Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004846.1 Hibiscus syriacus cultivar Beakdansim tig00010927_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: 1467214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:825026 original size:76 final size:77
Alignment explanation
Indices: 824859--825029 Score: 218
Period size: 76 Copynumber: 2.2 Consensus size: 77
824849 TCTCTTCTCA
* * * * *
824859 TTCTGTGATAGAATCGAGCAAAAAGTTGATGTTGATCCAACTCCTTCTGTGCCAGACGAAAATAT
1 TTCTGTGATAGATTTGAACAAAAAATTGATGTTGATCCAACTCCTTCTGTACCAGACGAAAATAT
824924 TGATCCACCTCT
66 TGATCCACCTCT
* * * ** *
824936 TTCTGTGATGGATTTGAACAAAAAATTGATGTTGATCCAACTTCTT-TGTACCATATTAAAATGT
1 TTCTGTGATAGATTTGAACAAAAAATTGATGTTGATCCAACTCCTTCTGTACCAGACGAAAATAT
* *
825000 TGATTCACCTTT
66 TGATCCACCTCT
825012 TTCTGTGATAGATTTGAA
1 TTCTGTGATAGATTTGAA
825030 ATGTTGATCC
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
76 40 0.50
77 40 0.50
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (77 bp):
TTCTGTGATAGATTTGAACAAAAAATTGATGTTGATCCAACTCCTTCTGTACCAGACGAAAATAT
TGATCCACCTCT
Found at i:825035 original size:34 final size:34
Alignment explanation
Indices: 824991--825564 Score: 665
Period size: 34 Copynumber: 17.1 Consensus size: 34
824981 TTGTACCATA
* * * *
824991 TTAAAATGTTGATTCACCTTTTTCTGTGATAGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* *
825025 TTGAAATGTTGATCCACCTCTTTCTGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* *
825059 TAAAAATGTTGATCCACCTCTTTCTGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* * * *
825093 TAAAAATATCGATCCACCTATTTCTATGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* **
825127 TAAAAATGTTAATCCACCTCTTTCTGTG-TGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* *
825160 TT-GAATGTCGGTCCACCTCTTTCTGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
*
825193 TT-GAATGTCGATCCACCTCTTTCTGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
*
825226 TTGAAATGTCGATCCACCTCTTTCTGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* *
825260 TTGAAATGTCGATCCACATCTTTCTGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* *
825294 TTAAAATGTCGATCAACCTCTTTTTGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* *
825328 TT-GAATGTCGATCCACCACTTTCTGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* * * *
825361 TAAAAATGTTGATCTACCTCTTTCTATGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* * * *
825395 TAAAAATGTCGATCCACCTATTTTTATGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* ** *
825429 TAAAAATGTTAATCCACCTCTTTATGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* * * * * *
825463 TAAAAATGTTGATCCACTTATTTCTATGATGAAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
* * * * *
825497 TAAAAATATCGA-ACACCTCTTTTTATGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
*
825530 TT-GAATGTCGATCCACCTCTTTCTGTGATGGAT
1 TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
825563 TT
1 TT
825565 GAGAAAAAAG
Statistics
Matches: 471, Mismatches: 65, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
32 28 0.06
33 110 0.23
34 333 0.71
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (34 bp):
TTAAAATGTCGATCCACCTCTTTCTGTGATGGAT
Found at i:825359 original size:135 final size:136
Alignment explanation
Indices: 824993--825564 Score: 681
Period size: 135 Copynumber: 4.2 Consensus size: 136
824983 GTACCATATT
* * * * * *
824993 AAAATGTTGATTCACCTTTTTCTGTGATAGATTTGAAATGTTGATCCACCTCTTTCTGTGATGGA
1 AAAATGTCGATCCACCTCTTTCTGTGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGA
* * *
825058 TTAAAAATGTTGATCCACCTCTTTCTGTGATGGATTAAAAATATCGATCCACCTATTTCTATGAT
66 TTAAAAATGTCGATCCACCACTTTCTGTGATGGATTAAAAATATCGATCCACCTCTTTCTATGAT
825123 GGATTA
131 GGATTA
** * *
825129 AAAATGTTAATCCACCTCTTTCTGTG-TGGATTT-GAATGTCGGTCCACCTCTTTCTGTGATGGA
1 AAAATGTCGATCCACCTCTTTCTGTGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGA
** * ** * *
825192 TT-TGAATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGAT
66 TTAAAAATGTCGATCCACCACTTTCTGTGATGGATTAAAAATATCGATCCACCTCTTTCTATGAT
*
825256 GGATTT
131 GGATTA
* * * *
825262 GAAATGTCGATCCACATCTTTCTGTGATGGATTTAAAATGTCGATCAACCTCTTTTTGTGATGGA
1 AAAATGTCGATCCACCTCTTTCTGTGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGA
** * * *
825327 TT-TGAATGTCGATCCACCACTTTCTGTGATGGATTAAAAATGTTGATCTACCTCTTTCTATGAT
66 TTAAAAATGTCGATCCACCACTTTCTGTGATGGATTAAAAATATCGATCCACCTCTTTCTATGAT
825391 GGATTA
131 GGATTA
* * * * ** *
825397 AAAATGTCGATCCACCTATTTTTATGATGGATTAAAAATGTTAATCCACCTCTTTATGTGATGGA
1 AAAATGTCGATCCACCTCTTTCTGTGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGA
* * * * * *
825462 TTAAAAATGTTGATCCACTTA-TTTCTATGATGAATTAAAAATATCGA-ACACCTCTTTTTATGA
66 TTAAAAATGTCGATCCAC-CACTTTCTGTGATGGATTAAAAATATCGATCCACCTCTTTCTATGA
825525 TGGATT-
130 TGGATTA
**
825531 TGAATGTCGATCCACCTCTTTCTGTGATGGATTT
1 AAAATGTCGATCCACCTCTTTCTGTGATGGATTT
825565 GAGAAAAAAG
Statistics
Matches: 374, Mismatches: 58, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
133 81 0.22
134 64 0.17
135 171 0.46
136 57 0.15
137 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (136 bp):
AAAATGTCGATCCACCTCTTTCTGTGATGGATTTAAAATGTCGATCCACCTCTTTCTGTGATGGA
TTAAAAATGTCGATCCACCACTTTCTGTGATGGATTAAAAATATCGATCCACCTCTTTCTATGAT
GGATTA
Found at i:827618 original size:22 final size:23
Alignment explanation
Indices: 827593--827657 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
827583 ACCTATTGTC
827593 TTCTTTTT-TT-TCATTTTTTTCT
1 TTCTTTTTGTTGT-ATTTTTTTCT
*
827615 TTCTTTTTGTTGTTTTTTTTTCT
1 TTCTTTTTGTTGTATTTTTTTCT
* * *
827638 TT-TTGTTGTTTTGTTTTTTT
1 TTCTTTTTGTTGTATTTTTTT
827658 TCTATATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 23 0.62
23 13 0.35
24 1 0.03
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.83
Consensus pattern (23 bp):
TTCTTTTTGTTGTATTTTTTTCT
Found at i:827630 original size:19 final size:19
Alignment explanation
Indices: 827608--827649 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
827598 TTTTTTCATT
827608 TTTTTCTTTCTTTTTGTTG
1 TTTTTCTTTCTTTTTGTTG
*
827627 TTTTTTTTTCTTTTTGTTG
1 TTTTTCTTTCTTTTTGTTG
827646 TTTT
1 TTTT
827650 GTTTTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (19 bp):
TTTTTCTTTCTTTTTGTTG
Found at i:827651 original size:24 final size:23
Alignment explanation
Indices: 827606--827660 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
827596 TTTTTTTTCA
827606 TTTTTTTCTTTCTTTTTGTTGTT
1 TTTTTTTCTTTCTTTTTGTTGTT
* *
827629 TTTTTTTCTTT-TTGTTGTTTTGT
1 TTTTTTTCTTTCTTTTTGTTGT-T
827652 TTTTTTTCT
1 TTTTTTTCT
827661 ATATATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.28
23 21 0.72
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (23 bp):
TTTTTTTCTTTCTTTTTGTTGTT
Found at i:827654 original size:19 final size:19
Alignment explanation
Indices: 827614--827658 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
827604 CATTTTTTTC
*
827614 TTTCTTTTTGTTGTTTTTT
1 TTTCTTTTTGTTGTTTTGT
827633 TTTCTTTTTGTTGTTTTGT
1 TTTCTTTTTGTTGTTTTGT
827652 TTT-TTTT
1 TTTCTTTT
827659 CTATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.84
Consensus pattern (19 bp):
TTTCTTTTTGTTGTTTTGT
Found at i:835425 original size:33 final size:34
Alignment explanation
Indices: 835366--835488 Score: 187
Period size: 33 Copynumber: 3.7 Consensus size: 34
835356 CTCATGTGCA
* *
835366 AAGTTGGTCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
*
835400 AAGTTGGCCACCAACC-AAGATGAATTTTTCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
* *
835433 AAGTTGGCCATCGACC-AAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
835466 AAGTTGGCCACCAACCAAAGATG
1 AAGTTGGCCACCAACCAAAGATG
835489 TCAACTTTGC
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
33 60 0.75
34 20 0.25
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
Found at i:836999 original size:23 final size:24
Alignment explanation
Indices: 836973--837018 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
836963 GGAATTGAGA
836973 AAGGAGTTAGGGATTTT-AATTTG
1 AAGGAGTTAGGGATTTTGAATTTG
836996 AAGGAGTTAGGGATTTTGAATTT
1 AAGGAGTTAGGGATTTTGAATTT
837019 ACCCGATGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.39
Consensus pattern (24 bp):
AAGGAGTTAGGGATTTTGAATTTG
Found at i:842142 original size:24 final size:24
Alignment explanation
Indices: 842114--842160 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
842104 GGAATTGAGA
842114 AAGGAGTTAGGGATTTCGAATTTG
1 AAGGAGTTAGGGATTTCGAATTTG
*
842138 AAGGAGTTAGGGATTTTGAATTT
1 AAGGAGTTAGGGATTTCGAATTT
842161 ACCTGATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (24 bp):
AAGGAGTTAGGGATTTCGAATTTG
Found at i:842232 original size:18 final size:19
Alignment explanation
Indices: 842206--842244 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
842196 AAGAAGGGAT
*
842206 GATGGTAATCGGGCT-AAG
1 GATGATAATCGGGCTGAAG
*
842224 GATGATAATTGGGCTGAAG
1 GATGATAATCGGGCTGAAG
842243 GA
1 GA
842245 GTCAACAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.31, C:0.08, G:0.38, T:0.23
Consensus pattern (19 bp):
GATGATAATCGGGCTGAAG
Found at i:844678 original size:20 final size:20
Alignment explanation
Indices: 844653--844713 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
844643 CCAAAGATAG
844653 ACATCCTGAAGGGCTTTGTA
1 ACATCCTGAAGGGCTTTGTA
*
844673 ACATCCTGAAGTGCTTTGTA
1 ACATCCTGAAGGGCTTTGTA
844693 ACATCCTGAAGGGCTTTGTA
1 ACATCCTGAAGGGCTTTGTA
844713 A
1 A
844714 AAGTCCTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (20 bp):
ACATCCTGAAGGGCTTTGTA
Found at i:846563 original size:16 final size:16
Alignment explanation
Indices: 846544--846617 Score: 130
Period size: 16 Copynumber: 4.6 Consensus size: 16
846534 ACCTGTTTTC
846544 AACCTGACCTATGATG
1 AACCTGACCTATGATG
*
846560 AACCTGACATATGATG
1 AACCTGACCTATGATG
846576 AACCTGACCTATGATG
1 AACCTGACCTATGATG
*
846592 AACCTGACATATGATG
1 AACCTGACCTATGATG
846608 AACCTGACCT
1 AACCTGACCT
846618 GGTTTTAACC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (16 bp):
AACCTGACCTATGATG
Found at i:846627 original size:16 final size:16
Alignment explanation
