Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009581.1 Hibiscus syriacus cultivar Beakdansim tig00116958_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: 2551150
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1443452 original size:30 final size:29
Alignment explanation
Indices: 1443416--1443485 Score: 122
Period size: 30 Copynumber: 2.4 Consensus size: 29
1443406 CAAAAATCAT
1443416 AGTTTAGGGATGAAGTTGAAATGCTTAAA
1 AGTTTAGGGATGAAGTTGAAATGCTTAAA
*
1443445 AGTTTTAGGGATGAAGTTGAAATGCTTAAT
1 AG-TTTAGGGATGAAGTTGAAATGCTTAAA
1443475 AGTTTAGGGAT
1 AGTTTAGGGAT
1443486 TAAATTGGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 11 0.28
30 28 0.72
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
AGTTTAGGGATGAAGTTGAAATGCTTAAA
Found at i:1449639 original size:127 final size:127
Alignment explanation
Indices: 1449413--1449666 Score: 508
Period size: 127 Copynumber: 2.0 Consensus size: 127
1449403 TGCGCGAAAA
1449413 TATCTAATAGAATTAGGGAATTTTGTGGAGGGAAGGTCAAGACAAGGAAAGAAGGGAAAAAGAAA
1 TATCTAATAGAATTAGGGAATTTTGTGGAGGGAAGGTCAAGACAAGGAAAGAAGGGAAAAAGAAA
1449478 ACAAAATTGAATAGTGAAAACGCAACAGTTATTCTTACGTGGCGGCTTGGACAGGTGTTGAC
66 ACAAAATTGAATAGTGAAAACGCAACAGTTATTCTTACGTGGCGGCTTGGACAGGTGTTGAC
1449540 TATCTAATAGAATTAGGGAATTTTGTGGAGGGAAGGTCAAGACAAGGAAAGAAGGGAAAAAGAAA
1 TATCTAATAGAATTAGGGAATTTTGTGGAGGGAAGGTCAAGACAAGGAAAGAAGGGAAAAAGAAA
1449605 ACAAAATTGAATAGTGAAAACGCAACAGTTATTCTTACGTGGCGGCTTGGACAGGTGTTGAC
66 ACAAAATTGAATAGTGAAAACGCAACAGTTATTCTTACGTGGCGGCTTGGACAGGTGTTGAC
1449667 CGCTGGCAAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.39, C:0.10, G:0.28, T:0.22
Consensus pattern (127 bp):
TATCTAATAGAATTAGGGAATTTTGTGGAGGGAAGGTCAAGACAAGGAAAGAAGGGAAAAAGAAA
ACAAAATTGAATAGTGAAAACGCAACAGTTATTCTTACGTGGCGGCTTGGACAGGTGTTGAC
Found at i:1454956 original size:29 final size:29
Alignment explanation
Indices: 1454922--1454999 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
1454912 TGGTGATTGG
*
1454922 TATATTTATCGATCTAACACTGGTCAGAT
1 TATATTTCTCGATCTAACACTGGTCAGAT
*
1454951 TATATTTCTCGATCTAATACTGGTCAGAT
1 TATATTTCTCGATCTAACACTGGTCAGAT
1454980 TATATTTCTCGATCTAACAC
1 TATATTTCTCGATCTAACAC
1455000 CTGTAGCAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (29 bp):
TATATTTCTCGATCTAACACTGGTCAGAT
Found at i:1461017 original size:17 final size:18
Alignment explanation
Indices: 1460997--1461037 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1460987 AAATTATATT
1460997 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
*
1461014 AGTAAAATACTTAACTAA
1 AGTAAAATACTTAAATAA
*
1461032 ATTAAA
1 AGTAAA
1461038 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1469660 original size:160 final size:159
Alignment explanation
Indices: 1469389--1469707 Score: 613
Period size: 160 Copynumber: 2.0 Consensus size: 159
1469379 GGAAATGGAA
1469389 CACTTAAAGTATCTTTGTCCCTCACTAGGATCCAACATATCTTACCACTTCAACAAGATTAATGT
1 CACTTAAAGTATCTTTGTCCCTCACTAGGATCCAACATATCTTACCACTTCAACAAGATTAATGT
1469454 GATGTTTAATATTTCAGATTGGTGTACTTCTTGAAGACAAAGAATTCGTTGATTCATGGATGGGA
66 GATGTTTAATATTTCAGATTGGTGTACTTCTTGAAGACAAAGAATTCGTTGATTCATGGATGGGA
1469519 GGAAAGCA-TGGAAGGCCGGGAAATTTGC
131 GGAAAGCATTGGAAGGCCGGGAAATTTGC
1469547 CACTTAAACGTATCTTTGTCCCTCACTAGGATCCAACATATCTTTACCACTTCAACAAGATTAAT
1 CACTTAAA-GTATCTTTGTCCCTCACTAGGATCCAACATATC-TTACCACTTCAACAAGATTAAT
1469612 GTGATGTTTAATATTTCAGATTGGTGTACTTCTTGAAGACAAAGAATTCGTTGATTCATGGATGG
64 GTGATGTTTAATATTTCAGATTGGTGTACTTCTTGAAGACAAAGAATTCGTTGATTCATGGATGG
1469677 GAGGAAAGCATTGGAAGGCCGGGAAATTTGC
129 GAGGAAAGCATTGGAAGGCCGGGAAATTTGC
1469708 TTTGAGTCTT
Statistics
Matches: 158, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
158 8 0.05
159 33 0.21
160 97 0.61
161 20 0.13
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (159 bp):
CACTTAAAGTATCTTTGTCCCTCACTAGGATCCAACATATCTTACCACTTCAACAAGATTAATGT
GATGTTTAATATTTCAGATTGGTGTACTTCTTGAAGACAAAGAATTCGTTGATTCATGGATGGGA
GGAAAGCATTGGAAGGCCGGGAAATTTGC
Found at i:1472168 original size:29 final size:29
Alignment explanation
Indices: 1472126--1472370 Score: 490
Period size: 29 Copynumber: 8.4 Consensus size: 29
1472116 AGACCATAAC
1472126 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1472155 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1472184 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1472213 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1472242 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1472271 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1472300 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1472329 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1 AGAAGTTCGGTGATTAAAACGTAAGCTTT
1472358 AGAAGTTCGGTGA
1 AGAAGTTCGGTGA
1472371 CATACTCAAA
Statistics
Matches: 216, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 216 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (29 bp):
AGAAGTTCGGTGATTAAAACGTAAGCTTT
Found at i:1472911 original size:23 final size:21
Alignment explanation
Indices: 1472863--1472903 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1472853 ATTTTTTTTA
*
1472863 ATTTTTCCATCTAAATGTATT
1 ATTTTTCCATCTAAATATATT
1472884 ATTTTTCACAT-TAAATATAT
1 ATTTTTC-CATCTAAATATAT
1472904 AATATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTTTCCATCTAAATATATT
Found at i:1473583 original size:29 final size:29
Alignment explanation
Indices: 1473546--1473641 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
1473536 CATAAGCCTC
* *
1473546 ATTTTAAATTAGTCCTTAAACTTTTAAAT
1 ATTTCAAATTAGTCCTTAAACTTTTGAAT
* * *
1473575 ATTTCAAATTAATCCTTAAAC-TATGACT
1 ATTTCAAATTAGTCCTTAAACTTTTGAAT
* *
1473603 ACTATTCTAAATTAGTCCTCAAACTTTTGAAC
1 A-T-TTC-AAATTAGTCCTTAAACTTTTGAAT
1473635 ATTTCAA
1 ATTTCAA
1473642 TTTCATCCCC
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
28 5 0.09
29 22 0.42
30 6 0.11
31 15 0.28
32 5 0.09
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.42
Consensus pattern (29 bp):
ATTTCAAATTAGTCCTTAAACTTTTGAAT
Found at i:1473618 original size:60 final size:60
Alignment explanation
Indices: 1473545--1473690 Score: 159
Period size: 60 Copynumber: 2.4 Consensus size: 60
1473535 CCATAAGCCT
* * **
1473545 CATTTTAAATTAGTCCTTAAACTTTTAAATATTTCAAATTAATCCTTAAACTATGA-CTA
1 CATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAAATTAATCCCCAAACTATGACCTA
* * * * * *
1473604 CTATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTTCATCCCCAGACTATGACCTT
1 C-ATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAAATTAATCCCCAAACTATGACCTA
* * *
1473665 CATTCTAAATTGGTACATAAACTTTT
1 CATTCTAAATTAGTCCTTAAACTTTT
1473691 TTGAGCATTC
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.01
60 67 0.94
61 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.40
Consensus pattern (60 bp):
CATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAAATTAATCCCCAAACTATGACCTA
Found at i:1473945 original size:60 final size:57
Alignment explanation
Indices: 1473840--1474027 Score: 178
Period size: 60 Copynumber: 3.1 Consensus size: 57
1473830 TATTTGGATG
* * * * *
1473840 AATTTGAGGATGAAATTGGAAGATTCAAAATTTTAGGTACCAATTTAGAAAGAGGGTCAT
1 AATTTG-GGATGAAATTAGAATATTCAAAGTTTAAGG-ACTAATTTA-AAAGAGGGTCAT
* *
1473900 AATTTAGGGATGAAATTAGAATATTCATAAGTTTAAGGACTAATTTAAAATGAGAGACAT
1 AATTT-GGGATGAAATTAGAATATTCA-AAGTTTAAGGACTAATTTAAAA-GAGGGTCAT
* * * * * *
1473960 AGTTTGGAGATGAAATTAAAATATTCAAAAGTTTAAAGAATAATTTAAAGTGAGGGTTAT
1 AATTTGG-GATGAAATTAGAATATTC-AAAGTTTAAGGACTAATTTAAA-AGAGGGTCAT
1474020 AATTTGGG
1 AATTTGGG
1474028 GCATAAGATG
Statistics
Matches: 106, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
59 6 0.06
60 90 0.85
61 10 0.09
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (57 bp):
AATTTGGGATGAAATTAGAATATTCAAAGTTTAAGGACTAATTTAAAAGAGGGTCAT
Found at i:1474440 original size:112 final size:112
Alignment explanation
Indices: 1474243--1474593 Score: 553
Period size: 112 Copynumber: 3.1 Consensus size: 112
1474233 TTGTCGGTTT
* * * *
1474243 GTGTCGATACTTTATAAAAATATATTGAT-TATAACAATATAACAAGTAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
*
1474307 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
1474355 GTGTCGATACTTTATAAAAATGTATCT-ATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTAT-TGATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
*
1474419 CGGTCTATAAATGACAAAACAGGTAAAGTACTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
* * *
1474467 GTGTCTATACTTTATAAAAATGTATTGATCCATAACAATATGACAGGTAAAAAAATGACAAATCC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
1474532 GGTCTATAAATGACAAAACAGGTAAAGTGCAACCGAATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
1474579 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
1474594 TATAGGTATC
Statistics
Matches: 221, Mismatches: 15, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
111 1 0.00
112 203 0.92
113 17 0.08
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
Found at i:1474771 original size:182 final size:182
Alignment explanation
Indices: 1474464--1474916 Score: 726
Period size: 182 Copynumber: 2.5 Consensus size: 182
1474454 GGATATATTG
* * * *
1474464 AAAGTGTCTATACTTTATAAAAATGTATTGATCCATAACAATATGACAGGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* ** * *
1474529 TCCGGTCTATAAATGACAAAACAGGTAAAGTGCAACCGAATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCAACCGAATATGTTGATAGTGTCGATACTTTAT
* * * * *
1474594 TATAGGTATCGACACTTTTGGAATTTAAAAGAGAAGACGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAAAAAAGAAGTTATAGCGCCAAT
1474646 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
1474711 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCAACCGAATATGTTGATAGTGTCGATACTTTAT
*
1474776 TATAAGTATCGACACTTTTGGAATTTAAAAAAAAATAAGTTATAGCGCCAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAAAAAAGAAGTTATAGCGCCAAT
*
1474828 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
1474893 ATCGATCTCGAAATGACAAAACCG
66 ACCGGTCTCGAAATGACAAAACCG
1474917 ATAGTAAAAA
Statistics
Matches: 251, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
182 251 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCAACCGAATATGTTGATAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAAAAAAGAAGTTATAGCGCCAAT
Found at i:1495606 original size:31 final size:31
Alignment explanation
