Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008930.1 Hibiscus syriacus cultivar Beakdansim tig00112236_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: 792381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:770065 original size:21 final size:21
Alignment explanation
Indices: 770004--770059 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
769994 TCACAATGAT
770004 TTTGGACTATCGCAACGCGAA
1 TTTGGACTATCGCAACGCGAA
*
770025 TTCGGACTATCGCAACGCGAA
1 TTTGGACTATCGCAACGCGAA
770046 TTTGGACTATCGCA
1 TTTGGACTATCGCA
770060 TTGCGATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
TTTGGACTATCGCAACGCGAA
Found at i:770610 original size:18 final size:19
Alignment explanation
Indices: 770576--770626 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
770566 AATTAATATA
*
770576 AATAAAATTGATA-ATTTAT
1 AATAAAA-TAATAGATTTAT
* *
770595 TA-AAAATATTAGATTTAT
1 AATAAAATAATAGATTTAT
770613 AATAAAATAATAGA
1 AATAAAATAATAGA
770627 AAGTTTAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
17 3 0.12
18 11 0.44
19 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (19 bp):
AATAAAATAATAGATTTAT
Found at i:771260 original size:32 final size:31
Alignment explanation
Indices: 771187--771296 Score: 112
Period size: 32 Copynumber: 3.5 Consensus size: 31
771177 GATCTAAAGG
* * * * *
771187 TTAACCTAAACCGAAAATAAATCGATCCGATA
1 TTAACCCAACCCG-AAATCAATCGATCAGGTA
*
771219 TTAACCCAACCCGAAATCTAATCGATCTGGTA
1 TTAACCCAACCCGAAATC-AATCGATCAGGTA
* *
771251 TTAACCCAACCCAAAAATCAACCGATCAGGTA
1 TTAACCCAACCC-GAAATCAATCGATCAGGTA
*
771283 TTGACCCAACCCGA
1 TTAACCCAACCCGA
771297 TATTGACCAG
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
31 5 0.08
32 56 0.85
33 5 0.08
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.20
Consensus pattern (31 bp):
TTAACCCAACCCGAAATCAATCGATCAGGTA
Found at i:772150 original size:22 final size:23
Alignment explanation
Indices: 772125--772198 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
772115 GAACAGTCAA
*
772125 ATAACTAAAAATGTGTCA-AAAG
1 ATAACTAAAAATATGTCACAAAG
** *
772147 ATAAAGAAAAATATGTCATAAAG
1 ATAACTAAAAATATGTCACAAAG
772170 ATGGAA--AAAAATATGTCACAAAG
1 AT--AACTAAAAATATGTCACAAAG
772193 ATAACT
1 ATAACT
772199 TTTTTAAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.05
22 15 0.35
23 24 0.56
25 2 0.05
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.22
Consensus pattern (23 bp):
ATAACTAAAAATATGTCACAAAG
Found at i:772169 original size:23 final size:21
Alignment explanation
Indices: 772131--772196 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 21
772121 TCAAATAACT
*
772131 AAAAATGTGTCAAAAGATAAA
1 AAAAATATGTCAAAAGATAAA
*
772152 GAAAAATATGTCATAAAGATGGAA
1 -AAAAATATGTCA-AAAGAT-AAA
772176 AAAAATATGTCACAAAGATAA
1 AAAAATATGTCA-AAAGATAA
772197 CTTTTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.32
23 24 0.63
24 2 0.05
ACGTcount: A:0.59, C:0.06, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAAATATGTCAAAAGATAAA
Found at i:774350 original size:21 final size:21
Alignment explanation
Indices: 774326--774367 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
774316 CCAAGGAATT
774326 TCTTGATAATTTTTTAATTAA
1 TCTTGATAATTTTTTAATTAA
774347 TCTTGATAATTTTTTAATTAA
1 TCTTGATAATTTTTTAATTAA
774368 AATAAGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TCTTGATAATTTTTTAATTAA
Found at i:774768 original size:70 final size:69
Alignment explanation
Indices: 774611--775148 Score: 379