Indices: 846608--846647 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
846598 ACATATGATG
*
846608 AACCTGACCTGGTTTT
1 AACCTGACATGGTTTT
* *
846624 AACCTGGCATGTTTTT
1 AACCTGACATGGTTTT
846640 AACCTGAC
1 AACCTGAC
846648 TTGTAAATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (16 bp):
AACCTGACATGGTTTT
Found at i:846629 original size:32 final size:32
Alignment explanation
Indices: 846544--846617 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
846534 ACCTGTTTTC
846544 AACCTGACCTATGATGAACCTGACATATGATG
1 AACCTGACCTATGATGAACCTGACATATGATG
846576 AACCTGACCTATGATGAACCTGACATATGATG
1 AACCTGACCTATGATGAACCTGACATATGATG
846608 AACCTGACCT
1 AACCTGACCT
846618 GGTTTTAACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (32 bp):
AACCTGACCTATGATGAACCTGACATATGATG
Found at i:846944 original size:14 final size:14
Alignment explanation
Indices: 846922--846968 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
846912 TGCAAAGGAA
*
846922 AATTAATATAGTTT
1 AATTTATATAGTTT
846936 AATTTATATA----
1 AATTTATATAGTTT
846946 AA-TTATATAGTTT
1 AATTTATATAGTTT
846959 AATTTATATA
1 AATTTATATA
846969 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:846955 original size:23 final size:24
Alignment explanation
Indices: 846921--846970 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
846911 ATGCAAAGGA
846921 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
846945 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
846968 AAA
1 AAA
846971 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:847538 original size:10 final size:10
Alignment explanation
Indices: 847523--847624 Score: 69
Period size: 10 Copynumber: 11.1 Consensus size: 10
847513 ATAAATTACA
847523 AGGCAACAAC
1 AGGCAACAAC
847533 AGG---CAAC
1 AGGCAACAAC
847540 AGGCAACAAC
1 AGGCAACAAC
* *
847550 AGG---TAGC
1 AGGCAACAAC
847557 AGGCAACAAC
1 AGGCAACAAC
*
847567 AGG---CAGC
1 AGGCAACAAC
847574 AGGCAACAAC
1 AGGCAACAAC
* *
847584 ATGCAACAGC
1 AGGCAACAAC
*
847594 AGGAAACAAC
1 AGGCAACAAC
* *
847604 ATGCAACAGC
1 AGGCAACAAC
847614 AGGCAACAAC
1 AGGCAACAAC
847624 A
1 A
847625 TGTAGAATTT
Statistics
Matches: 67, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
7 18 0.27
10 49 0.73
ACGTcount: A:0.46, C:0.27, G:0.24, T:0.03
Consensus pattern (10 bp):
AGGCAACAAC
Found at i:847545 original size:17 final size:17
Alignment explanation
Indices: 847523--847592 Score: 104
Period size: 17 Copynumber: 4.1 Consensus size: 17
847513 ATAAATTACA
847523 AGGCAACAACAGGCAAC
1 AGGCAACAACAGGCAAC
* *
847540 AGGCAACAACAGGTAGC
1 AGGCAACAACAGGCAAC
*
847557 AGGCAACAACAGGCAGC
1 AGGCAACAACAGGCAAC
*
847574 AGGCAACAACATGCAAC
1 AGGCAACAACAGGCAAC
847591 AG
1 AG
847593 CAGGAAACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.44, C:0.27, G:0.26, T:0.03
Consensus pattern (17 bp):
AGGCAACAACAGGCAAC
Found at i:847593 original size:20 final size:20
Alignment explanation
Indices: 847554--847626 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
847544 AACAACAGGT
*
847554 AGCAGGCAACAACA-G--GC
1 AGCAGGCAACAACATGCAAC
847571 AGCAGGCAACAACATGCAAC
1 AGCAGGCAACAACATGCAAC
*
847591 AGCAGGAAACAACATGCAAC
1 AGCAGGCAACAACATGCAAC
847611 AGCAGGCAACAACATG
1 AGCAGGCAACAACATG
847627 TAGAATTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
17 14 0.28
18 1 0.02
20 35 0.70
ACGTcount: A:0.45, C:0.27, G:0.23, T:0.04
Consensus pattern (20 bp):
AGCAGGCAACAACATGCAAC
Found at i:850513 original size:25 final size:25
Alignment explanation
Indices: 850467--850514 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
850457 CGGTTAGGGT
* * **
850467 TTTTTAGGTTCAGGTTTGGGTTTAA
1 TTTTTAAGTTCAGGATCAGGTTTAA
850492 TTTTTAAGTTCAGGATCAGGTTT
1 TTTTTAAGTTCAGGATCAGGTTT
850515 TGGATTTGGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (25 bp):
TTTTTAAGTTCAGGATCAGGTTTAA
Found at i:850522 original size:6 final size:6
Alignment explanation
Indices: 850513--850617 Score: 111
Period size: 6 Copynumber: 17.3 Consensus size: 6
850503 AGGATCAGGT
* * * **
850513 TTTGGA TTTGGG TTCGGG TTTGGA TTCAGG TTTGGG TTTGGG TTTGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * * *
850561 TTTGGG TTCGGG TTCGGG TTTAGG TTTGGG TTTGGG TTTTGG TTTAGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTT-GGG
*
850610 TTTAGG TT
1 TTTGGG TT
850618 CTAGTTTAAG
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
6 77 0.94
7 5 0.06
ACGTcount: A:0.06, C:0.04, G:0.43, T:0.48
Consensus pattern (6 bp):
TTTGGG
Found at i:854347 original size:16 final size:16
Alignment explanation
Indices: 854328--854401 Score: 130
Period size: 16 Copynumber: 4.6 Consensus size: 16
854318 ACCTGTTTTC
854328 AACCTGACCTATGATG
1 AACCTGACCTATGATG
*
854344 AACCTGACATATGATG
1 AACCTGACCTATGATG
854360 AACCTGACCTATGATG
1 AACCTGACCTATGATG
*
854376 AACCTGACATATGATG
1 AACCTGACCTATGATG
854392 AACCTGACCT
1 AACCTGACCT
854402 GGTTTTAACC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 54 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (16 bp):
AACCTGACCTATGATG
Found at i:854411 original size:16 final size:16
Alignment explanation
Indices: 854392--854431 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
854382 ACATATGATG
*
854392 AACCTGACCTGGTTTT
1 AACCTGACATGGTTTT
* *
854408 AACCTGGCATGTTTTT
1 AACCTGACATGGTTTT
854424 AACCTGAC
1 AACCTGAC
854432 TTGTAAATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (16 bp):
AACCTGACATGGTTTT
Found at i:854413 original size:32 final size:32
Alignment explanation
Indices: 854328--854401 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
854318 ACCTGTTTTC
854328 AACCTGACCTATGATGAACCTGACATATGATG
1 AACCTGACCTATGATGAACCTGACATATGATG
854360 AACCTGACCTATGATGAACCTGACATATGATG
1 AACCTGACCTATGATGAACCTGACATATGATG
854392 AACCTGACCT
1 AACCTGACCT
854402 GGTTTTAACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (32 bp):
AACCTGACCTATGATGAACCTGACATATGATG
Found at i:854728 original size:14 final size:14
Alignment explanation
Indices: 854706--854752 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
854696 TGCAAAGGAA
*
854706 AATTAATATAGTTT
1 AATTTATATAGTTT
854720 AATTTATATA----
1 AATTTATATAGTTT
854730 AA-TTATATAGTTT
1 AATTTATATAGTTT
854743 AATTTATATA
1 AATTTATATA
854753 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:854739 original size:23 final size:24
Alignment explanation
Indices: 854705--854754 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
854695 ATGCAAAGGA
854705 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
854729 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
854752 AAA
1 AAA
854755 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:855307 original size:17 final size:17
Alignment explanation
Indices: 855285--855386 Score: 123
Period size: 17 Copynumber: 5.6 Consensus size: 17
855275 ATAAATTACA
855285 AGGCAACAACAGGCAGC
1 AGGCAACAACAGGCAGC
*
855302 AGGCAACAACAGGTAGC
1 AGGCAACAACAGGCAGC
855319 AGGCAACAACAGGCAGC
1 AGGCAACAACAGGCAGC
*
855336 AGGCAACAACATGCAACAGC
1 AGGCAACAACA-G--GCAGC
*
855356 AGGCAACAACATGCAACAGC
1 AGGCAACAACA-G--GCAGC
855376 AGGCAACAACA
1 AGGCAACAACA
855387 TGTAGAATTT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
17 43 0.54
18 1 0.01
20 35 0.44
ACGTcount: A:0.44, C:0.28, G:0.25, T:0.03
Consensus pattern (17 bp):
AGGCAACAACAGGCAGC
Found at i:855311 original size:20 final size:20
Alignment explanation
Indices: 855288--855386 Score: 79
Period size: 20 Copynumber: 5.2 Consensus size: 20
855278 AATTACAAGG
855288 CAACAACAGGCAGCAGG---
1 CAACAACAGGCAGCAGGCAA
*
855305 CAACAACAGGTAGCAGG---
1 CAACAACAGGCAGCAGGCAA
855322 CAACAACAGGCAGCAGGCAA
1 CAACAACAGGCAGCAGGCAA
* *
855342 CAACATGCA-ACAGCAGGCAA
1 CAACA-ACAGGCAGCAGGCAA
* *
855362 CAACATGCA-ACAGCAGGCAA
1 CAACA-ACAGGCAGCAGGCAA
855382 CAACA
1 CAACA
855387 TGTAGAATTT
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
17 32 0.43
20 40 0.54
21 2 0.03
ACGTcount: A:0.44, C:0.29, G:0.23, T:0.03
Consensus pattern (20 bp):
CAACAACAGGCAGCAGGCAA
Found at i:855314 original size:10 final size:10
Alignment explanation
Indices: 855285--855386 Score: 69
Period size: 10 Copynumber: 11.1 Consensus size: 10
855275 ATAAATTACA
855285 AGGCAACAAC
1 AGGCAACAAC
*
855295 AGG---CAGC
1 AGGCAACAAC
855302 AGGCAACAAC
1 AGGCAACAAC
* *
855312 AGGTAGC-A-
1 AGGCAACAAC
855320 -GGCAACAAC
1 AGGCAACAAC
*
855329 AGG---CAGC
1 AGGCAACAAC
855336 AGGCAACAAC
1 AGGCAACAAC
* *
855346 ATGCAACAGC
1 AGGCAACAAC
855356 AGGCAACAAC
1 AGGCAACAAC
* *
855366 ATGCAACAGC
1 AGGCAACAAC
855376 AGGCAACAAC
1 AGGCAACAAC
855386 A
1 A
855387 TGTAGAATTT
Statistics
Matches: 67, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
7 16 0.24
8 1 0.01
9 1 0.01
10 49 0.73
ACGTcount: A:0.44, C:0.28, G:0.25, T:0.03
Consensus pattern (10 bp):
AGGCAACAAC
Found at i:855387 original size:20 final size:20
Alignment explanation
Indices: 855316--855388 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
855306 AACAACAGGT
*
855316 AGCAGGCAACAACA-G--GC
1 AGCAGGCAACAACATGCAAC
855333 AGCAGGCAACAACATGCAAC
1 AGCAGGCAACAACATGCAAC
855353 AGCAGGCAACAACATGCAAC
1 AGCAGGCAACAACATGCAAC
855373 AGCAGGCAACAACATG
1 AGCAGGCAACAACATG
855389 TAGAATTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
17 14 0.27
18 1 0.02
20 37 0.71
ACGTcount: A:0.44, C:0.29, G:0.23, T:0.04
Consensus pattern (20 bp):
AGCAGGCAACAACATGCAAC
Found at i:858280 original size:6 final size:6
Alignment explanation
Indices: 858271--858374 Score: 109
Period size: 6 Copynumber: 17.2 Consensus size: 6
858261 GGATCAGGTA
* * * **
858271 TTGGAT TTGGGT TCGGGT TTGGAT TCAGGT TTGGGT TTGGGT TTGGGT
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT
* * * *
858319 TTGGGT TTTGGT TCGGGT TTAGGT TTGGGT TTGGGT TTTGGT TTAGGGT
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TT-GGGT
*
858368 TTAGGT T
1 TTGGGT T
858375 CTAGTTTAAG
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
6 74 0.94
7 5 0.06
ACGTcount: A:0.06, C:0.03, G:0.42, T:0.49
Consensus pattern (6 bp):
TTGGGT
Found at i:862013 original size:23 final size:23
Alignment explanation
