Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008881.1 Hibiscus syriacus cultivar Beakdansim tig00112127_pilon, 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: 608427
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 3
Found at i:393 original size:24 final size:24
Alignment explanation
Indices: 366--516 Score: 128
Period size: 24 Copynumber: 6.4 Consensus size: 24
356 TATATCAAAA
* * *
366 ATCAAATCATAATTCACGTCAAGT
1 ATCATATCATAATCCAAGTCAAGT
* *
390 ATCATATCAAAATCCAGGTCAAGT
1 ATCATATCATAATCCAAGTCAAGT
*
414 ATCAGATC-TAATCCAAGTCAAGT
1 ATCATATCATAATCCAAGTCAAGT
* *
437 ATCATATCAGAATCCATGTCATA-T
1 ATCATATCATAATCCAAGTCA-AGT
* * * *
461 ATCAGATCAGAATCCATGTCGA-T
1 ATCATATCATAATCCAAGTCAAGT
* * *
484 ATCATAGCAGAATCCATGTCAAGT
1 ATCATATCATAATCCAAGTCAAGT
*
508 ATCAGATCA
1 ATCATATCA
517 GAAATCAAAT
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
23 41 0.38
24 65 0.61
25 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (24 bp):
ATCATATCATAATCCAAGTCAAGT
Found at i:452 original size:47 final size:48
Alignment explanation
Indices: 383--519 Score: 190
Period size: 47 Copynumber: 2.9 Consensus size: 48
373 CATAATTCAC
* * *
383 GTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATC-TAATCCAA
1 GTCAAGTATCATATCAGAATCCATGTCAAGTATCAGATCAGAATCCAA
*
430 GTCAAGTATCATATCAGAATCCATGTCATA-TATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCATGTCA-AGTATCAGATCAGAATCCAA
* *
478 GTCGA-TATCATAGCAGAATCCATGTCAAGTATCAGATCAGAA
1 GTCAAGTATCATATCAGAATCCATGTCAAGTATCAGATCAGAA
520 ATCAAATCGA
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
46 1 0.01
47 69 0.85
48 11 0.14
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCATGTCAAGTATCAGATCAGAATCCAA
Found at i:518 original size:24 final size:24
Alignment explanation
Indices: 383--519 Score: 163
Period size: 24 Copynumber: 5.8 Consensus size: 24
373 CATAATTCAC
* * *
383 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
* *
407 GTCAAGTATCAGATC-TAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
430 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
454 GTCATA-TATCAGATCAGAATCCAT
1 GTCA-AGTATCAGATCAGAATCCAT
* * *
478 GTCGA-TATCATAGCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
501 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
520 ATCAAATCGA
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
23 41 0.42
24 55 0.57
25 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:4682 original size:2 final size:2
Alignment explanation
Indices: 4675--4723 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
4665 GCACTGGAAC
4675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4717 TA -A TA TA
1 TA TA TA TA
4724 CTTTTAAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6275 original size:14 final size:14
Alignment explanation
Indices: 6258--6299 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
6248 ACCATATCTT
*
6258 CATAACCTCTAAAC
1 CATAAACTCTAAAC
*
6272 CATAAACTCTAAAT
1 CATAAACTCTAAAC
6286 CATAAACTCTAAAC
1 CATAAACTCTAAAC
6300 ACTAAATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
CATAAACTCTAAAC
Found at i:6305 original size:14 final size:14
Alignment explanation
Indices: 6264--6305 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
6254 TCTTCATAAC
6264 CTCTAAAC-CATAAA
1 CTCTAAACAC-TAAA
6278 CTCTAAATCA-TAAA
1 CTCTAAA-CACTAAA
6292 CTCTAAACACTAAA
1 CTCTAAACACTAAA
6306 TCATTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.08
14 22 0.88
15 1 0.04
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (14 bp):
CTCTAAACACTAAA
Found at i:6906 original size:31 final size:31
Alignment explanation
Indices: 6868--6944 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
6858 GTGTTCAAGT
6868 AATTATGTATATAATATATTTTCTTTTATAA
1 AATTATGTATATAATATATTTTCTTTTATAA
6899 AATTATGTATATAATATATTTTCTTTTATAA
1 AATTATGTATATAATATATTTTCTTTTATAA
*
6930 AATTACGTATTATAA
1 AATTATGTA-TATAA
6945 AAATTTAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 39 0.89
32 5 0.11
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (31 bp):
AATTATGTATATAATATATTTTCTTTTATAA
Found at i:7544 original size:23 final size:23
Alignment explanation
Indices: 7518--7567 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
7508 GGTAAATAAG
7518 AATACAATATCA-TATATAATTAT
1 AATACAAT-TCAGTATATAATTAT
* * *
7541 AATATAATTGAGTATATTATTAT
1 AATACAATTCAGTATATAATTAT
7564 AATA
1 AATA
7568 TTTAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (23 bp):
AATACAATTCAGTATATAATTAT
Found at i:7653 original size:39 final size:36
Alignment explanation
Indices: 7578--7669 Score: 89
Period size: 39 Copynumber: 2.4 Consensus size: 36
7568 TTTAAAAATA
7578 TAATATTATATTTTATTAAAATTATTAATTAATATTT
1 TAATATTATATTTTATTAAAATTATT-ATTAATATTT
7615 TAATAATTAATATTTTCATTAAAA-TATT-TTCAATTATTT
1 TAAT-ATT-ATATTTT-ATTAAAATTATTATT-AA-TATTT
*
7654 TGAGTATTTATATTTT
1 T-AATA-TTATATTTT
7670 TGAAGCGAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
37 6 0.13
38 5 0.11
39 25 0.53
40 11 0.23
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (36 bp):
TAATATTATATTTTATTAAAATTATTATTAATATTT
Found at i:16169 original size:21 final size:20
Alignment explanation
Indices: 16143--16188 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
16133 AGTGAATGTC
* * *
16143 AATTACAGATATTATATTGTA
1 AATTACAAATATAAAATT-TA
16164 AATTACAAATATAAAATTTA
1 AATTACAAATATAAAATTTA
16184 AATTA
1 AATTA
16189 TATTTACACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (20 bp):
AATTACAAATATAAAATTTA
Found at i:16898 original size:6 final size:6
Alignment explanation
Indices: 16887--16926 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
16877 GCGAAGGTAT
16887 GAAATA GAAATA GAAATA GAAATA GAAATA GAAATA GAAA
1 GAAATA GAAATA GAAATA GAAATA GAAATA GAAATA GAAA
16927 GATACTGCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (6 bp):
GAAATA
Found at i:23088 original size:30 final size:30
Alignment explanation
Indices: 22879--23071 Score: 359
Period size: 30 Copynumber: 6.4 Consensus size: 30
22869 TCCGAAGGAC
22879 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
22909 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
22939 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
22969 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
22999 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
23029 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
23059 CTATCCATAGGTC
1 CTATCCAGAGGTC
23072 CCGAAGAACC
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 158 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:23111 original size:31 final size:31
Alignment explanation
Indices: 23057--23149 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
23047 GATCCTCGGT
* *
23057 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
23088 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
23119 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
23150 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:27616 original size:30 final size:30
Alignment explanation
Indices: 27317--27599 Score: 566
Period size: 30 Copynumber: 9.4 Consensus size: 30
27307 TCCGAATGAC
27317 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27347 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27377 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27407 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27437 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27467 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27497 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27527 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27557 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
27587 CTATCCAGAGGTC
1 CTATCCAGAGGTC
27600 CCGAAGAACC
Statistics
Matches: 253, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 253 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:27984 original size:2 final size:2
Alignment explanation
Indices: 27972--28018 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
27962 TACACAACTC
27972 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28013 AT AT AT
1 AT AT AT
28019 TGTAACATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32748 original size:23 final size:22
Alignment explanation
Indices: 32718--32763 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
32708 AATCTAACCT
* * *
32718 AGAAAATTATGTGGCATTTAAA
1 AGAAAATTAAGAGGCATTGAAA
32740 AGAATAATTAAGAGGCATTGAAA
1 AGAA-AATTAAGAGGCATTGAAA
32763 A
1 A
32764 AAATTACCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (22 bp):
AGAAAATTAAGAGGCATTGAAA
Found at i:39388 original size:25 final size:25
Alignment explanation
Indices: 39360--39409 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39350 TCCCTCTGCT
39360 GTGATGGTCGTGTTTTGTTCGTGTA
1 GTGATGGTCGTGTTTTGTTCGTGTA
