Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 93 of 187
Found at i:27808237 original size:32 final size:32
Alignment explanation
Indices: 27808162--27808238 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
27808152 TGATTTACTG
* **
27808162 GAAAATATTTTCTGGTGTTTGATTGAATCTGT
1 GAAAATATTTTCTGCTGTTTGATCAAATCTGT
27808194 GTAAAATATTTTCTGCTGTTTGA-CAAATTTCT-T
1 G-AAAATATTTTCTGCTGTTTGATCAAA--TCTGT
27808227 GAAAATATTTTC
1 GAAAATATTTTC
27808239 CGGAAAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 14 0.36
33 22 0.56
34 3 0.08
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (32 bp):
GAAAATATTTTCTGCTGTTTGATCAAATCTGT
Found at i:27809161 original size:53 final size:52
Alignment explanation
Indices: 27809050--27809152 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 52
27809040 CTAATGACCA
* * *
27809050 ACACCCTTGTACCAGATTAAAAAAAAAAAAGGGTACTGGGACACTGATGGCTG
1 ACACCCTTGCACCAAATTAAAAAAAAAAAAGGGTA-TGGGACACTAATGGCTG
* *
27809103 ACACCCTTGCACCAAAATTAAAAAAAAAAATGGTGT-TGGGATACTAATGG
1 ACACCCTTGCACC-AAATTAAAAAAAAAAAAGG-GTATGGGACACTAATGG
27809153 TCGGCACCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
53 24 0.56
54 17 0.40
55 2 0.05
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (52 bp):
ACACCCTTGCACCAAATTAAAAAAAAAAAAGGGTATGGGACACTAATGGCTG
Found at i:27809531 original size:12 final size:13
Alignment explanation
Indices: 27809509--27809537 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27809499 TCCAACACTA
27809509 AAAAACTTTTTTT
1 AAAAACTTTTTTT
27809522 AAAAACTTTTTTT
1 AAAAACTTTTTTT
27809535 AAA
1 AAA
27809538 TATTGGTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAACTTTTTTT
Found at i:27810229 original size:22 final size:22
Alignment explanation
Indices: 27810173--27810222 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
27810163 TAAGATTCAA
**
27810173 TTTT-TTGAAATTTGAGTTTTT
1 TTTTCTTGAAATTTGAGAATTT
27810194 TTTTCTTGAAATTTGAGAATTT
1 TTTTCTTGAAATTTGAGAATTT
27810216 TTTTCTT
1 TTTTCTT
27810223 TTAATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.64
Consensus pattern (22 bp):
TTTTCTTGAAATTTGAGAATTT
Found at i:27810476 original size:29 final size:30
Alignment explanation
Indices: 27810415--27810489 Score: 125
Period size: 29 Copynumber: 2.5 Consensus size: 30
27810405 CTAGAATTTT
27810415 GCCCAGGCCCGGCCCGGGAAAAAATTCATAA
1 GCCC-GGCCCGGCCCGGGAAAAAATTCATAA
*
27810446 GCCCGGCCCGGCCCGGG-AAAATTTCATAA
1 GCCCGGCCCGGCCCGGGAAAAAATTCATAA
27810475 GCCCGGCCCGGCCCG
1 GCCCGGCCCGGCCCG
27810490 TTTTTTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 26 0.60
30 13 0.30
31 4 0.09
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.09
Consensus pattern (30 bp):
GCCCGGCCCGGCCCGGGAAAAAATTCATAA
Found at i:27811018 original size:49 final size:49
Alignment explanation
Indices: 27810939--27811035 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
27810929 TTATGCTATG
* * * *
27810939 CATTTCTAAACTTGGTTTTCCACTGCCTACACTCTTATCACTATTTATA
1 CATTGCTAAACTTAGTCTTCCACTGCCTACACTCTTACCACTATTTATA
*
27810988 CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTACCACTATTTAT
1 CATTGCTAAACTTAGTCTTCCACTGCCTACACTCTTACCACTATTTAT
27811036 CCCTTCTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (49 bp):
CATTGCTAAACTTAGTCTTCCACTGCCTACACTCTTACCACTATTTATA
Found at i:27812378 original size:16 final size:16
Alignment explanation
Indices: 27812357--27812421 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
27812347 ATCTCATAAT
27812357 CATTTCTCATATTTGC
1 CATTTCTCATATTTGC
* *
27812373 CATTTC-AATATTTTC
1 CATTTCTCATATTTGC
27812388 TCA--TCTCATA-TT--
1 -CATTTCTCATATTTGC
*
27812400 CATTTCTCATATTTGT
1 CATTTCTCATATTTGC
27812416 CATTTC
1 CATTTC
27812422 AATATCAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
11 2 0.05
13 7 0.18
14 6 0.15
15 10 0.26
16 14 0.36
ACGTcount: A:0.22, C:0.23, G:0.03, T:0.52
Consensus pattern (16 bp):
CATTTCTCATATTTGC
Found at i:27812390 original size:43 final size:43
Alignment explanation
Indices: 27812341--27812426 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
27812331 TCATATTTGA
27812341 TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
* *
27812384 TTTCTCATCTCATATTCATTTCTCATATTTGTCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
27812427 CAATCACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.24, C:0.22, G:0.02, T:0.51
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTGCCATTTCAATAT
Found at i:27815461 original size:12 final size:12
Alignment explanation
Indices: 27815444--27815498 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
27815434 GTCATTTCTG
*
27815444 CTTCTTCATCAC
1 CTTCTTCATCAT
27815456 CTTCTTCATCAT
1 CTTCTTCATCAT
* *
27815468 CATCATCATCAT
1 CTTCTTCATCAT
* *
27815480 CATCATCATCAT
1 CTTCTTCATCAT
27815492 CTTCTTC
1 CTTCTTC
27815499 TTCTTCTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.22, C:0.36, G:0.00, T:0.42
Consensus pattern (12 bp):
CTTCTTCATCAT
Found at i:27815467 original size:3 final size:3
Alignment explanation
Indices: 27815461--27815492 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
27815451 ATCACCTTCT
27815461 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
27815493 TTCTTCTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:27815978 original size:36 final size:36
Alignment explanation
Indices: 27815938--27816010 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
27815928 CAAGGGAGAC
27815938 AACTTTATTGGTAGGTTGTTGAGGATTTGGGAGTTT
1 AACTTTATTGGTAGGTTGTTGAGGATTTGGGAGTTT
27815974 AACTTTATTGGTAGGTTGTTGAGGATTTGGGAGTTT
1 AACTTTATTGGTAGGTTGTTGAGGATTTGGGAGTTT
27816010 A
1 A
27816011 GTGCTTCATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.03, G:0.33, T:0.44
Consensus pattern (36 bp):
AACTTTATTGGTAGGTTGTTGAGGATTTGGGAGTTT
Found at i:27824906 original size:21 final size:21
Alignment explanation
Indices: 27824880--27824926 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
27824870 ATGATGATGA
* * *
27824880 TGAGATTAGTTACTGTAGTGG
1 TGAGATTAGATACTATAATGG
*
27824901 TGAGATTTGATACTATAATGG
1 TGAGATTAGATACTATAATGG
27824922 TGAGA
1 TGAGA
27824927 ATAAAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (21 bp):
TGAGATTAGATACTATAATGG
Found at i:27826672 original size:14 final size:14
Alignment explanation
Indices: 27826653--27826691 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
27826643 TTGTTTCACT
27826653 GAAAATGACTTTCG
1 GAAAATGACTTTCG
* *
27826667 GAAAATGATTTTTG
1 GAAAATGACTTTCG
27826681 GAAAATGACTT
1 GAAAATGACTT
27826692 ACTTTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (14 bp):
GAAAATGACTTTCG
Found at i:27827450 original size:23 final size:24
Alignment explanation
Indices: 27827424--27827472 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
27827414 TTGAACATCA
27827424 ATAATTTGAG-TTTTAAATATGTC
1 ATAATTTGAGATTTTAAATATGTC
27827447 ATAATTTGAGCATTTTTAAATATGTC
1 ATAATTTGAG-A-TTTTAAATATGTC
27827473 CTAAGTGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.43
26 13 0.57
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (24 bp):
ATAATTTGAGATTTTAAATATGTC
Found at i:27827544 original size:21 final size:20
Alignment explanation
Indices: 27827510--27827548 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
27827500 AGGCCCAATA
27827510 CACCTAAACAAACCCAAACC
1 CACCTAAACAAACCCAAACC
*
27827530 CACCTAAAACTAACCCAAA
1 CACCT-AAACAAACCCAAA
27827549 TACAGCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.51, C:0.41, G:0.00, T:0.08
Consensus pattern (20 bp):
CACCTAAACAAACCCAAACC
Found at i:27828562 original size:3 final size:3
Alignment explanation
Indices: 27828528--27828596 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
27828518 CCCTTTGTAG
* * *
27828528 TAT TTT TAT TAT T-T TGT TCAT TAT T-C TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
* *
27828572 TAT TATT TAA TAT TAT TTT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT
27828597 CATCGTATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
2 3 0.06
3 45 0.85
4 5 0.09
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:27829677 original size:111 final size:111
Alignment explanation
Indices: 27829473--27829677 Score: 374
Period size: 111 Copynumber: 1.8 Consensus size: 111
27829463 TCAAAAAAGG
* *
27829473 AAAATATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
*
27829538 GGGTGCCGATTTTTCTCGTTTAACCAAATGGCTTAATATCCTTTTA
66 GGGTGCCGATTTTTCTCATTTAACCAAATGGCTTAATATCCTTTTA
27829584 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
*
27829649 GGGTGTCGATTTTTCTCATTTAACCAAAT
66 GGGTGCCGATTTTTCTCATTTAACCAAAT
27829678 TGCCAAAATA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 90 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (111 bp):
AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
GGGTGCCGATTTTTCTCATTTAACCAAATGGCTTAATATCCTTTTA
Found at i:27830125 original size:26 final size:27
Alignment explanation
Indices: 27830082--27830146 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
27830072 TTATTATGTG
27830082 TTTAATTG-GTCT-TAGTTTAGAC-AA
1 TTTAATTGTGTCTATAGTTTAGACAAA
* *
27830106 TTTAATTGTGTCTATTGTTTGGACAAA
1 TTTAATTGTGTCTATAGTTTAGACAAA
* *
27830133 TTAAAGTGTGTCTA
1 TTTAATTGTGTCTA
27830147 AATTAAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.24
25 4 0.12
26 8 0.24
27 14 0.41
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (27 bp):
TTTAATTGTGTCTATAGTTTAGACAAA
Found at i:27831775 original size:20 final size:20
Alignment explanation
Indices: 27831746--27831783 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27831736 AATAAAATTG
*
27831746 AAATATTAAATAATTTATTA
1 AAATAATAAATAATTTATTA
*
27831766 AAATAATAAATTATTTAT
1 AAATAATAAATAATTTAT
27831784 ATGATTAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATAAATAATTTATTA
Found at i:27836384 original size:7 final size:7
Alignment explanation
Indices: 27836372--27836461 Score: 108
Period size: 7 Copynumber: 12.9 Consensus size: 7
27836362 AAAAAAATAT
27836372 TTGAGAA
1 TTGAGAA