Indices: 861982--862026 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
861972 TTATGATACC
*
861982 TGACCTGGATTCTGATCTGATAT
1 TGACATGGATTCTGATCTGATAT
862005 TGACATGGATTCTGATCTGATA
1 TGACATGGATTCTGATCTGATA
862027 CATGTCCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (23 bp):
TGACATGGATTCTGATCTGATAT
Found at i:862026 original size:47 final size:48
Alignment explanation
Indices: 861966--862056 Score: 121
Period size: 47 Copynumber: 1.9 Consensus size: 48
861956 TCGAATTTGA
* * *
861966 ATTCTGTTATGATACCTGACCTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTAATCTGATACTTGACATGG
* * *
862013 ATTCTGATCTGATACATGTCCTGGATTTTAATCTGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTAATCTGATACTTGAC
862057 CTAAATTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
47 32 0.86
48 5 0.14
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTAATCTGATACTTGACATGG
Found at i:862046 original size:24 final size:24
Alignment explanation
Indices: 861966--862058 Score: 98
Period size: 24 Copynumber: 3.9 Consensus size: 24
861956 TCGAATTTGA
* * *
861966 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACATGACCTGG
* *
861990 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACATGACCTGG
*
862013 ATTCTGATCTGATACATGTCCTGG
1 ATTCTGATCTGATACATGACCTGG
* * *
862037 ATTTTAATCTGATACTTGACCT
1 ATTCTGATCTGATACATGACCT
862059 AAATTATGTT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 21 0.37
24 36 0.63
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACATGACCTGG
Found at i:866579 original size:24 final size:23
Alignment explanation
Indices: 866517--866601 Score: 98
Period size: 24 Copynumber: 3.6 Consensus size: 23
866507 TTATGATACC
*
866517 TGACCTGGATTTTGATCTGATAC
1 TGACCTGGATTTTGATCTGATAA
* *
866540 TGACATGGATTCTGATCTGATATA
1 TGACCTGGATTTTGATCTGATA-A
* *
866564 TGGCCTGGATTTTGATCTGATACT
1 TGACCTGGATTTTGATCTGATA-A
*
866588 TGACCTGAATTTTG
1 TGACCTGGATTTTG
866602 TTTTTATTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 20 0.39
24 31 0.61
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.40
Consensus pattern (23 bp):
TGACCTGGATTTTGATCTGATAA
Found at i:867719 original size:21 final size:21
Alignment explanation
Indices: 867680--867835 Score: 180
Period size: 21 Copynumber: 7.4 Consensus size: 21
867670 ATAATTAAAT
*
867680 TTAAAATAATTATATATTAATA
1 TTAATATAATTA-ATATTAATA
867702 TTAATATAATTAATATTAATA
1 TTAATATAATTAATATTAATA
867723 TTAATATAATTAATATTAATA
1 TTAATATAATTAATATTAATA
867744 TTAATATAATTAATATATAATA
1 TTAATATAATTAATAT-TAATA
867766 TTAATATAA-T-A-ATTAATA
1 TTAATATAATTAATATTAATA
867784 TTAACTAT-ATTAATA-TAATA
1 TTAA-TATAATTAATATTAATA
* **
867804 -TAGTTTATAATTTGTAATTAATA
1 TTA--ATATAATTAAT-ATTAATA
867827 TTAATATAA
1 TTAATATAA
867836 ACTATATGTT
Statistics
Matches: 118, Mismatches: 5, Indels: 22
0.81 0.03 0.15
Matches are distributed among these distances:
18 10 0.08
19 8 0.07
20 10 0.08
21 52 0.44
22 31 0.26
23 5 0.04
24 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
TTAATATAATTAATATTAATA
Found at i:867799 original size:6 final size:6
Alignment explanation
Indices: 867688--867787 Score: 103
Period size: 6 Copynumber: 17.8 Consensus size: 6
867678 ATTTAAAATA
867688 ATTATAT ATTAAT ATTAAT A-T-A- ATTAAT ATTAAT ATTAAT A-T-A-
1 ATTA-AT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
867731 ATTAAT ATTAAT ATTAAT A-T-A- ATTAAT ATATAAT ATTAAT A-TAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT-TAAT ATTAAT ATTAAT
867776 AATTAAT ATTAA
1 -ATTAAT ATTAA
867788 CTATATTAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 25
0.76 0.00 0.24
Matches are distributed among these distances:
3 3 0.04
4 6 0.07
5 10 0.12
6 48 0.59
7 14 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTAAT
Found at i:867813 original size:61 final size:64
Alignment explanation
Indices: 867680--867835 Score: 184
Period size: 61 Copynumber: 2.5 Consensus size: 64
867670 ATAATTAAAT
*
867680 TTAAAATAATTATATATTAATATTAATATAATTAATATTAATATTAATATAATTAATATTAATA
1 TTAATATAATTATATATTAATATTAATATAATTAATATTAATATTAATATAATTAATATTAATA
867744 TTAATATAATTA-ATATATAATATTAATATAA-T-A-ATTAATATTAACTAT-ATTAATA-TAAT
1 TTAATATAATTATATAT-TAATATTAATATAATTAATATTAATATTAA-TATAATTAATATTAAT
867803 A
64 A
* *
867804 -TAGTTTATAATT-TGTAATTAATATTAATATAA
1 TTA--ATATAATTATAT-ATTAATATTAATATAA
867836 ACTATATGTT
Statistics
Matches: 83, Mismatches: 3, Indels: 15
0.82 0.03 0.15
Matches are distributed among these distances:
59 2 0.02
60 5 0.06
61 40 0.48
62 6 0.07
63 5 0.06
64 25 0.30
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (64 bp):
TTAATATAATTATATATTAATATTAATATAATTAATATTAATATTAATATAATTAATATTAATA
Found at i:867868 original size:14 final size:14
Alignment explanation
Indices: 867851--867912 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
867841 ATGTTATAAA
867851 TTATATATTATAGT
1 TTATATATTATAGT
* *
867865 TTATAAACTATAGT
1 TTATATATTATAGT
*
867879 TAATATAATTAATA-T
1 TTATAT-ATT-ATAGT
*
867894 TAATATATTATAGT
1 TTATATATTATAGT
867908 TTATA
1 TTATA
867913 AACTATATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.08
14 24 0.62
15 9 0.23
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (14 bp):
TTATATATTATAGT
Found at i:867919 original size:14 final size:14
Alignment explanation
Indices: 867859--867919 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
867849 AATTATATAT
*
867859 TATAGTTTATAAAC
1 TATAGTTAATAAAC
*
867873 TATAGTTAATATAAT
1 TATAGTTAATA-AAC
* *
867888 TAATA-TTAATATAT
1 T-ATAGTTAATAAAC
*
867902 TATAGTTTATAAAC
1 TATAGTTAATAAAC
867916 TATA
1 TATA
867920 TACTATATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (14 bp):
TATAGTTAATAAAC
Found at i:867961 original size:65 final size:64
Alignment explanation
Indices: 867844--867965 Score: 165
Period size: 65 Copynumber: 1.9 Consensus size: 64
867834 AAACTATATG
* * * * *
867844 TTATAAATTATATATTATAGTTTATAAACTATAGTTAATATAATTAATATTAATATATTATAGT
1 TTATAAACTATATACTATAGTTTATAAACTATAGTTAAGATAAATAACATTAATATATTATAGT
*
867908 TTATAAACTATATACTATA-TTAATATAAATTATAGTTAAGATAAATAACATTAATATA
1 TTATAAACTATATACTATAGTT--TATAAACTATAGTTAAGATAAATAACATTAATATA
867966 AACTATATAG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 2 0.04
64 17 0.34
65 31 0.62
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.44
Consensus pattern (64 bp):
TTATAAACTATATACTATAGTTTATAAACTATAGTTAAGATAAATAACATTAATATATTATAGT
Found at i:867980 original size:22 final size:22
Alignment explanation
Indices: 867955--868057 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
867945 AAGATAAATA
867955 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
867977 ACATTAATATAAACTAT-T-GT
1 ACATTAATATAAACTATATAGT
** * * *
867997 TTATAAATTATATACTATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
868019 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
868041 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
868058 TGATTATAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
20 6 0.09
21 26 0.39
22 31 0.47
23 3 0.05
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.38
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:868013 original size:21 final size:21
Alignment explanation
Indices: 867984--868036 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
867974 AGTACATTAA
* * *
867984 TATAAACTATTGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
868005 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
868026 TATAAACTATA
1 TATAAACTATA
868037 TAGTACACTA
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:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:868094 original size:2 final size:2
Alignment explanation
Indices: 868079--868167 Score: 78
Period size: 2 Copynumber: 45.5 Consensus size: 2
868069 TATAGGTTAC
* * * * *
868079 AT AT AT AGT TT AT AT A- AC AT AT AA AT AG AT -T AT AT AT AT AC
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
868120 AT AT ACT AT AT GT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
868162 AT -T AT A
1 AT AT AT A
868168 CATAGTTTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
1 4 0.06
2 64 0.90
3 3 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:868276 original size:7 final size:7
Alignment explanation
Indices: 868264--868319 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
868254 TATGTATAGT
868264 GTTTAGG
1 GTTTAGG
868271 GTTTAGG
1 GTTTAGG
* *
868278 ATTTATG
1 GTTTAGG
*
868285 ATTCTA-G
1 GTT-TAGG
*
868292 GTTTATG
1 GTTTAGG
*
868299 ATTTAGG
1 GTTTAGG
868306 GTTTAGG
1 GTTTAGG
868313 GTTTAGG
1 GTTTAGG
868320 ATTTTTATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 2 0.05
7 37 0.90
8 2 0.05
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:868295 original size:21 final size:21
Alignment explanation
Indices: 868265--868323 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
868255 ATGTATAGTG
*
868265 TTTAGGGTTTAGGATTTATGA
1 TTTAGGGTTTAGGATTTAGGA
* *
868286 TTCTA-GGTTTATGATTTAGGG
1 TT-TAGGGTTTAGGATTTAGGA
868307 TTTAGGGTTTAGGATTT
1 TTTAGGGTTTAGGATTT
868324 TTATAAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTAGGATTTAGGA
Found at i:868317 original size:14 final size:14
Alignment explanation
Indices: 868265--868323 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
868255 ATGTATAGTG
868265 TTTAGGGTTTAGGA
1 TTTAGGGTTTAGGA
* *
868279 TTTATGATTCTAGG-
1 TTTAGGGTT-TAGGA
* * *
868293 TTTATGATTTAGGG
1 TTTAGGGTTTAGGA
868307 TTTAGGGTTTAGGA
1 TTTAGGGTTTAGGA
868321 TTT
1 TTT
868324 TTATAAACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 4 0.11
14 30 0.79
15 4 0.11
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTAGGA
Found at i:868426 original size:17 final size:18
Alignment explanation
Indices: 868398--868432 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
868388 TAATTTACTT
868398 TATATGGTTATATATATA
1 TATATGGTTATATATATA
868416 TATAT-GTTATATATATA
1 TATATGGTTATATATATA
868433 GTGTATAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
TATATGGTTATATATATA
Found at i:868448 original size:20 final size:20
Alignment explanation