39385 GTGATGGTCGTGTTTTGTTCGTGTA
1 GTGATGGTCGTGTTTTGTTCGTGTA
39410 CGTGGGGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.08, C:0.08, G:0.36, T:0.48
Consensus pattern (25 bp):
GTGATGGTCGTGTTTTGTTCGTGTA
Found at i:52536 original size:21 final size:21
Alignment explanation
Indices: 52507--52546 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52497 TTTTTATTAT
* *
52507 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
52528 TTTAGTAAAACACTTGGTA
1 TTTAGTAAAACAATTGGTA
52547 CATTTAGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:54251 original size:21 final size:21
Alignment explanation
Indices: 54218--54270 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
54208 ATTCTGACTA
54218 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
54239 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
54260 TCGCAATGCGA
1 TCGCATTGCGA
54271 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:54285 original size:20 final size:20
Alignment explanation
Indices: 54260--54573 Score: 529
Period size: 20 Copynumber: 15.7 Consensus size: 20
54250 TTTTCCTAAT
54260 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
54280 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
54301 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
54321 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
54341 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
54361 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
54381 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* **
54401 TCGCAATACGAATATATAAA
1 TCGCAATGCGAATACGTAAA
54421 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
54441 TCGCAATGCGCATACGTAAA
1 TCGCAATGCGAATACGTAAA
54461 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
54481 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
54501 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
54521 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
54541 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
54561 TCGCAACGCGAAT
1 TCGCAATGCGAAT
54574 CTGACTATCG
Statistics
Matches: 275, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
20 259 0.94
21 16 0.06
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:54795 original size:22 final size:22
Alignment explanation
Indices: 54770--54835 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
54760 GGCGACATCC
54770 GTCCTCATCTCCGACGAAATCA
1 GTCCTCATCTCCGACGAAATCA
* *
54792 GTCCCCATCTCCGACGATATCA
1 GTCCTCATCTCCGACGAAATCA
**
54814 GT-CTCCATCTCCGGTGAAATCA
1 GTCCT-CATCTCCGACGAAATCA
54836 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 1 0.03
22 36 0.97
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.24
Consensus pattern (22 bp):
GTCCTCATCTCCGACGAAATCA
Found at i:55244 original size:20 final size:20
Alignment explanation
Indices: 55171--55261 Score: 85
Period size: 20 Copynumber: 4.6 Consensus size: 20
55161 ACGATTCTGT
*
55171 CGTTGCAATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
55190 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
55210 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
* *
55230 TGTTGCGATTTTCATTTTGG
1 CGTTGCGATTTTCATTTTCG
*
55250 TGTTGCGATTTT
1 CGTTGCGATTTT
55262 AAGTTTCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 11 0.18
20 50 0.82
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:57162 original size:20 final size:20
Alignment explanation
Indices: 57137--57298 Score: 180
Period size: 20 Copynumber: 8.5 Consensus size: 20
57127 AGAATAGTTT
*
57137 ACTATCGCAATGCGAAAATA
1 ACTATCGCAATGCGAAAATG
* *
57157 ACTATCGCGACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
57177 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
57193 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
57210 AAAATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
57230 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
57250 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
57270 ACTAT-GCAATGC-AAATTTG
1 ACTATCGCAATGCGAAA-ATG
57289 ACTATCGCAA
1 ACTATCGCAA
57299 CGAAAGAATT
Statistics
Matches: 123, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.06
16 6 0.05
17 4 0.03
18 5 0.04
19 24 0.20
20 77 0.63
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:57237 original size:39 final size:38
Alignment explanation
Indices: 57140--57330 Score: 136
Period size: 40 Copynumber: 5.2 Consensus size: 38
57130 ATAGTTTACT
* * * **
57140 ATCGCAATGCGAAAATAACTATCGCGACGCGAAAATGACT
1 ATCGCAA-GCGAAAATGACTATCGCAATGCG-AAATGAAA
*
57180 ATCGCAA-CG-AGA-GA--ATCGCAATGCGAAATGAAA
1 ATCGCAAGCGAAAATGACTATCGCAATGCGAAATGAAA
**
57213 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACT
1 ATCGCAA-GCGAAAATGACTATCGCAATGCG-AAATGAAA
**
57253 ATCGCAATGCGAAAATGACTAT-GCAATGC-AAATTTGACT
1 ATCGCAA-GCGAAAATGACTATCGCAATGCGAAA--TGAAA
*
57292 ATCGCAA-CG-AAA-GA--ATTGCAATGCGAAATGAAA
1 ATCGCAAGCGAAAATGACTATCGCAATGCGAAATGAAA
57325 ATCGCA
1 ATCGCA
57331 TTGCAATTCT
Statistics
Matches: 128, Mismatches: 12, Indels: 29
0.76 0.07 0.17
Matches are distributed among these distances:
33 24 0.19
34 16 0.12
35 7 0.05
36 6 0.05
37 9 0.07
38 2 0.02
39 30 0.23
40 34 0.27
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (38 bp):
ATCGCAAGCGAAAATGACTATCGCAATGCGAAATGAAA
Found at i:57370 original size:20 final size:20
Alignment explanation
Indices: 57345--57471 Score: 202
Period size: 20 Copynumber: 6.3 Consensus size: 20
57335 AATTCTCTCG
*
57345 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTC-ATTTTCGCA
**
57365 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
57385 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
57405 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
57425 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
57445 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
57465 TTGCGAT
1 TTGCGAT
57472 TTTAAGTTTC
Statistics
Matches: 102, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
19 4 0.04
20 98 0.96
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:57996 original size:18 final size:19
Alignment explanation
Indices: 57957--57998 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
57947 CTCACCTGTC
57957 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
57978 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
57996 ATC
1 ATC
57999 ATTCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:59462 original size:14 final size:14
Alignment explanation
Indices: 59443--59478 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
59433 ATTGTTTAAT
59443 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
59457 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
59471 TGATTTGT
1 TGATTTGT
59479 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:59672 original size:34 final size:33
Alignment explanation
Indices: 59584--59673 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
59574 AAAACAGACT
* **
59584 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
59618 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
59651 ATCGCAATGCGAAAATGAAAATC
1 ATCGCAATGCG-AAATGAAAATC
59674 ACAATGCGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 31 0.61
34 20 0.39
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:59753 original size:20 final size:20
Alignment explanation
Indices: 59728--59816 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
59718 GTGATTCACT
*
59728 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
59748 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
59768 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
59788 TGTTGCGATAGTCATATT-TG
1 CGTTGCGATAGTCAT-TTCCG
59808 CGTTGCGAT
1 CGTTGCGAT
59817 TTCCGCGTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:62277 original size:25 final size:24
Alignment explanation
Indices: 62237--62291 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
62227 TTGAAAAATC
62237 ATCAAAATCCGAGTATAGACCAAG
1 ATCAAAATCCGAGTATAGACCAAG
* * *
62261 ATGCAAAGTCCGGGTATTGACCAAG
1 AT-CAAAATCCGAGTATAGACCAAG
62286 ATCAAA
1 ATCAAA
62292 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (24 bp):
ATCAAAATCCGAGTATAGACCAAG
Found at i:63176 original size:20 final size:20
Alignment explanation
Indices: 63132--63179 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
63122 GAAATTCAGT
*
63132 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCGC
*
63152 ATTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCGC
*
63172 GTTGCGAT
1 ATTGCGAT
63180 TTACGTATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCGC
Found at i:63189 original size:20 final size:20
Alignment explanation
Indices: 63166--63257 Score: 130
Period size: 20 Copynumber: 4.5 Consensus size: 20
63156 CGATAGTCAG
*
63166 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
63186 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