27836379 TTGAGAA
1 TTGAGAA
*
27836386 TTAAGAA
1 TTGAGAA
27836393 TTGAGAA
1 TTGAGAA
*
27836400 TTGAAAA
1 TTGAGAA
27836407 TTGAGAA
1 TTGAGAA
* *
27836414 TCGAGGA
1 TTGAGAA
*
27836421 TTAAGAA
1 TTGAGAA
27836428 TTGAGAA
1 TTGAGAA
27836435 TTGAGAA
1 TTGAGAA
**
27836442 TTGATTA
1 TTGAGAA
*
27836449 TTGAGTA
1 TTGAGAA
27836456 TTGAGA
1 TTGAGA
27836462 TAAAAAGAAT
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 69 1.00
ACGTcount: A:0.42, C:0.01, G:0.26, T:0.31
Consensus pattern (7 bp):
TTGAGAA
Found at i:27837491 original size:12 final size:11
Alignment explanation
Indices: 27837476--27837516 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
27837466 CAGCAAAAAA
27837476 AAAAGAAAATGC
1 AAAA-AAAATGC
27837488 --AAAAAATGC
1 AAAAAAAATGC
27837497 AAAAAAAATCGC
1 AAAAAAAAT-GC
27837509 AAAAAAAA
1 AAAAAAAA
27837517 AGTTGCCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 7 0.27
12 10 0.38
ACGTcount: A:0.73, C:0.10, G:0.10, T:0.07
Consensus pattern (11 bp):
AAAAAAAATGC
Found at i:27837573 original size:6 final size:6
Alignment explanation
Indices: 27837562--27837590 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
27837552 CCTATTGTTG
27837562 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
27837591 CCAAAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:27843888 original size:65 final size:65
Alignment explanation
Indices: 27843806--27843992 Score: 232
Period size: 65 Copynumber: 2.9 Consensus size: 65
27843796 TATAAGATAA
* * * * * *
27843806 ATAATTTGTGTATTTATATTTGGTATTTAGATATCTTATTGAATTATAATCATATTTATTTTAAT
1 ATAATTTGTATATTTATAATTGGTATTTAAATATTTTATTGAATTATAATAATATTTATCTTAAT
* * *
27843871 ATAATTTGTATATTTATAACTAGTATTTAAATATTTTATTAAATTATAATAATATTTATCTTAAT
1 ATAATTTGTATATTTATAATTGGTATTTAAATATTTTATTGAATTATAATAATATTTATCTTAAT
* * * ** *
27843936 ATAATTTTTAGATTTTTAATTGACATTAAAATATTTTATTGAATTATAATAA-ATTTA
1 ATAATTTGTATATTTATAATTGGTATTTAAATATTTTATTGAATTATAATAATATTTA
27843993 ATTTGTAATC
Statistics
Matches: 104, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
64 5 0.05
65 99 0.95
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (65 bp):
ATAATTTGTATATTTATAATTGGTATTTAAATATTTTATTGAATTATAATAATATTTATCTTAAT
Found at i:27843986 original size:18 final size:20
Alignment explanation
Indices: 27843949--27843986 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
27843939 ATTTTTAGAT
27843949 TTTTAATTGACATTAAAATA
1 TTTTAATTGACATTAAAATA
*
27843969 TTTT-ATTGA-ATTATAATA
1 TTTTAATTGACATTAAAATA
27843987 AATTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTAATTGACATTAAAATA
Found at i:27847692 original size:161 final size:157
Alignment explanation
Indices: 27847433--27847754 Score: 428
Period size: 161 Copynumber: 2.0 Consensus size: 157
27847423 CAGAAATTGA
* * * * *
27847433 TTACAATGCTTCTTTTTTTTTTGTACAAAATTTGTTCATTCATTTTTTTGTATTTCATTTGTATT
1 TTACAATGCTTCTTTTTTTCTTATACAAAATCTATCCATTCATTTTTTTGTATTTCATTTGTATT
* * * * *
27847498 TTTAACTATCTACTAACATTCATATAGTGGAAAATTTGCTATTTTAAGTGTTACATCAAATACAA
66 TGTAACCATCTACTAACATTCATATAGTGGAAAAATAGCTACTTTAAGTGTTACATCAAATACAA
* *
27847563 ATTATAATTTCTCTGGCGATTGAACTT
131 ATTACAATTTCTCTGGCGATTGAACAT
*
27847590 TTACAATGCTTCTTTTTTTCTTATGCAAAATCTATCCATTCATTTTTTTTTGGGTATTTCATTTG
1 TTACAATGCTTCTTTTTTTCTTATACAAAATCTATCCATTCA--TTTTTTT--GTATTTCATTTG
* * * * *
27847655 TATTTGTCACCGTCTACTAACATTCATATAGTGGAAAAATAGCTACTTTAAGTTTTACGTCAAGT
62 TATTTGTAACCATCTACTAACATTCATATAGTGGAAAAATAGCTACTTTAAGTGTTACATCAAAT
* *
27847720 ACCAATTACAATTTCTTTGGCGATTGAACAT
127 ACAAATTACAATTTCTCTGGCGATTGAACAT
27847751 TTAC
1 TTAC
27847755 CATTTTTACT
Statistics
Matches: 141, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
157 36 0.26
159 7 0.05
161 98 0.70
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (157 bp):
TTACAATGCTTCTTTTTTTCTTATACAAAATCTATCCATTCATTTTTTTGTATTTCATTTGTATT
TGTAACCATCTACTAACATTCATATAGTGGAAAAATAGCTACTTTAAGTGTTACATCAAATACAA
ATTACAATTTCTCTGGCGATTGAACAT
Found at i:27850158 original size:18 final size:17
Alignment explanation
Indices: 27850132--27850165 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27850122 TATATATATT
27850132 TTTAGAATTTTTTAAAAA
1 TTTAGAA-TTTTTAAAAA
*
27850150 TTTATAATTTTTAAAA
1 TTTAGAATTTTTAAAA
27850166 TATATATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAGAATTTTTAAAAA
Found at i:27850169 original size:40 final size:41
Alignment explanation
Indices: 27850090--27850170 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
27850080 AAAATTATTA
* *
27850090 TTTTAGAAATTTTTTAAAATTTTAACTTTCTTTATATATAT
1 TTTTAGAAATTTTTTAAAATTTTAACTTTCTTAAAATATAT
27850131 TTTTAG-AATTTTTTAAAAATTTATAA-TTT-TTAAAATATAT
1 TTTTAGAAATTTTTT-AAAATTT-TAACTTTCTTAAAATATAT
27850171 ATAAAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
40 17 0.47
41 16 0.44
42 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (41 bp):
TTTTAGAAATTTTTTAAAATTTTAACTTTCTTAAAATATAT
Found at i:27850173 original size:18 final size:18
Alignment explanation
Indices: 27850140--27850184 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
27850130 TTTTTAGAAT
*
27850140 TTTTTAAAA-ATTTATAA
1 TTTTTAAAATATATATAA
27850157 TTTTTAAAATATATATAA
1 TTTTTAAAATATATATAA
**
27850175 AATTTAAAAT
1 TTTTTAAAAT
27850185 TTTTTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTTAAAATATATATAA
Found at i:27850846 original size:2 final size:2
Alignment explanation
Indices: 27850835--27850865 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
27850825 TATCAAATTT
27850835 TA TA -A 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
27850866 AAGGATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:27853431 original size:36 final size:35
Alignment explanation
Indices: 27853391--27853462 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
27853381 AATGAGGCAG
* *
27853391 TCCAAAATGTGTTCTCAAACTACGGAATCTTAACAT
1 TCCAAAATCTATTCTCAAACTACGGAATCTT-ACAT
*
27853427 TCCAAAATCTATTCTCAAATTACGGAATCTTACAT
1 TCCAAAATCTATTCTCAAACTACGGAATCTTACAT
27853462 T
1 T
27853463 GGAGGATCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 5 0.15
36 28 0.85
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.33
Consensus pattern (35 bp):
TCCAAAATCTATTCTCAAACTACGGAATCTTACAT
Found at i:27857517 original size:26 final size:26
Alignment explanation
Indices: 27857488--27857677 Score: 128
Period size: 26 Copynumber: 7.5 Consensus size: 26
27857478 ATCCTCTCTC
27857488 GAGCCATATAA-CAGGAAGCTCACAAA
1 GAGCCAT-TAATCAGGAAGCTCACAAA
*
27857514 GAGCCATTAATCGGGAAGCTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* * *
27857540 GAGTC-TT--TCAGGAAGCTTATC--C
1 GAGCCATTAATCAGGAAGCTCA-CAAA
* * * *
27857562 GGGCTATATAAT-GGGAAGCTCACACA
1 GAGCCAT-TAATCAGGAAGCTCACAAA
* *
27857588 GAGCCA-TAATCA-GAAGGTTCACATA
1 GAGCCATTAATCAGGAA-GCTCACAAA
* **
27857613 GAACTTTTAATCAGGAAGCTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* * * *
27857639 GAGCCTTTAAACGGGAAGCTCACGAA
1 GAGCCATTAATCAGGAAGCTCACAAA
27857665 GAGCCATTAATCA
1 GAGCCATTAATCA
27857678 AGAGCTCCAG
Statistics
Matches: 123, Mismatches: 29, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
22 2 0.02
23 11 0.09
24 10 0.08
25 23 0.19
26 74 0.60
27 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACAAA
Found at i:27857805 original size:65 final size:64
Alignment explanation
Indices: 27857729--27857910 Score: 204
Period size: 65 Copynumber: 2.8 Consensus size: 64
27857719 ATATCAGGAT
* *
27857729 GCTCACAAAGAGCTGCGTTTGAGTCTGCAACATATGCAGGATCACAGCCGATCATAAAACAAGAC
1 GCTCACAAAGAGCTGCGTTT-AGTCCGCAACATATGCAGGATCACAACCGATCATAAAACAAGAC
** * * * * * * *
27857794 GCTCACAAAGAGCTATGTTTCTGTCCGCAATATATGCAAGATTACAACTGATCATATAACAGGAC
1 GCTCACAAAGAGCTGCGTTT-AGTCCGCAACATATGCAGGATCACAACCGATCATAAAACAAGAC
* * * *
27857859 GCTCACAAAGAGCTGCG-GTAGTCCGCAACACATGCAGGATCACTACCAATCA
1 GCTCACAAAGAGCTGCGTTTAGTCCGCAACATATGCAGGATCACAACCGATCA
27857911 GGATGCTCGT
Statistics
Matches: 94, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
63 25 0.27
64 1 0.01
65 68 0.72
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (64 bp):
GCTCACAAAGAGCTGCGTTTAGTCCGCAACATATGCAGGATCACAACCGATCATAAAACAAGAC
Found at i:27863061 original size:2 final size:2
Alignment explanation
Indices: 27863056--27863081 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27863046 CAAAAAAAAA
27863056 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
27863082 TTAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27864353 original size:6 final size:6
Alignment explanation
Indices: 27864342--27864375 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
27864332 CTTCACCCCA
* *
27864342 TCCTAT TCCTAT TCCTAT TCCTAT CCCTAG TCCT
1 TCCTAT TCCTAT TCCTAT TCCTAT TCCTAT TCCT
27864376 CCCCCATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.15, C:0.38, G:0.03, T:0.44
Consensus pattern (6 bp):
TCCTAT
Found at i:27875479 original size:20 final size:20
Alignment explanation
Indices: 27875422--27875483 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
27875412 AAAATAGATT
** *
27875422 ATGATTTTTTGAAATTTTTC
1 ATGATTTTTTTTAATTTTTA
*
27875442 ATGATTTTTTTTGGATTTTTA
1 ATGATTTTTTTT-AATTTTTA
27875463 ATGATTTTTTTTAATTTTTA
1 ATGATTTTTTTTAATTTTTA
27875483 A
1 A
27875484 GTAAAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.65
Consensus pattern (20 bp):
ATGATTTTTTTTAATTTTTA
Found at i:27879241 original size:2 final size:2
Alignment explanation
Indices: 27879234--27879263 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27879224 AAATCAAAGT
27879234 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
27879264 AAAGCCTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27879489 original size:20 final size:20
Alignment explanation
Indices: 27879453--27879497 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
27879443 TTTATGTAAT
* *
27879453 AATA-ATATTTTAATTTTAG
1 AATATATATATTAATTTTAA
*
27879472 AATATATATATTAGTTTTAA
1 AATATATATATTAATTTTAA
27879492 AATATA
1 AATATA