Indices: 868425--868464 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
868415 ATATATGTTA
* *
868425 TATATATAGTGTATAGATAC
1 TATACATAGTGTATACATAC
*
868445 TATACATAGTTTATACATAC
1 TATACATAGTGTATACATAC
868465 ATGTACTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
TATACATAGTGTATACATAC
Found at i:868490 original size:35 final size:36
Alignment explanation
Indices: 868450--868523 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
868440 GATACTATAC
*
868450 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
868485 ATAGTTTACATGTATACATATACTATAGGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
868522 AT
1 AT
868524 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:868586 original size:16 final size:16
Alignment explanation
Indices: 868565--868595 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
868555 TACATATATA
868565 ATTTATATAAACTATT
1 ATTTATATAAACTATT
868581 ATTTATATAAACTAT
1 ATTTATATAAACTAT
868596 ATATGAATTA
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:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTATATAAACTATT
Found at i:868644 original size:7 final size:7
Alignment explanation
Indices: 868634--868672 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
868624 AGTTTATAAA
868634 GTTTAGG
1 GTTTAGG
868641 GTTTAGG
1 GTTTAGG
*
868648 GTTTACG
1 GTTTAGG
*
868655 TTTTAGG
1 GTTTAGG
*
868662 GTATAGG
1 GTTTAGG
868669 GTTT
1 GTTT
868673 TTATAAACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.03, G:0.36, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:870836 original size:2 final size:2
Alignment explanation
Indices: 870831--870865 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
870821 TTTTTTTCTT
870831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
870866 GTTTGTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:876641 original size:29 final size:28
Alignment explanation
Indices: 876583--876734 Score: 135
Period size: 29 Copynumber: 5.2 Consensus size: 28
876573 ACTTTCATTT
* * * *
876583 TAATTTGTAAAAAGATTTGTCTTTTTATTG
1 TAATTTATAAAAAGATTTATC--CTTATTA
* * *
876613 TAAATTATAAAAATATTTATCCTTGATTG
1 TAATTTATAAAAAGATTTATCCTT-ATTA
* *
876642 TAATTTATAAAATA-ATTTTTCTCCTATTA
1 TAATTTATAAAA-AGATTTATC-CTTATTA
876671 TAATTTATAAAAAGATTTATCCTATATTA
1 TAATTTATAAAAAGATTTATCCT-TATTA
* *
876700 TAATTTACAAAAAGATTTATCCTATGTTA
1 TAATTTATAAAAAGATTTATCCT-TATTA
876729 TAATTT
1 TAATTT
876735 GTTGTCCTAC
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
28 4 0.04
29 80 0.77
30 20 0.19
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (28 bp):
TAATTTATAAAAAGATTTATCCTTATTA
Found at i:877209 original size:18 final size:17
Alignment explanation
Indices: 877182--877217 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
877172 GTTTATACAT
877182 ATATAATTTATAATATAA
1 ATATAATTTAT-ATATAA
*
877200 ATATAGTTTATATATAA
1 ATATAATTTATATATAA
877217 A
1 A
877218 CTTATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATAATTTATATATAA
Found at i:880810 original size:24 final size:24
Alignment explanation
Indices: 880783--880834 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
880773 AACATCAAAT
*
880783 ACAATAA-AATTATATTATTTATTA
1 ACAATAATAATAATATTATTT-TTA
*
880807 ACAA-AATAGTAATATTATTTTTA
1 ACAATAATAATAATATTATTTTTA
880830 A-AATA
1 ACAATA
880835 TTAGAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 2 0.08
23 7 0.29
24 15 0.62
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
ACAATAATAATAATATTATTTTTA
Found at i:880862 original size:14 final size:14
Alignment explanation
Indices: 880843--880887 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
880833 TATTAGAATA
*
880843 ATTTATTTAATATT
1 ATTTATTAAATATT
880857 ATTTATGTAAATATT
1 ATTTAT-TAAATATT
880872 A-TTATTAAAATATT
1 ATTTATT-AAATATT
880886 AT
1 AT
880888 ATTTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:880961 original size:16 final size:16
Alignment explanation
Indices: 880920--880980 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 16
880910 AATTATGATT
880920 ATTATATTTTATTA-AA
1 ATTATA-TTTATTATAA
* *
880936 A-TAAAATTATTATAA
1 ATTATATTTATTATAA
880951 ATTATATTTATTAT--
1 ATTATATTTATTATAA
880965 -TTATTATTTATTATAA
1 ATTA-TATTTATTATAA
880981 TAAGAATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.08
14 16 0.44
15 6 0.17
16 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATATTTATTATAA
Found at i:881340 original size:14 final size:15
Alignment explanation
Indices: 881321--881351 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
881311 TATGCCCAAC
881321 AATAACAAAAC-GGT
1 AATAACAAAACAGGT
881335 AATAACAAAACAGGT
1 AATAACAAAACAGGT
881350 AA
1 AA
881352 AAATAGACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAACAAAACAGGT
Found at i:881669 original size:21 final size:20
Alignment explanation
Indices: 881583--881740 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
881573 AAATGACCAA
**
881583 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
881602 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
881622 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
881642 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
881663 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
881684 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
881704 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
881725 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
881741 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 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:881769 original size:20 final size:20
Alignment explanation
Indices: 881708--881936 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
881698 GATTTTCAAG
* ** *
881708 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
881728 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
881748 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
881768 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
881788 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
881808 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
881828 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
881848 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
881868 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
881888 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
881908 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
881928 AATCACAAC
1 AATCGCAAC
881937 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:882668 original size:24 final size:24
Alignment explanation
Indices: 882629--882675 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
882619 AAATTTGGTC
882629 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
882653 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
882676 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:882867 original size:12 final size:12
Alignment explanation
Indices: 882850--882874 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
882840 ATATAATCCT
882850 GAAGAAGAAAAA
1 GAAGAAGAAAAA
882862 GAAGAAGAAAAA
1 GAAGAAGAAAAA
882874 G
1 G
882875 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:885199 original size:33 final size:34
Alignment explanation
Indices: 885148--885394 Score: 176
Period size: 33 Copynumber: 7.2 Consensus size: 34
885138 CGGAAATTAC
* *
885148 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
885181 AATCCCAAC-ATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
885214 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATAAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
885252 AATCGCAACGA-GAGAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* * *
885286 AATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
* *
885324 AAT-GCGA-AATGAAAATCGCAA--CGAGAATCG-C
1 AATCGCAACAATGAAAATCGCAATGCGA-AAT-GAA
*
885355 AAT-GCGGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACAATGAAAATCGCAATGCGAAATGAA
885388 AATCGCA
1 AATCGCA
885395 TTGCGATTCT
Statistics
Matches: 178, Mismatches: 16, Indels: 40
0.76 0.07 0.17
Matches are distributed among these distances:
31 14 0.08
32 22 0.12
33 64 0.36
34 21 0.12
35 1 0.01
36 2 0.01
37 5 0.03
38 47 0.26
39 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:885212 original size:19 final size:19
Alignment explanation
Indices: 885162--885400 Score: 254
Period size: 19 Copynumber: 13.7 Consensus size: 19
885152 GCAACGAGAG
885162 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
885181 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
885195 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
885214 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
885233 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
*
885252 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
885266 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
885286 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
885304 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
885318 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
885337 AATCGCAA--CG--A-G--
1 AATCGCAATGCGAAATGAA
885349 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
885369 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
885388 AATCGCATTGCGA
1 AATCGCAATGCGA
885401 TTCTCTCGTT
Statistics
Matches: 186, Mismatches: 9, Indels: 50
0.76 0.04 0.20
Matches are distributed among these distances:
12 8 0.04
13 1 0.01
14 32 0.17
15 3 0.02
16 6 0.03
17 7 0.04
18 11 0.06
19 94 0.51
20 24 0.13
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:885221 original size:52 final size:51
Alignment explanation
Indices: 885162--885394 Score: 223
Period size: 52 Copynumber: 4.5 Consensus size: 51
885152 GCAACGAGAG
*
885162 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAAT-CGAAATGAA
* *
885214 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATAAAAATCGCAA-CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATGAAAATCGCAATCGAAATGAA
* * * *
885266 AATCGCAATGCGGAAATGAAAATCGC-A-ATGCGAAAT-GAAATCGCAACGAGA
1 AATCGCAATGC-GAAATGAAAATCGCAACATG-AAAATCGCAATCGAAATGA-A
