Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 7 of 322
Found at i:1672381 original size:5 final size:5
Alignment explanation
Indices: 1672371--1672438 Score: 66
Period size: 5 Copynumber: 13.0 Consensus size: 5
1672361 ACAACCTAAT
* * *
1672371 TTTTA TTTTA TTTTA GTTTA TTTTA TTTTTA TTTATT TTTTC TTATTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTT-TA TTTTA TT-TTA
1672419 TTTTA TTTT- TTCTTA TTTTA
1 TTTTA TTTTA TT-TTA TTTTA
1672439 AAATATTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 2 0.04
5 36 0.68
6 15 0.28
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1672392 original size:15 final size:14
Alignment explanation
Indices: 1672372--1672438 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 14
1672362 CAACCTAATT
1672372 TTTATTTTATTTTA
1 TTTATTTTATTTTA
1672386 GTTTATTTTATTTTTA
1 -TTTATTTTA-TTTTA
1672402 TTTATTTT-TTCTTA
1 TTTATTTTATT-TTA
*
1672416 -TTATTTTATTTTT
1 TTTATTTTATTTTA
1672429 TCTTATTTTA
1 T-TTATTTTA
1672439 AAATATTAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
13 11 0.24
14 5 0.11
15 25 0.54
16 5 0.11
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:1672445 original size:28 final size:28
Alignment explanation
Indices: 1672388--1672446 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1672378 TTATTTTAGT
****
1672388 TTATTTTATTTTTATTTATTTTTTCTTA
1 TTATTTTATTTTTATTTATTTTAAAATA
1672416 TTATTTTATTTTT-TCTTATTTTAAAATA
1 TTATTTTATTTTTAT-TTATTTTAAAATA
1672444 TTA
1 TTA
1672447 ATAAAATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (28 bp):
TTATTTTATTTTTATTTATTTTAAAATA
Found at i:1674033 original size:20 final size:20
Alignment explanation
Indices: 1674008--1674047 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1673998 TAATTTTAGG
1674008 ATTTATTT-TCATTTATCTTT
1 ATTTATTTGT-ATTTATCTTT
1674028 ATTTATTTGTATTTATCTTT
1 ATTTATTTGTATTTATCTTT
1674048 TACAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (20 bp):
ATTTATTTGTATTTATCTTT
Found at i:1679760 original size:26 final size:26
Alignment explanation
Indices: 1679728--1679777 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1679718 ATAAGGAAAA
*
1679728 TTTACAAATTTTTCATCTTCACAATT
1 TTTACAAATTTTACATCTTCACAATT
1679754 TTTACAAATTTTACATCTTCACAA
1 TTTACAAATTTTACATCTTCACAA
1679778 AAAATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTACAAATTTTACATCTTCACAATT
Found at i:1685427 original size:69 final size:69
Alignment explanation
Indices: 1685288--1685438 Score: 167
Period size: 69 Copynumber: 2.2 Consensus size: 69
1685278 TCGTTTTCTT
* * * * *
1685288 CAAGAAAAAGAGCCCCCTGTTGCTGGAAAAAAAAAACCGTCTGAAATGCTAAATAAACGACTTCT
1 CAAGAAAAAGAGCCACCTGTCGCTGGAAAAAAAAAACCGTCAGAAACGCTAAATAAACGACCTCT
1685353 ACTC
66 ACTC
* ** * * * * *
1685357 CAAGAAAAAGAGCCACCTGTCGCTGGACACGAAGAGCCGTCAGAAACGCTAGATCAACTACCTCT
1 CAAGAAAAAGAGCCACCTGTCGCTGGAAAAAAAAAACCGTCAGAAACGCTAAATAAACGACCTCT
*
1685422 CCTC
66 ACTC
*
1685426 CAAGGAAAAGAGC
1 CAAGAAAAAGAGC
1685439 GACATGTTCC
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.15
Consensus pattern (69 bp):
CAAGAAAAAGAGCCACCTGTCGCTGGAAAAAAAAAACCGTCAGAAACGCTAAATAAACGACCTCT
ACTC
Found at i:1685557 original size:69 final size:68
Alignment explanation
Indices: 1685464--1685661 Score: 256
Period size: 69 Copynumber: 2.9 Consensus size: 68
1685454 GTAAAGAGCG
* * *
1685464 GGAAATGCTAGATAAACAAGGTCGAAACCAAGAAAATGAGCTCCATGTTACCGGACATGAAGAGC
1 GGAAATGCTAGATAAAC-ACGTCGAATCCAAGAAAATGAGCTCCATGTTACTGGACATGAAGAGC
1685529 CATC
65 CATC
* *
1685533 GGAAATGCTAAATAAACGACGTCGACTCCAAGAAAATGAGCTCCATGTTGA-TGGACATGAAGAG
1 GGAAATGCTAGATAAAC-ACGTCGAATCCAAGAAAATGAGCTCCATGTT-ACTGGACATGAAGAG
*
1685597 CCCTC
64 CCATC
* * *
1685602 GGAAATACTAGATCAACAGCGTC-AACTCCAAGAAAATGAGCTCCATGTTGCTGGACATGA
1 GGAAATGCTAGATAAACA-CGTCGAA-TCCAAGAAAATGAGCTCCATGTTACTGGACATGA
1685662 GCTAGATAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
68 2 0.02
69 110 0.97
70 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (68 bp):
GGAAATGCTAGATAAACACGTCGAATCCAAGAAAATGAGCTCCATGTTACTGGACATGAAGAGCC
ATC
Found at i:1685727 original size:123 final size:123
Alignment explanation
Indices: 1685539--1685786 Score: 318
Period size: 123 Copynumber: 2.0 Consensus size: 123
1685529 CATCGGAAAT
** ** * *
1685539 GCTAAATAAACGACGTCGACTCCAAGAAAATGAGCTCCATGTTGATGGACATGAAGAGCCCTCGG
1 GCTAAATAAACGACGTCGACTCCAAGAAAACAAAATCCATGTTGACGGACATGAAGAGCCATCGG
* *
1685604 AAATACTAGATCAAC-AGCGTCAACTCCAAGAAAATGAGCTCCATGTTGCTGGACATGA
66 AAATACTAGATAAACGA-CGTCAACTCCAAGAAAATGAGCTCCAAGTTGCTGGACATGA
* * * **
1685662 GCTAGATAAACTAGGTCGACTCCAAGAAAACAAAATCCATGTTTCCGGACATGAAGAGCCATCGG
1 GCTAAATAAACGACGTCGACTCCAAGAAAACAAAATCCATGTTGACGGACATGAAGAGCCATCGG
** * * *
1685727 AAATGTTAGATAAACGACGTCGACTCCTAGAAAATGAGCTCCAAGTTGGTGGACATGA
66 AAATACTAGATAAACGACGTCAACTCCAAGAAAATGAGCTCCAAGTTGCTGGACATGA
1685785 GC
1 GC
1685787 AGCCATTAGA
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
123 105 0.99
124 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (123 bp):
GCTAAATAAACGACGTCGACTCCAAGAAAACAAAATCCATGTTGACGGACATGAAGAGCCATCGG
AAATACTAGATAAACGACGTCAACTCCAAGAAAATGAGCTCCAAGTTGCTGGACATGA
Found at i:1685824 original size:192 final size:192
Alignment explanation
Indices: 1685470--1685827 Score: 520
Period size: 192 Copynumber: 1.9 Consensus size: 192
1685460 AGCGGGAAAT
** **
1685470 GCTAGATAAACAAGGTCGAAACCAAGAAAATGAGCTCCATGTTACCGGACATGAAGAGCCATCGG
1 GCTAGATAAACAAGGTCGAAACCAAGAAAACAAAATCCATGTTACCGGACATGAAGAGCCATCGG
* *
1685535 AAATGCTAAATAAACGACGTCGACTCCAAGAAAATGAGCTCCATGTTGATGGACATGAAGAGCCC
66 AAATGCTAAATAAACGACGTCGACTCCAAGAAAATGAGCTCCAAGTTGATGGACATGAAGAGCCA
* *
1685600 TCGGAAATACTAGATCAACAGCGTCAACTCCAAGAAAATGAGCTCCATGTTGCTGGACATGA
131 TCAGAAATACTAGATAAACAGCGTCAACTCCAAGAAAATGAGCTCCATGTTGCTGGACATGA
* ** *
1685662 GCTAGATAAACTAGGTCGACTCCAAGAAAACAAAATCCATGTTTCCGGACATGAAGAGCCATCGG
1 GCTAGATAAACAAGGTCGAAACCAAGAAAACAAAATCCATGTTACCGGACATGAAGAGCCATCGG
* * * *
1685727 AAATGTTAGATAAACGACGTCGACTCCTAGAAAATGAGCTCCAAGTTGGTGGACATG-AGCAGCC
66 AAATGCTAAATAAACGACGTCGACTCCAAGAAAATGAGCTCCAAGTTGATGGACATGAAG-AGCC
* * * *
1685791 ATTAGAAATGCTAGATAAACGGCGTCGACTCCAAGAA
130 ATCAGAAATACTAGATAAACAGCGTCAACTCCAAGAA
1685828 CATATCGATG
Statistics
Matches: 145, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
191 2 0.01
192 143 0.99
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.19
Consensus pattern (192 bp):
GCTAGATAAACAAGGTCGAAACCAAGAAAACAAAATCCATGTTACCGGACATGAAGAGCCATCGG
AAATGCTAAATAAACGACGTCGACTCCAAGAAAATGAGCTCCAAGTTGATGGACATGAAGAGCCA
TCAGAAATACTAGATAAACAGCGTCAACTCCAAGAAAATGAGCTCCATGTTGCTGGACATGA
Found at i:1685875 original size:129 final size:128
Alignment explanation
Indices: 1685708--1687108 Score: 1475
Period size: 129 Copynumber: 10.9 Consensus size: 128
1685698 CCATGTTTCC
* * * * * *
1685708 GGACATGAAGAGCCATCGGAAATGTTAGATAAACGACGTCGACTCCTAGA-AAATGAGCTCCAAG
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAA-GAACTCCAAG
* * * *
1685772 TTGGTGGACATGAGCAGCCATTAGAAATGCTAGATAAACGGCGTCGACTCCAAGAACATATCGAT
65 TTGATGGACATGAG-AGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
1685837 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
* * *
1685902 TGATGGACATGGACAGCCCTCAGAAATGCTAGATAAACAGCGTCAACTCAAAGAACATATCGAT
66 TGATGGACAT-GAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
*
1685966 GGGCACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
*
1686031 TGATGGACATGGAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGA-
66 TGATGGACAT-GAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
* * * *
1686094 GAGACACAAAGAGCCCTTGGAAATGCTAGATAAACGACGTCGACTGCAAGAGAAAGAACTCCAAG
1 G-GACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAG
* *
1686159 TTGATAGACATGAAGAGCCCTCAGAAATGCTAGATAAACAGCGTC-ACCTCAAAGAACATATCGA
65 TTGATGGACATG-AGAGCCCTCAGAAATGCTAGATAAACGGCGTCGA-CTCAAAGAACATATCGA
1686223 T
128 T
*
1686224 GGGCACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
* *
1686289 TGATGGACATGAAAAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGAT
66 TGATGGACATG-AGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
* * * *
1686353 AGACACAAAGAGCCCTTGGAAATGCTAGATAAAAGACGTCGACTGCAAGAGAAAGAACTCCAAGT
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
1686418 TGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
66 TGATGGACATG-AGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
* *
1686482 GGACACGAAGAGCCTTCGGAAATGCTAGATAAAAGACGTCGACTTCAAGAGAAAGAACTCCAAGT
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
*
1686547 TGATAGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
66 TGATGGACATG-AGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
* * * * * * * *
1686611 CGACACGAAGAGACCTCGAAAATGCTAGATAAACGGCGTCGAAT-CAA-A-CAA-CA-T---A-T
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
* * * * * *
1686667 TGATGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAAAATGAGCTCC
66 TGATGGACATG-AGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACAT-A--T-C
1686732 AAGTTGAT
126 -----GAT
* * * * *
1686740 GGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACT-CAA-AG-AA-CA-T---A-T
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
* ** * * ** *
1686796 CGATGGACACAAAGAGCCCT-TGAAAATGCTAGATAAAAGATGTCTACTCCAAGAGAAAGAACTA
66 TGATGGACA-TGAGAGCCCTCAG-AAATGCTAGATAAACGGCGTCGACT-C-----AAAGAAC-A
* *
1686860 CAGGTTGAT
122 TA--TCGAT
* * * * *
1686869 GGACATGAAGAGCCCTCAGAAATGCTAGATAAACGACATCGACT-CAA-A-AAACATA-T-C-A-
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGA-ACTCCAAG
* * * * * * * *
1686927 ---ATGGACACGAAGAGCCCTCTGAAATGCTAGATAAAAGACGTCGACTCAAGGAAAATGTTGAT
65 TTGATGGACATG-AGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
* ** * * *
1686989 GGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGTCTCCAAGA-AAATGAGCTCCAAG
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAA-GAACTCCAAG
* * * * * *
1687053 TTGACGGACATGAAGAGCCCTC-GAAAATGCTATATAAAAGACATCGACTCCAAGAA
65 TTGATGGACATG-AGAGCCCTCAG-AAATGCTAGATAAACGGCGTCGACTCAAAGAA
1687109 AATGAGCTAC
Statistics
Matches: 1126, Mismatches: 103, Indels: 86
0.86 0.08 0.07
Matches are distributed among these distances:
120 98 0.09
121 5 0.00
122 5 0.00
123 8 0.01
124 3 0.00
125 2 0.00
126 2 0.00
127 1 0.00
128 9 0.01
129 971 0.86
130 10 0.01
131 2 0.00
132 1 0.00
135 8 0.01
136 1 0.00
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.17
