Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 101 of 168
Found at i:29688202 original size:76 final size:74
Alignment explanation
Indices: 29687802--29688500 Score: 710
Period size: 76 Copynumber: 9.2 Consensus size: 74
29687792 TGTTTTTTTT
* * * ** *
29687802 AAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTTGGGCACATGCCAAGGTATTTCTCAATTTC
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGTCACATGCTGAGGTATTT-TTAATTTC
* *
29687867 TGTTTTTCAAAAAA
65 T-ATTTTC---CAA
* * * *
29687881 AAATTTAACTCATAATGCGAGAGGTGGGTTGAGCCTCGAGTCACATCCTGAGGTATTTTCAATTT
1 AAA-TCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG-GTCACATGCTGAGGTATTTTTAATTT
*
29687946 CTATTTTTCAA
64 CTATTTTCCAA
* * * *
29687957 AAATCAACTCATAATGCGAGAAGTGAGTTAAGCCTCGGGC-CATGCTGAGGTATTTTCAATTTCT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGTCACATGCTGAGGTATTTTTAATTTCT
*
29688021 ACTTTTCAAA
66 A-TTTTCCAA
* *
29688031 AATATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTATTTTCAATTT
1 AA-ATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCTGAGGTATTTTTAATTT
* *
29688094 CTGTTTTTCAAAA
64 CT-ATTTTC-CAA
* ** *
29688107 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGTCACATGTTGAGGTATATTTTAATTT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCTGAGGTAT-TTTTAATTT
29688172 CTATTTTCCAA
64 CTATTTTCCAA
* *
29688183 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTAC--GCTGAGGTATTTTTAATTCC
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCTGAGGTATTTTTAATTTC
*
29688246 TGTTTTCCAAAAA
65 TATTTTCC---AA
*
29688259 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTAC--GCTGAGGTATTTTTAATTTC
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCTGAGGTATTTTTAATTTC
*
29688322 TTGTTTTCCAAAA
65 -TATTTTCC--AA
* * * * *
29688335 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCTATACGCCGAGGCATTTTTAATTTC
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGTC-ACATGCTGAGGTATTTTTAATTTC
* *
29688400 TGTTTTTCAA
65 TATTTTCCAA
* * * * *
29688410 AAATCAACTCATATTGCGAGATGTGAGTTGAGCCTAGGGTCATATGCCGAGGTATTTTTCAATTT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCT-CGGTCACATGCTGAGGTATTTTT-AATTT
*
29688475 CTATTTTTCAA
64 CTATTTTCCAA
**
29688486 AGGTCAACTCATAAT
1 AAATCAACTCATAAT
29688501 CTGAGAAATG
Statistics
Matches: 544, Mismatches: 56, Indels: 43
0.85 0.09 0.07
Matches are distributed among these distances:
73 40 0.07
74 19 0.03
75 178 0.33
76 188 0.35
77 30 0.06
78 28 0.05
79 7 0.01
80 39 0.07
81 15 0.03
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (74 bp):
AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGTCACATGCTGAGGTATTTTTAATTTCT
ATTTTCCAA
Found at i:29688516 original size:227 final size:226
Alignment explanation
Indices: 29687802--29688500 Score: 874
Period size: 227 Copynumber: 3.1 Consensus size: 226
29687792 TGTTTTTTTT
* * **
29687802 AAATCAACTCATAATGCAAGAGGTGAGTTGAGCCTTGGG-CACATGCCAAGGTATTTCTCAATTT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTATTT-TCAATTT
* * * *
29687866 CTGTTTTTCAAAAAAAAATTTAACTCATAATGCGAGAGGTGGGTTGAGCCTCGAGTCACATC-CT
63 CTG-TTTTC-CAAAAAAA-TCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CGCT
* *
29687930 GAGGTATTTTCAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTAAGCCTCGG
124 GAGGTATTTTTAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGG
* *
29687995 G-CCATGCTGAGGTA-TTTTCAATTTCTACTTTTCAAA
189 GTCTATGCTGAGGTATTTTTCAATTTCTATTTTTCAAA
*
29688031 AATATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCT
1 AA-ATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCT
* * ** * * *
29688096 GTTTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGTCACATGTTGAGGTA
65 GTTTTCCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
* *
29688161 TATTTTAATTTCTATTTTCCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT-TA
130 T-TTTTAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCTA
* * * *
29688225 CGCTGAGGTATTTTT-AATTCCTGTTTTCCAAAAA
194 TGCTGAGGTATTTTTCAATTTCTATTTTTC--AAA
* *
29688259 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTTACGCTGAGGTATTTTTAATTTCTT
1 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTC-T
* * *
29688324 GTTTTCCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CTATACGCCGAGGC
65 GTTTTCCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC-ACACGCTGAGGT
* * * *
29688388 ATTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCTAGGGTCAT
129 ATTTTTAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTC-T
*
29688453 ATGCCGAGGTATTTTTCAATTTCTATTTTTC-AA
193 ATGCTGAGGTATTTTTCAATTTCTATTTTTCAAA
**
29688486 AGGTCAACTCATAAT
1 AAATCAACTCATAAT
29688501 CTGAGAAATG
Statistics
Matches: 406, Mismatches: 51, Indels: 28
0.84 0.11 0.06
Matches are distributed among these distances:
225 42 0.10
226 82 0.20
227 137 0.34
228 70 0.17
229 27 0.07
230 45 0.11
231 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (226 bp):
AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTCAATTTCTG
TTTTCCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTAT
TTTTAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAAGTGAGTTGAGCCTCGGGTCTATG
CTGAGGTATTTTTCAATTTCTATTTTTCAAA
Found at i:29688984 original size:30 final size:29
Alignment explanation
Indices: 29688835--29688995 Score: 119
Period size: 30 Copynumber: 5.4 Consensus size: 29
29688825 CAAAAAATAC
* * *
29688835 AAATTACATTTTAGCCCCTGAACTTTTCAA
1 AAATTACATTTTGGCCCCTAAAC-TTTCTA
* **
29688865 AAATTACATTTTGACCCCTAATTTTTTCTA
1 AAATTACATTTTGGCCCCTAA-ACTTTCTA
* ** * *
29688895 AAATTACATCTTAACCCCTAATAATTTGT-
1 AAATTACATTTTGGCCCCTAA-ACTTTCTA
*
29688924 AAATTACATTTAGGCCCCTAAACTTTCTAA
1 AAATTACATTTTGGCCCCTAAACTTTCT-A
* * *
29688954 AAATTACATTTTGGCCTC-ATATTTTCCTA
1 AAATTACATTTTGGCCCCTAAACTTT-CTA
29688983 AAATTACACTTTT
1 AAATTACA-TTTT
29688996 ATCCTAGAAA
Statistics
Matches: 105, Mismatches: 21, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
28 5 0.05
29 31 0.30
30 69 0.66
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTGGCCCCTAAACTTTCTA
Found at i:29689289 original size:15 final size:15
Alignment explanation
Indices: 29689269--29689302 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
29689259 GTCGATTCCC
*
29689269 CCACCGTCACCGCAA
1 CCACCGCCACCGCAA
29689284 CCACCGCCACCGCAA
1 CCACCGCCACCGCAA
29689299 CCAC
1 CCAC
29689303 AACATCGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.59, G:0.12, T:0.03
Consensus pattern (15 bp):
CCACCGCCACCGCAA
Found at i:29689394 original size:11 final size:11
Alignment explanation
Indices: 29689373--29689402 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
29689363 ACCAAAAAAA
29689373 AAGAGAA-AAG
1 AAGAGAAGAAG
29689383 AAGAGAAGAAG
1 AAGAGAAGAAG
29689394 AAGAGAAGA
1 AAGAGAAGA
29689403 GGAGACGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
AAGAGAAGAAG
Found at i:29689508 original size:16 final size:15
Alignment explanation
Indices: 29689475--29689518 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
29689465 GAAGGGAAAG
* *
29689475 AAGAAGAAGAGAAGA
1 AAGAAGAAGAAAAAA
29689490 AAGAAGGAAGAAAAAA
1 AAGAA-GAAGAAAAAA
29689506 AAGAAAGAAGAAA
1 AAG-AAGAAGAAA
29689519 GGGAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.20
16 18 0.72
17 2 0.08
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGAAAAAA
Found at i:29689514 original size:27 final size:28
Alignment explanation
Indices: 29689479--29689564 Score: 81
Period size: 27 Copynumber: 3.1 Consensus size: 28
29689469 GGAAAGAAGA
29689479 AGAAGAGAAGAAAGAAGGAAGAAAAAAA-
1 AGAA-AGAAGAAAGAAGGAAGAAAAAAAG
29689507 AGAAAGAAGAAAG--GGAAAGAAAAAAAG
1 AGAAAGAAGAAAGAAGG-AAGAAAAAAAG
* * ** *
29689534 GGAAAAAAG-AAGAAAAAAGAAAAAAAT
1 AGAAAGAAGAAAGAAGGAAGAAAAAAAG
29689561 AGAA
1 AGAA
29689565 TAGTCGGGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
25 2 0.04
26 13 0.27
27 29 0.60
28 4 0.08
ACGTcount: A:0.73, C:0.00, G:0.26, T:0.01
Consensus pattern (28 bp):
AGAAAGAAGAAAGAAGGAAGAAAAAAAG
Found at i:29690476 original size:17 final size:17
Alignment explanation
Indices: 29690453--29690693 Score: 188
Period size: 17 Copynumber: 13.8 Consensus size: 17
29690443 TTTAAAAAAA
29690453 CCGTGTTTCAAAAATCTT
1 CCGTGTTTCAAAAAT-TT
29690471 CC-TGTTTTCAAAAA-TT
1 CCGTG-TTTCAAAAATTT
29690487 CCGGTGTTTCAAAAATCTT
1 CC-GTGTTTCAAAAAT-TT
29690506 -CGTGTTTTC-AAAATTT
1 CCGTG-TTTCAAAAATTT
*
29690522 CCGGTGTTTTAAAAATTT
1 CC-GTGTTTCAAAAATTT
* *
29690540 TCGTGTTTTCAAAAAATTC
1 CCGTG-TTTC-AAAAATTT
29690559 CCGTGTTTCAAAAATTT
1 CCGTGTTTCAAAAATTT
* * * *
29690576 TCATGTTTTCAACAATTC
1 CCGTG-TTTCAAAAATTT
*
29690594 CCGTGTTTCACAAATTT
1 CCGTGTTTCAAAAATTT
29690611 CCGTGTTTTCAAAAATTT
1 CCGTG-TTTCAAAAATTT
* *
29690629 TCGTGTTTTAAAAATTT
1 CCGTGTTTCAAAAATTT
** *
29690646 TTGTG-TTCTTAAAA-TT
1 CCGTGTTTC-AAAAATTT
* *
29690662 CTCGTATTTCAAAAGTTT
1 C-CGTGTTTCAAAAATTT
*
29690680 TCGTGTTTCAAAAA
1 CCGTGTTTCAAAAA
29690694 AAATTCTCAT
Statistics
Matches: 177, Mismatches: 29, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
16 10 0.06
17 85 0.48
18 69 0.39
19 13 0.07
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (17 bp):
CCGTGTTTCAAAAATTT
Found at i:29690481 original size:18 final size:17
Alignment explanation
Indices: 29690458--29690645 Score: 152
Period size: 18 Copynumber: 10.7 Consensus size: 17
29690448 AAAAACCGTG
29690458 TTTCAAAAATCTTCCTGT
1 TTTCAAAAAT-TTCCTGT
*
29690476 TTTCAAAAA-TTCCGGT
1 TTTCAAAAATTTCCTGT
*
29690492 GTTTCAAAAATCTTCGTGT
1 -TTTCAAAAAT-TTCCTGT
29690511 TTTC-AAAATTTCCGGTGT
1 TTTCAAAAATTTCC--TGT
*
29690529 TTT-AAAAATTTTCGTGT
1 TTTCAAAAA-TTTCCTGT
* *
29690546 TTTCAAAAAATTCCCGT
1 TTTCAAAAATTTCCTGT
*
29690563 GTTTCAAAAATTTTCATGT
1 -TTTCAAAAA-TTTCCTGT
* *
29690582 TTTCAACAA-TTCCCGT
1 TTTCAAAAATTTCCTGT
*
29690598 GTTTCACAAATTTCCGTGT
1 -TTTCAAAAATTTCC-TGT
*
29690617 TTTCAAAAATTTTCGTGT
1 TTTCAAAAA-TTTCCTGT
29690635 TTT-AAAAATTT
1 TTTCAAAAATTT
29690646 TTGTGTTCTT
Statistics
Matches: 137, Mismatches: 19, Indels: 30
0.74 0.10 0.16
Matches are distributed among these distances:
16 17 0.12
17 37 0.27
18 63 0.46
19 20 0.15
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (17 bp):
TTTCAAAAATTTCCTGT
Found at i:29690644 original size:35 final size:35
Alignment explanation
Indices: 29690453--29690693 Score: 281
Period size: 35 Copynumber: 6.9 Consensus size: 35
29690443 TTTAAAAAAA
* *
29690453 CCGTGTTTCAAAAATCTTCCTGTTTTCAAAAATTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* * *
29690488 CGGTGTTTCAAAAATCTTCGTGTTTTCAAAATTTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* *
29690523 CGGTGTTTTAAAAATTTTCGTGTTTTCAAAAAATTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTC-AAAAATTC
* *
29690559 CCGTGTTTCAAAAATTTTCATGTTTTCAACAATTC
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* * *