*
885317 GAATCGCAATGCGAAATGAAAATCGCAAC--GAGAATCGCAATGCGGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAAT-C-GAAATGAA
885369 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
885395 TTGCGATTCT
Statistics
Matches: 151, Mismatches: 12, Indels: 37
0.75 0.06 0.19
Matches are distributed among these distances:
46 5 0.03
47 6 0.04
49 1 0.01
50 5 0.03
51 45 0.30
52 54 0.36
53 20 0.13
54 1 0.01
55 2 0.01
57 12 0.08
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (51 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATCGAAATGAA
Found at i:885275 original size:104 final size:104
Alignment explanation
Indices: 885148--885344 Score: 285
Period size: 104 Copynumber: 1.9 Consensus size: 104
885138 CGGAAATTAC
* *
885148 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAACATG-AAAATCGCAATGCGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCC-A-ATGCAAAAT-GAAAT-CGAAAC
885211 GA-A-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATAAA
62 GAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATAAA
* * *
885252 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAGA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAATGCAAAATGAAATCGAAACGAGA
885317 GAATCGCAATGCGAAATGAAAATCGCAA
66 GAATCGCAATGCGAAATGAAAATCGCAA
885345 CGAGAATCGC
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
102 6 0.07
103 8 0.10
104 57 0.68
105 13 0.15
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (104 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAATGCAAAATGAAATCGAAACGAGA
GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATAAA
Found at i:885353 original size:31 final size:32
Alignment explanation
Indices: 885286--885376 Score: 150
Period size: 32 Copynumber: 2.8 Consensus size: 32
885276 CGGAAATGAA
885286 AATCGCAATGCGAAATG-AAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAAC-AGAG
885318 AATCGCAATGCGAAATGAAAATCGCAAC-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACAGAG
885349 AATCGCAATGCGGAAATGAAAATCGCAA
1 AATCGCAATGC-GAAATGAAAATCGCAA
885377 TGCGAAATGA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
31 14 0.25
32 33 0.58
33 10 0.18
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (32 bp):
AATCGCAATGCGAAATGAAAATCGCAACAGAG
Found at i:885458 original size:54 final size:52
Alignment explanation
Indices: 885390--885507 Score: 218
Period size: 54 Copynumber: 2.2 Consensus size: 52
885380 GAAATGAAAA
885390 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
885443 TCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
885496 TCGCATTGCGAT
1 TCGCATTGCGAT
885508 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
52 11 0.17
53 20 0.31
54 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:885515 original size:19 final size:19
Alignment explanation
Indices: 885409--885507 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
885399 GATTCTCTCG
885409 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
885429 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
885449 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
885463 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
885482 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
885501 TTGCGAT
1 TTGCGAT
885508 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 5 0.07
17 6 0.08
18 3 0.04
19 26 0.36
20 26 0.36
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:885633 original size:14 final size:14
Alignment explanation
Indices: 885614--885650 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
885604 CATCAATTAC
885614 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
885628 ACAAATCATCTTTT
1 ACAAATCAACTTTT
885642 ACAAATCAA
1 ACAAATCAA
885651 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:887617 original size:19 final size:19
Alignment explanation
Indices: 887575--887747 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
887565 TAGTTTACTT
* *
887575 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
887595 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
887614 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
887633 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
887652 TCGCAACGTGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
887671 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
887685 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
887704 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
887718 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
887737 TCGCAATGCGA
1 TCGCAACGCGA
887748 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.06
17 6 0.05
18 1 0.01
19 81 0.64
20 12 0.10
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:887688 original size:14 final size:14
Alignment explanation
Indices: 887669--887725 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
887659 GTGAAATGAA
*
887669 AATCGCAACGACAG
1 AATCGCAACGAAAG
887683 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
887700 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
887716 AATCGCAACG
1 AATCGCAACG
887726 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:887698 original size:33 final size:33
Alignment explanation
Indices: 887650--887742 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
887640 GCGAAACCAA
*
887650 AATCGCAACGTGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
887683 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
887716 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
887743 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:887739 original size:52 final size:52
Alignment explanation
Indices: 887609--887747 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
887599 AACGCGAAAT
* * * *
887609 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGT
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
887661 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
887713 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
887748 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:887765 original size:19 final size:18
Alignment explanation
Indices: 887743--887834 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
887733 AAAATCGCAA
887743 TGCGATTTTGGTTTCACGT
1 TGCGATTTTGGTTTC-CGT
887762 TGCGATTTT-G--T-CGT
1 TGCGATTTTGGTTTCCGT
887776 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTC-CGT
*
887795 TGCGATTCT-G--T-CGT
1 TGCGATTTTGGTTTCCGT
**
887809 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTC-CGT
887828 TGCGATT
1 TGCGATT
887835 CTCTCTTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.09, C:0.17, G:0.27, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGGTTTCCGT
Found at i:887778 original size:14 final size:14
Alignment explanation
Indices: 887759--887817 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
887749 TTTGGTTTCA
887759 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
887773 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
887790 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
887806 CGTTGCGATTTT
1 CGTTGCGATTTT
887818 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:887785 original size:33 final size:33
Alignment explanation
Indices: 887743--887866 Score: 167
Period size: 33 Copynumber: 3.7 Consensus size: 33
887733 AAAATCGCAA
* *
887743 TGCGATTTTGGTTTCACGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
887776 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** * *
887809 TGCGATTTTCATTTCGCGTTGCGATTCTCTCTT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
887842 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
887867 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 69 0.85
34 12 0.15
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:888123 original size:93 final size:93
Alignment explanation
Indices: 887964--888279 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
887954 TCAGGGTATT
887964 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
888029 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
888057 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
888122 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
888150 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
888215 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
888243 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
888280 AAGCAATCTA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:889851 original size:21 final size:21
Alignment explanation
Indices: 889797--889861 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
889787 TCTTTTGGTT
*
889797 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAAAGAGA
***
889818 G-AATGACTGTCGCAAAGAGA
1 GAAATGAAAATCGCAAAGAGA
*
889838 GAAATGAAAATCGCAATGAGA
1 GAAATGAAAATCGCAAAGAGA
889859 GAA
1 GAA
889862 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.49, C:0.12, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAATGAAAATCGCAAAGAGA
Found at i:889884 original size:19 final size:19
Alignment explanation
Indices: 889860--889910 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
889850 GCAATGAGAG
889860 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
889879 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
889898 AATCGCAATGCGA
1 AATCGCAACGCGA
889911 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:889941 original size:14 final size:14
Alignment explanation
Indices: 889922--889978 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
889912 TTTGGTTTCG
889922 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
889936 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
889955 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
889969 CGTTGCGATT
1 CGTTGCGATT
889979 TTCATTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:889954 original size:33 final size:33
Alignment explanation
Indices: 889906--889985 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
889896 AAAATCGCAA
** *
889906 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
889939 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