Indices: 1495570--1495629 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1495560 TCATTTTGTT
*
1495570 TGAATAAGTTGTTTTTAGTCATTACATTGAA
1 TGAATAAATTGTTTTTAGTCATTACATTGAA
1495601 TGAATAAATTGTTTTTAGTCATTACATTG
1 TGAATAAATTGTTTTTAGTCATTACATTG
1495630 GAAATAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (31 bp):
TGAATAAATTGTTTTTAGTCATTACATTGAA
Found at i:1497562 original size:16 final size:16
Alignment explanation
Indices: 1497541--1497571 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1497531 ATAAATAAAT
1497541 GAACATAAACGAACAC
1 GAACATAAACGAACAC
1497557 GAACATAAACGAACA
1 GAACATAAACGAACA
1497572 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:1497663 original size:16 final size:16
Alignment explanation
Indices: 1497642--1497702 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
1497632 TAATAAATAA
1497642 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1497658 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1497674 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1497690 ACGAACATAAACG
1 ACGAACATAAACG
1497703 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1498559 original size:13 final size:13
Alignment explanation
Indices: 1498543--1498568 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1498533 TGCACTATAA
1498543 TATAACTTGTTTT
1 TATAACTTGTTTT
1498556 TATAACTTGTTTT
1 TATAACTTGTTTT
1498569 GAATCTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TATAACTTGTTTT
Found at i:1498819 original size:24 final size:24
Alignment explanation
Indices: 1498791--1498865 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
1498781 GATTGTGTTA
*
1498791 AACATAAAAGAATGAACATAAACG
1 AACATAAAAGAACGAACATAAACG
**
1498815 AACATAATCGAACGAACATAAACG
1 AACATAAAAGAACGAACATAAACG
* *
1498839 AACATAACCA-AACGAACATAACCG
1 AACATAA-AAGAACGAACATAAACG
1498863 AAC
1 AAC
1498866 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.57, C:0.21, G:0.11, T:0.11
Consensus pattern (24 bp):
AACATAAAAGAACGAACATAAACG
Found at i:1498828 original size:14 final size:14
Alignment explanation
Indices: 1498811--1498866 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1498801 AATGAACATA
*
1498811 AACGAACATAATCG
1 AACGAACATAACCG
1498825 AACGAACAT-A---
1 AACGAACATAACCG
*
1498835 AACGAACATAACCA
1 AACGAACATAACCG
1498849 AACGAACATAACCG
1 AACGAACATAACCG
1498863 AACG
1 AACG
1498867 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1498876 original size:24 final size:24
Alignment explanation
Indices: 1498804--1498865 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
1498794 ATAAAAGAAT
*
1498804 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
*
1498828 GAACATAAACGAACATAACCAAAC
1 GAACATAAACGAACATAACCGAAC
*
1498852 GAACATAACCGAAC
1 GAACATAAACGAAC
1498866 GTTCACGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.55, C:0.24, G:0.11, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:1500660 original size:20 final size:20
Alignment explanation
Indices: 1500637--1500678 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1500627 GAAATTTGAA
*
1500637 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATAAATTACAT
1500657 TTCTGGAAAATAAATTACAT
1 TTCTGGAAAATAAATTACAT
1500677 TT
1 TT
1500679 TTTAAAAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (20 bp):
TTCTGGAAAATAAATTACAT
Found at i:1500803 original size:22 final size:22
Alignment explanation
Indices: 1500777--1500849 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 22
1500767 ATTTATTAAA
1500777 ATTATTAAATATAATAAATAAT
1 ATTATTAAATATAATAAATAAT
* * * *
1500799 ATTATTTATCATAAAACTTAATATT
1 ATTA-TTA-AATATAA-TAAATAAT
*
1500824 ATTATTAAATATTA-AAATAAT
1 ATTATTAAATATAATAAATAAT
1500845 -TTATT
1 ATTATT
1500850 TATTATTAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
20 5 0.13
21 5 0.13
22 4 0.10
23 7 0.18
24 8 0.21
25 10 0.26
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTATTAAATATAATAAATAAT
Found at i:1501045 original size:27 final size:25
Alignment explanation
Indices: 1501014--1501185 Score: 121
Period size: 26 Copynumber: 6.8 Consensus size: 25
1501004 TTTACTAAAA
1501014 TATTATTTAAATATATAATAATATAT
1 TATTA-TTAAATATATAATAATATAT
*
1501040 TCATTATTAAATATATAA-AAAATTAT
1 T-ATTATTAAATATATAATAATA-TAT
1501066 ATATTATTAAA-ATA-AA-AATATAAT
1 -TATTATTAAATATATAATAATAT-AT
* * *
1501090 ATATATATTATATAATATAATATTATTTT
1 -TAT-TATTAAAT-ATATAATAATA-TAT
*
1501119 ATATATATTAAA-ATATAATATTATAT
1 -TAT-TATTAAATATATAATAATATAT
1501145 TATTA-TAAATAT-TAATAA-ATA-
1 TATTATTAAATATATAATAATATAT
*
1501166 TATT-TTAAATATTTAATAAT
1 TATTATTAAATATATAATAAT
1501186 TAATATTTTG
Statistics
Matches: 124, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
21 11 0.09
22 9 0.07
23 10 0.08
24 15 0.12
25 15 0.12
26 27 0.22
27 19 0.15
28 2 0.02
29 15 0.12
30 1 0.01
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTATTAAATATATAATAATATAT
Found at i:1501122 original size:29 final size:29
Alignment explanation
Indices: 1501063--1501192 Score: 109
Period size: 27 Copynumber: 4.8 Consensus size: 29
1501053 TATAAAAAAT
* * * *
1501063 TATATATTAT-TAAAATAAAAATATAATA
1 TATATATTATATAATATAATATTATATTA
*
1501091 TATATATTATATAATATAATATTATTTTA
1 TATATATTATATAATATAATATTATATTA
1501120 TATATATTA-A-AATATAATATTATATTA
1 TATATATTATATAATATAATATTATATTA
* *
1501147 T-TATA-AATATTAATA-AATA-TATTTTA
1 TATATATTATA-TAATATAATATTATATTA
*
1501173 AATAT-TTA-ATAAT-TAATATT
1 TATATATTATATAATATAATATT
1501193 TTGACGAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
25 9 0.11
26 13 0.15
27 25 0.30
28 15 0.18
29 22 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TATATATTATATAATATAATATTATATTA
Found at i:1501133 original size:22 final size:22
Alignment explanation
Indices: 1501087--1501158 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
1501077 ATAAAAATAT
*
1501087 AATATATATATTATA-TAATAT-
1 AATAT-TATATTATATTATTATA
*
1501108 AATATTATTTTATATATATTA-A
1 AATATTATATTATAT-TATTATA
*
1501130 AATATAATATTATATTATTATA
1 AATATTATATTATATTATTATA
1501152 AATATTA
1 AATATTA
1501159 ATAAATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 8 0.19
21 10 0.24
22 24 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTATATTATATTATTATA
Found at i:1501165 original size:32 final size:28
Alignment explanation
Indices: 1501063--1501167 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 28
1501053 TATAAAAAAT
* * **
1501063 TATATATTATTAAA-ATAAAAATATAATA
1 TATATATTA-TAAATATAATATTATTTTA
1501091 TATATATTATATAATATAATATTATTTTA
1 TATATATTATA-AATATAATATTATTTTA
1501120 TATATATTA-AAATATAATATTATATTATTA
1 TATATATTATAAATATAATA-T-TATT-TTA
*
1501150 TAAATATTAATAAATATA
1 TATATATT-ATAAATATA
1501168 TTTTAAATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
27 11 0.17
28 13 0.20
29 23 0.35
30 10 0.15
31 1 0.02
32 7 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TATATATTATAAATATAATATTATTTTA
Found at i:1501166 original size:22 final size:22
Alignment explanation
Indices: 1501119--1501184 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
1501109 ATATTATTTT
*
1501119 ATATATATTA-AAATA-TAATATT
1 ATAT-TATTATAAATATTAATA-A
1501141 ATATTATTATAAATATTAATAA
1 ATATTATTATAAATATTAATAA
*
1501163 ATA-TATTTTAAATATTTAATAA
1 ATATTATTATAAATA-TTAATAA
1501185 TTAATATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 15 0.38
22 19 0.49
23 5 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATTATAAATATTAATAA
Found at i:1501169 original size:21 final size:21
Alignment explanation
Indices: 1501121--1501184 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
1501111 ATTATTTTAT
*
1501121 ATATATTA-AAATA-TAATATT
1 ATATATTATAAATATTAATA-A
1501141 ATATTATTATAAATATTAATAA
1 ATA-TATTATAAATATTAATAA
*
1501163 ATATATTTTAAATATTTAATAA
1 ATATATTATAAATA-TTAATAA
1501185 TTAATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.08
21 15 0.39
22 15 0.39
23 5 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATATTATAAATATTAATAA
Found at i:1501414 original size:42 final size:43
Alignment explanation
Indices: 1501366--1501481 Score: 155
Period size: 42 Copynumber: 2.7 Consensus size: 43
1501356 ATGAATTACA
1501366 TTCCGGAAAATGAATTACGTGAAACAAACACGGA-AAAACATT
1 TTCCGGAAAATGAATTACGTGAAACAAACACGGAGAAAACATT
* * *
1501408 TTCCGGAAAATAAATTACGTGAAATAAACAC-GAGAAAATATT
1 TTCCGGAAAATGAATTACGTGAAACAAACACGGAGAAAACATT
* * * *
1501450 TTACAGAAAACGAATTACATGAAACAAACACG
1 TTCCGGAAAATGAATTACGTGAAACAAACACG
1501482 AGATTTCAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 2 0.03
42 61 0.97
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.20
Consensus pattern (43 bp):
TTCCGGAAAATGAATTACGTGAAACAAACACGGAGAAAACATT
Found at i:1511101 original size:21 final size:21
Alignment explanation
Indices: 1511060--1511100 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1511050 TTATATGTAT
*
1511060 TGAAGAAAACAAATATGAAAA
1 TGAAGAAAACAAATATAAAAA
*
1511081 TGAAGAGAACAAAT-TAAAAA
1 TGAAGAAAACAAATATAAAAA
1511101 AACAACCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (21 bp):
TGAAGAAAACAAATATAAAAA
Found at i:1515207 original size:29 final size:27
Alignment explanation
Indices: 1515169--1515250 Score: 67
Period size: 29 Copynumber: 2.9 Consensus size: 27
1515159 AAATTCTCTA
*
1515169 TTATTAAATTTAAAATTCAAAAATATAT
1 TTATTTAATTTAAAATTCAAAAA-ATAT
*** *
1515197 TTAATTTAATTCTATTTTTCAAATAATAT
1 TT-ATTTAATT-TAAAATTCAAAAAATAT
1515226 TTATTT-ATTTAAAATATCTAAAAAA
1 TTATTTAATTTAAAAT-TC-AAAAAA
1515251 CTTCTCTTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
26 3 0.07
27 5 0.12
28 11 0.27
29 13 0.32
30 9 0.22
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (27 bp):
TTATTTAATTTAAAATTCAAAAAATAT
Found at i:1515416 original size:16 final size:15
Alignment explanation
Indices: 1515377--1515427 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
1515367 AAAAATGTTT
1515377 AACAATATA--ATAA
1 AACAATATATTATAA
*
1515390 AACAAAAATATTACTAA
1 AAC-AATATATTA-TAA
1515407 AACAATATATTA-AA
1 AACAATATATTATAA
1515421 AACAATA
1 AACAATA
1515428 AACTAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 3 0.09
14 14 0.44
16 9 0.28
17 6 0.19
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (15 bp):
AACAATATATTATAA
Found at i:1515442 original size:18 final size:19
Alignment explanation
Indices: 1515419--1515454 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1515409 CAATATATTA
