Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000121.1 Hibiscus syriacus cultivar Beakdansim tig00000218_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2099483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1704556 original size:3 final size:3
Alignment explanation
Indices: 1704548--1704602 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
1704538 TTTAATAACC
* * * *
1704548 TTA TTA TTA TTCT TTA TTG TTA TTG TTA TTG TTA TT- TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1704593 TT- TTA TTA TT
1 TTA TTA TTA TT
1704603 TTCAATTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
2 4 0.10
3 35 0.85
4 2 0.05
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:1704561 original size:42 final size:43
Alignment explanation
Indices: 1704467--1704562 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 43
1704457 ATTTTTATTT
* *
1704467 TTATTTTCTTTTTTATTTATATATATATTTTTTATTACCTTAA
1 TTATTTTCTTTTTTATTTATATATATATTTTTAATAACCTTAA
* * *
1704510 TTTTTTTCTTTTTTATTTAT-TTTCTATTTTTAATAACCTT-A
1 TTATTTTCTTTTTTATTTATATATATATTTTTAATAACCTTAA
1704551 TTATTATTCTTT
1 TTATT-TTCTTT
1704563 ATTGTTATTG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 5 0.11
42 22 0.48
43 19 0.41
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (43 bp):
TTATTTTCTTTTTTATTTATATATATATTTTTAATAACCTTAA
Found at i:1704603 original size:19 final size:18
Alignment explanation
Indices: 1704548--1704604 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
1704538 TTTAATAACC
*
1704548 TTATTATTATTCTTTATT
1 TTATTATTATTTTTTATT
* *
1704566 GTTATTGTTA-TTGTTATT
1 -TTATTATTATTTTTTATT
1704584 TTATTATTATTTTATTATT
1 TTATTATTATTTT-TTATT
1704603 TT
1 TT
1704605 CAATTTCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 8 0.26
18 8 0.26
19 15 0.48
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (18 bp):
TTATTATTATTTTTTATT
Found at i:1704604 original size:8 final size:9
Alignment explanation
Indices: 1704548--1704602 Score: 51
Period size: 8 Copynumber: 6.2 Consensus size: 9
1704538 TTTAATAACC
1704548 TTATTATTA
1 TTATTATTA
* *
1704557 TTCTTTATTG
1 TT-ATTATTA
*
1704567 TTATTGTTA
1 TTATTATTA
*
1704576 TTGTTATT-
1 TTATTATTA
1704584 TTATTATTA
1 TTATTATTA
1704593 TT-TTATTA
1 TTATTATTA
1704601 TT
1 TT
1704603 TTCAATTTCT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
8 15 0.42
9 14 0.39
10 7 0.19
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (9 bp):
TTATTATTA
Found at i:1709371 original size:110 final size:110
Alignment explanation
Indices: 1708435--1709358 Score: 1434
Period size: 110 Copynumber: 8.4 Consensus size: 110
1708425 CTGAGTCTCG
* * * *
1708435 TTCAAAGTCAATTTCAACTTCACATCGAATGATATTGGACTCGAGATAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * * *
1708500 CAGTGAAGGGGGGACTGACTGTTAACAAACAACTTTTTAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* ** *
1708545 TTCAGAGTCAATTTCAACTTCACAGCGAAGTATATTACACTCGAGATAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
*
1708610 CAGCGAAGAGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* *
1708655 TTCAGAGTCAATTTCAACTTCACAACGAATGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1708720 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
*
1708765 TTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
*
1708830 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCATTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
*
1708875 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * *
1708940 CAGCGAAGGGGCGATTGAATGTCAACAAACAAATTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* *
1708985 TTTAGAGTCAATTTCAACTTCATAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * *
1709050 CAACGAAGGGGCGACTGACTATCAATAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* *
1709095 TTCAGAGTCAATTTCAACTTCACAGCAAATGATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* *
1709160 CAGCGAATGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* ** * * *
1709205 TTCAGAGTCAATTTCAACTTCACAACGAAATATATTCGCCTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* ** * ** * *
1709270 CAGCGAATGGGCGGTTGGCTGTCAACAAACAACTTCCCAATTTTA
66 CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* *
1709315 TTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGA
1 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
1709359 AACAGTACAA
Statistics
Matches: 749, Mismatches: 65, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 749 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (110 bp):
TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
CAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCA
Found at i:1709757 original size:84 final size:84
Alignment explanation
Indices: 1709616--1710009 Score: 502
Period size: 84 Copynumber: 4.7 Consensus size: 84
1709606 GATATCGTGT
** * * * *
1709616 TCATTTGCAATATAGCTCAAGGAAAGAAGGACTATTTGCCAACAAAAGACATTCGAGTTCGACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
1709681 CGCTCAGCTCCAAGGCACA
66 CACTCAACTCAAAGGCACA
* * *
1709700 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
1709765 CGCTCAGCTCCAAGGCACA
66 CACTCAACTCAAAGGCACA
* * * *
1709784 TCATTTGCAACATAGCTCAAGTCAAGAAGGGCTATTTGCCAACAAAATACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
1709849 CACTCAACTCAAAGGCACA
66 CACTCAACTCAAAGGCACA
* * * *
1709868 TCATTTGTAGCATAGCTTAAGGCAAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
*
1709933 CACTCAACTTAAAGGCACA
66 CACTCAACTCAAAGGCACA
* * * * * * *
1709952 TCATTTACAGCTTAGCTCAAGGCAAGAAGTGATATCTGACAATAAAA-ACCATCGAGTT
1 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTT
1710010 GATTCCATTC
Statistics
Matches: 272, Mismatches: 38, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
83 10 0.04
84 262 0.96
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (84 bp):
TCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
CACTCAACTCAAAGGCACA
Found at i:1710332 original size:22 final size:20
Alignment explanation
Indices: 1710303--1710369 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 20
1710293 CTTAAAAAAT
1710303 ATTA-TATTGTTATTATAATA
1 ATTATTATT-TTATTATAATA
* *
1710323 ATTACTTATTATTATTATTATT
1 ATTA-TTATT-TTATTATAATA
* *
1710345 ATTATTAATTTA-TATTATA
1 ATTATTATTTTATTATAATA
1710364 ATTATT
1 ATTATT
1710370 TTGTGGGCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.30
20 7 0.17
21 4 0.10
22 17 0.43
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (20 bp):
ATTATTATTTTATTATAATA
Found at i:1710334 original size:3 final size:3
Alignment explanation
Indices: 1710302--1710369 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
1710292 GCTTAAAAAA
* * *
1710302 TAT TA- TAT TGT TAT TAT AAT AAT TACT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* *
1710347 TAT TAA T-T TA- TAT TAT AAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1710370 TTGTGGGCCA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1710351 original size:25 final size:25
Alignment explanation
Indices: 1710304--1710369 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
1710294 TTAAAAAATA
* * *
1710304 TTATATTGTTATTATAATAATT-AC
1 TTATATTATTATTATTATAATTAAT
*
1710328 TTATTATTATTATTATTATTATTAAT
1 TTA-TATTATTATTATTATAATTAAT
*
1710354 TTATATTATAATTATT
1 TTATATTATTATTATT
1710370 TTGTGGGCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 3 0.09
25 28 0.80
26 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATATTATTATTATTATAATTAAT
Found at i:1711523 original size:45 final size:46
Alignment explanation
Indices: 1711474--1711561 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
1711464 TCGATACTAC
* **
1711474 TTATATATATATATTATT-CTTTTTCTTTTTATTTTCTTTTTTTAT
1 TTATATATATATATTATTACCTTAACTTTTTATTTTCTTTTTTTAT
* * *
1711519 TTATATATATTTTTTATTACCTTAACTTTTTTTTTTCTTTTTT
1 TTATATATATATATTATTACCTTAACTTTTTATTTTCTTTTTT
1711562 AATAACCTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 16 0.44
46 20 0.56
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (46 bp):
TTATATATATATATTATTACCTTAACTTTTTATTTTCTTTTTTTAT
Found at i:1712143 original size:17 final size:16
Alignment explanation
Indices: 1712123--1712210 Score: 65
Period size: 17 Copynumber: 5.3 Consensus size: 16
1712113 TATAATCATA
1712123 TGATATATGCAAATATC
1 TGATATATG-AAATATC
*
1712140 TGATA-ACTGTAATCATC
1 TGATATA-TGAAAT-ATC
1712157 TGATATATGTAAATATC
1 TGATATATG-AAATATC
* *
1712174 TTATA-ATTGTAATCATC
1 TGATATA-TGAAAT-ATC
*
1712191 TGATATGT-AAATATC
1 TGATATATGAAATATC
1712206 TGATA
1 TGATA
1712211 ATTGAAAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
15 8 0.14
16 11 0.19
17 34 0.60
18 4 0.07
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (16 bp):
TGATATATGAAATATC
Found at i:1712146 original size:34 final size:34
Alignment explanation
Indices: 1712104--1712228 Score: 146
Period size: 34 Copynumber: 3.7 Consensus size: 34
1712094 TTAATATATG
*
1712104 TCTGATAACTATAATCATATGATATATGCAAATA
1 TCTGATAACTATAATCATATGATATATGTAAATA
* *
1712138 TCTGATAACTGTAATCATCTGATATATGTAAATA
1 TCTGATAACTATAATCATATGATATATGTAAATA
* * * *
1712172 TCTTATAATTGTAATCATCTG--ATATGTAAATA
1 TCTGATAACTATAATCATATGATATATGTAAATA
* *
1712204 TCTGATAATTGAAAATCATATGATA
1 TCTGATAACT-ATAATCATATGATA
1712229 ACTGTAACGT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
32 20 0.25
33 8 0.10
34 50 0.63
35 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (34 bp):
TCTGATAACTATAATCATATGATATATGTAAATA
Found at i:1712644 original size:97 final size:98
Alignment explanation
Indices: 1712540--1712726 Score: 245
Period size: 97 Copynumber: 1.9 Consensus size: 98
1712530 GTTTACACAA
* * *
1712540 TTTAATCTCACTTTATATC-TTTATAATTGAAGCATTTAATTTTTTCAATCCCACATTTTCCCTT
1 TTTAATCTAACTTTATA-CATTTATAATTGAAGCACTTAATTTTTTCAATCCCACATTTTACCTT
1712604 TATAATTGAAGCTC-CT-ATTTTTTCCCTAACTTT
65 TATAATTG-AGCTCTCTGATTTTTTCCCTAACTTT
* * * * * *
1712637 TTTAATCTAACTTTTTACATTTATAATTGAGGCCCTTAATTTTTTCAATCTCACTTTTTATCTTT
1 TTTAATCTAACTTTATACATTTATAATTGAAGCACTTAATTTTTTCAATCCCACATTTTACCTTT
*
1712702 ATAATTGAGGTCTCTGATTTTTTCC
66 ATAATTGAGCTCTCTGATTTTTTCC
1712727 AGTCTCACTT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
96 5 0.06
97 63 0.82
98 9 0.12
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.51
Consensus pattern (98 bp):
TTTAATCTAACTTTATACATTTATAATTGAAGCACTTAATTTTTTCAATCCCACATTTTACCTTT
ATAATTGAGCTCTCTGATTTTTTCCCTAACTTT
Found at i:1712746 original size:44 final size:43
Alignment explanation
Indices: 1712629--1712793 Score: 167
