Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007884.1 Hibiscus syriacus cultivar Beakdansim tig00110264_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: 2814991
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 13
Found at i:1549631 original size:36 final size:36
Alignment explanation
Indices: 1549584--1549659 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
1549574 ATTGAAAACA
* * *
1549584 TTTCCATTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCATTGAAACGAATTTTATCTCCCTTGAGACAG
* *
1549620 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCATTGAAACGAATTTTATCTCCCTTGAGACAG
1549656 TTTC
1 TTTC
1549660 TCTCCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCATTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:1550057 original size:105 final size:105
Alignment explanation
Indices: 1549859--1550489 Score: 914
Period size: 105 Copynumber: 6.0 Consensus size: 105
1549849 ATATCGTGAC
* * * * * * * *
1549859 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACAGTTGGTTTTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
1549924 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
1549965 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
1550030 ATTTCAGATCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1550070 ACTTCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
1550135 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1550175 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
1550240 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1550280 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
1550341 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
1550380 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
* * *
1550445 GATTCCAGAGCCAATTTCAACTTCACGAC-AGAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGA-AGGATATTGG
1550486 ACTC
1 ACTC
1550490 GGAACAATGC
Statistics
Matches: 480, Mismatches: 38, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
100 81 0.17
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 304 0.63
106 82 0.17
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1551089 original size:37 final size:37
Alignment explanation
Indices: 1551032--1551136 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
1551022 CATTTTCGTC
*
1551032 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
1551069 TTGCTATGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
1551106 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
1551137 CCACAAACAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1551531 original size:18 final size:17
Alignment explanation
Indices: 1551492--1551534 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1551482 ATTATATAGA
1551492 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1551508 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1551526 TATTATTAT
1 TATTATTAT
1551535 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1551544 original size:56 final size:55
Alignment explanation
Indices: 1551476--1551603 Score: 136
Period size: 58 Copynumber: 2.3 Consensus size: 55
1551466 ATTAGTCCAT
* * *
1551476 TTATTTAT-TATATAGATATT-TTA-TTCATTTATTTTTATTATTCATGTTATTATTA
1 TTATATATATATATAGATATTATTATTTCATTTATTTTT-TTACT-ATATT-TTATTA
* *
1551531 TTATATGTATATATATATATTAAATTATTTTCATTTATTTTTTTACTATATTTTATTA
1 TTATATATATATATAGATATT--ATTA-TTTCATTTATTTTTTTACTATATTTTATTA
1551589 TTATATATATATATA
1 TTATATATATATATA
1551604 TTTCTTTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
55 6 0.10
56 11 0.18
58 20 0.33
59 7 0.11
60 4 0.07
61 13 0.21
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (55 bp):
TTATATATATATATAGATATTATTATTTCATTTATTTTTTTACTATATTTTATTA
Found at i:1557089 original size:66 final size:68
Alignment explanation
Indices: 1557005--1557142 Score: 262
Period size: 68 Copynumber: 2.1 Consensus size: 68
1556995 AAAATTTGGA
1557005 TTGAATTTC-TT-TATATATATATGAAAGCGTGTTGATAAACTGGATAGAATCTAAATTAGGATC
1 TTGAATTTCTTTATATATATATATGAAAGCGTGTTGATAAACTGGATAGAATCTAAATTAGGATC
1557068 TAT
66 TAT
1557071 TTGAATTTCTTTATATATATATATGAAAGCGTGTTGATAAACTGGATAGAATCTAAATTAGGATC
1 TTGAATTTCTTTATATATATATATGAAAGCGTGTTGATAAACTGGATAGAATCTAAATTAGGATC
1557136 TAT
66 TAT
1557139 TTGA
1 TTGA
1557143 CTGTTAATTT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 9 0.13
67 2 0.03
68 59 0.84
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (68 bp):
TTGAATTTCTTTATATATATATATGAAAGCGTGTTGATAAACTGGATAGAATCTAAATTAGGATC
TAT
Found at i:1563082 original size:3 final size:3
Alignment explanation
Indices: 1563063--1563096 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1563053 ATTAGGATAG
* *
1563063 TAT TGT TAT TGT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1563097 TTCAAGTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1563423 original size:21 final size:22
Alignment explanation
Indices: 1563392--1563433 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1563382 ATATCTCTCT
*
1563392 TTTATTTTTATCTATTTTTATA
1 TTTATTTTTATCCATTTTTATA
1563414 TTTA-TTTTATCCATTTTTAT
1 TTTATTTTTATCCATTTTTAT
1563434 TATCCTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTATTTTTATCCATTTTTATA
Found at i:1567311 original size:308 final size:309
Alignment explanation
Indices: 1566745--1567359 Score: 1006
Period size: 308 Copynumber: 2.0 Consensus size: 309
1566735 CCTTTCCTGG
* *
1566745 TTCACCATTTGATTGGTAGATTAAATTTATTGAATTAAATTTTTTTGGACCAAAATGATAGAATA
1 TTCACCATCTGATTGGTAGATTAAATTTATTGAATTAAATTTTTTTAGACCAAAATGATAGAATA
*
1566810 TATAAGTATTGAGGACTAAACATATAATTATACCGATTTTATTAGCTGTCACATCAACATTTCCA
66 TATAAGTATTGAGGACTAAACACATAATTATACCGATTTTATTAGCTGTCACATCAACATTTCCA
*
1566875 TTAAATATTAATAGAAAGTGACTTGATTGAATACAATTAAATAGTTAATAGTCTGATTGATAAAA
131 TTAAATATTAATAGAAAGTGACTTGATTGAATACAATTAAATAGTTAATAGTCTAATTGATAAAA
* *
1566940 TTGAAAGATCAATAGTAAAACTAAAAGGGCTAAATAATTAAGTTGTTAGTGATATAGTTTATACT
196 TTGAAAGATCAATAGTAAAACTAAAAAGGCTAAATAATTAAGTGGTTAGTGATATAGTTTATACT
1567005 ATCATTAGTTAGTTTGAATAATTATTATCTTGTAAATATA-CAAAAAGC
261 ATCATTAGTTAGTTTGAATAATTATTATCTTGTAAATATACCAAAAAGC
*
1567053 TTCACCATCTGATTGGTAGATTTAAATTTATTGAATT-AA-TTTTTTAGACCAAATTGATAGAAT
1 TTCACCATCTGATTGGTAGA-TTAAATTTATTGAATTAAATTTTTTTAGACCAAAATGATAGAAT
* * * * *
1567116 TTATAAGTATTGAGGACTAAATACATAATTATACTGATTTTATTAGCTGTCACATCAATATTTCT
65 ATATAAGTATTGAGGACTAAACACATAATTATACCGATTTTATTAGCTGTCACATCAACATTTCC
* * * *
1567181 GTTAGATGTTCAT-GATAAGTGACTTGATTGAATACAATTAAATAGTTAA-ATGATCTAATTGAT
130 ATTAAATATTAATAGA-AAGTGACTTGATTGAATACAATTAAATAGTTAATA-G-TCTAATTGAT
*
1567244 AAAATTGAGAGATCAATAGTAAAACTAAAAAGGCTAAATAATTAAGTGGTTAGTGATATAGTTTA
192 AAAATTGAAAGATCAATAGTAAAACTAAAAAGGCTAAATAATTAAGTGGTTAGTGATATAGTTTA
1567309 TACTATCATTAGTTAGTTTGAATAATTATTATCTTGTAAATATACCAAAAA
257 TACTATCATTAGTTAGTTTGAATAATTATTATCTTGTAAATATACCAAAAA
1567360 AACACATGTT
Statistics
Matches: 285, Mismatches: 17, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
306 3 0.01
307 124 0.44
308 136 0.48
309 22 0.08
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (309 bp):
TTCACCATCTGATTGGTAGATTAAATTTATTGAATTAAATTTTTTTAGACCAAAATGATAGAATA
TATAAGTATTGAGGACTAAACACATAATTATACCGATTTTATTAGCTGTCACATCAACATTTCCA
TTAAATATTAATAGAAAGTGACTTGATTGAATACAATTAAATAGTTAATAGTCTAATTGATAAAA
TTGAAAGATCAATAGTAAAACTAAAAAGGCTAAATAATTAAGTGGTTAGTGATATAGTTTATACT
ATCATTAGTTAGTTTGAATAATTATTATCTTGTAAATATACCAAAAAGC
Found at i:1576847 original size:12 final size:13
Alignment explanation
Indices: 1576824--1576852 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1576814 GTACTAACAT
1576824 AAATACATTTCCA
1 AAATACATTTCCA
1576837 AAATA-ATTTCCA
1 AAATACATTTCCA
1576849 AAAT
1 AAAT
1576853 CAGATAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATACATTTCCA
Found at i:1582607 original size:51 final size:51
Alignment explanation
Indices: 1582537--1582659 Score: 176
Period size: 51 Copynumber: 2.4 Consensus size: 51
1582527 AAAGCGCACA
* *
1582537 CCCCCTGCACCGCGCTATACGATGATTTGGCA-CCACGTGGGGTATAGCGCG
1 CCCCCTGCACCGCGCTATACGATGATCTGGCATACACGT-GGGTATAGCGCG
* *
1582588 CCCCCTGCACCGCGTTATACGTTGATCTGGCATACACGTGGGTATAGCGCG
1 CCCCCTGCACCGCGCTATACGATGATCTGGCATACACGTGGGTATAGCGCG
* *
1582639 GCCCCTGCAGCGCGCTATACG
1 CCCCCTGCACCGCGCTATACG
1582660 CCACGTAGGG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
51 59 0.92
52 5 0.08
ACGTcount: A:0.17, C:0.34, G:0.28, T:0.20
Consensus pattern (51 bp):
CCCCCTGCACCGCGCTATACGATGATCTGGCATACACGTGGGTATAGCGCG
Found at i:1586488 original size:3 final size:3
Alignment explanation
Indices: 1586482--1586510 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1586472 ATCACCATCT
1586482 TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
1586511 TTGCGCAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.31, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:1587547 original size:7 final size:7