Period size: 70 Copynumber: 7.8 Consensus size: 69
774601 ATTCCATACA
* * * * ** * *
774611 AGTCACCTAGAATTAATTACTGA-TAGATGCTCAT-GTACAAGTCACTCTAATATTTCAGGACTA
1 AGTCACCCAGAATTAAATAC-GATTAGGTGCTC-TCGTACGAGTCACTCTAATCCTTC-GGGCTC
*
774674 TCATACG
63 TCGTACG
* * * * *
774681 AGTCACCC-GAAAATAAATACGATTAGGTGCACCCATACGAGTCACTATAATCCTTCGGGACTCT
1 AGTCACCCAG-AATTAAATACGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCGGG-CTCT
774745 CGTACG
64 CGTACG
* ** * *
774751 AGTCACCCAGAGTTAAATATAATTAGGTGCTCTCGTATGAGTCACTCTAATCCTCCGAGGCTACT
1 AGTCACCCAGAATTAAATACGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCG-GGCT-CT
*
774816 -GTACA
64 CGTACG
** * * * *
774821 AGTCATTCAAAATTAAATACGATTAGGTGCTCTTGTACGAGCCACTCTAATCCTCCGAGGCTACT
1 AGTCACCCAGAATTAAATACGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCG-GGCT-CT
*
774886 -GTACA
64 CGTACG
** * * * * *
774891 AGTCATTCAAAATTAAATACGATTAGGTGCTCTTGTACGAGCCACTCTAATCCTTTGGGGCTCCC
1 AGTCACCCAGAATTAAATACGATTAGGTGCTCTCGTACGAGTCACTCTAATCC-TTCGGGCTCTC
774956 GTACG
65 GTACG
** * * *
774961 AGTCACCC-GAAATTAAATATTATTAGGTGCTCTCATACGAGTCACTATAATCTTTCAGGG-T-T
1 AGTCACCCAG-AATTAAATACGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTC-GGGCTCT
*
775023 C---CC
64 CGTACG
* ** * *
775026 A-TCACCCAAAATT--ATGTGATTAGGTGCTC-CTGTACGAGCCACTCTAATCCTTCAGGCTCTC
1 AGTCACCCAGAATTAAATACGATTAGGTGCTCTC-GTACGAGTCACTCTAATCCTTCGGGCTCTC
*
775087 ATACG
65 GTACG
* * * * *
775092 AGTCACTC-GAAATTAAATATGATTGGGTGCTCTCGTATGAGTCACTCTGATCCTTCG
1 AGTCACCCAG-AATTAAATACGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCG
775149 ACGCACCTAA
Statistics
Matches: 377, Mismatches: 68, Indels: 47
0.77 0.14 0.10
Matches are distributed among these distances:
61 3 0.01
62 33 0.09
63 2 0.01
64 10 0.03
65 2 0.01
66 2 0.01
67 9 0.02
68 1 0.00
69 42 0.11
70 266 0.71
71 7 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (69 bp):
AGTCACCCAGAATTAAATACGATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCGGGCTCTCG
TACG
Found at i:774979 original size:210 final size:201
Alignment explanation
Indices: 774638--775148 Score: 506
Period size: 210 Copynumber: 2.5 Consensus size: 201
774628 TACTGATAGA
* * * ** * * * *
774638 TGCTCATGTACAAGTCACTCTAATATTTCAGGACTATCATACGAGTCACCCGAAAA-TAAATACG
1 TGCTCCTGTACGAGCCACTCTAATCCTCCAGG-CTCTCATACAAGTCACTC-AAAATTAAATACG
* * * * * *
774702 ATTAGGTGCACCCATACGAGTCACTATAATCCTTCGGGACTCTCGTACGAGTCACCCAGAGTTAA
64 ATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCGGGACTCCCGTACGAGTCACCCAGAATTAA
* * * **
774767 ATATAATTAGGTGCTCTCGTATGAGTCACTCTAATCCTCCGAGGCTACTGTACAAGTCATTCAAA
129 ATATAATTAGGTGCTCTCATACGAGTCACTATAATCCTCC-AGG---CT-TACAA-TCACCCAAA
774832 ATTAAATACGATTAGG
188 ATT--ATACGATTAGG
* * *
774848 TGCTCTTGTACGAGCCACTCTAATCCTCCGAGGCTACT-GTACAAGTCATTCAAAATTAAATACG
1 TGCTCCTGTACGAGCCACTCTAATCCTCC-AGGCT-CTCATACAAGTCACTCAAAATTAAATACG
* * * *
774912 ATTAGGTGCTCTTGTACGAGCCACTCTAATCCTTTGGGGCTCCCGTACGAGTCACCC-GAAATTA
64 ATTAGGTGCTCTCGTACGAGTCACTCTAATCCTTCGGGACTCCCGTACGAGTCACCCAG-AATTA
* * * * * *
774976 AATATTATTAGGTGCTCTCATACGAGTCACTATAATCTTTCAGGGTTCCCATCACCCAAAATTAT
128 AATATAATTAGGTGCTCTCATACGAGTCACTATAATCCTCCAGGCTTACAATCACCCAAAATTAT
**
775041 GTGATTAGG
193 ACGATTAGG
* * * *
775050 TGCTCCTGTACGAGCCACTCTAATCCTTCAGGCTCTCATACGAGTCACTCGAAATTAAATATGAT
1 TGCTCCTGTACGAGCCACTCTAATCCTCCAGGCTCTCATACAAGTCACTCAAAATTAAATACGAT
* * *
775115 TGGGTGCTCTCGTATGAGTCACTCTGATCCTTCG
66 TAGGTGCTCTCGTACGAGTCACTCTAATCCTTCG
775149 ACGCACCTAA