29690594 CCGTGTTTCACAAATTTCCGTGTTTTCAAAAATTT
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
* * *
29690629 TCGTGTTTTAAAAATTTTTGTGTTCTT--AAAATTC
1 CCGTGTTTCAAAAATTTTCGTGTT-TTCAAAAATTC
* * *
29690663 TCGTATTTCAAAAGTTTTCGTG-TTTCAAAAA
1 CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAA
29690694 AAATTCTCAT
Statistics
Matches: 177, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
32 2 0.01
33 1 0.01
34 28 0.16
35 113 0.64
36 33 0.19
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (35 bp):
CCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTC
Found at i:29693079 original size:23 final size:24
Alignment explanation
Indices: 29693052--29693097 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29693042 TAAATTTTGT
29693052 TCTATTATT-TAAA-TTTTATTTTA
1 TCTA-TATTATAAATTTTTATTTTA
29693075 TCTATATTATAAATTTTTATTTT
1 TCTATATTATAAATTTTTATTTT
29693098 TATTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 8 0.38
24 9 0.43
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TCTATATTATAAATTTTTATTTTA
Found at i:29693107 original size:25 final size:22
Alignment explanation
Indices: 29693056--29693108 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 22
29693046 TTTTGTTCTA
29693056 TTATTTAAATTTTATTTTATCT
1 TTATTTAAATTTTATTTTATCT
* *
29693078 ATATTATAAATTTTTATTTTTATTT
1 TTATT-TAAA-TTTTA-TTTTATCT
29693103 TTATTT
1 TTATTT
29693109 TGATGTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 4 0.16
23 4 0.16
24 6 0.24
25 11 0.44
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTAAATTTTATTTTATCT
Found at i:29697011 original size:3 final size:3
Alignment explanation
Indices: 29697005--29697032 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29696995 TGTTAAAATT
29697005 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
29697033 CATCTACCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:29697208 original size:16 final size:16
Alignment explanation
Indices: 29697179--29697229 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
29697169 TGAATTATTA
** *
29697179 ATTACAGCTTTATTTC
1 ATTACAGCCCTATTCC
*
29697195 ATTACAGTCCTATTCC
1 ATTACAGCCCTATTCC
29697211 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCC
29697227 ATT
1 ATT
29697230 CCCCCCAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:29697588 original size:30 final size:30
Alignment explanation
Indices: 29697552--29697611 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
29697542 ACTTAACAAG
29697552 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
29697582 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
29697612 TAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:29698668 original size:14 final size:13
Alignment explanation
Indices: 29698643--29698672 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
29698633 ATAATTTATA
29698643 TATATTTATATTT
1 TATATTTATATTT
29698656 TATATTCTATATTT
1 TATATT-TATATTT
29698670 TAT
1 TAT
29698673 TATATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TATATTTATATTT
Found at i:29699224 original size:11 final size:10
Alignment explanation
Indices: 29699192--29699248 Score: 53
Period size: 11 Copynumber: 5.4 Consensus size: 10
29699182 TTAAAATTAT
29699192 AAAAATT-AA
1 AAAAATTAAA
* *
29699201 AATATTTATAA
1 AAAAATTA-AA
29699212 AAAAATTACAA
1 AAAAATTA-AA
29699223 AAAAATTAAA
1 AAAAATTAAA
29699233 AAAATTATTAAA
1 AAAA--ATTAAA
29699245 AAAA
1 AAAA
29699249 TAAAAACTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
9 5 0.13
10 6 0.15
11 18 0.46
12 10 0.26
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:29699232 original size:20 final size:20
Alignment explanation
Indices: 29699208--29699254 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
29699198 TAAAATATTT
29699208 ATAAAAAAATTA-CAAAAAA
1 ATAAAAAAATTATCAAAAAA
*
29699227 ATTAAAAAAATTATTAAAAAA
1 A-TAAAAAAATTATCAAAAAA
29699248 ATAAAAA
1 ATAAAAA
29699255 CTACTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.68
21 7 0.28
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (20 bp):
ATAAAAAAATTATCAAAAAA
Found at i:29699529 original size:15 final size:13
Alignment explanation
Indices: 29699495--29699525 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29699485 AAATGTAATG
29699495 AATATTTGATATA
1 AATATTTGATATA
*
29699508 AATATTTGGTATA
1 AATATTTGATATA
29699521 AATAT
1 AATAT
29699526 ATTTTAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (13 bp):
AATATTTGATATA
Found at i:29703503 original size:2 final size:2
Alignment explanation
Indices: 29703496--29703524 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29703486 CTTTATTTGA
29703496 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
29703525 CNNNNNNNNN
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:29703670 original size:2 final size:2
Alignment explanation
Indices: 29703632--29703659 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29703622 NNNNGTTGTA
29703632 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
29703660 GTTTAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29723641 original size:6 final size:6
Alignment explanation
Indices: 29723630--29723655 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29723620 GTTAAGTCAT
29723630 ATTTTA ATTTTA ATTTTA ATTTTA AT
1 ATTTTA ATTTTA ATTTTA ATTTTA AT
29723656 ATCTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
ATTTTA
Found at i:29729192 original size:22 final size:21
Alignment explanation
Indices: 29729167--29729212 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
29729157 TAAAAAATAT
29729167 TAAAATT-ACATATAAAATTTTA
1 TAAAATTAAC-TA-AAAATTTTA
29729189 TAAAAATTAACTAAAAATTTTA
1 T-AAAATTAACTAAAAATTTTA
29729211 TA
1 TA
29729213 TTAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.05
22 11 0.50
23 8 0.36
24 2 0.09
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAATTAACTAAAAATTTTA
Found at i:29729256 original size:5 final size:5
Alignment explanation
Indices: 29729248--29729272 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29729238 TTAATATTAC
29729248 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
29729273 CTATCCCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:29739563 original size:28 final size:27
Alignment explanation
Indices: 29739530--29739628 Score: 103
Period size: 28 Copynumber: 3.6 Consensus size: 27
29739520 TAATGAGATT
29739530 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTTTAATTGAA
* *
29739557 ATGCACTAAGTGTGCGAGTATAAGGGTG-A
1 A-GCACTAAGTGTGCGAGTTTAA--TTGAA
* *
29739586 AGCACTAAGTGTGCAAGTTTGATT-ATTA
1 AGCACTAAGTGTGCGAGTTTAATTGA--A
29739614 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
29739629 TACTTATCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 53 0.90
29 2 0.03
30 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTTAATTGAA
Found at i:29740679 original size:47 final size:47
Alignment explanation
Indices: 29740607--29740923 Score: 471
Period size: 47 Copynumber: 6.8 Consensus size: 47
29740597 AAATTTGATA
29740607 TATAATGCTGTCC-ATTTTAAGTATATTGATGCTGTCCATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATG
* * *
29740653 TGTAATGCTGTCCAATTTTGAGTATATTGATGCTGCCCATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATG
29740700 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATG
*
29740747 TATAATGCTGTCCAATTTTGAGTATATTGATGCTG-CTCATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTC-CATTTTAATG
* *
29740794 TATAATGCTGTCCAATTTTAAGTATATTTATGTTGTCCATTTTAATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATG
* * * * * *
29740841 TATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCTAATTTGATG
1 TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATG
*
29740888 TATAATGCTGTCC-ATTTTAAGCATATT-ATTGCTGTC
1 TATAATGCTGTCCAATTTTAAGTATATTGA-TGCTGTC
29740924 TAATTTGATG
Statistics
Matches: 248, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
45 1 0.00
46 31 0.12
47 215 0.87
48 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (47 bp):
TATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCATTTTAATG
Found at i:29752782 original size:2 final size:2
Alignment explanation
Indices: 29752775--29752874 Score: 75
Period size: 2 Copynumber: 52.5 Consensus size: 2
29752765 TATAAAGATG
* * *
29752775 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A GA TA TA AA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
29752815 AA TA TA TA TG TA TA TA AA GA TA TA TA TA TA TA TA -A TA -A GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
29752855 TA TA -A AA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
29752875 GTATGAAAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
1 5 0.06
2 76 0.94
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (2 bp):
TA
Found at i:29756481 original size:29 final size:30
Alignment explanation
Indices: 29756442--29756499 Score: 91
Period size: 29 Copynumber: 1.9 Consensus size: 30
29756432 AATTGGTCTC
29756442 TTCTTTTTGAGAA-ACTCTGTAATTATTCT
1 TTCTTTTTGAGAAGACTCTGTAATTATTCT
*
29756471 TTCTTTTTGAGAAGGTCTCTGTAATTATT
1 TTCTTTTTGAGAA-GACTCTGTAATTATT
29756500 ATAGTGAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 13 0.50
31 13 0.50
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (30 bp):
TTCTTTTTGAGAAGACTCTGTAATTATTCT
Found at i:29772991 original size:3 final size:3
Alignment explanation
Indices: 29772983--29773009 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29772973 TATATTAACC
29772983 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
29773010 TAAAGAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29773834 original size:52 final size:52
Alignment explanation
Indices: 29773753--29773903 Score: 257
Period size: 52 Copynumber: 2.9 Consensus size: 52
29773743 ATAGGGGATA
* * *
29773753 AAAGCTAAACGAGCAGATAAGAGGAAATCTGCTTTTACAAAGTGTAAGTCAT
1 AAAGCTAAACGAGCAGATAAGAGGGAATCTGCTTTTACAAAGTGAAAGACAT
*
29773805 AAAGCTAAACGAGCAGATAAGAGGGAATCTGTTTTTACAAAGTGAAAGACAT
1 AAAGCTAAACGAGCAGATAAGAGGGAATCTGCTTTTACAAAGTGAAAGACAT
*
29773857 AAAGCTAAACGAGCAGATAAGAGGGAATCTGCTTTCACAAAGTGAAA
1 AAAGCTAAACGAGCAGATAAGAGGGAATCTGCTTTTACAAAGTGAAA
29773904 AACAATTATT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 93 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (52 bp):
AAAGCTAAACGAGCAGATAAGAGGGAATCTGCTTTTACAAAGTGAAAGACAT
Found at i:29774672 original size:3 final size:3
Alignment explanation
Indices: 29774659--29774692 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
29774649 AACCTTCATT
29774659 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29774693 GAAGAAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:29779518 original size:68 final size:67
Alignment explanation