Alignment explanation
Indices: 1587535--1587570 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
1587525 AAATACTGTA
1587535 TGAATAG
1 TGAATAG
1587542 TGAATAG
1 TGAATAG
1587549 TGAATAG
1 TGAATAG
*
1587556 TAAATAG
1 TGAATAG
1587563 TGAATAG
1 TGAATAG
1587570 T
1 T
1587571 ACGATGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (7 bp):
TGAATAG
Found at i:1587683 original size:12 final size:12
Alignment explanation
Indices: 1587666--1587690 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1587656 TTACTGTTCA
1587666 TGCTACAGTAAT
1 TGCTACAGTAAT
1587678 TGCTACAGTAAT
1 TGCTACAGTAAT
1587690 T
1 T
1587691 TTCGAAAATT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGCTACAGTAAT
Found at i:1588470 original size:21 final size:21
Alignment explanation
Indices: 1588421--1588484 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
1588411 CATATGAAAT
*
1588421 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
1588442 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
*
1588464 TTGTCCCAAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
1588485 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:1588784 original size:14 final size:15
Alignment explanation
Indices: 1588757--1588785 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1588747 ATATCATATA
1588757 TCTTATGTTTTATGC
1 TCTTATGTTTTATGC
1588772 TCTTATG-TTTATGC
1 TCTTATGTTTTATGC
1588786 ATATCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TCTTATGTTTTATGC
Found at i:1591155 original size:110 final size:111
Alignment explanation
Indices: 1590961--1591181 Score: 390
Period size: 110 Copynumber: 2.0 Consensus size: 111
1590951 ATTACAAAAA
* * *
1590961 TTAATTCTTAATCTACTAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
1591026 AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTAGAGATAT
1591072 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
1591136 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTAGAGATAT
1591182 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 34 0.32
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCATATCAGCAAAGTGTAGAGATAT
Found at i:1591511 original size:51 final size:51
Alignment explanation
Indices: 1591426--1591527 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
1591416 CCCCCTGCGC
* * *
1591426 CGCGCTATACCCACGTGTATGCCAGATCACCGTATGGCGCGGTGCAGGGGG
1 CGCGCTATACCCACGTGTACGCCAAATCACCGTATAGCGCGGTGCAGGGGG
* *
1591477 CGCGCTATACCCCACGTG-GCGCCAAATCATCGTATAGCGCGGTGCAGGGGG
1 CGCGCTATA-CCCACGTGTACGCCAAATCACCGTATAGCGCGGTGCAGGGGG
1591528 TGCACTTTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
51 37 0.82
52 8 0.18
ACGTcount: A:0.19, C:0.30, G:0.34, T:0.17
Consensus pattern (51 bp):
CGCGCTATACCCACGTGTACGCCAAATCACCGTATAGCGCGGTGCAGGGGG
Found at i:1591607 original size:30 final size:29
Alignment explanation
Indices: 1591545--1591607 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
1591535 TACTGCTAAG
*
1591545 GGTGTTAGATCGAGAAATATAATCTGACC
1 GGTGTTAGATCGAGAAATATAATCTCACC
*
1591574 GGTGTTAGATCGAGAAATATAATGTTCACC
1 GGTGTTAGATCGAGAAATATAAT-CTCACC
1591604 GGTG
1 GGTG
1591608 ATATATCGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGAGAAATATAATCTCACC
Found at i:1598588 original size:15 final size:17
Alignment explanation
Indices: 1598563--1598611 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
1598553 CGAATATCTG
1598563 ATCCGAAA-TTTCGGAT
1 ATCCGAAATTTTCGGAT
1598579 ATCC-AAATTTTCGGAT
1 ATCCGAAATTTTCGGAT
**
1598595 ATCCGATTTTTTCGGAT
1 ATCCGAAATTTTCGGAT
1598612 CGAATACGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 3 0.10
16 16 0.55
17 10 0.34
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (17 bp):
ATCCGAAATTTTCGGAT
Found at i:1598665 original size:16 final size:17
Alignment explanation
Indices: 1598636--1598668 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1598626 TATTTTAGTA
*
1598636 ATCCGAAATTTTCGGAT
1 ATCCGAAATATTCGGAT
1598653 ATCCGAAA-ATTCGGAT
1 ATCCGAAATATTCGGAT
1598669 CGGATAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (17 bp):
ATCCGAAATATTCGGAT
Found at i:1600807 original size:21 final size:20
Alignment explanation
Indices: 1600721--1600878 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1600711 AAATGACCAA
**
1600721 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1600740 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1600760 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1600780 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1600801 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1600822 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1600842 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1600863 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1600879 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1600907 original size:20 final size:20
Alignment explanation
Indices: 1600845--1601038 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1600835 CGATTTTCCA
* ** *
1600845 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1600865 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1600885 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1600905 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1600925 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1600945 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1600965 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1600985 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1601005 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1601026 AAATCGCAACGCG
1 AAATCGCAACGCG
1601039 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1600929 original size:60 final size:60
Alignment explanation
Indices: 1600845--1601038 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1600835 CGATTTTCCA
* ** * *
1600845 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
1600905 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
1600965 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
1601026 AAATCGCAACGCG
1 AAATCGCAACGCG
1601039 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:1601459 original size:33 final size:33
Alignment explanation
Indices: 1601420--1601490 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1601410 TTCACTTAGA
* *
1601420 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
1601453 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
1601486 TTTCA
1 TTTCA
1601491 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:1601596 original size:21 final size:20
Alignment explanation
Indices: 1601570--1601675 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
1601560 TGCAGAAGAG
1601570 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
1601591 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
1601611 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
1601632 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1601646 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1601665 TCGCAACGAGA
1 TCGCAACGAGA
1601676 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1601614 original size:20 final size:21
Alignment explanation
Indices: 1601568--1601646 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
1601558 TTTGCAGAAG
*
1601568 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
1601590 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
1601609 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
1601631 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
1601647 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:1601627 original size:41 final size:38
Alignment explanation
Indices: 1601563--1601679 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
1601553 TTCAATTTGC
* *
1601563 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1601601 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1601642 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1601675 AGAAT
1 AGAAT
1601680 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1601652 original size:14 final size:14
Alignment explanation
Indices: 1601633--1601686 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1601623 AAATGAAAAG
1601633 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
1601647 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
1601666 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
1601680 CGCAACG
1 CGCAACG
1601687 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:1601662 original size:33 final size:33
Alignment explanation
Indices: 1601622--1601691 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
1601612 CGCAACGAGA
1601622 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
1601655 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1601688 GAAA