*
1515419 AAAACA-ATAAACTAAATG
1 AAAACATATAAAATAAATG
1515437 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
1515455 AACTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.19
Consensus pattern (19 bp):
AAAACATATAAAATAAATG
Found at i:1516701 original size:3 final size:3
Alignment explanation
Indices: 1516693--1516805 Score: 144
Period size: 3 Copynumber: 38.7 Consensus size: 3
1516683 TTATTTATTA
* *
1516693 AAT AAT AAT AAT -AT AAT ATAT AAT ATT AAT AAT AAT AAT ACT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
** *
1516738 AAT AAT AAT AAT AAT -AT AAT AA- AAT AAT GCT AAT -AT AAT AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1516783 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
1516806 AATGGATAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
2 8 0.08
3 84 0.88
4 3 0.03
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1516776 original size:48 final size:49
Alignment explanation
Indices: 1516693--1516808 Score: 177
Period size: 48 Copynumber: 2.4 Consensus size: 49
1516683 TTATTTATTA
* *
1516693 AATAATAATAATATAAT-ATATAATATTAATAATAATAATACTAATAAT
1 AATAATAATAATATAATAAAATAATACTAATAATAATAATACTAATAAT
*
1516741 AATAATAATAATATAATAAAATAATGCTAAT-ATAATAATACTAATAAT
1 AATAATAATAATATAATAAAATAATACTAATAATAATAATACTAATAAT
1516789 AATAATAAT-A-ATAATAAAAT
1 AATAATAATAATATAATAAAAT
1516809 GGATAAAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
46 10 0.16
47 1 0.02
48 43 0.67
49 10 0.16
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (49 bp):
AATAATAATAATATAATAAAATAATACTAATAATAATAATACTAATAAT
Found at i:1517407 original size:110 final size:109
Alignment explanation
Indices: 1516979--1517967 Score: 1370
Period size: 110 Copynumber: 9.0 Consensus size: 109
1516969 GATATCAAAC
*
1516979 AAAGG-TGAACAAGCTCTTCTCATTATGAAACTTCTTCTTCCTTCTTCAGATGAG-TC-TCTCAT
1 AAAGGTTGAACAAGTTCTTCTCATTATG-AACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
* ** * *
1517041 TCATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
64 T-ATGAACTTTCTCTGG--A-AATGATCCATCAAATGATGAATTCAAGCA
*
1517091 AAAAG-TGAACAAG-TCTTCTC--T-TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
* * * * *
1517151 ATGAACTTTCTCTGGAAAGAGATCCACCAAATGATGGATTCAGGTA
65 ATGAACTTTCTCTGGAAA-TGATCCATCAAATGATGAATTCAAGCA
*
1517197 AAAGGTTGAACAAATTCTTCTCATTATG---TTCTTC--CTTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
* * *
1517257 TGAACTTTC-CTGGAAAGATGATCCACCAAATGATGGATTCAGGCA
66 TGAACTTTCTCTGG-AA-ATGATCCATCAAATGATGAATTCAAGCA
1517302 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-T-TTCTTCAGATGACGAGTTC-TCTCA
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT---GAGTTCTTCTCA
*
1517364 TTATGAACTTTCCTCTGGAAATGATCCATCAAGTGATGAATTCAAGCA
63 TTATGAACTTT-CTCTGGAAATGATCCATCAAATGATGAATTCAAGCA
1517412 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
1517477 ATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCA
65 ATGAACTTTCTCTGGAAA---TGATCCATCAAATGATGAATTCAAGCA
1517525 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
1517590 ATGAACTTTCTCTGGAAATGATCCATC-AATGATGAATTCAAGCA
65 ATGAACTTTCTCTGGAAATGATCCATCAAATGATGAATTCAAGCA
1517634 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
* *
1517699 ATGAACCTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATT-AAACA
65 ATGAA-CTTTCTCTGG---A-AATGATCCATCAAATGATGAATTCAAGCA
1517748 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
1517813 ATGAACTTTCTCTGGAAATGTGATCCATC-AATGATGAATTCAAGCA
65 ATGAACTTTCTCTGGAAA--TGATCCATCAAATGATGAATTCAAGCA
*
1517859 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
*
1517924 ATGAACTTTCCTCTGGAAATGATCCATCAATTTGATGAATTCAA
65 ATGAACTTT-CTCTGGAAATGATCCATCAA-ATGATGAATTCAA
1517968 ATCTTTGCTA
Statistics
Matches: 812, Mismatches: 27, Indels: 76
0.89 0.03 0.08
Matches are distributed among these distances:
104 4 0.00
105 89 0.11
106 26 0.03
107 33 0.04
108 47 0.06
109 97 0.12
110 132 0.16
111 122 0.15
112 37 0.05
113 130 0.16
114 85 0.10
115 10 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (109 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAATGATCCATCAAATGATGAATTCAAGCA
Found at i:1517550 original size:223 final size:221
Alignment explanation
Indices: 1516979--1517968 Score: 1450
Period size: 223 Copynumber: 4.5 Consensus size: 221
1516969 GATATCAAAC
*
1516979 AAAGG-TGAACAAGCTCTTCTCATTATGAAACTTCTTCTTCCTTCTTCAGATGAG-TC-TCTCAT
1 AAAGGTTGAACAAGTTCTTCTCATTATG-AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
1517041 TCATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAAAAAG-TGAACAAG-
65 T-ATGAACTTTCTCTGG-AAAGATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGT
1517104 TCTTCTC--T-TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
128 TCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * * * *
1517166 AAAGAGATCCACCAAATGATGGATTCAGGTA
192 AAAGTGATCCATC-AATGATGAATTCAAGCA
*
1517197 AAAGGTTGAACAAATTCTTCTCATTATG------TTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * **
1517256 ATGAACTTTC-CTGGAAAGATGATCCACCAAATGATGGATTCAGGCAAAAGGTTGAACAAGTTCT
66 ATGAACTTTCTCTGGAAAGATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCT
1517320 TCTCATTATGAACTTCTTC-T-TTCTTCAGATGACGAGTTC-TCTCATTATGAACTTTCCTCTGG
131 TCTCATTATGAACTTCTTCTTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTT-CTCTGG
1517382 AAA-TGATCCATCAAGTGATGAATTCAAGCA
192 AAAGTGATCCATCAA-TGATGAATTCAAGCA
1517412 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
1517477 ATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAGTTC
66 ATGAACTTTCTCTGGAAA-GATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTC
1517542 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
130 TTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1517607 A-TGATCCATCAATGATGAATTCAAGCA
194 AGTGATCCATCAATGATGAATTCAAGCA
1517634 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1517699 ATGAACCTTTCTCTGGAAAAGAATGATCCATCAAGTGATGAATT-AAACAAAAGGTTGAACAAGT
66 ATGAA-CTTTCTCTGG-AAAG-ATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGT
1517763 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
128 TCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1517828 AAATGTGATCCATCAATGATGAATTCAAGCA
192 AAA-GTGATCCATCAATGATGAATTCAAGCA
*
1517859 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
1517924 ATGAACTTTCCTCTGG-AA-ATGATCCATCAATTTGATGAATTCAAA
66 ATGAACTTT-CTCTGGAAAGATGATCCATCAA-ATGATGAATTCAAA
1517969 TCTTTGCTAA
Statistics
Matches: 712, Mismatches: 27, Indels: 61
0.89 0.03 0.08
Matches are distributed among these distances:
211 28 0.04
212 31 0.04
213 29 0.04
214 9 0.01
215 64 0.09
216 26 0.04
218 5 0.01
219 20 0.03
221 53 0.07
222 101 0.14
223 191 0.27
224 44 0.06
225 101 0.14
226 10 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (221 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAGATGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCT
TCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAG
TGATCCATCAATGATGAATTCAAGCA
Found at i:1518636 original size:51 final size:51
Alignment explanation
Indices: 1518585--1519289 Score: 1139
Period size: 51 Copynumber: 13.9 Consensus size: 51
1518575 GATTCCCAAT
1518585 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAATC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAA-C
*
1518637 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGTCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAAC
*
1518688 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-TATCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAAC
*
1518737 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGTCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAAC
1518788 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAAC
1518839 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG----G-CAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAAC
*
1518885 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCATCTTCTAATC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC-T-GTC-AA-C
* * *
1518940 CAGATCAGATATCTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAAC
*
1518991 CAGATCAGATAACTCAAAGAACACTTCCAG-AGATGCTATGTTATGATCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCAAC
1519042 CAGATCAGATAACTCAAAGAACACTTCC---AGATGCTATGTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT-CAAC
*
1519091 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCAAC
1519143 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-GTTCTGTCCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGT-CAAC
*
1519194 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCAAC
1519246 CAGATCAGATAACTCAAAGAACACTT-CAGAAGATGCTATGTTCT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT
1519290 TGATGCTTTC
Statistics
Matches: 615, Mismatches: 18, Indels: 41
0.91 0.03 0.06
Matches are distributed among these distances:
46 45 0.07
47 1 0.00
48 1 0.00
49 93 0.15
50 16 0.03
51 265 0.43
52 143 0.23
53 5 0.01
54 3 0.00
55 43 0.07
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (51 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAAC
Found at i:1518945 original size:203 final size:200
Alignment explanation
Indices: 1518585--1519286 Score: 1130
Period size: 203 Copynumber: 3.5 Consensus size: 200
1518575 GATTCCCAAT
*
1518585 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCAATCCAGATCAGATAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAA-CCAGATCAGATAA
1518649 CTCAAAGAACACTTCCAGAAGATGCTATGTTATGTCAACCAGATCAGATAACTCAAAGAACACTT
65 CTCAAAGAACACTTCCAGAAGATGCTATG---TG-CAACCAGATCAGATAACTCAAAGAACACTT
1518714 CCAGAAGATGCTATGTTA-TCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
126 CCAGAAGATGCTATGTTATTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
1518778 TTATGTCAAC
191 TTCTGTCAAC
*
1518788 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCAACCAGATCAGATAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACCAGATCAGATAAC
1518852 TCAAAGAACACTTCCAGAAGATGCTATG-GCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
66 TCAAAGAACACTTCCAGAAGATGCTATGTGCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
* *
1518916 AGATGCTATGTTCATCTTCTAATCCAGATCAGATATCTCAAAGAACACTTCCAGAAAATGCTATG
131 AGATGCTATGTT-A--TTC-AA-CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