63206 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
63227 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
63247 ATTCGCATTGC
1 ATTCGCATTGC
63258 AAATTAGGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.74
21 16 0.26
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:63301 original size:21 final size:21
Alignment explanation
Indices: 63249--63301 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
63239 ATTTACGTAT
* *
63249 TCGCATTGCAAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
63270 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
63291 TCGCAATGCGA
1 TCGCAATGCGA
63302 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:64076 original size:22 final size:22
Alignment explanation
Indices: 64051--64105 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
64041 CCGAAATAAT
* *
64051 AATAAAAATATTATTTTAATTC
1 AATAAAAATAATAATTTAATTC
64073 AATAAAAATAATAATTTAATT-
1 AATAAAAATAATAATTTAATTC
*
64094 GA-AAAAATAATA
1 AATAAAAATAATA
64106 TATAGAGAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 10 0.33
21 1 0.03
22 19 0.63
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAAAAATAATAATTTAATTC
Found at i:73205 original size:6 final size:6
Alignment explanation
Indices: 73194--73226 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
73184 GGAATCGTAG
73194 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGG
1 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT TGG
73227 AATAAGCGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
TGGGAT
Found at i:88789 original size:28 final size:30
Alignment explanation
Indices: 88756--88831 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
88746 ATGTCTATCG
**
88756 TTTATTTTTAAAAAAATTTAAAAAAA-ATA
1 TTTATTTTTAAAAAAAAATAAAAAAATATA
*
88785 -TTATTTTTAATAAAAAAATAAAAAAATGTA
1 TTTATTTTTAA-AAAAAAATAAAAAAATATA
88815 TTTATTTATTAAAAAAA
1 TTTATTT-TTAAAAAAA
88832 CAAATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 10 0.25
29 13 0.32
30 2 0.05
31 11 0.28
32 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
TTTATTTTTAAAAAAAAATAAAAAAATATA
Found at i:90548 original size:23 final size:23
Alignment explanation
Indices: 90522--90569 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
90512 ATAAAGTACA
* *
90522 ATAACATACTAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
90545 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
90568 AT
1 AT
90570 TTACATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:91022 original size:23 final size:23
Alignment explanation
Indices: 90996--91058 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
90986 ATATAACCAC
90996 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
91019 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
91042 TACCTATTACATCATAT
1 TACCTATTACATTATAT
91059 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:91531 original size:39 final size:39
Alignment explanation
Indices: 91477--91562 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
91467 CAAGTTGTAG
*
91477 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
91516 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
91555 ATTTTGAT
1 ATTTTGAT
91563 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:91842 original size:18 final size:18
Alignment explanation
Indices: 91819--91855 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
91809 CGAAATATAT
91819 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
91837 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
91855 A
1 A
91856 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:92313 original size:23 final size:23
Alignment explanation
Indices: 92287--92349 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
92277 ATATAACCAC
92287 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
92310 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
92333 TACCTATTACATCATAT
1 TACCTATTACATTATAT
92350 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:92740 original size:25 final size:25
Alignment explanation
Indices: 92683--92748 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
92673 CACTCAAAAG
*
92683 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*** *
92708 ACAAACATATCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
92733 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
92749 TTAATGATAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:95515 original size:183 final size:183
Alignment explanation
Indices: 95212--95884 Score: 1127
Period size: 183 Copynumber: 3.7 Consensus size: 183
95202 TTAAAATTAC
*
95212 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATTTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
95277 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
95342 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTTCGATGT-AAAAT-T
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGAAAATGT
95393 ACCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACA
1 --CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACA
* * *
95458 ATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGATATATTTATACCGG
64 ATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGG
*
95523 TTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
129 TTATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGAAAATGT
* * * *
95578 CGATACTTTTTTAAATCGTATCTACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
95643 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAATCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
95708 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGAAAATGT
*
95761 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
* *
95825 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAAAAAACCGGTATATTTATA
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATA
95885 ATATGTTGAA
Statistics
Matches: 466, Mismatches: 21, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
183 458 0.98
184 7 0.02
185 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGAAAATGT
Found at i:97347 original size:3 final size:3
Alignment explanation
Indices: 97339--97407 Score: 57
Period size: 3 Copynumber: 23.0 Consensus size: 3
97329 ACTTGTTTGG
* * * ** * *
97339 ATC ATC ATC TTC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
97387 ATC GTC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC
97408 GTCAGCTTCA
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:97356 original size:12 final size:12
Alignment explanation
Indices: 97339--97422 Score: 69
Period size: 12 Copynumber: 7.0 Consensus size: 12
97329 ACTTGTTTGG
97339 ATCATCATCTTC
1 ATCATCATCTTC
*
97351 ATCATCATCATC
1 ATCATCATCTTC
*
97363 GTCATCATCTTC
1 ATCATCATCTTC
** *
97375 ATCGCCAGCTTC
1 ATCATCATCTTC
* *
97387 ATCGTCATCATC
1 ATCATCATCTTC
* *
97399 ATCGTCATCGTC
1 ATCATCATCTTC
* *
97411 AGCTTCATCTTC
1 ATCATCATCTTC
97423 TGCGACCGCT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 58 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:97362 original size:18 final size:18
Alignment explanation
Indices: 97339--97422 Score: 78
Period size: 18 Copynumber: 4.7 Consensus size: 18
97329 ACTTGTTTGG
*
97339 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCGTC
* * *
97357 ATCATCGTCATCATCTTC
1 ATCATCATCTTCATCGTC
** *
97375 ATCGCCAGCTTCATCGTC
1 ATCATCATCTTCATCGTC
*
97393 ATCATCATCGTCATCGTC
1 ATCATCATCTTCATCGTC
* *
97411 AGCTTCATCTTC
1 ATCATCATCTTC
97423 TGCGACCGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCGTC
Found at i:97389 original size:30 final size:30
Alignment explanation
Indices: 97355--97419 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
97345 ATCTTCATCA
* *
97355 TCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCGTCATCGCCAGCT
* *
97385 TCATCGTCATCATCATCGTCATCGTCAGCT
1 TCATCATCATCATCATCGTCATCGCCAGCT
97415 TCATC
1 TCATC
97420 TTCTGCGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.11, T:0.34
Consensus pattern (30 bp):
TCATCATCATCATCATCGTCATCGCCAGCT
Found at i:97422 original size:6 final size:6
Alignment explanation
Indices: 97343--97422 Score: 52
Period size: 6 Copynumber: 13.3 Consensus size: 6
97333 GTTTGGATCA
* * * * * * * *
97343 TCATCT TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
97391 TCATCA TCATCG TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TC
97423 TGCGACCGCT
Statistics
Matches: 58, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.20, C:0.35, G:0.09, T:0.36
Consensus pattern (6 bp):
TCATCT
Found at i:99583 original size:199 final size:199
Alignment explanation
Indices: 99005--100013 Score: 1839
Period size: 199 Copynumber: 5.1 Consensus size: 199
98995 GATGATTTTG
99005 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
*
99070 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