1 GAAA
1601692 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:1601698 original size:33 final size:33
Alignment explanation
Indices: 1601628--1601702 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
1601618 GAGAGAAATG
* **
1601628 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1601661 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1601694 AAAATCGCA
1 AAAATCGCA
1601703 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:1601720 original size:19 final size:19
Alignment explanation
Indices: 1601698--1601795 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1601688 GAAACCAAAA
*
1601698 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1601717 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1601731 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1601750 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1601764 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1601783 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1601796 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1601739 original size:14 final size:14
Alignment explanation
Indices: 1601720--1601809 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1601710 TTTCATTTCG
1601720 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1601734 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1601753 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1601767 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1601784 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1601800 CGTTGCGATT
1 CGTTGCGATT
1601810 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1601745 original size:33 final size:33
Alignment explanation
Indices: 1601703--1601817 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1601693 CAAAATCGCA
1601703 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1601736 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1601769 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1601802 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1601818 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1603675 original size:93 final size:93
Alignment explanation
Indices: 1603516--1603988 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
1603506 TAGATTGCTT
*
1603516 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1603581 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1603609 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1603674 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1603701 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1603766 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1603794 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1603859 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1603887 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1603952 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1603980 AGTAAATTT
1 AGTAAATTT
1603989 ATCCATTCAA
Statistics
Matches: 376, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 92 0.24
93 284 0.76
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1603746 original size:185 final size:186
Alignment explanation
Indices: 1603516--1603988 Score: 921
Period size: 185 Copynumber: 2.5 Consensus size: 186
1603506 TAGATTGCTT
*
1603516 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1603581 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
1603646 GTGTATTCTTTAACACTGTGAAATAGTATTTGTC-TTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1603701 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1603766 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1603831 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1603887 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1603952 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
1603989 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 162 0.57
186 123 0.43
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1604072 original size:19 final size:19
Alignment explanation
Indices: 1604032--1604160 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1604022 TAGTTTACTT
* *
1604032 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1604052 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1604071 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1604090 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1604104 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1604123 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1604137 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1604156 TCGCA
1 TCGCA
1604161 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1604111 original size:33 final size:32
Alignment explanation
Indices: 1604068--1604160 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1604058 CGCGAAACCA
**
1604068 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1604100 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1604133 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1604161 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1604158 original size:52 final size:52
Alignment explanation
Indices: 1604032--1604160 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1604022 TAGTTTACTT
**
1604032 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1604084 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1604137 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1604161 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1604178 original size:19 final size:19
Alignment explanation
Indices: 1604156--1604289 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1604146 GAAACCAAAA
*
1604156 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1604175 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1604191 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1604208 TCGCATTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1604224 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
**
1604240 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1604259 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1604279 TCGTGTTGCGA
1 TCGCGTTGCGA
1604290 AAGTAAACTA
Statistics
Matches: 96, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 15 0.16
15 3 0.03
16 12 0.12
17 9 0.09
18 8 0.08
19 37 0.39
20 12 0.12
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1604197 original size:14 final size:14
Alignment explanation
Indices: 1604178--1604234 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
1604168 TTTCATTTCG
1604178 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1604192 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
1604209 CGCATTGCGATTCTTT
1 CG--TTGCGATTCTTT
1604225 CGTTGCGATT
1 CGTTGCGATT
1604235 TCATTTCGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 16 0.42
16 8 0.21
17 8 0.21
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1604242 original size:32 final size:33
Alignment explanation
Indices: 1604161--1604252 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1604151 CAAAATCGCA
1604161 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
1604194 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1604227 TTGCGA-TTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1604253 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 19 0.33
33 38 0.67
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:1604261 original size:51 final size:47
Alignment explanation
Indices: 1604178--1604271 Score: 125
Period size: 51 Copynumber: 1.9 Consensus size: 47
1604168 TTTCATTTCG
1604178 CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTTT
1 CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTTT
** *
1604225 CGTTGCGATTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATT
1 CGTTGCGA-TTC-TTT--CGTTGCGATTTTCATTTCGCATTGCGATT
1604272 TTAAGTTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
47 8 0.20
48 3 0.08
49 3 0.08
51 26 0.65
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (47 bp):
CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTTT
Found at i:1606200 original size:14 final size:14
Alignment explanation
Indices: 1606181--1606216 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1606171 ATTGTTTAAT
1606181 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1606195 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1606209 TGATTTGT
1 TGATTTGT
1606217 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1606347 original size:19 final size:19
Alignment explanation
Indices: 1606323--1606420 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1606313 AAAATTGACT