27879498 ATTACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
AATATATATATTAATTTTAA
Found at i:27881989 original size:3 final size:3
Alignment explanation
Indices: 27881978--27882042 Score: 53
Period size: 3 Copynumber: 21.0 Consensus size: 3
27881968 TAATAATTTC
* * *
27881978 AAT ATT AAT AAT AAT AAT AAAT AAT AAT GAT AAAC AAGT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AA-T AAT AAT AAT
27882025 AAT -AT AAT AAT AAAT AAT
1 AAT AAT AAT AAT -AAT AAT
27882043 TAAATAGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
2 4 0.08
3 37 0.74
4 9 0.18
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27882002 original size:13 final size:13
Alignment explanation
Indices: 27881984--27882042 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
27881974 TTTCAATATT
27881984 AATAATAATAATA
1 AATAATAATAATA
*
27881997 AATAATAATGATA
1 AATAATAATAATA
*
27882010 AACAAGTAATAATA
1 AATAA-TAATAATA
27882024 TAAT-ATAATAATA
1 -AATAATAATAATA
27882037 AATAAT
1 AATAAT
27882043 TAAATAGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 3 0.08
13 26 0.67
14 8 0.21
15 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:27883555 original size:44 final size:44
Alignment explanation
Indices: 27883490--27883606 Score: 200
Period size: 44 Copynumber: 2.7 Consensus size: 44
27883480 AACTTCAGGG
* *
27883490 AGACAAGA-CTTCTATCTTCGATCTACTTCACGCCAATACATGA
1 AGACAAGATCTACTTTCTTCGATCTACTTCACGCCAATACATGA
*
27883533 AGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGA
1 AGACAAGATCTACTTTCTTCGATCTACTTCACGCCAATACATGA
27883577 AGACAAGATCTACTTTCTTCGATCTACTTC
1 AGACAAGATCTACTTTCTTCGATCTACTTC
27883607 GCCACCAGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 8 0.11
44 62 0.89
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (44 bp):
AGACAAGATCTACTTTCTTCGATCTACTTCACGCCAATACATGA
Found at i:27883765 original size:44 final size:44
Alignment explanation
Indices: 27883706--27884066 Score: 184
Period size: 44 Copynumber: 8.2 Consensus size: 44
27883696 CTGTAACCTC
* * * *
27883706 AGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACTACTGCCT
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTACTGCCT
* * * *
27883750 AGGGAGATAAGATCTGTAATCTTCAATCTAGTCCACTGCTGCCC
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTACTGCCT
* *** * * *
27883794 AGGGAGAT-AGAAT-TACTGGCTTCAATGTACTCCACT-GTAACCT
1 AGGGAGATAAG-ATCTGCAATCTTCAATCTACTCCACTACT-GCCT
* * * * * * *
27883837 CAGTGAGGTAAAATCTGCCATCCTT-GATCTGCTCCACTACTGCTT
1 -AGGGAGATAAGATCTGCAAT-CTTCAATCTACTCCACTACTGCCT
* * * *
27883882 AGGGAGATAAGATATGTAATCTTCAATCTATTCCACTGCTG-CT
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTACTGCCT
* *** * * *
27883925 CAGGGAGAT-AGAAT-TACTGGCTTCAATGTACTCCACT-GTAACCT
1 -AGGGAGATAAG-ATCTGCAATCTTCAATCTACTCCACTACT-GCCT
* * * * * * *
27883969 CAGGGAGGTAAAATCCGCCATCGTT-GATCTGCTCCACTACTGCTT
1 -AGGGAGATAAGATCTGCAATC-TTCAATCTACTCCACTACTGCCT
* *
27884014 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTACTGTCC-
1 AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTACTG-CCT
27884058 AGGGAGATA
1 AGGGAGATA
27884067 GAATTACTGG
Statistics
Matches: 226, Mismatches: 73, Indels: 36
0.67 0.22 0.11
Matches are distributed among these distances:
42 2 0.01
43 44 0.19
44 142 0.63
45 31 0.14
46 7 0.03
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (44 bp):
AGGGAGATAAGATCTGCAATCTTCAATCTACTCCACTACTGCCT
Found at i:27883866 original size:132 final size:132
Alignment explanation
Indices: 27883647--27884115 Score: 769
Period size: 132 Copynumber: 3.6 Consensus size: 132
27883637 TCTTTGATCG
* * * * *
27883647 ATTCCACTGCCGACCAGGAAGTTAGAATTACTGGCTTCAATATACTCCACTGTAACCTCAGGGAG
1 ATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
* *
27883712 GTAAAATCTGCCAT-CTTCGATCTACTCCACTACTGCCTAGGGAGATAAGATCTGTAATCTTCAA
66 GTAAAATCTGCCATCCTT-GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
27883776 TCT
130 TCT
* *
27883779 AGTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGTGAG
1 ATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
*
27883844 GTAAAATCTGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATCTTCAAT
66 GTAAAATCTGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
27883909 CT
131 CT
*
27883911 ATTCCACTGCTGCTCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
1 ATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
* *
27883976 GTAAAATCCGCCATCGTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
66 GTAAAATCTGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
27884041 CT
131 CT
* * * *
27884043 ATTCCACTACTGTCCAGGGAGATAGAATTACTGGCTTCAATGTACTCAACTGTAACCTCCGGGAG
1 ATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
27884108 GTAAAATC
66 GTAAAATC
27884116 CGTCATCAAC
Statistics
Matches: 315, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
132 312 0.99
133 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
ATTCCACTGCTGCCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
GTAAAATCTGCCATCCTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
CT
Found at i:27884932 original size:13 final size:13
Alignment explanation
Indices: 27884914--27884938 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27884904 AAATTGTCGA
27884914 GGATAACAAAGAT
1 GGATAACAAAGAT
27884927 GGATAACAAAGA
1 GGATAACAAAGA
27884939 AATTGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.24, T:0.12
Consensus pattern (13 bp):
GGATAACAAAGAT
Found at i:27888288 original size:13 final size:13
Alignment explanation
Indices: 27888270--27888295 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27888260 TGTTCAATTT
27888270 TTTACTAGAAAAC
1 TTTACTAGAAAAC
27888283 TTTACTAGAAAAC
1 TTTACTAGAAAAC
27888296 AGATATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:27890352 original size:3 final size:3
Alignment explanation
Indices: 27890341--27890405 Score: 53
Period size: 3 Copynumber: 21.0 Consensus size: 3
27890331 TAATAATTTC
* * *
27890341 AAT ATT AAT AAT AAT AAT AAAT AAT AAT GAT AAAC AAGT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AA-T AAT AAT AAT
27890388 AAT -AT AAT AAT AAAT AAT
1 AAT AAT AAT AAT -AAT AAT
27890406 TAAATAGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
2 4 0.08
3 37 0.74
4 9 0.18
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27890365 original size:13 final size:13
Alignment explanation
Indices: 27890347--27890405 Score: 75
Period size: 13 Copynumber: 4.5 Consensus size: 13
27890337 TTTCAATATT
27890347 AATAATAATAATA
1 AATAATAATAATA
*
27890360 AATAATAATGATA
1 AATAATAATAATA
*
27890373 AACAAGTAATAATA
1 AATAA-TAATAATA
27890387 TAAT-ATAATAATA
1 -AATAATAATAATA
27890400 AATAAT
1 AATAAT
27890406 TAAATAGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 3 0.08
13 26 0.67
14 8 0.21
15 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:27890843 original size:113 final size:107
Alignment explanation
Indices: 27890655--27891229 Score: 486
Period size: 114 Copynumber: 5.2 Consensus size: 107
27890645 CGGATATACG
*
27890655 AAAAAA-ACGAAAAAAA-AATTTTTTTTTGGGTGCTGG-CCTGTCAATGGCCGGCACCCAGTACA
1 AAAAAATACGAAAAAAATAA-ATTTTTTTGGGTGCTGGCCCTGTCAATGGCCGGCACCCAGTACA
27890717 CAGTACAAAAAATTTTTTTTTATTTTTTTTCGTGTCAGAATCAGGATA
65 CAGTAC--AAAA-TTTTTTTT-TTTTTTTTCGTGTCAGAATCA-GATA
27890765 AAAAAATACGAAAAAAATATATATTTTTTTGGGTGCTGGCCCTGTCAATGGCCGGGCACCCAAGT
1 AAAAAATACGAAAAAAATA-A-ATTTTTTTGGGTGCTGGCCCTGTCAATGGCC-GGCACCC-AGT
27890830 ACACAGTAC-AAA---TTTTTTTTTTTTTCGTGGTCAGAATCAGATA
62 ACACAGTACAAAATTTTTTTTTTTTTTTTCGT-GTCAGAATCAGATA
* * *
27890873 TAAAAATACGAAAAAAAAAATTAAAAAAAAATTTTTTTGGGGTGCTGGCCCTGTCAAATGGTCAG
1 AAAAAATACG---AAAAAAA-T------AAATTTTTTT-GGGTGCTGGCCCTGTC-AATGGCCGG
* *
27890938 CACCCAGTACACAATACAAAA------TTTTTTTTTTCGTGTCCGAATCAGATA
54 CACCCAGTACACAGTACAAAATTTTTTTTTTTTTTTTCGTGTCAGAATCAGATA
* * * *
27890986 AAAAAATATG--AAAAATAAA--ATTTTGGATTCTGGCCCTGTCAATGGGCCCGGCCACCCAGTA
1 AAAAAATACGAAAAAAATAAATTTTTTTGGGTGCTGGCCCTGTCAAT-GG-CCGG-CACCCAGTA
* * * *
27891047 CACAGGAACAAAAAAATTTCTTTTTATTTTTTTATCGTGGTCGGATTCAGATT
63 CACA-GTAC---AAAATTT-TTTTT-TTTTTTT-TCGT-GTCAGAATCAGATA
** **
27891100 TGAAAATACGAAAAAATTATAAA-AATTTTGGGTGCTGG-CCTGTCAATGGCCGGCACCCAGTAC
1 AAAAAATACGAAAAAA--ATAAATTTTTTTGGGTGCTGGCCCTGTCAATGGCCGGCACCCAGTAC
* *
27891163 ACAGTACAAAAATTTTTTTTTTATTTTTTTGTATCAGAATCAGATA
64 ACAGTAC-AAAATTTTTTTTTT-TTTTTTCGTGTCAGAATCAGATA
*
27891209 TAAAAATACGAAAAAAATAAA
1 AAAAAATACGAAAAAAATAAA
27891230 AAAAATGAAG
Statistics
Matches: 392, Mismatches: 30, Indels: 89
0.77 0.06 0.17
Matches are distributed among these distances:
97 3 0.01
98 16 0.04
99 6 0.02
100 13 0.03
101 5 0.01
104 4 0.01
107 6 0.02
108 29 0.07
109 40 0.10
110 11 0.03
111 29 0.07
112 17 0.04
113 46 0.12
114 47 0.12
115 20 0.05
116 39 0.10
117 28 0.07
118 21 0.05
119 12 0.03
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (107 bp):
AAAAAATACGAAAAAAATAAATTTTTTTGGGTGCTGGCCCTGTCAATGGCCGGCACCCAGTACAC
AGTACAAAATTTTTTTTTTTTTTTTCGTGTCAGAATCAGATA
Found at i:27890926 original size:117 final size:112
Alignment explanation
Indices: 27890787--27891007 Score: 309
Period size: 113 Copynumber: 1.9 Consensus size: 112
27890777 AAAAATATAT
* * *
27890787 ATTTTTTTGGGTGCTGGCCCTGTC-AATGGCCGGGCACCCAAGTACACAGTACAAATTTTTTTTT
1 ATTTTTTTGGGTGCTGGCCCTGTCAAATGGCC-AGCACCC-AGTACACAATACAAA--ATTTTTT
*
27890851 TTTTCGTGGTCAGAATCAGATATAAAAATACGAAAAAAAAAATTAAAAAAAA
62 TTTTCGT-GTCAGAATCAGATAAAAAAATACGAAAAAAAAAATTAAAAAAAA
*
27890903 ATTTTTTTGGGGTGCTGGCCCTGTCAAATGGTCAGCACCCAGTACACAATACAAAATTTTTTTTT
1 ATTTTTTT-GGGTGCTGGCCCTGTCAAATGGCCAGCACCCAGTACACAATACAAAATTTTTTTTT
* * *
27890968 TCGTGTCCGAATCAGATAAAAAAATATGAAAAATAAAATT
65 TCGTGTCAGAATCAGATAAAAAAATACGAAAAAAAAAATT
27891008 TTGGATTCTG
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
113 32 0.34
114 13 0.14
116 22 0.23
117 22 0.23
118 6 0.06
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (112 bp):
ATTTTTTTGGGTGCTGGCCCTGTCAAATGGCCAGCACCCAGTACACAATACAAAATTTTTTTTTT
CGTGTCAGAATCAGATAAAAAAATACGAAAAAAAAAATTAAAAAAAA