99135 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
99200 ATAT
196 ATAT
99204 GGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
* *
99267 --TATTAGTGTCGACACATTTTTTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
99330 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
99395 ATAT
196 ATAT
*
99399 GGATCAACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
* *
99464 TATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTATACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
99529 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
99594 ATAT
196 ATAT
*
99598 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCAACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
99663 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
*
99728 GATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTCGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
99792 ATAT
196 ATAT
99796 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAAATATCGACACAAA
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAAATATCGACACAAA
* * *
99861 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGACTTGTACCGGTT
65 CTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTT
* * *
99926 AGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACACTTTTT
130 AGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTT
99991 ATATAT
194 ATATAT
99997 GGATCGACACTTTATGG
1 GGATCGACACTTTATGG
100014 TAAATTTGCC
Statistics
Matches: 784, Mismatches: 19, Indels: 12
0.96 0.02 0.01
Matches are distributed among these distances:
195 143 0.18
196 28 0.04
197 40 0.05
198 122 0.16
199 387 0.49
200 16 0.02
201 48 0.06
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (199 bp):
GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
TATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
ATAT
Found at i:99609 original size:394 final size:395
Alignment explanation
Indices: 99005--100014 Score: 1844
Period size: 394 Copynumber: 2.5 Consensus size: 395
98995 GATGATTTTG
99005 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
99070 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
99135 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
*
99200 ATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACA
196 ATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCAACACA
* *
99264 AAC-TATTAGTGTCGACACATTTTTTATACATATTATCTCATAAAACCGGTATAATTGTACCGGT
261 AACATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGT
*
99328 TAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTT
326 TAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTCGGATCGACACTTTTT
99393 ATATAT
390 ATATAT
*
99399 GGATCAACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
* * *
99464 TATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTATACCGGTTA
66 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
99529 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
131 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
99594 ATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCAACAC
196 ATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCAACAC
99659 AAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCG
260 AAAC-ATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCG
99724 GTTAGATTGAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTCGGATCGACACTTTT
324 GTTAGATTGAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTCGGATCGACACTTTT
99789 TATATAT
389 TATATAT
99796 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAAATATCGACACAAA
1 GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAAATATCGACACAAA
* *
99861 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGACTTGTACCGGTT
65 CTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTT
* * *
99926 AGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACACTTTTT
130 AGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTT
99991 ATATATGGATCGACACTTTATGGT
194 ATATATGGATCGACACTTTATGGT
100015 AAATTTGCCT
Statistics
Matches: 593, Mismatches: 17, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
394 210 0.35
395 28 0.05
396 19 0.03
397 93 0.16
398 196 0.33
399 47 0.08
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (395 bp):
GGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAC
TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
ATATGGATCGACACTTTATGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCAACACA
AACATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATAATTGTACCGGT
TAGATTGAAAAATTACATATACATTATACTTTTGGGTTCGATGATTTTCGGATCGACACTTTTTA
TATAT
Found at i:100168 original size:19 final size:19
Alignment explanation
Indices: 100122--100170 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
100112 TTATATTCAC
*
100122 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
100141 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
100160 ATACAAAATTA
1 ATACAAAATTA
100171 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:102085 original size:21 final size:21
Alignment explanation
Indices: 102060--102124 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
102050 CCCCTTATGC
* *
102060 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
102081 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
102102 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
102123 CT
1 CT
102125 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:104530 original size:20 final size:20
Alignment explanation
Indices: 104503--104549 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
104493 TCCGGTAACG
104503 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
104522 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
104543 TTTTACC
1 TTTTACC
104550 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:104763 original size:181 final size:180
Alignment explanation
Indices: 104337--104761 Score: 629
Period size: 181 Copynumber: 2.4 Consensus size: 180
104327 ATATATCCGG
* *
104337 TATCATTTTAT--CGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTT
1 TATCATTTTATACCGGTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTT
* * *
104400 TAAAGTATCGACACATTATAGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCT
66 AAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCT
* * * *
104465 TATATAAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTT
131 TATATAAAGTACCGACACTTTAAATATATCCGGTAACGCTTGACCGGTTT
* *
104515 TATCATTTTGTTACCGGTTTTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTT
1 TATCATTTT-ATACCGGTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
* ** *
104580 TAAAAGTATCGACACTTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCC
65 TAAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCC
* *
104645 TTATATTAAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTT
130 TTATA-TAAAGTACCGACACTTTAAATATATCCGGTAACGCTTGACCGGTTT
* * *
104697 TATCATTTCTATACCGGTTTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
1 TATCATTT-TATACCGGTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
104762 AATTTGGATC
Statistics
Matches: 220, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
178 9 0.04
179 1 0.00
181 111 0.50
182 98 0.45
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (180 bp):
TATCATTTTATACCGGTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTT
AAAAGTATCGACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCT
TATATAAAGTACCGACACTTTAAATATATCCGGTAACGCTTGACCGGTTT
Found at i:118929 original size:22 final size:21
Alignment explanation
Indices: 118893--118954 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 21
118883 GAACCAGTGG
* *
118893 GGGGGTATCGATTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
118913 GGAGGGAATCGGTTTCCCATTCAAA
1 GG-GGGAATCGG-TTCCC--TCAAA
118938 GGGGGAATCGGTTCCCT
1 GGGGGAATCGGTTCCCT
118955 TATGGGGGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
20 2 0.06
21 8 0.23
22 5 0.14
23 5 0.14
24 11 0.31
25 4 0.11
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:123659 original size:153 final size:148
Alignment explanation
Indices: 123363--123664 Score: 475
Period size: 153 Copynumber: 2.0 Consensus size: 148
123353 GATGAATATC
*
123363 ATCATACACCTCTTCCAATGACAATAATTTGTTCCATGAATGTGGAGCACGTAATAGGTCTGGAT
1 ATCATACACCTCTTCCAATGACAATAATTTGTTCCATGAATGTGGAGCACGCAATAGGTCTGGAT
*
123428 TCTTCCATGGAGAACAGGAAGTAGACGCCATCTTTATCTATTTAATCTTCCCGTATCGACTCAAG
66 TCTTCCATGGAGAACAGGAAGTA-ACGCCATCTTTA-CTATTTAATCTTCCCGGATCGACTCAAG
123493 AGGTGATTAAACCTTCAAAG
129 AGGTGATTAAACCTTCAAAG
123513 ATCATACACCTCTTCCAATGACAATAATTTGTTCCATAGAAATGTGGAGGCACGCAATAGGTCTG
1 ATCATACACCTCTTCCAATGACAATAATTTGTTCCAT-G-AATGTGGA-GCACGCAATAGGTCTG
123578 GATTCTTCCATGGAGAATGAACAGGAAGT-ACGCCATCTTTA-TATTTAACTCTTCCCGGATCGA
63 GATTCTTCCAT-G-G-A-GAACAGGAAGTAACGCCATCTTTACTATTTAA-TCTTCCCGGATCGA
123641 CTCAAGAGGTGATT-AACCTTCAAA
