTTGAATGTTCGGGGGT
46619 AAAATGGTAA-TTTT-AATGTTCGGGGGT
1 AAAATGGTAATTTTTGAATGTTCGGGGGT
* * * ** *
46646 AAAAAT-GTAGTTTTAGAAAAGTTTAGGGTT
1 -AAAATGGTAATTTTTG-AATGTTCGGGGGT
**
46676 AAAATGGTAATTTTT-AGATGTTTAGGGGT
1 AAAATGGTAATTTTTGA-ATGTTCGGGGGT
46705 AAAA
1 AAAA
46709 ATGCAATTTT
Statistics
Matches: 116, Mismatches: 24, Indels: 18
0.73 0.15 0.11
Matches are distributed among these distances:
27 14 0.12
28 13 0.11
29 51 0.44
30 38 0.33
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTGAATGTTCGGGGGT
Found at i:46679 original size:29 final size:29
Alignment explanation
Indices: 46642--46892 Score: 172
Period size: 29 Copynumber: 8.6 Consensus size: 29
46632 TAATGTTCGG
* *
46642 GGGTAAAAATGTAGTTTTAGAAAAGTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA
*
46671 GGGTTAAAATGGTAATTTTTAG--ATGTTTA
1 GGGTTAAAAT-GTAA-TTTTAGAAAAGTTTA
* * *
46700 GGGGTAAAAATGCAATTTTAGAAAAGTTAA
1 -GGGTTAAAATGTAATTTTAGAAAAGTTTA
* * * * * *
46730 GAGTCAAAATGTAATTTTTG-GATGCTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA
* * * * *
46758 GGAG-CAAAATGATAATTTT-TATATGTAT-
1 GG-GTTAAAATG-TAATTTTAGAAAAGTTTA
* * * *
46786 GGGGTAAAATGTAATTTTGGAAAAATTTG
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA
* *
46815 GGGTTAAAATGTAATTTTGGAAAACTTTAA
1 GGGTTAAAATGTAATTTTAGAAAAGTTT-A
*
46845 GGGTTAAAATGTAACTTTAGAAAAGTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA
*
46874 GGGGTTAAAATATAATTTT
1 -GGGTTAAAATGTAATTTT
46893 TAAATAAAAC
Statistics
Matches: 175, Mismatches: 34, Indels: 25
0.75 0.15 0.11
Matches are distributed among these distances:
27 8 0.05
28 30 0.17
29 73 0.42
30 58 0.33
31 6 0.03
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTAGAAAAGTTTA
Found at i:46690 original size:86 final size:88
Alignment explanation
Indices: 46498--46697 Score: 230
Period size: 86 Copynumber: 2.3 Consensus size: 88
46488 GAAAATTTAA
* ** * *
46498 GGTCGAAAAT-GTGATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGGATGCTCGAGGGAAA
1 GGTC-AAAATGGTAATTTTTGGATGTTCGAGGGCAAAATGGTAATTTTTGAATGCTCGAGGGAAA
*
46562 AATGGTGATTTTAGAAAAGTTCGG
65 AATGGTGATTTTAGAAAAGTTCAG
* * *
46586 GGTCAAAATGGTAATTTTTGGATGTTCGAGGGTAAAATGGTAA-TTTT-AATGTTCGGGGGTAAA
1 GGTCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAATGGTAATTTTTGAATGCTCGAGGG-AAA
*
46649 AAT-GT-AGTTTTAGAAAAGTTTAG
65 AATGGTGA-TTTTAGAAAAGTTCAG
* *
46672 GGTTAAAATGGTAATTTTTAGATGTT
1 GGTCAAAATGGTAATTTTTGGATGTT
46698 TAGGGGTAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
85 1 0.01
86 49 0.51
87 15 0.15
88 32 0.33
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (88 bp):
GGTCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAATGGTAATTTTTGAATGCTCGAGGGAAAA
ATGGTGATTTTAGAAAAGTTCAG
Found at i:46709 original size:59 final size:59
Alignment explanation
Indices: 46614--46759 Score: 183
Period size: 59 Copynumber: 2.5 Consensus size: 59
46604 TGGATGTTCG
** * * *
46614 AGGG-TAAAATGGTAA-TTTTA-ATGTTCGGGGGTAAAAATGTAGTTTTAGAAAAGTTT
1 AGGGTTAAAATGGTAATTTTTAGATGTTTAGGGGTAAAAATGCAATTTTAGAAAAGTTA
46670 AGGGTTAAAATGGTAATTTTTAGATGTTTAGGGGTAAAAATGCAATTTTAGAAAAGTTA
1 AGGGTTAAAATGGTAATTTTTAGATGTTTAGGGGTAAAAATGCAATTTTAGAAAAGTTA
* * * *
46729 AGAGTCAAAAT-GTAATTTTTGGATGCTTAGG
1 AGGGTTAAAATGGTAATTTTTAGATGTTTAGG
46760 AGCAAAATGA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
56 4 0.05
57 11 0.14
58 23 0.29
59 40 0.51
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (59 bp):
AGGGTTAAAATGGTAATTTTTAGATGTTTAGGGGTAAAAATGCAATTTTAGAAAAGTTA
Found at i:46775 original size:58 final size:59
Alignment explanation
Indices: 46619--46776 Score: 164
Period size: 59 Copynumber: 2.7 Consensus size: 59
46609 GTTCGAGGGT
* * * * * *
46619 AAAATGGTAA-TTTTA-ATG-TTCGGGGGTAAAAATGTAGTTTTAGAAAAGTTTAGGGTT