1518981 TTCTGTCAAT
191 TTCTGTCAAC
1518991 CAGATCAGATAACTCAAAGAACACTTCCAG-AGATGCTATGTTATGATCAACCAGATCAGATAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACCAGATCAGATAAC
* * * *
1519055 TCAAAGAACACTTCCAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
66 TCAAAGAACACTTCCAGAAG--ATGCTATGTGCAACCAGATCAGATAACTCAAAGAACACTTCCA
1519120 GAAGATGCTATGTTATGATCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-GT
129 GAAGATGCTATGTTAT--TCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGT
1519184 TCTGTCCAAC
192 TCTGT-CAAC
1519194 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACCAGATCAGATAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACCAGATCAGATAAC
1519259 TCAAAGAACACTT-CAGAAGATGCTATGT
66 TCAAAGAACACTTCCAGAAGATGCTATGT
1519287 TCTTGATGCT
Statistics
Matches: 470, Mismatches: 15, Indels: 30
0.91 0.03 0.06
Matches are distributed among these distances:
197 47 0.10
198 2 0.00
201 9 0.02
202 65 0.14
203 242 0.51
204 49 0.10
205 9 0.02
206 47 0.10
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.24
Consensus pattern (200 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACCAGATCAGATAAC
TCAAAGAACACTTCCAGAAGATGCTATGTGCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
AGATGCTATGTTATTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG
TCAAC
Found at i:1518988 original size:152 final size:150
Alignment explanation
Indices: 1518585--1519289 Score: 1106
Period size: 152 Copynumber: 4.6 Consensus size: 150
1518575 GATTCCCAAT
1518585 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTC-TGTCAATCCAGATCAGATAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCATGTCAA-CCAGATCAGATAA
*
1518649 CTCAAAGAACACTTCCAGAAGATGCTATGTTATGTCAACCAGATCAGATAACTCAAAGAACACTT
65 CTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAACCAGATCAGATAACTCAAAGAACACTT
*
1518714 CCAGAAGATGCTATGTTATCAAC
130 CCAGAAGATGCTATG-T-GCAAC
1518737 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTT-ATGTCAACCAGATCAGATAAC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCATGTCAACCAGATCAGATAAC
1518801 TCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAACCAGATCAGATAACTCAAAGAACACTTC
66 TCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAACCAGATCAGATAACTCAAAGAACACTTC
1518866 CAGAAGATGCTATG-GCAAC
131 CAGAAGATGCTATGTGCAAC
*
1518885 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCATCTTCTAATCCAGATCAGAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCAT-GTC-AA-CCAGATCAGAT
* * *
1518950 ATCTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCAATCAGATCAGATAACTCAAAGAACAC
63 AACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAACCAGATCAGATAACTCAAAGAACAC
1519015 TTCCAG-AGATGCTATGTTATGATCAAC
128 TTCCAGAAGATGCTATG---TG--CAAC
1519042 CAGATCAGATAACTCAAAGAACACTTCC---AGATGCTATGTTC-TGTCCAACCAGATCAGATAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCATGT-CAACCAGATCAGATAA
*
1519103 CTCAAAGAACACTTCCAGAAGATGCTATGTTATGATCAACCAGATCAGATAACTCAAAGAACACT
65 CTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCAACCAGATCAGATAACTCAAAGAACACT
*
1519168 TCCAGAAGATGCTAGTTCTGTCCAAC
129 TCCAGAAGATGCTA----TGTGCAAC
1519194 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTT-ATGATCAACCAGATCAGATAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCATG-TCAACCAGATCAGATAA
1519258 CTCAAAGAACACTT-CAGAAGATGCTATGTTCT
65 CTCAAAGAACACTTCCAGAAGATGCTATGTTCT
1519290 TGATGCTTTC
Statistics
Matches: 517, Mismatches: 13, Indels: 44
0.90 0.02 0.08
Matches are distributed among these distances:
148 47 0.09
149 2 0.00
150 2 0.00
151 148 0.29
152 197 0.38
153 10 0.02
154 31 0.06
155 45 0.09
156 1 0.00
157 34 0.07
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (150 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCATGTCAACCAGATCAGATAAC
TCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCAACCAGATCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATGTGCAAC
Found at i:1520266 original size:1 final size:1
Alignment explanation
Indices: 1520260--1520331 Score: 63
Period size: 1 Copynumber: 72.0 Consensus size: 1
1520250 ACCTTGACCC
* * ** * * * * *
1520260 TTTTTTTTTTCTTTTCTTTTTTCCTTTTTTTTTTTTCTTTTTCTTTTTCTTTTCTTTTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1520325 TTTTTTT
1 TTTTTTT
1520332 CTTCAAGCAT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:1520287 original size:21 final size:21
Alignment explanation
Indices: 1520263--1520334 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
1520253 TTGACCCTTT
1520263 TTTTTTTCTTTTCTTTTTTCC
1 TTTTTTTCTTTTCTTTTTTCC
*
1520284 TTTTTTTTTTTTC-TTTTT-C
1 TTTTTTTCTTTTCTTTTTTCC
* *
1520303 TTTTTCTT-TTCTTTTTTTTTCT
1 TTTTT-TTCTT-TTCTTTTTTCC
1520325 TTTTTTTCTT
1 TTTTTTTCTT
1520335 CAAGCATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
19 8 0.19
20 9 0.21
21 19 0.44
22 7 0.16
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTTTTCTTTTCTTTTTTCC
Found at i:1520289 original size:26 final size:25
Alignment explanation
Indices: 1520260--1520331 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 25
1520250 ACCTTGACCC
1520260 TTTTTTTTTTCTTTTCTTTTTTCCTT
1 TTTTTTTTTTCTTTT-TTTTTTCCTT
*
1520286 TTTTTTTTTTCTTTTTCTTTTTCTTT
1 TTTTTTTTTTCTTTTT-TTTTTCCTT
1520312 TCTTTTTTTTTCTTTTTTTT
1 T-TTTTTTTTTCTTTTTTTT
1520332 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 1 0.02
26 27 0.63
27 15 0.35
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (25 bp):
TTTTTTTTTTCTTTTTTTTTTCCTT
Found at i:1520330 original size:38 final size:37
Alignment explanation
Indices: 1520259--1520334 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 37
1520249 CACCTTGACC
1520259 CTTTTTTTTTTCTTTTCTTTTTTCCTTTTTTTTTTTT
1 CTTTTTTTTTTCTTTTCTTTTTTCCTTTTTTTTTTTT
*
1520296 CTTTTTCTTTTTCTTTTCTTTTTT--TTTCTTTTTTTT
1 CTTTTT-TTTTTCTTTTCTTTTTTCCTTTTTTTTTTTT
1520332 CTT
1 CTT
1520335 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 14 0.38
37 6 0.16
38 17 0.46
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (37 bp):
CTTTTTTTTTTCTTTTCTTTTTTCCTTTTTTTTTTTT
Found at i:1533003 original size:3 final size:3
Alignment explanation
Indices: 1532995--1533114 Score: 147
Period size: 3 Copynumber: 40.7 Consensus size: 3
1532985 TTAATATATT
*
1532995 TAA TAA TAA -AA TAA T-A TAA TAA TAA TAA CAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
1533040 TAA CAA TGA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAT TAA AAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1533086 TGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1533115 TGGATAAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
2 6 0.06
3 90 0.91
4 3 0.03
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1547980 original size:31 final size:31
Alignment explanation
Indices: 1547942--1548004 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1547932 AGTTGGAACT
*
1547942 CTTCCAATGACTGGCTCTCACAACGGTCGAG
1 CTTCCAATGACTGGCTCCCACAACGGTCGAG
1547973 CTTCCAATGACTGGCTCCCACAACGGTCGAG
1 CTTCCAATGACTGGCTCCCACAACGGTCGAG
1548004 C
1 C
1548005 ATTACGCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.21
Consensus pattern (31 bp):
CTTCCAATGACTGGCTCCCACAACGGTCGAG
Found at i:1548132 original size:15 final size:15
Alignment explanation
Indices: 1548112--1548141 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1548102 TATATATTTT
1548112 CTTTAAAAATTATAA
1 CTTTAAAAATTATAA
1548127 CTTTAAAAATTATAA
1 CTTTAAAAATTATAA
1548142 ATTCATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
CTTTAAAAATTATAA
Found at i:1549436 original size:34 final size:34
Alignment explanation
Indices: 1549370--1549436 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
1549360 AATCTAACCA
* *
1549370 AATATATTTTAATATTCAACATTAAACCGATAAT
1 AATATATTTTAATATTAAACATTAAAACGATAAT
* *
1549404 AATATATTTTAAT-TTGAAATATTAAAATGATAA
1 AATATATTTTAATATT-AAACATTAAAACGATAA
1549437 AACTTCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (34 bp):
AATATATTTTAATATTAAACATTAAAACGATAAT
Found at i:1549491 original size:71 final size:71
Alignment explanation
Indices: 1549405--1549547 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
1549395 ACCGATAATA
1549405 ATATATTTTAATTTGAAATATTAAAATGATAAAACTTCTTTTACCATTCAAACTTAAATACGTAT
1 ATATATTTTAATTTGAAATATTAAAATGATAAAACTTCTTTTACCATTCAAACTTAAATACGTAT
1549470 TATTTT
66 TATTTT
1549476 ATATATTTTAATTTGAAATATTAAAATGATAAAACTTCTTTTACCATTCAAACTTAAATACGTAT
1 ATATATTTTAATTTGAAATATTAAAATGATAAAACTTCTTTTACCATTCAAACTTAAATACGTAT
1549541 TATTTT
66 TATTTT
1549547 A
1 A
1549548 ATTTAAAATA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (71 bp):
ATATATTTTAATTTGAAATATTAAAATGATAAAACTTCTTTTACCATTCAAACTTAAATACGTAT
TATTTT
Found at i:1554855 original size:34 final size:34
Alignment explanation
Indices: 1554816--1554900 Score: 143
Period size: 34 Copynumber: 2.5 Consensus size: 34
1554806 TGATTATATA
* *
1554816 TATATATATAATATTTTTTATTTTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
1554850 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
1554884 TATATATAAAATATTTT
1 TATATATATAATATTTT
1554901 CGGGTTCAGG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:1555546 original size:39 final size:38
Alignment explanation
Indices: 1555517--1555622 Score: 133
Period size: 39 Copynumber: 2.8 Consensus size: 38
1555507 ACTTCATGAT
1555517 TGCATGGCGTCTTCAGACAAATGAAGAAGACCCCACGAC
1 TGCATGGCGTCTTCAGACAAATGAAGAAGA-CCCACGAC
* * * *
1555556 TGCATGACGTCTTCAGACAAATGGAGAAGACCCTAGGAG
1 TGCATGGCGTCTTCAGACAAATGAAGAAGACCC-ACGAC
* *
1555595 TGAATGGCGTCTTCAGACTAAT-AAGAAG
1 TGCATGGCGTCTTCAGACAAATGAAGAAG
1555623 CCCTAATTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 8 0.14
39 50 0.86
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (38 bp):
TGCATGGCGTCTTCAGACAAATGAAGAAGACCCACGAC
Found at i:1563320 original size:13 final size:13
Alignment explanation
Indices: 1563302--1563335 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1563292 TGTCACGTTC
1563302 ATATTTTAAAAAA
1 ATATTTTAAAAAA
* *
1563315 ATATTTTTAAATA
1 ATATTTTAAAAAA
1563328 ATATTTTA
1 ATATTTTA
1563336 TTTTTAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATTTTAAAAAA
Found at i:1565073 original size:29 final size:29
Alignment explanation
Indices: 1565022--1565079 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1565012 GTGTTAGCCG
* *