Consensus pattern (128 bp):
GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
TGATGGACATGAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
Found at i:1686743 original size:258 final size:255
Alignment explanation
Indices: 1685708--1687363 Score: 1548
Period size: 258 Copynumber: 6.5 Consensus size: 255
1685698 CCATGTTTCC
* * * * * *
1685708 GGACATGAAGAGCCATCGGAAATGTTAGATAAACGACGTCGACTCCTAGA-AAATGAGCTCCAAG
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAA-GAACTCCAAG
* * * * *
1685772 TTGGTGGACATG-AGCAGCCATTAGAAATGCTAGATAAACGGCGTCGACTCCAAGAACATATCGA
65 TTGATGGACATGAAG-AGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGA
* * *
1685836 TGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAG
129 TAGACACGAAGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTGCAAGAGAAAGAACT-C-AG
* * *
1685901 TTGATGGACATGGACAGCCCTCAGAAATGCTAGATAAACAGCGTCAACTCAAAGAACATATCGAT
192 TTGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAA-AGCGTCGACTCAAAGAACATATCGAT
*
1685966 GGGCACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
* *
1686031 TGATGGACATGGAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGAGA
66 TGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGATA
* *
1686096 GACACAAAGAGCCCTTGGAAATGCTAGATAAACGACGTCGACTGCAAGAGAAAGAACTCCAAGTT
131 GACACGAAGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTGCAAGAGAAAGAACT-C-AGTT
*
1686161 GATAGACATGAAGAGCCCTCAGAAATGCTAGATAAACAGCGTC-ACCTCAAAGAACATATCGAT
194 GATGGACATGAAGAGCCCTCAGAAATGCTAGATAAA-AGCGTCGA-CTCAAAGAACATATCGAT
*
1686224 GGGCACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
*
1686289 TGATGGACATGAAAAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGATA
66 TGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGATA
* * *
1686354 GACACAAAGAGCCCTTGGAAATGCTAGATAAAAGACGTCGACTGCAAGAGAAAGAACTCCAAGTT
131 GACACGAAGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTGCAAGAGAAAGAACT-C-AGTT
*
1686419 GATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGAT
194 GATGGACATGAAGAGCCCTCAGAAATGCTAGATAAA-AGCGTCGACTCAAAGAACATATCGAT
* *
1686482 GGACACGAAGAGCCTTCGGAAATGCTAGATAAAAGACGTCGACTTCAAGAGAAAGAACTCCAAGT
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
* * *
1686547 TGATAGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATCGATC
66 TGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGATA
* * * * * *
1686612 GACACGAAGAGACCTCGAAAATGCTAGATAAACGGCGTCGAAT-CAA-A-CAA-CA-T-A-TTGA
131 GACACGAAGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTGCAAGAGAAAGAACTCAGTTGA
* * * *
1686670 TGGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAAAATGAGCTCCAAG
196 TGGACATGAAGAGCCCTCAGAAATGCTAGATAAAAG-CGTCGACTCAAAGAACAT-A--T-C---
1686735 TTGAT
253 --GAT
* * * * *
1686740 GGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACT-CAA-AG-AA-CA-T---A-T
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
* ** * * ** *
1686796 CGATGGACACAAAGAGCCCT-TGAAAATGCTAGATAAAAGATGTCTACTCCAAGAGAAAGAACTA
66 TGATGGACATGAAGAGCCCTCAG-AAATGCTAGATAAACGGCGTCGACT-C-----AAAGAAC-A
* * * * * *
1686860 CAGGTTGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGACATCGACT-CAA-A-AAACA
123 TA--TTGATAGACACGAAGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTGCAAGAGAAAGA
* * * *
1686922 TA-TCA----ATGGACACGAAGAGCCCTCTGAAATGCTAGATAAAAGACGTCGACTCAAGGAAAA
186 -ACTCAGTTGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAAAG-CGTCGACTCAAAGAACA
* *
1686982 TGTTGAT
249 TATCGAT
* ** * * *
1686989 GGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGTCTCCAAGA-AAATGAGCTCCAAG
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAA-GAACTCCAAG
* * * * *
1687053 TTGACGGACATGAAGAGCCCTC-GAAAATGCTATATAAAAGACATCGACTCCAAGAAAATGAGCT
65 TTGATGGACATGAAGAGCCCTCAG-AAATGCTAGATAAACGGCGTCGACT-C----AAA-GA---
* * * * ** * *
1687117 ACATGTTGCTAGACAC-AGAGAACTCTTTGAAATGCTAGATAAACGACGTCGACTCCAA-AAAAA
120 ACATATTGATAGACACGA-AGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTGCAAGAGAAA
* * * * * * * *
1687180 TGAGCTCCATGTTGTTAGACATCAAGAGCCCTC-GAAAATGCTAGA-AAATGAG-C--TTC-ATG
184 -GAACT-CA-GTTGATGGACATGAAGAGCCCTCAG-AAATGCTAGATAAAAGCGTCGACTCAAAG
*
1687239 ----T-T-GCT
245 AACATATCGAT
* * * * ** *
1687244 GGACATGAAGAGCCCTCGGAAATGCTAGATAAACGGCGTCAACTCCAAGA-AAATGGGCTCCATG
1 GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAA-GAACTCCAAG
* * * * * *
1687308 TTGCTGGACATGAAGAGGCGTCGGAAATGCTAGATAAACGACGTCGACTCCAAGAA
65 TTGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAA
1687364 GTTGAGCACC
Statistics
Matches: 1207, Mismatches: 136, Indels: 122
0.82 0.09 0.08
Matches are distributed among these distances:
246 1 0.00
248 2 0.00
249 134 0.11
250 9 0.01
251 3 0.00
252 1 0.00
253 3 0.00
254 4 0.00
255 109 0.09
256 7 0.01
257 14 0.01
258 861 0.71
259 10 0.01
260 6 0.00
261 7 0.01
262 4 0.00
264 1 0.00
265 1 0.00
266 5 0.00
267 25 0.02
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (255 bp):
GGACACGAAGAGCCCTCGGAAATGCTAGATAAAAGACGTCGACTCCAAGAGAAAGAACTCCAAGT
TGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACATATTGATA
GACACGAAGAGCCCTCGGAAATGCTAGATAAACGACGTCGACTGCAAGAGAAAGAACTCAGTTGA
TGGACATGAAGAGCCCTCAGAAATGCTAGATAAAAGCGTCGACTCAAAGAACATATCGAT
Found at i:1687041 original size:60 final size:60
Alignment explanation
Indices: 1686734--1687112 Score: 303
Period size: 60 Copynumber: 6.0 Consensus size: 60
1686724 TGAGCTCCAA
* * * * * *
1686734 GTTGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGGCGTCGACTCAAAGAACAT
1 GTTGATGGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCCAAGAAAAT
* * ** ** ** *
1686794 ATCGATGGACACAAAGAGCCCTTGAAAATGCTAGATAAAAGATGTCTACTCCAAGAGAAAGAACT
1 GTTGATGGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCC-A-AG-AA-AA-T
* * *
1686859 ACAGGTTGATGGACATGAAGAGCCCTCAGAAATGCTAGATAAACGACATCGACT-CAAAAAACAT
1 ----GTTGATGGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCCAAGAAA-AT
* ** * ** *
1686923 ATCAATGGACACGAAGAGCCCTCTGAAATGCTAGATAAAAGACGTCGACT-CAAGGAAAAT
1 GTTGATGGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCCAA-GAAAAT
*
1686983 GTTGATGGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGTCTCCAAGAAAATGAGCT
1 GTTGATGGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCCAAG-AAA--A--T
* * *
1687048 CCAAGTTGACGGACATGAAGAGCCCTCGAAAATGCTATATAAAAGACATCGACTCCAAGAAAAT
1 ----GTTGATGGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCCAAGAAAAT
1687112 G
1 G
1687113 AGCTACATGT
Statistics
Matches: 253, Mismatches: 45, Indels: 42
0.74 0.13 0.12
Matches are distributed among these distances:
60 132 0.52
61 10 0.04
62 2 0.01
63 3 0.01
64 4 0.02
65 5 0.02
66 2 0.01
67 1 0.00
68 4 0.02
69 90 0.36
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (60 bp):
GTTGATGGACATGAAGAGCCCTCAAAAATGCTAGATAAAAGACATCGACTCCAAGAAAAT
Found at i:1687249 original size:48 final size:48
Alignment explanation
Indices: 1687176--1687272 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
1687166 CGACTCCAAA
*
1687176 AAAATGAGCTCCATGTTGTTAGACATCAAGAGCCCTCGAAAATGCTAG
1 AAAATGAGCTCCATGTTGCTAGACATCAAGAGCCCTCGAAAATGCTAG
* * * *
1687224 AAAATGAGCTTCATGTTGCTGGACATGAAGAGCCCTCGGAAATGCTAG
1 AAAATGAGCTCCATGTTGCTAGACATCAAGAGCCCTCGAAAATGCTAG
1687272 A
1 A
1687273 TAAACGGCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (48 bp):
AAAATGAGCTCCATGTTGCTAGACATCAAGAGCCCTCGAAAATGCTAG
Found at i:1687318 original size:117 final size:117
Alignment explanation
Indices: 1687105--1687341 Score: 305
Period size: 117 Copynumber: 2.0 Consensus size: 117
1687095 ATCGACTCCA
* ** *
1687105 AGAAAATGAGCTACATGTTGCTAGACACAGAGAACTCTTTGAAATGCTAGATAAACGACGTCGAC
1 AGAAAATGAGCTACATGTTGCTAGACACAGAGAACCCTCGGAAATGCTAGATAAACGACGTCAAC
*
1687170 TCCAAAAAAATGAGCTCCATGTTGTTAGACATCAAGAGCCCTCGAAAATGCT
66 TCCAAAAAAATGAGCTCCATGTTGCTAGACATCAAGAGCCCTCGAAAATGCT
* * * * *
1687222 AGAAAATGAGCTTCATGTTGCTGGACA-TGAAGAGCCCTCGGAAATGCTAGATAAACGGCGTCAA
1 AGAAAATGAGCTACATGTTGCTAGACACAG-AGAACCCTCGGAAATGCTAGATAAACGACGTCAA
* * * * * * *
1687286 CTCCAAGAAAATGGGCTCCATGTTGCTGGACATGAAGAGGCGTCGGAAATGCT
65 CTCCAAAAAAATGAGCTCCATGTTGCTAGACATCAAGAGCCCTCGAAAATGCT
1687339 AGA
1 AGA
1687342 TAAACGACGT
Statistics
Matches: 102, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
116 1 0.01
117 101 0.99
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (117 bp):
AGAAAATGAGCTACATGTTGCTAGACACAGAGAACCCTCGGAAATGCTAGATAAACGACGTCAAC
TCCAAAAAAATGAGCTCCATGTTGCTAGACATCAAGAGCCCTCGAAAATGCT
Found at i:1687333 original size:69 final size:69
Alignment explanation
Indices: 1687222--1687573 Score: 379
Period size: 69 Copynumber: 5.1 Consensus size: 69
1687212 CGAAAATGCT
* * * * *
1687222 AGAAAATGAGCTTCATGTTGCTGGACATGAAGAGCCCTCGGAAATGCTAGATAAACGGCGTCAAC
1 AGAAAATGAGCTCCATGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTAC
1687287 TCCA
66 TCCA
* * * *
1687291 AGAAAATGGGCTCCATGTTGCTGGACATGAAGAGGCGTCGGAAATGCTAGATAAACGACGTCGAC
1 AGAAAATGAGCTCCATGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTAC
1687356 TCCA
66 TCCA
** * * * ** * *
1687360 AGAAGTTGAGCACCCTATTTTTGGACATGAAGAGCCGT-TGAAAGTGCTAGATAATATC--CGTT
1 AGAAAATGAGCTCCATGTTGCTGGACATGAAGAGCCGTCAGAAA-TGCTAGATAA-A-CGACGTC
*
1687422 TACTCCG
63 TACTCCA
* * *
1687429 AGAAAATGAG-TCCACTGTTGCTGGACATGAAGAACTGTCAGAAATGCTAGATAAACCACGTCTA
1 AGAAAATGAGCTCCA-TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTA
1687493 CTCCA
65 CTCCA
* * * * * *
1687498 AGAAAAGGAGCCCCCTGTTGCTGGACATGAAGAGCCATCAGAAATTCTAGATAAACAACGTCTAC
1 AGAAAATGAGCTCCATGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTAC
1687563 TCCA
66 TCCA
1687567 AGGAAAA
1 A-GAAAA
1687574 CAGTCCCCTG
Statistics
Matches: 235, Mismatches: 39, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
67 1 0.00
68 7 0.03
69 214 0.91
70 12 0.05
71 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (69 bp):
AGAAAATGAGCTCCATGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTAC
TCCA
Found at i:1687395 original size:186 final size:185
Alignment explanation
Indices: 1687036--1687410 Score: 450
Period size: 186 Copynumber: 2.0 Consensus size: 185
1687026 ATCGTCTCCA
* *
1687036 AGAAAATGAGCTCCAAGTTGACGGACATGAAGAGCCCTCGAAAATGCTATATAAAAGACATCGAC
1 AGAAAATGAGCTCCAAGTTGACGGACATGAAGAGCCCTCGAAAATGCTAGATAAAAGACATCAAC
* *
1687101 TCCAAGAAAATGAGCTACATGTTGCTAGACACAGAGAACTCTTTGAAATGCTAGATAAACGACGT
66 TCCAAGAAAATGAGCTACATGTTGCTAGACAAAGAGAACTC-TGGAAATGCTAGATAAACGACGT