Period size: 44 Copynumber: 3.8 Consensus size: 43
1712619 TATTTTTTCC
* * * *
1712629 CTAACTTTTTT-AATCTAACTTTTTACATTTATAATTGAGG-CC
1 CTAA-TTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGTCA
* * *
1712671 CTTAATTTTTTCAATCTCACTTTTTATCTTTATAATTGAGGTCT
1 C-TAATTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGTCA
* * *
1712715 CTGATTTTTTCCAGTCTCACTTTCTACCTTTATAATTGAAGTCA
1 CTAATTTTTT-CAATCTCACTTTCTACCTTTATAATTGAGGTCA
*
1712759 CTAACTTTTT-AATCTCAC-TTCTTACCTTTATAATT
1 CTAATTTTTTCAATCTCACTTTC-TACCTTTATAATT
1712794 AAGACCTCTA
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
41 3 0.03
42 27 0.26
43 37 0.35
44 38 0.36
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (43 bp):
CTAATTTTTTCAATCTCACTTTCTACCTTTATAATTGAGGTCA
Found at i:1712788 original size:42 final size:43
Alignment explanation
Indices: 1712629--1712793 Score: 172
Period size: 43 Copynumber: 3.8 Consensus size: 43
1712619 TATTTTTTCC
* * * * *
1712629 CTAACTTTTTTAATCTAACTTTTTACATTTATAATTG-AGGCC
1 CTAACTTTTTCAATCTCACTTTTTACCTTTATAATTGAAGTCA
* * * *
1712671 CTTAATTTTTTCAATCTCACTTTTTATCTTTATAATTGAGGTCT
1 C-TAACTTTTTCAATCTCACTTTTTACCTTTATAATTGAAGTCA
* * * *
1712715 CTGATTTTTTCCAGTCTCACTTTCTACCTTTATAATTGAAGTCA
1 CTAACTTTTT-CAATCTCACTTTTTACCTTTATAATTGAAGTCA
*
1712759 CTAACTTTTT-AATCTCACTTCTTACCTTTATAATT
1 CTAACTTTTTCAATCTCACTTTTTACCTTTATAATT
1712794 AAGACCTCTA
Statistics
Matches: 101, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
42 23 0.23
43 39 0.39
44 39 0.39
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (43 bp):
CTAACTTTTTCAATCTCACTTTTTACCTTTATAATTGAAGTCA
Found at i:1712808 original size:86 final size:87
Alignment explanation
Indices: 1712646--1712810 Score: 208
Period size: 86 Copynumber: 1.9 Consensus size: 87
1712636 TTTTAATCTA
* * * * * *
1712646 ACTTTTTACATTTATAATTGAGGCCCTTAATTTTTTCAATCTCACTTTTTATCTTTATAATTGAG
1 ACTTTCTACATTTATAATTGAGGCACTTAACTTTTTCAATCTCACTTCTTACCTTTATAATTAAG
** *
1712711 GTCTCTGATTTTTTCCAGTCTC
66 ACCTCTAATTTTTTCCAGTCTC
* *
1712733 ACTTTCTACCTTTATAATTGAAGTCAC-TAACTTTTT-AATCTCACTTCTTACCTTTATAATTAA
1 ACTTTCTACATTTATAATTG-AGGCACTTAACTTTTTCAATCTCACTTCTTACCTTTATAATTAA
1712796 GACCTCTAATTTTTT
65 GACCTCTAATTTTTT
1712811 AATAATTTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
86 36 0.55
87 26 0.39
88 4 0.06
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (87 bp):
ACTTTCTACATTTATAATTGAGGCACTTAACTTTTTCAATCTCACTTCTTACCTTTATAATTAAG
ACCTCTAATTTTTTCCAGTCTC
Found at i:1712810 original size:42 final size:42
Alignment explanation
Indices: 1712629--1712813 Score: 176
Period size: 42 Copynumber: 4.3 Consensus size: 42
1712619 TATTTTTTCC
* * *
1712629 CTAACTTTTTTAATCTAACTTTTTACATTTATAATTGAGGCC-
1 CTAA-TTTTTTAATCTCACTTTTTACCTTTATAATTAAGGCCT
* * *
1712671 CTTAATTTTTTCAATCTCACTTTTTATCTTTATAATTGAGGTCT
1 C-TAATTTTTT-AATCTCACTTTTTACCTTTATAATTAAGGCCT
* * * * *
1712715 CTGATTTTTTCCAGTCTCACTTTCTACCTTTATAATTGAA-GTCA
1 CTAATTTTTT--AATCTCACTTTTTACCTTTATAATT-AAGGCCT
* * *
1712759 CTAACTTTTTAATCTCACTTCTTACCTTTATAATTAAGACCT
1 CTAATTTTTTAATCTCACTTTTTACCTTTATAATTAAGGCCT
1712801 CTAATTTTTTAAT
1 CTAATTTTTTAAT
1712814 AATTTAAGAT
Statistics
Matches: 118, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
41 2 0.02
42 42 0.36
43 38 0.32
44 35 0.30
45 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (42 bp):
CTAATTTTTTAATCTCACTTTTTACCTTTATAATTAAGGCCT
Found at i:1718133 original size:123 final size:124
Alignment explanation
Indices: 1717893--1718137 Score: 462
Period size: 123 Copynumber: 2.0 Consensus size: 124
1717883 GATTTTAAGA
1717893 TGGTGCGGTGAATTTTATAATTTGAATATTTTAAATGAATTATTTTAAATTATTTGTATTTATAA
1 TGGTGCGGTGAATTTTATAATTTGAATATTTTAAATGAATTATTTTAAATTATTTGTATTTATAA
1717958 TTTTTTATTTAAATAAATCATTTTAAAAGAAATTTTAGCCCATTAGAATTTCTTCTGAT
66 TTTTTTATTTAAATAAATCATTTTAAAAGAAATTTTAGCCCATTAGAATTTCTTCTGAT
1718017 TGGTGCGGTGAATTTTATAATTTGAATATTTTAAATGAATT-TTTTAAATTATTTGTATTTATAA
1 TGGTGCGGTGAATTTTATAATTTGAATATTTTAAATGAATTATTTTAAATTATTTGTATTTATAA
1718081 TTTTTTATTTAAATAAATCATTTTAAAAG-AA-TTTAGCCCATTAGAATTT-TTCTGAT
66 TTTTTTATTTAAATAAATCATTTTAAAAGAAATTTTAGCCCATTAGAATTTCTTCTGAT
1718137 T
1 T
1718138 AAAAAATAGT
Statistics
Matches: 121, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
120 8 0.07
121 18 0.15
122 2 0.02
123 52 0.43
124 41 0.34
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (124 bp):
TGGTGCGGTGAATTTTATAATTTGAATATTTTAAATGAATTATTTTAAATTATTTGTATTTATAA
TTTTTTATTTAAATAAATCATTTTAAAAGAAATTTTAGCCCATTAGAATTTCTTCTGAT
Found at i:1719613 original size:73 final size:75
Alignment explanation
Indices: 1719481--1719629 Score: 284
Period size: 73 Copynumber: 2.0 Consensus size: 75
1719471 AGTCCGTTGT
1719481 GTGCACGGCAGTCATTCAGCACTTAAATGGCTTCGACGAAACTGTTGTAAGCTAGAAGTGGAGCC
1 GTGCACGGCAGTCATTCAGCACTTAAATGGCTTCGACGAAACTGTTGTAAGCTAGAAGTGGAGCC
1719546 TTGGCTGGAA
66 TTGGCTGGAA
1719556 GTGCACGGCAGTCATTCAGCACTTAAAT-G-TTCGACGAAACTGTTGTAAGCTAGAAGTGGAGCC
1 GTGCACGGCAGTCATTCAGCACTTAAATGGCTTCGACGAAACTGTTGTAAGCTAGAAGTGGAGCC
1719619 TTGGCTGGAA
66 TTGGCTGGAA
1719629 G
1 G
1719630 ACAAACATAC
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
73 45 0.61
74 1 0.01
75 28 0.38
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (75 bp):
GTGCACGGCAGTCATTCAGCACTTAAATGGCTTCGACGAAACTGTTGTAAGCTAGAAGTGGAGCC
TTGGCTGGAA
Found at i:1721210 original size:29 final size:29
Alignment explanation
Indices: 1721176--1721234 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1721166 CCTAAATTAA
1721176 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1721205 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1721234 T
1 T
1721235 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1725873 original size:29 final size:29
Alignment explanation
Indices: 1725839--1725897 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1725829 CCTAAATTAA
1725839 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1725868 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1725897 T
1 T
1725898 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1727821 original size:9 final size:9
Alignment explanation
Indices: 1727807--1727832 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1727797 GAAATCGGTT
1727807 AATTAACCG
1 AATTAACCG
1727816 AATTAACCG
1 AATTAACCG
1727825 AATTAACC
1 AATTAACC
1727833 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:1727876 original size:11 final size:11
Alignment explanation
Indices: 1727860--1727887 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1727850 TAAGAGGCCC
1727860 AATCCATTTAA
1 AATCCATTTAA
1727871 AATCCATTTAA
1 AATCCATTTAA
1727882 AATCCA
1 AATCCA
1727888 AATCAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.32
Consensus pattern (11 bp):
AATCCATTTAA
Found at i:1727969 original size:17 final size:17
Alignment explanation
Indices: 1727947--1727985 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1727937 TGAATCAAAT
1727947 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1727964 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1727981 -AATTA
1 TAATTA
1727986 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1728511 original size:3 final size:3
Alignment explanation
Indices: 1728503--1728539 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1728493 ATATTTATAC
1728503 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1728540 ATATAAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1728585 original size:27 final size:27
Alignment explanation
Indices: 1728505--1728587 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
1728495 ATTTATACAT
* *
1728505 AATAAT-AATAATAATAATAAT-AATAAT
1 AATAATAAAT-ATAA-AACAATAAATAAA
*
1728532 AATAATAAATATAAAACAATAACTAAA
1 AATAATAAATATAAAACAATAAATAAA
*
1728559 AATAATGAAAT-TAAAACTATAAATAAA
1 AATAAT-AAATATAAAACAATAAATAAA
1728586 AA
1 AA
1728588 ACTAGTAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
26 5 0.10
27 36 0.75
28 7 0.15
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.27
Consensus pattern (27 bp):
AATAATAAATATAAAACAATAAATAAA
Found at i:1729771 original size:19 final size:19
Alignment explanation
Indices: 1729747--1729783 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1729737 GGTTTCCTTT
1729747 GCATCTGGGTTGGGTCTCC
1 GCATCTGGGTTGGGTCTCC
1729766 GCATCTGGGTTGGGTCTC
1 GCATCTGGGTTGGGTCTC
1729784 TAGATCTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.24, G:0.38, T:0.32
Consensus pattern (19 bp):
GCATCTGGGTTGGGTCTCC
Found at i:1729790 original size:19 final size:19
Alignment explanation
Indices: 1729747--1729793 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1729737 GGTTTCCTTT
*
1729747 GCATCTGGGTTGGGTCTCC
1 GCATCTGGGTTGGGTCTCA
1729766 GCATCTGGGTTGGGTCTCTA
1 GCATCTGGGTTGGGTCTC-A
1729786 G-ATCTGGG
1 GCATCTGGG
1729794 CCGGTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 25 0.96
20 1 0.04
ACGTcount: A:0.09, C:0.21, G:0.38, T:0.32
Consensus pattern (19 bp):
GCATCTGGGTTGGGTCTCA
Found at i:1729819 original size:3 final size:3
Alignment explanation
Indices: 1729811--1729932 Score: 151
Period size: 3 Copynumber: 40.0 Consensus size: 3
1729801 ATTTGGCTTG
1729811 TAA TAA TAA TAA TAA TAA TAA TAAA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA
* *
1729858 TAA TAA TAA -AA TGA TAA TAA TAA TAA TAA TAA T-A TAA TAT TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
*
1729904 TAA TAAA TAA AAA TAA TAA TAAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA T-AA TAA TAA
1729933 AAAAACAAAT
Statistics
Matches: 106, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
2 5 0.05
3 87 0.82
4 14 0.13
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1729848 original size:26 final size:25
Alignment explanation
Indices: 1729812--1729932 Score: 153
Period size: 23 Copynumber: 4.9 Consensus size: 25
1729802 TTTGGCTTGT
1729812 AATAATAATAATAATAATAATAAATA
1 AATAATAATAATAATAATAAT-AATA
1729838 AATAATAATAATAATAATAATAAT-
1 AATAATAATAATAATAATAATAATA
*
1729862 AATAA-AATGATAATAATAATAAT-
1 AATAATAATAATAATAATAATAATA
*
1729885 AATAAT-ATAATATTAA-ATATAATA
1 AATAATAATAATAATAATA-ATAATA
*
1729909 AATAAAAATAATAATAAATAATAA
1 AATAATAATAATAAT-AATAATAA
1729933 AAAAACAAAT
Statistics
Matches: 84, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
22 1 0.01
23 35 0.42
24 10 0.12
25 10 0.12
26 27 0.32
27 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (25 bp):
AATAATAATAATAATAATAATAATA
Found at i:1730282 original size:111 final size:111