1606323 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1606342 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1606361 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1606375 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1606394 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1606414 ATCGCAA
1 ATCGCAA
1606421 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1606452 original size:53 final size:53
Alignment explanation
Indices: 1606323--1606439 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1606313 AAAATTGACT
1606323 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1606375 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1606428 ATCGCAATGCGA
1 ATCGCAATGCGA
1606440 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1608772 original size:12 final size:12
Alignment explanation
Indices: 1608755--1608779 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1608745 TCTTCGGGGA
1608755 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1608767 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1608779 C
1 C
1608780 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1608987 original size:24 final size:24
Alignment explanation
Indices: 1608953--1608999 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1608943 CTGAAACATC
1608953 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1608977 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1609000 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1609710 original size:20 final size:20
Alignment explanation
Indices: 1609682--1609931 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
1609672 AAATTTCAGT
* * *
1609682 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1609702 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1609722 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1609742 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1609762 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
1609782 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1609802 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1609822 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
*
1609842 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1609862 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1609882 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1609902 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1609922 GTTGCGATTT
1 GTTGCGATTT
1609932 TGGAAAATCG
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1609948 original size:21 final size:21
Alignment explanation
Indices: 1609918--1610000 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1609908 ATTTTCATAT
*
1609918 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1609939 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1609960 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1609981 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1610001 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1609991 original size:42 final size:43
Alignment explanation
Indices: 1609898--1609996 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1609888 ATTTATGTGT
* *
1609898 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1609939 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1609981 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1609997 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1613998 original size:26 final size:26
Alignment explanation
Indices: 1613968--1614021 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1613958 ATAAATAGAC
1613968 AAATACAAATATAATCTTGTTCATTT
1 AAATACAAATATAATCTTGTTCATTT
*
1613994 AAATATAAATATAATCTTGTTCATTT
1 AAATACAAATATAATCTTGTTCATTT
1614020 AA
1 AA
1614022 GCTTAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (26 bp):
AAATACAAATATAATCTTGTTCATTT
Found at i:1618828 original size:3 final size:3
Alignment explanation
Indices: 1618820--1618869 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
1618810 CATTTTACTT
* *
1618820 TTA TTA TTA TTA TCA TTA TTA ATA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1618867 TTA
1 TTA
1618870 AATACATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1620283 original size:21 final size:22
Alignment explanation
Indices: 1620232--1620286 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1620222 AATTAATAAT
**
1620232 TTAATAATTTATGTATTTATTTG
1 TTAAT-ATTTATGTATTTATTCA
*
1620255 TTATTATTTATGT-TTTATTCA
1 TTAATATTTATGTATTTATTCA
1620276 TTAATATTTAT
1 TTAATATTTAT
1620287 ATGAAATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 16 0.57
22 8 0.29
23 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (22 bp):
TTAATATTTATGTATTTATTCA
Found at i:1624727 original size:20 final size:20
Alignment explanation
Indices: 1624702--1624794 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
1624692 TTTTCCCAAT
*
1624702 TCGCAATTCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1624722 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1624743 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1624763 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1624784 TCGCAATGCGA
1 TCGCAATGCGA
1624795 TACTGACTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.46
21 31 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1624745 original size:21 final size:21
Alignment explanation
Indices: 1624719--1624794 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1624709 TCGAATAAGT
1624719 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1624740 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1624760 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
1624781 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1624795 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1624759 original size:41 final size:41
Alignment explanation
Indices: 1624702--1624794 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1624692 TTTTCCCAAT
*
1624702 TCGCAATTCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1624743 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1624784 TCGCAATGCGA
1 TCGCAATGCGA
1624795 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1624825 original size:41 final size:41
Alignment explanation
Indices: 1624780--1624857 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1624770 GCGAATTGGG
* * *
1624780 AAAATCGCAATGCGATACTGACTATCACAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCACAACGCGATAATAA
* * *
1624821 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCACAACGCGATA
1624858 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCACAACGCGATAATAA
Found at i:1624850 original size:20 final size:20
Alignment explanation
Indices: 1624825--1624877 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1624815 TAATAAAAAA
* *
1624825 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
1624845 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
1624865 TCGCAACGCGATA
1 TCGCAACGCGATA
1624878 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1625093 original size:22 final size:22
Alignment explanation
Indices: 1625065--1625108 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1625055 CACTCTCTCA
1625065 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1625087 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1625109 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1625395 original size:20 final size:20
Alignment explanation
Indices: 1625370--1625407 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1625360 CGATTCTCTC
1625370 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1625390 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1625408 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1626728 original size:18 final size:18
Alignment explanation
Indices: 1626707--1626751 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1626697 TCCACTTCGG
*
1626707 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1626725 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1626743 GAGCCATCA
1 GAGCCATCA
1626752 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1627287 original size:19 final size:20
Alignment explanation
Indices: 1627233--1627299 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1627223 TAGTTTACTT
* *
1627233 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1627253 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1627273 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1627292 TCGCAACG
1 TCGCAACG
1627300 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1627307 original size:14 final size:14
Alignment explanation
Indices: 1627288--1627345 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1627278 ATGCGAAATG
1627288 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1627302 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1627318 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1627334 AAAATCGCAACG