* *
1687166 CGACTCCAAAAAAATGAGCTCCATGTTGTTAGACATCAAGAGCCCTCGAAAATGCT
130 CGACTCCAAAAAAATGAGCACCATATTGTTAGACATCAAGAGCCCTCGAAAATGCT
* * * * * *
1687222 AGAAAATGAGCTTCATGTTG-CTGGACATGAAGAGCCCTCGGAAATGCTAGATAAACGGCGTCAA
1 AGAAAATGAGCTCCAAGTTGAC-GGACATGAAGAGCCCTCGAAAATGCTAGATAAAAGACATCAA
* * * *
1687286 CTCCAAGAAAATGGGCTCCATGTTGCTGGACATGAAGAG-GCGTC-GGAAATGCTAGATAAACGA
65 CTCCAAGAAAATGAGCTACATGTTGCTAGACA--AAGAGAAC-TCTGGAAATGCTAGATAAACGA
* ** * * * * * * *
1687349 CGTCGACTCCAAGAAGTTGAGCACCCTATTTTTGGACATGAAGAGCCGTTGAAAGTGCT
127 CGTCGACTCCAAAAAAATGAGCACCATATTGTTAGACATCAAGAGCCCTCGAAAATGCT
1687408 AGA
1 AGA
1687411 TAATATCCGT
Statistics
Matches: 159, Mismatches: 26, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
185 1 0.01
186 151 0.95
187 1 0.01
188 6 0.04
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.21
Consensus pattern (185 bp):
AGAAAATGAGCTCCAAGTTGACGGACATGAAGAGCCCTCGAAAATGCTAGATAAAAGACATCAAC
TCCAAGAAAATGAGCTACATGTTGCTAGACAAAGAGAACTCTGGAAATGCTAGATAAACGACGTC
GACTCCAAAAAAATGAGCACCATATTGTTAGACATCAAGAGCCCTCGAAAATGCT
Found at i:1687582 original size:69 final size:68
Alignment explanation
Indices: 1687237--1687641 Score: 345
Period size: 69 Copynumber: 5.9 Consensus size: 68
1687227 ATGAGCTTCA
* * * * *
1687237 TGTTGCTGGACATGAAGAGCCCTCGGAAATGCTAGATAAACGGCGTCAACTCCAAGAAAATG-GG
1 TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTACTCCAAGAAAA-GAGT
*
1687301 CTCCA
65 C-CCC
* * * **
1687306 TGTTGCTGGACATGAAGAGGCGTCGGAAATGCTAGATAAACGACGTCGACTCCAAGAAGTTGAG-
1 TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTACTCCAAGAA-AAGAGT
1687370 CACCC
65 C-CCC
* ** * * *
1687375 TATTTTTGGACATGAAGAGCCGT-TGAAAGTGCTAGATAATATC--CGTTTACTCCGAGAAAATG
1 TGTTGCTGGACATGAAGAGCCGTCAGAAA-TGCTAGATAA-A-CGACGTCTACTCCAAGAAAA-G
*
1687437 AGTCCAC
62 AGTCCCC
* * * *
1687444 TGTTGCTGGACATGAAGAACTGTCAGAAATGCTAGATAAACCACGTCTACTCCAAGAAAAGGAGC
1 TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTACTCCAAGAAAA-GAGT
1687509 CCCC
65 CCCC
* * * *
1687513 TGTTGCTGGACATGAAGAGCCATCAGAAATTCTAGATAAACAACGTCTACTCCAAGGAAAACAGT
1 TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTACTCCAA-GAAAAGAGT
1687578 CCCC
65 CCCC
** * ** ** * * *
1687582 TGGTT-CTGGACACAAAGAACCACCAGAAATGCTCCATAAACGACCTGTACTCCAAAAAAA
1 T-GTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTACTCCAAGAAAA
1687642 AGAACCACCT
Statistics
Matches: 276, Mismatches: 48, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
67 1 0.00
68 9 0.03
69 250 0.91
70 15 0.05
71 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.20
Consensus pattern (68 bp):
TGTTGCTGGACATGAAGAGCCGTCAGAAATGCTAGATAAACGACGTCTACTCCAAGAAAAGAGTC
CCC
Found at i:1688864 original size:5 final size:5
Alignment explanation
Indices: 1688854--1688882 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1688844 AATATACCAT
1688854 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1688883 AGCTCTCCAA
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:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:1696504 original size:21 final size:21
Alignment explanation
Indices: 1696478--1696519 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1696468 CGCATCTCGA
1696478 ATGCCAAAAAGCTCAATTTCC
1 ATGCCAAAAAGCTCAATTTCC
1696499 ATGCCAAAAAGCTCAATTTCC
1 ATGCCAAAAAGCTCAATTTCC
1696520 TTTTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.10, T:0.24
Consensus pattern (21 bp):
ATGCCAAAAAGCTCAATTTCC
Found at i:1704407 original size:26 final size:26
Alignment explanation
Indices: 1704376--1704483 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
1704366 TGAAATGCCC
* *
1704376 ATCATGGAACATTTAACTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
1704402 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
1704428 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
1704454 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1704480 ATCA
1 ATCA
1704484 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1711469 original size:26 final size:26
Alignment explanation
Indices: 1711438--1711571 Score: 223
Period size: 26 Copynumber: 5.2 Consensus size: 26
1711428 TGAAATGCCC
*
1711438 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
1711464 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
1711490 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
1711516 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
1711542 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1711568 ATCA
1 ATCA
1711572 ATTTGTACCA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 103 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1713659 original size:20 final size:21
Alignment explanation
Indices: 1713634--1713677 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1713624 GTAAGTTCTA
* *
1713634 TAAAAAATATA-TATTTAATT
1 TAAAAAACATATTATTGAATT
1713654 TAAAAAACATATTATTGAATT
1 TAAAAAACATATTATTGAATT
1713675 TAA
1 TAA
1713678 TAATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAAAACATATTATTGAATT
Found at i:1717652 original size:85 final size:85
Alignment explanation
Indices: 1717509--1717679 Score: 306
Period size: 85 Copynumber: 2.0 Consensus size: 85
1717499 TAGCTTATAG
1717509 ATCAAGTAAGCCAGTTTCCTTAATTGCCACAAAGAATGCTATAAGATCAGTTGGTTTATACAATC
1 ATCAAGTAAGCCAGTTTCCTTAATTGCCACAAAGAATGCTATAAGATCAGTTGGTTTATACAATC
*
1717574 AGTTTTAAGAGGTGATATCC
66 AGTTTTAAGAGGTGACATCC
* * *
1717594 ATCAAGTAAGCCAGTTTCCTTATTTGGCACAAAGAATGCTATGAGATCAGTTGGTTTATACAATC
1 ATCAAGTAAGCCAGTTTCCTTAATTGCCACAAAGAATGCTATAAGATCAGTTGGTTTATACAATC
1717659 AGTTTTAAGAGGTGACATCC
66 AGTTTTAAGAGGTGACATCC
1717679 A
1 A
1717680 ATAAGTTTGA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (85 bp):
ATCAAGTAAGCCAGTTTCCTTAATTGCCACAAAGAATGCTATAAGATCAGTTGGTTTATACAATC
AGTTTTAAGAGGTGACATCC
Found at i:1720335 original size:24 final size:24
Alignment explanation
Indices: 1720305--1720406 Score: 104
Period size: 23 Copynumber: 4.3 Consensus size: 24
1720295 TTTGAATATA
* *
1720305 TATATATATATACTGTATATGTTTT
1 TATATATAT-TAATGTATATATTTT
*
1720330 TCATATATA-TAATGTATGTATTTT
1 T-ATATATATTAATGTATATATTTT
1720354 TA-ATATTATTAAT-TATATATTTT
1 TATATA-TATTAATGTATATATTTT
*
1720377 TATATATATT-ATGTATACATTTT
1 TATATATATTAATGTATATATTTT
*
1720400 TAAATAT
1 TATATAT
1720407 CATACTGTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
22 5 0.08
23 33 0.50
24 20 0.30
25 1 0.02
26 7 0.11
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (24 bp):
TATATATATTAATGTATATATTTT
Found at i:1721764 original size:24 final size:23
Alignment explanation
Indices: 1721737--1721782 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1721727 ATCCATAGTA
1721737 AAAATAAAAT-ATAATGTGCAATAT
1 AAAATAAAATGA-AATGTG-AATAT
*
1721761 AAAATATAATGAAATGTGAATA
1 AAAATAAAATGAAATGTGAATA
1721783 CTATTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 15 0.75
25 1 0.05
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (23 bp):
AAAATAAAATGAAATGTGAATAT
Found at i:1722029 original size:19 final size:19
Alignment explanation
Indices: 1722005--1722045 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1721995 TACTAAATTC
1722005 ATAAATAAAATGT-ATAATA
1 ATAAATAAAAT-TAATAATA
*
1722024 ATAAATATAATTAATAATA
1 ATAAATAAAATTAATAATA
1722043 ATA
1 ATA
1722046 TAAAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAATAAAATTAATAATA
Found at i:1724123 original size:21 final size:21
Alignment explanation
Indices: 1724092--1724155 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1724082 ATTATAATTA
1724092 TTATTAT-TATTAGTATATGT
1 TTATTATATATTAGTATATGT
*
1724112 TTATTATATATTTA-TATATCT
1 TTATTATATA-TTAGTATATGT
*
1724133 TTAATATATA-T-GTATATGT
1 TTATTATATATTAGTATATGT
1724152 TTAT
1 TTAT
1724156 GCAGTATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.27
20 7 0.19
21 17 0.46
22 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (21 bp):
TTATTATATATTAGTATATGT
Found at i:1732748 original size:16 final size:16
Alignment explanation
Indices: 1732727--1732759 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1732717 GTAATGGAAC
1732727 TAGAAATATATTGGTG
1 TAGAAATATATTGGTG
1732743 TAGAAATATATTGGTG
1 TAGAAATATATTGGTG
1732759 T
1 T
1732760 TCTTAATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.39
Consensus pattern (16 bp):
TAGAAATATATTGGTG
Found at i:1737394 original size:220 final size:219
Alignment explanation
Indices: 1737019--1737502 Score: 752
Period size: 220 Copynumber: 2.2 Consensus size: 219
1737009 AGATTTGACC
* * * * ** * * *
1737019 TTCAGGTGTTTACACTGAAGTGGATCCAAGATGATTTAACATCTTTGTATTATTAGAGAACAAAT
1 TTCACGTGTTTACGCTGAAGTAGATCTAAGATGATTTGGCATCTCTGTACTATCAGAGAACAAAT
*
1737084 CGAAGAAACAGATTTGGCATATCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAAC
66 CAAAGAAACAGATTTGGCATATCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAAC
* *
1737149 CTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTTGCATTGACAAGGAGCA
131 CTTCAGATGTCTTCACATAGAAGTAGATCCAAGATGATTTGGCATCCTTGCATTGACAAGGAGCA
** *
1737214 GATTGAAGACATAGTAGATTTGGAT
196 GATCAAAGACATAGCA-ATTTGGAT
* * *
1737239 TTCACGTGTTTATGCTGAAGTAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGAGCAAAT
1 TTCACGTGTTTACGCTGAAGTAGATCTAAGATGATTTGGCATCTCTGTACTATCAGAGAACAAAT
* *
1737304 CAAAGAAACAGATTTGGCATCTCTATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAAC
66 CAAAGAAACAGATTTGGCATATCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAAC
* *
1737369 CTTCGGATGTCTTCACATAGAAGTAGATCCAAGATGATTTGGCATCCTTGCGTTGACAAGGAGCA
131 CTTCAGATGTCTTCACATAGAAGTAGATCCAAGATGATTTGGCATCCTTGCATTGACAAGGAGCA
*
1737434 GATCAAAGACATAGCAATTTGGCT
196 GATCAAAGACATAGCAATTTGGAT
1737458 TTCACGTGTTTACGCTGAAGTAGATCTAAGATGATTTGGCATCTC
1 TTCACGTGTTTACGCTGAAGTAGATCTAAGATGATTTGGCATCTC
1737503 CATATTCGAC
Statistics
Matches: 240, Mismatches: 24, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
219 51 0.21
220 189 0.79
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Consensus pattern (219 bp):
TTCACGTGTTTACGCTGAAGTAGATCTAAGATGATTTGGCATCTCTGTACTATCAGAGAACAAAT
CAAAGAAACAGATTTGGCATATCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAAC
CTTCAGATGTCTTCACATAGAAGTAGATCCAAGATGATTTGGCATCCTTGCATTGACAAGGAGCA
GATCAAAGACATAGCAATTTGGAT
Found at i:1737602 original size:78 final size:78
Alignment explanation
Indices: 1737473--1737706 Score: 344