1565022 TAGGTTGTCATGCCTTTCGGGCGACCTAC
1 TAGGTCGTCATGCCTTTCGGGCGAACTAC
* **
1565051 TAGGTCGTCATGTCTTTTTGGCGAACTAC
1 TAGGTCGTCATGCCTTTCGGGCGAACTAC
1565080 AAGAGATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (29 bp):
TAGGTCGTCATGCCTTTCGGGCGAACTAC
Found at i:1565167 original size:34 final size:34
Alignment explanation
Indices: 1565118--1565184 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1565108 AATACGCTGG
*
1565118 GCATCTGAGGCCATCCGACCGAGGCCATCCGAAA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAAA
* *
1565152 GCATCCGAGGTCATCCGACCGAGGTCATCCGAA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAA
1565185 CGAGCTATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.34, G:0.27, T:0.13
Consensus pattern (34 bp):
GCATCCGAGGCCATCCGACCGAGGCCATCCGAAA
Found at i:1565175 original size:14 final size:14
Alignment explanation
Indices: 1565156--1565188 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1565146 CCGAAAGCAT
1565156 CCGAGGTCATCCGA
1 CCGAGGTCATCCGA
1565170 CCGAGGTCATCCGA
1 CCGAGGTCATCCGA
*
1565184 ACGAG
1 CCGAG
1565189 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.33, G:0.30, T:0.12
Consensus pattern (14 bp):
CCGAGGTCATCCGA
Found at i:1565222 original size:33 final size:33
Alignment explanation
Indices: 1565170--1565253 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
1565160 GGTCATCCGA
* * * *
1565170 CCGAGGTCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1565203 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
*
1565236 CCGATGG-AAGCCGAGCGA
1 CCGAGGGCAA-CCGAGCGA
1565254 AGGTAGGTCG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
32 2 0.04
33 43 0.96
ACGTcount: A:0.26, C:0.26, G:0.37, T:0.11
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:1565384 original size:19 final size:19
Alignment explanation
Indices: 1565360--1565397 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1565350 AAGCAAGGGT
1565360 AGGTCGCCCA-GAGTGCATG
1 AGGTCG-CCATGAGTGCATG
1565379 AGGTCGCCATGAGTGCATG
1 AGGTCGCCATGAGTGCATG
1565398 GCGACCTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.21, C:0.24, G:0.37, T:0.18
Consensus pattern (19 bp):
AGGTCGCCATGAGTGCATG
Found at i:1565421 original size:29 final size:29
Alignment explanation
Indices: 1565379--1565435 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1565369 AGAGTGCATG
* * *
1565379 AGGTCGCCATGAGTGCATGGCGACCTACA
1 AGGTCGCCAGGAGTACATGGAGACCTACA
*
1565408 AGGTCGCCCGGAGTACATGGAGACCTAC
1 AGGTCGCCAGGAGTACATGGAGACCTAC
1565436 GGCCAACACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.32, T:0.16
Consensus pattern (29 bp):
AGGTCGCCAGGAGTACATGGAGACCTACA
Found at i:1566028 original size:3 final size:3
Alignment explanation
Indices: 1566020--1566052 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1566010 TAGATGTTAC
*
1566020 ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1566053 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1566905 original size:7 final size:7
Alignment explanation
Indices: 1566878--1566922 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
1566868 AATTTAATTT
1566878 AATT-TA
1 AATTATA
1566884 AATT-TA
1 AATTATA
*
1566890 AAATA-A
1 AATTATA
1566896 AATTATA
1 AATTATA
1566903 AATTATA
1 AATTATA
1566910 AATTATA
1 AATTATA
1566917 AATTAT
1 AATTAT
1566923 TTGAATTCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 14 0.40
7 21 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTATA
Found at i:1567097 original size:34 final size:32
Alignment explanation
Indices: 1567059--1567121 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 32
1567049 CCATAATTCA
* *
1567059 AAAATATTTTTTTAAAATATTATTAAATTATTTT
1 AAAATAATTTGTTAAAATATTA--AAATTATTTT
*
1567093 AAAATAATTTGTTAAACTATTAAAATTAT
1 AAAATAATTTGTTAAAATATTAAAATTAT
1567122 AAAATGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 7 0.27
34 19 0.73
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (32 bp):
AAAATAATTTGTTAAAATATTAAAATTATTTT
Found at i:1567107 original size:23 final size:21
Alignment explanation
Indices: 1567068--1567113 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
1567058 AAAAATATTT
*
1567068 TTTTAAAATATTATTAAATTA
1 TTTTAAAATATTATTAAACTA
*
1567089 TTTTAAAATAATTTGTTAAACTA
1 TTTTAAAAT-A-TTATTAAACTA
1567112 TT
1 TT
1567114 AAAATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 1 0.05
23 11 0.52
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTTAAAATATTATTAAACTA
Found at i:1572802 original size:12 final size:12
Alignment explanation
Indices: 1572785--1572816 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1572775 TAATGTTTGA
1572785 TTAAAAAAATAT
1 TTAAAAAAATAT
1572797 TTAAAAAAATAT
1 TTAAAAAAATAT
*
1572809 ATAAAAAA
1 TTAAAAAA
1572817 GAATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAAAAAATAT
Found at i:1574966 original size:89 final size:93
Alignment explanation
Indices: 1574760--1574967 Score: 325
Period size: 93 Copynumber: 2.3 Consensus size: 93
1574750 GTAAATTTAA
* * *
1574760 AATAATTTTCTTAACCATAATTTTATCCACAGATCAATTATAAATTTAATAACATAAAAAATAAT
1 AATAATTTTCTTATCCATAATCTTATCCAAAGATCAATTATAAATTTAATAACATAAAAAATAAT
*
1574825 TAATAATAAAAATATATTTGTTATCAAT
66 TAATAATAAAAATATATTTGTTATCAAG
* * *
1574853 AATAATTTTCTTATCCATAATCTTATCCAAAGATCAATTATAAATTTAATAATAT-AAATATATT
1 AATAATTTTCTTATCCATAATCTTATCCAAAGATCAATTATAAATTTAATAACATAAAAAATAAT
1574917 TAATAA-AAAAA-A-ATTTGTTATCAAG
66 TAATAATAAAAATATATTTGTTATCAAG
1574942 AATAATTTTCTTATCCATAATCTTAT
1 AATAATTTTCTTATCCATAATCTTAT
1574968 GCTTATTTCA
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
89 38 0.35
90 1 0.01
91 5 0.05
92 13 0.12
93 51 0.47
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.40
Consensus pattern (93 bp):
AATAATTTTCTTATCCATAATCTTATCCAAAGATCAATTATAAATTTAATAACATAAAAAATAAT
TAATAATAAAAATATATTTGTTATCAAG
Found at i:1580584 original size:47 final size:46
Alignment explanation
Indices: 1580497--1580586 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 46
1580487 CTTAAAAGTT
**
1580497 TTAAATTTTTATATAATTTATATAATTTTATTATTTTTTAAATCAC
1 TTAAATTTTTATATAATTTATATAATTTTATTATAATTTAAATCAC
*
1580543 TTAAATTTTTAATATAATTT-TTTGAACTTTTA-TATAATTTAAAT
1 TTAAATTTTT-ATATAATTTATAT-AA-TTTTATTATAATTTAAAT
1580587 ATATTTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
46 12 0.32
47 21 0.55
48 5 0.13
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (46 bp):
TTAAATTTTTATATAATTTATATAATTTTATTATAATTTAAATCAC
Found at i:1585661 original size:55 final size:54
Alignment explanation
Indices: 1585596--1585734 Score: 147
Period size: 57 Copynumber: 2.5 Consensus size: 54
1585586 TATTTTTTAG
*
1585596 ATATATTCGATTCTGAGCCCTTATTTTTATGCTTCTTAATAGAAACAACTGATAA
1 ATATATTCGATTCTGAGCCC-TATTTTTATGCTTATTAATAGAAACAACTGATAA
* * * * *
1585651 ATATATTCGATT-TAAAGACCCCCTATTTGTATGCTTATTAATGGCAACAACTGATAG
1 ATATATTCGATTCT---GA-GCCCTATTTTTATGCTTATTAATAGAAACAACTGATAA
*
1585708 AGATATTCGATTC-GAGCTCCTATTTTT
1 ATATATTCGATTCTGAGC-CCTATTTTT
1585735 TGGGGACCCT
Statistics
Matches: 69, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
53 1 0.01
54 11 0.16
55 12 0.17
57 42 0.61
58 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (54 bp):
ATATATTCGATTCTGAGCCCTATTTTTATGCTTATTAATAGAAACAACTGATAA
Found at i:1596189 original size:24 final size:25
Alignment explanation
Indices: 1596141--1596190 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1596131 AGGAAACTTG
*
1596141 CAGCAGAAACTCCAATCGTCTGTAA
1 CAGCAGAAACTCCAATCCTCTGTAA
* *
1596166 CAGCAGAGACTGC-ATCCTCTGTAA
1 CAGCAGAAACTCCAATCCTCTGTAA
1596190 C
1 C
1596191 TAAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (25 bp):
CAGCAGAAACTCCAATCCTCTGTAA
Found at i:1597311 original size:463 final size:456
Alignment explanation
Indices: 1596446--1597343 Score: 1123
Period size: 463 Copynumber: 1.9 Consensus size: 456
1596436 TAAGTAACTA
** *
1596446 TGATCGAGCTCATATCTAGAAGAGATGGGTATCATTCAAATGCGATCATGATAGACCAATATAAA
1 TGATCGAGCTCATATCTAGAAGAGATGAATATCATTCAAATGCAATCATGATAGACCAATATAAA
*
1596511 ACATGGAATTCATATCGAATGTTCACATCACAAATCAAAATTTAGTCTTATATTAAGTTATTAAC
66 ACATGGAATTCATATCGAATGTTCACATCACAAATCAAAATTTAGTCCTATATTAA--TATT---
* * *
1596576 ATAAGCCAAATATCTCTCATCACCAAAGAATCTGCACAACAGGCATCTGAAGGAAAATCGAAAGA
126 ATAAGCCAAATATCTCTAATCACCAAAGAATCTGCACAACAGGCACCTAAAGGAAAATCGAAAGA
* * * * *
1596641 CAAGCGGACAAGCGAGTGTTGGGTACGGGTATGTGTTTATCTCGGCTATGCTCATTTCTTTCAAA
191 CAAGCGGACAAGCGAGTATTGGGTACGGGTATGTGTTTAACTAGGATATGCTAATTTCTTTCAAA
* ** **** *
1596706 GGTTTTTTCTTTTCTAAATTTTCTAATATTTCGAAGATGATATCAGTCGGTATAACATAGGACAG
256 GGTATTCCCCCCCCTAAATTTTCTAATATTTCGAAGATGATACCAGTC-G-ATAACATAGGACAG
* * **
1596771 ACAGAATTTATAAACTGGCCAAATCATCCACATTCTTTCCAACTTACAACAATTCATATCCTAAG
319 AAAGAATTTATAAACTGACCAAATCATCCACATTCTTTCCAACTTACAACAACCCATATCCTAAG
* *
1596836 CATTCTGATTTCCATAATTG-ATAAGCCACAAATTTGCATTTATGAATGTAAGTGGTTTGTCTAA
384 CATTCTGATTTCCATAACTGAATAA-CCAAAAATTTGCATTTATGAATGTAAGTGGTTTGTCTAA
1596900 AAGAGTGTC
448 AAGAGTGTC
* * * *
1596909 TGATCGAGCTCATATCTAGAAGGGATGAATATCATTCAAATTCAATCATGATGGACTAATATAAA
1 TGATCGAGCTCATATCTAGAAGAGATGAATATCATTCAAATGCAATCATGATAGACCAATATAAA
*
1596974 ACATGGAATTCATATCGAATGTTTACATCACAAATCAAAATTTAGTCCTATATTAA-A-T-TAAG
66 ACATGGAATTCATATCGAATGTTCACATCACAAATCAAAATTTAGTCCTATATTAATATTATAAG
* *
1597036 CCAAATATCTC-AAGTCACCAAAGAATCTGCACAACAGGCACCTAAAGGAAAATTGAACGACAA-
131 CCAAATATCTCTAA-TCACCAAAGAATCTGCACAACAGGCACCTAAAGGAAAATCGAAAGACAAG
** * *
1597099 CTGGACAATTGAGTATTAGACATGTATCATATGATGAGTGTGTGTTTAACTAGGATATGCTAATT
195 C-GGACAAGCGAGTATT-G---GGTA-C----G--G-GTATGTGTTTAACTAGGATATGCTAATT
* * *
1597164 TC-TTCTAAAGGTATTCCCCCCCCTATATTTT-TTATATTTGGAAGATGATACCAGTC-ATAACA
247 TCTTTC-AAAGGTATTCCCCCCCCTAAATTTTCTAATATTTCGAAGATGATACCAGTCGATAACA
* *
1597226 TAGGGCAGAAAGCATTTATAAACTGACCAAATCA-CCTACATTCTTTCCAACTTACAACAACCCA
311 TAGGACAGAAAGAATTTATAAACTGACCAAATCATCC-ACATTCTTTCCAACTTACAACAACCCA
*
1597290 TATCCTAAGCATTTTGATTTCCATAACTGAATAACCAAAAATTTGCATTTATGA
375 TATCCTAAGCATTCTGATTTCCATAACTGAATAACCAAAAATTTGCATTTATGA
1597344 GTACAAACAC
Statistics
Matches: 375, Mismatches: 43, Indels: 34
0.83 0.10 0.08
Matches are distributed among these distances:
454 2 0.01
455 72 0.19
456 1 0.00
459 4 0.01
460 2 0.01
462 2 0.01
463 219 0.58
464 5 0.01
466 26 0.07
467 42 0.11