Statistics
Matches: 249, Mismatches: 47, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
200 2 0.01
201 56 0.22
202 36 0.14
204 10 0.04
205 3 0.01
206 1 0.00
209 8 0.03
210 129 0.52
211 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (201 bp):
TGCTCCTGTACGAGCCACTCTAATCCTCCAGGCTCTCATACAAGTCACTCAAAATTAAATACGAT
TAGGTGCTCTCGTACGAGTCACTCTAATCCTTCGGGACTCCCGTACGAGTCACCCAGAATTAAAT
ATAATTAGGTGCTCTCATACGAGTCACTATAATCCTCCAGGCTTACAATCACCCAAAATTATACG
ATTAGG
Found at i:775422 original size:57 final size:57
Alignment explanation
Indices: 775333--775446 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
775323 ATAATTCCAT
** * *
775333 CAGTGAAACTTAACATAGATTTACACCGGTGAAACTATCACTTGATTTCAGCACTGA
1 CAGTGAAACTTAACATAGACATACACCGGTGAAACTACCACTTAATTTCAGCACTGA
* * *
775390 CAGTGAAACTTAACATAGGCATACACCTGTGAAATTACCACTTAATTTCAGCACTGA
1 CAGTGAAACTTAACATAGACATACACCGGTGAAACTACCACTTAATTTCAGCACTGA
775447 ACTTAACACA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (57 bp):
CAGTGAAACTTAACATAGACATACACCGGTGAAACTACCACTTAATTTCAGCACTGA
Found at i:775498 original size:133 final size:133
Alignment explanation
Indices: 775257--775523 Score: 354
Period size: 133 Copynumber: 2.0 Consensus size: 133
775247 GTACTTACAC
* * * * *
775257 CAGTGAAACTTAATATAGACTTACACAGGTGAAACTAACACTTAGTTCCGGCATTGAACTTAACA
1 CAGTGAAACTTAACATAGACATACACAGGTGAAACTAACACTTAATTCCAGCACTGAACTTAACA
* ** * * * *
775322 CATAATTCCATCAGTGAAACTTAACATAGATTTACACCGGTGAAACTATCACTTGATTTCAGCAC
66 CACAATTCCATCAAAGAAACTTAACATAGACTTACACCAGTGAAACTAACACTTAATTTCAGCAC
775387 TGA
131 TGA
* ** * * *
775390 CAGTGAAACTTAACATAGGCATACACCTGTGAAATTACCACTTAATTTCAGCACTGAACTTAACA
1 CAGTGAAACTTAACATAGACATACACAGGTGAAACTAACACTTAATTCCAGCACTGAACTTAACA
* *
775455 CACAATTCCATCAAAGAAACTTAACATAGACTTACACCAGTGAAAGTAACACTTAATTTTAGCAC
66 CACAATTCCATCAAAGAAACTTAACATAGACTTACACCAGTGAAACTAACACTTAATTTCAGCAC
775520 TGA
131 TGA
775523 C
1 C
775524 GTTAACACAT
Statistics
Matches: 114, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
133 114 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.27
Consensus pattern (133 bp):
CAGTGAAACTTAACATAGACATACACAGGTGAAACTAACACTTAATTCCAGCACTGAACTTAACA
CACAATTCCATCAAAGAAACTTAACATAGACTTACACCAGTGAAACTAACACTTAATTTCAGCAC
TGA
Found at i:775520 original size:76 final size:76
Alignment explanation
Indices: 775393--775660 Score: 358
Period size: 76 Copynumber: 3.5 Consensus size: 76
775383 GCACTGACAG
* * * * * *
775393 TGAAACTTAACATAGGCATACACCTGTGAAATTACCACTTAATTTCAGCACTGAACTTAACACAC
1 TGAAACTTAACATAGACTTACACCAGTGAAACTAACACTTAATTTCAGCACTGAACTTAACACAT
775458 AATTCCATCAA
66 AATTCCATCAA
* * *
775469 AGAAACTTAACATAGACTTACACCAGTGAAAGTAACACTTAATTTTAGCACTG-ACGTTAACACA
1 TGAAACTTAACATAGACTTACACCAGTGAAACTAACACTTAATTTCAGCACTGAAC-TTAACACA
*
775533 TAATTCCATCAG
65 TAATTCCATCAA
* ***
775545 TGAAACTTAACATAGACTTACACCGGTGAAACTAACACTTAATTTCAGTGTTGAACTTAACACAT
1 TGAAACTTAACATAGACTTACACCAGTGAAACTAACACTTAATTTCAGCACTGAACTTAACACAT
*
775610 AATTCTATCAA
66 AATTCCATCAA
* * *
775621 TGAAACTTAACATAGATTTATACCAGTAAAACTAACACTT
1 TGAAACTTAACATAGACTTACACCAGTGAAACTAACACTT
775661 GATTCTAGCA
Statistics
Matches: 168, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
75 2 0.01
76 164 0.98
77 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (76 bp):
TGAAACTTAACATAGACTTACACCAGTGAAACTAACACTTAATTTCAGCACTGAACTTAACACAT
AATTCCATCAA
Found at i:775574 original size:152 final size:152
Alignment explanation
Indices: 775390--775670 Score: 409