Indices: 29779337--29779587 Score: 190
Period size: 65 Copynumber: 3.8 Consensus size: 67
29779327 TGAGACGGGA
* * * * * *
29779337 TCATCATTTACACTGATCTTAGAACATCTATCTCAATTTAT-AGGAATTCTTGAACAAATGAGAT
1 TCATCA-TTACACTGATCTTAGGACTTTTATCTCATTTTATCA-GAATTCTAGAACAAAGGAGAT
*
29779401 GGAG
64 GGAC
** * * *
29779405 TCAT--TTACACCAAGCCTAGGACTTTCT-TCCTCATTTGATCAGAATTCTAGAACAAAGGAGAT
1 TCATCATTACACTGATCTTAGGACTTT-TAT-CTCATTTTATCAGAATTCTAGAACAAAGGAGAT
29779467 GGAC
64 GGAC
* * **
29779471 TCATCATTCACACTGATCTTAGGACTTTTATCTCATTTTATCAGAATTCTTGATCAAACAAGATG
1 TCATCATT-ACACTGATCTTAGGACTTTTATCTCATTTTATCAGAATTCTAGAACAAAGGAGATG
**
29779536 GGG
65 GAC
* * ** * * *
29779539 TAAT--TTGCACCAATTTTAGGACTTCTATCTCATTTTATCGGAATTCTAG
1 TCATCATTACACTGATCTTAGGACTTTTATCTCATTTTATCAGAATTCTAG
29779588 TCTAGAACAA
Statistics
Matches: 145, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
65 51 0.35
66 37 0.26
67 1 0.01
68 40 0.28
69 16 0.11
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (67 bp):
TCATCATTACACTGATCTTAGGACTTTTATCTCATTTTATCAGAATTCTAGAACAAAGGAGATGG
AC
Found at i:29779627 original size:70 final size:70
Alignment explanation
Indices: 29779474--29779717 Score: 257
Period size: 71 Copynumber: 3.5 Consensus size: 70
29779464 GATGGACTCA
* * * * *
29779474 TCATTCACACTGATCTTAGGACTTTTATCTCATTTTATCAGAATTC---T-T-GATCAAACAAGA
1 TCATTTACACTGATCTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAAA
29779534 TGGGG
66 TGGGG
* * ** *
29779539 TAATTTGCACCAATTTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAAA
1 TCATTTACACTGATCTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAAA
29779604 TGGGG
66 TGGGG
* * * **
29779609 TCATTTACACTGATTTTAGGACTTCTGTCTCATCTTTTTCGGAATTCTAGTCTAGAACAAATTAA
1 TCATTTACACTGATCTTAGGACTTCTATCTCAT-TTTATCGGAATTCTAGTCTAGAACAAACAAA
* *
29779674 ACGGGA
65 ATGGGG
* *
29779680 TCATTTAC-GTCGATCTTAGGACTTCTATCTCATCTTAT
1 TCATTTACACT-GATCTTAGGACTTCTATCTCATTTTAT
29779718 AAGCTGTATG
Statistics
Matches: 147, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
65 38 0.26
68 1 0.01
69 1 0.01
70 47 0.32
71 60 0.41
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (70 bp):
TCATTTACACTGATCTTAGGACTTCTATCTCATTTTATCGGAATTCTAGTCTAGAACAAACAAAA
TGGGG
Found at i:29791798 original size:27 final size:27
Alignment explanation
Indices: 29791767--29791865 Score: 76
Period size: 27 Copynumber: 3.7 Consensus size: 27
29791757 TTCGGTTTAG
*
29791767 AAAATTATTAAAATA-CCCTCGACTTGT
1 AAAATTATCAAAATACCCCT-GACTTGT
* * *
29791794 AAAATTACCAAAGTACCCCTGATTTGT
1 AAAATTATCAAAATACCCCTGACTTGT
* * * * *
29791821 AAAATTATCGAAAGA-CCCTCATTTTGG
1 AAAATTATCAAAATACCCCTGA-CTTGT
*
29791848 AAAATTATCGAAATACCC
1 AAAATTATCAAAATACCC
29791866 TTATAGGTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
26 5 0.09
27 47 0.81
28 6 0.10
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.29
Consensus pattern (27 bp):
AAAATTATCAAAATACCCCTGACTTGT
Found at i:29794073 original size:2 final size:2
Alignment explanation
Indices: 29794066--29794090 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29794056 CTATTATCAT
29794066 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
29794091 TCAGCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29794919 original size:41 final size:41
Alignment explanation
Indices: 29794869--29794971 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
29794859 TGATCCAGTA
*
29794869 CACCGGCATTAAGCTTGCTAGACGTATAGTCTGAAATATTT
1 CACCGGCATTAAGCTTGCTAGACGTATAGTCTAAAATATTT
* *
29794910 CACCAGCATTAAGCCTGCTAGACGTATAGTCTAAAATATTT
1 CACCGGCATTAAGCTTGCTAGACGTATAGTCTAAAATATTT
* *
29794951 CACCGGCACTAAGTTTGCTAG
1 CACCGGCATTAAGCTTGCTAG
29794972 GCACAAACCT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCTTGCTAGACGTATAGTCTAAAATATTT
Found at i:29801756 original size:5 final size:5
Alignment explanation
Indices: 29801746--29801771 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29801736 TGAGCATTCG
29801746 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
29801772 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:29803813 original size:20 final size:20
Alignment explanation
Indices: 29803790--29803851 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
29803780 AAAGCATACT
*
29803790 TGGCACACAAAGTACATTCC
1 TGGCACACAAAGTGCATTCC
* * *
29803810 TGGCACA-TAAGCGCATAT-T
1 TGGCACACAAAGTGCAT-TCC
29803829 TGGCACACAAAGTGCATTCC
1 TGGCACACAAAGTGCATTCC
29803849 TGG
1 TGG
29803852 TGCATAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (20 bp):
TGGCACACAAAGTGCATTCC
Found at i:29803865 original size:39 final size:39
Alignment explanation
Indices: 29803783--29803865 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
29803773 TGTACAAAAA
*
29803783 GCATACTTGGCACACAAAGTACATTCCTGGCACATAAGC
1 GCATACTTGGCACACAAAGTACATTCCTGGCACATAAAC
* * ** *
29803822 GCATATTTGGCACACAAAGTGCATTCCTGGTGCATAAAT
1 GCATACTTGGCACACAAAGTACATTCCTGGCACATAAAC
29803861 GCATA
1 GCATA
29803866 ATCTCATACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (39 bp):
GCATACTTGGCACACAAAGTACATTCCTGGCACATAAAC
Found at i:29818509 original size:6 final size:6
Alignment explanation
Indices: 29818495--29818525 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
29818485 ACCATGCCCG
*
29818495 ACATAT ACATGT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT ACATAT A
29818526 TATAACACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:29818769 original size:49 final size:49
Alignment explanation
Indices: 29818697--29818795 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
29818687 AAAAAAATAG
29818697 AGTAAAATTTTGGGTAGGAAATGAAGATTTTACCTGAATTAACTCTACT
1 AGTAAAATTTTGGGTAGGAAATGAAGATTTTACCTGAATTAACTCTACT
29818746 AGTAAAATTTTGGGTAGGAAATGAAGATTTTACCTGAATTAACTCTACT
1 AGTAAAATTTTGGGTAGGAAATGAAGATTTTACCTGAATTAACTCTACT
29818795 A
1 A
29818796 ACATGATGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.34
Consensus pattern (49 bp):
AGTAAAATTTTGGGTAGGAAATGAAGATTTTACCTGAATTAACTCTACT
Found at i:29822175 original size:91 final size:92
Alignment explanation
Indices: 29822012--29822223 Score: 268
Period size: 91 Copynumber: 2.3 Consensus size: 92
29822002 ACTATTATTC
* * * * * *
29822012 AAAATGTTCATATTATTTTTGTATTTGT--AAATCAATTTTAGTCAGTATTATTTTTTGGTCAAA
1 AAAATATTCGTATTATTTTTGTATATGTAAAAATCAATTTTAGCCAGTATTATTTATCGGTCAAA
* *
29822075 TTTTATATTTTCGTATATTAATTTTGT
66 TTTTATATTTTCGTATATCAATTTTCT
* * * * *
29822102 AAAATATTTGTATTATTTTTGGATATGTAAAAAT-ATTTTTAGCCCGTATTATTTATCGGTCGAA
1 AAAATATTCGTATTATTTTTGTATATGTAAAAATCAATTTTAGCCAGTATTATTTATCGGTCAAA
29822166 TTTTATATTTTCGTATATCAATTTTCT
66 TTTTATATTTTCGTATATCAATTTTCT
* *
29822193 AAAATGTTCGTATTATTTTTGTATCTGTAAA
1 AAAATATTCGTATTATTTTTGTATATGTAAA
29822224 TAAAATTTAA
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
90 23 0.22
91 76 0.74
92 4 0.04
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (92 bp):
AAAATATTCGTATTATTTTTGTATATGTAAAAATCAATTTTAGCCAGTATTATTTATCGGTCAAA
TTTTATATTTTCGTATATCAATTTTCT
Found at i:29822311 original size:16 final size:17
Alignment explanation
Indices: 29822286--29822319 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29822276 GAATGTTTGT
29822286 ATTTTCTTATATATGTA
1 ATTTTCTTATATATGTA
*
29822303 ATTTT-TTATATCTGTA
1 ATTTTCTTATATATGTA
29822319 A
1 A
29822320 ATAAAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (17 bp):
ATTTTCTTATATATGTA
Found at i:29832871 original size:96 final size:96
Alignment explanation
Indices: 29832755--29832949 Score: 381
Period size: 96 Copynumber: 2.0 Consensus size: 96
29832745 AATGCACAAA
*
29832755 TTTCAACTAGCTTATGCTTATTGTTAAGAATTAACCCCTTGAAGTAGTTAACAATCCCCAAAGTA
1 TTTCAACTAGCTTATGCTTATTGTTAAGAATTAACCCCTTGAAGTAGTTAACAATCCCCAAAGAA
29832820 ACAAGAAAAACATCACCATAAAGTACATATT
66 ACAAGAAAAACATCACCATAAAGTACATATT
29832851 TTTCAACTAGCTTATGCTTATTGTTAAGAATTAACCCCTTGAAGTAGTTAACAATCCCCAAAGAA
1 TTTCAACTAGCTTATGCTTATTGTTAAGAATTAACCCCTTGAAGTAGTTAACAATCCCCAAAGAA
29832916 ACAAGAAAAACATCACCATAAAGTACATATT
66 ACAAGAAAAACATCACCATAAAGTACATATT
29832947 TTT
1 TTT
29832950 AAGTTTAAAC
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (96 bp):
TTTCAACTAGCTTATGCTTATTGTTAAGAATTAACCCCTTGAAGTAGTTAACAATCCCCAAAGAA
ACAAGAAAAACATCACCATAAAGTACATATT
Found at i:29848662 original size:20 final size:20
Alignment explanation
Indices: 29848639--29848679 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29848629 CTATTCAAAC
* *
29848639 AATATTACTTGAATAGTTAT
1 AATATTACATGAATAATTAT
*
29848659 AATATTAGATGAATAATTAT
1 AATATTACATGAATAATTAT
29848679 A
1 A
29848680 TGTCTTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.41
Consensus pattern (20 bp):
AATATTACATGAATAATTAT
Found at i:29850107 original size:22 final size:23
Alignment explanation
Indices: 29850065--29850107 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
29850055 TGACATTAGT
*
29850065 GTAATTTTTAAAGTTATGTAAGG
1 GTAATTTTTAAAGTTAAGTAAGG
29850088 GTAATTTTGT-AA-TTAAGTAA
1 GTAATTTT-TAAAGTTAAGTAA
29850108 TTAATGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 10 0.56
24 1 0.06
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (23 bp):
GTAATTTTTAAAGTTAAGTAAGG
Found at i:29852277 original size:56 final size:56
Alignment explanation
Indices: 29852198--29852309 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
29852188 ATTCAGTAGG
** * *
29852198 CTCACACGGCTTAACACACGGGCGTGTGGCTTGGCCGTGTGACCCAAGTCAGTATA
1 CTCACACGGCTTAACACACGGGCGTGTGGCTCAGCCATGTGACACAAGTCAGTATA
* * *
29852254 CTCACACGGCTTAGCACATGGGCGTGTGGCTCAGCCATGTGTCACAAGTCAGTATA
1 CTCACACGGCTTAACACACGGGCGTGTGGCTCAGCCATGTGACACAAGTCAGTATA
29852310 TTCAAATTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (56 bp):
CTCACACGGCTTAACACACGGGCGTGTGGCTCAGCCATGTGACACAAGTCAGTATA
Found at i:29853593 original size:105 final size:101
Alignment explanation
Indices: 29853415--29853608 Score: 280
Period size: 105 Copynumber: 1.9 Consensus size: 101
29853405 ATTTGACGGA
* * *
29853415 TAAGACCATGGTTGGACCATGGCAATGTTCAAATGTAAGACCATAGCTGGGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATACAAATGTAAGACCATAGCTGGGCTATGGCATTCTAA
29853480 TGAAAAGACCATAACTAGGTTATGACACCTTGAACG
66 TGAAAAGACCATAACTAGGTTATGACACCTTGAACG
**
29853516 TAAGACCATGGTTGGACCATGGCAGTATAAATACATGTGTAAGACCATAGCTGGGCTATGGCATT
1 TAAGACCATGGTTGGACCATGGCA--AT--ATACAAATGTAAGACCATAGCTGGGCTATGGCATT
* * *
29853581 CTGATGATAAGACCATAACTGGGTTATG
62 CTAATGAAAAGACCATAACTAGGTTATG
29853609 GCACTAAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 24 0.30
103 2 0.02
105 55 0.68
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATACAAATGTAAGACCATAGCTGGGCTATGGCATTCTAA
TGAAAAGACCATAACTAGGTTATGACACCTTGAACG
Found at i:29853624 original size:105 final size:101
Alignment explanation
Indices: 29853415--29853646 Score: 277