1 AAAATCGCAACG
1627346 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1627330 original size:32 final size:33
Alignment explanation
Indices: 1627272--1627362 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1627262 GGAAATGGCT
1627272 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1627305 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1627337 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1627363 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1627398 original size:14 final size:14
Alignment explanation
Indices: 1627379--1627436 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1627369 TTGTGTTTCG
1627379 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1627393 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1627409 CACGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
1627425 CGTTGTGATTTT
1 CGTTGCGATTTT
1627437 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1627418 original size:32 final size:33
Alignment explanation
Indices: 1627374--1627452 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
1627364 GCGATTTGTG
1627374 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
* *
1627406 TTTCACGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1627439 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1627453 AGCCATTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 25 0.60
33 17 0.40
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1627471 original size:20 final size:19
Alignment explanation
Indices: 1627437--1627491 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1627427 TTGTGATTTT
*
1627437 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1627456 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1627476 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1627492 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1629748 original size:20 final size:19
Alignment explanation
Indices: 1629717--1629896 Score: 112
Period size: 19 Copynumber: 9.8 Consensus size: 19
1629707 TCTTTTGGTT
1629717 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1629736 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1629757 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
1629776 G--A-G--AATCGCAAC-A
1 GAAATGAAAATCGCAACGA
**
1629789 CGAAATGACTATCG---CGA
1 -GAAATGAAAATCGCAACGA
** * * *
1629806 -CCA-GACAATCGTAACGC
1 GAAATGAAAATCGCAACGA
*
1629823 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
1629843 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1629862 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
1629881 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1629897 TGCGATTTTG
Statistics
Matches: 129, Mismatches: 17, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
13 1 0.01
14 16 0.12
15 1 0.01
16 3 0.02
17 5 0.04
18 1 0.01
19 53 0.41
20 47 0.36
21 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1629799 original size:33 final size:33
Alignment explanation
Indices: 1629742--1629840 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
1629732 ACGAGATAAT
*
1629742 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
1629776 GAGAATCGCAACACGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * **
1629809 GACAATCGTAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
1629841 GCGAAATAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
33 43 0.77
34 13 0.23
ACGTcount: A:0.40, C:0.25, G:0.22, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1629834 original size:19 final size:19
Alignment explanation
Indices: 1629812--1629901 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
1629802 GCGACCAGAC
*
1629812 AATCGTAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1629831 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
1629851 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1629870 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1629889 AATCGCAATGCGA
1 AATCGCAACGCGA
1629902 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
19 48 0.73
20 18 0.27
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1629855 original size:39 final size:38
Alignment explanation
Indices: 1629812--1629901 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
1629802 GCGACCAGAC
*
1629812 AATCGTAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
1629851 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
1629889 AATCGCAATGCGA
1 AATCGCAACGCGA
1629902 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 22 0.46
39 26 0.54
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:1629930 original size:19 final size:19
Alignment explanation
Indices: 1629897--1629963 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1629887 AAAATCGCAA
**
1629897 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1629916 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1629935 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1629955 TGCGATTTT
1 TGCGATTTT
1629964 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1630568 original size:20 final size:20
Alignment explanation
Indices: 1630483--1630576 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1630473 TGCTATGTAA
* *
1630483 ATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1630503 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1630523 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1630544 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1630564 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1630577 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.72
21 12 0.20
22 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1630594 original size:21 final size:21
Alignment explanation
Indices: 1630565--1630657 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
1630555 ATAGTAAGTA
1630565 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1630586 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1630606 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1630627 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1630647 TCGCATTGCGA
1 TCGCATTGCGA
1630658 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1630595 original size:41 final size:41
Alignment explanation
Indices: 1630504--1630638 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1630494 AAAGTCAGAA
* * * * ** *
1630504 TCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
1630544 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1630586 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1630627 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1630639 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1630639 original size:41 final size:41
Alignment explanation
Indices: 1630565--1630657 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1630555 ATAGTAAGTA
1630565 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1630606 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1630647 TCGCATTGCGA
1 TCGCATTGCGA
1630658 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1633786 original size:24 final size:23
Alignment explanation
Indices: 1633738--1633794 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
1633728 TTTGCAAACG
* *
1633738 TGTTCGTTTAATGTTCGTGAGCA
1 TGTTCGTTTAATGTTCGCGAACA
*
1633761 TGTTTGTTTAAATGTTCGCGAACA
1 TGTTCGTTT-AATGTTCGCGAACA
*
1633785 TGGTCGTTTA
1 TGTTCGTTTA
1633795 TATATTTGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (23 bp):
TGTTCGTTTAATGTTCGCGAACA
Found at i:1633827 original size:35 final size:34
Alignment explanation
Indices: 1633781--1633863 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
1633771 AATGTTCGCG
* *
1633781 AACATGGTCGTTTATATATTTGTTTAGCATTCGTA
1 AACATGTTCGTTTA-ACATTTGTTTAGCATTCGTA
* * *
1633816 AACATGTTCGTTTAGCATTTGTTTATCATTCGTG
1 AACATGTTCGTTTAACATTTGTTTAGCATTCGTA
1633850 AACATGCTT-GTTTA
1 AACATG-TTCGTTTA
1633864 GCGTTCATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 27 0.64
35 15 0.36
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (34 bp):
AACATGTTCGTTTAACATTTGTTTAGCATTCGTA
Found at i:1633846 original size:34 final size:34
Alignment explanation
Indices: 1633798--1633865 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
1633788 TCGTTTATAT
1633798 ATTTGTTTAGCATTCGTAAACATG-TTCGTTTAGC
1 ATTTGTTTAGCATTCGTAAACATGCTT-GTTTAGC
* *
1633832 ATTTGTTTATCATTCGTGAACATGCTTGTTTAGC
1 ATTTGTTTAGCATTCGTAAACATGCTTGTTTAGC
1633866 GTTCATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.46
Consensus pattern (34 bp):
ATTTGTTTAGCATTCGTAAACATGCTTGTTTAGC
Found at i:1633875 original size:34 final size:34
Alignment explanation
Indices: 1633803--1633876 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
1633793 TATATATTTG
* **
1633803 TTTAGCATTCGTAAACATGTTCGTTTAGCATTTG