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (456 bp):
TGATCGAGCTCATATCTAGAAGAGATGAATATCATTCAAATGCAATCATGATAGACCAATATAAA
ACATGGAATTCATATCGAATGTTCACATCACAAATCAAAATTTAGTCCTATATTAATATTATAAG
CCAAATATCTCTAATCACCAAAGAATCTGCACAACAGGCACCTAAAGGAAAATCGAAAGACAAGC
GGACAAGCGAGTATTGGGTACGGGTATGTGTTTAACTAGGATATGCTAATTTCTTTCAAAGGTAT
TCCCCCCCCTAAATTTTCTAATATTTCGAAGATGATACCAGTCGATAACATAGGACAGAAAGAAT
TTATAAACTGACCAAATCATCCACATTCTTTCCAACTTACAACAACCCATATCCTAAGCATTCTG
ATTTCCATAACTGAATAACCAAAAATTTGCATTTATGAATGTAAGTGGTTTGTCTAAAAGAGTGT
C
Found at i:1598585 original size:59 final size:61
Alignment explanation
Indices: 1598453--1598599 Score: 165
Period size: 59 Copynumber: 2.4 Consensus size: 61
1598443 AATTATAATT
* * * * * *
1598453 TTTAAAAGTTTGAGGACTAATTTAAGATAAAGATCATAAGTTTGGGGATGAATTTAGAATT
1 TTTAAAAGTTTAAGGACAAATTTAAAATAAAGACCATAAGTTTGGGGATGAATTTAAAATA
* * * *
1598514 TTTTAAAGTTTAAGGACCAATTTAAAATGATAG-CCATATG-TTGGGG-TGAATTTAAAATA
1 TTTAAAAGTTTAAGGACAAATTTAAAAT-AAAGACCATAAGTTTGGGGATGAATTTAAAATA
*
1598573 TTTAAAAGTTTAAGAACAAATTTAAAA
1 TTTAAAAGTTTAAGGACAAATTTAAAA
1598600 GGCTTAAGTA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
59 35 0.48
60 6 0.08
61 29 0.40
62 3 0.04
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (61 bp):
TTTAAAAGTTTAAGGACAAATTTAAAATAAAGACCATAAGTTTGGGGATGAATTTAAAATA
Found at i:1607430 original size:84 final size:86
Alignment explanation
Indices: 1607247--1607448 Score: 252
Period size: 84 Copynumber: 2.4 Consensus size: 86
1607237 AGTTAAAAAG
** *
1607247 ACAATTAA-AATCAACTCCACCAAGAATGAAAACATGTATGTCGAAGTCATAGATTCTTTCATAC
1 ACAATTAACAATC-ACTCTGCCAAGAATGAAAACATGTATGT--AAGTCATAGACTCTTTCATAC
* *
1607311 GATTATGGTATTTTAGTAAAATAT
63 AATTATGGTAATTTAGTAAAATAT
* * * *
1607335 ACAATTAACAATGACTCTAG-CAAGAATGAAAACATGTATGT-TGTCCTATACTCTTTCATACAA
1 ACAATTAACAATCACTCT-GCCAAGAATGAAAACATGTATGTAAGTCATAGACTCTTTCATACAA
1607398 TTATGG-AATTTAGTAAAATAT
65 TTATGGTAATTTAGTAAAATAT
1607419 ACAATTAACAATCACTCTGCCAAGAA-GAAA
1 ACAATTAACAATCACTCTGCCAAGAATGAAA
1607449 GTCCTAGACT
Statistics
Matches: 101, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
83 5 0.05
84 37 0.37
85 23 0.23
88 33 0.33
89 3 0.03
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (86 bp):
ACAATTAACAATCACTCTGCCAAGAATGAAAACATGTATGTAAGTCATAGACTCTTTCATACAAT
TATGGTAATTTAGTAAAATAT
Found at i:1608302 original size:75 final size:75
Alignment explanation
Indices: 1608179--1608333 Score: 274
Period size: 75 Copynumber: 2.1 Consensus size: 75
1608169 AGTGAAAGTT
* *
1608179 CTTCAATTTCACCTGAATTTTCTTTCCTATGAGTAGTTTGTACTTCCTCATTGATCTGGTCTTCA
1 CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATTGATCTGGTCTTCA
*
1608244 CCTACATGAG
66 CCTACATAAG
1608254 CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATTGATCTGGTCTTCA
1 CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATTGATCTGGTCTTCA
*
1608319 CCTTCATAAG
66 CCTACATAAG
1608329 CTTCA
1 CTTCA
1608334 TCATAATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.43
Consensus pattern (75 bp):
CTTCAATTTCACCTGAATTTTCTTTCATATGAGCAGTTTGTACTTCCTCATTGATCTGGTCTTCA
CCTACATAAG
Found at i:1610062 original size:11 final size:11
Alignment explanation
Indices: 1610046--1610113 Score: 70
Period size: 11 Copynumber: 6.2 Consensus size: 11
1610036 GCTTCATTAC
1610046 TATAATTAGTA
1 TATAATTAGTA
1610057 TATAATTATAGTA
1 TATAA-T-TAGTA
*
1610070 TATAATTACTA
1 TATAATTAGTA
*
1610081 TAATCATTAG--
1 T-ATAATTAGTA
1610091 TATAATTAGTA
1 TATAATTAGTA
1610102 TATAATT-GTA
1 TATAATTAGTA
1610112 TA
1 TA
1610114 ACAGTTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
9 7 0.15
10 6 0.12
11 17 0.35
12 8 0.17
13 10 0.21
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (11 bp):
TATAATTAGTA
Found at i:1610070 original size:13 final size:13
Alignment explanation
Indices: 1610052--1610077 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1610042 TTACTATAAT
1610052 TAGTATATAATTA
1 TAGTATATAATTA
1610065 TAGTATATAATTA
1 TAGTATATAATTA
1610078 CTATAATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TAGTATATAATTA
Found at i:1611121 original size:27 final size:29
Alignment explanation
Indices: 1611083--1611142 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
1611073 TGATGATATT
1611083 ATAATT-TT-TTATTATTATTTTTCAAAG
1 ATAATTATTATTATTATTATTTTTCAAAG
1611110 ATAATTTATTATTATTATTATTTTTCAAAG
1 ATAA-TTATTATTATTATTATTTTTCAAAG
1611140 ATA
1 ATA
1611143 GTGTGACACT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 4 0.13
28 2 0.07
29 2 0.07
30 22 0.73
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (29 bp):
ATAATTATTATTATTATTATTTTTCAAAG
Found at i:1615151 original size:12 final size:12
Alignment explanation
Indices: 1615134--1615184 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
1615124 GGCAAATAAG
*
1615134 CTCATTTATTGA
1 CTCATTTATCGA
1615146 CTCATTTATCGA
1 CTCATTTATCGA
* *
1615158 CTCGTTTAT-AA
1 CTCATTTATCGA
*
1615169 GCTCAGTTATCGA
1 -CTCATTTATCGA
1615182 CTC
1 CTC
1615185 GCTCATAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 1 0.03
12 29 0.94
13 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (12 bp):
CTCATTTATCGA
Found at i:1615173 original size:24 final size:24
Alignment explanation
Indices: 1615150--1615342 Score: 194
Period size: 24 Copynumber: 8.1 Consensus size: 24
1615140 TATTGACTCA
*
1615150 TTTATCGACTCGTTTATAAGCTCAG
1 TTTATCGACTCGTTCATAAGCTC-G
*
1615175 -TTATCGACTCGCTCATAAGC-CTG
1 TTTATCGACTCGTTCATAAGCTC-G
*
1615198 TTTATCGACTCGTTCATAAGCCCG
1 TTTATCGACTCGTTCATAAGCTCG
* *
1615222 TTTATCGACTCGTTCATAAGCCCT
1 TTTATCGACTCGTTCATAAGCTCG
* *
1615246 TTTATTGACTCGTTCATAAGC-CC
1 TTTATCGACTCGTTCATAAGCTCG
* * *
1615269 TTTATAGACTCTTTTATAAGCTCG
1 TTTATCGACTCGTTCATAAGCTCG
* * * * *
1615293 TTTGTGGAGTCGTTTATAAGCACG
1 TTTATCGACTCGTTCATAAGCTCG
* *
1615317 TTTATGGACTCGTTTATAAGCTCG
1 TTTATCGACTCGTTCATAAGCTCG
1615341 TT
1 TT
1615343 CGATTATGAA
Statistics
Matches: 146, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
23 21 0.14
24 124 0.85
25 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (24 bp):
TTTATCGACTCGTTCATAAGCTCG
Found at i:1615312 original size:71 final size:72
Alignment explanation
Indices: 1615150--1615337 Score: 207
Period size: 71 Copynumber: 2.6 Consensus size: 72
1615140 TATTGACTCA
* * * * *
1615150 TTTATCGACTCGTTTATAAGCTCAGTTATCGACTCGCTCATAAGCCTGTTTATCGACTCGTTCAT
1 TTTATCGACTCGTTTATAAGCACATTTATCGACTCGTTCATAAGCCTCTTTATAGACTCGTTCAT
1615215 AAGCCCG
66 AAGCCCG
* * * * * *
1615222 TTTATCGACTCGTTCATAAGCCCTTTTATTGACTCGTTCATAAGCC-CTTTATAGACTCTTTTAT
1 TTTATCGACTCGTTTATAAGCACATTTATCGACTCGTTCATAAGCCTCTTTATAGACTCGTTCAT
*
1615286 AAGCTCG
66 AAGCCCG
* * * * * *
1615293 TTTGTGGAGTCGTTTATAAGCACGTTTATGGACTCGTTTATAAGC
1 TTTATCGACTCGTTTATAAGCACATTTATCGACTCGTTCATAAGC
1615338 TCGTTCGATT
Statistics
Matches: 97, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
71 57 0.59
72 40 0.41
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.38
Consensus pattern (72 bp):
TTTATCGACTCGTTTATAAGCACATTTATCGACTCGTTCATAAGCCTCTTTATAGACTCGTTCAT
AAGCCCG
Found at i:1615340 original size:12 final size:12
Alignment explanation
Indices: 1615206--1615342 Score: 61
Period size: 12 Copynumber: 11.5 Consensus size: 12
1615196 TGTTTATCGA
*
1615206 CTCGTTCATAAG
1 CTCGTTTATAAG
* *
1615218 CCCGTTTAT-CG
1 CTCGTTTATAAG
*
1615229 ACTCGTTCATAAG
1 -CTCGTTTATAAG
* * *
1615242 CCCTTTTAT-TG
1 CTCGTTTATAAG
*
1615253 ACTCGTTCATAAG
1 -CTCGTTTATAAG
*
1615266 C-CCTTTAT-AG
1 CTCGTTTATAAG
*
1615276 ACTCTTTTATAAG
1 -CTCGTTTATAAG
* *
1615289 CTCGTTTGTGGAG
1 CTCGTTTAT-AAG
1615302 -TCGTTTATAAG
1 CTCGTTTATAAG
* *
1615313 CACGTTTAT-GG
1 CTCGTTTATAAG
1615324 ACTCGTTTATAAG
1 -CTCGTTTATAAG
1615337 CTCGTT
1 CTCGTT
1615343 CGATTATGAA
Statistics
Matches: 88, Mismatches: 26, Indels: 22
0.65 0.19 0.16
Matches are distributed among these distances:
10 2 0.02
11 11 0.12
12 68 0.77
13 7 0.08
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (12 bp):
CTCGTTTATAAG
Found at i:1615408 original size:23 final size:24
Alignment explanation
Indices: 1615378--1615435 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
1615368 GTTCAATCAC
1615378 GGACTTGTTTACAAGCTC-TTTGG
1 GGACTTGTTTACAAGCTCGTTTGG
*
1615401 GGACTTGTTTATAAGCTCGTTTGG
1 GGACTTGTTTACAAGCTCGTTTGG
1615425 GGACTTGTTTA
1 GGACTTGTTTA
1615436 TAAGTTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (24 bp):
GGACTTGTTTACAAGCTCGTTTGG
Found at i:1615428 original size:24 final size:23
Alignment explanation
Indices: 1615378--1615439 Score: 106
Period size: 24 Copynumber: 2.7 Consensus size: 23
1615368 GTTCAATCAC
*
1615378 GGACTTGTTTACAAGCTCTTTGG
1 GGACTTGTTTATAAGCTCTTTGG
1615401 GGACTTGTTTATAAGCTCGTTTGG
1 GGACTTGTTTATAAGCTC-TTTGG
1615425 GGACTTGTTTATAAG
1 GGACTTGTTTATAAG
1615440 TTCATTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 17 0.46
24 20 0.54
ACGTcount: A:0.19, C:0.13, G:0.27, T:0.40
Consensus pattern (23 bp):
GGACTTGTTTATAAGCTCTTTGG
Found at i:1615447 original size:12 final size:12
Alignment explanation
Indices: 1615432--1615521 Score: 83
Period size: 12 Copynumber: 7.5 Consensus size: 12
1615422 TGGGGACTTG
*
1615432 TTTATAAGTTCA
1 TTTATAAGCTCA
* *
1615444 TTTATAAGTTCG
1 TTTATAAGCTCA
*
1615456 TTTACAAGC-CTA
1 TTTATAAGCTC-A
**
1615468 TTTATAAGCTTG
1 TTTATAAGCTCA
1615480 TTTATAAGCTCA
1 TTTATAAGCTCA
* * *
1615492 TTTATAAACCCC
1 TTTATAAGCTCA
1615504 TTTATAAGCTCA
1 TTTATAAGCTCA
1615516 TTTATA
1 TTTATA
1615522 GACTCTTTTA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
11 1 0.02
12 60 0.98
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (12 bp):
TTTATAAGCTCA
Found at i:1615458 original size:24 final size:24
Alignment explanation
Indices: 1615431--1615521 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
1615421 TTGGGGACTT
*
1615431 GTTTATAAGTTCATTTATAAGTTC
1 GTTTATAAGCTCATTTATAAGTTC
*
1615455 GTTTACAAGC-CTATTTATAAGCTT-
1 GTTTATAAGCTC-ATTTATAAG-TTC
***
1615479 GTTTATAAGCTCATTTATAAACCC
1 GTTTATAAGCTCATTTATAAGTTC
*
1615503 CTTTATAAGCTCATTTATA
1 GTTTATAAGCTCATTTATA
1615522 GACTCTTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
23 1 0.02
24 52 0.93
25 3 0.05
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (24 bp):
GTTTATAAGCTCATTTATAAGTTC
Found at i:1615472 original size:36 final size:36
Alignment explanation