Found at i:27892743 original size:220 final size:219
Alignment explanation
Indices: 27892316--27893106 Score: 1179
Period size: 220 Copynumber: 3.6 Consensus size: 219
27892306 CCCCAAAAAA
*
27892316 TTTATTTTTTTCGTATTTTTAAATCTGATTCTGACACGAAAAAAAATTTAAAATTTTTTTTTCTT
1 TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAA--T-AAA----TTTTT-TT
* *
27892381 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA-----ATTT-TTTTTTTCGT
58 TGTACTATGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTATTTTTTTCGT
27892440 ATTTTT-TATCTGATTCTGACACGAAAAAAAATAAAAAAAATTTTTTGTACTGTGTACTGGGTGC
123 ATTTTTATATCTGATTCTGACACGAAAAAAAATAAAAAAAATTTTTTGTACTGTGTACTGGGTGC
27892504 CGGCCATTGACAGGCCAGCACCCAAAATTTTT
188 CGGCCATTGACAGGCCAGCACCCAAAATTTTT
27892536 TTTA-TTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAA-AAATTTTTTTTGTACTAT
1 TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAATTTTTTTTGTACTAT
* *
27892599 GTACTGGGTGCCAGCCATTGACAGGCCAACACCCAAATTTTTTTTTTATTTTTTTCGTATTTTTA
66 GTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA-TTTTTTTTTATTTTTTTCGTATTTTTA
* * *
27892664 TATCTGATTCTGACACGAAAAAAAATAAAAGAAAGTTTTTTTGTACTGTGTACTGGGTGTCGACC
130 TATCTGATTCTGACACGAAAAAAAATAAAA-AAA-ATTTTTTGTACTGTGTACTGGGTGCCGGCC
*
27892729 ATTTACAGGCCAGCACCCAAAA-TTTT
193 ATTGACAGGCCAGCACCCAAAATTTTT
*
27892755 TTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAATAAATTTTTTTTGTACTAT
1 TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAATTTTTTTTGTACTAT
* *
27892820 GTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTTTTCGTCTTTTTAT
66 GTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTTTTAT
* * *
27892885 ATCTGATTTTGACACGAAAAAAATTAAAAAAAATTTTTTGTGCTGTGTACTGGGTGCCGGCCATT
131 ATCTGATTCTGACACGAAAAAAAATAAAAAAAATTTTTTGTACTGTGTACTGGGTGCCGGCCATT
27892950 GACAGGCCAGCACCCAAAAAATTTTTT
196 GACAGGCCAGCACCC--AAAA-TTTTT
*
27892977 TTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAATTTTTTTTGTACTG
1 TTTA-TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAATTTTTTTTGTACTA
*
27893042 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTTTTTTTGTTTTTTTCGTAT
65 TGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC---AAA--TTTTTTTTTATTTTTTTCGTAT
27893107 ATCCGTATAT
Statistics
Matches: 523, Mismatches: 26, Indels: 36
0.89 0.04 0.06
Matches are distributed among these distances:
210 44 0.08
211 5 0.01
215 3 0.01
216 3 0.01
217 16 0.03
218 73 0.14
219 54 0.10
220 149 0.28
221 53 0.10
222 8 0.02
223 93 0.18
226 3 0.01
228 19 0.04
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (219 bp):
TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAATTTTTTTTGTACTAT
GTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTATTTTTTTCGTATTTTTAT
ATCTGATTCTGACACGAAAAAAAATAAAAAAAATTTTTTGTACTGTGTACTGGGTGCCGGCCATT
GACAGGCCAGCACCCAAAATTTTT
Found at i:27892791 original size:112 final size:111
Alignment explanation
Indices: 27892316--27893093 Score: 1071
Period size: 112 Copynumber: 7.1 Consensus size: 111
27892306 CCCCAAAAAA
* ***
27892316 TTTATTTTTTTCGTATTTTTAAATCTGATTCTGACACGAAAAAAAATTTAAAATTTTTTTTTCTT
1 TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAA--TAAAA-AAATTTTT-TT
27892381 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA----
62 TGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTT
*
27892427 TTT-TTTTTTTCGTATTTTT-TATCTGATTCTGACACGAAAAAAAATAAAAAAA-ATTTTTTGTA
1 TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAAAAAATTTTTTTTGTA
27892489 CTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTT
66 CTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTT
27892535 TTT-TATTTTTTCGTATTTTTATATCTGATTCTGACACG----AAAA-AAAAAAATTTTTTTTGT
1 TTTAT-TTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAAAAAATTTTTTTTGT
* * * *
27892594 ACTATGTACTGGGTGCCAGCCATTGACAGGCCAACACCCAAATTTTTTT
65 ACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA--ATTTT
*
27892643 TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAAAGAAAGTTTTTTTGT
1 TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAAA-AAATTTTTTTTGT
* * *
27892708 ACTGTGTACTGGGTGTCGACCATTTACAGGCCAGCACCCAAAATTTT
65 ACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTT
*
27892755 TTTATTTTTTTCGTATTTTTTTATCTGATTCTGACACGAAAAAAAAT----AAATTTTTTTTGTA
1 TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAAAAAATTTTTTTTGTA
*
27892816 CTATGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTT
66 CTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAA-TTTT
* * * * *
27892863 TTTATTTTTTTCGTCTTTTTATATCTGATTTTGACACGAAAAAAATTAAAAAAA-ATTTTTTGTG
1 TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAAAAAATTTTTTTTGTA
27892927 CTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTTTTT
66 CTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCC--AAAA--TTTT
27892977 TTTATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAAT----AAATTTTTTTTGT
1 TTTA-TTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAAAAAATTTTTTTTGT
**
27893038 ACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATT
65 ACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTT
27893085 TTT-TTTTTT
1 TTTATTTTTT
27893094 GTTTTTTTCG
Statistics
Matches: 603, Mismatches: 38, Indels: 57
0.86 0.05 0.08
Matches are distributed among these distances:
104 48 0.08
105 10 0.02
106 57 0.09
107 56 0.09
108 96 0.16
109 40 0.07
110 37 0.06
111 51 0.08
112 103 0.17
113 8 0.01
114 57 0.09
115 40 0.07
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (111 bp):
TTTATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAAAATAAAAAAATTTTTTTTGTA
CTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTT
Found at i:27898473 original size:4 final size:4
Alignment explanation
Indices: 27898459--27898516 Score: 107
Period size: 4 Copynumber: 14.5 Consensus size: 4
27898449 CTGCAGCAGT
*
27898459 ATAC CTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
27898507 ATAC ATAC AT
1 ATAC ATAC AT
27898517 GTATATATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:27915841 original size:24 final size:23
Alignment explanation
Indices: 27915810--27915857 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
27915800 ATAAGGAATT
**
27915810 TAAATTTAATATTTTTTAAATAA
1 TAAATTTAATATTTTAAAAATAA
*
27915833 TAAATTTTATTATTTTAAAAATAA
1 TAAA-TTTAATATTTTAAAAATAA
27915857 T
1 T
27915858 TAAAATTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTTAATATTTTAAAAATAA
Found at i:27918377 original size:16 final size:17
Alignment explanation
Indices: 27918356--27918390 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
27918346 AATTAATTTA
*
27918356 AATTAATTAATTTT-TC
1 AATTAAATAATTTTCTC
27918372 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
27918389 AA
1 AA
27918391 CTCAATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:27919260 original size:17 final size:17
Alignment explanation
Indices: 27919238--27919272 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
27919228 CAATCATCCA
*
27919238 CTTAGGATTAATGTATG
1 CTTAGGATTAAGGTATG
27919255 CTTAGGATTAAGGTATG
1 CTTAGGATTAAGGTATG
27919272 C
1 C
27919273 CACACAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.37
Consensus pattern (17 bp):
CTTAGGATTAAGGTATG
Found at i:27921988 original size:238 final size:238
Alignment explanation
Indices: 27921564--27922251 Score: 1058
Period size: 238 Copynumber: 2.9 Consensus size: 238
27921554 TAAACCTATG
**
27921564 ATGATTATAATGTTTGTCACTCCTAGCTAAGAATCTCCTTT-GAGTCTCATCCTAGACTAAAAGA
1 ATGATTATAATGTTTGTCACTTTTAGCTAAGAATCTCCTTTCG-GTCTCATCCTAGACTAAAAGA
** * * * *
27921628 TGCCACTTAGGTTCTCCTCTCGGTCTCACCTAGGCATATAGATCTCCTCTTGGTTTCACTATTCG
65 TGCTTCCTAGGTTCT-CTCTCGATCTCACCTAGGCATATAGATCTCCTCTTGATCTCACTATTCG
* * * * * *
27921693 ACACAAGTGTATCAAATTCCTATACGATAGAGTTTCCTCTTAGCCTCATCTATCTAAATCTTTCA
129 ACACAAGTGTATCAAAATCCTACACGATAGAGTCTCCTCTCAGTCTCATCTATCTAAATCTTCCA
* *
27921758 TTAGATGCGTCAATTCTAGTATAATAAGTAATTTAATACACTTGA
194 CTAGATGCGTCAATTCTAGTATAATAAGCAATTTAATACACTTGA
*
27921803 ATGATTATAATGTTTGTCACTTTTAGCTAAGAATCTCCTTTCGGTCTCATCTTAGACTAAAAGAT
1 ATGATTATAATGTTTGTCACTTTTAGCTAAGAATCTCCTTTCGGTCTCATCCTAGACTAAAAGAT
* *
27921868 GCTTCCTAGGTTCTCTCTCGAACTCACCTAGGCATATAGATCTCTTCTTGATCTCACTATTCGAC
66 GCTTCCTAGGTTCTCTCTCGATCTCACCTAGGCATATAGATCTCCTCTTGATCTCACTATTCGAC
* *
27921933 ATAAGTGTATCAAAATCGTACACGATAGAGTCTCCTCTCAGTCTCATCTATCTAAATCTTCCACT
131 ACAAGTGTATCAAAATCCTACACGATAGAGTCTCCTCTCAGTCTCATCTATCTAAATCTTCCACT
* *
27921998 AAATGCGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
196 AGATGCGTCAATTCTAGTATAATAAGCAATTTAATACACTTGA
*
27922041 ATGATTATAATAG-TTGTCACTTTTAGCTAAGAATCTCCTTTCGATCTCATCCTAGACTAAAAGA
1 ATGATTATAAT-GTTTGTCACTTTTAGCTAAGAATCTCCTTTCGGTCTCATCCTAGACTAAAAGA
* *
27922105 TGCTTACTAGGTTCTCTCTCGATCTCACCT-GGACATATAAATCTCCTCTTGATCTCACTATTCG
65 TGCTTCCTAGGTTCTCTCTCGATCTCACCTAGG-CATATAGATCTCCTCTTGATCTCACTATTCG
* *
27922169 ACACAAGTGTATGAAAGTCCTACACGATAGAGTCTCCTCTCAGTCTCATCTATCTAAATCTTCCA
129 ACACAAGTGTATCAAAATCCTACACGATAGAGTCTCCTCTCAGTCTCATCTATCTAAATCTTCCA
*
27922234 CTAGAGGCGTCAATTCTA
194 CTAGATGCGTCAATTCTA
27922252 TTATTGTTGG
Statistics
Matches: 411, Mismatches: 35, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
237 2 0.00
238 336 0.82
239 72 0.18
240 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (238 bp):
ATGATTATAATGTTTGTCACTTTTAGCTAAGAATCTCCTTTCGGTCTCATCCTAGACTAAAAGAT
GCTTCCTAGGTTCTCTCTCGATCTCACCTAGGCATATAGATCTCCTCTTGATCTCACTATTCGAC
ACAAGTGTATCAAAATCCTACACGATAGAGTCTCCTCTCAGTCTCATCTATCTAAATCTTCCACT
AGATGCGTCAATTCTAGTATAATAAGCAATTTAATACACTTGA
Found at i:27924074 original size:12 final size:12
Alignment explanation
Indices: 27924059--27924084 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27924049 AAAAGAAAAG
27924059 AAAACCTAAACT
1 AAAACCTAAACT
27924071 AAAACCTAAACT
1 AAAACCTAAACT
27924083 AA
1 AA
27924085 GAGCTATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAACCTAAACT
Found at i:27927856 original size:16 final size:16
Alignment explanation