123 CTCAAGAGGTGATTAAACCTTCAAA
123665 TAAGTGAGGC
Statistics
Matches: 142, Mismatches: 2, Indels: 13
0.90 0.01 0.08
Matches are distributed among these distances:
150 37 0.26
151 1 0.01
152 8 0.06
153 43 0.30
154 28 0.20
155 13 0.09
156 1 0.01
157 11 0.08
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (148 bp):
ATCATACACCTCTTCCAATGACAATAATTTGTTCCATGAATGTGGAGCACGCAATAGGTCTGGAT
TCTTCCATGGAGAACAGGAAGTAACGCCATCTTTACTATTTAATCTTCCCGGATCGACTCAAGAG
GTGATTAAACCTTCAAAG
Found at i:125920 original size:17 final size:17
Alignment explanation
Indices: 125887--125920 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
125877 TTGACCCCCG
*
125887 TTTTTATGCTCATACTC
1 TTTTTATGCTCAGACTC
*
125904 TTTTTATGCTCCGACTC
1 TTTTTATGCTCAGACTC
125921 CATACAGCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.09, T:0.50
Consensus pattern (17 bp):
TTTTTATGCTCAGACTC
Found at i:126041 original size:18 final size:18
Alignment explanation
Indices: 126020--126079 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
126010 TATAAGATAA
*
126020 TTAAAATTAATTAATTTT
1 TTAAAATTAATTAAGTTT
*
126038 TTAAAAATAATT-AGTTT
1 TTAAAATTAATTAAGTTT
*
126055 TTAAAA-TAATATAAGTAT
1 TTAAAATTAAT-TAAGTTT
126073 TTAAAAT
1 TTAAAAT
126080 ATAAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.11
17 11 0.31
18 21 0.58
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTAAAATTAATTAAGTTT
Found at i:135515 original size:14 final size:14
Alignment explanation
Indices: 135498--135524 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
135488 TTACATCTTT
135498 TGAAAAATATTTTC
1 TGAAAAATATTTTC
135512 TGAAAAATATTTT
1 TGAAAAATATTTT
135525 ACGGTGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
TGAAAAATATTTTC
Found at i:135689 original size:14 final size:14
Alignment explanation
Indices: 135670--135705 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
135660 TATTAAAATT
135670 AATATTATTGTTAA
1 AATATTATTGTTAA
*
135684 AATATTATTTTTAA
1 AATATTATTGTTAA
*
135698 AATTTTAT
1 AATATTAT
135706 AAAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
AATATTATTGTTAA
Found at i:135807 original size:10 final size:10
Alignment explanation
Indices: 135794--135836 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 10
135784 ATATTGTATT
135794 ATATTTTTAA
1 ATATTTTTAA
135804 ATATTATTAATAA
1 ATATT-TT--TAA
135817 ATATATTTTAA
1 ATAT-TTTTAA
135828 ATATTTTTA
1 ATATTTTTA
135837 TTAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
13 9 0.31
14 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:135843 original size:25 final size:24
Alignment explanation
Indices: 135793--135849 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
135783 AATATTGTAT
135793 TATATTTTTAAATATTATTAATAAA
1 TATA-TTTTAAATATTATTAATAAA
* *
135818 TATATTTTAAATATTTTTATTAAA
1 TATATTTTAAATATTATTAATAAA
*
135842 -ATAATTTA
1 TATATTTTA
135850 GACTATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 7 0.24
24 18 0.62
25 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATATTTTAAATATTATTAATAAA
Found at i:136044 original size:23 final size:23
Alignment explanation
Indices: 135986--136045 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
135976 TTTATAATAT
135986 CAAATA-ATTTTAAAAAATTTAA
1 CAAATATATTTTAAAAAATTTAA
* *
136008 -TATTATATTATT-AAAAATATTAA
1 CAAATATATT-TTAAAAAAT-TTAA
136031 CAAATATATTTTAAA
1 CAAATATATTTTAAA
136046 TATTTTAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
21 3 0.10
22 9 0.31
23 8 0.28
24 9 0.31
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (23 bp):
CAAATATATTTTAAAAAATTTAA
Found at i:136053 original size:23 final size:23
Alignment explanation
Indices: 135986--136053 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
135976 TTTATAATAT
*
135986 CAAATA-ATTTTAAAAAATTTAA
1 CAAATATATTTTAAAAATTTTAA
* * *
136008 -TATTATATTATTAAAAATATTAA
1 CAAATATATT-TTAAAAATTTTAA
*
136031 CAAATATATTTTAAATATTTTAA
1 CAAATATATTTTAAAAATTTTAA
136054 TGATCAATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 3 0.09
22 3 0.09
23 22 0.63
24 7 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
CAAATATATTTTAAAAATTTTAA
Found at i:137814 original size:12 final size:12
Alignment explanation
Indices: 137789--137827 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
137779 GGAAAATGAT
137789 GAAGAACAAG-AA
1 GAAGAA-AAGAAA
*
137801 GAAGAGAAGAAA
1 GAAGAAAAGAAA
137813 GAAGAAAAGAAA
1 GAAGAAAAGAAA
137825 GAA
1 GAA
137828 AATTGTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAAAGAAA
Found at i:137816 original size:15 final size:16
Alignment explanation
Indices: 137796--137828 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
137786 GATGAAGAAC
*
137796 AAGAAGAAGAG-AAGA
1 AAGAAGAAAAGAAAGA
137811 AAGAAGAAAAGAAAGA
1 AAGAAGAAAAGAAAGA
137827 AA
1 AA
137829 ATTGTATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
AAGAAGAAAAGAAAGA
Found at i:153923 original size:39 final size:39
Alignment explanation
Indices: 153850--153927 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
153840 TGCGTTTTTT
* * *
153850 ATTAAATGAAGAACATGAACAAGATTTTGTGTTCGTTTA
1 ATTAAATGAAGAACATGAACAAGAGTCTGCGTTCGTTTA
153889 ATTAAATGAACGAACATGAACATAG-GTCT-CGTTCGTTTA
1 ATTAAATGAA-GAACATGAACA-AGAGTCTGCGTTCGTTTA
153928 TTTATGTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 19 0.56
40 13 0.38
41 2 0.06
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (39 bp):
ATTAAATGAAGAACATGAACAAGAGTCTGCGTTCGTTTA
Found at i:153961 original size:14 final size:14
Alignment explanation
Indices: 153942--153973 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
153932 TGTTCGTGAA
153942 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
153956 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
153970 CGTT
1 CGTT
153974 TATGTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:153990 original size:24 final size:24
Alignment explanation
Indices: 153943--153993 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
153933 GTTCGTGAAC
* *
153943 GTTCGATTATGTTCGTTCGGTTAT
1 GTTCGATTATGTTCATTCAGTTAT
* *
153967 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGATTATGTTCATTCAGTTAT
153991 GTT
1 GTT
153994 TAACCCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGATTATGTTCATTCAGTTAT
Found at i:155076 original size:10 final size:10
Alignment explanation
Indices: 155061--155147 Score: 53
Period size: 10 Copynumber: 10.3 Consensus size: 10
155051 GGGTCTCCAA
155061 CGTTTATGTT
1 CGTTTATGTT
155071 CGTTTA---T
1 CGTTTATGTT
155078 -GTTTATGTT
1 CGTTTATGTT
155087 CGTTTATGTT
1 CGTTTATGTT
155097 C----ATGTT
1 CGTTTATGTT
155103 CGTTTATGTT
1 CGTTTATGTT
155113 C----ATGTT
1 CGTTTATGTT
*
155119 CATTTATGTT
1 CGTTTATGTT
155129 CG----TGTT
1 CGTTTATGTT
155135 CGTTTATGTT
1 CGTTTATGTT
155145 CGT
1 CGT
155148 GTTCATTTAT
Statistics
Matches: 60, Mismatches: 1, Indels: 32
0.65 0.01 0.34
Matches are distributed among these distances:
6 23 0.38
7 1 0.02
9 1 0.02
10 35 0.58
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:155083 original size:16 final size:16
Alignment explanation
Indices: 155066--155163 Score: 151
Period size: 16 Copynumber: 6.1 Consensus size: 16
155056 TCCAACGTTT
*
155066 ATGTTCGTTTATGTTT
1 ATGTTCGTTTATGTTC
155082 ATGTTCGTTTATGTTC
1 ATGTTCGTTTATGTTC
155098 ATGTTCGTTTATGTTC
1 ATGTTCGTTTATGTTC
*
155114 ATGTTCATTTATGTTC
1 ATGTTCGTTTATGTTC
*
155130 GTGTTCGTTTATGTTC
1 ATGTTCGTTTATGTTC
* *
155146 GTGTTCATTTATGTTC
1 ATGTTCGTTTATGTTC
155162 AT
1 AT
155164 TTATTTATTA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 76 1.00
ACGTcount: A:0.13, C:0.11, G:0.18, T:0.57
Consensus pattern (16 bp):
ATGTTCGTTTATGTTC
Found at i:155101 original size:6 final size:6
Alignment explanation
Indices: 155092--155163 Score: 52
Period size: 6 Copynumber: 13.3 Consensus size: 6
155082 ATGTTCGTTT
* *
155092 ATGTTC ATGTTC --GTTT ATGTTC ATGTTC AT-TT- ATGTTC GTGTTC
1 ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC
* *
155136 --GTTT ATGTTC GTGTTC AT-TT- ATGTTC AT
1 ATGTTC ATGTTC ATGTTC ATGTTC ATGTTC AT
155164 TTATTTATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
4 10 0.20
5 8 0.16
6 33 0.65
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.56
Consensus pattern (6 bp):
ATGTTC
Found at i:155256 original size:16 final size:16
Alignment explanation
Indices: 155232--155264 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
155222 AAAAAAAATT
*
155232 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
155248 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
155264 T
1 T
155265 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.24, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:155559 original size:20 final size:19
Alignment explanation
Indices: 155498--155569 Score: 81
Period size: 22 Copynumber: 3.6 Consensus size: 19
155488 TGCATTCATA
*