1 TTTATCATTCGTAAACATGTTCGTTTAGCATTCA
* *
1633837 TTTATCATTCGTGAACATGCTT-GTTTAGCGTTCA
1 TTTATCATTCGTAAACATG-TTCGTTTAGCATTCA
1633871 TTTATC
1 TTTATC
1633877 GTTCCCGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (34 bp):
TTTATCATTCGTAAACATGTTCGTTTAGCATTCA
Found at i:1633897 original size:34 final size:34
Alignment explanation
Indices: 1633816--1633898 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
1633806 AGCATTCGTA
** **
1633816 AACATGTTCGTTTAGCATTTGTTTATCATTCGTG
1 AACATGTTCGTTTAGCATTCATTTATCATTCCCG
* *
1633850 AACATGCTT-GTTTAGCGTTCATTTATCGTTCCCG
1 AACATG-TTCGTTTAGCATTCATTTATCATTCCCG
*
1633884 AATATGTTCGTTTAG
1 AACATGTTCGTTTAG
1633899 AATAAATGGG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
33 2 0.05
34 36 0.90
35 2 0.05
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (34 bp):
AACATGTTCGTTTAGCATTCATTTATCATTCCCG
Found at i:1634577 original size:12 final size:12
Alignment explanation
Indices: 1634562--1634640 Score: 70
Period size: 12 Copynumber: 6.6 Consensus size: 12
1634552 ATAAACAAAG
*
1634562 TTCTAAATAAGC
1 TTCTAAATGAGC
*
1634574 TTCTAAACGAGC
1 TTCTAAATGAGC
*
1634586 TTATAAATGAGC
1 TTCTAAATGAGC
*
1634598 TTCTAAACGAGC
1 TTCTAAATGAGC
*
1634610 ATT-TAAATGAGA
1 -TTCTAAATGAGC
* *
1634622 ATCTAAACGAGC
1 TTCTAAATGAGC
*
1634634 TTATAAA
1 TTCTAAA
1634641 CGAATTTGTT
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
11 1 0.02
12 49 0.94
13 2 0.04
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (12 bp):
TTCTAAATGAGC
Found at i:1634641 original size:12 final size:12
Alignment explanation
Indices: 1634571--1634643 Score: 76
Period size: 12 Copynumber: 6.1 Consensus size: 12
1634561 GTTCTAAATA
1634571 AGCTTCTAAACG
1 AGCTTCTAAACG
* *
1634583 AGCTTATAAATG
1 AGCTTCTAAACG
1634595 AGCTTCTAAACG
1 AGCTTCTAAACG
*
1634607 AGCATT-TAAATG
1 AGC-TTCTAAACG
**
1634619 AGAATCTAAACG
1 AGCTTCTAAACG
*
1634631 AGCTTATAAACG
1 AGCTTCTAAACG
1634643 A
1 A
1634644 ATTTGTTCGT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
11 1 0.02
12 45 0.94
13 2 0.04
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.26
Consensus pattern (12 bp):
AGCTTCTAAACG
Found at i:1644130 original size:59 final size:59
Alignment explanation
Indices: 1644017--1644140 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 59
1644007 ATCATACATT
* * *
1644017 CTCAAATTATGATTTTCATTTTAAACTGCTTCTTAAAATTTTGAATGTACTAGTTTTATC
1 CTCAAAATATGATTTTCATTTTAAACTGCTCCTTAAAATTTTGAATGTA-TAGTTTCATC
* *
1644077 CTCAAAATATGATTTT-ATTTTAAATTAG-TCCTTAAACTTTTGAACATGT-TAGTTTCATC
1 CTCAAAATATGATTTTCATTTTAAACT-GCTCCTTAAAATTTTG-A-ATGTATAGTTTCATC
1644136 C-CAAA
1 CTCAAA
1644141 CATAGGTTCA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
58 4 0.07
59 31 0.55
60 17 0.30
61 4 0.07
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (59 bp):
CTCAAAATATGATTTTCATTTTAAACTGCTCCTTAAAATTTTGAATGTATAGTTTCATC
Found at i:1646336 original size:20 final size:19
Alignment explanation
Indices: 1646311--1646364 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1646301 GTGAAATAAA
1646311 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
1646331 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
1646351 AATCGCAACGCGAT
1 AATCGCAACGCGAT
1646365 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:1646375 original size:21 final size:20
Alignment explanation
Indices: 1646351--1646483 Score: 90
Period size: 20 Copynumber: 6.5 Consensus size: 20
1646341 CAGTTCCCAG
1646351 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
* *
1646371 GAATCGCAATGCGA-TATTACA
1 -AATCGCAACGCGATTATGA-A
** * * *
1646392 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
1646414 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
1646434 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
1646454 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
1646474 TATCGCAACG
1 AATCGCAACG
1646484 AGTATCCGTA
Statistics
Matches: 88, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.01
20 47 0.53
21 35 0.40
22 4 0.05
23 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:1646439 original size:20 final size:20
Alignment explanation
Indices: 1646351--1646524 Score: 84
Period size: 20 Copynumber: 8.5 Consensus size: 20
1646341 CAGTTCCCAG
*
1646351 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGAATATGAA
* *
1646371 GAATCGCAATGCG-ATATTACA
1 -AATCGCAACGCGAATATGA-A
** * * * *
1646392 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGAATAT-GAA
1646414 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATATGAA
*
1646434 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
1646454 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATATGAA
* * * **
1646474 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATATG-AA
* *
1646495 AATCGCAACGCGTATCA-GTA
1 AATCGCAACGCGAAT-ATGAA
1646515 AATCGCAACG
1 AATCGCAACG
1646525 AGTATACGTA
Statistics
Matches: 116, Mismatches: 29, Indels: 17
0.72 0.18 0.10
Matches are distributed among these distances:
19 1 0.01
20 62 0.53
21 48 0.41
22 4 0.03
23 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATATGAA
Found at i:1646506 original size:41 final size:40
Alignment explanation
Indices: 1646475--1646605 Score: 163
Period size: 41 Copynumber: 3.2 Consensus size: 40
1646465 GATTCTGACT
*
1646475 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCAGTAA
1 ATCGCAACGAGTATACGT-AAATCGCAACGCGTATCAGTAA
* *
1646516 ATCGCAACGAGTATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATACGTAAATCGCAACGCGTATCAGTAA
* ** * *
1646556 ATTGCAACGACAATACGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGTATACGT-AAATCGCAACGCGTATCAGTAA
*
1646597 ATTGCAACG
1 ATCGCAACG
1646606 CGATTTTTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 35 0.43
41 46 0.57
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAGTATACGTAAATCGCAACGCGTATCAGTAA
Found at i:1646606 original size:20 final size:20
Alignment explanation
Indices: 1646475--1646607 Score: 142
Period size: 20 Copynumber: 6.5 Consensus size: 20
1646465 GATTCTGACT
*
1646475 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
1646496 ATCGCAACGCGTATCAGTAA
1 ATCGCAACGCGTATCCGTAA
* *
1646516 ATCGCAACGAGTATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
1646536 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1646556 ATTGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
1646577 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
1646597 ATTGCAACGCG
1 ATCGCAACGCG
1646608 ATTTTTAAAG
Statistics
Matches: 91, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
20 60 0.66
21 31 0.34
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:1647225 original size:21 final size:21
Alignment explanation
Indices: 1647165--1647243 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
1647155 TTCTAAACTT
1647165 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
*
1647185 AAAATTGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
1647205 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
1647226 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
1647244 TAGCAACTCG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 28 0.56
21 22 0.44
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1649210 original size:93 final size:94
Alignment explanation
Indices: 1649050--1649428 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
1649040 TAGATTGCTT
* * *
1649050 AGTAAATTTATTCGGTTGCTACCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1649115 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* *
1649144 AGTAAATTTATTC-GTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1649208 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1649237 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1649302 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
1649331 AGTAAATTTGTTCGGTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1649396 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1649424 AGTAA
1 AGTAA
1649429 TGCAATCCAT
Statistics
Matches: 272, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
92 20 0.07
93 72 0.26
94 180 0.66
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1649538 original size:17 final size:17
Alignment explanation
Indices: 1649516--1649598 Score: 64
Period size: 19 Copynumber: 4.8 Consensus size: 17
1649506 AAAAATGACT
1649516 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
*
1649533 ATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATG--A
* *
1649552 ATCACAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
**
1649566 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAA--TGA
1649585 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1649599 CTATAATCGC
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 7 0.13
16 5 0.10
17 18 0.35
19 22 0.42