Period size: 78 Copynumber: 3.0 Consensus size: 78
1737463 GTGTTTACGC
* ** * * * *
1737473 TGAAGTAGATCTAAGATGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACACAGCAG
1 TGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAG
1737538 ATCTGACCTTCAT
66 ATCTGACCTTCAT
* * *
1737551 TGAAGCAGATCCAAGGTGATTTGGCATATCTGTATTAGACGGGGAGCAGATCGAAGACATAACAG
1 TGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAG
1737616 AT-TGGACCTTCAT
66 ATCT-GACCTTCAT
* *
1737629 TGAAGTAGATGCAAGATGATTTGGAATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAG
1 TGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAG
1737694 ATCTGACCTTCAT
66 ATCTGACCTTCAT
1737707 GTGTTTACAT
Statistics
Matches: 139, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
77 1 0.01
78 137 0.99
79 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (78 bp):
TGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAG
ATCTGACCTTCAT
Found at i:1737840 original size:45 final size:45
Alignment explanation
Indices: 1737646--1737874 Score: 207
Period size: 45 Copynumber: 5.1 Consensus size: 45
1737636 GATGCAAGAT
* *
1737646 GATTTGGAATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATC-AA-AGATAACA
* * * * * * * *
1737693 GATCTGACCT-TCATGTGTTTACATC--GAAGCAGATCCAAGATGACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCAAAGATAACA
* * *
1737738 GATTTGGCATCTCTATATTAGACGGGGAGCA-AACTAAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATC-AAAGATAACA
* *
1737782 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACA
* * *
1737827 GATTTGGCGTCTCTGTATTAGATGGGGAGCAGATCAAAGATATCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACA
1737872 GAT
1 GAT
1737875 ATCGCCTTCC
Statistics
Matches: 144, Mismatches: 29, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
43 1 0.01
44 41 0.28
45 74 0.51
46 5 0.03
47 18 0.12
48 4 0.03
49 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGATAACA
Found at i:1738244 original size:17 final size:17
Alignment explanation
Indices: 1738224--1738286 Score: 83
Period size: 17 Copynumber: 3.5 Consensus size: 17
1738214 AATGATATGT
1738224 AATCTTAGATATGATAC
1 AATCTTAGATATGATAC
1738241 AATCTTAGATATGATTGA-
1 AATCTTAGATATGA-T-AC
1738259 AATCTTAGATATGATATGC
1 AATCTTAGATATGATA--C
1738278 AATCTTAGA
1 AATCTTAGA
1738287 AGATATGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.02
17 15 0.37
18 15 0.37
19 10 0.24
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (17 bp):
AATCTTAGATATGATAC
Found at i:1738264 original size:18 final size:18
Alignment explanation
Indices: 1738224--1738286 Score: 85
Period size: 18 Copynumber: 3.5 Consensus size: 18
1738214 AATGATATGT
1738224 AATCTTAGATATGA-T-A
1 AATCTTAGATATGATTGA
1738240 CAATCTTAGATATGATTGA
1 -AATCTTAGATATGATTGA
*
1738259 AATCTTAGATATGATATGC
1 AATCTTAGATATGAT-TGA
1738278 AATCTTAGA
1 AATCTTAGA
1738287 AGATATGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
17 14 0.33
18 16 0.38
19 12 0.29
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (18 bp):
AATCTTAGATATGATTGA
Found at i:1738264 original size:35 final size:37
Alignment explanation
Indices: 1738215--1738294 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 37
1738205 ATAATCTTCA
*
1738215 ATGATATGTAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGAAATCTTAGATATGATAGCAATCTTAGAT
1738251 ATGAT-TGAAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGAAATCTTAGATATGATA-GCAATCTTAGAT
1738287 A-GATATGA
1 ATGATATGA
1738295 TTTTGTAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
35 21 0.52
36 9 0.22
37 10 0.25
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36
Consensus pattern (37 bp):
ATGATATGAAATCTTAGATATGATAGCAATCTTAGAT
Found at i:1738293 original size:17 final size:19
Alignment explanation
Indices: 1738215--1738286 Score: 105
Period size: 19 Copynumber: 3.9 Consensus size: 19
1738205 ATAATCTTCA
*
1738215 ATGATATGTAATCTTAGAT
1 ATGATATGCAATCTTAGAT
1738234 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
1738251 ATGAT-TGAAATCTTAGAT
1 ATGATATGCAATCTTAGAT
1738269 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
1738287 AGATATGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
17 15 0.32
18 15 0.32
19 17 0.36
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:1738293 original size:22 final size:23
Alignment explanation
Indices: 1738265--1738309 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1738255 TTGAAATCTT
1738265 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
1738287 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
1738310 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:1747246 original size:20 final size:20
Alignment explanation
Indices: 1747221--1747261 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1747211 ACTTTACTTC
1747221 TAATTTCCAATTGATCTGAT
1 TAATTTCCAATTGATCTGAT
1747241 TAATTTCCAATTGATCTGAT
1 TAATTTCCAATTGATCTGAT
1747261 T
1 T
1747262 TCAAGAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (20 bp):
TAATTTCCAATTGATCTGAT
Found at i:1748389 original size:37 final size:37
Alignment explanation
Indices: 1748343--1748413 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
1748333 TAACAATAGG
* * *
1748343 AGATTTATTGAAAAATAATTATTATACTCAAATTAAA
1 AGATGTATTGAAAAATAATTATAATACTAAAATTAAA
*
1748380 AGATGTATTGAATAATAATTATAATACTAAAATT
1 AGATGTATTGAAAAATAATTATAATACTAAAATT
1748414 GTAATTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (37 bp):
AGATGTATTGAAAAATAATTATAATACTAAAATTAAA
Found at i:1749741 original size:13 final size:13
Alignment explanation
Indices: 1749723--1749760 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1749713 AACAACACAC
*
1749723 ATATATTAAATAA
1 ATATATAAAATAA
1749736 ATATATAAAATAA
1 ATATATAAAATAA
1749749 A-ATA-AAAATAA
1 ATATATAAAATAA
1749760 A
1 A
1749761 AAAATAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.33
12 3 0.12
13 13 0.54
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATATATAAAATAA
Found at i:1751616 original size:54 final size:54
Alignment explanation
Indices: 1751548--1751937 Score: 753
Period size: 54 Copynumber: 7.2 Consensus size: 54
1751538 ATTATGGTAG
*
1751548 AGCCACCAGAACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1751602 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1751656 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1751710 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1751764 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1751818 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
* *
1751872 AGCCACCAGGACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGTAT
1 AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
1751926 AGCCACCAGGAC
1 AGCCACCAGGAC
1751938 GCTTCCTCCA
Statistics
Matches: 333, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 333 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (54 bp):
AGCCACCAGGACAGATATATGTGGCAGAGCCACCGGATCAGATAATTGTGGCAT
Found at i:1751913 original size:27 final size:27
Alignment explanation
Indices: 1751524--1751934 Score: 436
Period size: 27 Copynumber: 15.2 Consensus size: 27
1751514 GTGACGAAGT
* * *
1751524 CACCAGATAAAGATAT-TATGGTAGAGC
1 CACCAGAT-CAGATATATGTGGCAGAGC
*
1751551 CACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATATATGTGGCAGAGC
* *
1751578 CACCGGATCAGATA-ATTGTGGCATAGC
1 CACCAGATCAGATATA-TGTGGCAGAGC
1751605 CACCAGGA-CAGATATATGTGGCAGAGC
1 CACCA-GATCAGATATATGTGGCAGAGC
* *
1751632 CACCGGATCAGATA-ATTGTGGCATAGC
1 CACCAGATCAGATATA-TGTGGCAGAGC
1751659 CACCAGGA-CAGATATATGTGGCAGAGC
1 CACCA-GATCAGATATATGTGGCAGAGC
* *
1751686 CACCGGATCAGATA-ATTGTGGCATAGC
1 CACCAGATCAGATATA-TGTGGCAGAGC
1751713 CACCAGGA-CAGATATATGTGGCAGAGC
1 CACCA-GATCAGATATATGTGGCAGAGC
* *
1751740 CACCGGATCAGATA-ATTGTGGCATAGC
1 CACCAGATCAGATATA-TGTGGCAGAGC
1751767 CACCAGGA-CAGATATATGTGGCAGAGC
1 CACCA-GATCAGATATATGTGGCAGAGC
* *
1751794 CACCGGATCAGATA-ATTGTGGCATAGC
1 CACCAGATCAGATATA-TGTGGCAGAGC
1751821 CACCAGGA-CAGATATATGTGGCAGAGC
1 CACCA-GATCAGATATATGTGGCAGAGC
* *
1751848 CACCGGATCAGATA-ATTGTGGCATAGC
1 CACCAGATCAGATATA-TGTGGCAGAGC
1751875 CACCAGGA-CAGATATATGTGGCAGAGC
1 CACCA-GATCAGATATATGTGGCAGAGC
* *
1751902 CACCAGATCAGATA-ATTGTGGTATAGC
1 CACCAGATCAGATATA-TGTGGCAGAGC
1751929 CACCAG
1 CACCAG
1751935 GACGCTTCCT
Statistics
Matches: 327, Mismatches: 31, Indels: 52
0.80 0.08 0.13
Matches are distributed among these distances:
26 25 0.08
27 284 0.87
28 18 0.06
ACGTcount: A:0.33, C:0.22, G:0.27, T:0.19
Consensus pattern (27 bp):
CACCAGATCAGATATATGTGGCAGAGC
Found at i:1753536 original size:180 final size:180
Alignment explanation
Indices: 1753234--1753593 Score: 702
Period size: 180 Copynumber: 2.0 Consensus size: 180
1753224 ACATGTTGTC
*
1753234 TTCAACAACATGTTGCTGGCCACTTCTTGTAAAATGGGAGGTTTGACATGCAAATCCTCCTATTT
1 TTCAACAACATGTTGCTGGCCACTTCTTGTAAAATGGGAGGTTTGACATGCAAATCATCCTATTT
1753299 TGCACTACTATTTATTTGGCCACTACAAATTAGCCTATAGCATTTTCAAACATTTTCACATAGGT
66 TGCACTACTATTTATTTGGCCACTACAAATTAGCCTATAGCATTTTCAAACATTTTCACATAGGT
1753364 CCTATTTCATAATTTCACTCACAAATGACAAAATCAAAGCATGAAATTTT
131 CCTATTTCATAATTTCACTCACAAATGACAAAATCAAAGCATGAAATTTT
1753414 TTCAACAACATGTTGCTGGCCACTTCTTGTAAAATGGGAGGTTTGACATGCAAATCATCCTATTT
1 TTCAACAACATGTTGCTGGCCACTTCTTGTAAAATGGGAGGTTTGACATGCAAATCATCCTATTT
*
1753479 TGCACTACTATTTATTTGGCCACTACAAATTAGCCTATAGCATTTTCAAACATTTTCACGTAGGT
66 TGCACTACTATTTATTTGGCCACTACAAATTAGCCTATAGCATTTTCAAACATTTTCACATAGGT
1753544 CCTATTTCATAATTTCACTCACAAATGACAAAATCAAAGCATGAAATTTT
131 CCTATTTCATAATTTCACTCACAAATGACAAAATCAAAGCATGAAATTTT
1753594 GCCAACATTC
Statistics
Matches: 178, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 178 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (180 bp):
TTCAACAACATGTTGCTGGCCACTTCTTGTAAAATGGGAGGTTTGACATGCAAATCATCCTATTT
TGCACTACTATTTATTTGGCCACTACAAATTAGCCTATAGCATTTTCAAACATTTTCACATAGGT
CCTATTTCATAATTTCACTCACAAATGACAAAATCAAAGCATGAAATTTT
Found at i:1759250 original size:27 final size:27
Alignment explanation
Indices: 1759220--1759279 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
1759210 GTGACGAAGT
1759220 CACCAGATACAGATAT-TGTAGCAGAGC
1 CACCAGA-ACAGATATATGTAGCAGAGC
*
1759247 CACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAACAGATATATGTAGCAGAGC
1759274 CACCAG
1 CACCAG
1759280 GATGCTTCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.15
Consensus pattern (27 bp):
CACCAGAACAGATATATGTAGCAGAGC