Alignment explanation
Indices: 1730157--1730716 Score: 620
Period size: 111 Copynumber: 4.9 Consensus size: 111
1730147 TGTAATCTAA
* * * * *
1730157 CAAAATGTTGAACAAATTCTTCTCATTATGAACTCCTTCTTCCTCTTCAGATAAGTTCTTTTCAT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
*
1730222 TATGAACTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAG
66 TATGAACTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAG
* * *
1730268 CAAAAAGTTGAACAAGTTCTTCTCATTATGAAATTCTTATTCTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
* ** * * ** * *
1730333 TATGAACACTTCTACAAATGTTAATGCTGATCTATCTTCTTCTGTGA-AAGAGTCAAG
66 TATGAACTCTTCT-GGAA----AA-GTTGATC---CATC--GAGTGATGA-ATTCAAG
* * *
1730390 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
* * *
1730455 TATGAACT-TTCTGGCAACGTTGATCCATCGAATGATGAATTCAAG
66 TATGAACTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAG
* * * *
1730500 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCATCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCCTCTTCAGATGAGTTCTTCTCA
* * ** * * *
1730565 TTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAG
65 TTATGAACTCT-TCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAG
*
1730613 CAAAAAGTTGAACAAGTTCTTCTCATTGTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCA
* * *
1730678 TTATGAACTCTTCTGGAAATGTTGATCCATTGAATGATG
65 TTATGAACTCTTCTGGAAAAGTTGATCCATCGAGTGATG
1730717 GATTTGAATC
Statistics
Matches: 372, Mismatches: 60, Indels: 33
0.80 0.13 0.07
Matches are distributed among these distances:
110 46 0.12
111 101 0.27
112 30 0.08
113 96 0.26
115 6 0.02
116 3 0.01
117 6 0.02
120 4 0.01
121 5 0.01
122 75 0.20
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (111 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAG
Found at i:1730570 original size:233 final size:223
Alignment explanation
Indices: 1730157--1730716 Score: 728
Period size: 233 Copynumber: 2.5 Consensus size: 223
1730147 TGTAATCTAA
* * * *
1730157 CAAAATGTTGAACAAATTCTTCTCATTATGAACTCCTTCTTCCTCTTCAGATAAGTTCTTTTCAT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
* * *
1730222 TATGAACTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCAAAAAGTTGAACAAGTTC
66 TATGAACTCTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAATTC
*
1730287 TTCTCATTATGAAATTCTTATTCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTACAAAT
131 TTCTCATTATGAAATTCTTATTCTTCATCAGATGAGTTCTTCTCATTATG-A-AC-TCT--AAAT
** * *
1730352 GTTAATGCTGATCTATCTTCTTCTGTGAA-AGAGTCAAG
191 GGCAATGCTGATCCA-C--C--CAGTGAAGA-AGTCAAG
* *
1730390 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
* * *
1730455 TATGAACT-TTCTGGCAACGTTGATCCATCGAATGATGAATTCAAGCAAAAGGTTGAACAAATTC
66 TATGAACTCTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAATTC
* * *
1730519 TTCTCATTATGAACTTCTTCTTTCTTCATCAGATGAGTTCTTCTCATTATGAACTCTAACTGGCA
131 TTCTCATTATGAAATTCTT-ATTCTTCATCAGATGAGTTCTTCTCATTATGAACTCTAAATGGCA
* * * * *
1730584 CTGCTGATCCACCGAGTGATGAATTTAAG
195 ATGCTGATCCACCCAGTGAAGAAGTCAAG
* *
1730613 CAAAAAGTTGAACAAGTTCTTCTCATTGTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCA
* *
1730678 TTATGAACTCTTCTGGAAATGTTGATCCATTGAATGATG
65 TTATGAACTCTTCTGGAAAAGTTGATCCATCGAATGATG
1730717 GATTTGAATC
Statistics
Matches: 292, Mismatches: 31, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
223 49 0.17
224 30 0.10
225 27 0.09
227 1 0.00
228 14 0.05
230 3 0.01
231 2 0.01
232 69 0.24
233 97 0.33
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (223 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
TATGAACTCTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCAAAAAGTTGAACAAATTC
TTCTCATTATGAAATTCTTATTCTTCATCAGATGAGTTCTTCTCATTATGAACTCTAAATGGCAA
TGCTGATCCACCCAGTGAAGAAGTCAAG
Found at i:1730624 original size:113 final size:111
Alignment explanation
Indices: 1730157--1730706 Score: 600
Period size: 113 Copynumber: 4.8 Consensus size: 111
1730147 TGTAATCTAA
* * * * * *
1730157 CAAAATGTTGAACAAATTCTTCTCATTATGAACTCCTTCTTCCTCTTCAGATAAGTTCTTTTCAT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
1730222 TATGAACTCTTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAG
66 TATGAACTCTACTGGCAATGCTGATCCACCGAGTGATGAATTCAAG
* *
1730268 CAAAAAGTTGAACAAGTTCTTCTCATTATGAAATTCTTATTCTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
** * ** * *
1730333 TATGAACACTTCTACAAATGTTAATGCTGATCTATCTTCTTCTGTGA-AAGAGTCAAG
66 TATG-A-AC-TCTAC---TGGCAATGCTGATCCA-C--C--GAGTGATGA-ATTCAAG
* * * *
1730390 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
1730455 TATGAACT-TTCTGGCAACGTTGATCCATCGAATGATGAATTCAAG
66 TATGAACTCTACTGGCAATGCTGATCCACCGAGTGATGAATTCAAG
* * *
1730500 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCATCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATGAGTTCTTCTCA
* *
1730565 TTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAG
65 TTATGAACTCT-ACTGGCAATGCTGATCCACCGAGTGATGAATTCAAG
*
1730613 CAAAAAGTTGAACAAGTTCTTCTCATTGTGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
* * *
1730678 TTATGAACTCTTCTGGAAATGTTGATCCA
65 TTATGAACTCTACTGGCAATGCTGATCCA
1730707 TTGAATGATG
Statistics
Matches: 364, Mismatches: 58, Indels: 33
0.80 0.13 0.07
Matches are distributed among these distances:
110 46 0.13
111 93 0.26
112 19 0.05
113 100 0.27
114 4 0.01
115 11 0.03
117 11 0.03
118 2 0.01
119 1 0.00
120 3 0.01
121 2 0.01
122 72 0.20
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (111 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTACTGGCAATGCTGATCCACCGAGTGATGAATTCAAG
Found at i:1731891 original size:18 final size:19
Alignment explanation
Indices: 1731863--1731918 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1731853 TTTACAAAAT
1731863 AAAAGAATAAATTGAATTTC
1 AAAA-AATAAATTGAATTTC
* *
1731883 -GAAAATAAATTGAATCTC
1 AAAAAATAAATTGAATTTC
1731901 AAAAAATAAATTGAATTT
1 AAAAAATAAATTGAATTT
1731919 AGAGAAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.30
Consensus pattern (19 bp):
AAAAAATAAATTGAATTTC
Found at i:1732277 original size:9 final size:10
Alignment explanation
Indices: 1732263--1732310 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1732253 TTGACCCTCA
1732263 TTTTTTATTT
1 TTTTTTATTT
1732273 TTTTTTATTT
1 TTTTTTATTT
*
1732283 TTTCTTTCTTT
1 TTT-TTTATTT
1732294 TTTCATTTCATTT
1 TTT--TTT-ATTT
1732307 TTTT
1 TTTT
1732311 AAGCATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 13 0.41
11 10 0.31
12 3 0.09
13 6 0.19
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:1732284 original size:17 final size:19
Alignment explanation
Indices: 1732260--1732301 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1732250 ATCTTGACCC
1732260 TCATTTTTTATTT-TTTTT
1 TCATTTTTTATTTCTTTTT
*
1732278 T-ATTTTTTCTTTCTTTTT
1 TCATTTTTTATTTCTTTTT
1732296 TCATTT
1 TCATTT
1732302 CATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 10 0.48
18 7 0.33
19 4 0.19
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (19 bp):
TCATTTTTTATTTCTTTTT
Found at i:1739652 original size:15 final size:15
Alignment explanation
Indices: 1739629--1739660 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1739619 TGCAATAAAT
1739629 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1739644 AATGCATGTATGCAA
1 AATGAATGTATGCAA
1739659 AA
1 AA
1739661 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1742649 original size:33 final size:33
Alignment explanation
Indices: 1742607--1742674 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1742597 CTCTGACAGA
*
1742607 AAAATAAATAATGAAATA-AAATACT-TGCAAAT
1 AAAATAAATAAT-AAATATAAATACTATGAAAAT
*
1742639 AAAATGAAATAATATATATAAATACTATGAAAAT
1 AAAAT-AAATAATAAATATAAATACTATGAAAAT
1742673 AA
1 AA
1742675 TAAGTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 9 0.29
33 14 0.45
34 8 0.26
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.26
Consensus pattern (33 bp):
AAAATAAATAATAAATATAAATACTATGAAAAT
Found at i:1743428 original size:3 final size:3
Alignment explanation
Indices: 1743420--1743480 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
1743410 ATATTTATAC
*
1743420 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA A-A ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1743466 ATA ACTA AAA ATA AT
1 ATA A-TA ATA ATA AT
1743481 GAAATTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1744756 original size:3 final size:3
Alignment explanation
Indices: 1744735--1744845 Score: 102
Period size: 3 Copynumber: 36.0 Consensus size: 3
1744725 ATTTAGCCTG
* * *
1744735 TAA TAA CAA TAA TAT TAA TAA TAA TAA TAA TAAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
1744781 -AA TGA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAT TAA -ATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
1744824 TAAA TAAA TAAA TAAA TAA TAA
1 T-AA T-AA T-AA T-AA TAA TAA
1744846 ATAAAAACAA
Statistics
Matches: 92, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
2 5 0.05
3 68 0.74
4 19 0.21
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1744797 original size:36 final size:37
Alignment explanation
Indices: 1744750--1744847 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 37
1744740 ACAATAATAT
1744750 TAATAATAATAATAATAAATTATAATAATAAAATGATAA
1 TAATAATAATAATAATAAATTATAATAAT-AAAT-ATAA
*
1744789 TAATAATAATAATAAT-AA-TATAATATTAAATATAA
1 TAATAATAATAATAATAAATTATAATAATAAATATAA
1744824 TAAATAAATAAATAAATAATAAAT
1 T-AAT-AAT-AAT-AATAATAAAT
1744848 AAAAACAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
35 5 0.10
36 7 0.13
37 11 0.21
38 5 0.10
39 22 0.42
40 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (37 bp):
TAATAATAATAATAATAAATTATAATAATAAATATAA
Found at i:1744831 original size:4 final size:4
Alignment explanation
Indices: 1744815--1744850 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
1744805 AATATAATAT
1744815 TAAA TATAA TAAA TAAA TAAA TAAA T-AA TAAA TAAA
1 TAAA TA-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1744851 AACAAATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:1753293 original size:20 final size:20
Alignment explanation
Indices: 1753249--1753465 Score: 139
Period size: 20 Copynumber: 10.6 Consensus size: 20
1753239 AATGACCAAT
* *
1753249 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1753268 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1753288 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
1753308 AAAATCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * * *
1753331 AAAATCGCAATGCAATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1753351 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1753371 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1753391 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1753411 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1753434 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
*
1753454 AGAATCGCAACG
1 AAAATCGCAACG
1753466 TTGAAAATCG
Statistics
Matches: 158, Mismatches: 33, Indels: 13
0.77 0.16 0.06
Matches are distributed among these distances:
19 17 0.11
20 109 0.69
23 32 0.20
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1753426 original size:60 final size:62
Alignment explanation
Indices: 1753333--1753448 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 62
1753323 TTTAGAAGAA
* * *
1753333 AATCGCAATGCAATTGATAGAATCGCAATGCGATTTA-TAG-AATCGCAATGCGATTTATAT
1 AATCGCAATGCAATTGAGAGAATCGCAACGCGATTTAGAAGAAATCGCAATGCGATTTATAT
* *
1753393 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGA
1 AATCGCAATGCAATTGAGAGAATCGCAACGCGATTTAGAAG-AAATCGCAATGCGA
1753449 CTGAGAGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 33 0.69
61 2 0.04
63 13 0.27
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (62 bp):
AATCGCAATGCAATTGAGAGAATCGCAACGCGATTTAGAAGAAATCGCAATGCGATTTATAT
Found at i:1753579 original size:6 final size:6
Alignment explanation
Indices: 1753568--1753616 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
1753558 GACACGTATT
1753568 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1753616 A
1 A
1753617 GACGGCGGCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1754315 original size:6 final size:6
Alignment explanation
Indices: 1754299--1754402 Score: 201
Period size: 6 Copynumber: 17.5 Consensus size: 6
1754289 TCTCGTCTCG
1754299 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1754346 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1754394 GGTCGT GGT
1 GGTCGT GGT
1754403 AATACGTGTC
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.05
6 93 0.95
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1754505 original size:20 final size:20
Alignment explanation
Indices: 1754480--1754523 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1754470 TTTTTAACTA
*
1754480 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
1754500 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
1754520 TTCT
1 TTCT
1754524 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:1754533 original size:20 final size:20
Alignment explanation
Indices: 1754510--1754807 Score: 161
Period size: 20 Copynumber: 14.6 Consensus size: 20
1754500 TTCTTTTTAA
1754510 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1754530 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1754550 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1754570 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
1754590 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
1754613 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1754633 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
1754653 CATTGTGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
1754673 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
1754696 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
1754717 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
1754735 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
1754757 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1754777 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
1754796 CGTTGCGATTTT
1 CGTTGCGATTTT
1754808 ATTGGTCATT
Statistics
Matches: 225, Mismatches: 42, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 158 0.70
21 14 0.06
22 6 0.03
23 28 0.12
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:1754556 original size:40 final size:40
Alignment explanation
Indices: 1754512--1754703 Score: 231
Period size: 40 Copynumber: 4.7 Consensus size: 40
1754502 CTTTTTAACG
1754512 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * *
1754552 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
1754592 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * *
1754635 TTGCGATTCTATAAATCGCATTGTGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1754675 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
1754704 ACTTGGAAGC
Statistics
Matches: 125, Mismatches: 21, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
40 73 0.58
41 2 0.02
42 4 0.03
43 46 0.37
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:1754628 original size:83 final size:83
Alignment explanation
Indices: 1754520--1754703 Score: 305
Period size: 83 Copynumber: 2.2 Consensus size: 83
1754510 CGTTGCGATT
* * * * *
1754520 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
*
1754585 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
*
1754603 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGTGATTCTATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1754668 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
1754686 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
1754704 ACTTGGAAGC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 94 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:1754797 original size:19 final size:20
Alignment explanation
Indices: 1754757--1754807 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1754747 TTCTTTTTAA
*
1754757 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
1754777 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
1754796 CGTTGCGATTTT
1 CGTTGCGATTTT
1754808 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:1757693 original size:42 final size:42
Alignment explanation
Indices: 1757578--1757679 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 42
1757568 TCCACTTTAG
* * * *
1757578 ATGCCATCTCCTCACGGGCATATGCCAAGCCCACCAGTTCAT
1 ATGCCATCTCCGCATGGGTATATGCCAAGCCCACCAATTCAT
*
1757620 ATGCCATCTCCGTATGGGTATATGCCAAGCCCACCAATTCAT
1 ATGCCATCTCCGCATGGGTATATGCCAAGCCCACCAATTCAT
1757662 AT-CTCATCTCCGCA-GGGT
1 ATGC-CATCTCCGCATGGGT
1757680 TGCATTCCTA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 5 0.09
42 48 0.91
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCATCTCCGCATGGGTATATGCCAAGCCCACCAATTCAT
Found at i:1757722 original size:21 final size:21
Alignment explanation
Indices: 1757671--1757722 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1757661 TATCTCATCT
* *
1757671 CCGCAGGGTTGCATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
1757692 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
1757713 CCGCAGGGTT
1 CCGCAGGGTT
1757723 TTATACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.15, C:0.35, G:0.29, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:1758278 original size:34 final size:34
Alignment explanation
Indices: 1758235--1758319 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
1758225 ATAAATGTTT
1758235 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
1758269 TTAAAATACAAATAATATTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
1758303 TTTAAATATAAATTATA
1 TTAAAATACAAATTATA
1758320 CAAACACAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:1775456 original size:14 final size:14
Alignment explanation
Indices: 1775434--1775517 Score: 52
Period size: 14 Copynumber: 6.1 Consensus size: 14
1775424 TTATATTTTG
1775434 ATAAAATATTTAAT
1 ATAAAATATTTAAT
*
1775448 AT--AATATATAA-
1 ATAAAATATTTAAT
*
1775459 AT-ATATATTT-AT
1 ATAAAATATTTAAT
*
1775471 TTAAAAATATTTAAT
1 AT-AAAATATTTAAT
* **
1775486 TTAATTTATTTATTAT
1 ATAAAATATTTA--AT
1775502 ATAAAATATTTAAT
1 ATAAAATATTTAAT
1775516 AT
1 AT
1775518 GATACTTAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
11 3 0.06
12 14 0.26
14 21 0.40
15 4 0.08
16 11 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAAAATATTTAAT
Found at i:1775471 original size:28 final size:26
Alignment explanation
Indices: 1775440--1775502 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 26
1775430 TTTGATAAAA
1775440 TATTTAATATAATATATAAATATATATT
1 TATTTAATATAATAT-TAAATATA-ATT
* *
1775468 TATTTAA-A-AATATTTAATTTAATT
1 TATTTAATATAATATTAAATATAATT
*
1775492 TATTTATTATA
1 TATTTAATATA
1775503 TAAAATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 9 0.30
25 7 0.23
26 6 0.20
27 1 0.03
28 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTTAATATAATATTAAATATAATT
Found at i:1775528 original size:68 final size:65
Alignment explanation
Indices: 1775405--1775536 Score: 162
Period size: 68 Copynumber: 2.0 Consensus size: 65
1775395 TATATGTAAT
1775405 TTTAAAAAATTTAATGTATTTATATTTTGATAAAATATTTAATATAATATATAAA-TATATATTT
1 TTTAAAAAATTTAATGTATTTATATTTTGATAAAATATTTAATATAATATATAAATTAT-TATTT
1775469 A
65 A
* * *
1775470 TTTAAAAATATTTAATTTAATTTAT-TTATTATATAAAATATTTAATATGATACT-TAAATTATT
1 TTTAAAAA-ATTTAATGT-ATTTATATT-TT-GATAAAATATTTAATATAATA-TATAAATTATT
1775533 ATTT
61 ATTT
1775537 TGTATATTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
65 8 0.14
66 10 0.17
67 8 0.14
68 28 0.48
69 4 0.07
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (65 bp):
TTTAAAAAATTTAATGTATTTATATTTTGATAAAATATTTAATATAATATATAAATTATTATTTA
Found at i:1775666 original size:30 final size:28
Alignment explanation
Indices: 1775629--1775699 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 28
1775619 AATGAATATT
* *
1775629 CAAATATTATATGGATATTTTAATAAAGTA
1 CAAATATTATATGAACATTTT-A-AAAGTA
*
1775659 CATATATTATATTGAACATTTTAAAAGTA
1 CAAATATTATA-TGAACATTTTAAAAGTA
1775688 CAAATATTATAT
1 CAAATATTATAT
1775700 TAAATATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 16 0.44
30 11 0.31
31 8 0.22
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (28 bp):
CAAATATTATATGAACATTTTAAAAGTA
Found at i:1775694 original size:29 final size:30
Alignment explanation
Indices: 1775629--1775742 Score: 108
Period size: 31 Copynumber: 3.8 Consensus size: 30
1775619 AATGAATATT
*
1775629 CAAATATTATA-TGGATATTTTAATAAAGTA
1 CAAATATTATATTGAATATTTT-ATAAAGTA
* *
1775659 CATATATTATATTGAACATTTTA-AAAGTA
1 CAAATATTATATTGAATATTTTATAAAGTA
* **
1775688 CAAATATTATATTAAATATTTTATTAAAAAA
1 CAAATATTATATTGAATATTTTA-TAAAGTA
* *
1775719 TAAATATTAAATTTG-ATATTTTAT
1 CAAATATTATA-TTGAATATTTTAT
1775743 TAAAAGATAA
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
29 26 0.38
30 12 0.17
31 29 0.42
32 2 0.03
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (30 bp):
CAAATATTATATTGAATATTTTATAAAGTA
Found at i:1775727 original size:31 final size:31