889972 TGCGATTTTCATTT
1 TGCGATTTTCATTT
889986 TTCTCGTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
Found at i:889991 original size:21 final size:21
Alignment explanation
Indices: 889966--890037 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
889956 GTTACGATTC
889966 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
889987 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
890008 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
890029 TCTCGTTGC
1 TCTCGTTGC
890038 AACTCTTCTG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.14
21 30 0.71
22 6 0.14
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.49
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:890164 original size:33 final size:33
Alignment explanation
Indices: 890119--890189 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
890109 AATACTAACT
890119 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* * *
890152 TGAAAATTGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
890185 TGAAA
1 TGAAA
890190 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.15, G:0.24, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:890593 original size:20 final size:20
Alignment explanation
Indices: 890568--890760 Score: 255
Period size: 20 Copynumber: 9.6 Consensus size: 20
890558 CTTTAAAAAT
890568 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
890588 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
890608 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
890629 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
890649 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
890669 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
890689 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
890709 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
890729 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
890749 CGCGTTGCGATT
1 CGCGTTGCGATT
890761 CTGGAAAATC
Statistics
Matches: 154, Mismatches: 14, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
20 136 0.88
21 18 0.12
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:891090 original size:24 final size:25
Alignment explanation
Indices: 891063--891131 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 25
891053 AACATCAAAT
891063 ACAATAA-AATAATATTATTTATTA
1 ACAATAAGAATAATATTATTTATTA
* *
891087 ACAA-AATAATAATAATATTT-TTA
1 ACAATAAGAATAATATTATTTATTA
891110 A-AATATTAGAATAAT-TTATTTA
1 ACAATA--AGAATAATATTATTTA
891132 ATATTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 2 0.05
23 7 0.19
24 21 0.57
25 7 0.19
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (25 bp):
ACAATAAGAATAATATTATTTATTA
Found at i:891181 original size:28 final size:28
Alignment explanation
Indices: 891149--891235 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
891139 TTATGTTAAC
891149 ATTATTATTAAAATATTAT-ATCTATAAT
1 ATTATTATTAAAATATTATGAT-TATAAT
* * * * *
891177 TTTATAAATAAAAAATTATGATTATTAT
1 ATTATTATTAAAATATTATGATTATAAT
** *
891205 ATT-TTATTAAAATAAAATTATTATAA-
1 ATTATTATTAAAATATTATGATTATAAT
891231 ATTAT
1 ATTAT
891236 ATTTATTATT
Statistics
Matches: 44, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
26 3 0.07
27 17 0.39
28 22 0.50
29 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
ATTATTATTAAAATATTATGATTATAAT
Found at i:891238 original size:31 final size:31
Alignment explanation
Indices: 891175--891243 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
891165 TATATCTATA
*
891175 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
891205 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
891236 A-TTTATTA
1 ATTTTATTA
891244 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:891493 original size:20 final size:20
Alignment explanation
Indices: 891464--891502 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
891454 GGTAAAGCGC
891464 TATCGATTTTGTTATTTTTT
1 TATCGATTTTGTTATTTTTT
*
891484 TATCGGTTTTGTTATTTTT
1 TATCGATTTTGTTATTTTT
891503 GGGAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.05, G:0.13, T:0.69
Consensus pattern (20 bp):
TATCGATTTTGTTATTTTTT
Found at i:891946 original size:14 final size:14
Alignment explanation
Indices: 891921--892023 Score: 50
Period size: 14 Copynumber: 7.2 Consensus size: 14
891911 TAAATTATTT
891921 AATATTATTTATGT-A
1 AATATTA-TTAT-TAA
891936 AATATTATTATTAA
1 AATATTATTATTAA
*
891950 AATATTA-TATCTAT
1 AATATTATTAT-TAA
* * *
891964 AATTTTATAAATAAA
1 AATATTAT-TATTAA
* * *
891979 AAAATTATGATTAT
1 AATATTATTATTAA
*
891993 TATATT-TTATTAA
1 AATATTATTATTAA
**
892006 AATAAAATTATTATA
1 AATATTATTATTA-A
892021 AAT
1 AAT
892024 TATATTTATT
Statistics
Matches: 65, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
13 12 0.18
14 33 0.51
15 18 0.28
16 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:891980 original size:29 final size:32
Alignment explanation
Indices: 891948--892034 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 32
891938 TATTATTATT
891948 AAAATATTATATCTA-TA-ATTTTA-T-AAATA
1 AAAATATTATAT-TATTATATTTTATTAAAATA
*
891977 AAAAAATTATGATTATTATATTTTATTAAAATA
1 AAAATATTAT-ATTATTATATTTTATTAAAATA
* *
892010 AAATTATTATA-AATTATA-TTTATTA
1 AAAATATTATATTATTATATTTTATTA
892035 TTTATTATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
29 11 0.22
30 11 0.22
31 12 0.24
32 2 0.04
33 13 0.27
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (32 bp):
AAAATATTATATTATTATATTTTATTAAAATA
Found at i:892000 original size:31 final size:31
Alignment explanation
Indices: 891965--892030 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
891955 TATATCTATA
*
891965 ATTTTATAAATAAAAAAATTATGAT-TATTAT
1 ATTTTATAAA-AAAAAAATTATGATAAATTAT
* * *
891996 ATTTTATTAAAATAAAATTATTATAAATTAT
1 ATTTTATAAAAAAAAAATTATGATAAATTAT
892027 ATTT
1 ATTT
892031 ATTATTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
ATTTTATAAAAAAAAAATTATGATAAATTAT
Found at i:892015 original size:30 final size:32
Alignment explanation
Indices: 891965--892034 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
891955 TATATCTATA
* *
891965 ATTTTATAAATAAAAAAATTATGAT-TATTAT
1 ATTTTATTAATAAAAAAATTATGATAAATTAT
* *
891996 ATTTTATTAA-AATAAAATTATTATAAATTAT
1 ATTTTATTAATAAAAAAATTATGATAAATTAT
892027 A-TTTATTA
1 ATTTTATTA
892035 TTTATTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
ATTTTATTAATAAAAAAATTATGATAAATTAT
Found at i:892591 original size:196 final size:197
Alignment explanation
Indices: 892135--892621 Score: 606
Period size: 196 Copynumber: 2.5 Consensus size: 197
892125 CACATATGTT
* *
892135 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTAATCGCTATAAATATACCGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACT-GGTATAAATATACCGG
*
892200 TTTTATGAGAGAATAGATCAACATAATGTATCGAAACAAATTTAAAAAGTGTCGATACATTTTGT
65 TTTTATGAGAAAATAGATCAACATAATGTATC-AAACAAATTTAAAAAGTGTCGATACATTTTGT
892265 CCAGAATGAATGCCAAACGAGGTGCACGCATAAAACGTCGATACATTTATTAAAAGTATCGATCC
129 CCAGAATGAATGCCAAACGAGGTGCACGCATAAAACGTCGATACATTTA-TAAAAGTATCGATCC
892330 CAAAA
193 CAAAA
** * * * *
892335 ACATCGAAACCGATAATTGCAATGTAATAGGTAAATTTACAATATACCCGGTAGAAATATACAGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTA-CTGGTATAAATATACCGG
* * * *** *
892400 TTTTATGAGAAAATATG-TCTACATAATGTAT-TAAC-ATTTTAAGTTTGTGTCGATAC-TTTTT
65 TTTTATGAGAAAATA-GATCAACATAATGTATCAAACAAATTTAA-AAAGTGTCGATACATTTTG
* * ** *
892461 TCCATAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA-AAATTGTATCGATC
128 TCCAGAATGAATGCCAAACGAGGTGCACGCATAAAACGTCGATACATTTATAAA-AGTATCGATC
892525 CCAAAA
192 CCAAAA
* * *
892531 ATATCGAAACCAATAATTATAATGTAATAGGTAAATTTGCAATGTTACTGGTATAAATATACCGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG-TACTGGTATAAATATACCGG
** * * *
892596 TTTGGTTAGAAAATAGGTCAATATAA
65 TTTTATGAGAAAATAGATCAACATAA
892622 GCGCTACCTA
Statistics
Matches: 246, Mismatches: 35, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
195 4 0.02
196 87 0.35
197 58 0.24
198 13 0.05
200 83 0.34
201 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (197 bp):
ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACTGGTATAAATATACCGGT
TTTATGAGAAAATAGATCAACATAATGTATCAAACAAATTTAAAAAGTGTCGATACATTTTGTCC
AGAATGAATGCCAAACGAGGTGCACGCATAAAACGTCGATACATTTATAAAAGTATCGATCCCAA
AA
Found at i:892749 original size:23 final size:23
Alignment explanation
Indices: 892699--892743 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
892689 TACCTATTTT
**
892699 ATTATATAAGCGCTACATGTTAC
1 ATTATATAAGCGCTACATAATAC
*
892722 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACATAATA
892744 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACATAATAC
Found at i:892802 original size:23 final size:23
Alignment explanation
Indices: 892776--892824 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
892766 TCCGGTTAAA
**
892776 TACCTATTTTATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
892799 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
892822 TAC
1 TAC
892825 ATGTTATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGC
Found at i:892923 original size:23 final size:23
Alignment explanation
Indices: 892873--892917 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
892863 TGCCTATTTT
*
892873 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
892896 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
892918 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:892951 original size:87 final size:87
Alignment explanation
Indices: 892616--892950 Score: 600
Period size: 87 Copynumber: 3.9 Consensus size: 87
892606 AAATAGGTCA
892616 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
892681 -CGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
* *
892702 ATATAAGCGCTACATGTTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
892767 CCGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
* **
892789 ATATAAGCGCTACCTATTACATTATATAAGCGCTACATGTTATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
892854 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