1 AAAATGGTAATTTTTAGATGCTT-AGGAGTAAAAATGTAATTTTAGAAAAGTTAAGAGTC
* * *
46676 AAAATGGTAATTTTTAGATGTTTAGGGGTAAAAATGCAATTTTAGAAAAGTTAAGAGTC
1 AAAATGGTAATTTTTAGATGCTTAGGAGTAAAAATGTAATTTTAGAAAAGTTAAGAGTC
* *
46735 AAAAT-GTAATTTTTGGATGCTTAGGAG-CAAAATGATAATTTT
1 AAAATGGTAATTTTTAGATGCTTAGGAGTAAAAATG-TAATTTT
46777 TATATGTATG
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
57 16 0.19
58 30 0.35
59 38 0.44
60 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGATGCTTAGGAGTAAAAATGTAATTTTAGAAAAGTTAAGAGTC
Found at i:46851 original size:30 final size:30
Alignment explanation
Indices: 46786--46892 Score: 146
Period size: 30 Copynumber: 3.6 Consensus size: 30
46776 TTATATGTAT
46786 GGGG-TAAAATGTAATTTTGGAAAAATTT-
1 GGGGTTAAAATGTAATTTTGGAAAAATTTA
*
46814 GGGGTTAAAATGTAATTTTGGAAAACTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAATTTA
* * * *
46844 AGGGTTAAAATGTAACTTTAGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAATTTA
*
46874 GGGGTTAAAATATAATTTT
1 GGGGTTAAAATGTAATTTT
46893 TAAATAAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 4 0.06
29 23 0.33
30 42 0.61
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTGGAAAAATTTA
Found at i:46854 original size:144 final size:143
Alignment explanation
Indices: 46569--46871 Score: 346
Period size: 144 Copynumber: 2.1 Consensus size: 143
46559 AAAAATGGTG
** * * *
46569 ATTTTAGAAAAGTTCGGGGTCAAAATGGTAATTTTTGGATGTTCGAGGGTAAAATGGTAATTTTA
1 ATTTTAGAAAAGTTAAGAGTCAAAATGGTAATTTTTGGATGTTC-AGGGCAAAATGATAATTTTA
* * * * **
46634 ATGTTCGGGGGTAAAAATGTAGTTTTAGAAAAGTTTAGGGTTAAAATGGTAATTTTTAGATGTTT
65 ATGTTC-GGGGTAAAAATGTAATTTTAGAAAAATTTAGGGTTAAAATGGTAATTTTGAAAACTTT
*
46699 AGGGGTAAAAATGCA
129 AAGGGTAAAAATGCA
46714 ATTTTAGAAAAGTTAAGAGTCAAAAT-GTAATTTTTGGATGCTT-AGGAGCAAAATGATAATTTT
1 ATTTTAGAAAAGTTAAGAGTCAAAATGGTAATTTTTGGATG-TTCAGG-GCAAAATGATAA-TTT
* *
46777 TATATGTAT-GGGGT-AAAATGTAATTTTGGAAAAATTTGGGGTTAAAAT-GTAATTTTGGAAAA
63 TA-ATGT-TCGGGGTAAAAATGTAATTTTAGAAAAATTTAGGGTTAAAATGGTAATTTT-GAAAA
* *
46839 CTTTAAGGGTTAAAATGTA
125 CTTTAAGGGTAAAAATGCA
*
46858 ACTTTAGAAAAGTT
1 ATTTTAGAAAAGTT
46872 TAGGGGTTAA
Statistics
Matches: 135, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
143 11 0.08
144 84 0.62
145 35 0.26
146 4 0.03
147 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (143 bp):
ATTTTAGAAAAGTTAAGAGTCAAAATGGTAATTTTTGGATGTTCAGGGCAAAATGATAATTTTAA
TGTTCGGGGTAAAAATGTAATTTTAGAAAAATTTAGGGTTAAAATGGTAATTTTGAAAACTTTAA
GGGTAAAAATGCA
Found at i:47718 original size:17 final size:17
Alignment explanation
Indices: 47698--47736 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
47688 TTTCCTTTTT
47698 ATTTTGTTTTTTAATCC
1 ATTTTGTTTTTTAATCC
* *
47715 ATTTCGTTTTTTTATCC
1 ATTTTGTTTTTTAATCC
*
47732 CTTTT
1 ATTTT
47737 CTATTTAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.13, C:0.15, G:0.05, T:0.67
Consensus pattern (17 bp):
ATTTTGTTTTTTAATCC
Found at i:62346 original size:21 final size:22
Alignment explanation
Indices: 62305--62348 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
62295 ATATCTTGTA
*
62305 TTTTAATTTCATCAATTTTAGT
1 TTTTAATTTCATCAATATTAGT
62327 TTTTATATTTC-TCAA-ATTAGT
1 TTTTA-ATTTCATCAATATTAGT
62348 T
1 T
62349 ATGTTTAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTTAATTTCATCAATATTAGT
Found at i:78760 original size:33 final size:33
Alignment explanation
Indices: 78695--78761 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
78685 GGAGGGGATG
**
78695 GGGCTTGGGATGTGATGGAGGTGGAGGTTTGTA
1 GGGCTTGGGATGTGATGGAGGTGGAGACTTGTA
* * *
78728 GGGCTTGGGATGTGGTGGTGGTGGTGACTTGTA
1 GGGCTTGGGATGTGATGGAGGTGGAGACTTGTA
78761 G
1 G
78762 ATATAATGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.12, C:0.04, G:0.52, T:0.31
Consensus pattern (33 bp):
GGGCTTGGGATGTGATGGAGGTGGAGACTTGTA
Done.