Found at i:1769641 original size:2 final size:2
Alignment explanation
Indices: 1769636--1769660 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1769626 AAAAAAAAAA
1769636 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 A
1769661 CATACACTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1774352 original size:69 final size:69
Alignment explanation
Indices: 1774241--1774379 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
1774231 CACAATTACT
1774241 GCTTCTCCGTCATGGATATTACGTTTTCGTTTTACAAGGGAAGTGCTACCTGCGGATCCATCCTT
1 GCTTCTCCGTCATGGATATTACGTTTTCGTTTTACAAGGGAAGTGCTACCTGCGGATCCATCCTT
1774306 GTCG
66 GTCG
*
1774310 GCTTCTCCGTCATGGATATTACGTTTTCGTTTTACAGGGGAAGTGCTACCTGCGGATCCATCCTT
1 GCTTCTCCGTCATGGATATTACGTTTTCGTTTTACAAGGGAAGTGCTACCTGCGGATCCATCCTT
1774375 GTCG
66 GTCG
1774379 G
1 G
1774380 TAGAGTGATG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (69 bp):
GCTTCTCCGTCATGGATATTACGTTTTCGTTTTACAAGGGAAGTGCTACCTGCGGATCCATCCTT
GTCG
Found at i:1775345 original size:16 final size:16
Alignment explanation
Indices: 1775320--1775352 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1775310 ATTCCCCATT
*
1775320 CATTTCGAGTTCTAAA
1 CATTTAGAGTTCTAAA
1775336 CATTTAGAGTTCTAAA
1 CATTTAGAGTTCTAAA
1775352 C
1 C
1775353 TGTGTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (16 bp):
CATTTAGAGTTCTAAA
Found at i:1779834 original size:162 final size:156
Alignment explanation
Indices: 1779554--1779868 Score: 427
Period size: 162 Copynumber: 2.0 Consensus size: 156
1779544 ACATGTGATA
1779554 GATAAAATGATCAAATCAAAATATTCGAAAAAATTAAAAATAATATTTCTGTGACTTTTTCTGTT
1 GATAAAATGATCAAATCAAAATATTCG-AAAAATTAAAAATAATATTTCTGTGACTTTTTCTGTT
* *
1779619 GTTTCCATGACTTTTTTGTGTACTGCACATTTCATACAATTAGAATAAAGTTTTGAAAATGATAT
65 GTTTCCATGACTTTTTTGTGTACTACACATTTCATACAATTAAAATAAAGTTTTGAAAATGATAT
1779684 TCATATGAATTATGTTGGACCTATTGTG
130 TCATATGAATTATGTT-GACCTATTGTG
* * **
1779712 GATAAAATTATCAAATCAAAATATTTG-AAAATTCCAAAAATTGTATTTCTGTGACTACTTTT-T
1 GATAAAATGATCAAATCAAAATATTCGAAAAATT--AAAAATAATATTTCTGTGACT--TTTTCT
* * * *
1779775 GTTGTTTTCATGATTTTCTTTTTGTGTACTATACATTTCATATAATTAAAATAAAGTTTTGAAAA
62 GTTGTTTCCATGA--CT-TTTTTGTGTACTACACATTTCATACAATTAAAATAAAGTTTTGAAAA
* *
1779840 TTATATTCATATTAATTATGTTGACCTAT
124 TGATATTCATATGAATTATGTTGACCTAT
1779869 GATAGATATG
Statistics
Matches: 138, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
156 6 0.04
158 44 0.32
159 13 0.09
160 4 0.03
161 8 0.06
162 63 0.46
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (156 bp):
GATAAAATGATCAAATCAAAATATTCGAAAAATTAAAAATAATATTTCTGTGACTTTTTCTGTTG
TTTCCATGACTTTTTTGTGTACTACACATTTCATACAATTAAAATAAAGTTTTGAAAATGATATT
CATATGAATTATGTTGACCTATTGTG
Found at i:1781205 original size:29 final size:30
Alignment explanation
Indices: 1781150--1781215 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
1781140 GTTCGATGTG
* *
1781150 CAATGTTATACATGAACTTTAATTTTG-TA
1 CAATTTTATACATGAAATTTAATTTTGATA
* *
1781179 CAATTTTATACATTAAATCTTAA-TTTGATT
1 CAATTTTATACATGAAAT-TTAATTTTGATA
1781209 CAATTTT
1 CAATTTT
1781216 CACAAGTCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (30 bp):
CAATTTTATACATGAAATTTAATTTTGATA
Found at i:1781706 original size:10 final size:10
Alignment explanation
Indices: 1781691--1781728 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1781681 ATTTTAGCTT
1781691 TTATCTTTAA
1 TTATCTTTAA
1781701 TTATCTTTAA
1 TTATCTTTAA
*
1781711 TTAT-TTGTAT
1 TTATCTT-TAA
1781721 TTATCTTT
1 TTATCTTT
1781729 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:1782782 original size:14 final size:14
Alignment explanation
Indices: 1782763--1782792 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1782753 AAAAACCCAC
1782763 CTCACCAGCAACAA
1 CTCACCAGCAACAA
1782777 CTCACCAGCAACAA
1 CTCACCAGCAACAA
1782791 CT
1 CT
1782793 TTGGATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.43, G:0.07, T:0.10
Consensus pattern (14 bp):
CTCACCAGCAACAA
Found at i:1790130 original size:19 final size:19
Alignment explanation
Indices: 1790106--1790145 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1790096 GTGTACTTCT
*
1790106 TTTTTTTTTAATTTTTAAA
1 TTTTTTTATAATTTTTAAA
1790125 TTTTTTTATAATTTTTAAA
1 TTTTTTTATAATTTTTAAA
1790144 TT
1 TT
1790146 ATTTATTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTTTTATAATTTTTAAA
Found at i:1792844 original size:10 final size:10
Alignment explanation
Indices: 1792831--1792876 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
1792821 CAATTTATTT
1792831 TTTTCTTTTA
1 TTTTCTTTTA
1792841 TTTTCTTTTAA
1 TTTTCTTTT-A
*
1792852 CTTTCTTTTA
1 TTTTCTTTTA
*
1792862 TTTTCTTTTT
1 TTTTCTTTTA
1792872 TTTTC
1 TTTTC
1792877 ATTCTCTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:1807560 original size:79 final size:79
Alignment explanation
Indices: 1807458--1807605 Score: 172
Period size: 79 Copynumber: 1.9 Consensus size: 79
1807448 TCATGCTTAT
* * * ** * *
1807458 ATATATATTATAAATTGATATATAATAACGGCCTTTCCATAACATGCAAAATTTTAAC-AGACAA
1 ATATATATTATAAATAGACATATAACAACAACCTGTCCATAACATACAAAATTTT-ACTAGACAA
1807522 ATAGAATTATTATAA
65 ATAGAATTATTATAA
* * * * *
1807537 ATATATATTATAGATAGGCATATAACAACAATCTGTCCATAATATACAAAATTTTACTAGATAAA
1 ATATATATTATAAATAGACATATAACAACAACCTGTCCATAACATACAAAATTTTACTAGACAAA
1807602 TAGA
66 TAGA
1807606 GTTTTAAATT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
78 2 0.04
79 54 0.96
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (79 bp):
ATATATATTATAAATAGACATATAACAACAACCTGTCCATAACATACAAAATTTTACTAGACAAA
TAGAATTATTATAA
Found at i:1808490 original size:22 final size:21
Alignment explanation
Indices: 1808452--1808494 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1808442 TGGTATAATA
1808452 ACATATTTAGTCCTCAATACTT
1 ACATATTTAGTCCTCAA-ACTT
*
1808474 ACATATTCTA-TCTTCAAACTT
1 ACATATT-TAGTCCTCAAACTT
1808495 GTTAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 13 0.68
23 2 0.11
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (21 bp):
ACATATTTAGTCCTCAAACTT
Found at i:1810190 original size:16 final size:16
Alignment explanation
Indices: 1810169--1810200 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1810159 TAATTATATA
1810169 ATTTTAAATTTAAAAT
1 ATTTTAAATTTAAAAT
*
1810185 ATTTTAAATTTTAAAT
1 ATTTTAAATTTAAAAT
1810201 TAAATGGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTAAATTTAAAAT
Found at i:1827121 original size:21 final size:21
Alignment explanation
Indices: 1827095--1827147 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1827085 AAAGGAGTAA
1827095 TTTTACGTTGACTGAAAAATC
1 TTTTACGTTGACTGAAAAATC
1827116 TTTTACGTTGACTGAAAAATC
1 TTTTACGTTGACTGAAAAATC
1827137 TTTTACGTTGA
1 TTTTACGTTGA
1827148 TCATCCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (21 bp):
TTTTACGTTGACTGAAAAATC
Found at i:1830033 original size:31 final size:31
Alignment explanation
Indices: 1829998--1830056 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1829988 GAAAGTGATC
* **
1829998 ACTGAACTAATTAAAAGTTTTCATTTAAGTA
1 ACTGAACTAATCAAAAAATTTCATTTAAGTA
1830029 ACTGAACTAATCAAAAAATTTCATTTAA
1 ACTGAACTAATCAAAAAATTTCATTTAA
1830057 ATCATTGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.36
Consensus pattern (31 bp):
ACTGAACTAATCAAAAAATTTCATTTAAGTA
Found at i:1832935 original size:11 final size:10
Alignment explanation
Indices: 1832920--1832944 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1832910 AGAAGAGAAT
1832920 GAAAAAAAAA
1 GAAAAAAAAA
1832930 GAAAAAAAAA
1 GAAAAAAAAA
1832940 GAAAA
1 GAAAA
1832945 TTTAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:1837489 original size:21 final size:21
Alignment explanation
Indices: 1837440--1837562 Score: 102
Period size: 21 Copynumber: 5.9 Consensus size: 21
1837430 AAGCCCGAAG
* **
1837440 GCTGAACAGAAGCTCATTGGA
1 GCTGAACAGAAACTCATAAGA
* * *
1837461 ACTAAACAGAAACTCATAAGG
1 GCTGAACAGAAACTCATAAGA
* *
1837482 GTTGAACAGAAGCTCATAAGA
1 GCTGAACAGAAACTCATAAGA
* *
1837503 GCTGAACAGAAACCCATAAGG
1 GCTGAACAGAAACTCATAAGA
* * * *
1837524 GTTAAACAGAAGCTCAAAAGA
1 GCTGAACAGAAACTCATAAGA
**
1837545 GCTGAATGGAAACTCATA
1 GCTGAACAGAAACTCATA
1837563 TGAGTTAAAC
Statistics
Matches: 75, Mismatches: 27, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (21 bp):
GCTGAACAGAAACTCATAAGA
Found at i:1837588 original size:42 final size:42
Alignment explanation
Indices: 1837444--1837598 Score: 166
Period size: 42 Copynumber: 3.7 Consensus size: 42
1837434 CCGAAGGCTG
** * * * *
1837444 AACAGAAGCTCATTGGAACTAAACAGAAACTCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGGGTTA
* *
1837486 AACAGAAGCTCATAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGGGTTA
* * * *
1837528 AACAGAAGCTCAAAAGAGCTGAATGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGGGTTA
* * * *
1837570 AACAAAAGCTCGTGAGAGCTAAACGGAAA
1 AACAGAAGCTCATAAGAGCTGAACGGAAA
1837599 GTAAACACGA
Statistics
Matches: 95, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 95 1.00
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACGGAAACTCATAAGGGTTA
Found at i:1844299 original size:26 final size:26
Alignment explanation
Indices: 1844270--1844351 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
1844260 TTGTAATATT
1844270 TATATTTATTTTTAGAGTAAAAATTC
1 TATATTTATTTTTAGAGTAAAAATTC
* * *
1844296 TATATTTATTTAATA-AGTCGAGAA-T-
1 TATATTTATTT-TTAGAGT-AAAAATTC
* *
1844321 GATATATATTTTTAGAGTAAAAATTC
1 TATATTTATTTTTAGAGTAAAAATTC
1844347 TATAT
1 TATAT
1844352 ATTTGATCAT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
24 5 0.12
25 13 0.31
26 19 0.45
27 5 0.12
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (26 bp):
TATATTTATTTTTAGAGTAAAAATTC
Found at i:1845842 original size:17 final size:16
Alignment explanation
Indices: 1845820--1845853 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1845810 CTTTTAAATT
1845820 AAAAAATAAAAGAGAAA
1 AAAAAATAAAAGA-AAA
*
1845837 AAAAAATGAAAGAAAA
1 AAAAAATAAAAGAAAA
1845853 A
1 A
1845854 GGTAATGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAAATAAAAGAAAA
Found at i:1848743 original size:21 final size:20
Alignment explanation
Indices: 1848709--1848753 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1848699 ATTCTTGCTG
**
1848709 TTTTTTTTTCTTTTTTTCTA
1 TTTTTTTTTCTTTTTCACTA
*
1848729 TTTTTTGTTTTTTTTTCACTA
1 TTTTTT-TTTCTTTTTCACTA
1848750 TTTT
1 TTTT
1848754 GCTACCATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTCTTTTTCACTA
Found at i:1848836 original size:17 final size:19
Alignment explanation
Indices: 1848803--1848837 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1848793 ATTGTTTGGA
1848803 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
1848822 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
1848838 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:1850803 original size:31 final size:31
Alignment explanation
Indices: 1850768--1850850 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
1850758 CGAGTGAGTT
*
1850768 ATTATTTTAATATT-TATTTAATGTCTACAAG
1 ATTATTTTAAGATTGTA-TTAATGTCTACAAG
* *
1850799 ATTATTTTAAGGTTGTATTAATGTCTACAAT
1 ATTATTTTAAGATTGTATTAATGTCTACAAG
*
1850830 ATTATTTTAAGGTTGTATTAA
1 ATTATTTTAAGATTGTATTAA
1850851 AATTTTGTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
31 46 0.96
32 2 0.04
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.51
Consensus pattern (31 bp):
ATTATTTTAAGATTGTATTAATGTCTACAAG
Found at i:1852397 original size:18 final size:18
Alignment explanation
Indices: 1852374--1852413 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1852364 AATGATATTA
1852374 TGCTTATTCTATAAATTG
1 TGCTTATTCTATAAATTG
1852392 TGCTTATTCTATAAATTG
1 TGCTTATTCTATAAATTG
1852410 TGCT
1 TGCT
1852414 AATGAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (18 bp):
TGCTTATTCTATAAATTG
Found at i:1862175 original size:29 final size:30
Alignment explanation
Indices: 1862146--1862367 Score: 182
Period size: 30 Copynumber: 7.4 Consensus size: 30
1862136 TTCGGCTATC
*
1862146 AATTATGAAAAGGGATTGTGACGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
1862176 AATTATGAAAAGGGATGGTGACGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
* ** * * *
1862206 AATTATAAAAAGGGATGGCT-TTGGCTATCG
1 AATTATGAAAAGGGATGG-TGACGACCATCA
* * * * *
1862236 TATGATGAAAAGGGATGGCT-TCGGCTATC-
1 AATTATGAAAAGGGATGG-TGACGACCATCA
* * *
1862265 AATCTATGAAAAGGGATGGCT-TCGACTATTA
1 AAT-TATGAAAAGGGATGG-TGACGACCATCA
*
1862296 AATTATGAAAAGGGATGTTGACGACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
** * ** *
1862326 AACAATAAAAATTGATGGTGACAACCATCA
1 AATTATGAAAAGGGATGGTGACGACCATCA
1862356 AATTATGAAAAG
1 AATTATGAAAAG
1862368 AGATAGTTTC
Statistics
Matches: 158, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
29 3 0.02
30 151 0.96
31 4 0.03
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (30 bp):
AATTATGAAAAGGGATGGTGACGACCATCA
Found at i:1862182 original size:30 final size:31
Alignment explanation
Indices: 1862121--1862367 Score: 181
Period size: 30 Copynumber: 8.3 Consensus size: 31
1862111 TCATTGACGA
* * * *
1862121 ATGAAAAGGGATAGCT-TCGGCTATC-AATT
1 ATGAAAAGGGATGGCTGACGACCATCAAATT
*
1862150 ATGAAAAGGGATTG-TGACGACCATCAAATT
1 ATGAAAAGGGATGGCTGACGACCATCAAATT
1862180 ATGAAAAGGGATGG-TGACGACCATCAAATT
1 ATGAAAAGGGATGGCTGACGACCATCAAATT
* ** * * ** *
1862210 ATAAAAAGGGATGGCT-TTGGCTATCGTATG
1 ATGAAAAGGGATGGCTGACGACCATCAAATT
* * *
1862240 ATGAAAAGGGATGGCT-TCGGCTATC-AATCT
1 ATGAAAAGGGATGGCTGACGACCATCAAAT-T
* * *
1862270 ATGAAAAGGGATGGCT-TCGACTATTAAATT
1 ATGAAAAGGGATGGCTGACGACCATCAAATT
* **
1862300 ATGAAAAGGGAT-GTTGACGACCATCAAACA
1 ATGAAAAGGGATGGCTGACGACCATCAAATT
* ** *
1862330 ATAAAAATTGATGG-TGACAACCATCAAATT
1 ATGAAAAGGGATGGCTGACGACCATCAAATT
1862360 ATGAAAAG
1 ATGAAAAG
1862368 AGATAGTTTC
Statistics
Matches: 178, Mismatches: 33, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
28 1 0.01
29 23 0.13
30 149 0.84
31 5 0.03
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (31 bp):
ATGAAAAGGGATGGCTGACGACCATCAAATT
Found at i:1862426 original size:30 final size:30
Alignment explanation
Indices: 1862352--1862427 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
1862342 GGTGACAACC
**
1862352 ATCAAATTATGAAAAGAGATAGTTTCGCCT
1 ATCAAATTATGAAAAGAGATAACTTCGCCT
* **
1862382 GTCGAAA-TATGAAAAGAGATAACTTCGGTT
1 ATC-AAATTATGAAAAGAGATAACTTCGCCT
*
1862412 ATCAAATTACGAAAAG
1 ATCAAATTATGAAAAG
1862428 GGATGTGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 3 0.08
30 31 0.84
31 3 0.08
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.26
Consensus pattern (30 bp):
ATCAAATTATGAAAAGAGATAACTTCGCCT
Found at i:1867886 original size:21 final size:20
Alignment explanation
Indices: 1867862--1867934 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
1867852 ATTTTATCCA
1867862 TTTTTATTTAATTAGT-TTAT
1 TTTTTATTTAATTA-TATTAT
1867882 TTTTTATTCTAATTATATTAT
1 TTTTTATT-TAATTATATTAT
*
1867903 TTTTATTTTTAAGGTT-TATTACT
1 TTTT-TATTTAA--TTATATTA-T
1867926 TTTTTATTT
1 TTTTTATTT
1867935 TTTAAAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
20 9 0.20
21 17 0.38
22 12 0.27
23 7 0.16
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTTTATTTAATTATATTAT
Found at i:1867887 original size:20 final size:19
Alignment explanation
Indices: 1867861--1867910 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
1867851 TATTTTATCC
1867861 ATTTTTATTTAATTAGT-TT
1 ATTTTTATTTAATTA-TATT
1867880 ATTTTTTATTCTAATTATATT
1 A-TTTTTATT-TAATTATATT
1867901 ATTTTTATTT
1 ATTTTTATTT
1867911 TTAAGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 2 0.07
20 17 0.61
21 9 0.32
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTTATTTAATTATATT
Found at i:1869922 original size:33 final size:33
Alignment explanation
Indices: 1869879--1869943 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
1869869 TGTATGTGTG
*
1869879 TGTGTGTTGATTTCTATAACATTTTTCTTTGTA
1 TGTGCGTTGATTTCTATAACATTTTTCTTTGTA
*
1869912 TGTGCGTTGATTTTTATAACATTTTTCTTTGT
1 TGTGCGTTGATTTCTATAACATTTTTCTTTGT
1869944 TAAATATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.17, C:0.09, G:0.15, T:0.58
Consensus pattern (33 bp):
TGTGCGTTGATTTCTATAACATTTTTCTTTGTA
Found at i:1873308 original size:21 final size:21
Alignment explanation
Indices: 1873273--1873332 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1873263 ATAAACATAT
* *
1873273 AAAAATACAAAAAT-ATTTTCA
1 AAAAATATAAAAATAAATTT-A
*
1873294 AAAAATATAATAATAAATTTA
1 AAAAATATAAAAATAAATTTA
*
1873315 AAAATATATAAAGATAAA
1 AAAA-ATATAAAAATAAA
1873333 AAATAATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAATATAAAAATAAATTTA
Found at i:1873378 original size:54 final size:50
Alignment explanation
Indices: 1873264--1873384 Score: 129
Period size: 56 Copynumber: 2.3 Consensus size: 50
1873254 TAAAATTAAA
*
1873264 TAAACATATAAAAATACAAAAATATTTTCAAAAAATATAATAATAAA-TT
1 TAAAAATATAAAAATACAAAAATATTTTCAAAAAATATAATAATAAATTT
* *
1873313 TAAAAATATATAAAGATA-AAAAATAATTATTGACAAAATAATAATAGATAAATTTT
1 TAAAAATATA-AAA-ATACAAAAAT-ATT-TTCAAAAAAT-ATAATA-ATAAA-TTT
*
1873369 TAAAAATATATAAATA
1 TAAAAATATAAAAATA
1873385 TACGTAAACA
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
49 9 0.15
50 9 0.15
51 6 0.10
52 8 0.13
53 6 0.10
54 8 0.13
55 2 0.03
56 12 0.20
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (50 bp):
TAAAAATATAAAAATACAAAAATATTTTCAAAAAATATAATAATAAATTT
Found at i:1886198 original size:24 final size:24
Alignment explanation
Indices: 1886162--1886210 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1886152 CCAGCAAAGA
* *
1886162 CTTCCAACTGATTCGCCTGAGAGG
1 CTTCCAACAGATTCGCCTAAGAGG
*
1886186 CTTCCAACAGATTCTCCTAAGAGG
1 CTTCCAACAGATTCGCCTAAGAGG
1886210 C
1 C
1886211 CGAGGGAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (24 bp):
CTTCCAACAGATTCGCCTAAGAGG
Found at i:1886868 original size:6 final size:6
Alignment explanation
Indices: 1886857--1886888 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1886847 TCTACATATG
*
1886857 TACATA TACATA TACATA TATATA TACATA TA
1 TACATA TACATA TACATA TACATA TACATA TA
1886889 TAATTGGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (6 bp):
TACATA
Found at i:1886889 original size:12 final size:12
Alignment explanation
Indices: 1886852--1886890 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1886842 TTGCTTCTAC
*
1886852 ATATGTACATAT
1 ATATATACATAT
*
1886864 ACATATACATAT
1 ATATATACATAT
1886876 ATATATACATAT
1 ATATATACATAT
1886888 ATA
1 ATA
1886891 ATTGGTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (12 bp):
ATATATACATAT
Found at i:1890639 original size:9 final size:9
Alignment explanation
Indices: 1890559--1890786 Score: 54
Period size: 10 Copynumber: 24.0 Consensus size: 9
1890549 TAATCTATTT
1890559 TTATAAAAA
1 TTATAAAAA
*
1890568 CGTATAAAAA
1 -TTATAAAAA
*
1890578 TTCTTAAAAA
1 TT-ATAAAAA
*
1890588 CTTATAAAAG
1 -TTATAAAAA
*
1890598 TCATTAAAAA
1 TTA-TAAAAA
1890608 -TA-AAAAA
1 TTATAAAAA
* * *
1890615 TAATATACAC
1 TTATA-AAAA
1890625 TTATAAAAA
1 TTATAAAAA
*
1890634 TTATAATAA
1 TTATAAAAA
*
1890643 -TATAATAA
1 TTATAAAAA
*
1890651 TATGTAAAAA
1 T-TATAAAAA
* *
1890661 ATAT-AAAT
1 TTATAAAAA
**
1890669 TTAATGAAATGT
1 TT-AT-AAA-AA
* *
1890681 TTTTAAAATT
1 TTATAAAA-A
1890691 TTATAAAAA
1 TTATAAAAA
1890700 CTTATAAAAAA
1 -TTAT-AAAAA
** *
1890711 TTCCCAAAAT
1 TT-ATAAAAA
1890721 TTATAAATAA
1 TTATAAA-AA
1890731 -TATAAAAAA
1 TTAT-AAAAA
* *
1890740 TTCTAATAAG
1 TTATAA-AAA
1890750 TTATATAGAAA
1 TTATA-A-AAA
1890761 TTATAAAAA
1 TTATAAAAA
1890770 TT-TAAAAA
1 TTATAAAAA
*
1890778 TTTTAAAAA
1 TTATAAAAA
1890787 ATAATCATTT
Statistics
Matches: 159, Mismatches: 37, Indels: 45
0.66 0.15 0.19
Matches are distributed among these distances:
7 5 0.03
8 21 0.13
9 40 0.25
10 72 0.45
11 18 0.11
12 3 0.02
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:1890738 original size:29 final size:30
Alignment explanation
Indices: 1890685--1890742 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 30
1890675 AAATGTTTTT
1890685 AAAATTTTATAAAAACTTATAAAAAATTCCC
1 AAAATTTTATAAAAAC-TATAAAAAATTCCC
1890716 AAAA-TTTATAAATAA-TATAAAAAATTC
1 AAAATTTTATAAA-AACTATAAAAAATTC
1890743 TAATAAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 12 0.46
30 8 0.31
31 6 0.23
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAATTTTATAAAAACTATAAAAAATTCCC
Found at i:1890909 original size:14 final size:15
Alignment explanation
Indices: 1890890--1890925 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1890880 GTTCCTCTCT
1890890 TTTTTATTTAT-AAA
1 TTTTTATTTATAAAA
*
1890904 TTTTTATTTTTAAAA
1 TTTTTATTTATAAAA
1890919 TTTTTAT
1 TTTTTAT
1890926 CTCCAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTATTTATAAAA
Found at i:1891341 original size:10 final size:10
Alignment explanation
Indices: 1891326--1891516 Score: 58