Indices: 27927808--27927856 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 16
27927798 TATTCTAAAA
27927808 ATAAGCTCATTAATAATT
1 ATAA-CTCA-TAATAATT
27927826 ATAAC-CAT-ATAAATT
1 ATAACTCATAAT-AATT
27927841 ATAACTCATAATAATT
1 ATAACTCATAATAATT
27927857 TTTGTACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.07
15 10 0.36
16 9 0.32
17 3 0.11
18 4 0.14
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAACTCATAATAATT
Found at i:27932943 original size:24 final size:24
Alignment explanation
Indices: 27932912--27932970 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
27932902 TATTTTCTTA
27932912 TAAT-TTAAAATAAAATAAAATAT
1 TAATATTAAAATAAAATAAAATAT
* *
27932935 TAATATTAAAATATAGTAAAATAT
1 TAATATTAAAATAAAATAAAATAT
* *
27932959 TAAAATAAAAAT
1 TAATATTAAAAT
27932971 GTTATACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 4 0.13
24 27 0.87
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
TAATATTAAAATAAAATAAAATAT
Found at i:27933024 original size:26 final size:26
Alignment explanation
Indices: 27932982--27933033 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
27932972 TTATACTTTT
27932982 TAATTTTATTTTAATATTAAAATATA
1 TAATTTTATTTTAATATTAAAATATA
*
27933008 TAATTTTATATTT-ATATTAATATATA
1 TAATTTTAT-TTTAATATTAAAATATA
27933034 AATATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATTTTATTTTAATATTAAAATATA
Found at i:27933098 original size:8 final size:8
Alignment explanation
Indices: 27933085--27933120 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
27933075 ATAATATCTA
27933085 TATAATTT
1 TATAATTT
27933093 TATAATTT
1 TATAATTT
27933101 TATATATTT
1 TATA-ATTT
27933110 T-TAATTT
1 TATAATTT
27933117 TATA
1 TATA
27933121 TAAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 5 0.19
8 16 0.62
9 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATAATTT
Found at i:27933114 original size:16 final size:17
Alignment explanation
Indices: 27933072--27933122 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 17
27933062 AGTATTAAAA
*
27933072 TTTATAATATCTATATAAT
1 TTTATAAT-TTTATAT-AT
27933091 TTTATAATTTTATATAT
1 TTTATAATTTTATATAT
27933108 TTT-TAATTTTATATA
1 TTTATAATTTTATATA
27933123 AAATATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 12 0.39
17 5 0.16
18 6 0.19
19 8 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATAATTTTATATAT
Found at i:27936440 original size:24 final size:24
Alignment explanation
Indices: 27936361--27936440 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
27936351 CCGGGTAATA
* *
27936361 TAACGGGAAGCTCACAAAGAGC-CT
1 TAACGGGTAGCTC-CAAAGAGCAAT
* * *
27936385 ATAACGGATAGCTCCAAATAGTAAT
1 -TAACGGGTAGCTCCAAAGAGCAAT
*
27936410 TAACGGGTAGCTCCGAAGAGCAAT
1 TAACGGGTAGCTCCAAAGAGCAAT
27936434 TAACGGG
1 TAACGGG
27936441 AAGCATCGGA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
24 33 0.73
25 12 0.27
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (24 bp):
TAACGGGTAGCTCCAAAGAGCAAT
Found at i:27937211 original size:20 final size:20
Alignment explanation
Indices: 27937186--27937228 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
27937176 AGCCCATGAA
*
27937186 TTCCATGAAATTTCA-AAATT
1 TTCCATG-AATTTAACAAATT
27937206 TTCCATGAATTTAACAAATT
1 TTCCATGAATTTAACAAATT
27937226 TTC
1 TTC
27937229 AATTTAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (20 bp):
TTCCATGAATTTAACAAATT
Found at i:27940185 original size:27 final size:27
Alignment explanation
Indices: 27940155--27940225 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
27940145 AGAGTCCACC
* *
27940155 GGGACAGTAAACATTAGGTAGTCTGCT
1 GGGACAGTAAACATGAGGTAGTCCGCT
* *
27940182 GGGATAGTAAACACGAGGTAGTCCGCT
1 GGGACAGTAAACATGAGGTAGTCCGCT
** *
27940209 AAGACAGTATACATGAG
1 GGGACAGTAAACATGAG
27940226 TCCATACTGT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (27 bp):
GGGACAGTAAACATGAGGTAGTCCGCT
Found at i:27945525 original size:23 final size:23
Alignment explanation
Indices: 27945499--27945549 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
27945489 GGCTCGATTT
*
27945499 GTTTAGCATTTGCGAACATGTTC
1 GTTTAGCATTCGCGAACATGTTC
*
27945522 GTTTAGCATTCGTGAACATGTTC
1 GTTTAGCATTCGCGAACATGTTC
27945545 GTTTA
1 GTTTA
27945550 ATGCTCGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (23 bp):
GTTTAGCATTCGCGAACATGTTC
Found at i:27945557 original size:23 final size:22
Alignment explanation
Indices: 27945512--27945565 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
27945502 TAGCATTTGC
27945512 GAACATGTTCGTTTAGCATTCGT
1 GAACATGTTCGTTTAGCA-TCGT
27945535 GAACATGTTCGTTTAATGC-TCGT
1 GAACATGTTCGTTT-A-GCATCGT
27945558 GAACATGT
1 GAACATGT
27945566 CTGTTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 26 0.90
24 1 0.03
25 2 0.07
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (22 bp):
GAACATGTTCGTTTAGCATCGT
Found at i:27945956 original size:3 final size:3
Alignment explanation
Indices: 27945948--27945992 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
27945938 TTGTTTGATC
27945948 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
27945993 AAGAAAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:27950001 original size:8 final size:8
Alignment explanation
Indices: 27949988--27950041 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
27949978 AGGTATACGT
27949988 ATAAAATA
1 ATAAAATA
27949996 ATAAAAT-
1 ATAAAATA
*
27950003 AT-ATA-A
1 ATAAAATA
27950009 ATAAAATA
1 ATAAAATA
27950017 ATAAAATGA
1 ATAAAAT-A
* *
27950026 TTCAAATA
1 ATAAAATA
27950034 ATAAAATA
1 ATAAAATA
27950042 GAATTACAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
6 4 0.11
7 4 0.11
8 22 0.61
9 6 0.17
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (8 bp):
ATAAAATA
Found at i:27950005 original size:21 final size:21
Alignment explanation
Indices: 27949988--27950051 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
27949978 AGGTATACGT
*
27949988 ATAAAATAATAAAATATATAA
1 ATAAAATAATAAAATATACAA
*
27950009 ATAAAATAATAAAATGATTCAA
1 ATAAAATAATAAAAT-ATACAA
*
27950031 ATAATAA-AATAGAAT-TACAA
1 ATAA-AATAATAAAATATACAA
27950051 A
1 A
27950052 AGTAATAGNN
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 5 0.14
21 15 0.41
22 15 0.41
23 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (21 bp):
ATAAAATAATAAAATATACAA
Found at i:27952209 original size:89 final size:89
Alignment explanation
Indices: 27951686--27952749 Score: 1272
Period size: 89 Copynumber: 12.0 Consensus size: 89
27951676 ATCTGCTGTA
* * * *
27951686 TTTGATCTACTTCACGACAATACATGAAGACAAGATCCGTTTTCTTCGATCTACTTCACCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
*
27951751 TATGGGAAGACAAGATCTGCTATC
66 TATGGGAAGACAAGATCTGTTATC
* * * *
27951775 TTTGATCTACTTCACGCCAATACATGAAGACAATATCTGTTTTC-TCGATCTACTCCACCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
* *
27951839 TATGGGGAGACAAGATCTGTTGTC
66 TATGGGAAGACAAGATCTGTTATC
* * * * * * *
27951863 TTGGATCTACTTCACGCCAATACATGTAGACAAGATCTGTTTTCTTCAATCTACTTC-ACGCCAA
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
*** * * *
27951927 TACATGAAGATAAGATTTACTT-TC
66 TATGGGAAGACAAGATCT-GTTATC
** * * * * *
27951951 TTCAATCTACCTCACGCCAATACATGAAGATAAGATTTATTTTCTTCGATCTACTTCGCCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
* *
27952016 TATGGGAAGACAAGATCTGTTTTA
66 TATGGGAAGACAAGATCTGTTATC
* * * * *** * ** *
27952040 TTTAATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTTTATTTAATCTGCTTCACCACCA
1 TTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCA
* *
27952105 GTATGGGAAGGCAAGATCTGGTATC
65 GTATGGGAAGACAAGATCTGTTATC
* * * * *
27952130 TCTGATCTACTTCACGCCAATACATGAATACAAGATCTGCTTTCTTCGGTCTGTTTCGCCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
* *
27952195 TATGGGAAGACAAGATATGTTGTC
66 TATGGGAAGACAAGATCTGTTATC
* * * *
27952219 TTTGATCTACTTCACGCCAGTACATGAAGACAAGATATGTTTTCTTTGATCTGCTTCACCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
* *
27952284 TATGGGAAGGCAAGATCTGGTATC
66 TATGGGAAGACAAGATCTGTTATC
* * ** *
27952308 TCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTGTTTCGCCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
*
27952373 TATGGGAAGATAAGATCTGTTATC
66 TATGGGAAGACAAGATCTGTTATC
* * * * *
27952397 TTTGATCTACTTCACGCCAGTACATAAAGACAAGATCTGCTTTCTTCAATCTGTTTCGCCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
*
27952462 TATGGGAAGATAAGATCTGTTATC
66 TATGGGAAGACAAGATCTGTTATC
* * * * *
27952486 TTTGATCTACTTCACGCCAGTACATGAAGACAAAATATGTTTTCTTTGATCTGCTTCACCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
* *
27952551 TATGGGAAGGCAAGATCTGGTATC
66 TATGGGAAGACAAGATCTGTTATC
* * ** *
27952575 TCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTCGATCTGTTTCGCCACCAG
1 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
*
27952640 TATGGGAAGATAAGATCTGTTATC
66 TATGGGAAGACAAGATCTGTTATC
* * * *
27952664 TTTGATCTACTTCACG-CAAGTACATGAAGATAAAATCTGCTTTCTTCGATCTGTTTCGCCACCA
1 TTTGATCTACTTCACGCCAA-TACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCA
*
27952728 GTATGGGGAGACAAGATCTGTT
65 GTATGGGAAGACAAGATCTGTT
27952750 GCTACTCCAC
Statistics
Matches: 833, Mismatches: 136, Indels: 12
0.85 0.14 0.01
Matches are distributed among these distances:
88 152 0.18
89 612 0.73
90 69 0.08
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (89 bp):
TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCACCAG
TATGGGAAGACAAGATCTGTTATC
Found at i:27959033 original size:2 final size:2
Alignment explanation
Indices: 27959026--27959055 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27959016 AGCGTTAAAA
27959026 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27959056 AAATGCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27959827 original size:15 final size:13
Alignment explanation
Indices: 27959799--27959832 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
27959789 TATATAACCG
27959799 AAAATAAAAAAAT
1 AAAATAAAAAAAT
27959812 AAAATACAAAATAAT
1 AAAATA-AAAA-AAT
27959827 AAAATA
1 AAAATA
27959833 TTTTCTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 4 0.21