Indices: 1615432--1615521 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
1615422 TGGGGACTTG
* * * *
1615432 TTTATAAGTTCATTTATAAGTTCGTTTACAAGCCTA
1 TTTATAAGTTCATTTATAAGCTCATTTACAAACCCA
* * *
1615468 TTTATAAGCTT-GTTTATAAGCTCATTTATAAACCCC
1 TTTATAAG-TTCATTTATAAGCTCATTTACAAACCCA
*
1615504 TTTATAAGCTCATTTATA
1 TTTATAAGTTCATTTATA
1615522 GACTCTTTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
35 1 0.02
36 40 0.93
37 2 0.05
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (36 bp):
TTTATAAGTTCATTTATAAGCTCATTTACAAACCCA
Found at i:1615531 original size:24 final size:24
Alignment explanation
Indices: 1615480--1615586 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
1615470 TATAAGCTTG
* * *
1615480 TTTATAAGCTCATTTATAAACCCC
1 TTTATAAGCTCATTTATAGACTCT
1615504 TTTATAAGCTCATTTATAGACTCT
1 TTTATAAGCTCATTTATAGACTCT
* *** * * * *
1615528 TTTATACGCTTGGTTCTGGAGTCA
1 TTTATAAGCTCATTTATAGACTCT
* *
1615552 TTTATAAGCTCGTTTATGGACTCT
1 TTTATAAGCTCATTTATAGACTCT
*
1615576 TTAATAAGCTC
1 TTTATAAGCTC
1615587 GTTCGATTAT
Statistics
Matches: 65, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (24 bp):
TTTATAAGCTCATTTATAGACTCT
Found at i:1615610 original size:28 final size:28
Alignment explanation
Indices: 1615565--1615645 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
1615555 ATAAGCTCGT
* *
1615565 TTATGGACTC-TTTAATAAGCTCGTTCGA
1 TTATGAACTCGTTT-ATAAGCTCGTTCAA
*
1615593 TTATGAACTCGTTTATAAGTTCGTTCAA
1 TTATGAACTCGTTTATAAGCTCGTTCAA
* * * *
1615621 TCACGAATTTGTTTATAAGCTCGTT
1 TTATGAACTCGTTTATAAGCTCGTT
1615646 TATAAGCTCG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 41 0.93
29 3 0.07
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (28 bp):
TTATGAACTCGTTTATAAGCTCGTTCAA
Found at i:1615648 original size:12 final size:12
Alignment explanation
Indices: 1615631--1615655 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1615621 TCACGAATTT
1615631 GTTTATAAGCTC
1 GTTTATAAGCTC
1615643 GTTTATAAGCTC
1 GTTTATAAGCTC
1615655 G
1 G
1615656 GGGACTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTTATAAGCTC
Found at i:1615702 original size:24 final size:24
Alignment explanation
Indices: 1615664--1615718 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1615654 CGGGGACTTG
1615664 TTTATAAGTTCGTTTACAAGC-CTA
1 TTTATAAGTTCGTTTACAAGCTC-A
*
1615688 TTTATAAGCTT-GTTTATAAGCTCA
1 TTTATAAG-TTCGTTTACAAGCTCA
1615712 TTTATAA
1 TTTATAA
1615719 ACCCCTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 25 0.89
25 3 0.11
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (24 bp):
TTTATAAGTTCGTTTACAAGCTCA
Found at i:1615703 original size:12 final size:12
Alignment explanation
Indices: 1615660--1615746 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
1615650 AGCTCGGGGA
1615660 CTTGTTTATAAG
1 CTTGTTTATAAG
*
1615672 -TTCGTTTACAAG
1 CTT-GTTTATAAG
* *
1615684 CCTATTTATAAG
1 CTTGTTTATAAG
1615696 CTTGTTTATAAG
1 CTTGTTTATAAG
** *
1615708 CTCATTTATAAA
1 CTTGTTTATAAG
***
1615720 CCCCTTTATAAG
1 CTTGTTTATAAG
* *
1615732 CTCGTTTATGAG
1 CTTGTTTATAAG
1615744 CTT
1 CTT
1615747 CGATTTATTT
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
11 2 0.04
12 54 0.95
13 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (12 bp):
CTTGTTTATAAG
Found at i:1615703 original size:36 final size:36
Alignment explanation
Indices: 1615660--1615745 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
1615650 AGCTCGGGGA
* * * *
1615660 CTTGTTTATAAGTTCGTTTACAAGCCTATTTATAAG
1 CTTGTTTATAAGCTCATTTACAAACCCATTTATAAG
* *
1615696 CTTGTTTATAAGCTCATTTATAAACCCCTTTATAAG
1 CTTGTTTATAAGCTCATTTACAAACCCATTTATAAG
* *
1615732 CTCGTTTATGAGCT
1 CTTGTTTATAAGCT
1615746 TCGATTTATT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (36 bp):
CTTGTTTATAAGCTCATTTACAAACCCATTTATAAG
Found at i:1621571 original size:26 final size:27
Alignment explanation
Indices: 1621521--1621572 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
1621511 ATATTCTAAT
*
1621521 GATTGAAATACCCCTGAACCTCAAAAA
1 GATTAAAATACCCCTGAACCTCAAAAA
* *
1621548 GATTAAAATA-CCTTGAACTTCAAAA
1 GATTAAAATACCCCTGAACCTCAAAA
1621573 TGACTGAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (27 bp):
GATTAAAATACCCCTGAACCTCAAAAA
Found at i:1624237 original size:32 final size:31
Alignment explanation
Indices: 1624200--1624260 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
1624190 TATCTTAAAT
1624200 TTTAAAAATATATTTATTTTTGTT-TTAACTTA
1 TTTAAAAATATA-TTATTTTT-TTCTTAACTTA
*
1624232 TTTAAATATATATTATTTTTTTCTTAACT
1 TTTAAAAATATATTATTTTTTTCTTAACT
1624261 AATTAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 2 0.07
31 14 0.52
32 11 0.41
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.61
Consensus pattern (31 bp):
TTTAAAAATATATTATTTTTTTCTTAACTTA
Found at i:1624241 original size:30 final size:29
Alignment explanation
Indices: 1624205--1624279 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
1624195 TAAATTTTAA
*
1624205 AAATATATTTATTTTTGTT-TTAACTTATTT
1 AAATATATTTATTTTT-TTCTTAAC-TAATT
1624235 AAATATATATTATTTTTTTCTTAACTAATT
1 AAATATAT-TTATTTTTTTCTTAACTAATT
*
1624265 AAATATTTTTTATTT
1 AAATA-TATTTATTT
1624280 CAATGTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 25 0.62
31 15 0.38
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (29 bp):
AAATATATTTATTTTTTTCTTAACTAATT
Found at i:1624570 original size:30 final size:30
Alignment explanation
Indices: 1624513--1624583 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
1624503 ATTAAAATAC
* *
1624513 AAAATATATTTAAGAAGTTAAGGCAAAAGT
1 AAAATATATTTAAGAAGTTAAGACAAAAAT
*
1624543 AAAATATATTTAATAAGTTATA-ACAAAAAT
1 AAAATATATTTAAGAAGTTA-AGACAAAAAT
*
1624573 AAAAGATATTT
1 AAAATATATTT
1624584 TTAAAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (30 bp):
AAAATATATTTAAGAAGTTAAGACAAAAAT
Found at i:1624826 original size:16 final size:17
Alignment explanation
Indices: 1624805--1624840 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1624795 CTGATTGAAG
*
1624805 AAAAAATATATTAA-AT
1 AAAAAATAAATTAATAT
1624821 AAAAAATAAATTAATAT
1 AAAAAATAAATTAATAT
1624838 AAA
1 AAA
1624841 TTTAGTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAAATAAATTAATAT
Found at i:1629141 original size:32 final size:32
Alignment explanation
Indices: 1629095--1629158 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1629085 CCAATTCAGG
1629095 TGAACCATGCATGTGAAACAATTGAATGATGT
1 TGAACCATGCATGTGAAACAATTGAATGATGT
* *
1629127 TGAATCATGCATGTGAAACAATTGTATGATGT
1 TGAACCATGCATGTGAAACAATTGAATGATGT
1629159 CTAAACATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (32 bp):
TGAACCATGCATGTGAAACAATTGAATGATGT
Found at i:1629168 original size:32 final size:32
Alignment explanation
Indices: 1629095--1629168 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
1629085 CCAATTCAGG
*
1629095 TGAACCATGCATGTGAAACAATTGAATGATGT
1 TGAAACATGCATGTGAAACAATTGAATGATGT
* *
1629127 TGAATCATGCATGTGAAACAATTGTATGATGT
1 TGAAACATGCATGTGAAACAATTGAATGATGT
1629159 CT-AAACATGC
1 -TGAAACATGC
1629169 TAAGAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 37 0.97
33 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (32 bp):
TGAAACATGCATGTGAAACAATTGAATGATGT
Found at i:1630305 original size:150 final size:149
Alignment explanation
Indices: 1630027--1630450 Score: 649
Period size: 150 Copynumber: 2.8 Consensus size: 149
1630017 CTGATCCTGA
* * * * *
1630027 TGAAGCCGAAGCTAAGGATTTGCGTAACGGACCTCTTGT-AGCAGAGGGAGAAAACACCACCCTG
1 TGAAGCCGAAGCTAAGGATTTGAGTAACGGACCGCTTGTCA-AAGAGGAAG-AAA-A-CACCTTG
* * *
1630091 GATGGAGGAGTATCACAAACACATGAAGCTCCTTCTTCTGTTCAAACAGAGGAAT-CAACGCAAC
62 GATGGAGGACTAACACAAACACAGGAAGCTCC-TCTTCTGTTCAAACAGAGGAATCCAA-GCAAC
1630155 AACTAATAAAAGAACTTGATCATCC
125 AACTAATAAAAGAACTTGATCATCC
*
1630180 TGAAGCCGAAGCTAAGGATTTGAGTACCGGACCGCTTGTCAAAGAGGAAGAAAACACCTTGGATG
1 TGAAGCCGAAGCTAAGGATTTGAGTAACGGACCGCTTGTCAAAGAGGAAGAAAACACCTTGGATG
1630245 GAGGACTAACACAAACACAGGAAGCTCCGTCTTCTGTTCAAACAGAGGAATCCAAGCAACAACTA
66 GAGGACTAACACAAACACAGGAAGCTCC-TCTTCTGTTCAAACAGAGGAATCCAAGCAACAACTA
1630310 ATAAAAGAACTTGATCATCC
130 ATAAAAGAACTTGATCATCC
* *
1630330 TGAAGCCGAAGCTAAGGATTTGAGTAGCGGACCGCTTGTCAAAGGGGAAGAAAACACCTTGGATG
1 TGAAGCCGAAGCTAAGGATTTGAGTAACGGACCGCTTGTCAAAGAGGAAGAAAACACCTTGGATG
*
1630395 GAGGACTAACACAAACACAGGAAGCT-C-CTTCTGTTCAAACAGAGGAATCTAAGCAA
66 GAGGACTAACACAAACACAGGAAGCTCCTCTTCTGTTCAAACAGAGGAATCCAAGCAA
1630451 TAGCTTACAA
Statistics
Matches: 256, Mismatches: 13, Indels: 10
0.92 0.05 0.04
Matches are distributed among these distances:
147 28 0.11
149 1 0.00
150 176 0.69
151 4 0.02
152 3 0.01
153 43 0.17
154 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (149 bp):
TGAAGCCGAAGCTAAGGATTTGAGTAACGGACCGCTTGTCAAAGAGGAAGAAAACACCTTGGATG
GAGGACTAACACAAACACAGGAAGCTCCTCTTCTGTTCAAACAGAGGAATCCAAGCAACAACTAA
TAAAAGAACTTGATCATCC
Found at i:1641514 original size:33 final size:33
Alignment explanation
Indices: 1641477--1641539 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1641467 TGCAGAGGAT
*
1641477 GCATCCACCGCATCTGATGCAGCAGACCTTGGA
1 GCATCCACCACATCTGATGCAGCAGACCTTGGA
* *
1641510 GCATCCACCACGTCTGTTGCAGCAGACCTT
1 GCATCCACCACATCTGATGCAGCAGACCTT
1641540 CGATGTCGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.21
Consensus pattern (33 bp):
GCATCCACCACATCTGATGCAGCAGACCTTGGA
Found at i:1644064 original size:7 final size:7
Alignment explanation
Indices: 1644052--1644088 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
1644042 GTCAAAGAAA
1644052 GTCAACG
1 GTCAACG
1644059 GTCAACG
1 GTCAACG
1644066 GTC-ACG
1 GTCAACG
1644072 GTCAACG
1 GTCAACG
1644079 GTCAACG
1 GTCAACG
1644086 GTC
1 GTC
1644089 GGGTCAACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:1644074 original size:13 final size:14
Alignment explanation
Indices: 1644052--1644088 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
1644042 GTCAAAGAAA
1644052 GTCAACGGTCAACG
1 GTCAACGGTCAACG
1644066 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
1644079 GTCAACGGTC
1 GTCAACGGTC
1644089 GGGTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:1644131 original size:19 final size:19
Alignment explanation
Indices: 1644107--1644196 Score: 85
Period size: 19 Copynumber: 4.7 Consensus size: 19
1644097 AGTCGGGTCG
*
1644107 GGTCAACCCGATTCAGACC
1 GGTCAAACCGATTCAGACC
*
1644126 GGTCAAACC-AGTTCAGATC
1 GGTCAAACCGA-TTCAGACC