155498 CATCCCTGCACCTGTAGTG
1 CATCCATGCACCTGTAGTG
*
155517 CATCCATGCACCTCCACTAGTG
1 CATCCATGCACCT---GTAGTG
*
155539 CATCGATGCACCATGTAGTG
1 CATCCATGCACC-TGTAGTG
155559 CATCCATGCAC
1 CATCCATGCAC
155570 TCCATTTCGA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 12 0.27
20 15 0.34
22 16 0.36
23 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (19 bp):
CATCCATGCACCTGTAGTG
Found at i:156412 original size:21 final size:20
Alignment explanation
Indices: 156361--156398 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
156351 TTGAAAGCAA
156361 AAAAT-AGATTTTGAAAAAC
1 AAAATGAGATTTTGAAAAAC
*
156380 AAAATGAAATTTTGAAAAA
1 AAAATGAGATTTTGAAAAA
156399 TAATGTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (20 bp):
AAAATGAGATTTTGAAAAAC
Found at i:170118 original size:20 final size:21
Alignment explanation
Indices: 170072--170124 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
170062 ATAATAATAA
170072 ATTTTTAATAAATTTAATGAT
1 ATTTTTAATAAATTTAATGAT
*
170093 ATTTTTTAA-AAA-TTAATTATT
1 A-TTTTTAATAAATTTAATGA-T
170114 ATTTTATAATA
1 ATTTT-TAATA
170125 TTTTAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 10 0.37
21 9 0.33
22 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTTAATAAATTTAATGAT
Found at i:170138 original size:19 final size:19
Alignment explanation
Indices: 170116--170195 Score: 53
Period size: 19 Copynumber: 4.3 Consensus size: 19
170106 TAATTATTAT
170116 TTTATAATATTTTAATAAA
1 TTTATAATATTTTAATAAA
*
170135 -TT-TAATATTTTGTAAT-TA
1 TTTATAATA-TTT-TAATAAA
**
170153 TTTGATAA-A-TTTAATATT
1 TTT-ATAATATTTTAATAAA
*
170171 TTTATAATATATTAATAAA
1 TTTATAATATTTTAATAAA
*
170190 ATTATA
1 TTTATA
170196 TAAATATAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
17 13 0.28
18 13 0.28
19 17 0.36
20 1 0.02
21 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTATAATATTTTAATAAA
Found at i:170145 original size:27 final size:27
Alignment explanation
Indices: 170113--170189 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
170103 AATTAATTAT
170113 TATTTTATAATATTTTAATAAATTTAA
1 TATTTTATAATATTTTAATAAATTTAA
* *
170140 TATTTTGTAAT-TATTTGATAAATTTAA
1 TATTTTATAATAT-TTTAATAAATTTAA
*
170167 TATTTTTATAATATATTAATAAA
1 TA-TTTTATAATATTTTAATAAA
170190 ATTATATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
26 1 0.02
27 25 0.60
28 15 0.36
29 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (27 bp):
TATTTTATAATATTTTAATAAATTTAA
Found at i:170196 original size:27 final size:28
Alignment explanation
Indices: 170107--170197 Score: 91
Period size: 27 Copynumber: 3.3 Consensus size: 28
170097 TTTAAAAATT
*
170107 AATTAT-TATTTTATAATATTTTAATAA
1 AATTATATATTTTATAATATATTAATAA
* * *
170134 ATTTA-ATATTTTGTAAT-TATTTGATAA
1 AATTATATATTTTATAATATA-TTAATAA
*
170161 ATTTA-ATATTTTTATAATATATTAATAA
1 AATTATATA-TTTTATAATATATTAATAA
170189 AATTATATA
1 AATTATATA
170198 AATATAATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
26 1 0.02
27 28 0.54
28 18 0.35
29 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
AATTATATATTTTATAATATATTAATAA
Found at i:172387 original size:31 final size:31
Alignment explanation
Indices: 172349--172420 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
172339 CGGCGGTGAT
172349 CGATTTGTTATAAATAGATAACATTAGTAAC
1 CGATTTGTTATAAATAGATAACATTAGTAAC
* * * *
172380 CGATTTGTTATAGATCGATAACATTTGTGAC
1 CGATTTGTTATAAATAGATAACATTAGTAAC
*
172411 CAATTTGTTA
1 CGATTTGTTA
172421 CTTTTGAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (31 bp):
CGATTTGTTATAAATAGATAACATTAGTAAC
Found at i:172651 original size:62 final size:62
Alignment explanation
Indices: 172554--172677 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
172544 GGACATAAAG
*
172554 GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCACAAAGCCCAGTGTCCAAAAACT
1 GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCACAAAGCCCAGGGTCCAAAAACT
172616 GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCACAAAGCCCAGGGTCCAAAAACT
1 GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCACAAAGCCCAGGGTCCAAAAACT
172678 ATGTCATGGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (62 bp):
GTGACCTCAAGAAGATATCAACAATTTCAAAGTAAAAGCACAAAGCCCAGGGTCCAAAAACT
Found at i:186183 original size:21 final size:21
Alignment explanation
Indices: 186127--186176 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
186117 TGTCCCTTTA
186127 TGTCAGATATGTATCTGAATG
1 TGTCAGATATGTATCTGAATG
186148 TGTCAGATATGTATCTGAATG
1 TGTCAGATATGTATCTGAATG
186169 TGTCAGAT
1 TGTCAGAT
186177 GCTTATCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (21 bp):
TGTCAGATATGTATCTGAATG
Found at i:193212 original size:21 final size:20
Alignment explanation
Indices: 193186--193298 Score: 61
Period size: 21 Copynumber: 5.3 Consensus size: 20
193176 GGAAACTGAT
193186 TTGCGATAGTTGAAGTTCGCG
1 TTGCGATAGTTGAAGTTC-CG
* * *
193207 TTGCGATTTATTTCAAATT-CG
1 TTGCGA--TAGTTGAAGTTCCG
*
193228 TTGCGAATAGTCGAAGTTCACG
1 TTGCG-ATAGTTGAAGTTC-CG
* *
193250 TTGCGATTTA-TTCCAAATT-CG
1 TTGCGA--TAGTT-GAAGTTCCG
*
193271 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTTGAAGTTC-CG
193292 TTGCGAT
1 TTGCGAT
193299 TTATTCCAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 22
0.66 0.13 0.21
Matches are distributed among these distances:
19 6 0.09
20 8 0.12
21 31 0.46
22 9 0.13
23 14 0.21
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTTGAAGTTCCG
Found at i:193294 original size:42 final size:42
Alignment explanation
Indices: 193186--193323 Score: 231
Period size: 42 Copynumber: 3.3 Consensus size: 42
193176 GGAAACTGAT
* *
193186 TTGCGATAGTTGAAGTTCGCGTTGCGATTTATTTCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
193228 TTGCGAATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCG
1 TTGCG-ATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
193271 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
193313 TTGCGGTAGTC
1 TTGCGATAGTC
193324 CAAAATCGCA
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 51 0.57
43 39 0.43
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:193314 original size:21 final size:21
Alignment explanation
Indices: 193205--193317 Score: 97
Period size: 21 Copynumber: 5.3 Consensus size: 21
193195 TTGAAGTTCG
*
193205 CGTTGCGATTTATTTCAAATT
1 CGTTGCGATTTATTCCAAATT
* * * *
193226 CGTTGCGA-ATAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
193246 CACGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
* * *
193269 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
193288 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
193311 CGTTGCG
1 CGTTGCG
193318 GTAGTCCAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
19 8 0.11
20 7 0.10
21 31 0.44
22 8 0.11
23 16 0.23
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:194068 original size:19 final size:20
Alignment explanation
Indices: 194046--194225 Score: 98
Period size: 23 Copynumber: 8.6 Consensus size: 20
194036 TGCGATTTTC
*
194046 GACTATCGCAACG-ATCTTG
1 GACTATCGCAACGAAACTTG
* *
194065 GACTATCGCAACGCGAATTTG
1 GACTATCGCAACG-AAACTTG
* *
194086 GAATAAATCACAACGCAAACTTG
1 GACT--ATCGCAACG-AAACTTG
* *
194109 GACTATCACAACG-AATTTG
1 GACTATCGCAACGAAACTTG
* *
194128 GAATAAATCGCAAAACG-AACTTC
1 GACT--ATCGC--AACGAAACTTG
194151 GACTATCGCAACG-AACTTG
1 GACTATCGCAACGAAACTTG
* *
194170 GACTATCGCAACGTGAATTTG
1 GACTATCGCAACG-AAACTTG
* *
194191 GAATAAATCGCAACGCGAACTTG
1 GACT--ATCGCAACG-AAACTTG
*
194214 GAGTATCGCAAC
1 GACTATCGCAAC
194226 TAATTTGGAA
Statistics
Matches: 130, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
19 43 0.33
21 41 0.32
23 46 0.35
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
GACTATCGCAACGAAACTTG
Found at i:194125 original size:42 final size:42
Alignment explanation
Indices: 194061--194171 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
194051 TCGCAACGAT
**
194061 CTTGGACTATCGCAACGCGAATTTGGAATAAATCACAACGCAAA
1 CTTGGACTATCGCAA--CGAATTTGGAATAAATCACAAAACAAA
* * *
194105 CTTGGACTATCACAACGAATTTGGAATAAATCGCAAAACGAA
1 CTTGGACTATCGCAACGAATTTGGAATAAATCACAAAACAAA
* *
194147 CTTCGACTATCGCAACGAACTTGGA
1 CTTGGACTATCGCAACGAATTTGGA
194172 CTATCGCAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 45 0.76
44 14 0.24
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
CTTGGACTATCGCAACGAATTTGGAATAAATCACAAAACAAA
Found at i:194160 original size:21 final size:21
Alignment explanation
Indices: 194134--194180 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
194124 TTTGGAATAA
194134 ATCGCAAAACGAACTTCGACT
1 ATCGCAAAACGAACTTCGACT
*
194155 ATCGC--AACGAACTTGGACT
1 ATCGCAAAACGAACTTCGACT
194174 ATCGCAA
1 ATCGCAA
194181 CGTGAATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 18 0.78
21 5 0.22
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (21 bp):
ATCGCAAAACGAACTTCGACT
Found at i:194163 original size:63 final size:62
Alignment explanation