15 9 0.47
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:27964563 original size:13 final size:13
Alignment explanation
Indices: 27964545--27964569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27964535 TCTACGCAGT
27964545 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
27964558 TTTTTTTCTTTT
1 TTTTTTTCTTTT
27964570 GTGTGTTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:27983674 original size:25 final size:25
Alignment explanation
Indices: 27983646--27983699 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
27983636 TGTAGTGGCA
*
27983646 AGGTGGAGACACAAGTGTGGCAAGG
1 AGGTGGAGACACAAGTGTGGCAAAG
* * *
27983671 AGGTGGTGTCACAAGTGTGGTAAAG
1 AGGTGGAGACACAAGTGTGGCAAAG
27983696 AGGT
1 AGGT
27983700 TAGAGGTTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.43, T:0.19
Consensus pattern (25 bp):
AGGTGGAGACACAAGTGTGGCAAAG
Found at i:27985224 original size:26 final size:27
Alignment explanation
Indices: 27985195--27985245 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
27985185 GACCGTAATG
27985195 CCCCTAGAGGGTAAATGACT-ATTTTT
1 CCCCTAGAGGGTAAATGACTGATTTTT
* *
27985221 CCCCTCGTGGGTAAATGACTGATTT
1 CCCCTAGAGGGTAAATGACTGATTT
27985246 GTGTTATGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (27 bp):
CCCCTAGAGGGTAAATGACTGATTTTT
Found at i:27986408 original size:25 final size:25
Alignment explanation
Indices: 27986371--27986458 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 25
27986361 TACCGATTGC
* * * *
27986371 AGCTCATAAGAGCTTATCGATTCGT
1 AGCTCGTATGAGCTTACCGATTCAT
* *
27986396 AGCTCGTATGAGCTTACCGATTTAC
1 AGCTCGTATGAGCTTACCGATTCAT
*
27986421 AGCTCGTGA-GAGCATACCGATTCAT
1 AGCTCGT-ATGAGCTTACCGATTCAT
*
27986446 AGCTTGTATGAGC
1 AGCTCGTATGAGC
27986459 ATACATGTAC
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
24 1 0.02
25 49 0.96
26 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGATTCAT
Found at i:27986442 original size:50 final size:49
Alignment explanation
Indices: 27986360--27986458 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 49
27986350 TCATTAAGGA
* * * *
27986360 TTACCGATTGCAGCTCATAAGAGCTTATCGATTCGTAGCTCGTATGAGC
1 TTACCGATTACAGCTCATAAGAGCATACCGATTCATAGCTCGTATGAGC
* * *
27986409 TTACCGATTTACAGCTCGTGAGAGCATACCGATTCATAGCTTGTATGAGC
1 TTACCGA-TTACAGCTCATAAGAGCATACCGATTCATAGCTCGTATGAGC
27986459 ATACATGTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 7 0.17
50 35 0.83
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (49 bp):
TTACCGATTACAGCTCATAAGAGCATACCGATTCATAGCTCGTATGAGC
Found at i:27986459 original size:25 final size:25
Alignment explanation
Indices: 27986388--27986462 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
27986378 AAGAGCTTAT
* *
27986388 CGATTCGTAGCTCGTATGAGCTTAC
1 CGATTCATAGCTCGTATGAGCATAC
* *
27986413 CGATTTACAGCTCGTGA-GAGCATAC
1 CGATTCATAGCTCGT-ATGAGCATAC
*
27986438 CGATTCATAGCTTGTATGAGCATAC
1 CGATTCATAGCTCGTATGAGCATAC
27986463 ATGTACAGGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (25 bp):
CGATTCATAGCTCGTATGAGCATAC
Found at i:27987605 original size:15 final size:16
Alignment explanation
Indices: 27987585--27987614 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27987575 TGGTGCCTTA
27987585 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
27987600 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
27987615 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:27990924 original size:20 final size:20
Alignment explanation
Indices: 27990882--27990925 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
27990872 CTTGTGTTTG
* * * *
27990882 AAAAAAAATGAAGATTTAGA
1 AAAAAAAATGAAAAATGAAA
27990902 AAAAAAAATGAAAAATGAAA
1 AAAAAAAATGAAAAATGAAA
27990922 AAAA
1 AAAA
27990926 GAGAAAAGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (20 bp):
AAAAAAAATGAAAAATGAAA
Found at i:27994218 original size:2 final size:2
Alignment explanation
Indices: 27994211--27994252 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27994201 TATTATATGC
27994211 AT AT AT 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
27994253 CAATGAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28004594 original size:21 final size:21
Alignment explanation
Indices: 28004570--28004639 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
28004560 GCATAATGTC
*
28004570 TTTCAACTATGGTCTTATTCA
1 TTTCAACTATGGTCATATTCA
* *
28004591 TTTCCAGTATAGTGTCATAGTGTC-
1 TTTCAACTAT-G-GTCATA-T-TCA
28004615 TTTCAACTATGGT-AGTATTCA
1 TTTCAACTATGGTCA-TATTCA
28004636 TTTC
1 TTTC
28004640 CGGTATAGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.05
21 14 0.37
22 5 0.13
23 6 0.16
24 9 0.24
25 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (21 bp):
TTTCAACTATGGTCATATTCA
Found at i:28004739 original size:45 final size:45
Alignment explanation
Indices: 28004469--28004769 Score: 308
Period size: 45 Copynumber: 6.7 Consensus size: 45
28004459 TTTTCAAGGA
* * * * * *
28004469 TGCCATAGCGTCTTTCAGCCACGGTCTTATTAATTTCC-G-ACATG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTATA-G
* *
28004513 ATGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTC-GTCAT-G
1 -TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGT-ATAG
*
28004558 TTG-CATAATGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAG
1 -TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAG
* ** *
28004603 TGTCATAGTGTCTTTCAACTATGGTAGTATTCATTTCCGGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAG
* ** * *
28004648 TGCCATATTGTCTTTCAACTATGGTAGTATTCATTTCCGGTTTAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAG
* *
28004693 TGCCATAGTGTCTTTCAATTATGGTCTTATTCATTTCTAGTATAG
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAG
* * *
28004738 TGTCACCA-TATCTTTCAACTATGGTCTTATTC
1 TGCCA-TAGTGTCTTTCAACTATGGTCTTATTC
28004770 GTTTTTCAAG
Statistics
Matches: 221, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
44 36 0.16
45 183 0.83
46 1 0.00
47 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAG
Found at i:28004752 original size:135 final size:134
Alignment explanation
Indices: 28004514--28004762 Score: 342
Period size: 135 Copynumber: 1.9 Consensus size: 134
28004504 TCCGACATGA
** * *
28004514 TGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTCGTCATGTTGCATAATGTCTTTCAACTA
1 TGCCATAGTGTCTTTCAACTATGGTAGTATTCATTTCCGTCATGTTGCATAATGTCTTTCAACTA
* *
28004579 TGGTCTTATTCATTTCCAGTATAGTGTCATAGTGTCTTTCAACTATGGTAGTATTCATTTCCGGT
66 TGGTCTTATTCATTTCCAGTATAGTGTCACAGTATCTTTCAACTATGGTAGTATTCATTTCCGGT
28004644 ATAG
131 ATAG
* * *
28004648 TGCCATATTGTCTTTCAACTATGGTAGTATTCATTTCCGGT-TTAG-TGCCATAGTGTCTTTCAA
1 TGCCATAGTGTCTTTCAACTATGGTAGTATTCATTTCC-GTCAT-GTTG-CATAATGTCTTTCAA
* *
28004711 TTATGGTCTTATTCATTTCTAGTATAGTGTCACCA-TATCTTTCAACTATGGT
63 CTATGGTCTTATTCATTTCCAGTATAGTGTCA-CAGTATCTTTCAACTATGGT
28004763 CTTATTCGTT
Statistics
Matches: 100, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
134 36 0.36
135 63 0.63
136 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.45
Consensus pattern (134 bp):
TGCCATAGTGTCTTTCAACTATGGTAGTATTCATTTCCGTCATGTTGCATAATGTCTTTCAACTA
TGGTCTTATTCATTTCCAGTATAGTGTCACAGTATCTTTCAACTATGGTAGTATTCATTTCCGGT
ATAG
Found at i:28004769 original size:135 final size:134
Alignment explanation
Indices: 28004491--28004769 Score: 341
Period size: 135 Copynumber: 2.1 Consensus size: 134
28004481 TTTCAGCCAC
* ** * *
28004491 GGTCTTATTAATTTCCGACATGATGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTTCGTCA
1 GGTCTTATTCATTTCCGACATGATGCCATAGTGTCTTTCAACTATGGTAGTATTCATTTCCGTCA
* *
28004556 TGTTGCATAATGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAGTGTCATAGTGTCTTTCAA
66 TGTTGCATAATGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAGTGTCACAGTATCTTTCAA
28004621 CTAT
131 CTAT
** ** *
28004625 GGTAGTATTCATTTCCGGTAT-AGTGCCATATTGTCTTTCAACTATGGTAGTATTCATTTCCGGT
1 GGTCTTATTCATTTCCGACATGA-TGCCATAGTGTCTTTCAACTATGGTAGTATTCATTTCC-GT
* * * *
28004689 -TTAG-TGCCATAGTGTCTTTCAATTATGGTCTTATTCATTTCTAGTATAGTGTCACCA-TATCT
64 CAT-GTTG-CATAATGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAGTGTCA-CAGTATCT
28004751 TTCAACTAT
126 TTCAACTAT
28004760 GGTCTTATTC
1 GGTCTTATTC
28004770 GTTTTTCAAG
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
133 1 0.01
134 52 0.43
135 68 0.56
136 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (134 bp):
GGTCTTATTCATTTCCGACATGATGCCATAGTGTCTTTCAACTATGGTAGTATTCATTTCCGTCA
TGTTGCATAATGTCTTTCAACTATGGTCTTATTCATTTCCAGTATAGTGTCACAGTATCTTTCAA
CTAT
Found at i:28007671 original size:73 final size:72
Alignment explanation
Indices: 28007548--28007752 Score: 250
Period size: 73 Copynumber: 2.8 Consensus size: 72
28007538 CAGACATATT
** * * *
28007548 AATTGCTTGTTCGAGCTGTACATATAATCATGTCAGGCTACCCGTTCGGGCTAAACCTTTATATA
1 AATTGCTCATTCGAGCTG-ACATATAATCGTGTCAGGTTACCCGTCCGGGCTAAACCTTTATATA
28007613 AATACATC
65 AATACATC
*
28007621 AATTGCTCA-TCTGAGCTGACCATATAATCGTATCAGGTTACCCGTCCGGGCTAAACCTTTATAT
1 AATTGCTCATTC-GAGCTGA-CATATAATCGTGTCAGGTTACCCGTCCGGGCTAAACCTTTATAT
*
28007685 GAATACATC
64 AAATACATC
* * * * * *
28007694 AGTTGCTCGTTCGAACTGAGCATATAATTGTGTCAGGTTACCTGTCCGAGCTAAACCTT
1 AATTGCTCATTCGAGCTGA-CATATAATCGTGTCAGGTTACCCGTCCGGGCTAAACCTT
28007753 AATGTAGACA
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
72 3 0.03
73 109 0.96
74 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (72 bp):
AATTGCTCATTCGAGCTGACATATAATCGTGTCAGGTTACCCGTCCGGGCTAAACCTTTATATAA
ATACATC
Found at i:28010787 original size:16 final size:16
Alignment explanation
Indices: 28010766--28010818 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
28010756 TTGGTTCGCT
*
28010766 GTAATGGAATAGGGGC
1 GTAATGGAATAGAGGC
28010782 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
28010798 ATAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
28010814 GTAAT
1 GTAAT
28010819 AGATAATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:28010853 original size:46 final size:44
Alignment explanation
Indices: 28010800--28010893 Score: 152