Alignment explanation
Indices: 1775689--1775773 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
1775679 TTAAAAGTAC
1775689 AAATATTATATTAAATATTTTATTAAAAAAT
1 AAATATTATATTAAATATTTTATTAAAAAAT
* ** *
1775720 AAATATTAAATTTGATATTTTATTAAAAGAT
1 AAATATTATATTAAATATTTTATTAAAAAAT
* * *
1775751 AAGTATCATATTAAACATTTTAT
1 AAATATTATATTAAATATTTTAT
1775774 CAGCCAATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (31 bp):
AAATATTATATTAAATATTTTATTAAAAAAT
Found at i:1776186 original size:20 final size:20
Alignment explanation
Indices: 1776148--1776186 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1776138 TTAAAGGATC
* *
1776148 TCTACATCTTAGAGTTCACG
1 TCTACATCTCAGAGCTCACG
*
1776168 TCTACATCTCGGAGCTCAC
1 TCTACATCTCAGAGCTCAC
1776187 ACACCCCTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (20 bp):
TCTACATCTCAGAGCTCACG
Found at i:1776557 original size:20 final size:20
Alignment explanation
Indices: 1776534--1776583 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1776524 TGGTCTTACA
1776534 GTATCGATACCCAACCCAAT
1 GTATCGATACCCAACCCAAT
*
1776554 GTATCGATACCCAACCCATT
1 GTATCGATACCCAACCCAAT
*
1776574 GTATCAATAC
1 GTATCGATAC
1776584 TCCAGTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (20 bp):
GTATCGATACCCAACCCAAT
Found at i:1778124 original size:37 final size:37
Alignment explanation
Indices: 1778072--1778160 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
1778062 TTTTGTTCAG
* * *
1778072 GTCGGGTCGGGTTTTTTAATTGTGGTATTCGGGTCGA
1 GTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGA
* *
1778109 GTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTCGG
1 GTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGA
1778146 GTCGGGTTCGAGTTT
1 GTCGGG-TCGAGTTT
1778161 AGGGTGAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
37 38 0.84
38 7 0.16
ACGTcount: A:0.11, C:0.11, G:0.37, T:0.40
Consensus pattern (37 bp):
GTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:1778263 original size:248 final size:248
Alignment explanation
Indices: 1777861--1778444 Score: 910
Period size: 248 Copynumber: 2.4 Consensus size: 248
1777851 TCGGGTTGGA
* * *
1777861 TCGGGTTTTTTTAAGTGTGATATTCCGATCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCGGA
1 TCGGATTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTG-AAAAAATCGGA
1777926 CCGACCCGAAAATATATATAATTCAGGTCGGGTCGAATTAAGTCACTGTTTTTATTAAATAAAAA
65 CCGACCCGAAAATATATATAA-T----TCGGGTCGAATTAAGTCACTGTTTTTATTAAATAAAAA
* *
1777991 TAATTTTTTATTATTTCGGGTCGGGTTAGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAA
125 TAATTTTTTATTATTTCAGGTCGGGTCAGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAA
* * * *
1778056 ACTTTATTTTGTTCAGGTCGGGTCGGGTTTTTTAATTGTGGTATTCGGGTCGAGTCGGG
190 AATTTATTTTGTTCAGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGAGTCGAGTCGGG
* *
1778115 TC-GATTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAACCCGGA
1 TCGGATTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAA-TCGGA
*
1778179 CCGACCCGAAAATATATATAATTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATT
65 CCGACCCGAAAATATATATAATTCGGGTCGAATTAAGTCACTGTTTTTATTAAATAAAAATAATT
*
1778244 TTTTATTATTTCAGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAAATTT
130 TTTTATTATTTCAGGTCGGGTCAGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAAATTT
* *
1778309 ATTTTGTTCAGGTTGGGTCGGGTTTTTTAAGTGTGATATTCGAGTCTAGTCGGG
195 ATTTTGTTCAGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGAGTCGAGTCGGG
*
1778363 TCGGGTTTTTTTAAGTGTGATATTCGGGT----T-GGGTTCGGGTTTAGGGTGAAAAAATCGGAC
1 TCGGATTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAATCGGAC
*
1778423 CGACCCGAAAAAATATATAATT
66 CGACCCGAAAATATATATAATT
1778445 TTACCTTATA
Statistics
Matches: 309, Mismatches: 19, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
243 26 0.08
244 23 0.07
245 1 0.00
248 154 0.50
249 25 0.08
252 7 0.02
253 71 0.23
254 2 0.01
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.37
Consensus pattern (248 bp):
TCGGATTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAATCGGAC
CGACCCGAAAATATATATAATTCGGGTCGAATTAAGTCACTGTTTTTATTAAATAAAAATAATTT
TTTATTATTTCAGGTCGGGTCAGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAAATTTA
TTTTGTTCAGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGAGTCGAGTCGGG
Found at i:1778985 original size:16 final size:18
Alignment explanation
Indices: 1778964--1779008 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1778954 TATAGAATTG
1778964 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
1778980 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
1778998 GATTCTAATTC
1 GATTCCAATTC
1779009 TCTCATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 13 0.50
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1779941 original size:2 final size:2
Alignment explanation
Indices: 1779934--1779971 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1779924 TATAGTAATT
1779934 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1779972 GTTTGATGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1781988 original size:29 final size:29
Alignment explanation
Indices: 1781924--1781981 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1781914 CAATAAACTG
1781924 AAATAAATACAACATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
*
1781953 AAATAAATACAAGATACAAATTAGAAACC
1 AAATAAATACAACATACAAATTAGAAACC
1781982 GATTAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.17
Consensus pattern (29 bp):
AAATAAATACAACATACAAATTAGAAACC
Found at i:1784841 original size:64 final size:63
Alignment explanation
Indices: 1784768--1784888 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 63
1784758 ATTGTTCAAG
* *
1784768 GTGTATCGATGCACATGAAGTGCATCGATGCA-CTAATTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCATCCAA-TT-AAATAAAAACATCGAATGTCATCA
* * *
1784832 GTGTATCGATGCACAAGTAGTGCATCGATGCATCCCATTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATG
1784889 AGATTTATGC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
63 17 0.33
64 32 0.63
65 2 0.04
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGTCATCA
Found at i:1785597 original size:23 final size:23
Alignment explanation
Indices: 1785571--1785630 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
1785561 AATCTTATAT
*
1785571 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
1785594 GGCACTTCGGTACAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
1785617 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1785631 TTTATATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.20, C:0.28, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1792561 original size:23 final size:23
Alignment explanation
Indices: 1792509--1792569 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1792499 CAATCTTATA
* *
1792509 TGGCACTACGGTACAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1792532 CGACACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1792555 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1792570 TTTATACGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1793947 original size:24 final size:24
Alignment explanation
Indices: 1793920--1793969 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1793910 CATAATTTAC
1793920 CATTATATACCTGACAATGTACTG
1 CATTATATACCTGACAATGTACTG
1793944 CATTATATACCTGACAATGTACTG
1 CATTATATACCTGACAATGTACTG
1793968 CA
1 CA
1793970 GGATATAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (24 bp):
CATTATATACCTGACAATGTACTG
Found at i:1793975 original size:24 final size:24
Alignment explanation
Indices: 1793924--1793976 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1793914 ATTTACCATT
**
1793924 ATATACCTGACAATGTACTGCATT
1 ATATACCTGACAATGTACTGCAGG
1793948 ATATACCTGACAATGTACTGCAGG
1 ATATACCTGACAATGTACTGCAGG
1793972 ATATA
1 ATATA
1793977 ACGAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (24 bp):
ATATACCTGACAATGTACTGCAGG
Found at i:1798704 original size:14 final size:15
Alignment explanation
Indices: 1798685--1798718 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1798675 AATTATTATT
1798685 AAATATTA-TTTAAA
1 AAATATTATTTTAAA
1798699 AAATATTATTTTAAA
1 AAATATTATTTTAAA
1798714 AAATA
1 AAATA
1798719 CTAATAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATATTATTTTAAA
Found at i:1802490 original size:26 final size:27
Alignment explanation
Indices: 1802445--1802495 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
1802435 GAAATTTGTA
*
1802445 AAATATATGATAATATTTTAGAAAAGT
1 AAATATATGATAATATTTTAAAAAAGT
*
1802472 AAATATATTAT-ATATTTTAAAAAA
1 AAATATATGATAATATTTTAAAAAA
1802496 TGATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (27 bp):
AAATATATGATAATATTTTAAAAAAGT
Found at i:1802738 original size:18 final size:19
Alignment explanation
Indices: 1802704--1802739 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1802694 AAAATAATAC
*
1802704 ATTTTTATTAATTATAGAG
1 ATTTTTATTAATAATAGAG
1802723 ATTTTTATT-ATAATAGA
1 ATTTTTATTAATAATAGA
1802740 AGGAAGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
ATTTTTATTAATAATAGAG
Found at i:1802995 original size:2 final size:2
Alignment explanation
Indices: 1802984--1803038 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1802974 TTTTAAATTA
1802984 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1803025 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1803039 TATTTTTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1807017 original size:3 final size:3
Alignment explanation
Indices: 1807009--1807037 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1806999 TTGAACCTCA
1807009 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1807038 AACTTTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1807634 original size:20 final size:21
Alignment explanation
Indices: 1807601--1807643 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
1807591 ACTAAAAATA
1807601 TACTCTCTTTTTTTAGACCTT
1 TACTCTCTTTTTTTAGACCTT
1807622 TACTCTC-TTTTTTAGACCTT
1 TACTCTCTTTTTTTAGACCTT
1807642 TA
1 TA
1807644 ACATTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.56
Consensus pattern (21 bp):
TACTCTCTTTTTTTAGACCTT
Found at i:1808446 original size:22 final size:23
Alignment explanation
Indices: 1808418--1808464 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1808408 TAATTTTTCA
*
1808418 ATAAATTATAAT-TTTTTATTTT
1 ATAAATTATAATATTTTGATTTT
*
1808440 ATAAATTCTAATATTTTGATTTT
1 ATAAATTATAATATTTTGATTTT