*
1644145 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGATTCAG-ACC
* * *
1644164 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGATTC-AGACC
1644184 GGTCAAACCGATT
1 GGTCAAACCGATT
1644197 TTCCAGCAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.03
19 43 0.73
20 14 0.24
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGATTCAGACC
Found at i:1644150 original size:38 final size:39
Alignment explanation
Indices: 1644107--1644196 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 39
1644097 AGTCGGGTCG
* * *
1644107 GGTCAACCCGATTC-AGACCGGTCAAACCAGTTCAGATC-
1 GGTCAAACCGATTCGA-ACCGGTCAAACCAGTTCAAAACT
* *
1644145 GGTCAAACCGGTTCGAACCGGTCAAACCGGTTCAAAACT
1 GGTCAAACCGATTCGAACCGGTCAAACCAGTTCAAAACT
1644184 GGTCAAACCGATT
1 GGTCAAACCGATT
1644197 TTCCAGCAGC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 31 0.70
39 13 0.30
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (39 bp):
GGTCAAACCGATTCGAACCGGTCAAACCAGTTCAAAACT
Found at i:1644172 original size:9 final size:9
Alignment explanation
Indices: 1644123--1644193 Score: 61
Period size: 9 Copynumber: 7.4 Consensus size: 9
1644113 CCCGATTCAG
1644123 ACCGGTCAA
1 ACCGGTCAA
* *
1644132 ACCAGTTCAG
1 ACC-GGTCAA
*
1644142 ATCGGTCAA
1 ACCGGTCAA
*
1644151 ACCGGTTCGA
1 ACCGG-TCAA
1644161 ACCGGTCAA
1 ACCGGTCAA
1644170 ACCGGTTCAAA
1 ACCGG-TC-AA
*
1644181 ACTGGTCAA
1 ACCGGTCAA
1644190 ACCG
1 ACCG
1644194 ATTTTCCAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
9 24 0.50
10 18 0.38
11 6 0.12
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.17
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1647560 original size:60 final size:60
Alignment explanation
Indices: 1647484--1647599 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
1647474 CACAGGGTTT
* * *
1647484 GTCACTGGTGTACTCACTGGGACTCCTCCAGTGGGAGCAGGATACGTCGTTACCGGATTC
1 GTCACCGGTGTACTCACCGGGACTCCTCCAGTCGGAGCAGGATACGTCGTTACCGGATTC
* * ** *
1647544 GTCACCGGTGTGCTCACCGGGACTCCTCCAGTCGGTGTGGGGTACGTCGTTACCGG
1 GTCACCGGTGTACTCACCGGGACTCCTCCAGTCGGAGCAGGATACGTCGTTACCGG
1647600 CTGCTGCGCC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.24
Consensus pattern (60 bp):
GTCACCGGTGTACTCACCGGGACTCCTCCAGTCGGAGCAGGATACGTCGTTACCGGATTC
Found at i:1648215 original size:2 final size:2
Alignment explanation
Indices: 1648208--1648237 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1648198 AAAGATCGTG
1648208 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
1648238 GAAAAGCTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1649828 original size:16 final size:17
Alignment explanation
Indices: 1649803--1649838 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1649793 TTCAAATCTC
*
1649803 TTAAATTTTTTATAATT
1 TTAAATTTTTTAAAATT
1649820 TTAAA-TTTTTAAAATT
1 TTAAATTTTTTAAAATT
1649836 TTA
1 TTA
1649839 TTAACTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAAATTTTTTAAAATT
Found at i:1650100 original size:13 final size:13
Alignment explanation
Indices: 1650082--1650108 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1650072 TATCTAAAAT
1650082 AAAAATATAATTA
1 AAAAATATAATTA
1650095 AAAAATATAATTA
1 AAAAATATAATTA
1650108 A
1 A
1650109 TAATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAAATATAATTA
Found at i:1650114 original size:3 final size:3
Alignment explanation
Indices: 1650101--1650132 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
1650091 ATTAAAAAAT
1650101 ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA A
1650133 AAGCTTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1651016 original size:21 final size:22
Alignment explanation
Indices: 1650990--1651042 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
1650980 CCCTAACTTA
*
1650990 AAACCCTAAATTATAAAC-CAT
1 AAACCCTAAATCATAAACTCAT
*
1651011 AAACCCTAAATCATAACCTCAT
1 AAACCCTAAATCATAAACTCAT
1651033 AAACCCTAAA
1 AAACCCTAAA
1651043 CCCTAAACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (22 bp):
AAACCCTAAATCATAAACTCAT
Found at i:1655527 original size:66 final size:66
Alignment explanation
Indices: 1655421--1655554 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
1655411 GAGACATAAA
1655421 GTCCAGCAATATTCTGATCGATGATGACTTCAACTCCAAGGTTTCCGATTTCGGTCTGGCGAAGT
1 GTCCAGCAATATTCTGATCGATGATGACTTCAACTCCAAGGTTTCCGATTTCGGTCTGGCGAAGT
1655486 T
66 T
1655487 GTCCAGCAATATTCTGATCGATGATGACTTCAACTCCAAGGTTTCCGATTTCGGTCTGGCGAAGT
1 GTCCAGCAATATTCTGATCGATGATGACTTCAACTCCAAGGTTTCCGATTTCGGTCTGGCGAAGT
1655552 T
66 T
1655553 GT
1 GT
1655555 TAGGTGCCGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (66 bp):
GTCCAGCAATATTCTGATCGATGATGACTTCAACTCCAAGGTTTCCGATTTCGGTCTGGCGAAGT
T
Found at i:1656757 original size:6 final size:6
Alignment explanation
Indices: 1656746--1656772 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1656736 TATGAAGCAC
1656746 CATATA CATATA CATATA CATATA CAT
1 CATATA CATATA CATATA CATATA CAT
1656773 GTTCTGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:1661517 original size:23 final size:23
Alignment explanation
Indices: 1661479--1661537 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1661469 TAGTTTAAGG
*
1661479 ATAAATTTTTAATTTAACATTCGT
1 ATAAA-TTTTATTTTAACATTCGT
*
1661503 ATAAATTTTATTTTAACCTTCGT
1 ATAAATTTTATTTTAACATTCGT
* *
1661526 AGAATTTTTATT
1 ATAAATTTTATT
1661538 ATTCAACGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 26 0.84
24 5 0.16
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (23 bp):
ATAAATTTTATTTTAACATTCGT
Found at i:1661884 original size:21 final size:21
Alignment explanation
Indices: 1661860--1661902 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1661850 AACGTGATGC
1661860 ACCCTTAATATACGGTTAAGA
1 ACCCTTAATATACGGTTAAGA
1661881 ACCCTTAATATACGGTTAAGA
1 ACCCTTAATATACGGTTAAGA
1661902 A
1 A
1661903 AATATGTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (21 bp):
ACCCTTAATATACGGTTAAGA
Found at i:1667478 original size:11 final size:10
Alignment explanation
Indices: 1667439--1667484 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
1667429 CCAAGTAACC
*
1667439 AACAACT-AC
1 AACAACTAAT
1667448 AACAAACTAAT
1 AAC-AACTAAT
1667459 AACAACTAAT
1 AACAACTAAT
1667469 AACAAGCTAAT
1 AACAA-CTAAT
1667480 AACAA
1 AACAA
1667485 ACCAAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
9 3 0.09
10 16 0.48
11 14 0.42
ACGTcount: A:0.61, C:0.22, G:0.02, T:0.15
Consensus pattern (10 bp):
AACAACTAAT
Found at i:1667478 original size:21 final size:20
Alignment explanation
Indices: 1667439--1667484 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1667429 CCAAGTAACC
1667439 AACAACTACAACAAACTAAT
1 AACAACTACAACAAACTAAT
* *
1667459 AACAACTAATAACAAGCTAAT
1 AACAACT-ACAACAAACTAAT
1667480 AACAA
1 AACAA
1667485 ACCAAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.61, C:0.22, G:0.02, T:0.15
Consensus pattern (20 bp):
AACAACTACAACAAACTAAT
Found at i:1667493 original size:21 final size:21
Alignment explanation
Indices: 1667448--1667497 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1667438 CAACAACTAC
*
1667448 AACAAACTAATAACAACTAAT
1 AACAAACTAATAACAACCAAT
*
1667469 AACAAGCTAATAACAAACCAA-
1 AACAAACTAATAAC-AACCAAT
1667490 AACAAACT
1 AACAAACT
1667498 CTAACATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.62, C:0.22, G:0.02, T:0.14
Consensus pattern (21 bp):
AACAAACTAATAACAACCAAT
Found at i:1674023 original size:10 final size:10
Alignment explanation
Indices: 1673997--1674031 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1673987 CCAAGTAACC
1673997 AACAACT-AT
1 AACAACTAAT
1674006 AACAAACTAAT
1 AAC-AACTAAT
1674017 AACAACTAAT
1 AACAACTAAT
1674027 AACAA
1 AACAA
1674032 ACCATAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 3 0.12
10 16 0.67
11 5 0.21
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (10 bp):
AACAACTAAT
Found at i:1683574 original size:33 final size:33
Alignment explanation
Indices: 1683525--1683639 Score: 176
Period size: 33 Copynumber: 3.5 Consensus size: 33
1683515 TTAGTGTTGT
* *
1683525 ATGAAACAGTCTATATTAGTGTACCAGAACGAA
1 ATGAAACAGTCGATATTAGTGTACAAGAACGAA
*
1683558 ATGAAACGGTCGATATTAGTGTACAAGAACGAA
1 ATGAAACAGTCGATATTAGTGTACAAGAACGAA
* *
1683591 ATGAAACAGTCGATATTAGTGCACGAGAACGAA
1 ATGAAACAGTCGATATTAGTGTACAAGAACGAA
*
1683624 ATGAAGCAGTCGATAT
1 ATGAAACAGTCGATAT
1683640 GTACGAGAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.22
Consensus pattern (33 bp):
ATGAAACAGTCGATATTAGTGTACAAGAACGAA
Found at i:1683646 original size:29 final size:30
Alignment explanation
Indices: 1683541--1683653 Score: 120
Period size: 33 Copynumber: 3.6 Consensus size: 30
1683531 CAGTCTATAT
* *
1683541 TAGTGTACCAGAACGAAATGAAACGGTCGATA
1 TAGTGTACGAGAACGAAATGAAACAGTCG--A
*
1683573 TTAGTGTACAAGAACGAAATGAAACAGTCGATA
1 -TAGTGTACGAGAACGAAATGAAACAGTCG--A
* *
1683606 TTAGTGCACGAGAACGAAATGAAGCAGTCGA
1 -TAGTGTACGAGAACGAAATGAAACAGTCGA
1683637 TA-TGTACGAGAACGAAA
1 TAGTGTACGAGAACGAAA
1683654 CAGATTCCAT
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
29 14 0.19
30 2 0.03
31 1 0.01
33 57 0.77
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (30 bp):
TAGTGTACGAGAACGAAATGAAACAGTCGA
Found at i:1690222 original size:21 final size:22
Alignment explanation
Indices: 1690198--1690249 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
1690188 ATTAATATTC
* *
1690198 ATTTTAGGTAG-CGAAATTAAT
1 ATTTTAGGTAGACAAAAATAAT
*
1690219 ATTTTCGGT-GACAAAAATAAT
1 ATTTTAGGTAGACAAAAATAAT
1690240 ATTTTAGGTA
1 ATTTTAGGTA
1690250 ACACTCTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (22 bp):
ATTTTAGGTAGACAAAAATAAT
Found at i:1690806 original size:60 final size:60
Alignment explanation
Indices: 1690684--1690806 Score: 131
Period size: 60 Copynumber: 2.0 Consensus size: 60
1690674 GGTCCCCGAT
* * * * * * *
1690684 TATGGGGTATTATTTTGTTGAGTTCTCTAACTATTAAAAATTATAAAATAGTCCCTTGAC
1 TATGGGATATTATTTTGTGGAGATCTCCAACTACTAAAAATTAAAAAATAGTCCCTTAAC
* * **
1690744 TATGGGATATTATTTTGTGGA-ATCATCCAACTACTAAAAGTTAAAAAATGGTTGCTTAAC
1 TATGGGATATTATTTTGTGGAGATC-TCCAACTACTAAAAATTAAAAAATAGTCCCTTAAC
1690804 TAT
1 TAT
1690807 TCATATAGTT
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 2 0.04
60 49 0.96
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (60 bp):
TATGGGATATTATTTTGTGGAGATCTCCAACTACTAAAAATTAAAAAATAGTCCCTTAAC
Done.