Period size: 105 Copynumber: 2.3 Consensus size: 101
29853405 ATTTGACGGA
* * *
29853415 TAAGACCATGGTTGGACCATGGCAATGTTCAAATGTAAGACCATAGCTGGGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATACAAATGTAAGACCATAGCTGGGCTATGGCATTCTAA
**
29853480 TGAAAAGACCATAACTAGGTTATGACACCTTGAACG
66 TGAAAAGACCATAACTAGGTTATGACACCTAAAACG
**
29853516 TAAGACCATGGTTGGACCATGGCAGTATAAATACATGTGTAAGACCATAGCTGGGCTATGGCATT
1 TAAGACCATGGTTGGACCATGGCA--AT--ATACAAATGTAAGACCATAGCTGGGCTATGGCATT
* * * * *
29853581 CTGATGATAAGACCATAACTGGGTTATGGCA-CTAAAAATG
62 CTAATGAAAAGACCATAACTAGGTTATGACACCT-AAAACG
** *
29853621 TAAGACCATGGCAGGGCCATGGCAAT
1 TAAGACCATGGTTGGACCATGGCAAT
29853647 GCATGTGTAA
Statistics
Matches: 111, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
101 24 0.22
103 4 0.04
104 2 0.02
105 81 0.73
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATACAAATGTAAGACCATAGCTGGGCTATGGCATTCTAA
TGAAAAGACCATAACTAGGTTATGACACCTAAAACG
Found at i:29853625 original size:33 final size:32
Alignment explanation
Indices: 29853553--29853629 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
29853543 TAAATACATG
* ****
29853553 TGTAAGACCATAGCTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGGCATAAAAA
*
29853585 TGATAAGACCATAACTGGGTTATGGCACTAAAAA
1 TG-TAAGACCATAACTGGGCTATGGCA-TAAAAA
29853619 TGTAAGACCAT
1 TGTAAGACCAT
29853630 GGCAGGGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 31 0.84
34 4 0.11
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGGCATAAAAA
Found at i:29853675 original size:66 final size:65
Alignment explanation
Indices: 29853553--29853683 Score: 149
Period size: 66 Copynumber: 2.0 Consensus size: 65
29853543 TAAATACATG
* * * ***
29853553 TGTAAGACCATAGCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCACTAAAA
1 TGTAAGACCATAGCAGGGCCATGGCATGCTGATGATAAGACCATAACTGAACTATGGCAC-AAAA
29853618 A
65 A
* *
29853619 TGTAAGACCATGGCAGGGCCATGGCAATGCATG-TG-TAAGACCATAATTGAACTATGGCACAAA
1 TGTAAGACCATAGCAGGGCCATGGC-ATGC-TGATGATAAGACCATAACTGAACTATGGCACAAA
29853682 AA
64 AA
29853684 GAATGATGTA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
65 5 0.09
66 43 0.78
67 5 0.09
68 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (65 bp):
TGTAAGACCATAGCAGGGCCATGGCATGCTGATGATAAGACCATAACTGAACTATGGCACAAAAA
Found at i:29855633 original size:46 final size:46
Alignment explanation
Indices: 29855566--29855658 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
29855556 ATATAAGTAA
29855566 ACCATCTTGCCTCACTACTGTGTGAAAACCTACATTTCTACTCCCT
1 ACCATCTTGCCTCACTACTGTGTGAAAACCTACATTTCTACTCCCT
29855612 ACCATCTTGCCTCACTACTGTGTGAAAACCTACATTTCTACTCCCT
1 ACCATCTTGCCTCACTACTGTGTGAAAACCTACATTTCTACTCCCT
29855658 A
1 A
29855659 TCCTTTTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.25, C:0.34, G:0.09, T:0.32
Consensus pattern (46 bp):
ACCATCTTGCCTCACTACTGTGTGAAAACCTACATTTCTACTCCCT
Found at i:29864200 original size:14 final size:14
Alignment explanation
Indices: 29864183--29864216 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
29864173 TCATTTTTAA
29864183 TTTT-AAAATATATT
1 TTTTAAAAATA-ATT
29864197 TTTTAAAAATAATT
1 TTTTAAAAATAATT
29864211 TTTTAA
1 TTTTAA
29864217 TGTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAAAATAATT
Found at i:29873702 original size:6 final size:6
Alignment explanation
Indices: 29873691--29873731 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
29873681 ATATTTATTA
29873691 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
29873732 AATAATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:29877334 original size:22 final size:22
Alignment explanation
Indices: 29877277--29877335 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
29877267 ACATATCGTG
*
29877277 TAACATATCATAACACATCTCA
1 TAACATATCATAGCACATCTCA
*
29877299 TAACATATCTTAGCA-AGTCTCA
1 TAACATATCATAGCACA-TCTCA
29877321 -AATCATATCATAGCA
1 TAA-CATATCATAGCA
29877336 TATCGCATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.09
22 29 0.91
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (22 bp):
TAACATATCATAGCACATCTCA
Found at i:29877370 original size:22 final size:22
Alignment explanation
Indices: 29877322--29877372 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
29877312 CAAGTCTCAA
* *
29877322 ATCATATCATAGCATATCGCAT
1 ATCATATCATAGCATAACACAT
* **
29877344 GTCATATTGTAGCATAACACAT
1 ATCATATCATAGCATAACACAT
29877366 ATCATAT
1 ATCATAT
29877373 ATTAACATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCATATCATAGCATAACACAT
Found at i:29890644 original size:19 final size:21
Alignment explanation
Indices: 29890622--29890664 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
29890612 TATATTAACT
*
29890622 TATATCATATAAT-ATA-AAA
1 TATATAATATAATAATATAAA
*
29890641 TATATAATATTATAATATAAA
1 TATATAATATAATAATATAAA
29890662 TAT
1 TAT
29890665 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 3 0.15
21 6 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TATATAATATAATAATATAAA
Found at i:29890645 original size:14 final size:15
Alignment explanation
Indices: 29890628--29890674 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
29890618 AACTTATATC
29890628 ATATAATA-TAAAAT
1 ATATAATATTAAAAT
*
29890642 ATATAATATTATAAT
1 ATATAATATTAAAAT
*
29890657 ATA-AATATTAAAAA
1 ATATAATATTAAAAT
29890671 ATAT
1 ATAT
29890675 TTTGAGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATAATATTAAAAT
Found at i:29891515 original size:31 final size:28
Alignment explanation
Indices: 29891469--29891532 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
29891459 AATCTCAAAA
* *
29891469 TTATATAAAATTTTGATTTAATATGTAATT
1 TTATACAAAATTTTGAATT--TATGTAATT
*
29891499 TTATACAAGAATTTTGAATTTGTGTAATT
1 TTATACAA-AATTTTGAATTTATGTAATT
29891528 TTATA
1 TTATA
29891533 TGTGAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 13 0.43
30 7 0.23
31 10 0.33
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (28 bp):
TTATACAAAATTTTGAATTTATGTAATT
Found at i:29894081 original size:135 final size:135
Alignment explanation
Indices: 29893839--29894249 Score: 687
Period size: 135 Copynumber: 3.0 Consensus size: 135
29893829 AGTGGGAGGC
29893839 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
*
29893904 CGAGTTTGAAGCAGACAAATCAGATCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCCGGTT
66 CGAGTTTGAAGCAGACAAATCAGATCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCCAGTT
29893969 TTTCT
131 TTTCT
* * *
29893974 TCTGGATCATATTGTCTATATCCGACGGTATTAGTTTCATTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
* * * * *
29894039 CAAGTTTGAAGCAGAAAAATCGGATCCTCCATCTTTTTTGGCCCAATTCCTCGTCTTTTCCTGTT
66 CGAGTTTGAAGCAGACAAATCAGATCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCCAGTT
29894104 TTTCT
131 TTTCT
*
29894109 TCTGGATCATATTGTCTATGTCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
1 TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
* *
29894174 CGAGTTTGAAGCAGACGAATCAGATCCTCCTCCATCTTTCTTGGCCCAATTCCTCGACTTTTCCA
66 CGAGTTTGAAGCAGACAAATCAGA---TCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCCA
29894239 GTTTTTCT
128 GTTTTTCT
29894247 TCT
1 TCT
29894250 CTAGTTGCTT
Statistics
Matches: 254, Mismatches: 19, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
135 208 0.82
138 46 0.18
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (135 bp):
TCTGGATCATATTGTCTATATCCAATGGTATTAGTTTCGTTATTATTAACAGCATTCACCTGCCT
CGAGTTTGAAGCAGACAAATCAGATCCTCCATCTTTCTTGGCCCAATTCCTCGTCTTTTCCAGTT
TTTCT
Found at i:29897257 original size:24 final size:24
Alignment explanation
Indices: 29897229--29897304 Score: 152
Period size: 24 Copynumber: 3.2 Consensus size: 24
29897219 ATTGGAGAAC
29897229 ATAAACTTTAATCTTAGCAACGAA
1 ATAAACTTTAATCTTAGCAACGAA
29897253 ATAAACTTTAATCTTAGCAACGAA
1 ATAAACTTTAATCTTAGCAACGAA
29897277 ATAAACTTTAATCTTAGCAACGAA
1 ATAAACTTTAATCTTAGCAACGAA
29897301 ATAA
1 ATAA
29897305 GGATGTCCCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (24 bp):
ATAAACTTTAATCTTAGCAACGAA
Found at i:29898516 original size:83 final size:82
Alignment explanation
Indices: 29898377--29898618 Score: 405
Period size: 83 Copynumber: 2.9 Consensus size: 82
29898367 TAGTCATGAG
*
29898377 TGTTCACCAAATAAGTTCATAAAAAATGACAATTTCAAATAAATTAAAAGCAATTAAA-AGTATA
1 TGTTCACCAAATAAGTTCAT-AAAAATGACAATTTAAAATAAATTAAAAGCAATTAAATA-TATA
29898441 CATTAACCAAATTCAATTA
64 CATTAACCAAATTCAATTA
* * *
29898460 TGTTCACCGAATAAGTTCATAAAAAGTAACAATTTAAAATAAATTAAAAGCCATTAAATATATAC
1 TGTTCACCAAATAAGTTCATAAAAA-TGACAATTTAAAATAAATTAAAAGCAATTAAATATATAC
29898525 ATTAACCAAATTCAATTA
65 ATTAACCAAATTCAATTA
29898543 TGTTCACCAAATAAGTTCATAAAAATGACAATTTAAAATAAATTAAAAGCAATTAAATATATACA
1 TGTTCACCAAATAAGTTCATAAAAATGACAATTTAAAATAAATTAAAAGCAATTAAATATATACA
*
29898608 TTAACCGAATT
66 TTAACCAAATT
29898619 TAAATTGCCG
Statistics
Matches: 149, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
82 53 0.36
83 95 0.64
84 1 0.01
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (82 bp):
TGTTCACCAAATAAGTTCATAAAAATGACAATTTAAAATAAATTAAAAGCAATTAAATATATACA
TTAACCAAATTCAATTA
Found at i:29902046 original size:31 final size:31
Alignment explanation
Indices: 29902011--29902072 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
29902001 TTAGAGGAGA
29902011 ATGAAAGAAATAATGAAAACTTGATAGAGCT
1 ATGAAAGAAATAATGAAAACTTGATAGAGCT
*
29902042 ATGAAAGAAATGATGAAAACTTGATAGAGCT
1 ATGAAAGAAATAATGAAAACTTGATAGAGCT
29902073 CATTGACACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.23
Consensus pattern (31 bp):
ATGAAAGAAATAATGAAAACTTGATAGAGCT
Found at i:29911624 original size:9 final size:9
Alignment explanation
Indices: 29911610--29911640 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29911600 GTAGTGATTC
*
29911610 AATTCGGGT
1 AATTCGGTT
29911619 AATTCGGTT
1 AATTCGGTT
29911628 AATTCGGTT
1 AATTCGGTT
29911637 AATT
1 AATT
29911641 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:29916878 original size:18 final size:19
Alignment explanation
Indices: 29916855--29916890 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29916845 ATCTAAGAAA
29916855 ATTAAAAATTAT-TAAATT
1 ATTAAAAATTATATAAATT
*
29916873 ATTAAAAGTTATATAAAT
1 ATTAAAAATTATATAAAT
29916891 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTAAAAATTATATAAATT
Found at i:29921121 original size:16 final size:16
Alignment explanation
Indices: 29921100--29921141 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29921090 TTATTAAATT
*
29921100 ATATATTTTAATTATA
1 ATATATTTTAATAATA
29921116 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
29921131 AT-TATGTTTAA
1 ATATAT-TTTAA
29921142 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:29921126 original size:15 final size:15
Alignment explanation