Period size: 152 Copynumber: 1.8 Consensus size: 152
775380 TCAGCACTGA
* * * *
775390 CAGTGAAACTTAACATAGGCATACACCTGTGAAATTACCACTTAATTTCAGCACTGAACTTAACA
1 CAGTGAAACTTAACATAGACATACACCGGTGAAACTAACACTTAATTTCAGCACTGAACTTAACA
* * *
775455 CACAATTCCATCAAAGAAACTTAACATAGACTTACACCAGTGAAAGTAACACTTAATTTTAGCAC
66 CACAATTCCATCAAAGAAACTTAACATAGACTTACACCAGTAAAACTAACACTTAATTCTAGCAC
775520 TGACGTTAACACATAATTCCAT
131 TGACGTTAACACATAATTCCAT
* ***
775542 CAGTGAAACTTAACATAGACTTACACCGGTGAAACTAACACTTAATTTCAGTGTTGAACTTAACA
1 CAGTGAAACTTAACATAGACATACACCGGTGAAACTAACACTTAATTTCAGCACTGAACTTAACA
* * * * * *
775607 CATAATTCTATCAATGAAACTTAACATAGATTTATACCAGTAAAACTAACACTTGATTCTAGCA
66 CACAATTCCATCAAAGAAACTTAACATAGACTTACACCAGTAAAACTAACACTTAATTCTAGCA
775671 TTGGACTTAA
Statistics
Matches: 112, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
152 112 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (152 bp):
CAGTGAAACTTAACATAGACATACACCGGTGAAACTAACACTTAATTTCAGCACTGAACTTAACA
CACAATTCCATCAAAGAAACTTAACATAGACTTACACCAGTAAAACTAACACTTAATTCTAGCAC
TGACGTTAACACATAATTCCAT
Found at i:777243 original size:2 final size:2
Alignment explanation
Indices: 777236--777275 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
777226 TTATGTAATC
777236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
777276 TACATGATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:777948 original size:32 final size:32
Alignment explanation
Indices: 777901--778070 Score: 179
Period size: 32 Copynumber: 5.4 Consensus size: 32
777891 AAGAGTCGAG
* * * *
777901 GATTACTTATATCTTTCGGGACATATAGATAG
1 GATTACCTATGTCTTTCGGGACATATAGACAT
*
777933 GATTACCTATGTCTTTCGGGACATATGGACAT
1 GATTACCTATGTCTTTCGGGACATATAGACAT
* * *
777965 GATTACCTATGTCTTTTGAGACATATGGACAT
1 GATTACCTATGTCTTTCGGGACATATAGACAT
* *
777997 GATTACCTATGTCTTTTGTGACATA-AGGACAT
1 GATTACCTATGTCTTTCGGGACATATA-GACAT
*
778029 GATTACATATGTCCTTT-GGGACATAT-GAACA-
1 GATTACCTATGT-CTTTCGGGACATATAG-ACAT
778060 G-TTACCTATGT
1 GATTACCTATGT
778071 TCTTAGGAAC
Statistics
Matches: 122, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
30 9 0.07
31 2 0.02
32 107 0.88
33 4 0.03
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (32 bp):
GATTACCTATGTCTTTCGGGACATATAGACAT
Found at i:778002 original size:64 final size:63
Alignment explanation
Indices: 777901--778070 Score: 207
Period size: 64 Copynumber: 2.7 Consensus size: 63
777891 AAGAGTCGAG
* * * * * *
777901 GATTACTTATATCTTTCGGGACATATAGATAGGATTACCTATGTCTTTCGGGACATATGGACAT
1 GATTACATATGTCTTTTGGGACATATGGACA-GATTACCTATGTCTTTCGGGACATAAGGACAT
* * * *
777965 GATTACCTATGTCTTTTGAGACATATGGACATGATTACCTATGTCTTTTGTGACATAAGGACAT
1 GATTACATATGTCTTTTGGGACATATGGACA-GATTACCTATGTCTTTCGGGACATAAGGACAT
* *
778029 GATTACATATGTCCTTTGGGACATATGAACAG-TTACCTATGT
1 GATTACATATGTCTTTTGGGACATATGGACAGATTACCTATGT
778071 TCTTAGGAAC
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
62 10 0.11
63 1 0.01
64 81 0.88
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (63 bp):
GATTACATATGTCTTTTGGGACATATGGACAGATTACCTATGTCTTTCGGGACATAAGGACAT
Found at i:778727 original size:22 final size:21
Alignment explanation
Indices: 778676--778727 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
778666 GGCCGAAATT
*
778676 ACTGTAGCAAGGTATCGGTAC
1 ACTGTAGCAAGGTATCGATAC
*
778697 ACTGTAGCAGGGTATCGATAC
1 ACTGTAGCAAGGTATCGATAC
*
778718 CCTTGTAGCA
1 AC-TGTAGCA
778728 TTCTGGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAAGGTATCGATAC
Found at i:781372 original size:20 final size:20
Alignment explanation
Indices: 781349--781403 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
781339 GCACTAACTC
781349 TATTATACT-GCCACCACTAA
1 TATT-TACTGGCCACCACTAA
*
781369 TATTTGCTGGCCACCACTAA
1 TATTTACTGGCCACCACTAA
*
781389 TATTTGCTGGCCACC
1 TATTTACTGGCCACC
781404 CATGTTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
TATTTACTGGCCACCACTAA
Found at i:789160 original size:7 final size:7
Alignment explanation
Indices: 789148--789208 Score: 50
Period size: 7 Copynumber: 7.7 Consensus size: 7
789138 TAAAGATAAA
789148 AAAAATG
1 AAAAATG
789155 AAAAATG
1 AAAAATG
789162 AAAAAAAATG
1 ---AAAAATG
789172 AAAAAAATG
1 --AAAAATG
*
789181 AAAAAAG
1 AAAAATG
789188 AAAAATAG
1 AAAAAT-G
789196 AAAAATAG
1 AAAAAT-G
789204 AAAAA
1 AAAAA
789209 AATAAAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
7 18 0.38
8 14 0.29
9 9 0.19
10 7 0.15
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (7 bp):
AAAAATG
Found at i:789167 original size:9 final size:9
Alignment explanation
Indices: 789146--789236 Score: 81
Period size: 8 Copynumber: 10.8 Consensus size: 9
789136 CTTAAAGATA
789146 AAAAAAATG
1 AAAAAAATG
789155 --AAAAATG
1 AAAAAAATG
789162 AAAAAAAATG
1 -AAAAAAATG
789172 AAAAAAATG
1 AAAAAAATG
789181 -AAAAAA-G
1 AAAAAAATG
*
789188 AAAAATA-G
1 AAAAAAATG
*
789196 AAAAATA-G
1 AAAAAAATG
789204 AAAAAAAT-
1 AAAAAAATG
789212 AAAAAAAT-
1 AAAAAAATG
*
789220 AAAAAAAAG
1 AAAAAAATG
789229 AAGAAAAA
1 AA-AAAAA
789237 AAGAAGAAGA
Statistics
Matches: 72, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
7 8 0.11
8 41 0.57
9 11 0.15
10 12 0.17
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:789167 original size:17 final size:18
Alignment explanation
Indices: 789145--789186 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
789135 GCTTAAAGAT
789145 AAAAAAAATG-AAAAATG
1 AAAAAAAATGAAAAAATG
789162 AAAAAAAATGAAAAAAATG
1 AAAAAAAATG-AAAAAATG
789181 AAAAAA
1 AAAAAA
789187 GAAAAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.43
19 13 0.57
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAAAAAATGAAAAAATG
Found at i:789192 original size:17 final size:17
Alignment explanation
Indices: 789145--789253 Score: 77
Period size: 16 Copynumber: 6.5 Consensus size: 17
789135 GCTTAAAGAT
*
789145 AAAAAAAATGAAAAATG
1 AAAAAAAATGAAAAAAG
789162 AAAAAAAATGAAAAAA-
1 AAAAAAAATGAAAAAAG
*
789178 ATGAAAAAA-GAAAAATAG
1 A-AAAAAAATGAAAAA-AG
*
789196 -AAAAATA-GAAAAAA-
1 AAAAAAAATGAAAAAAG
*
789210 ATAAAAAAATAAAAAAAAG
1 A-AAAAAAAT-GAAAAAAG
* *
789229 AAGAAAAAAAG-AAGAAG
1 AA-AAAAAATGAAAAAAG
789246 AAAAAAAA
1 AAAAAAAA
789254 AAATAAATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 19
0.73 0.09 0.19
Matches are distributed among these distances:
15 1 0.01
16 30 0.41
17 29 0.39
18 7 0.09
19 7 0.09
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (17 bp):
AAAAAAAATGAAAAAAG
Found at i:789226 original size:8 final size:8
Alignment explanation
Indices: 789163--789265 Score: 68
Period size: 8 Copynumber: 12.5 Consensus size: 8
789153 TGAAAAATGA
789163 AAAAAAAT
1 AAAAAAAT
789171 GAAAAAAAT
1 -AAAAAAAT
* *
789180 GAAAAAAG
1 AAAAAAAT
* *
789188 AAAAATAG
1 AAAAAAAT
* *
789196 AAAAATAG
1 AAAAAAAT
789204 AAAAAAAT
1 AAAAAAAT
789212 AAAAAAAT
1 AAAAAAAT
789220 AAAAAAA-
1 AAAAAAAT
789227 AGAAGAAAA-
1 A-AA-AAAAT
*
789236 AAAGAAGAAG
1 AAA-AA-AAT
789246 AAAAAAA-
1 AAAAAAAT
789253 AAAATAAAT
1 AAAA-AAAT