Period size: 44 Copynumber: 2.1 Consensus size: 44
28010790 ATAGAGGCAT
*
28010800 AATGGAATAGAGGCGTAATAGATAATCATTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAG-TAATC-TTGTGTTTGGTTGAATGG
*
28010846 AATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAATGG
28010890 AATG
1 AATG
28010894 ATGTTGTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 21 0.46
45 4 0.09
46 21 0.46
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAATGG
Found at i:28011075 original size:18 final size:18
Alignment explanation
Indices: 28011052--28011185 Score: 81
Period size: 18 Copynumber: 7.9 Consensus size: 18
28011042 TTATTATTAA
28011052 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
28011070 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
*
28011087 ATATGAATTTACT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * * *
28011105 -CATAATAT-ATAATACT
1 ATATAATTTAATAAAAAT
* * *
28011121 ATAAAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
28011140 A-ATTA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
*
28011152 ATATAATTTAACAAAAAT
1 ATATAATTTAATAAAAAT
28011170 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
28011186 TTCTTAGTGT
Statistics
Matches: 86, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
12 1 0.01
13 5 0.06
14 2 0.02
15 3 0.03
16 8 0.09
17 20 0.23
18 42 0.49
19 5 0.06
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:28011228 original size:120 final size:120
Alignment explanation
Indices: 28011086--28011401 Score: 587
Period size: 120 Copynumber: 2.6 Consensus size: 120
28011076 TTTAATAAAA
28011086 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
* *
28011151 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTGTTAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATGAAATATTCT
*
28011206 TATATGAATTTACTAAACTCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
* *
28011271 AATATAATTTAATAATAATATATAATTTAATAAAATTCTTAGTATGAAATATTCT
66 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATGAAATATTCT
28011326 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
28011391 AATATAATTTA
66 AATATAATTTA
28011402 TAATCTACTT
Statistics
Matches: 190, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 190 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTATGAAATATTCT
Found at i:28011235 original size:61 final size:59
Alignment explanation
Indices: 28011167--28011357 Score: 192
Period size: 61 Copynumber: 3.2 Consensus size: 59
28011157 ATTTAACAAA
28011167 AATATATAATTTAATAAAATTCTTAGTGTTAAATATTCTTATATGAATTTACTAAACTCAT
1 AATATATAATTTAATAAAATTCTTAGT-TTAAATATTCTTATATGAATTTACTAAA-TCAT
* * * * * * * * *
28011228 AATATATAATACT-ATAAAA-T-ATAATTTAAAATAATTATTAT-TAAATATAATTTAATAAT
1 AATATATAAT-TTAATAAAATTCTTAGTTT-AAAT-ATTCTTATATGAAT-TTACTAAATCAT
*
28011287 AATATATAATTTAATAAAATTCTTAGTATGAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAGT-TTAAATATTCTTATATGAATTTACT-AAATCAT
28011348 AATATATAAT
1 AATATATAAT
28011358 ACTATAAAAT
Statistics
Matches: 101, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
58 3 0.03
59 30 0.30
60 24 0.24
61 42 0.42
62 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (59 bp):
AATATATAATTTAATAAAATTCTTAGTTTAAATATTCTTATATGAATTTACTAAATCAT
Found at i:28011274 original size:26 final size:28
Alignment explanation
Indices: 28011244--28011307 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
28011234 TAATACTATA
*
28011244 AAATATAATTTAA-AATAAT-TATTATT
1 AAATATAATTTAATAATAATATATAATT
28011270 AAATATAATTTAATAATAATATATAATT
1 AAATATAATTTAATAATAATATATAATT
* *
28011298 TAATAAAATT
1 AAATATAATT
28011308 CTTAGTATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATATAATTTAATAATAATATATAATT
Found at i:28019583 original size:31 final size:30
Alignment explanation
Indices: 28019548--28019607 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28019538 GGAGGTGGGA
*
28019548 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
28019579 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
28019608 TAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:28019837 original size:9 final size:9
Alignment explanation
Indices: 28019823--28019862 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
28019813 TATAGTTTGA
28019823 TATTCGAAT
1 TATTCGAAT
28019832 TATTCGAAT
1 TATTCGAAT
28019841 TATTCGAAT
1 TATTCGAAT
*
28019850 TATTCGAGT
1 TATTCGAAT
28019859 TATT
1 TATT
28019863 ATTCGAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28019905 original size:9 final size:9
Alignment explanation
Indices: 28019888--28019918 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28019878 TCGAGTTGAT
28019888 TCGAATAAC
1 TCGAATAAC
*
28019897 TCGATTAAC
1 TCGAATAAC
28019906 TCGAATAAC
1 TCGAATAAC
28019915 TCGA
1 TCGA
28019919 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:28021912 original size:34 final size:34
Alignment explanation
Indices: 28021868--28021933 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
28021858 CAGTAAAATA
*
28021868 TTTTCCGTAAAATAAATTT-TAGAAAATATTTTAT
1 TTTTCCGTAAAAT-AATTTACAGAAAATATTTTAT
*
28021902 TTTTCTGTAAAATAATTTACAGAAAATATTTT
1 TTTTCCGTAAAATAATTTACAGAAAATATTTT
28021934 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 24 0.83
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (34 bp):
TTTTCCGTAAAATAATTTACAGAAAATATTTTAT
Found at i:28023316 original size:35 final size:36
Alignment explanation
Indices: 28023270--28023338 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
28023260 TGTCAATCAT
28023270 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
28023305 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
28023339 TCTAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:28023336 original size:27 final size:28
Alignment explanation
Indices: 28023306--28023375 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
28023296 AATAATAAAT
*
28023306 TCAATATCCAACAAGCTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
28023333 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
28023361 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
28023376 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:28026455 original size:41 final size:41
Alignment explanation
Indices: 28026410--28026535 Score: 153
Period size: 41 Copynumber: 3.1 Consensus size: 41
28026400 TTTATTGTCA
* *
28026410 GTGAAATAATTCAGACTTTATGTCTAGCAGGCTTAATGCCG
1 GTGAAATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
28026451 GTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGAAATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
* * * * * * * *
28026492 ATGATACATTTCGGACAATAAGTCTAGCAGGCTAAAAGCCG
1 GTGAAATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
28026533 GTG
1 GTG
28026536 TACCGATTCA
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (41 bp):
GTGAAATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:28026830 original size:32 final size:33
Alignment explanation
Indices: 28026770--28026836 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
28026760 CAATTATTAA
* * * *
28026770 ATATATATATATATATGTGCATTCGGTATATGC
1 ATATATATAAATATATATGCAATAGGTATATGC
28026803 ATATAT-TAAATATATATGCAATAGGTATATGC
1 ATATATATAAATATATATGCAATAGGTATATGC
28026835 AT
1 AT
28026837 TTGGTAAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 24 0.80
33 6 0.20
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.40
Consensus pattern (33 bp):
ATATATATAAATATATATGCAATAGGTATATGC
Found at i:28029263 original size:10 final size:10
Alignment explanation
Indices: 28029248--28029273 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
28029238 TCATTAAGTG
28029248 CTAACAAATA
1 CTAACAAATA
28029258 CTAACAAATA
1 CTAACAAATA
28029268 CTAACA
1 CTAACA
28029274 GATCAGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (10 bp):
CTAACAAATA
Found at i:28031746 original size:28 final size:28
Alignment explanation
Indices: 28031715--28031772 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
28031705 GTGTTTAGGG
28031715 TTAGGG-TTAT-GATTTTTGAAAAAATAAA
1 TTAGGGTTTATGGA-TTTT-AAAAAATAAA
*
28031743 TTAGGGTTTATGGATTTTAAAAATTAAA
1 TTAGGGTTTATGGATTTTAAAAAATAAA
28031771 TT
1 TT
28031773 TGAGTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 17 0.63
29 8 0.30
30 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (28 bp):
TTAGGGTTTATGGATTTTAAAAAATAAA
Found at i:28031787 original size:27 final size:28
Alignment explanation
Indices: 28031728--28031788 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
28031718 GGGTTATGAT
* *
28031728 TTTTGAAAAAATAAATTAGGGTTTATGGA
1 TTTT-AAAAAATAAATTAGAGTTTAAGGA
* *
28031757 TTTTAAAAATTAAATTTGAGTTTAAGG-
1 TTTTAAAAAATAAATTAGAGTTTAAGGA
28031784 TTTTA
1 TTTTA
28031789 GAATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.18
28 19 0.68
29 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.44
Consensus pattern (28 bp):
TTTTAAAAAATAAATTAGAGTTTAAGGA
Found at i:28035769 original size:2 final size:2
Alignment explanation
Indices: 28035762--28035797 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28035752 GAAGATTTGA
28035762 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
28035798 TGAATTTAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28050617 original size:6 final size:6
Alignment explanation
Indices: 28050601--28050660 Score: 65
Period size: 6 Copynumber: 10.3 Consensus size: 6
28050591 ATAAAAATTA
28050601 AATATTT AATATT AATATT AATATT AATATT AATA-- AATATTT AAT-TT
1 AATA-TT AATATT AATATT AATATT AATATT AATATT AATA-TT AATATT
*
28050648 AAT-CT AATATT AA
1 AATATT AATATT AA
28050661 ATTTGCTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
4 4 0.09
5 9 0.19
6 27 0.57
7 7 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:28054624 original size:40 final size:40
Alignment explanation
Indices: 28054570--28054700 Score: 210
Period size: 41 Copynumber: 3.2 Consensus size: 40
28054560 AATATATTTA