Indices: 194103--194234 Score: 185
Period size: 63 Copynumber: 2.1 Consensus size: 62
194093 TCACAACGCA
194103 AACTTGGACTATCACAAC-GAATTTGGAATAAATCGCAAAACGAACTTCGACTATCGCAACG
1 AACTTGGACTATCACAACGGAATTTGGAATAAATCGCAAAACGAACTTCGACTATCGCAACG
* ** * * *
194164 AACTTGGACTATCGCAACGTGAATTTGGAATAAATCGCAACGCGAACTTGGAGTATCGCAACT
1 AACTTGGACTATCACAACG-GAATTTGGAATAAATCGCAAAACGAACTTCGACTATCGCAACG
*
194227 AATTTGGA
1 AACTTGGA
194235 AAATTGCATT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 17 0.27
63 45 0.73
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (62 bp):
AACTTGGACTATCACAACGGAATTTGGAATAAATCGCAAAACGAACTTCGACTATCGCAACG
Found at i:194201 original size:42 final size:41
Alignment explanation
Indices: 194155--194235 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
194145 AACTTCGACT
194155 ATCGCAA-CGAACTTGGACTATCGCAACGTGAATTTGGAATAA
1 ATCGCAACCGAACTTGGACTATCGCAAC-T-AATTTGGAATAA
*
194197 ATCGCAACGCGAACTTGGAGTATCGCAACTAATTTGGAA
1 ATCGCAAC-CGAACTTGGACTATCGCAACTAATTTGGAA
194236 AATTGCATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 16 0.44
43 1 0.03
44 19 0.53
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (41 bp):
ATCGCAACCGAACTTGGACTATCGCAACTAATTTGGAATAA
Found at i:194231 original size:105 final size:105
Alignment explanation
Indices: 194043--194235 Score: 323
Period size: 105 Copynumber: 1.8 Consensus size: 105
194033 CGTTGCGATT
*
194043 TTCGACTATCGCAACGATCTTGGACTATCGCAACGCGAATTTGGAATAAATCACAACGCAAACTT
1 TTCGACTATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAATAAATCACAACGCAAACTT
194108 GGACTATCACAACGAATTTGGAATAAATCGCAAAACGAAC
66 GGACTATCACAACGAATTTGGAATAAATCGCAAAACGAAC
* * *
194148 TTCGACTATCGCAACGAACTTGGACTATCGCAACGTGAATTTGGAATAAATCGCAACGCGAACTT
1 TTCGACTATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAATAAATCACAACGCAAACTT
* * *
194213 GGAGTATCGCAACTAATTTGGAA
66 GGACTATCACAACGAATTTGGAA
194236 AATTGCATTG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
105 81 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (105 bp):
TTCGACTATCGCAACGAACTTGGACTATCGCAACGCGAATTTGGAATAAATCACAACGCAAACTT
GGACTATCACAACGAATTTGGAATAAATCGCAAAACGAAC
Found at i:201443 original size:24 final size:25
Alignment explanation
Indices: 201411--201478 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
201401 TATTAAGTTA
*
201411 ATTAAATATTTTTTAA-ATATTTTT
1 ATTACATATTTTTTAATATATTTTT
201435 ATTACATATTATTTTAATATATTTTT
1 ATTACATATT-TTTTAATATATTTTT
201461 -TATACATGTATTTTTTAA
1 AT-TACA--TATTTTTTAA
201479 CTAGATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 9 0.24
25 7 0.18
26 12 0.32
27 6 0.16
28 4 0.11
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.60
Consensus pattern (25 bp):
ATTACATATTTTTTAATATATTTTT
Found at i:201456 original size:13 final size:11
Alignment explanation
Indices: 201412--201462 Score: 57
Period size: 12 Copynumber: 4.3 Consensus size: 11
201402 ATTAAGTTAA
201412 TTAAATATTTT
1 TTAAATATTTT
201423 TTAAATATTTTT
1 TTAAATA-TTTT
*
201435 ATTACATATTATT
1 -TTAAATATT-TT
201448 TTAATATATTTT
1 TTAA-ATATTTT
201460 TTA
1 TTA
201463 TACATGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
11 7 0.21
12 14 0.41
13 13 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TTAAATATTTT
Found at i:201472 original size:25 final size:25
Alignment explanation
Indices: 201421--201474 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
201411 ATTAAATATT
*
201421 TTTTAAATATTTTTATTACATATTA
1 TTTTAAATATTTTTATTACATAGTA
201446 TTTTAATATATTTTT-TATACAT-GTA
1 TTTTAA-ATATTTTTAT-TACATAGTA
201471 TTTT
1 TTTT
201475 TTAACTAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (25 bp):
TTTTAAATATTTTTATTACATAGTA
Found at i:204214 original size:21 final size:21
Alignment explanation
Indices: 204188--204232 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
204178 GATTTCTGGG
* *
204188 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
204209 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
204230 CAA
1 CAA
204233 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:204839 original size:18 final size:18
Alignment explanation
Indices: 204816--204850 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
204806 CTAAGAGATT
204816 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
204834 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
204851 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:205829 original size:149 final size:149
Alignment explanation
Indices: 205649--205952 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
205639 GAGTCGAGGG
205649 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
205714 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
205779 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
205798 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
205863 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
205928 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
205947 TCTACG
1 TCTACG
205953 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:205975 original size:23 final size:23
Alignment explanation
Indices: 205931--205975 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
205921 ATCATTATAT
*
205931 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
205954 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
205976 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:210848 original size:2 final size:2
Alignment explanation
Indices: 210841--210886 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
210831 AGAACCCTGC
*
210841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
210883 TA TA
1 TA TA
210887 AACTGACTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:215642 original size:17 final size:18
Alignment explanation
Indices: 215617--215652 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
215607 AATATCTATC
*
215617 ATTTTTAAA-TTATCTAA
1 ATTTGTAAATTTATCTAA
215634 ATTTGTAAATTTATCTAA
1 ATTTGTAAATTTATCTAA
215652 A
1 A
215653 AATTAAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTTGTAAATTTATCTAA
Found at i:219079 original size:21 final size:21
Alignment explanation
Indices: 219055--219110 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
219045 TAGAAATATT
*
219055 TATTTTAGGTAGCGAAATTAA
1 TATTTTAGGTAGCGAAAATAA
**
219076 TATTTTCA-GTAGAAAAAATAA
1 TATTTT-AGGTAGCGAAAATAA
219097 TATTTTAGGTAGCG
1 TATTTTAGGTAGCG
219111 TTCTACCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.38
Consensus pattern (21 bp):
TATTTTAGGTAGCGAAAATAA
Found at i:219289 original size:2 final size:2
Alignment explanation
Indices: 219282--219310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
219272 ATAATTTTTA
219282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
219311 AACGTAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:219864 original size:50 final size:51
Alignment explanation
Indices: 219751--219868 Score: 123
Period size: 50 Copynumber: 2.4 Consensus size: 51
219741 GATTTGGCGC
* * * * *
219751 CACGTGGGGTATAGCGCGCCCCCTGCACGGCGCTATACGCTAACTGGGTTA
1 CACGTGGGGTATAGCGCGCCCCCTGCACCGCACTATACGCTAACTAGCTGA
* * * ** *
219802 CACGT-GGCTATAGCGCGCGCCCTGCTCCGCACTATAC-CTATTTATCTGA
1 CACGTGGGGTATAGCGCGCCCCCTGCACCGCACTATACGCTAACTAGCTGA
219851 CACGTGGGGTATAGCGCG
1 CACGTGGGGTATAGCGCG
219869 GTGCAGGGGC
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
49 11 0.20
50 38 0.70
51 5 0.09
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.22
Consensus pattern (51 bp):
CACGTGGGGTATAGCGCGCCCCCTGCACCGCACTATACGCTAACTAGCTGA
Found at i:220066 original size:17 final size:18
Alignment explanation
Indices: 220031--220071 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
220021 ATATTCTATA
*
220031 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
220049 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
220066 TTTACT
1 TTTACT
220072 AATATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:225891 original size:50 final size:51
Alignment explanation
Indices: 225781--225905 Score: 139
Period size: 50 Copynumber: 2.5 Consensus size: 51
225771 TCTACACAGA
* * * * *
225781 TATAGCGCGGTTCAGGGTGAGCGCTATACCCCACGTGTAACCTAGTTAGCAG
1 TATAGCGCGGTGCAGGG-GAGCGCTATACCCCACGTGGAACCAAATCAGCAG
* *
225833 -ATAGCGCGGTGCAGGGGCGCGCTATACCCCACGTGGAGCCAAATCAGC-G
1 TATAGCGCGGTGCAGGGGAGCGCTATACCCCACGTGGAACCAAATCAGCAG
*
225882 TATAACGCGG-GTCAGGGGAGCGCT
1 TATAGCGCGGTG-CAGGGGAGCGCT
225906 TTACTGCTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
49 2 0.03
50 45 0.73
51 15 0.24
ACGTcount: A:0.22, C:0.26, G:0.34, T:0.18
Consensus pattern (51 bp):
TATAGCGCGGTGCAGGGGAGCGCTATACCCCACGTGGAACCAAATCAGCAG
Found at i:239997 original size:32 final size:32
Alignment explanation
Indices: 239947--240029 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
239937 TCGGATCGGG
* * *