Indices: 29921091--29921132 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29921081 NNNAGAATTT
*
29921091 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29921105 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29921119 TATTTAATAATAAT
1 TATTTAATTATAAT
29921133 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29921377 original size:16 final size:16
Alignment explanation
Indices: 29921356--29921409 Score: 99
Period size: 16 Copynumber: 3.4 Consensus size: 16
29921346 TTGATTTGCT
*
29921356 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
29921372 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
29921388 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
29921404 ATTACA
1 ATTACA
29921410 GCGAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:29928405 original size:18 final size:19
Alignment explanation
Indices: 29928370--29928416 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
29928360 CTAAAAATAA
29928370 TTAAAATATTATAAAAAAT-
1 TTAAAAT-TTATAAAAAATC
**
29928389 TTAAAATTTATGGAAAATC
1 TTAAAATTTATAAAAAATC
29928408 TATAAAATT
1 T-TAAAATT
29928417 AATTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 7 0.29
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
TTAAAATTTATAAAAAATC
Found at i:29928527 original size:19 final size:19
Alignment explanation
Indices: 29928505--29928642 Score: 68
Period size: 19 Copynumber: 6.8 Consensus size: 19
29928495 ATTTTAAAAC
29928505 ATTATAAAAACTATTAAAT
1 ATTATAAAAACTATTAAAT
*
29928524 ATTATAAAATATTATTAAGAT
1 ATTATAAAA-ACTATTAA-AT
* *
29928545 CTTATGAAAA-TATTAAATAGAT
1 ATTATAAAAACTATT--A-A-AT
*
29928567 ATTATAAAAAAT-TTAGAAT
1 ATTATAAAAACTATTA-AAT
29928586 ATTATATAAAA-TAATTAAA-
1 ATTATA-AAAACT-ATTAAAT
* * *
29928605 ATGATAAAATCTATAAAAATT
1 ATTATAAAAACTAT-TAAA-T
*
29928626 GTTATAAAAACTTATTA
1 ATTATAAAAAC-TATTA
29928643 GAAGTATATT
Statistics
Matches: 92, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
18 5 0.05
19 31 0.34
20 16 0.17
21 22 0.24
22 17 0.18
23 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (19 bp):
ATTATAAAAACTATTAAAT
Found at i:29928576 original size:22 final size:21
Alignment explanation
Indices: 29928505--29928603 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 21
29928495 ATTTTAAAAC
29928505 ATTATAAAAACTATT-A-A-AT
1 ATTATAAAAA-TATTAATAGAT
*
29928524 ATTAT-AAAATATTATTAAGAT
1 ATTATAAAAATATTAAT-AGAT
* *
29928545 CTTATGAAAATATTAAATAGAT
1 ATTATAAAAATATT-AATAGAT
29928567 ATTATAAAAA-ATT--TAGAAT
1 ATTATAAAAATATTAATAG-AT
29928586 ATTATATAAAATAATTAA
1 ATTATA-AAAAT-ATTAA
29928604 AATGATAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
17 4 0.06
18 7 0.11
19 13 0.21
20 5 0.08
21 9 0.14
22 23 0.37
23 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (21 bp):
ATTATAAAAATATTAATAGAT
Found at i:29928934 original size:21 final size:22
Alignment explanation
Indices: 29928902--29928956 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
29928892 GTATAAAGAA
29928902 AATTATAAAAAAAATTATAA-GTT
1 AATTA-AAAAAAAATTA-AATGTT
*
29928925 -ATTAAAAAAATATTAAATGTT
1 AATTAAAAAAAAATTAAATGTT
*
29928946 AATTTAAAAAA
1 AATTAAAAAAA
29928957 TACTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 13 0.46
22 13 0.46
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
AATTAAAAAAAAATTAAATGTT
Found at i:29928954 original size:22 final size:22
Alignment explanation
Indices: 29928902--29928958 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
29928892 GTATAAAGAA
*
29928902 AATTATAAAAAAAATTATAAGTT
1 AATT-TAAAAAATATTATAAGTT
*
29928925 -ATTAAAAAAATATTA-AATGTT
1 AATTTAAAAAATATTATAA-GTT
29928946 AATTTAAAAAATA
1 AATTTAAAAAATA
29928959 CTATTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 13 0.45
22 14 0.48
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
AATTTAAAAAATATTATAAGTT
Found at i:29929397 original size:2 final size:2
Alignment explanation
Indices: 29929390--29929418 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29929380 GTTGTGTTCA
29929390 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
29929419 ATAAATGAGT
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:29931081 original size:31 final size:31
Alignment explanation
Indices: 29931007--29931083 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 31
29930997 TTAGGTAATG
* *
29931007 AAATATATTTTAGGTACTACTTGTGACAAAA
1 AAATATAGTTTAGGTACTAATTGTGACAAAA
* *
29931038 AAA-A-GGTTTAGGTACTAATT-TGAGAAAA
1 AAATATAGTTTAGGTACTAATTGTGACAAAA
29931066 ACAATATAGTTTAGGTAC
1 A-AATATAGTTTAGGTAC
29931084 CATTTTATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 8 0.21
29 15 0.39
30 2 0.05
31 13 0.34
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (31 bp):
AAATATAGTTTAGGTACTAATTGTGACAAAA
Found at i:29935532 original size:17 final size:19
Alignment explanation
Indices: 29935496--29935538 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
29935486 CGAAATTAAG
29935496 AGAAATAAGAATGAGAGAGA
1 AGAAA-AAGAATGAGAGAGA
29935516 AGAAAAAGAA-GAG-GAGA
1 AGAAAAAGAATGAGAGAGA
*
29935533 ATAAAA
1 AGAAAA
29935539 TCGAAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 3 0.14
19 5 0.23
20 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.28, T:0.07
Consensus pattern (19 bp):
AGAAAAAGAATGAGAGAGA
Found at i:29936569 original size:19 final size:19
Alignment explanation
Indices: 29936518--29936569 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29936508 AGTGATATGG
**
29936518 CAACAAAATAATGATAAAA
1 CAACAAAATAATGGGAAAA
*
29936537 CAACAAAACAATGGGAAAA
1 CAACAAAATAATGGGAAAA
*
29936556 CAAGAAAATAATGG
1 CAACAAAATAATGG
29936570 ATTTTTTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.63, C:0.12, G:0.13, T:0.12
Consensus pattern (19 bp):
CAACAAAATAATGGGAAAA
Found at i:29942092 original size:21 final size:21
Alignment explanation
Indices: 29942067--29942225 Score: 176
Period size: 21 Copynumber: 7.6 Consensus size: 21
29942057 TTGTTTTACT
*
29942067 TTCTGTTTAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
29942088 TTCTGATT-AACTCTTACGAGT
1 TTCTG-TTCAGCTCTTATGAGC
*
29942109 TTCTGTTTAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * *
29942130 TTCTGTTAAACTCTTATGAGT
1 TTCTGTTCAGCTCTTATGAGC
*
29942151 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTATGAGC
* * * *
29942172 TTCTGTTCAACTGTTAAGAGT
1 TTCTGTTCAGCTCTTATGAGC
29942193 TTCTGTTCAGCTCTTATGAGC
1 TTCTGTTCAGCTCTTATGAGC
*
29942214 TTCTGTTAAGCT
1 TTCTGTTCAGCT
29942226 TTCGAGCTTC
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
20 2 0.02
21 110 0.96
22 2 0.02
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTATGAGC
Found at i:29942113 original size:42 final size:42
Alignment explanation
Indices: 29942066--29942222 Score: 235
Period size: 42 Copynumber: 3.7 Consensus size: 42
29942056 CTTGTTTTAC
* *
29942066 TTTCTGTTTAGCTCTTATGAGCTTCTGATT-AACTCTTACGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTG-TTAAACTCTTAAGAG
* *
29942108 TTTCTGTTTAGCTCTTATGAGCTTCTGTTAAACTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTAAACTCTTAAGAG
* * *
29942150 TTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACTGTTAAGAG
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTAAACTCTTAAGAG
29942192 TTTCTGTTCAGCTCTTATGAGCTTCTGTTAA
1 TTTCTGTTCAGCTCTTATGAGCTTCTGTTAA
29942223 GCTTTCGAGC
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
41 2 0.02
42 104 0.98
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.45
Consensus pattern (42 bp):
TTTCTGTTCAGCTCTTATGAGCTTCTGTTAAACTCTTAAGAG
Found at i:29942166 original size:63 final size:62
Alignment explanation
Indices: 29942067--29942236 Score: 200
Period size: 63 Copynumber: 2.7 Consensus size: 62
29942057 TTGTTTTACT
* * * * * *
29942067 TTCTGTTTAGCTCTTATGAGCTTCTGATTAACTCTTACGAGTTTCTGTTTAGCTCTTATGAGC
1 TTCTGTTAAGCTCTTATGAGCTTCTG-TTAGCTCTTACGAGCTTCTGTTCAACTCTTAAGAGC
* * * *
29942130 TTCTGTTAAACTCTTATGAGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAACTGTTAAGAGT
1 TTCTGTTAAGCTCTTATGAGCTTCTGTT-AGCTCTTACGAGCTTCTGTTCAACTCTTAAGAGC
*
29942193 TTCTGTTCAGCTCTTATGAGCTTCTGTTAAGCT-TT-CGAGCTTCT
1 TTCTGTTAAGCTCTTATGAGCTTCTGTT-AGCTCTTACGAGCTTCT
29942237 ATTAGTGTAT
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
61 9 0.10
62 4 0.04
63 79 0.86
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.45
Consensus pattern (62 bp):
TTCTGTTAAGCTCTTATGAGCTTCTGTTAGCTCTTACGAGCTTCTGTTCAACTCTTAAGAGC
Found at i:29948066 original size:24 final size:24
Alignment explanation
Indices: 29948007--29948066 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
29947997 CCACTCATCG
*
29948007 CCTTATTTCTCATTCTCTCACATT
1 CCTTATTTCTCCTTCTCTCACATT
* *
29948031 CCTTATTTCTCCTTCTTTCACCTT
1 CCTTATTTCTCCTTCTCTCACATT
29948055 CCTTATTTCTCC
1 CCTTATTTCTCC
29948067 ATGTAGGAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.12, C:0.37, G:0.00, T:0.52
Consensus pattern (24 bp):
CCTTATTTCTCCTTCTCTCACATT
Found at i:29949925 original size:5 final size:5
Alignment explanation
Indices: 29949915--29949943 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
29949905 TATTAAATAT
29949915 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
29949944 TATTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:29950505 original size:12 final size:12
Alignment explanation
Indices: 29950488--29950521 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
29950478 TGGCCCGCCC
29950488 ATATTAATTTTT
1 ATATTAATTTTT
*
29950500 ATATTATTTTTT
1 ATATTAATTTTT
29950512 ATA-TAATTTT
1 ATATTAATTTT
29950522 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:29950689 original size:30 final size:30
Alignment explanation
Indices: 29950645--29950707 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
29950635 ACCTAATAAG
*
29950645 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
* *
29950675 CAAATGTCTTTAAAATAATAAAAAAATTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTAA
29950705 CAA
1 CAA
29950708 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAAAAAAATTAA
Found at i:29955252 original size:16 final size:14
Alignment explanation
Indices: 29955233--29955280 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 14
29955223 TTATATTACG
29955233 ATAAAATATAAGATAA
1 ATAAAA-ATAA-ATAA
*
29955249 ATAAAAAATACATTAA
1 AT-AAAAATA-AATAA
29955265 ATAAAAATAAATAA
1 ATAAAAATAAATAA
29955279 AT
1 AT
29955281 TGCATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 6 0.21
15 7 0.25
16 10 0.36
17 5 0.18
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (14 bp):
ATAAAAATAAATAA
Found at i:29957741 original size:27 final size:27
Alignment explanation
Indices: 29957693--29957758 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
29957683 ACATATTTTC
29957693 TCAAAATTTTA-TCAGGGATAAAATCA