789262 AAAA
1 AAAA
789266 GGGGGGTTCA
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
7 5 0.06
8 53 0.65
9 21 0.26
10 3 0.04
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.08
Consensus pattern (8 bp):
AAAAAAAT
Found at i:789227 original size:41 final size:41
Alignment explanation
Indices: 789148--789266 Score: 126
Period size: 41 Copynumber: 3.0 Consensus size: 41
789138 TAAAGATAAA
*
789148 AAAAAT-GAAAAAT-GAAAAAAAATGAAAAAAAT-GAAAAAAG
1 AAAAATAGAAAAATAG-AAAAAAAT-AAAAAAATAAAAAAAAG
789188 AAAAATAGAAAAATAGAAAAAAATAAAAAAATAAAAAAAAG
1 AAAAATAGAAAAATAGAAAAAAATAAAAAAATAAAAAAAAG
* * *
789229 AAGAAA-A-AAAGA-AGAAGAAAA-AAAAAAATAAATAAAAG
1 AA-AAATAGAAAAATAGAAAAAAATAAAAAAATAAAAAAAAG
789267 GGGGGTTCAA
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
38 16 0.23
39 8 0.11
40 18 0.25
41 25 0.35
42 4 0.06
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (41 bp):
AAAAATAGAAAAATAGAAAAAAATAAAAAAATAAAAAAAAG
Found at i:790686 original size:51 final size:54
Alignment explanation
Indices: 790543--790818 Score: 409
Period size: 54 Copynumber: 5.1 Consensus size: 54
790533 TGAAGCAAAA
790543 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATAC-CTCTGAAGAAATA-GGGGGCAGACGCGATCGTT
* * *
790599 GAAGATTATTCGAGTCTTATA-CTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
790652 GAAGATTG-TGGA-TCTTATA-CTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
790703 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCATACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATAC-CTCTGAAGAAATAGGGGGCAGACGCGATCGTT
790758 GAAGATTGTTCGAGTC-TATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATAC-CTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
790812 GGAGATT
1 GAAGATT
790819 ATTGTTCGAG
Statistics
Matches: 201, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
51 45 0.22
52 6 0.03
53 31 0.15
54 54 0.27
55 45 0.22
56 20 0.10
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (54 bp):
GAAGATTGTTCGAGTCTTATACCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:790818 original size:109 final size:107
Alignment explanation
Indices: 790543--790821 Score: 431
Period size: 109 Copynumber: 2.6 Consensus size: 107
790533 TGAAGCAAAA
790543 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGGCAGACGCGATCGTTGAAGATTAT
1 GAAGATTGTTCGAGTC-TATACTCTCTGAAGAAATA-GGGGGCAGACGCGATCGTTGAAGATTAT
790608 TCGAGTCTTATACTCTGAAGAAATAGGGGGCAGACGCGATTGAT
64 TCGAGTCTTATACTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
790652 GAAGATTG-TGGA-TCT-TA-TACTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTATACT-CTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* * *
790713 CGAGTCTTATACTCTCTGAATAAATAGGGGGCATACGCGATTGTT
65 CGAGTCTTATA--CTCTGAAGAAATAGGGGGCAGACGCGATTGAT
*
790758 GAAGATTGTTCGAGTCTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 GAAGATTGTTCGAGTCTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
790822 GTTCGAGTTC
Statistics
Matches: 155, Mismatches: 8, Indels: 14
0.88 0.05 0.08
Matches are distributed among these distances:
104 40 0.26
105 15 0.10
106 38 0.25
107 5 0.03
108 6 0.04
109 50 0.32
110 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (107 bp):
GAAGATTGTTCGAGTCTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTC
GAGTCTTATACTCTGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:790869 original size:160 final size:158
Alignment explanation
Indices: 790543--791331 Score: 447