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.08
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:1649573 original size:33 final size:33
Alignment explanation
Indices: 1649531--1649593 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1649521 AACGCGAAAT
**
1649531 GAATCGCAACGAGAAATGAAAATCACAACGAGA
1 GAATCGCAACGAGAAACCAAAATCACAACGAGA
* *
1649564 GAATCGCAACGCGAAACCAAAATCGCAACG
1 GAATCGCAACGAGAAACCAAAATCACAACG
1649594 CGAAACTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.48, C:0.24, G:0.21, T:0.08
Consensus pattern (33 bp):
GAATCGCAACGAGAAACCAAAATCACAACGAGA
Found at i:1649671 original size:20 final size:20
Alignment explanation
Indices: 1649643--1649749 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
1649633 GATTCTCTCG
**
1649643 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1649663 TTGCAATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
1649683 TTGCGATTGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1649703 TTGCGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
*
1649723 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1649743 TTGCGAT
1 TTGCGAT
1649750 TTTAAGTTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1650324 original size:21 final size:21
Alignment explanation
Indices: 1650233--1650337 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
1650223 GACTCACCTG
*
1650233 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1650255 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1650275 TCATCCATCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1650296 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1650317 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1650338 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1650330 original size:42 final size:42
Alignment explanation
Indices: 1650230--1650340 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1650220 CCCGACTCAC
* * * *
1650230 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1650272 CTATCATCCATCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1650314 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1650341 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1651714 original size:14 final size:14
Alignment explanation
Indices: 1651695--1651730 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1651685 ATTGTTTAAT
1651695 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1651709 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1651723 TGATTTGT
1 TGATTTGT
1651731 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1651873 original size:33 final size:34
Alignment explanation
Indices: 1651836--1651907 Score: 128
Period size: 33 Copynumber: 2.1 Consensus size: 34
1651826 TAGACTATCA
1651836 CAACGAGAGAATCGCAATGCG-AAATGAAAATCG
1 CAACGAGAGAATCGCAATGCGAAAATGAAAATCG
*
1651869 CAACGAGTGAATCGCAATGCGAAAATGAAAATCG
1 CAACGAGAGAATCGCAATGCGAAAATGAAAATCG
1651903 CAACG
1 CAACG
1651908 CGAAACTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 20 0.54
34 17 0.46
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (34 bp):
CAACGAGAGAATCGCAATGCGAAAATGAAAATCG
Found at i:1651903 original size:20 final size:19
Alignment explanation
Indices: 1651845--1651912 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
1651835 ACAACGAGAG
1651845 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1651864 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
1651878 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1651898 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
1651913 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1651968 original size:34 final size:34
Alignment explanation
Indices: 1651925--1652017 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 34
1651915 AATTTCGCGT
1651925 TGCGATTTTCATTTTCGCATTGCGATTCACTCGG
1 TGCGATTTTCATTTTCGCATTGCGATTCACTCGG
* *
1651959 TGCGATTTTCA-TTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTTCGCATTGCGATTCACTCGG
** * *
1651992 TGCGATAGTCATTTCCGCGTTGCGAT
1 TGCGATTTTCATTTTCGCATTGCGAT
1652018 AGTCAATTCC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.56
34 23 0.44
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.41
Consensus pattern (34 bp):
TGCGATTTTCATTTTCGCATTGCGATTCACTCGG
Found at i:1652014 original size:20 final size:20
Alignment explanation
Indices: 1651989--1652073 Score: 127
Period size: 20 Copynumber: 4.2 Consensus size: 20
1651979 GCGATTCTCT
1651989 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1652009 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
1652029 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1652049 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
1652069 CGTTG
1 CGTTG
1652074 TGATTTCCGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 56 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1654535 original size:24 final size:24
Alignment explanation
Indices: 1654501--1654554 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1654491 CTGAAAAATC
1654501 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1654525 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1654549 ATCAAA
1 ATCAAA
1654555 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1654568 original size:24 final size:24
Alignment explanation
Indices: 1654501--1654568 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1654491 CTGAAAAATC
* * *
1654501 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1654525 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1654549 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1654569 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1655428 original size:20 final size:20
Alignment explanation
Indices: 1655405--1655988 Score: 142
Period size: 20 Copynumber: 28.9 Consensus size: 20
1655395 TTGCGATAGT
*
1655405 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
* *
1655425 CAGATTCGCATTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
* *
1655445 C-GTATTCGCATTGCGATTTA
1 CAG-AATCGCGTTGCGATTTA
*
1655465 C-GTATCCGCGTTGCGATTTA
1 CAGAAT-CGCGTTGCGATTTA
* *
1655485 C-GTAATCGCATTGCGATTTTC
1 CAG-AATCGCGTTGCGA-TTTA
*
1655506 CA-AATTTGCGTTGCGATTTA
1 CAGAA-TCGCGTTGCGATTTA
* *
1655526 -AGTAATCGCATTGCGATTTTC
1 CAG-AATCGCGTTGCGA-TTTA
*
1655547 CA-AATTCGCGTTGCGAGTTA
1 CAGAA-TCGCGTTGCGATTTA
*
1655567 C-GTAATCGCGTTGCAATTTA
1 CAG-AATCGCGTTGCGATTTA
* * *
1655587 C-GTATTCGCATTGCGAATTA
1 CAG-AATCGCGTTGCGATTTA
* * ***
1655607 GGAAAATCGCAACGCGAATTT-
1 -CAGAATCGCGTTGCG-ATTTA
** ** *
1655628 GGGAAATCGCAATGCGATAGT-
1 CAG-AATCGCGTTGCGAT-TTA
*
1655649 CAGAATCGCGTTGCGA-AT-
1 CAGAATCGCGTTGCGATTTA
* * **
1655667 CTGGAAACTGATTTGCGA--TA
1 C-AGAATC-GCGTTGCGATTTA
* *
1655687 CCGGAGATCGCGTTGCGAATTA
1 -CAGA-ATCGCGTTGCGATTTA
1655709 TC-G-ATCGCGTTGCGATTTA
1 -CAGAATCGCGTTGCGATTTA
* *
1655728 CGGATAT-GCATTGCGATTTTA
1 CAGA-ATCGCGTTGCGA-TTTA
* *
1655749 CA-TATTGTCGTTGCGATTTA
1 CAGAATCG-CGTTGCGATTTA
* *
1655769 CGGATAT-GCATTGCGATTTA
1 CAGA-ATCGCGTTGCGATTTA
* *
1655789 C-GTATTCTCGTTGCGATTTA
1 CAG-AATCGCGTTGCGATTTA
*
1655809 CAG-ATACGCATTGCGATTTA
1 CAGAAT-CGCGTTGCGATTTA
* * *
1655829 CATATTCTCGTTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
* *
1655849 C-GGATACGCATTGCGATTTTA
1 CAGAAT-CGCGTTGCGA-TTTA
* * *
1655870 C-GTATTGTCGTTACGATTTA
1 CAGAATCG-CGTTGCGATTTA
*
1655890 C-GGATACGCGTTGCGATTTTA
1 CAGAAT-CGCGTTGCGA-TTTA
* * *
1655911 C-GGATACTCGTTGCGATAGT-
1 CAGAAT-CGCGTTGCGAT-TTA
*
1655931 CAGAATCACGTTGCGATTTA
1 CAGAATCGCGTTGCGATTTA
* * *
1655951 TATG-TTCGCGTTGCGATTTT
1 CA-GAATCGCGTTGCGATTTA
* *
1655971 CATATTCGCGTTGCGATT
1 CAGAATCGCGTTGCGATT
1655989 CTGGAAATTC
Statistics
Matches: 428, Mismatches: 88, Indels: 96
0.70 0.14 0.16
Matches are distributed among these distances:
18 3 0.01
19 31 0.07
20 271 0.63
21 114 0.27
22 9 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
CAGAATCGCGTTGCGATTTA
Found at i:1655459 original size:40 final size:40
Alignment explanation
Indices: 1655415--1655988 Score: 222
Period size: 41 Copynumber: 14.2 Consensus size: 40
1655405 CAGAATCTCG
* *
1655415 TTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACAGATTCGCGTTGCGATTTACGTAATCGCA
*
1655455 TTGCGATTTAC-GTATCCGCGTTGCGATTTACGTAATCGCA
1 TTGCGATTTACAG-ATTCGCGTTGCGATTTACGTAATCGCA
* * * *
1655495 TTGCGATTTTCCAAATTTGCGTTGCGATTTAAGTAATCGCA
1 TTGCGA-TTTACAGATTCGCGTTGCGATTTACGTAATCGCA
* * * *
1655536 TTGCGATTTTCCAAATTCGCGTTGCGAGTTACGTAATCGCG
1 TTGCGA-TTTACAGATTCGCGTTGCGATTTACGTAATCGCA
* * * * *
1655577 TTGCAATTTAC-GTATTCGCATTGCGAATTAGGAAAATCGCA
1 TTGCGATTTACAG-ATTCGCGTTGCGATTTACG-TAATCGCA
** ** * ** * *
1655618 ACGCGAATTT-GGGAAATCGCAATGCGATAGT-CAG-AATCGCG
1 TTGCG-ATTTACAG-ATTCGCGTTGCGAT-TTAC-GTAATCGCA
* ** * * ** * *
1655659 TTGCGAATCTGGAAACT-GATTTGCGA--TACCGGAGATCGCG
1 TTGCG-ATTTACAGATTCGCGTTGCGATTTA-CGTA-ATCGCA