1808463 AT
1 AT
1808465 TTATTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATAAATTATAATATTTTGATTTT
Found at i:1809831 original size:19 final size:19
Alignment explanation
Indices: 1809791--1809830 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1809781 AATGATTTGT
*
1809791 AAATTTTTAATAAAAGTTA
1 AAATTATTAATAAAAGTTA
*
1809810 AAATTATTAATCAAA-TTA
1 AAATTATTAATAAAAGTTA
1809828 AAA
1 AAA
1809831 AGAGTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATTATTAATAAAAGTTA
Found at i:1813975 original size:12 final size:11
Alignment explanation
Indices: 1813960--1814100 Score: 132
Period size: 11 Copynumber: 12.6 Consensus size: 11
1813950 AGAAAGAATA
*
1813960 AGAAGGAGAAG
1 AGAAGAAGAAG
1813971 TAGAAGAAGAAG
1 -AGAAGAAGAAG
*
1813983 AGAAGAGGAAG
1 AGAAGAAGAAG
1813994 AGGAAAGAAGAAG
1 A-G-AAGAAGAAG
1814007 A-AAGAAAGAAG
1 AGAAG-AAGAAG
*
1814018 AAAAGAAGAAG
1 AGAAGAAGAAG
1814029 AAGAAG-AGAAG
1 -AGAAGAAGAAG
1814040 AAGAAGAAGAA-
1 -AGAAGAAGAAG
1814051 AGAAG-AGAAG
1 AGAAGAAGAAG
1814061 AAGAAGAAGAAG
1 -AGAAGAAGAAG
*
1814073 A-AA-AAAAAG
1 AGAAGAAGAAG
1814082 AGAAGAAGAAG
1 AGAAGAAGAAG
1814093 AAGAAGAA
1 -AGAAGAA
1814101 TGACGAGTTA
Statistics
Matches: 111, Mismatches: 6, Indels: 24
0.79 0.04 0.17
Matches are distributed among these distances:
9 10 0.09
10 12 0.11
11 46 0.41
12 34 0.31
13 9 0.08
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:1813980 original size:3 final size:3
Alignment explanation
Indices: 1813948--1814100 Score: 163
Period size: 3 Copynumber: 51.0 Consensus size: 3
1813938 GAGGAAGGAG
* * * *
1813948 GAA GAAA GAA TAA GAA GGA GAA GTA GAA GAA GAA G-A GAA GAG GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
1813993 GAG GAAA GAA GAA GAAA GAAA GAA GAA -AA GAA GAA GAA GAA G-A GAA
1 GAA G-AA GAA GAA G-AA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
1814039 GAA GAA GAA GAAA GAA G-A GAA GAA GAA GAA GAA GAA AAA AAA G-A
1 GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1814083 GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA
1814101 TGACGAGTTA
Statistics
Matches: 129, Mismatches: 12, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
2 10 0.08
3 104 0.81
4 15 0.12
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:1814025 original size:38 final size:38
Alignment explanation
Indices: 1813974--1814100 Score: 161
Period size: 38 Copynumber: 3.3 Consensus size: 38
1813964 GGAGAAGTAG
* * *
1813974 AAGAAGAAGAGAAGAGGAAGAGGAAAGAAGAAGAAAGA
1 AAGAAGAAAAGAAGAAGAAGAAGAAAGAAGAAGAAAGA
1814012 AAGAAGAAAAGAAGAAGAAGAAGAGAAGAAGAAG-AAGA
1 AAGAAGAAAAGAAGAAGAAGAAGA-AAGAAGAAGAAAGA
* *
1814050 AAGAAGAGAAGAAGAAGAAGAAGAAA-AAAAAGAGAAG-
1 AAGAAGAAAAGAAGAAGAAGAAGAAAGAAGAAGA-AAGA
1814087 AAGAAGAAGAAGAA
1 AAGAAGAA-AAGAA
1814101 TGACGAGTTA
Statistics
Matches: 79, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
36 5 0.06
37 9 0.11
38 56 0.71
39 9 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (38 bp):
AAGAAGAAAAGAAGAAGAAGAAGAAAGAAGAAGAAAGA
Found at i:1814029 original size:35 final size:35
Alignment explanation
Indices: 1813949--1814100 Score: 96
Period size: 32 Copynumber: 4.5 Consensus size: 35
1813939 AGGAAGGAGG
* * *
1813949 AAGAAAGAATAAGAAGGAGAAGTAG-AAGAAGAAGA
1 AAGAAAGAAGAA-AAGAAGAAGAAGAAAGAAGAAGA
*
1813984 GAAGAGGAAG-AGGAAAGAAGAAGAAAGAAAGAAG-A-A
1 -AAGA--AAGAAGAAAAGAAGAAG-AAGAAAGAAGAAGA
1814020 AAG-AAGAAG--AAGAAG-AGAAG-AAGAAGAAGA
1 AAGAAAGAAGAAAAGAAGAAGAAGAAAGAAGAAGA
*
1814050 AAGAAGAGAAG--AAGAAGAAGAAGAAA-AAAAAGA
1 AAGAA-AGAAGAAAAGAAGAAGAAGAAAGAAGAAGA
1814083 GAAG-AAGAAGAAGAAGAA
1 -AAGAAAGAAGAA-AAGAA
1814101 TGACGAGTTA
Statistics
Matches: 96, Mismatches: 5, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
28 6 0.06
29 4 0.04
30 6 0.06
31 7 0.07
32 19 0.20
33 14 0.15
34 5 0.05
35 8 0.08
36 13 0.14
37 5 0.05
38 9 0.09
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.01
Consensus pattern (35 bp):
AAGAAAGAAGAAAAGAAGAAGAAGAAAGAAGAAGA
Found at i:1815168 original size:46 final size:47
Alignment explanation
Indices: 1815081--1815182 Score: 152
Period size: 46 Copynumber: 2.2 Consensus size: 47
1815071 CATTTTTCCC
* *
1815081 GAGGCCATTTATTGCAATAAATAATTCACCGTTTAAACTACTTTTCA
1 GAGGCCATTTATTGCAATAAATAATGCACCGGTTAAACTACTTTTCA
* * *
1815128 GAGGTCATTTATTGCAAT-AATAATGCACTGGTTCAACTACTTTTCA
1 GAGGCCATTTATTGCAATAAATAATGCACCGGTTAAACTACTTTTCA
1815174 GAGGCCATT
1 GAGGCCATT
1815183 CAATGCAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
46 32 0.65
47 17 0.35
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (47 bp):
GAGGCCATTTATTGCAATAAATAATGCACCGGTTAAACTACTTTTCA
Found at i:1815395 original size:34 final size:34
Alignment explanation
Indices: 1815351--1815415 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
1815341 ATTATCACTA
* *
1815351 TTTTACCTACTTTTCGGTGCTCA-TCAATGCACCG
1 TTTTACCTACTTTT-AGAGCTCATTCAATGCACCG
*
1815385 TTTTAGCTACTTTTAGAGCTCATTCAATGCA
1 TTTTACCTACTTTTAGAGCTCATTCAATGCA
1815416 AAATTCAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 6 0.22
34 21 0.78
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (34 bp):
TTTTACCTACTTTTAGAGCTCATTCAATGCACCG
Found at i:1818285 original size:41 final size:41
Alignment explanation
Indices: 1818231--1818714 Score: 508
Period size: 41 Copynumber: 11.6 Consensus size: 41
1818221 GGTTCATCTA
* *
1818231 TAGTGGCGTTTTT-TCAACAAACGCCGCAAAAGAGTAGTACTT
1 TAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGACTAGTACTT
* *
1818273 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAATT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTT
* * * * *
1818314 TAATGGCATTTTTATACAAACGCCGCTATAGAATTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTT
* * * *
1818355 TAGTGGCGTTTTTATACAAACGCCGTTATACACATA-TACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGAC-TAGTACTT
* *
1818396 TAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCA-TAATT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACT-AGTACTT
*
1818439 TAGTGGCATTTTTATACAAACGCCGCTAAAGACTCA-TACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACT-AGTACTT
* **
1818480 TAGTGGCATTTTTATACAAACGCCGCTAAAGACGCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTT
* * * * * * *
1818521 TAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTT
* *
1818562 TAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTAGTAATT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTAGTACTT
* *
1818605 TAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTT
* * * * * *
1818646 TAGTGGCGTTTTTATTCAAACGCCGCTATACATTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTT
*
1818687 TAGTGGCGTTTGTGTTTACAAACGCCGC
1 TAGTGGCGTTT-T-TATACAAACGCCGC
1818715 AAGTTTACAA
Statistics
Matches: 375, Mismatches: 57, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
41 280 0.75
42 20 0.05
43 75 0.20
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTAGTACTT
Found at i:1818443 original size:166 final size:166
Alignment explanation
Indices: 1818228--1818713 Score: 717
Period size: 166 Copynumber: 2.9 Consensus size: 166
1818218 ATAGGTTCAT
* * * * *
1818228 CTATAGTGGCGTTT-T-TTCAACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCGTTTTTATACA
1 CTATAGTGGCGTTTGTGTT-TACAAACGCCGCTAAAGACTAGTAATTTAGTGGCATTTTTATACA
* *
1818291 AACGCCGCTAAAGACTCGTAATTTAATGGCATTTTTATACAAACGCCGCTATAGAATTGTACTTT
65 AACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGAATTGTACTTT
1818356 AGTGGCGTTTTTATACAAACGCCGTTATACACATATA
130 AGTGGCGTTTTTATACAAACGCCGTTATACACATATA
1818393 CTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCA-TAATTTAGTGGCATTTTTATACA
1 CTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACT-AGTAATTTAGTGGCATTTTTATACA
* * ***
1818457 AACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAACGCCGCTAAAGACGCGTACTTT
65 AACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGAATTGTACTTT
* * * *
1818522 AGTGGCATTTTTATTCAAACGCCGTTATACACTTGTA
130 AGTGGCGTTTTTATACAAACGCCGTTATACACATATA
1818559 CTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTAGTAATTTAGTGGCATTTTTATACAA
1 CTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTAGTAATTTAGTGGCATTTTTATACAA
* * * * *
1818624 ACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACGCCGCTATACATTTGTACTATA
66 ACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGAATTGTACTTTA
*
1818689 GTGGCGTTTGTGTTTACAAACGCCG
131 GTGGCGTTT-T-TATACAAACGCCG
1818714 CAAGTTTACA
Statistics
Matches: 287, Mismatches: 28, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
165 15 0.05
166 257 0.90
167 4 0.01
168 11 0.04
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (166 bp):
CTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTAGTAATTTAGTGGCATTTTTATACAA
ACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGAATTGTACTTTA
GTGGCGTTTTTATACAAACGCCGTTATACACATATA
Found at i:1818676 original size:125 final size:123
Alignment explanation
Indices: 1818247--1818714 Score: 528
Period size: 125 Copynumber: 3.8 Consensus size: 123
1818237 CGTTTTTTCA
* * * * *
1818247 ACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAA
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACGCCGCTAAACACTCGTAA
* * * * * *
1818312 TTTAATGGCATTTTTATACAAACGCCGCTATAGAATTGTACTTTAGTGGCGTTTTTAT
66 TATAGTGGCATTTTTATACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
* * * * * *
1818370 ACAAACGCCGTTATACACAT-ATACTATAGTGGCGTTTGTGT-TTACAAACGCCGCTAAAGACTC
1 ACAAACGCCGCTAAAGAC-TCGTACTTTAGTGGCGTTT-T-TATT-CAAACGCCGCTAAACACTC
* *
1818433 ATAATTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCA-TACTTTAGTGGCATTTTTAT
62 GTAATATAGTGGCATTTTTATACAAACGCCGCTAAAGACT-AGTACTTTAGTGGCATTTTTAT
* * * * * *
1818495 ACAAACGCCGCTAAAGACGCGTACTTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTAC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACGCCGCTAAACACTCGTAA
* * *
1818560 TATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTAGTAATTTAGTGGCATTTTTAT
66 TATAGTGGCATTT-T-TATACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
* * * *
1818620 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACGCCGCTATACATTTGTAC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACGCCGCTAAACACTCGTAA
* *
1818685 TATAGTGGCGTTTGTGTTTACAAACGCCGC
66 TATAGTGGCATTT-T-TATACAAACGCCGC
1818715 AAGTTTACAA
Statistics
Matches: 300, Mismatches: 35, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
123 57 0.19
124 8 0.03
125 235 0.78
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (123 bp):
ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACGCCGCTAAACACTCGTAA
TATAGTGGCATTTTTATACAAACGCCGCTAAAGACTAGTACTTTAGTGGCATTTTTAT
Found at i:1818835 original size:28 final size:27
Alignment explanation
Indices: 1818796--1818849 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
1818786 CCCGCCGTTT
*
1818796 ACCCAAACCCATCT-TCTTCACTACCAA
1 ACCCAAACCCATATGT-TTCACTACCAA
1818823 ACCCTAAACCCATATGTTTCACTACCA
1 ACCC-AAACCCATATGTTTCACTACCA
1818850 TTTTTATGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 19 0.79
29 1 0.04
ACGTcount: A:0.33, C:0.41, G:0.02, T:0.24
Consensus pattern (27 bp):
ACCCAAACCCATATGTTTCACTACCAA
Found at i:1823013 original size:43 final size:42
Alignment explanation
Indices: 1822966--1823270 Score: 226
Period size: 43 Copynumber: 7.1 Consensus size: 42
1822956 TAATTAGCGA
1822966 CGTTTGTATCAATAAACGCCGCTATAGGTCTGACTTTTTGCGG
1 CGTTTGTATCAA-AAACGCCGCTATAGGTCTGACTTTTTGCGG
* * *** *
1823009 CGTTTGTGTTAAAAAACGCTATTATAGGTCTGACCTTTTGCGG
1 CGTTTGT-ATCAAAAACGCCGCTATAGGTCTGACTTTTTGCGG
* * *
1823052 CATTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGG
1 CGTTTGTAT-CAAAAACGCCGCTATAGGTCTGACTTTTTGCGG
* *
1823095 CGTTTGTTAT-AAAAATGCCAG-TATAGGTCT-TCTCTTTTGCGG
1 CGTTTG-TATCAAAAACGCC-GCTATAGGTCTGACT-TTTTGCGG
* *
1823137 CATTTGTATCCAAAAACGCCGCTATAGATCTGA-TCTTTTGCGG
1 CGTTTGTAT-CAAAAACGCCGCTATAGGTCTGACT-TTTTGCGG
* * * ** * *
1823180 CGTTT-TTTCTAGACACGCCGCTATATATCATAACTTTTTACGG
1 CGTTTGTATC-AAAAACGCCGCTATAGGTC-TGACTTTTTGCGG
* * * * * *
1823223 CGTTTAT-TCCAAAAATGCCGTTATAGATATCGACCTTTTGCGG
1 CGTTTGTAT-CAAAAACGCCGCTATAGGTCT-GACTTTTTGCGG
1823266 CGTTT
1 CGTTT
1823271 TTCCTATCGC
Statistics
Matches: 210, Mismatches: 37, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
41 5 0.02
42 51 0.24
43 146 0.70
44 8 0.04
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (42 bp):
CGTTTGTATCAAAAACGCCGCTATAGGTCTGACTTTTTGCGG
Found at i:1823156 original size:85 final size:86
Alignment explanation
Indices: 1822968--1823184 Score: 307
Period size: 85 Copynumber: 2.5 Consensus size: 86
1822958 ATTAGCGACG
* * *
1822968 TTTGTAT-CAATAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTTAAAAAACGCTATT
1 TTTGTATCCAA-AAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTGTTAAAAAACGCCAGT
1823032 ATAGGTCTGACCTTTTGCGGCA
65 ATAGGTCTGACCTTTTGCGGCA
* *
1823054 TTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCG-TT-TGTTATAAAAATGCCAGT
1 TTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTGTTA-AAAAACGCCAGT
*
1823117 ATAGGTCT-TCTCTTTTGCGGCA
65 ATAGGTCTGAC-CTTTTGCGGCA
* *
1823139 TTTGTATCCAAAAACGCCGCTATAGATCTGATCTTTTGCGGCGTTT
1 TTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTT
1823185 TTTCTAGACA
Statistics
Matches: 118, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
84 6 0.05
85 70 0.59
86 39 0.33
87 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (86 bp):
TTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTGTTAAAAAACGCCAGTA
TAGGTCTGACCTTTTGCGGCA
Found at i:1823217 original size:85 final size:84
Alignment explanation
Indices: 1822979--1823272 Score: 279
Period size: 85 Copynumber: 3.4 Consensus size: 84
1822969 TTGTATCAAT
* * * * *
1822979 AAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTTA-AAAAACGCTATTATAGGTC-TGA
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTT-T-TTATAAAAACGCCAGTATAGATCAT-A
*
1823042 CCTTTTGCGGCATTTGTGTCCAA
63 ACTTTTGCGGCATTTGT-TCCAA
* * * * * **
1823065 AAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTATAAAAATGCCAGTATAGGTCTTCTCT
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTTTATAAAAACGCCAGTATAGATCATAACT
1823130 TTTGCGGCATTTGTATCCAA
66 TTTGCGGCATTTGT-TCCAA
* * * * *
1823150 AAACGCCGCTATAGATCTGATCTTTTGCGGCGTTTTTTCTAGACACGCC-GCTATATATCATAAC
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTTTATAAAAACGCCAG-TATAGATCATAAC
* * *
1823214 TTTTTACGGCGTTTATTCCAA
65 -TTTTGCGGCATTTGTTCCAA
* * *
1823235 AAATGCCGTTATAGATATCGACCTTTTGCGGCGTTTTT
1 AAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTTT
1823273 CCTATCGCCG
Statistics
Matches: 176, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
84 4 0.02
85 107 0.61
86 65 0.37
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (84 bp):
AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTTTTATAAAAACGCCAGTATAGATCATAACT
TTTGCGGCATTTGTTCCAA
Found at i:1827449 original size:23 final size:26
Alignment explanation
Indices: 1827409--1827459 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 26
1827399 CTCATGAGTT
*
1827409 AAAATTGAGTTTAATTAGA-A-AAAC
1 AAAATTGAGTCTAATTAGAGAGAAAC
1827433 AAAATTG-GTCTAATTAGAGAGAAAC
1 AAAATTGAGTCTAATTAGAGAGAAAC
1827458 AA
1 AA
1827460 GATATTTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 8 0.33
25 6 0.25
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.25
Consensus pattern (26 bp):
AAAATTGAGTCTAATTAGAGAGAAAC
Found at i:1828806 original size:24 final size:22
Alignment explanation
Indices: 1828759--1828804 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1828749 CAAAGCTTAT
*
1828759 TAAAATCTTGATATATTATATA
1 TAAAATCTTAATATATTATATA
1828781 TAAAATCTTAATATATTATATA
1 TAAAATCTTAATATATTATATA
1828803 TA
1 TA
1828805 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAAATCTTAATATATTATATA
Found at i:1831653 original size:96 final size:97
Alignment explanation
Indices: 1831488--1831680 Score: 361
Period size: 96 Copynumber: 2.0 Consensus size: 97
1831478 TCACTTTTAT
* *
1831488 TTTCGTTATACTTAAGGGTATTTTTTCATTTTAGCCAATTAGAAGTATTTTAGTAACTTATCCTA
1 TTTCGTTATACTTAAGGGTATTTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
1831553 AATCTTTTATTATTAGACATCCCTTAATCCAC
66 AATCTTTTATTATTAGACATCCCTTAATCCAC
1831585 TTTCGTTATACTTAAGGGTA-TTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
1 TTTCGTTATACTTAAGGGTATTTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
1831649 AATCTTTTATTATTAGACATCCCTTAATCCAC
66 AATCTTTTATTATTAGACATCCCTTAATCCAC
1831681 AAACATTTTA
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 74 0.79
97 20 0.21
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (97 bp):
TTTCGTTATACTTAAGGGTATTTTTTAATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTA
AATCTTTTATTATTAGACATCCCTTAATCCAC
Found at i:1831712 original size:96 final size:95
Alignment explanation
Indices: 1831515--1831710 Score: 259
Period size: 96 Copynumber: 2.1 Consensus size: 95
1831505 GTATTTTTTC
*
1831515 ATTTTAGCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
1 ATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
*** * * ** * *
1831580 TCCACTTTCGTTATACTTAAGGGTATTTTTA
66 TCCACAAACATTATAC-GAAGGAAAGTTTGA
1831611 ATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
1 ATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
*
1831676 TCCACAAACATTTTA-GAAGTGAAAGTTTGA
66 TCCACAAACATTATACGAAG-GAAAGTTTGA
*
1831706 CTTTT
1 ATTTT
1831711 TAAGTAGGGA
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
94 3 0.03
95 10 0.11
96 74 0.85
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (95 bp):
ATTTTACCCAATTAGAAGTATTTTAGTAACTTATCCTAAATCTTTTATTATTAGACATCCCTTAA
TCCACAAACATTATACGAAGGAAAGTTTGA
Found at i:1831874 original size:20 final size:20
Alignment explanation
Indices: 1831846--1831896 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1831836 TCTACCTTTG
* *
1831846 ATATGGATACTTGATGAACA
1 ATATCGATACTTCATGAACA
*
1831866 ATATCGATACTTCTTGAACA
1 ATATCGATACTTCATGAACA
*
1831886 ATATTGATACT
1 ATATCGATACT
1831897 CTTAGTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
ATATCGATACTTCATGAACA
Found at i:1832864 original size:2 final size:2
Alignment explanation
Indices: 1832857--1832881 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1832847 CATGACCTCA
1832857 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
1832882 GCTTGATATT
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:1835444 original size:32 final size:32
Alignment explanation
Indices: 1835408--1835471 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1835398 AACTGACGAA
1835408 ATGATATGTATCACATCACTCAAAGTGATGAT
1 ATGATATGTATCACATCACTCAAAGTGATGAT
* * **
1835440 ATGATATTTGTCATGTCACTCAAAGTGATGAT
1 ATGATATGTATCACATCACTCAAAGTGATGAT
1835472 GTTCATATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (32 bp):
ATGATATGTATCACATCACTCAAAGTGATGAT
Found at i:1835534 original size:32 final size:32
Alignment explanation
Indices: 1835418--1835537 Score: 93
Period size: 32 Copynumber: 3.8 Consensus size: 32
1835408 ATGATATGTA
* * * *
1835418 TCACATCA-CTCAAAGTGATGATATGATATTTG
1 TCACATCACCT-AAAGTGATGATGTAACATATG
** *
1835450 TCATGTCA-CTCAAAGTGATGATGT-TCATATG
1 TCACATCACCT-AAAGTGATGATGTAACATATG
* ** *
1835481 TCAGATCATTTAAAATGATGATGTAACATATG
1 TCACATCACCTAAAGTGATGATGTAACATATG
*
1835513 TCACATCACCTAAAGTAATGATGTA
1 TCACATCACCTAAAGTGATGATGTA
1835538 GTATATATCA
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
31 22 0.31
32 48 0.69
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (32 bp):
TCACATCACCTAAAGTGATGATGTAACATATG
Found at i:1839900 original size:20 final size:20
Alignment explanation
Indices: 1839869--1839919 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1839859 GTTTGATTAA
*
1839869 TTTAATTATTTTTT--AATC
1 TTTAAATATTTTTTAAAATC
*
1839887 TTTATAATATTTTTTAAAATT
1 TTTA-AATATTTTTTAAAATC
1839908 TTTAAATATTTT
1 TTTAAATATTTT
1839920 AGATGATGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.14
19 9 0.32
20 8 0.29
21 7 0.25
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAAATATTTTTTAAAATC
Found at i:1840067 original size:15 final size:16
Alignment explanation
Indices: 1840047--1840079 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1840037 TGAAATTTTT
1840047 TAACTTT-ATATATAA
1 TAACTTTGATATATAA
*
1840062 TAACTTTGATATTTAA
1 TAACTTTGATATATAA
1840078 TA
1 TA
1840080 TTTACAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
TAACTTTGATATATAA
Found at i:1842120 original size:18 final size:18
Alignment explanation
Indices: 1842097--1842132 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1842087 AAATAAATTT
1842097 ATTTTTTCTTTAATTTTA
1 ATTTTTTCTTTAATTTTA
*
1842115 ATTTTTTTTTTAATTTTA
1 ATTTTTTCTTTAATTTTA
1842133 TCCGGCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
ATTTTTTCTTTAATTTTA
Found at i:1843206 original size:24 final size:26
Alignment explanation
Indices: 1843163--1843213 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
1843153 CTCAAAACAT
1843163 TATTATTTTATATATGTAATATTAATA