Period size: 153 Copynumber: 5.0 Consensus size: 158
790533 TGAAGCAAAA
* * *
790543 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGGCAGACGCGATCGTTGAAGATTAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGGCATACGCGATAGTTGAAGATTGT
* * * * * * *
790608 TCGAGTCTTATACTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGATC---TTAT
65 TCGAGTCTTAT-CTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATTGTTCGAGTTCT
* ** *
790670 A--CTCTGAAGAAATAGGGGGCAGACGCGATCG
129 AGTCCCTGAAGAAA-ATTGGGCAGAC-CG-TAG
* *
790701 TTGAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCATACGCGATTGTTGAAGATTG
1 --GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATAGTTGAAGATTG
790766 TTCGAGTCTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATTGTTCGAGTT
64 TTCGAGTCT-TA-TCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATTGTTCGAGTT
790831 CTAGTCCCTGAAGAAAATTGGGCAGACCGTAG
127 CTAGTCCCTGAAGAAAATTGGGCAGACCGTAG
* * * ** * *
790863 GAAGATTATGTTCGAG--TTCTAGTCCCTGAAGAAA-ATTGGGCATTCTCG-TAG--GAAGATTA
1 GAAGA-T-TGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATAGTTGAAG---A
* * ** *
790922 TTGTTCAAGT-TCTAGTCCCTGAAGAAA-ATTGGGCAGAC-C---CGTAGGAAGATTATTGTTCG
61 TTGTTCGAGTCT-TA-TCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGG-AGATTATTGTTCG
*
790981 AGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAG
123 AGTTCTAGTCCCTGAAGAAAATTGGGCAGA-CCGTAG
* * * * ** * * ** *
791018 GAAGATTATTTTTCGAG--TTCTAGTCCCTGAAGAAA-ATTGGGCAGACCCG-TAGGAAGAAATA
1 GAAG---ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATA-GTTG-AAGA
** * * *
791079 TTGTTCGAGT-TCTAGTC-CTGAAGAAA-ATTGGGCAG--TC--TCGTAGGA-A-GATTGTTCGA
61 TTGTTCGAGTCT-TA-TCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATTGTTCGA
*
791135 GTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAG
124 GTTCTAGTCCCTGAAGAAAATTGGGCAGA-CCGTAG
* * * ** * *
791171 GAAGATTATTGTTCGAG--TTCTAGTCCCTGAAGAAA-ATTGGGCAGACCCG-TAG--GAAGATT
1 GAAG---ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATAGTTGAAG---
* * ** * *
791230 ATTGTTCGAGTTCTAATCCCTGAAGAAA-ATTGGGC-G--TC--TCGTAGGAAGATTATTGTTCG
60 ATTGTTCGAG-TCTTATCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGG-AGATTATTGTTCG
791289 AGTTCTAGTCCCTGAAGAAAATTGGGCAGACCGTAG
123 AGTTCTAGTCCCTGAAGAAAATTGGGCAGACCGTAG
791325 GAAGATT
1 GAAGATT
791332 ATTGTTCGAG
Statistics
Matches: 551, Mismatches: 46, Indels: 73
0.82 0.07 0.11
Matches are distributed among these distances:
149 2 0.00
150 1 0.00
151 3 0.01
152 23 0.04
153 117 0.21
154 55 0.10
155 49 0.09
156 67 0.12
157 28 0.05
158 17 0.03
159 54 0.10
160 98 0.18
161 2 0.00
162 10 0.02
163 6 0.01
164 9 0.02
165 10 0.02
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (158 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATAGTTGAAGATTGTT
CGAGTCTTATCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATTGTTCGAGTTCTAG
TCCCTGAAGAAAATTGGGCAGACCGTAG
Found at i:790949 original size:52 final size:52
Alignment explanation
Indices: 790814--791616 Score: 1261
Period size: 52 Copynumber: 15.6 Consensus size: 52
790804 CGATCGTTGG
790814 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGA-CCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
** *
790865 AGATTA-TGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCATTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
790916 AGATTATTGTTCAAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
790968 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