1 TCAAAATTTTACTCAGGGATAAAATCA
*
29957719 TCAAAAATTTTACT-AGAGG-TAAAATCG
1 TC-AAAATTTTACTCAG-GGATAAAATCA
*
29957746 TCAAAGTTTTACT
1 TCAAAATTTTACT
29957759 GGGAGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 12 0.34
27 20 0.57
28 3 0.09
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (27 bp):
TCAAAATTTTACTCAGGGATAAAATCA
Found at i:29957766 original size:26 final size:26
Alignment explanation
Indices: 29957693--29957769 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 26
29957683 ACATATTTTC
*
29957693 TCAAAATTTTATCAGGGA-TAAAATCA
1 TCAAAATTTTA-CTGGGAGTAAAATCA
* *
29957719 TCAAAAATTTTACT-AGAGGTAAAATCG
1 TC-AAAATTTTACTGGGA-GTAAAATCA
*
29957746 TCAAAGTTTTACTGGGAGTAAAAT
1 TCAAAATTTTACTGGGAGTAAAAT
29957770 AGGGATGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 2 0.05
26 20 0.48
27 20 0.48
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (26 bp):
TCAAAATTTTACTGGGAGTAAAATCA
Found at i:29967820 original size:23 final size:23
Alignment explanation
Indices: 29967794--29967841 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
29967784 AATCAACACC
29967794 AGTGTTTCTTCAAAAGGAAACAA
1 AGTGTTTCTTCAAAAGGAAACAA
29967817 AGTGTTTCTTCAAAAGGAAACAA
1 AGTGTTTCTTCAAAAGGAAACAA
29967840 AG
1 AG
29967842 GCCAGGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (23 bp):
AGTGTTTCTTCAAAAGGAAACAA
Found at i:29973604 original size:11 final size:12
Alignment explanation
Indices: 29973571--29973611 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
29973561 CCACATTCGT
29973571 AAATATATGTAA
1 AAATATATGTAA
29973583 AAATATATGTAA
1 AAATATATGTAA
*
29973595 AAAT-TGTGTATA
1 AAATATATGTA-A
29973607 AAATA
1 AAATA
29973612 ATATATAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (12 bp):
AAATATATGTAA
Found at i:29977824 original size:15 final size:15
Alignment explanation
Indices: 29977804--29977832 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29977794 GAACATATTG
29977804 AAACTCAAAAATATC
1 AAACTCAAAAATATC
29977819 AAACTCAAAAATAT
1 AAACTCAAAAATAT
29977833 AATAAAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (15 bp):
AAACTCAAAAATATC
Found at i:29985977 original size:24 final size:24
Alignment explanation
Indices: 29985945--29986026 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
29985935 GTGCTTCCCA
29985945 TTAATTGCT-TTTCGGAGCTACCCG
1 TTAATTGCTCTTT-GGAGCTACCCG
*
29985969 TTAATTGCTCTTTGGAGCTACCCA
1 TTAATTGCTCTTTGGAGCTACCCG
* * *
29985993 TT-ATAGACTCTTTTTGAGCTTCCCG
1 TTAATTG-CTC-TTTGGAGCTACCCG
29986018 TTATATTGC
1 TTA-ATTGC
29986027 CCGGTTAAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 3 0.06
24 24 0.51
25 16 0.34
26 1 0.02
27 3 0.06
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.41
Consensus pattern (24 bp):
TTAATTGCTCTTTGGAGCTACCCG
Found at i:29990346 original size:12 final size:13
Alignment explanation
Indices: 29990321--29990348 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29990311 AAAAAATGAT
29990321 AAAATCTTCAAAA
1 AAAATCTTCAAAA
29990334 AAAATCTTCAAAA
1 AAAATCTTCAAAA
29990347 AA
1 AA
29990349 TAAAAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATCTTCAAAA
Found at i:29990737 original size:16 final size:16
Alignment explanation
Indices: 29990718--29990757 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
29990708 ATTTGATAAA
29990718 TATTAAATTATATTA-T
1 TATTAAATT-TATTATT
29990734 TATTTAAATTTATTATT
1 TA-TTAAATTTATTATT
29990751 TATTAAA
1 TATTAAA
29990758 AACAAGAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTAAATTTATTATT
Found at i:29991564 original size:21 final size:21
Alignment explanation
Indices: 29991534--29991579 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
29991524 GGTTTAGAGA
*
29991534 TTTTTTTATATT-TTTAAGTT
1 TTTTTTTATATTCTTTAAATT
29991554 TTTTTTATATATTCTTTAAATT
1 TTTTTT-TATATTCTTTAAATT
29991576 TTTT
1 TTTT
29991580 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 6 0.26
22 11 0.48
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTTTTATATTCTTTAAATT
Found at i:29997499 original size:9 final size:9
Alignment explanation
Indices: 29997485--29997513 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
29997475 GTCTCCCACG
29997485 TTAGGGTTT
1 TTAGGGTTT
29997494 TTAGGGTTT
1 TTAGGGTTT
29997503 TTAGGGTTT
1 TTAGGGTTT
29997512 TT
1 TT
29997514 GGAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.31, T:0.59
Consensus pattern (9 bp):
TTAGGGTTT
Found at i:29997869 original size:125 final size:124
Alignment explanation
Indices: 29997626--29998147 Score: 697
Period size: 125 Copynumber: 4.2 Consensus size: 124
29997616 TATAAAATCA
* * * * * *
29997626 AAGCAGGATGATTTATCAGAAGGATTTTTGAACTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
29997691 AGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTT-AAAAACGCTTC
* * * * * *
29997751 AAGTAGGATGCTTTGTGAGAAGAATTTGTGAAATCACGCCCTCGTGGATGCGCTTTTACTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
29997816 TGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTAAAAATGCTTC
66 AGGTCCTGGAA-AAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAACGCTTC
* * * *
29997876 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCTCCCACGTGGGCGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
29997941 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAATATAAAACAACGCTAT-
66 AGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGT-TTAAA-AACGCT-TC
* *
29998002 AAGCAGCATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * *
29998066 TTGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAACCGCTTC
65 TAGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAACGCTTC
*
29998126 TAGCAGGATGCTTTATGAGAAG
1 AAGCAGGATGCTTTATGAGAAG
29998148 TGTAACAGGT
Statistics
Matches: 341, Mismatches: 49, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
123 3 0.01
124 54 0.16
125 144 0.42
126 137 0.40
127 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (124 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAACGCTTC
Found at i:29998054 original size:126 final size:125
Alignment explanation
Indices: 29997626--29998147 Score: 683
Period size: 126 Copynumber: 4.2 Consensus size: 125
29997616 TATAAAATCA
* * * * * *
29997626 AAGCAGGATGATTTATCAGAAGGATTTTTGAACTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
29997691 AGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * * * * *
29997751 AAGTAGGATGCTTTGTGAGAAGAATTTGTGAAATCACGCCCTCGTGGATGCGCTTTTACTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * * *
29997816 TGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGT-TTAAAAATGCTTC
66 AGGTCCT-GAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * * *
29997876 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCTCCCACGTGGGCGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
29997941 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAATATAAAACAACGCTAT-
66 AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAA-AACGCT-TC
* *
29998002 AAGCAGCATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* * *
29998066 TTGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTAT-AAAACCGCTTC
65 TAGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
*
29998126 TAGCAGGATGCTTTATGAGAAG
1 AAGCAGGATGCTTTATGAGAAG
29998148 TGTAACAGGT
Statistics
Matches: 340, Mismatches: 50, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
123 3 0.01
124 57 0.17
125 138 0.41
126 139 0.41
127 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:29998084 original size:250 final size:250
Alignment explanation
Indices: 29997626--29998147 Score: 771
Period size: 250 Copynumber: 2.1 Consensus size: 250
29997616 TATAAAATCA
* * * * *
29997626 AAGCAGGATGATTTATCAGAAGGATTTTTGAACTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATAAGAAGAATTTGTGAACTCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
29997691 AGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTCAAGTA
66 AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAATATAAAAAACGCTTCAAGCA
* *
29997756 GGATGCTTTGTGAGAAGAATTTGTGAAATCACGCCCTCGTGGATGCGCTTTTACTACAGTTGGTC
131 GCATGCTTTGTGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTACTACAGTTGGTC
* * * *
29997821 CTGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTAAAAATGCTTC
196 CTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTC
* * *
29997876 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCTCCCACGTGGGCGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATAAGAAGAATTTGTGAACTCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
29997941 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAATATAAAACAACGCTAT-AAG
66 AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAATATAAAA-AACGCT-TCAAG
* *
29998005 CAGCATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTG
129 CAGCATGCT-TTGTGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTACTACAGTTG
*
29998069 GTCCTGGAA-AAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAACCGCTTC
193 GTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTC
* *
29998126 TAGCAGGATGCTTTATGAGAAG
1 AAGCAGGATGCTTTATAAGAAG
29998148 TGTAACAGGT
Statistics
Matches: 244, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
250 167 0.68
251 74 0.30
252 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (250 bp):
AAGCAGGATGCTTTATAAGAAGAATTTGTGAACTCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAATATAAAAAACGCTTCAAGCA
GCATGCTTTGTGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTACTACAGTTGGTC
CTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAACGCTTC
Found at i:29999601 original size:24 final size:22
Alignment explanation
Indices: 29999556--29999605 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
29999546 AATTTTGTTA
* *
29999556 TATATATATACATGCGTTTTTT
1 TATATATATACATGCATATTTT
29999578 TATATATATACATGTACATATTTT
1 TATATATATACATG--CATATTTT
29999602 TATA
1 TATA
29999606 CATTGTCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.58
24 10 0.42
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (22 bp):
TATATATATACATGCATATTTT
Found at i:30000312 original size:109 final size:106
Alignment explanation
Indices: 30000122--30000350 Score: 377
Period size: 109 Copynumber: 2.1 Consensus size: 106
30000112 TACGCATACT
* * *
30000122 AATATCCTTTTAAAAATTTCAAAATAAGGCAATGTTTTGTTTTGGAAATTCGAGAAAACGTGCCC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATATTTTGGTTTGGAAATTCAAGAAAACGTGCCC
*
30000187 TAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
66 TAATGTGCTGGGTTTCGA--CTTCTCGTTCGACCAAATAGCCA
*
30000230 AATATCCTTTTAAAAATTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCAAGAAAGCGTGCC
1 AATATCCTTTTAAAAATTTCAAAATAAGGCAATATTTTG-GTTTGGAAATTCAAGAAAACGTGCC
30000295 CTAATGTGCTGGGTTTCGACTTCTCGTTCGACCAAATAGCCA