1 TATTATTTTATATA-GTAATATTAATA
*
1843190 TATTATTTTA-ATA-TAATTTTAATA
1 TATTATTTTATATAGTAATATTAATA
1843214 AAAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 10 0.43
26 3 0.13
27 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TATTATTTTATATAGTAATATTAATA
Found at i:1843497 original size:43 final size:43
Alignment explanation
Indices: 1843441--1843523 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 43
1843431 TAATTTTAAT
*
1843441 ATTTTAGTAAATAATTAATAT-AATTAATAATA-TTTTATTATC
1 ATTTTAATAAATAATTAATATAAATT-ATAATACTTTTATTATC
1843483 ATTTTAATAAAATAATTAATATAAATTATAATACTTTTATT
1 ATTTTAAT-AAATAATTAATATAAATTATAATACTTTTATT
1843524 TTAATAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 7 0.19
43 19 0.51
44 11 0.30
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (43 bp):
ATTTTAATAAATAATTAATATAAATTATAATACTTTTATTATC
Found at i:1843530 original size:33 final size:35
Alignment explanation
Indices: 1843493--1843576 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 35
1843483 ATTTTAATAA
*
1843493 AATAATTAATATA-AATTATAATACTTTTATTT-T
1 AATAATTAATATATAATCATAATACTTTTATTTAT
* *
1843526 AATAA--AATATAATAATCGTAATATTTTTATTTAT
1 AATAATTAATAT-ATAATCATAATACTTTTATTTAT
1843560 AA-AATTATATATATAAT
1 AATAATTA-ATATATAAT
1843577 ATTTTAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
31 5 0.12
32 1 0.02
33 23 0.55
34 3 0.07
35 6 0.14
36 4 0.10
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (35 bp):
AATAATTAATATATAATCATAATACTTTTATTTAT
Found at i:1843540 original size:43 final size:43
Alignment explanation
Indices: 1843449--1843541 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
1843439 ATATTTTAGT
* **
1843449 AAATAATTAATATAATTAATAATATTTTATTATCATTTTAATA
1 AAATAATTAATATAATTAATAATATTTTATTATCAATAAAATA
*
1843492 AAATAATTAATATAAATT-ATAATACTTTTATT-TTAATAAAATA
1 AAATAATTAATAT-AATTAATAATA-TTTTATTATCAATAAAATA
*
1843535 TAATAAT
1 AAATAAT
1843542 CGTAATATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
43 32 0.74
44 11 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (43 bp):
AAATAATTAATATAATTAATAATATTTTATTATCAATAAAATA
Found at i:1843579 original size:29 final size:32
Alignment explanation
Indices: 1843500--1843581 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 32
1843490 TAAAATAATT
* *
1843500 AATATAA-ATTATAATACTTTTATTTTAATAA
1 AATATAATAATATAATATTTTTATTTTAATAA
*
1843531 AATATAATAATCGTAATATTTTTA-TTT-ATAA
1 AATATAATAAT-ATAATATTTTTATTTTAATAA
1843562 AAT-T-ATATATATAATATTTT
1 AATATAATA-ATATAATATTTT
1843582 AATAATAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 12 0.27
30 3 0.07
31 14 0.32
32 5 0.11
33 10 0.23
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (32 bp):
AATATAATAATATAATATTTTTATTTTAATAA
Found at i:1843589 original size:28 final size:28
Alignment explanation
Indices: 1843544--1843607 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
1843534 ATAATAATCG
* * * * *
1843544 TAATATTTTTATTTATAAAATTATATATA
1 TAATA-TTTTAATAATAAAATGACATAAA
*
1843573 TAATATTTTAATAATAATATGACATAAA
1 TAATATTTTAATAATAAAATGACATAAA
1843601 TAATATT
1 TAATATT
1843608 AAATAAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
TAATATTTTAATAATAAAATGACATAAA
Found at i:1844034 original size:33 final size:33
Alignment explanation
Indices: 1843979--1844041 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1843969 TATTTCTATG
1843979 ATGTATTTATATGTAATCATTTA-AAATATCAA
1 ATGTATTTATATGTAATCATTTAGAAATATCAA
* * *
1844011 ATGTTTTTATTATTTAATTATTTAGAAATAT
1 ATGTATTTA-TATGTAATCATTTAGAAATAT
1844042 GTGTAACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 8 0.31
33 12 0.46
34 6 0.23
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (33 bp):
ATGTATTTATATGTAATCATTTAGAAATATCAA
Found at i:1847629 original size:164 final size:167
Alignment explanation
Indices: 1847358--1847684 Score: 633
Period size: 164 Copynumber: 2.0 Consensus size: 167
1847348 AAAGTCTCTC
1847358 TTTTTGATTCATTGAAGTACTTACTGACTTGCAATTCTCCATGTGAAACTTCTTCAAGATCTCTT
1 TTTTTGATTCATTGAAGTACTTACTGACTTGCAATTCTCCATGTGAAACTTCTTCAAGATCTCTT
1847423 TAGCATACTTTCTTTGACAAATAAAGACTCCTTGATGATCTTGTCTTACCT-CATCCCAAGAAAG
66 TAGCATACTTTCTTTGACAAATAAAGACTCCTTGATGATCTTGTCTTACCTCCATCCCAAGAAAG
1847487 TATGCCATGGTCCCC-AGTCTGTCA-TTCAAATACTT
131 TATGCCATGGTCCCCAAGTCTGTCATTTCAAATACTT
1847522 TTTTTGATTCATTGAAGTACTTACTGACTTGCAATTCTCCATGTGAAACTTCTTCAAGATCTCTT
1 TTTTTGATTCATTGAAGTACTTACTGACTTGCAATTCTCCATGTGAAACTTCTTCAAGATCTCTT
1847587 TAGCATACTTTCTTTGACAAATAAAGACTCCTTGATGATCTTGTCTTACCTCCATCCCAAGAAAG
66 TAGCATACTTTCTTTGACAAATAAAGACTCCTTGATGATCTTGTCTTACCTCCATCCCAAGAAAG
1847652 TATGCCATGGTCCCCAAGTCTGTCATTTCAAAT
131 TATGCCATGGTCCCCAAGTCTGTCATTTCAAAT
1847685 CGATTCTAGC
Statistics
Matches: 160, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
164 116 0.73
165 28 0.17
166 9 0.06
167 7 0.04
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (167 bp):
TTTTTGATTCATTGAAGTACTTACTGACTTGCAATTCTCCATGTGAAACTTCTTCAAGATCTCTT
TAGCATACTTTCTTTGACAAATAAAGACTCCTTGATGATCTTGTCTTACCTCCATCCCAAGAAAG
TATGCCATGGTCCCCAAGTCTGTCATTTCAAATACTT
Found at i:1848956 original size:23 final size:23
Alignment explanation
Indices: 1848930--1848974 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1848920 CACCACAGCT
*
1848930 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1848953 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1848975 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1849223 original size:149 final size:149
Alignment explanation
Indices: 1848953--1849402 Score: 861
Period size: 149 Copynumber: 3.0 Consensus size: 149
1848943 CGAAGTGCCC
1848953 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1849018 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
1849083 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
*
1849102 CGTAGAATTGCATCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
1849167 CATATACATATACTATGGATCAAATATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
1849232 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
1849251 CGTAGAATTGCACCGTAGTGCC--AT-ATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1849313 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
1849378 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
1849397 CGTAGA
1 CGTAGA
1849403 CCCTCTACCC
Statistics
Matches: 297, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
146 127 0.43
147 2 0.01
149 168 0.57
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:1849517 original size:24 final size:26
Alignment explanation
Indices: 1849490--1849550 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 26
1849480 TATCGCGTAG
1849490 ACATAGTAT-TTT-CATACCTTTATC
1 ACATAGTATATTTACATACCTTTATC
1849514 ACATAGGCATATCATTTACATACCTTTATC
1 ACATA-G--TAT-ATTTACATACCTTTATC
1849544 ACATAGT
1 ACATAGT
1849551 TCATATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
27 4 0.13
29 4 0.13
30 17 0.55
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (26 bp):
ACATAGTATATTTACATACCTTTATC
Found at i:1850033 original size:67 final size:66
Alignment explanation
Indices: 1849919--1850069 Score: 221
Period size: 67 Copynumber: 2.3 Consensus size: 66
1849909 TTTTTCTCAT
* *
1849919 GGGGGAATCGGTTCCCCCCCTGGGGTATCGATTCCCCACAAGCATTCTGGAATTTCATATACGAT
1 GGGGGTATCGGTT-CCCCCCTGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
1849984 GA
65 GA
* * * * *
1849986 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATCCGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGAT
1850051 GA
65 GA
1850053 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1850070 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 7 0.09
67 69 0.91
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCCACAAGCATTCTGGAAATTCATATACGATG
A
Found at i:1856142 original size:23 final size:23
Alignment explanation
Indices: 1856116--1856160 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1856106 CACCACAACT
*
1856116 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1856139 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1856161 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1856409 original size:149 final size:149
Alignment explanation
Indices: 1856139--1856591 Score: 888
Period size: 149 Copynumber: 3.0 Consensus size: 149
1856129 CGAAGTGCCC
1856139 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1856204 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
1856269 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
*
1856288 CGTAGAATTGCATCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
1856353 CATATACATATACTATGGATCAAATATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
1856418 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
1856437 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1856502 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
1856567 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
1856586 CGTAGA
1 CGTAGA
1856592 CCCTCTACCC
Statistics
Matches: 300, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 300 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:1856706 original size:24 final size:26
Alignment explanation
Indices: 1856679--1856739 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 26
1856669 TATCGCGTAG
1856679 ACATAGTAT-TTT-CATACCTTTATC
1 ACATAGTATATTTACATACCTTTATC
1856703 ACATAGGCATATCATTTACATACCTTTATC
1 ACATA-G--TAT-ATTTACATACCTTTATC
1856733 ACATAGT
1 ACATAGT
1856740 TCATATAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
27 4 0.13
29 4 0.13
30 17 0.55
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (26 bp):
ACATAGTATATTTACATACCTTTATC
Found at i:1857240 original size:67 final size:65
Alignment explanation
Indices: 1857108--1857255 Score: 208
Period size: 67 Copynumber: 2.3 Consensus size: 65
1857098 TTTTTCTCAT
* *
1857108 GGGGGAATCGGTT-CCCCCTGGGGTATCGATTCCCACAAGCATTCTGGAATTTCATATACGATGA
1 GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCACAAGCATTCTGGAAATTCATATACGATGA
* * * * *
1857172 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATCCGTT
1 GGGGGTATCGGTTCCCCCCT-GGGGTATCGATT-CCCACAAGCATTCTGGAAATTCATATACGAT
1857237 GA
64 GA
1857239 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1857256 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 12 0.16
65 6 0.08
66 12 0.16
67 44 0.59
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (65 bp):
GGGGGTATCGGTTCCCCCCTGGGGTATCGATTCCCACAAGCATTCTGGAAATTCATATACGATGA
Done.