Period size: 10 Copynumber: 19.4 Consensus size: 10
1891316 CCAGTTGAAG
*
1891326 TTTTTATGAT
1 TTTTTATAAT
1891336 TTTTTATAAT
1 TTTTTATAAT
*
1891346 TTTTTA-AAG
1 TTTTTATAAT
* *
1891355 TTTATATTATT
1 TTTTTA-TAAT
*
1891366 TTTTTATGAT
1 TTTTTATAAT
* *
1891376 TTTTTAAGAAA
1 TTTTT-ATAAT
*
1891387 CTTTTAT-AT
1 TTTTTATAAT
*
1891396 GTTTTTATAAA
1 -TTTTTATAAT
* *
1891407 ATTTTAAACAT
1 TTTTTATA-AT
*
1891418 GTTTTATTAA-
1 TTTTTA-TAAT
1891428 -TTTTATAAT
1 TTTTTATAAT
* *
1891437 TTATTAGAAT
1 TTTTTATAAT
** *
1891447 TTACTA-GA-
1 TTTTTATAAT
1891455 TTTTTAT-A-
1 TTTTTATAAT
1891463 TTTTTATAA-
1 TTTTTATAAT
** *
1891472 CATTTATAAG
1 TTTTTATAAT
*
1891482 TTTTTATTAT
1 TTTTTATAAT
1891492 TTTTTATAAAT
1 TTTTTAT-AAT
* *
1891503 TTTATATCAT
1 TTTTTATAAT
1891513 TTTT
1 TTTT
1891517 AATATCTTTA
Statistics
Matches: 131, Mismatches: 37, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
8 15 0.11
9 22 0.17
10 65 0.50
11 28 0.21
12 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:1891366 original size:29 final size:30
Alignment explanation
Indices: 1891323--1891382 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1891313 GGTCCAGTTG
*
1891323 AAGTTTTTATGA-TTTTTTATAATTTTTTA
1 AAGTTTATATGATTTTTTTATAATTTTTTA
* *
1891352 AAGTTTATATTATTTTTTTATGATTTTTTA
1 AAGTTTATATGATTTTTTTATAATTTTTTA
1891382 A
1 A
1891383 GAAACTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (30 bp):
AAGTTTATATGATTTTTTTATAATTTTTTA
Found at i:1891467 original size:9 final size:9
Alignment explanation
Indices: 1891419--1891508 Score: 53
Period size: 9 Copynumber: 9.8 Consensus size: 9
1891409 TTTAAACATG
1891419 TTTTATTAA-
1 TTTTA-TAAT
1891428 TTTTATAAT
1 TTTTATAAT
*
1891437 TTATTAGAA-
1 TT-TTATAAT
1891446 -TTTACTAGAT
1 TTTTA-TA-AT
1891456 TTTTAT-AT
1 TTTTATAAT
*
1891464 TTTTATAAC
1 TTTTATAAT
*
1891473 ATTTATAAGT
1 TTTTATAA-T
*
1891483 TTTTATTATT
1 TTTTA-TAAT
*
1891493 TTTTATAAA
1 TTTTATAAT
1891502 TTTTATA
1 TTTTATA
1891509 TCATTTTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.05
8 13 0.21
9 25 0.40
10 16 0.25
11 6 0.10
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1891476 original size:19 final size:19
Alignment explanation
Indices: 1891454--1891517 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
1891444 AATTTACTAG
1891454 ATTTTTATATTTTTATAAC
1 ATTTTTATATTTTTATAAC
* *
1891473 ATTTATA-AGTTTTTATTA-
1 ATTTTTATA-TTTTTATAAC
* * *
1891491 TTTTTTATAAATTTTATATC
1 ATTTTTAT-ATTTTTATAAC
1891511 ATTTTTA
1 ATTTTTA
1891518 ATATCTTTAG
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
18 6 0.18
19 20 0.61
20 7 0.21
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTATATTTTTATAAC
Found at i:1892159 original size:15 final size:16
Alignment explanation
Indices: 1892124--1892158 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1892114 GACATAATTT
1892124 AAAATGAATATTATAA
1 AAAATGAATATTATAA
* *
1892140 AAAATGTATATTACAA
1 AAAATGAATATTATAA
1892156 AAA
1 AAA
1892159 TCTTGATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATGAATATTATAA
Found at i:1894628 original size:19 final size:21
Alignment explanation
Indices: 1894604--1894647 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1894594 CATCGTTTTT
* *
1894604 AGAAGC-C-TGAAGGCTGAAC
1 AGAAGCTCATGAAAGCTAAAC
1894623 AGAAGCTCATGAAAGCTAAAC
1 AGAAGCTCATGAAAGCTAAAC
1894644 AGAA
1 AGAA
1894648 ACCCATAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.11
Consensus pattern (21 bp):
AGAAGCTCATGAAAGCTAAAC
Found at i:1894687 original size:42 final size:42
Alignment explanation
Indices: 1894620--1894755 Score: 134
Period size: 42 Copynumber: 3.2 Consensus size: 42
1894610 CTGAAGGCTG
* * *
1894620 AACAGAAGCTCATGAA-AGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCA-AAAGAGCTGAACAGAAACCCATAAGGGTTA
**
1894662 AAC-GAAAGCTCGTAAGAGCTGAACAGAAACCCATAAGGGTTA
1 AACAG-AAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
* * * *
1894704 AACAGAAGCTCAAAAGGGCTGAACGGAAACTCATATA-AGTTA
1 AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATA-AGGGTTA
*
1894746 AATAGAAGCT
1 AACAGAAGCT
1894756 AGTGAGAGCT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
41 3 0.04
42 74 0.94
43 2 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (42 bp):
AACAGAAGCTCAAAAGAGCTGAACAGAAACCCATAAGGGTTA
Found at i:1894698 original size:21 final size:21
Alignment explanation
Indices: 1894616--1894698 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
1894606 AAGCCTGAAG
* *
1894616 GCTGAACAGAAGCTCATGAA-A
1 GCTGAACAGAAACCCAT-AAGA
* *
1894637 GCTAAACAGAAACCCATAAGG
1 GCTGAACAGAAACCCATAAGA
* * *
1894658 GTTGAAC-GAAAGCTCGTAAGA
1 GCTGAACAGAAA-CCCATAAGA
1894679 GCTGAACAGAAACCCATAAG
1 GCTGAACAGAAACCCATAAG
1894699 GGTTAAACAG
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
20 6 0.13
21 37 0.79
22 4 0.09
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (21 bp):
GCTGAACAGAAACCCATAAGA
Found at i:1894707 original size:21 final size:21
Alignment explanation
Indices: 1894639--1894710 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
1894629 TCATGAAAGC
1894639 TAAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
* * * * *
1894660 TGAAC-GAAAGCTCGTAAGAGC
1 TAAACAGAAA-CCCATAAGGGT
*
1894681 TGAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
1894702 TAAACAGAA
1 TAAACAGAA
1894711 GCTCAAAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
20 4 0.10
21 31 0.79
22 4 0.10
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGGGT
Found at i:1894736 original size:21 final size:21
Alignment explanation
Indices: 1894615--1894736 Score: 70
Period size: 21 Copynumber: 5.8 Consensus size: 21
1894605 GAAGCCTGAA
*
1894615 GGCTGAACAGAAGCTCATGAAA-
1 GGCTGAACAGAAACTCA--AAAG
* * *
1894637 -GCTAAACAGAAACCCATAAG
1 GGCTGAACAGAAACTCAAAAG
* **
1894657 GGTTGAAC-GAAAGCTCGTAAG
1 GGCTGAACAGAAA-CTCAAAAG
* * *
1894678 AGCTGAACAGAAACCCATAAG
1 GGCTGAACAGAAACTCAAAAG
* * *
1894699 GGTTAAACAGAAGCTCAAAAG
1 GGCTGAACAGAAACTCAAAAG
*
1894720 GGCTGAACGGAAACTCA
1 GGCTGAACAGAAACTCA
1894737 TATAAGTTAA
Statistics
Matches: 74, Mismatches: 22, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
19 2 0.03
20 4 0.05
21 64 0.86
22 4 0.05
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.13
Consensus pattern (21 bp):
GGCTGAACAGAAACTCAAAAG
Found at i:1900304 original size:20 final size:20
Alignment explanation
Indices: 1900279--1900316 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1900269 TTTTTCGGGT
1900279 CAGGTTTTATGGGAAGAGGA
1 CAGGTTTTATGGGAAGAGGA
1900299 CAGGTTTTATGGGAAGAG
1 CAGGTTTTATGGGAAGAG
1900317 TGGGTTCGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.39, T:0.26
Consensus pattern (20 bp):
CAGGTTTTATGGGAAGAGGA
Found at i:1903846 original size:24 final size:23
Alignment explanation
Indices: 1903805--1903860 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
1903795 CTTGTTTAAG
* *
1903805 TTTATCTATTTATTTTTAT-TTTT
1 TTTAT-TAGTTATTTTTATATATT
1903828 ATTTATTAGTTATTATTTATATATT
1 -TTTATTAGTTATT-TTTATATATT
1903853 TTTATTAG
1 TTTATTAG
1903861 AATTATACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.25
24 18 0.64
25 3 0.11
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTATTAGTTATTTTTATATATT
Found at i:1905471 original size:19 final size:20
Alignment explanation
Indices: 1905444--1905481 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1905434 TTGTGATAAT
*
1905444 TATATTTTA-ATAGTTAAAA
1 TATAATTTATATAGTTAAAA
*
1905463 TATAATTTATATATTTAAA
1 TATAATTTATATAGTTAAA
1905482 TTAAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATAATTTATATAGTTAAAA
Found at i:1905485 original size:25 final size:25
Alignment explanation
Indices: 1905439--1905487 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1905429 TGAATTTGTG
1905439 ATAATTATATTTTAATAGTTAAAAT
1 ATAATTATATTTTAATAGTTAAAAT
1905464 ATAATTTATATATTTAA-A-TTAAAA
1 ATAA-TTATAT-TTTAATAGTTAAAA
1905488 ATTTACAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
ATAATTATATTTTAATAGTTAAAAT
Found at i:1906040 original size:19 final size:18
Alignment explanation
Indices: 1906018--1906071 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
1906008 ATTTTATGTT
1906018 ATTTTTTAAATTTTTATGA
1 ATTTTTTAAATTTTTAT-A
1906037 ATTTTTTATATATTTTT-TA
1 ATTTTTTA-A-ATTTTTATA
*
1906056 A-TTTTTAAATATTTAT
1 ATTTTTTAAATTTTTAT
1906072 TAACATTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
18 6 0.19
19 10 0.32
20 2 0.06
21 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTTTAAATTTTTATA
Found at i:1906060 original size:18 final size:18
Alignment explanation
Indices: 1906020--1906074 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
1906010 TTTATGTTAT
* *
1906020 TTTTTAAATTTTTATGAA
1 TTTTTAAATATTTATTAA
* *
1906038 TTTTTTATATATTTTTTAA
1 -TTTTTAAATATTTATTAA
1906057 TTTTTAAATATTTATTAA
1 TTTTTAAATATTTATTAA
1906075 CATTACATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTTAAATATTTATTAA
Found at i:1911268 original size:24 final size:24
Alignment explanation
Indices: 1911240--1911291 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1911230 TTCGTAGGCC
* *
1911240 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
1911264 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
1911288 AAAT
1 AAAT
1911292 GTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:1912446 original size:16 final size:15
Alignment explanation
Indices: 1912404--1912438 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1912394 GCCCATTAAA
1912404 CAAATAAATAAAACC
1 CAAATAAATAAAACC
*
1912419 TAAATAAATAAAACC
1 CAAATAAATAAAACC
1912434 CAAAT
1 CAAAT
1912439 CCAATAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (15 bp):
CAAATAAATAAAACC
Found at i:1913511 original size:9 final size:9
Alignment explanation
Indices: 1913497--1913529 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1913487 CCTAAAGTTA
1913497 ATATTATTT
1 ATATTATTT
1913506 ATATTATTT
1 ATATTATTT
1913515 ATA-TATTT
1 ATATTATTT
1913523 AT-TTATT
1 ATATTATT
1913530 ATTCTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 11 0.48
9 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATATTATTT
Found at i:1913531 original size:15 final size:15
Alignment explanation
Indices: 1913498--1913544 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
1913488 CTAAAGTTAA
1913498 TATTATTTATATTATT
1 TATTATTTAT-TTATT
1913514 TATATATTTATTTA-T
1 TAT-TATTTATTTATT
*
1913529 TATTCTTTATTT-TT