65 CTAATGTGCTGGGTTTCGACTTCTCGTTCGACCAAATAGCCA
*
30000337 AATATCCTCTTAAA
1 AATATCCTTTTAAA
30000351 TCTAAATCCA
Statistics
Matches: 114, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
107 35 0.31
108 38 0.33
109 41 0.36
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (106 bp):
AATATCCTTTTAAAAATTTCAAAATAAGGCAATATTTTGGTTTGGAAATTCAAGAAAACGTGCCC
TAATGTGCTGGGTTTCGACTTCTCGTTCGACCAAATAGCCA
Found at i:30003913 original size:21 final size:21
Alignment explanation
Indices: 30003887--30004760 Score: 859
Period size: 21 Copynumber: 40.7 Consensus size: 21
30003877 TCAAATTATA
30003887 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
30003908 TTTAAGTTAAAGGTTTAGAGTT
1 TTTAAGTT-AAGGGTTAGGGTT
30003930 TTTAAGTTAAGGGTCTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* * *
30003952 TTAAAATTAAAGGTTTAGGG-T
1 TTTAAGTT-AAGGGTTAGGGTT
* *
30003973 TTTCAGATT-AGGGTTAGGTTT
1 TTTAAG-TTAAGGGTTAGGGTT
*
30003994 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
30004016 TTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
30004037 TTTAAGTTAAGGTTTTATGGTT
1 TTTAAGTTAAGG-GTTAGGGTT
30004059 TTTAAGTTAAGGGTCTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
*
30004081 TTTAAGTTAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
30004102 TTTAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
30004123 TTTAGGTT--GGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
30004142 TTTAAGTTAAAGGTTAGGGGT
1 TTTAAGTTAAGGGTTAGGGTT
*
30004163 TTTGAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
30004185 TTTAAGTTAAGGGTCTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* *
30004207 TTAAAGTTAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
30004228 GTTAGGTTAAGGGTTAGTGG-T
1 TTTAAGTTAAGGGTTAG-GGTT
*
30004249 TTTAGGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGG-TTAGGGTT
* *
30004270 TTTAATTTAAGGGTTAAGG-T
1 TTTAAGTTAAGGGTTAGGGTT
30004290 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
30004312 TTAAAGTTAAGGATTTAAGG-T
1 TTTAAGTTAAGG-GTTAGGGTT
* *
30004333 TTAAAGTT-AGGGTTTAGAG-T
1 TTTAAGTTAAGGG-TTAGGGTT
* **
30004353 TTTAGGTTAAGGGTTAATGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
30004374 TTTAGGTTAAGGGTTTAGAGTT
1 TTTAAGTTAAGGG-TTAGGGTT
30004396 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
30004418 TTAAAGTTAAGGTTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
30004439 TTCAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
30004460 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
**
30004482 TTTAAGTTAAGGGTTAGTTTT
1 TTTAAGTTAAGGGTTAGGGTT
*
30004503 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
30004525 TTTAGGTTAAGGGTTTAGGATT
1 TTTAAGTTAAGGG-TTAGGGTT
*
30004547 TTTAAGTTAAAGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
30004568 TTTAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
30004589 TTTAATTTAAGGGTTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
30004610 TTTAATTTAAGAGTTTAGAGTTT
1 TTTAAGTTAAG-GGTTAG-GGTT
* *
30004633 TTTAGGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
30004655 TTAAAGTTAATGGTTAGGGTTT
1 TTTAAGTTAAGGGTTAGGG-TT
* *
30004677 TAGGTTAAGGGTTTAGGGTTAGTGTT
1 T---TTAA--GTTAAGGGTTAGGGTT
* *
30004703 TTTAGGTTAAGGGTTTAGGGGT
1 TTTAAGTTAAGGG-TTAGGGTT
30004725 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
30004746 TTTAGGTTAAGGGTT
1 TTTAAGTTAAGGGTT
30004761 TAAGGTTTGT
Statistics
Matches: 711, Mismatches: 108, Indels: 68
0.80 0.12 0.08
Matches are distributed among these distances:
19 17 0.02
20 46 0.06
21 322 0.45
22 286 0.40
23 23 0.03
25 3 0.00
26 3 0.00
27 11 0.02
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.45
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:30004329 original size:8 final size:7
Alignment explanation
Indices: 30004213--30004439 Score: 50
Period size: 7 Copynumber: 32.3 Consensus size: 7
30004203 GGTTTTAAAG
30004213 TTAAGGT
1 TTAAGGT
*
30004220 TTAGGGT
1 TTAAGGT
*
30004227 TGTTAGG-
1 T-TAAGGT
*
30004234 TTAAGGG
1 TTAAGGT
*
30004241 TTAGTGGT
1 TTA-AGGT
*
30004249 TTTAGG-
1 TTAAGGT
30004255 TTAAGGGT
1 TTAA-GGT
*
30004263 TTAGGGTT
1 TTAAGG-T
30004271 TTAA--T
1 TTAAGGT
*
30004276 TTAAGGG
1 TTAAGGT
30004283 TTAAGGTT
1 TTAAGG-T
30004291 TTAA-G-
1 TTAAGGT
30004296 TTAAGGGT
1 TTAA-GGT
*
30004304 TTAGGGTT
1 TTAAGG-T
*
30004312 TTAAAG-
1 TTAAGGT
30004318 TTAAGGAT
1 TTAAGG-T
30004326 TTAAGGT
1 TTAAGGT
*
30004333 TTAAAG-
1 TTAAGGT
*
30004339 TTAGGGT
1 TTAAGGT
30004346 TT-AGAGT
1 TTAAG-GT
*
30004353 TTTAGG-
1 TTAAGGT
*
30004359 TTAAGGG
1 TTAAGGT
*
30004366 TTAATGTT
1 TTAA-GGT
*
30004374 TTTAGG-
1 TTAAGGT
30004380 TTAAGGGT
1 TTAA-GGT
*
30004388 TTAGAGTTT
1 TTA-AG-GT
30004397 TTAA-G-
1 TTAAGGT
30004402 TTAAGGGT
1 TTAA-GGT
*
30004410 TTAGGGTT
1 TTAAGG-T
*
30004418 TTAAAG-
1 TTAAGGT
30004424 TTAAGGT
1 TTAAGGT
*
30004431 TTATGGT
1 TTAAGGT
30004438 TT
1 TT
30004440 TCAGGTTAAG
Statistics
Matches: 157, Mismatches: 34, Indels: 58
0.63 0.14 0.23
Matches are distributed among these distances:
5 13 0.08
6 30 0.19
7 58 0.37
8 51 0.32
9 5 0.03
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (7 bp):
TTAAGGT
Found at i:30004689 original size:14 final size:13
Alignment explanation
Indices: 30004666--30004718 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
30004656 TAAAGTTAAT
30004666 GGTTAGGGTTTTA
1 GGTTAGGGTTTTA
30004679 GGTTAAGGG-TTTA
1 GGTT-AGGGTTTTA
*
30004692 GGGTTAGTGTTTTTA
1 -GGTTAG-GGTTTTA
30004707 GGTTAAGGGTTT
1 GGTT-AGGGTTT
30004719 AGGGGTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 10 0.30
14 17 0.52
15 6 0.18
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (13 bp):
GGTTAGGGTTTTA
Found at i:30004712 original size:28 final size:27
Alignment explanation
Indices: 30004666--30004722 Score: 96
Period size: 28 Copynumber: 2.1 Consensus size: 27
30004656 TAAAGTTAAT
30004666 GGTTAGGGTTTTAGGTTAAGGGTTTAG
1 GGTTAGGGTTTTAGGTTAAGGGTTTAG
*
30004693 GGTTAGTGTTTTTAGGTTAAGGGTTTAG
1 GGTTAG-GGTTTTAGGTTAAGGGTTTAG
30004721 GG
1 GG
30004723 GTTTTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.18, C:0.00, G:0.40, T:0.42
Consensus pattern (27 bp):
GGTTAGGGTTTTAGGTTAAGGGTTTAG
Found at i:30004762 original size:43 final size:43
Alignment explanation
Indices: 30003887--30004760 Score: 956
Period size: 43 Copynumber: 20.3 Consensus size: 43
30003877 TCAAATTATA
* *
30003887 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
30003930 TTTAAGTTAAGGGTCTAGGGTTTTAAAATTAAAGGTTTAGGG-T
1 TTTAAGTTAAGGGT-TAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
30003973 TTTCAGATT-AGGGTTAGGTTTTTTAGGTTAAGGGTTTAGGGTT
1 TTTAAG-TTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
30004016 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGTTTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
30004059 TTTAAGTTAAGGGTCTAGGGTTTTTAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
30004102 TTTAGGTTAAGGGTTAGGGTTTTTAGGTT---GGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
30004142 TTTAAGTTAAAGGTTAGGGGTTTTGAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
30004185 TTTAAGTTAAGGGTCTAGGGTTTTAAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
30004228 GTTAGGTTAAGGGTTAGTGG-TTTTAGGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTAG-GGTTTTTAAGTTAAGGGTTTAGGGTT
* *
30004270 TTTAATTTAAGGGTTAAGG-TTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * *
30004312 TTAAAGTTAAGGATTTAAGG-TTTAAAGTT-AGGGTTTAGAG-T
1 TTTAAGTTAAGG-GTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* ** * *
30004353 TTTAGGTTAAGGGTTAATGTTTTTAGGTTAAGGGTTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
30004396 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAA-GGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
30004439 TTCAGGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
** *
30004482 TTTAAGTTAAGGGTTAGTTTTTTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
30004525 TTTAGGTTAAGGGTTTAGGATTTTTAAGTTAAAGG-TTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
30004568 TTTAGGTTAAGGGTTAGGGTTTTTAATTTAAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * * *
30004610 TTTAATTTAAGAGTTTAGAGTTTTTTAGGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAG-GGTTAG-GGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
30004655 TTAAAGTTAATGGTTAGGG-TTTTAGGTTAAGGGTTTAGGGTTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTA--G---G-GTT
* *
30004703 TTTAGGTTAAGGGTTTAGGGGTTTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
30004746 TTTAGGTTAAGGGTT
1 TTTAAGTTAAGGGTT
30004761 TAAGGTTTGT
Statistics
Matches: 709, Mismatches: 92, Indels: 61
0.82 0.11 0.07
Matches are distributed among these distances:
40 40 0.06
41 40 0.06
42 166 0.23
43 301 0.42
44 110 0.16
45 16 0.02
47 1 0.00
48 13 0.02
49 9 0.01
50 13 0.02
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.45
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:30005339 original size:18 final size:18
Alignment explanation
Indices: 30005313--30005378 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
30005303 GACTCGAAAA
* *
30005313 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
30005331 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
30005349 AGGTTAGGATACATAAAAGGGCT
1 AGG--A--A-ACATAAAAGGGCT
30005372 AGGAAAC
1 AGGAAAC
30005379 GCACCTGGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 20 0.51
19 1 0.03
20 1 0.03
21 1 0.03
23 16 0.41
ACGTcount: A:0.44, C:0.09, G:0.29, T:0.18
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:30005357 original size:23 final size:23
Alignment explanation
Indices: 30005327--30005374 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
30005317 AACATATAAG
30005327 GGTTAGGATACATAAAAGGGCTA
1 GGTTAGGATACATAAAAGGGCTA
30005350 GGTTAGGATACATAAAAGGGCTA
1 GGTTAGGATACATAAAAGGGCTA
30005373 GG
1 GG
30005375 AAACGCACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (23 bp):
GGTTAGGATACATAAAAGGGCTA
Found at i:30005977 original size:7 final size:7
Alignment explanation
Indices: 30005967--30006006 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
30005957 TTATATACAT
30005967 AATACTA
1 AATACTA
30005974 AATACTA
1 AATACTA
30005981 AATACTA
1 AATACTA
30005988 AATACTA
1 AATACTA
30005995 AATACTA
1 AATACTA
30006002 AATAC
1 AATAC
30006007 CAATCGACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:30006211 original size:20 final size:20
Alignment explanation
Indices: 30006174--30006211 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30006164 TTTATTTTTA
*
30006174 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
30006194 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
30006212 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:30007211 original size:51 final size:51