* *
1655699 TTGCGAATTATC-GA-TCGCGTTGCGATTTACGGATAT-GCA
1 TTGCGATTTA-CAGATTCGCGTTGCGATTTACGTA-ATCGCA
* *
1655738 TTGCGATTTTACATATT-GTCGTTGCGATTTACGGATAT-GCA
1 TTGCGA-TTTACAGATTCG-CGTTGCGATTTACGTA-ATCGCA
*
1655779 TTGCGATTTAC-GTATTCTCGTTGCGATTTAC--AGATACGCA
1 TTGCGATTTACAG-ATTCGCGTTGCGATTTACGTA-AT-CGCA
* * *
1655819 TTGCGATTTACATATTCTCGTTGCGATTTACG-GATACGCA
1 TTGCGATTTACAGATTCGCGTTGCGATTTACGTAAT-CGCA
* * *
1655859 TTGCGATTTTAC-GTATT-GTCGTTACGATTTACG-GATACGCG
1 TTGCGA-TTTACAG-ATTCG-CGTTGCGATTTACGTAAT-CGCA
* * * * * *
1655900 TTGCGATTTTACGGATACTCGTTGCGATAGT-CAG-AATCACG
1 TTGCGA-TTTACAGATTCGCGTTGCGAT-TTAC-GTAATCGCA
* * * * *
1655941 TTGCGATTTATATG-TTCGCGTTGCGATTTTCATATTCGCG
1 TTGCGATTTACA-GATTCGCGTTGCGATTTACGTAATCGCA
1655981 TTGCGATT
1 TTGCGATT
1655989 CTGGAAATTC
Statistics
Matches: 422, Mismatches: 74, Indels: 76
0.74 0.13 0.13
Matches are distributed among these distances:
37 1 0.00
38 5 0.01
39 23 0.05
40 184 0.44
41 185 0.44
42 22 0.05
43 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (40 bp):
TTGCGATTTACAGATTCGCGTTGCGATTTACGTAATCGCA
Found at i:1655616 original size:21 final size:21
Alignment explanation
Indices: 1655592--1655644 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1655582 ATTTACGTAT
*
1655592 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
1655613 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
1655634 TCGCAATGCGA
1 TCGCAATGCGA
1655645 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:1655763 original size:41 final size:41
Alignment explanation
Indices: 1655716--1655927 Score: 302
Period size: 41 Copynumber: 5.2 Consensus size: 41
1655706 TTATCGATCG
* *
1655716 CGTTGCGATTTACGGATATGCATTGCGATTTTACATATTGT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACATATTCT
* *
1655757 CGTTGCGATTTACGGATATGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACATATTCT
*
1655797 CGTTGCGATTTACAGATACGCATTGCGA-TTTACATATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACATATTCT
* *
1655837 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACATATTCT
* * ** *
1655878 CGTTACGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACATATTCT
1655919 CGTTGCGAT
1 CGTTGCGAT
1655928 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 74 0.47
41 82 0.53
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTTACATATTCT
Found at i:1656000 original size:21 final size:21
Alignment explanation
Indices: 1655955--1656091 Score: 61
Period size: 20 Copynumber: 6.7 Consensus size: 21
1655945 GATTTATATG
** *
1655955 TTCGCGTTGCGATT-TTCATA
1 TTCGCGTTGCGATTCTGGAAA
1655975 TTCGCGTTGCGATTCTGGAAA
1 TTCGCGTTGCGATTCTGGAAA
** * *
1655996 TTCGCAATGCGAATT-T-GTAC
1 TTCGCGTTGCG-ATTCTGGAAA
* * **
1656016 TATCGCATTACGATTCTTCATAA
1 T-TCGCGTTGCGATTCTGGA-AA
*
1656039 -TCGCGTTGCGATTCTGGGAA
1 TTCGCGTTGCGATTCTGGAAA
* ** *
1656059 CT-GATTTGCGATTCTGGAGA
1 TTCGCGTTGCGATTCTGGAAA
1656079 -TCGCGTTGCGATT
1 TTCGCGTTGCGATT
1656092 TTTATTTCGC
Statistics
Matches: 86, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
19 1 0.01
20 45 0.52
21 36 0.42
22 3 0.03
23 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATTCTGGAAA
Found at i:1656087 original size:20 final size:19
Alignment explanation
Indices: 1656038--1656091 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1656028 ATTCTTCATA
1656038 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
1656057 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
1656078 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
1656092 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:1656106 original size:19 final size:19
Alignment explanation
Indices: 1656079--1656131 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1656069 ATTCTGGAGA
*
1656079 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTTATT
1656098 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTTATT
1656117 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
1656132 GTTGGTCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.13, C:0.17, G:0.19, T:0.51
Consensus pattern (19 bp):
TCGCATTGCGATTTTTATT
Found at i:1668835 original size:16 final size:15
Alignment explanation
Indices: 1668799--1668843 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 15
1668789 TATAAGATAA
1668799 TTTTATTATAATT-T
1 TTTTATTATAATTAT
*
1668813 TTTTATTATACTTAT
1 TTTTATTATAATTAT
1668828 TGTTTATTATAATTAT
1 T-TTTATTATAATTAT
1668844 ATGAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 12 0.44
15 2 0.07
16 13 0.48
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:1671336 original size:13 final size:13
Alignment explanation
Indices: 1671318--1671356 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1671308 AATGATAAAT
*
1671318 AATAAAAAAGTCC
1 AATAAAAAAGTAC
* *
1671331 AATAAACAACTAC
1 AATAAAAAAGTAC
1671344 AATAAAAAAGTAC
1 AATAAAAAAGTAC
1671357 TAAATACAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.64, C:0.15, G:0.05, T:0.15
Consensus pattern (13 bp):
AATAAAAAAGTAC
Found at i:1671365 original size:26 final size:26
Alignment explanation
Indices: 1671318--1671378 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
1671308 AATGATAAAT
*
1671318 AATAAAAAAGTCCAATAAACAACTAC
1 AATAAAAAAGTCCAATAAACAAATAC
* * *
1671344 AATAAAAAAGTACTAA-ATACAAATAT
1 AATAAAAAAGT-CCAATAAACAAATAC
1671370 AATAAAAAA
1 AATAAAAAA
1671379 CAAAATCTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 27 0.90
27 3 0.10
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.18
Consensus pattern (26 bp):
AATAAAAAAGTCCAATAAACAAATAC
Found at i:1673685 original size:20 final size:20
Alignment explanation
Indices: 1673668--1673705 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1673658 ACAGAGAATA
*
1673668 TAAGAGTAATTGAGAGAAGT
1 TAAGAGAAATTGAGAGAAGT
*
1673688 TGAGAGAAATTGAGAGAA
1 TAAGAGAAATTGAGAGAA
1673706 CTTGGTGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (20 bp):
TAAGAGAAATTGAGAGAAGT
Found at i:1674803 original size:23 final size:23
Alignment explanation
Indices: 1674777--1674824 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1674767 CAGACATAAC
*
1674777 AAATGAACATAATCAA-ACACAAT
1 AAATGAACATAAACAACA-ACAAT
*
1674800 AAATGAACGTAAACAACAACAAT
1 AAATGAACATAAACAACAACAAT
1674823 AA
1 AA
1674825 CTACATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.62, C:0.17, G:0.06, T:0.15
Consensus pattern (23 bp):
AAATGAACATAAACAACAACAAT
Found at i:1675034 original size:24 final size:24
Alignment explanation
Indices: 1675007--1675099 Score: 116
Period size: 24 Copynumber: 3.9 Consensus size: 24
1674997 ATATACACAG
* *
1675007 ACATAAATGAATGAATATAAACGA
1 ACATAAATGAACGAACATAAACGA
* * *
1675031 ACATAAACGAACGAGCATACAC-A
1 ACATAAATGAACGAACATAAACGA
*
1675054 GACATAAATGAATGAACATAAACGA
1 -ACATAAATGAACGAACATAAACGA
1675079 ACATAAATGAACGAACATAAA
1 ACATAAATGAACGAACATAAA
1675100 TAAACGGATT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 1 0.02
24 55 0.96
25 1 0.02
ACGTcount: A:0.57, C:0.15, G:0.13, T:0.15
Consensus pattern (24 bp):
ACATAAATGAACGAACATAAACGA
Found at i:1675053 original size:48 final size:48
Alignment explanation
Indices: 1674999--1675097 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
1674989 ATACATAAAT
* *
1674999 ATACACAGACATAAATGAATGAATATAAACGAACATAAACGAACGAGC
1 ATACACAGACATAAATGAATGAACATAAACGAACATAAACGAACGAAC
*
1675047 ATACACAGACATAAATGAATGAACATAAACGAACATAAATGAACGAAC
1 ATACACAGACATAAATGAATGAACATAAACGAACATAAACGAACGAAC
1675095 ATA
1 ATA
1675098 AATAAACGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.15
Consensus pattern (48 bp):
ATACACAGACATAAATGAATGAACATAAACGAACATAAACGAACGAAC
Found at i:1675100 original size:14 final size:14
Alignment explanation
Indices: 1675055--1675105 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1675045 GCATACACAG
*
1675055 ACATAAATGAATGA
1 ACATAAATGAACGA
1675069 ACAT--A--AACGA
1 ACATAAATGAACGA
1675079 ACATAAATGAACGA
1 ACATAAATGAACGA
*
1675093 ACATAAATAAACG
1 ACATAAATGAACG
1675106 GATTACCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 8 0.26
12 2 0.06
14 21 0.68
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.16
Consensus pattern (14 bp):
ACATAAATGAACGA
Found at i:1675506 original size:52 final size:52
Alignment explanation
Indices: 1675435--1675534 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
1675425 TTGTAGTAAG
1675435 GCGCACCCCTGCAACGCGCTTTACGCTAATATGGCGCCAAGTGAGGTAAGGC
1 GCGCACCCCTGCAACGCGCTTTACGCTAATATGGCGCCAAGTGAGGTAAGGC
* * * *
1675487 GCGCCCCCCTGCAGA-GCGCTTTACGCTGATATGGCGCCACGTGGGGTA
1 GCGCACCCCTGCA-ACGCGCTTTACGCTAATATGGCGCCAAGTGAGGTA
1675535 TAACACGGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 42 0.98
53 1 0.02
ACGTcount: A:0.19, C:0.32, G:0.31, T:0.18
Consensus pattern (52 bp):
GCGCACCCCTGCAACGCGCTTTACGCTAATATGGCGCCAAGTGAGGTAAGGC
Done.