1 TATTATTTATTTATT
1913543 TA
1 TA
1913545 AATGCCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 11 0.39
15 4 0.14
16 6 0.21
17 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTATTTATT
Found at i:1913643 original size:4 final size:4
Alignment explanation
Indices: 1913634--1913691 Score: 75
Period size: 4 Copynumber: 15.0 Consensus size: 4
1913624 ATATGCTTGT
* * *
1913634 TTTA TTTA TTTA CTTA TTTA TTTA TTTA TTCA TTCA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1913682 -TTA TTT- TTTA
1 TTTA TTTA TTTA
1913692 AAATATTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 6 0.12
4 42 0.88
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:1916080 original size:20 final size:20
Alignment explanation
Indices: 1916055--1916094 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1916045 CGTAAAATGA
*
1916055 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1916075 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1916095 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1916084 original size:34 final size:35
Alignment explanation
Indices: 1916040--1916106 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1916030 CAGTAAAATA
*
1916040 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
1916074 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1916107 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:1916110 original size:14 final size:15
Alignment explanation
Indices: 1916034--1916110 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1916024 GATTGCCAGT
* *
1916034 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
1916048 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
1916062 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
1916082 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
1916097 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
1916111 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:1917042 original size:29 final size:30
Alignment explanation
Indices: 1917010--1917066 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
1917000 ATTGTAAAGA
*
1917010 TTAATAGA-AAATATTATT-AATAATATTTG
1 TTAATA-ACAAATATTATTGAAAAATATTTG
1917039 TTAATAACAAATATTATTGAAAAATATT
1 TTAATAACAAATATTATTGAAAAATATT
1917067 AAAATGCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 16 0.64
30 8 0.32
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
TTAATAACAAATATTATTGAAAAATATTTG
Found at i:1924174 original size:43 final size:41
Alignment explanation
Indices: 1924127--1924216 Score: 92
Period size: 43 Copynumber: 2.1 Consensus size: 41
1924117 ATGATTTTTC
1924127 AATAATATCAAACTTAAAAAT-ATAAATAAAATACTAATAAAAT
1 AATAATATC--ACTTAAAAATCA-AAATAAAATACTAATAAAAT
* * * *
1924170 AATAAAATATCATTTAAAAATCAAATTAAAATATTAATAAACT
1 AAT--AATATCACTTAAAAATCAAAATAAAATACTAATAAAAT
1924213 AATA
1 AATA
1924217 TTTATTTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
41 1 0.03
43 32 0.80
44 1 0.03
45 6 0.15
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (41 bp):
AATAATATCACTTAAAAATCAAAATAAAATACTAATAAAAT
Found at i:1928758 original size:16 final size:16
Alignment explanation
Indices: 1928739--1928776 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1928729 AAAATTTTCA
*
1928739 AAATTTAAAATAATTT
1 AAATTTAAAATAACTT
*
1928755 AAATTCAAAATAACTT
1 AAATTTAAAATAACTT
1928771 AAATTT
1 AAATTT
1928777 CAACCAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTTAAAATAACTT
Found at i:1932639 original size:3 final size:3
Alignment explanation
Indices: 1932631--1932671 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1932621 TTACTTCCTA
*
1932631 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1932672 AAATTTATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1935178 original size:2 final size:2
Alignment explanation
Indices: 1935173--1935202 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1935163 TCTCTTTTTT
1935173 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1935203 AAGCCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1938431 original size:20 final size:20
Alignment explanation
Indices: 1938406--1938470 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
1938396 ACATGGGCTA
1938406 TATTAATAAAATTGCACATT
1 TATTAATAAAATTGCACATT
* * **
1938426 TATTAA-GAAAGTGTTC-TT
1 TATTAATAAAATTGCACATT
1938444 ATATTAATAAAATTGCACATT
1 -TATTAATAAAATTGCACATT
1938465 TATTAA
1 TATTAA
1938471 GAAAGTGTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 2 0.06
19 12 0.35
20 18 0.53
21 2 0.06
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42
Consensus pattern (20 bp):
TATTAATAAAATTGCACATT
Found at i:1938447 original size:39 final size:39
Alignment explanation
Indices: 1938404--1938492 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 39
1938394 CAACATGGGC
1938404 TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
1 TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
1938443 TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
1 TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
*
1938482 TAT-TTAGTAAA
1 TATATTAATAAA
1938493 TTTTTCGTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 7 0.14
39 42 0.86
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (39 bp):
TATATTAATAAAATTGCACATTTATTAAGAAAGTGTTCT
Found at i:1938450 original size:19 final size:19
Alignment explanation
Indices: 1938426--1938484 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1938416 ATTGCACATT
1938426 TATTAAGAAAGTGTTCTTA
1 TATTAAGAAAGTGTTCTTA
* * **
1938445 TATTAATAAAATTGCACATT-
1 TATTAA-GAAAGTGTTC-TTA
1938465 TATTAAGAAAGTGTTCTTA
1 TATTAAGAAAGTGTTCTTA
1938484 T
1 T
1938485 TTAGTAAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 12 0.41
21 2 0.07
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (19 bp):
TATTAAGAAAGTGTTCTTA
Found at i:1945028 original size:161 final size:161
Alignment explanation
Indices: 1944841--1945168 Score: 647
Period size: 161 Copynumber: 2.0 Consensus size: 161
1944831 CTCTCTTGAT
1944841 TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
1 TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
*
1944906 CTACTGAATGTTTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
66 CTACTGAATGTGTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
1944971 GGGAGTGTTACTTTTTGTTGTTCACTGATGA
131 GGGAGTGTTACTTTTTGTTGTTCACTGATGA
1945002 TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
1 TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
1945067 CTACTGAATGTGTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
66 CTACTGAATGTGTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
1945132 GGGAGTGTTACTTTTTGTTGTTCACTGATGA
131 GGGAGTGTTACTTTTTGTTGTTCACTGATGA
1945163 TTATGG
1 TTATGG
1945169 TCGCATGAGT
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 166 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (161 bp):
TTATGGGAGGGGCGCATTTAAGGAAAGCAAACTAGGAAGCCATTTCCTGTTGGAAAAGCATAGAG
CTACTGAATGTGTAGAATTAATTCATGCTGGCCTATGTGGTGCTATGCAAACCGAGTCCTTGAGT
GGGAGTGTTACTTTTTGTTGTTCACTGATGA
Found at i:1948643 original size:6 final size:6
Alignment explanation
Indices: 1948611--1948660 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
1948601 ACAGCACCTA
* *
1948611 AACAGT AATCAGT AACGGT AGCAGT AACAGT AACAGT AACAGT AACAGT
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT
1948660 A
1 A
1948661 TTCAACACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (6 bp):
AACAGT
Found at i:1948981 original size:40 final size:40
Alignment explanation
Indices: 1948935--1949021 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
1948925 AATTCATTAC
* *
1948935 TTCAGTAA-TCTCACAGTTCAATGCAGTACACATAACAATA
1 TTCAGTAACT-TCACAATTCAATGCAGTACACAAAACAATA
* *
1948975 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
1949015 TTCAGTA
1 TTCAGTA
1949022 TTCCATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 41 0.98
41 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:1950563 original size:11 final size:11
Alignment explanation
Indices: 1950547--1950571 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1950537 ACTCAAGGTC
1950547 GAAGTATCCCT
1 GAAGTATCCCT
1950558 GAAGTATCCCT
1 GAAGTATCCCT
1950569 GAA
1 GAA
1950572 CTCTTCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (11 bp):
GAAGTATCCCT
Found at i:1951130 original size:6 final size:6
Alignment explanation
Indices: 1951098--1951147 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
1951088 ACAGCACCTA
* *
1951098 AACAGT AATCAGT AACGGT AGCAGT AACAGT AACAGT AACAGT AACAGT
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT
1951147 A
1 A
1951148 TTCAACACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (6 bp):
AACAGT
Found at i:1951468 original size:40 final size:40
Alignment explanation
Indices: 1951422--1951508 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
1951412 AATTCATTAC
* *
1951422 TTCAGTAA-TCTCACAGTTCAATGCAGTACACATAACAATA
1 TTCAGTAACT-TCACAATTCAATGCAGTACACAAAACAATA
* *
1951462 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
1951502 TTCAGTA
1 TTCAGTA
1951509 TTCCATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 41 0.98
41 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:1953050 original size:11 final size:11
Alignment explanation
Indices: 1953034--1953058 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1953024 ACTCAAGGTC
1953034 GAAGTATCCCT
1 GAAGTATCCCT
1953045 GAAGTATCCCT
1 GAAGTATCCCT
1953056 GAA
1 GAA
1953059 CTCTTCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (11 bp):
GAAGTATCCCT
Found at i:1954174 original size:13 final size:13
Alignment explanation
Indices: 1954152--1954257 Score: 52
Period size: 13 Copynumber: 7.7 Consensus size: 13
1954142 CAAATTTTCC
*
1954152 TCTTTTTTTTCTT
1 TCTTTCTTTTCTT
*
1954165 TCTTTCTTTTTCCT
1 TCTTTC-TTTTCTT
* *
1954179 TCTTTCCTTTCTC
1 TCTTTCTTTTCTT
* *
1954192 TGTTTCGTTCTACTT
1 TCTTTC-TT-TTCTT
1954207 CTCTGTTCTTTTTCTT
1 -TCT-TTC-TTTTCTT
* *
1954223 TCTTT-ATTTCAT
1 TCTTTCTTTTCTT
* *
1954235 TGTTTCTTTTATT
1 TCTTTCTTTTCTT
1954248 TCTTTACTTT
1 TCTTT-CTTT
1954258 ATATTATAAT
Statistics
Matches: 67, Mismatches: 19, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
12 9 0.13
13 22 0.33
14 19 0.28
15 6 0.09
16 6 0.09
17 5 0.07
ACGTcount: A:0.05, C:0.22, G:0.04, T:0.70
Consensus pattern (13 bp):
TCTTTCTTTTCTT
Done.