28054570 TTTTTTAATT-TTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTATTTTTAATTTTAAAATATTTTTAAAATAC
*
28054609 TTTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTA-TTTTTAATTTTAAAATATTTTTAAAATAC
* *
28054650 TTTTTAAATTTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTATTTTTAATTTTAAAATATTTTTAAAATAC
28054690 TTTTTTTAATT
1 -TTTTTTAATT
28054701 TTTAAAATAA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
39 9 0.11
40 29 0.35
41 46 0.55
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (40 bp):
TTTTTTAATTATTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:28054654 original size:30 final size:30
Alignment explanation
Indices: 28054598--28054661 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
28054588 TTTAAAATAT
** * *
28054598 TTTTAAAATACTTTTTTTATTATTTTTTAA
1 TTTTAAAATACTTTTTAAAATATTTTTAAA
28054628 TTTTAAAATA-TTTTTAAAATACTTTTTAAA
1 TTTTAAAATACTTTTTAAAATA-TTTTTAAA
28054658 TTTT
1 TTTT
28054662 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTAAAATACTTTTTAAAATATTTTTAAA
Found at i:28054655 original size:12 final size:11
Alignment explanation
Indices: 28054587--28054694 Score: 72
Period size: 11 Copynumber: 10.4 Consensus size: 11
28054577 ATTTTTTTAA
28054587 TTTTAAAATAT
1 TTTTAAAATAT
28054598 TTTTAAAATACT
1 TTTTAAAATA-T
** *
28054610 TTTTTTATTAT
1 TTTTAAAATAT
*
28054621 TTTT----TAA
1 TTTTAAAATAT
28054628 TTTTAAAATAT
1 TTTTAAAATAT
28054639 TTTTAAAATACT
1 TTTTAAAATA-T
28054651 TTTT-AAAT-T
1 TTTTAAAATAT
* *
28054660 TTTT---TTAA
1 TTTTAAAATAT
28054668 TTTTAAAATAT
1 TTTTAAAATAT
28054679 TTTTAAAATACT
1 TTTTAAAATA-T
28054691 TTTT
1 TTTT
28054695 TTAATTTTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.09
8 4 0.05
9 5 0.06
11 43 0.56
12 18 0.23
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:28054703 original size:40 final size:40
Alignment explanation
Indices: 28054570--28054703 Score: 225
Period size: 40 Copynumber: 3.3 Consensus size: 40
28054560 AATATATTTA
28054570 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
*
28054610 TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATAC-
1 TTTTTTAAT-TTTTTTAATTTTAAAATATTTTTAAAATACT
*
28054650 TTTTTAAATTTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAA-TTTTTTTAATTTTAAAATATTTTTAAAATACT
28054691 TTTTTTAATTTTT
1 TTTTTTAATTTTT
28054704 AAAATAAATT
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
40 49 0.56
41 38 0.44
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:28054715 original size:21 final size:21
Alignment explanation
Indices: 28054677--28054716 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28054667 ATTTTAAAAT
**
28054677 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
28054698 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
28054717 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:28054723 original size:22 final size:20
Alignment explanation
Indices: 28054676--28054730 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
28054666 AATTTTAAAA
* *
28054676 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
28054696 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
28054719 TATTTATTAAAA
1 TATTT-TTAAAA
28054731 AAAGGGCCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:28055144 original size:16 final size:16
Alignment explanation
Indices: 28055123--28055155 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28055113 TTCGCTGTAT
28055123 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
28055139 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
28055155 T
1 T
28055156 AGCAAATCAA
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:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:28055199 original size:45 final size:44
Alignment explanation
Indices: 28055135--28055224 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 44
28055125 GAATAGAGGC
28055135 GTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
28055180 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
28055224 G
1 G
28055225 GAATAGAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.43
45 23 0.55
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:28055406 original size:16 final size:16
Alignment explanation
Indices: 28055369--28055410 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28055359 TTAATCATAT
*
28055369 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28055385 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28055400 TTAAAATATAT
1 TTAAAATATAT
28055411 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28055417 original size:14 final size:15
Alignment explanation
Indices: 28055378--28055419 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28055368 TTTAAACATA
*
28055378 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28055393 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28055407 A-TATAATTTAATA
1 ATTATAATTAAATA
28055420 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28055517 original size:120 final size:120
Alignment explanation
Indices: 28055372--28055807 Score: 836
Period size: 120 Copynumber: 3.6 Consensus size: 120
28055362 ATCATATTTA
*
28055372 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAGTCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAGTCAA
28055437 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
28055492 AACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAGTCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAGTCAA
28055557 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
28055612 AACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAGTCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAGTCAA
28055677 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
28055732 AACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAGTCAA
*
28055797 TAATCTTATAT
66 TATTCTTATAT
28055808 ATTATATGAT
Statistics
Matches: 312, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 312 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAGTCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:28055819 original size:103 final size:102
Alignment explanation
Indices: 28055707--28055909 Score: 334
Period size: 103 Copynumber: 2.0 Consensus size: 102
28055697 CAAATCATAA
* *
28055707 TATATGATACTATAAAATATAAATTAACATAATTATTATTAAATATATTATAATTAAAATCTATA
1 TATATGATACTATAAAAGATAAATTAACATAATTATTATTAAATATATTATAATTAAAATATATA
* *
28055772 ATTTAATAAAATTCTTAATAATTAATAATCTTATATAT
66 ATTTAATAAAAGTC-TAATAATCAATAATCTTATATAT
* *
28055810 TATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATA
1 TATATGATACTATAAAAGATAAATTAACATAATTATTATTAAATATATTATAATTAAAATATATA
*
28055875 ATTTAATAAAAGTCTAATAATCAATATTCTTATAT
66 ATTTAATAAAAGTCTAATAATCAATAATCTTATAT
28055910 GAATTTACTA
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 19 0.20
103 74 0.80
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (102 bp):
TATATGATACTATAAAAGATAAATTAACATAATTATTATTAAATATATTATAATTAAAATATATA
ATTTAATAAAAGTCTAATAATCAATAATCTTATATAT
Found at i:28055873 original size:18 final size:17
Alignment explanation
Indices: 28055852--28055885 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28055842 TTATTATTAA
*
28055852 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28055870 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
28055886 GTCTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28055873 original size:59 final size:59
Alignment explanation
Indices: 28055810--28055995 Score: 173
Period size: 59 Copynumber: 3.1 Consensus size: 59
28055800 TCTTATATAT
28055810 TATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAAAA
1 TATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAAAA
* * * * * * * ** * *
28055869 TATATAAT-TTAATAAAAGTCTAA--TAATCA-ATATTCTTATATGAATTTACTAAAATCATAA
1 TATATGATACT-ATAAAAG-ATAATTTAA-CATA-ATTATTAT-TAAATATATTTTAATTAAAA
* * *
28055929 TATATGATACTATAAAATATAATTTAAAATAATTAATATTAAATATATTTTAATTAAAA
1 TATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAAAA
28055988 TATATGAT
1 TATATGAT
28055996 TTAATAAAAT
Statistics
Matches: 93, Mismatches: 25, Indels: 18
0.68 0.18 0.13
Matches are distributed among these distances:
58 5 0.05
59 47 0.51
60 36 0.39
61 5 0.05
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (59 bp):
TATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAAAA
Found at i:28055974 original size:222 final size:223
Alignment explanation
Indices: 28055587--28056006 Score: 716
Period size: 222 Copynumber: 1.9 Consensus size: 223
28055577 CAAATCATAA
* *
28055587 TATATGATACTATAAAATATAAATTAACATAATTATTATTAAATATATTATAATTAAAATCTATA
1 TATATGATACTATAAAAGATAAATTAACATAATTATTATTAAATATATTATAATTAAAATATATA
* * *
28055652 ATTTAATAAAATTCTTAATAGTCAATATTCTTATATGAATTTACTCAAATCATAATATATGATAC
66 ATTTAATAAAAGTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATAC
* * *
28055717 TATAAAATATAAATTAACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAA
131 TATAAAATATAAATTAAAATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAA
28055782 ATTCTTAATAATTAATAATCTTATATAT
196 ATTCTTAATAATTAATAATCTTATATAT
* *
28055810 TATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATA
1 TATATGATACTATAAAAGATAAATTAACATAATTATTATTAAATATATTATAATTAAAATATATA
28055875 ATTTAATAAAAGTC-TAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATAC
66 ATTTAATAAAAGTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATAC
* * *
28055939 TATAAAATATAATTTAAAATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAA
131 TATAAAATATAAATTAAAATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAA
28056004 ATT
196 ATT
28056007 TAAAATAATT
Statistics
Matches: 184, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
222 110 0.60
223 74 0.40
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (223 bp):
TATATGATACTATAAAAGATAAATTAACATAATTATTATTAAATATATTATAATTAAAATATATA
ATTTAATAAAAGTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATAC
TATAAAATATAAATTAAAATAATTAATATTAAATATATTATAATTAAAATATATAATTTAATAAA
ATTCTTAATAATTAATAATCTTATATAT
Done.