Alignment explanation
Indices: 30007150--30007247 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
30007140 AATTATTTAA
*
30007150 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGGAAATTGAAAAT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAACTTGAGAGCAAATTGAAAAT
* * * *
30007201 AAATATGGATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGA
30007248 GAGAAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.26, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAAAAT
Found at i:30007223 original size:11 final size:11
Alignment explanation
Indices: 30007209--30007283 Score: 68
Period size: 11 Copynumber: 6.7 Consensus size: 11
30007199 ATAAATATGG
30007209 ATTTGAGAGAA
1 ATTTGAGAGAA
*
30007220 ATTTTGA-AGGA
1 A-TTTGAGAGAA
30007231 ATTTGAGAGCAA
1 ATTTGAGAG-AA
30007243 A-TTGAGAGAAA
1 ATTTGAGAG-AA
30007254 ATTT-AGAAGAA
1 ATTTGAG-AGAA
30007265 A-TTGAGAGGAA
1 ATTTGAGA-GAA
30007276 ATTTGAGA
1 ATTTGAGA
30007284 TAGGATTAGT
Statistics
Matches: 53, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
10 8 0.15
11 28 0.53
12 17 0.32
ACGTcount: A:0.45, C:0.01, G:0.27, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:30007248 original size:33 final size:34
Alignment explanation
Indices: 30007209--30007283 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 34
30007199 ATAAATATGG
* *
30007209 ATTTGAGAG-AAATTTTGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAAATTTAGAA-GAAATTGAGAGCAA
*
30007243 A-TTGAGAGAAAATTTAGAAGAAATTGAGAGGAA
1 ATTTGAGAGAAAATTTAGAAGAAATTGAGAGCAA
30007276 ATTTGAGA
1 ATTTGAGA
30007284 TAGGATTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.45, C:0.01, G:0.27, T:0.27
Consensus pattern (34 bp):
ATTTGAGAGAAAATTTAGAAGAAATTGAGAGCAA
Found at i:30008498 original size:12 final size:12
Alignment explanation
Indices: 30008452--30008499 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
30008442 ATTTAATCAC
30008452 TTTAATATTAAA
1 TTTAATATTAAA
30008464 -TTAATA-TAATA
1 TTTAATATTAA-A
* *
30008475 TTTATTACTAAA
1 TTTAATATTAAA
30008487 TTTAATATTAAA
1 TTTAATATTAAA
30008499 T
1 T
30008500 CTTGTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
12 17 0.57
13 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:30008598 original size:25 final size:25
Alignment explanation
Indices: 30008544--30008598 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
30008534 AAACATTAAA
*
30008544 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
30008569 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
30008593 TATTAA
1 T-TTAA
30008599 GACAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:30010252 original size:16 final size:16
Alignment explanation
Indices: 30010231--30010261 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30010221 CTATGCATAC
*
30010231 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
30010247 AAAATACAAAAGACA
1 AAAATACAAAAGACA
30010262 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:30016880 original size:30 final size:30
Alignment explanation
Indices: 30016846--30016910 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
30016836 ACTTGTTTTA
30016846 TTGTTAATTTTGTTATTATTTTAGAAGCAT
1 TTGTTAATTTTGTTATTATTTTAGAAGCAT
30016876 TTGTTAATTTTGTTATTATTTTAGAAGCAT
1 TTGTTAATTTTGTTATTATTTTAGAAGCAT
30016906 TTGTT
1 TTGTT
30016911 TGTTAAGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAAGCAT
Found at i:30025474 original size:34 final size:34
Alignment explanation
Indices: 30025397--30025480 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 34
30025387 AAATAAAATG
* *
30025397 AAAATATAAAAAATATGTATATGTATATACATTT
1 AAAATATAAAAAATATGAATATGTATATACATAT
* **
30025431 ACAGCATAAAAGAA-ATGAATATGTATATATC-TAT
1 AAAATATAAAA-AATATGAATATGTATATA-CATAT
*
30025465 AAAATATAAAATATAT
1 AAAATATAAAAAATAT
30025481 AAAAGCTAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
33 1 0.03
34 34 0.89
35 3 0.08
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (34 bp):
AAAATATAAAAAATATGAATATGTATATACATAT
Found at i:30027526 original size:174 final size:174
Alignment explanation
Indices: 30027306--30027809 Score: 893
Period size: 174 Copynumber: 2.9 Consensus size: 174
30027296 TATGGGAAGA
* *
30027306 CAAGATCTACTTT-TTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTTTCGATC
1 CAAGATCT-GTTTCTTT-GATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCGATC
* *
30027370 GATTCCACTGCCGACCGAGGAGGTAAAATTACTAGCTTCAATATACTCCACTGCAACTTCAGGGA
64 GATTCCACTGCCGACCGAGGAGGTAGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGA
30027435 GGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGG
129 GGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGG
30027481 CAAGATCTGTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCGATCGA
1 CAAGATCTGTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCGATCGA
30027546 TTCCACTGCCGACCGAGGAGGTAGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGAGG
66 TTCCACTGCCGACCGAGGAGGTAGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGAGG
30027611 TAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGG
131 TAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGG
**
30027655 CAAGATCTGTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTTTCGATCGA
1 CAAGATCTGTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCGATCGA
*
30027720 TTCCACTGCCGACCGGGGAGGTAGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGAGG
66 TTCCACTGCCGACCGAGGAGGTAGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGAGG
* * *
30027785 TAAAATCTGCCGTCTACGATCTGCT
131 TAAAATCCGCCATCTTCGATCTGCT
30027810 TTGCTGTCTA
Statistics
Matches: 318, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
174 307 0.97
175 11 0.03
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (174 bp):
CAAGATCTGTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTCGATCGA
TTCCACTGCCGACCGAGGAGGTAGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGAGG
TAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGG
Found at i:30028012 original size:132 final size:132
Alignment explanation
Indices: 30027719--30028905 Score: 1605
Period size: 132 Copynumber: 9.0 Consensus size: 132
30027709 TTTTCGATCG
* * * * * * *
30027719 ATTCCACTGCCGACCGGGGAGGTAGAATTACTGGCTTCAATATACTCCACTGCAACTTCAGGGAG
1 ATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
** * ** * * * * * **
30027784 GTAAAATCTGCCGTCTACGATCTGCT---TTGCTGTCTATGCAAGAAGACAAGATCTAAAATCTT
66 GTAAAATCCACCATCTTTGATCTGCTCCACTACTG-CT-T--AGGGAGATAAGATCTGTAATCTT
30027846 CAATCT
127 CAATCT
* *
30027852 ATTCCACTGCTGCCCAGGGAAATAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAG
1 ATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
* ** **
30027917 GTAAAATCCACCATCTTTGACCTGCTCCACTACTGCTTAGGGAGGCAAGATCTAAAATCTTCAAT
66 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
30027982 CT
131 CT
* *
30027984 ATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
1 ATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
* * * ** ***
30028049 GTAAAATTCGCCATCTTTGATTTGCTCCACTACTGCTTAGGGAGGCAAGATCCAAAATCTTCAAT
66 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
30028114 CT
131 CT
* ** *
30028116 ATTCCACTGCTGCCCAGGGAAGTAGAATTATTGGCTTCAATACACTCCACTGTAACCACAGGGAG
1 ATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
*
30028181 GTAAAATCTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
66 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
30028246 CT
131 CT
*
30028248 ATTCCACTGTTGCCCAGGG-AGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
1 ATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
30028312 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
65 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
30028377 TCT
130 TCT
* * *
30028380 ATTCCACTGTTGCCCAGGG-AGATAGAATTTCCGGCTTCAATGTACTCCACTGTAACCTCAGGGA
1 ATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
* * * * * * * *
30028444 GGTAAAATTCGCCATCCTTGATATGCTCCACTACTGCTTAGGGAAATAAAATTTATAATCTTCAA
65 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
30028509 TCT
130 TCT
* * * *
30028512 ATTCTACTGCTGCCGAAGGAAGTAGAATTACTGGTTTCAATGTACTCCACTGTAACCAT-AGGGA
1 ATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACC-TCAGGGA
* * * * *
30028576 GGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAAGGAGACAAGATCTGAAATCTTTAA
65 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
30028641 TCT
130 TCT
* * *
30028644 ATTCCACTGCTGCCCAGGG-AGATAGAATTACTGGCTTCAATATACTCCACTGCAACCTCAGTGA
1 ATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
* *
30028708 GGTAAAATCTACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
65 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAA
30028773 TCT
130 TCT
* *
30028776 ATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAG
1 ATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
* * *
30028841 GTAAAATCCGCCATCTTTGATCTGCTCTATTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
66 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
30028906 TTGCTTCGCT
Statistics
Matches: 945, Mismatches: 100, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
131 5 0.01
132 852 0.90
133 81 0.09
134 1 0.00
135 2 0.00
136 4 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
ATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT
CT
Found at i:30028299 original size:43 final size:44
Alignment explanation
Indices: 30028107--30028432 Score: 126
Period size: 44 Copynumber: 7.4 Consensus size: 44
30028097 GATCCAAAAT
* * **
30028107 CTTCAATCTATTCCACTGCTGCCCAGGGA-AGTAGAAT-TATTGG
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGA-TAGAATCTACCGG
** * * **
30028150 CTTCAATAC-ACTCCACTGTAACCACAGGGAGGTAAAATCTACCAT
1 CTTCAAT-CTACTCCACTGTTGCC-CAGGGAGATAGAATCTACCGG
** * ** ** *****
30028195 CTTTGATCTGCTCCACTACTGCTTAGGGAGATA-AGATCTGTAAT
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGA-ATCTACCGG
* *
30028239 CTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGAATCTACCGG
* ** * * * **
30028282 CTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCAT
1 CTTCAATCTACTCCACTGTTGCC-CAGGGAGATAGAATCTACCGG
** * ** ** *****
30028327 CTTTGATCTGCTCCACTACTGCTTAGGGAGATA-AGATCTGTAAT
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGA-ATCTACCGG
* *
30028371 CTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAAT-TTCCGG
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGAATCTACCGG
*
30028414 CTTCAATGTACTCCACTGT
1 CTTCAATCTACTCCACTGT
30028433 AACCTCAGGG
Statistics
Matches: 196, Mismatches: 76, Indels: 22
0.67 0.26 0.07
Matches are distributed among these distances:
43 57 0.29
44 106 0.54
45 33 0.17
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGAATCTACCGG
Done.