892876 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
892941 TCGGTTAAAT
66 CCGGTTAAAT
892951 GTTATAATAT
Statistics
Matches: 236, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
86 63 0.27
87 173 0.73
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:892993 original size:16 final size:17
Alignment explanation
Indices: 892974--893009 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
892964 CGGTATAAAT
892974 TTTAACCGGTCAC-TTG
1 TTTAACCGGTCACGTTG
892990 TTTAACCGGTCACGTTG
1 TTTAACCGGTCACGTTG
893007 TTT
1 TTT
893010 TTTAACCGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (17 bp):
TTTAACCGGTCACGTTG
Found at i:894230 original size:2 final size:2
Alignment explanation
Indices: 894223--894249 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
894213 TTTAATTATG
894223 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
894250 TATTTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:895024 original size:12 final size:13
Alignment explanation
Indices: 895002--895030 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
894992 GAATCGAGTT
895002 TTTTAAATTTTAA
1 TTTTAAATTTTAA
895015 TTTT-AATTTTAA
1 TTTTAAATTTTAA
895027 TTTT
1 TTTT
895031 CTCTATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:897649 original size:95 final size:95
Alignment explanation
Indices: 897523--897700 Score: 270
Period size: 95 Copynumber: 1.9 Consensus size: 95
897513 ATATATATAC
* * * *
897523 AATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAG-CTTTATGGATAATATTC
1 AATAAAGCTTGAGATGTCCCTATAGAGCAATTGGTTAAAAG-CCCAGACTTTATGGATAAGATTC
*
897587 AGCTACCCTGATAAAGGTGATTACACAATAG
65 AGCTAACCTGATAAAGGTGATTACACAATAG
*
897618 AATAAAGCTTGAGATGTCCCTATA-AGACAATTGGTTAAAAGCCCTGACTTTATGGATAAGATTC
1 AATAAAGCTTGAGATGTCCCTATAGAG-CAATTGGTTAAAAGCCCAGACTTTATGGATAAGATTC
897682 AGCTAACCTGATAAAGGTG
65 AGCTAACCTGATAAAGGTG
897701 TTTGCATATT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 6 0.08
95 69 0.92
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (95 bp):
AATAAAGCTTGAGATGTCCCTATAGAGCAATTGGTTAAAAGCCCAGACTTTATGGATAAGATTCA
GCTAACCTGATAAAGGTGATTACACAATAG
Found at i:899169 original size:240 final size:238
Alignment explanation
Indices: 898735--899379 Score: 891
Period size: 240 Copynumber: 2.7 Consensus size: 238
898725 ACAAAACAAC
* * *
898735 TTTCACAGTTTCATTCAGAGCCAATTTCAACTTCATGGCAAAGGATATTGGACTCGAAACAATAC
1 TTTCCCAGTTTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATAC
** * * * *
898800 AAGCTTGGATTTCAACTTCACGATTAAGGATATTCAAGTCAAGGCTCAACTTCACAATGAAGGGG
66 AAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAAAGAG
*
898865 TCATCCACGATTTCAACTTCACGACGAAGGATATCATGCCAACTCTAGATTGGATTTAAACTTCA
131 CCATCCACGATTTCAACTTCACGACGAAGGATATCATGCCAACTCTAGATTGGATTTAAACTTCA
*
898930 CAAAAAAGGATATCCAAATCAAATATCAACTTCATGGCCAAGGGG
196 CAAAAAAGG--ATCCAAATCAAAGATCAACTTCATGGCCAAGGGG
898975 TTTCCCAGTTTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATAC
1 TTTCCCAGTTTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATAC
*
899040 AAGCTTGGATTTCAACTTCACGACGAAAGATATTCAAGTTAAGGCTCAACTTCACAACGAAAGAG
66 AAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAAAGAG
* * *
899105 CCATCCACGATTTCAACTTCATGACGAAGGATATTATGCCAACTCTAGATTGGATTTCAACTTCA
131 CCATCCACGATTTCAACTTCACGACGAAGGATATCATGCCAACTCTAGATTGGATTTAAACTTCA
* * * *
899170 CGAAAAAGGATCCAATTCAAAGCTCAACTTCATGGCGAAGGGG
196 CAAAAAAGGATCCAAATCAAAGATCAACTTCATGGCCAAGGGG
* **
899213 CTTCCCAGTTTCATTCAGAGCCAATTTCAACTTCACGAAGAAGGATATTGGACTCGAAGCAACAT
1 TTTCCCAGTTTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCG-A--AACA-
* * * * * *
899278 TCTTCTTTAGATTGGATTTTAACTTCACGACGAAGGATATCCAA-TTCAAGGCTCAACTTCACAA
62 -ATAC--AAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTT-AAGGCTCAACTTCACAA
* *
899342 CGAATAGA-CCATCCA-TAGTTTCAACTTCACGATGAAGG
123 CGAA-AGAGCCATCCACGA-TTTCAACTTCACGACGAAGG
899380 GAATCGTGCC
Statistics
Matches: 363, Mismatches: 32, Indels: 15
0.89 0.08 0.04
Matches are distributed among these distances:
238 83 0.23
239 1 0.00
240 189 0.52
241 4 0.01
243 2 0.01
244 3 0.01
245 78 0.21
246 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (238 bp):
TTTCCCAGTTTCATTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAATAC
AAGCTTGGATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAAAGAG
CCATCCACGATTTCAACTTCACGACGAAGGATATCATGCCAACTCTAGATTGGATTTAAACTTCA
CAAAAAAGGATCCAAATCAAAGATCAACTTCATGGCCAAGGGG
Found at i:899460 original size:124 final size:122
Alignment explanation
Indices: 899270--899627 Score: 486
Period size: 124 Copynumber: 2.9 Consensus size: 122
899260 TTGGACTCGA
* * *
899270 AGCAACATTCT-TCTTTAGATTGGATTTTAACTTCACGACGAAGGATATCCAATTCAAGGCTCAA
1 AGCAACATT-TATCTTCAAATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAA
* * *
899334 CTTCACAACGAATAGACCATCCATAGTTTCAACTTCACGATGAAGGGAATCGTGCCCACT
65 CTTCACAACGAAT-GACCATCCA-AGTTTCAACTTCACGACGAAGGGAATCATGCCCACC
* *
899394 AGCAACATTTATCTTCATATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTTAAC
1 AGCAACATTTATCTTCAAATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAAC
* * * *
899459 TTCACAACGAAGGGGCCATCCACGGTTTCAACTTCATGACGAAGGGAATCATGCCCACC
66 TTCACAACGAA-TGACCATCCA-AGTTTCAACTTCACGACGAAGGGAATCATGCCCACC
*
899518 AGCAACATTCATCTTCAAATTGGATTTCAACTTCACGACGAAGGATATCCAATTTC-AGGCTCAA
1 AGCAACATTTATCTTCAAATTGGATTTCAACTTCACGACGAAGGATATCCAA-TTCAAGGCTCAA
* * *
899582 CTTCACAATGAATGAGCCCTCCACGATTTCAACTTCACGACGAAGG
65 CTTCACAACGAATGA-CCATCCAAG-TTTCAACTTCACGACGAAGG
899628 ATATTCAATT
Statistics
Matches: 208, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
123 3 0.01
124 202 0.97
125 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (122 bp):
AGCAACATTTATCTTCAAATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAAC
TTCACAACGAATGACCATCCAAGTTTCAACTTCACGACGAAGGGAATCATGCCCACC
Found at i:899587 original size:34 final size:34
Alignment explanation
Indices: 899544--899669 Score: 89
Period size: 34 Copynumber: 3.7 Consensus size: 34
899534 AAATTGGATT
899544 TCAACTTCACGACGAAGGATATCCAATTTCAGGC
1 TCAACTTCACGACGAAGGATATCCAATTTCAGGC
* * * * * * **
899578 TCAACTTCACAATGAATG--AGCC--CTCCACGATT
1 TCAACTTCACGACGAAGGATATCCAATTTCA-G-GC
* *
899610 TCAACTTCACGACGAAGGATATTCAATTTAAGGC
1 TCAACTTCACGACGAAGGATATCCAATTTCAGGC
* *
899644 TCAACTTCATGACGAATGGACATCCA
1 TCAACTTCACGACGAA-GGATATCCA
899670 CGATTTCAAC
Statistics
Matches: 64, Mismatches: 21, Indels: 13
0.65 0.21 0.13
Matches are distributed among these distances:
30 3 0.05
31 1 0.02
32 18 0.28
34 32 0.50
35 8 0.12
36 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (34 bp):
TCAACTTCACGACGAAGGATATCCAATTTCAGGC
Found at i:899646 original size:66 final size:65
Alignment explanation
Indices: 899540--899697 Score: 244
Period size: 66 Copynumber: 2.4 Consensus size: 65
899530 CTTCAAATTG
* * * *
899540 GATTTCAACTTCACGACGAAGGATATCCAATTTCAGGCTCAACTTCACAATGAATGAGCCCTCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTTAAGGCTCAACTTCACAACGAATG-GACATCCA
899605 C
65 C
* **
899606 GATTTCAACTTCACGACGAAGGATATTCAATTTAAGGCTCAACTTCATGACGAATGGACATCCAC
1 GATTTCAACTTCACGACGAAGGATATCCAATTTAAGGCTCAACTTCACAACGAATGGACATCCAC
899671 GATTTCAACTTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
899698 GTGTTCATTT
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
65 33 0.39
66 51 0.61
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (65 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTTAAGGCTCAACTTCACAACGAATGGACATCCAC
Found at i:899843 original size:84 final size:84
Alignment explanation
Indices: 899726--900615 Score: 601
Period size: 84 Copynumber: 10.8 Consensus size: 84
899716 GATCAATGCA
* * * *
899726 AGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGACACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
899791 TGCAGCATAACTCAAGGCT
66 TGCAGCATAACTCAAGGCT
* * * * * * *
899810 AGAAGGGTTATCTACCAACAAAAGACCTTTGAGTTTGGCTACGCTTAGCTCCAAGACACATCAGT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
899875 TGCAACATAACTCAAGGCT
66 TGCAGCATAACTCAAGGCT
* * * * *
899894 AGAAGGGCTATTTACCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATTATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
899958 TGTAGCATAACTCAAGTCT
66 TGCAGCATAACTCAAGGCT
* * * * * * *
899977 AGAAGGGTTATCTGCCAATAAAAGACCTTCAAGTTCGATTCCACTTAGCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
900042 TGTAGCATAGCTCATGGCT
66 TGCAGCATAACTCAAGGCT
* * *
900061 AGAAGGGTTGTCTGCCATCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
900126 TACAACATAACTCAAGGC-
66 TGCAGCATAACTCAAGGCT
*** **** * * * * * * **
900144 AGAA-----A-C-AAAAGACCTTCGA-GTTTGACTACG-CT-CAGCTCCAAG--GCACA-TCATT
1 AGAAGGGTTATCTGCCA-ACAAAAGACCTTCGAGTTCGACTAC-GCT-C-AGCTCCA-AGGCACA
* * ** *
900196 TACAATAT--AGCTTAA-GGAAAG--
61 T-C-ATTTGCAGCATAACTCAAGGCT
* * * *** * * * ** * *** * * *
900217 A-AGGGTTATTTGCCAACAA-AATA-CCTTCGAG-TTCGA-CTACGTTCAGCTCTAAGGCATATC
1 AGAAGGGT-TAT-CTGCCAACAAAAGACCT-TCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
900277 ATTTGCAACATAACTCAAGGCT
63 ATTTGCAGCATAACTCAAGGCT
*
900299 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
900364 TGCAGCATAACTCAAGGCT
66 TGCAGCATAACTCAAGGCT
* * * *
900383 AGAAGGGTTATCTGCCAACAAAAGACCTTCGATTTCGATTACACTCAGCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
** *
900448 TGC-GTCATGGCTCAAGGCA
66 TGCAG-CATAACTCAAGGCT
* * * * * * *
900467 AGAAGAGCTATTTGCCAACAAAAGACCTTTGAGTTCAATTACACTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
900532 TACAGTATAACTCAAGGCA
66 TGCAGCATAACTCAAGGCT
** * * * * * *
900551 AGAAGGACTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACACTCACCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
900615 T
66 T
900616 TCATCATGGC
Statistics
Matches: 627, Mismatches: 144, Indels: 71
0.74 0.17 0.08
Matches are distributed among these distances:
72 1 0.00
73 1 0.00
74 4 0.01
75 16 0.03
76 11 0.02
77 14 0.02
78 3 0.00
79 17 0.03
80 7 0.01
81 7 0.01
82 7 0.01
83 121 0.19
84 417 0.67
85 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTCAAGGCT
Found at i:900140 original size:168 final size:168