239947 TATCGGGTCGGTTG-TTTTCAGTTC-GGATCAA
1 TATCGGATCGGTTGATTTTCAGGTCAGG-GCAA
* *
239978 TATCGGATTGGTTGATTTTCGGGTCAGGGCAA
1 TATCGGATCGGTTGATTTTCAGGTCAGGGCAA
240010 TATCGGATCGGTTGATTTTC
1 TATCGGATCGGTTGATTTTC
240030 TGTTTAGGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 12 0.27
32 30 0.68
33 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.39
Consensus pattern (32 bp):
TATCGGATCGGTTGATTTTCAGGTCAGGGCAA
Found at i:241369 original size:32 final size:33
Alignment explanation
Indices: 241333--241396 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
241323 CAATATGTTT
*
241333 GGGTTGCTTTTTGG-TCGGGTT-AAATTCGGTTC
1 GGGTTGC-TTTCGGATCGGGTTAAAATTCGGTTC
*
241365 GGGTTGCTTTCGGATTGGGTTAAAATTCGGTT
1 GGGTTGCTTTCGGATCGGGTTAAAATTCGGTT
241397 TGGATCAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.18
32 13 0.46
33 10 0.36
ACGTcount: A:0.12, C:0.11, G:0.34, T:0.42
Consensus pattern (33 bp):
GGGTTGCTTTCGGATCGGGTTAAAATTCGGTTC
Found at i:256210 original size:16 final size:16
Alignment explanation
Indices: 256189--256221 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
256179 GTAGAATAAC
256189 AGAAAAACTATTATAT
1 AGAAAAACTATTATAT
256205 AGAAAAACTATTATAT
1 AGAAAAACTATTATAT
256221 A
1 A
256222 AGGAATCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (16 bp):
AGAAAAACTATTATAT
Found at i:259224 original size:27 final size:25
Alignment explanation
Indices: 259181--259266 Score: 113
Period size: 24 Copynumber: 3.4 Consensus size: 25
259171 AAATTGAACG
*
259181 ACCGGTTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
259205 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT--AACCGGATAAAAA
*
259232 ACCGG-TTTTTTATCCGGATAAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
*
259256 ACCGGATTTTT
1 ACCGGTTTTTT
259267 GCAAATCGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
24 29 0.52
25 5 0.09
26 6 0.11
27 16 0.29
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATAAAAA
Found at i:263286 original size:31 final size:31
Alignment explanation
Indices: 263241--263323 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
263231 GTCACTTAAC
263241 TTTT-AAAAATTATAAAATGAT-CATTAAAT
1 TTTTCAAAAATTATAAAATGATACATTAAAT
* *
263270 TTTTCAAACAATTATAAAA-CATACATTAAGT
1 TTTTCAAA-AATTATAAAATGATACATTAAAT
*
263301 TTTATCAAAATATTACAAAATGA
1 TTT-TCAAAA-ATTATAAAATGA
263324 CAACGAAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.09
30 5 0.11
31 21 0.48
32 13 0.30
33 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (31 bp):
TTTTCAAAAATTATAAAATGATACATTAAAT
Found at i:268406 original size:105 final size:105
Alignment explanation
Indices: 268290--268982 Score: 1145
Period size: 105 Copynumber: 6.6 Consensus size: 105
268280 TTTGTCGGAT
* * * * * *
268290 GAGTTGTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCATTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
268355 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
268395 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
**
268460 GGAACATACTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* * *
268500 GAGTTCTTCTCATTATGAACTCTTATGGAAATATTGGTTCACCTCCTTCTGCGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
268565 GGAACAGGATCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
268605 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
268670 GGAACAGACTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* *
268710 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* * *
268775 GGAACAAGTTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
* * *
268815 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTTCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
268880 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTT-AGAAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAG-AC
* *
268920 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGA
268983 TTATTGTTGA
Statistics
Matches: 557, Mismatches: 30, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
104 1 0.00
105 556 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
Found at i:269905 original size:6 final size:7
Alignment explanation
Indices: 269887--269972 Score: 63
Period size: 8 Copynumber: 11.9 Consensus size: 7
269877 TCGAACCCTC
269887 CTTTTTT
1 CTTTTTT
269894 CTTTTTT
1 CTTTTTT
269901 C--TTTT
1 CTTTTTT
269906 CATTTTTT
1 C-TTTTTT
269914 CATTTTTTT
1 C--TTTTTT
269923 CATTTTTT
1 C-TTTTTT
269931 CATTTTTT
1 C-TTTTTT
* *
269939 -TCTCTT
1 CTTTTTT
269945 -TTTTTT
1 CTTTTTT
269951 CATTTTTT
1 C-TTTTTT
269959 CATTTTTT
1 C-TTTTTT
269967 CTTTTT
1 CTTTTT
269973 CACTTTTTCA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
5 5 0.07
6 8 0.12
7 13 0.19
8 34 0.51
9 7 0.10
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (7 bp):
CTTTTTT
Found at i:269924 original size:17 final size:16
Alignment explanation
Indices: 269902--269992 Score: 96
Period size: 17 Copynumber: 5.5 Consensus size: 16
269892 TTCTTTTTTC
269902 TTTTCATTTTTTCATTT
1 TTTTCATTTTTTCA-TT
269919 TTTTCATTTTTTCATTTT
1 TTTTCATTTTTTCA--TT
*
269937 TTTCTCTTTTTTTTCATT
1 TTT-TC-ATTTTTTCATT
269955 TTTTCATTTTTTC--T
1 TTTTCATTTTTTCATT
* *
269969 TTTTCACTTTTTCACT
1 TTTTCATTTTTTCATT
269985 TTTTCATT
1 TTTTCATT
269993 CATTCTTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
14 13 0.20
16 15 0.23
17 16 0.25
18 11 0.17
19 2 0.03
20 8 0.12
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTCATTTTTTCATT
Found at i:269980 original size:9 final size:8
Alignment explanation
Indices: 269902--269992 Score: 96
Period size: 8 Copynumber: 11.0 Consensus size: 8
269892 TTCTTTTTTC
269902 TTTTCATT
1 TTTTCATT
269910 TTTTCATTT
1 TTTTCA-TT
269919 TTTTCATT
1 TTTTCATT
269927 TTTTCATTTT
1 TTTTCA--TT
*
269937 TTTCTCTTTT
1 TTT-TC-ATT
269947 TTTTCATT
1 TTTTCATT
269955 TTTTCATT
1 TTTTCATT
269963 TTTTC--T
1 TTTTCATT
*
269969 TTTTCACT
1 TTTTCATT
*
269977 TTTTCACT
1 TTTTCATT
269985 TTTTCATT
1 TTTTCATT
269993 CATTCTTTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
6 6 0.08
8 45 0.62
9 10 0.14
10 10 0.14
11 2 0.03
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTCATT
Found at i:290801 original size:46 final size:46
Alignment explanation
Indices: 290748--290835 Score: 176
Period size: 46 Copynumber: 1.9 Consensus size: 46
290738 AAAAACCACC
290748 ACACTTGTTAGTGGTGAGAGTTTGCATATATATATTCAATTACATA
1 ACACTTGTTAGTGGTGAGAGTTTGCATATATATATTCAATTACATA
290794 ACACTTGTTAGTGGTGAGAGTTTGCATATATATATTCAATTA
1 ACACTTGTTAGTGGTGAGAGTTTGCATATATATATTCAATTA
290836 AATAGTGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (46 bp):
ACACTTGTTAGTGGTGAGAGTTTGCATATATATATTCAATTACATA
Found at i:297934 original size:20 final size:20
Alignment explanation
Indices: 297885--297936 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
297875 ATTACACATT
* *
297885 GGTACTGATACTGACCCTTC
1 GGTATTGATACTGAACCTTC
* * *
297905 AGTATCGATACTGAACCTTG
1 GGTATTGATACTGAACCTTC
297925 GGTATTGATACT
1 GGTATTGATACT
297937 CTAATGTTGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
GGTATTGATACTGAACCTTC
Found at i:302150 original size:5 final size:5
Alignment explanation
Indices: 302128--302177 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
302118 AATAAACCAA
* * *
302128 AAATA AAATT -AATC AAATT AAATT AAATT AAATT CAATT AATATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT AA-ATT AAATT
302178 TAAAACGAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
4 3 0.08
5 30 0.79
6 5 0.13
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:304764 original size:21 final size:24
Alignment explanation
Indices: 304722--304770 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
304712 TCAAAGCCTG
304722 TCATCTATATATATGATGAATTA-
1 TCATCTATATATATGATGAATTAC
* *
304745 TCATGTATATA-ATG-TTAATTAC
1 TCATCTATATATATGATGAATTAC
304767 TCAT
1 TCAT
304771 TAGTAACGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.26
22 7 0.30
23 10 0.43
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (24 bp):
TCATCTATATATATGATGAATTAC
Found at i:306349 original size:12 final size:12
Alignment explanation
Indices: 306330--306361 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
306320 TTGTGATGGG
306330 AAAGTAAAGTAA
1 AAAGTAAAGTAA
*
306342 ATAGTAAAGTAA
1 AAAGTAAAGTAA
306354 AAAGTAAA
1 AAAGTAAA
306362 TTTTAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (12 bp):
AAAGTAAAGTAA
Found at i:323054 original size:30 final size:30
Alignment explanation
Indices: 323014--323086 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
323004 CCCGAAGGAC
* *
323014 CTATCTAGAGGTTATAAAGATCCTCGGTAA
1 CTATCCAGAGGTTATAAAGATCCTCGGCAA
*
323044 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTTATAAAGATCCTCGGCAA
* *
323074 CTGTCCATAGGTT
1 CTATCCAGAGGTT
323087 CCGAAGAACC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (30 bp):
CTATCCAGAGGTTATAAAGATCCTCGGCAA
Done.