Alignment explanation
Indices: 899702--900615 Score: 964
Period size: 168 Copynumber: 5.5 Consensus size: 168
899692 GATATCGTGT
* * * *
899702 TCATTTGTAACATAGA-TCAATGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACT
1 TCATTTGCAACATA-ACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACT
* * *
899766 ACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAA
65 ACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAA
* * * * *
899831 AAGACCTTTGAGTTTGGCTACGCTTAGCTCCAAGACACA
130 AAGACCTTCGAGTTCGACTACACTTAGCTCCAAGGCACA
* * * *
899870 TCAGTTGCAACATAACTCAAGGCTAGAAGGGCTATTTACCAAC-AAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * * * *
899934 CGCTCAGCTCCAAGGCATATTATTTGTAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAATAAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
* * * *
899999 AGACCTTCAAGTTCGATTCCACTTAGCTCAAAGGCACA
131 AGACCTTCGAGTTCGACTACACTTAGCTCCAAGGCACA
* * * * * * * *
900037 TCATTTGTAGCATAGCTCATGGCTAGAAGGGTTGTCTGCCATCAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
900102 CGCTCAGCTCCAAGGCATATCATTTACAACATAACTCAAGGC----A--G--A------AACAAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
* * *
900153 AGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACA
131 AGACCTTCGAGTTCGACTACACTTAGCTCCAAGGCACA
* * * * * * * *
900191 TCATTTACAATATAGCTTAAGGAAAGAAGGGTTATTTGCCAACAAAATACCTTCGAGTTCGACTA
1 TCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
900256 CGTTCAGCTCTAAGGCATATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
*
900321 AGACCTTCGAGTTCGACTAC-GTTCAGCTCCAAGGCACA
131 AGACCTTCGAGTTCGACTACACTT-AGCTCCAAGGCACA
* * * * *
900359 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGATTTCGATTA
1 TCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * ** ** * * * *
900424 CACTCAGCTCAAAGGCACATCATTTGCGTCATGGCTCAAGGCAAGAAGAGCTATTTGCCAACAAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
* * * *
900489 AGACCTTTGAGTTCAATTACACTCAGCTCCAAGGCACA
131 AGACCTTCGAGTTCGACTACACTTAGCTCCAAGGCACA
* ** * * * *
900527 TCATTTACAGTATAACTCAAGGCAAGAAGGACTATCTGTCAAC-CAAGACCTTCGAGTTCGATTA
1 TCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
900591 CACTCACCTCAAAGGCACATCATTT
66 CGCTCAGCTCCAAGGCACATCATTT
900616 TCATCATGGC
Statistics
Matches: 628, Mismatches: 100, Indels: 37
0.82 0.13 0.05
Matches are distributed among these distances:
154 128 0.20
158 1 0.00
160 2 0.00
162 2 0.00
164 1 0.00
167 185 0.29
168 308 0.49
169 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (168 bp):
TCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
AGACCTTCGAGTTCGACTACACTTAGCTCCAAGGCACA
Found at i:900493 original size:406 final size:405
Alignment explanation
Indices: 899742--900550 Score: 1136
Period size: 406 Copynumber: 2.0 Consensus size: 405
899732 GCTATTTGCC
* * *
899742 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTCAAG
1 AACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTACAACATAACTCAAG
** * * *
899807 GCTAGAAGGGTTATCTACCAACAAAAGACCTTTGAGTTTGGCTACGCTTAGCTCCAAGACACATC
66 GAAAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGACACATC
*
899872 AGTTGCAACATAACTCAAGGCTAGAAGGGCTATTTACCAACAAAGACCTTCGAGTTCGACTACGC
131 AGTTGCAACATAACTCAAGGCTAGAAGGGCTATCTACCAACAAAGACCTTCGAGTTCGACTACGC
* * * * *
899937 TCAGCTCCAAGGCATATTATTTGTAGCATAACTCAAGTCTAGAAGGGTTATCTGCCAATAAAAGA
196 TCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGA
* * * * *
900002 CCTTCAAGTTCGATTCCACTTAGCTCAAAGGCACATCATTTGTAGCATAGCTCATGGCTAGAAGG
261 CCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGGCAAGAAGA
* * * * * *
900067 GTTGTCTGCCATCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAAC
326 GCTATCTGCCAACAAAAGACCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATCATTTACAAC
900132 ATAACTCAAGGCAGA
391 ATAACTCAAGGCAGA
* * * * *
900147 AACAAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTACAATATAGCTTAAG
1 AACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTACAACATAACTCAAG
* * * * * *
900212 GAAAGAAGGGTTATTTGCCAACAAAATACCTTCGAGTTCGACTACG-TTCAGCTCTAAGGCATAT
66 GAAAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACGCTT-AGCTCCAAGACACAT
* * *
900276 CATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTAC
130 CAGTTGCAACATAACTCAAGGCTAGAAGGGCTATCTACCAAC-AAAGACCTTCGAGTTCGACTAC
*
900341 GTTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
194 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
* * * *
900406 GACCTTCGATTTCGATTACACTCAGCTCAAAGGCACATCATTTG-CGTCATGGCTCAAGGCAAGA
259 GACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAG-CATAGCTCAAGGCAAGA
* * *
900470 AGAGCTATTTGCCAACAAAAGACCTTTGAGTTCAATTACACTCAGCTCCAAGGCACATCATTTAC
323 AGAGCTATCTGCCAACAAAAGACCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATCATTTAC
**
900535 AGTATAACTCAAGGCA
388 AACATAACTCAAGGCA
900551 AGAAGGACTA
Statistics
Matches: 352, Mismatches: 49, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
404 2 0.01
405 146 0.41
406 204 0.58
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (405 bp):
AACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTACAACATAACTCAAG
GAAAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGACACATC
AGTTGCAACATAACTCAAGGCTAGAAGGGCTATCTACCAACAAAGACCTTCGAGTTCGACTACGC
TCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGA
CCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTCAAGGCAAGAAGA
GCTATCTGCCAACAAAAGACCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATCATTTACAAC
ATAACTCAAGGCAGA
Found at i:902258 original size:7 final size:8
Alignment explanation
Indices: 902234--902363 Score: 53
Period size: 7 Copynumber: 16.8 Consensus size: 8
902224 ATTATATTTA
902234 ATTATGTAT
1 ATTAT-TAT
902243 A-TA-TAT
1 ATTATTAT
902249 ATT-TTAT
1 ATTATTAT
902256 ATTATTATT
1 ATTATTA-T
*
902265 ATTAGTAT
1 ATTATTAT
902273 -TTATCTATT
1 ATTAT-TA-T
902282 ATTATTA-
1 ATTATTAT
**
902289 ATGCTTAT
1 ATTATTAT
*
902297 ATTATTTT
1 ATTATTAT
* *
902305 TTTCTTAT
1 ATTATTAT
*
902313 -TAATTACT
1 ATTATTA-T
902321 ATTATTAT
1 ATTATTAT
*
902329 A-TATTTT
1 ATTATTAT
902336 ATT-TTAT
1 ATTATTAT
* *
902343 TTTATTTT
1 ATTATTAT
902351 ATT-TTAT
1 ATTATTAT
*
902358 TTTATT
1 ATTATT
902364 TGTTTTGTTT
Statistics
Matches: 88, Mismatches: 20, Indels: 27
0.65 0.15 0.20
Matches are distributed among these distances:
6 4 0.05
7 35 0.40
8 29 0.33
9 16 0.18
10 4 0.05
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.65
Consensus pattern (8 bp):
ATTATTAT
Found at i:902296 original size:20 final size:20
Alignment explanation
Indices: 902258--902296 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
902248 TATTTTATAT
* *
902258 TATTATTATTAGTATTTATC
1 TATTATTATTAATACTTATC
*
902278 TATTATTATTAATGCTTAT
1 TATTATTATTAATACTTAT
902297 ATTATTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
TATTATTATTAATACTTATC
Found at i:902340 original size:5 final size:5
Alignment explanation
Indices: 902330--902364 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
902320 TATTATTATA
902330 TATTT TATTT TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT
902365 GTTTTGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:905511 original size:29 final size:32
Alignment explanation
Indices: 905449--905513 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
905439 AACATTTGGT
**
905449 TTTTTATTATTATTTTTTTTGTTTTGTTTGTA
1 TTTTTATTATTATTTTTTTCCTTTTGTTTGTA
905481 TTTTTATTATTA-TTTTTTCCTTTT-TTT-TA
1 TTTTTATTATTATTTTTTTCCTTTTGTTTGTA
905510 TTTT
1 TTTT
905514 ATTTGATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 6 0.19
30 3 0.10
31 10 0.32
32 12 0.39
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (32 bp):
TTTTTATTATTATTTTTTTCCTTTTGTTTGTA
Found at i:905727 original size:6 final size:6
Alignment explanation
Indices: 905716--905742 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
905706 AATCGAGTTT
905716 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
905743 TCGCTATTAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:909197 original size:53 final size:52
Alignment explanation
Indices: 909134--909246 Score: 138
Period size: 53 Copynumber: 2.2 Consensus size: 52
909124 CACAATAAAC
** * *
909134 CAACACAAGATGTACAAAATAAAAATATTA-CATAAGAGTATCAAGTCTCAAA
1 CAACACAAGATGTACAAAATAAAAATACCACCACAAGAGTATCAAATCTC-AA
* * *
909186 TCAACACAAGATGTTCATATTAAAAATACCACCACAAGAGTATCAAATCTCAA
1 -CAACACAAGATGTACAAAATAAAAATACCACCACAAGAGTATCAAATCTCAA
909239 CAACACAA
1 CAACACAA
909247 TAAAATCAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 8 0.15
53 27 0.52
54 17 0.33
ACGTcount: A:0.51, C:0.20, G:0.08, T:0.20
Consensus pattern (52 bp):
CAACACAAGATGTACAAAATAAAAATACCACCACAAGAGTATCAAATCTCAA
Found at i:919751 original size:20 final size:19
Alignment explanation
Indices: 919726--919777 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
919716 ACTTGCCACC
919726 AGTATCGATACT-ACCCTGTG
1 AGTATCGATACTGACCC--TG
*
919746 AGTATCAATACTGGACCCTG
1 AGTATCGATACT-GACCCTG
919766 AGTATCGATACT
1 AGTATCGATACT
919778 CTTTGAGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 24 0.86
22 4 0.14
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (19 bp):
AGTATCGATACTGACCCTG
Found at i:928971 original size:20 final size:21
Alignment explanation
Indices: 928946--928988 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
928936 TGAGTGAATA
*
928946 TAGTTGCAATG-CTAATGAGC
1 TAGTTGCAATGAATAATGAGC
*
928966 TAGTTGGAATGAATAATGAGC
1 TAGTTGCAATGAATAATGAGC
928987 TA
1 TA
928989 AATAAACATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (21 bp):
TAGTTGCAATGAATAATGAGC
Found at i:930724 original size:17 final size:19
Alignment explanation
Indices: 930682--930727 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
930672 CTCCTATGGG
930682 GAGTATCGATACTCTACCAT
1 GAGTATCGATACTC-ACCAT
*
930702 GGGTATCGATAC-C-CCAT
1 GAGTATCGATACTCACCAT
930719 GAGTATCGA
1 GAGTATCGA
930728 CAACAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.50
19 1 0.04
20 11 0.46
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (19 bp):
GAGTATCGATACTCACCAT
Done.