791020 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
791072 AGAAATATTGTTCGAGTTCTAGT-CCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AG-ATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
791124 AG---ATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
791173 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
791225 AGATTATTGTTCGAGTTCTAATCCCTGAAGAAAATTGGGC-GTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
791276 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGA-CCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
791327 AGATTATTGTTCGAGTTCTAGTCCTTGATGAAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAG-AAAATTGGGCAGACCCGTAGGA
* * * **
791380 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTAGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
791432 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
791484 AGATTATTGTTCGAGTTCTAGT-CCTGAAGAAAATTGGACAGA-CCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
791534 AGATTA-TGTTCGAGTTCTAGTCCCTGAAG-AAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
791584 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
791617 TAGAGAGCGA
Statistics
Matches: 693, Mismatches: 45, Indels: 27
0.91 0.06 0.04
Matches are distributed among these distances:
48 17 0.02
49 53 0.08
50 67 0.10
51 141 0.20
52 362 0.52
53 53 0.08
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:790952 original size:28 final size:27
Alignment explanation
Indices: 790871--790952 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 27
790861 AGGAAGATTA
790871 TGTTCGAGTTCTAGTCCCTGAAGAAAAT
1 TGTTC-AGTTCTAGTCCCTGAAGAAAAT
** * ** **
790899 TGGGCA-TTCTCGT--AGGAAGATTAT
1 TGTTCAGTTCTAGTCCCTGAAGAAAAT
790923 TGTTCAAGTTCTAGTCCCTGAAGAAAAT
1 TGTTC-AGTTCTAGTCCCTGAAGAAAAT
790951 TG
1 TG
790953 GGCAGACCCG
Statistics
Matches: 36, Mismatches: 14, Indels: 8
0.62 0.24 0.14
Matches are distributed among these distances:
24 10 0.28
25 1 0.03
26 12 0.33
27 1 0.03
28 12 0.33
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (27 bp):
TGTTCAGTTCTAGTCCCTGAAGAAAAT
Found at i:791125 original size:24 final size:24
Alignment explanation
Indices: 791046--791126 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
791036 TCTAGTCCCT
* *
791046 GAAGAAAATTGGGCAGACCCGTAG
1 GAAGAAAATTGGGCAGTCTCGTAG
** * **
791070 GAAGAAATATTGTTCGAGTTCTAGTCCT
1 GAAGAAA-ATTGGGC-AG-TCTCGT-AG
791098 GAAGAAAATTGGGCAGTCTCGTAG
1 GAAGAAAATTGGGCAGTCTCGTAG
791122 GAAGA
1 GAAGA
791127 TTGTTCGAGT
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
24 12 0.29
25 10 0.24
26 4 0.10
27 8 0.20
28 7 0.17
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.22
Consensus pattern (24 bp):
GAAGAAAATTGGGCAGTCTCGTAG
Found at i:791157 original size:28 final size:28
Alignment explanation
Indices: 791126--791209 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
791116 TCGTAGGAAG
791126 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
1 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
* **
791154 ATTG---GA---C-AGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTAGTCCC-T--GAAGAAA
791178 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
1 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
791206 ATTG
1 ATTG
791210 GGCAGACCCG
Statistics
Matches: 40, Mismatches: 6, Indels: 20
0.61 0.09 0.30
Matches are distributed among these distances:
21 5 0.12
22 2 0.05
24 9 0.22
25 2 0.05
27 2 0.05
28 13 0.32
30 2 0.05
31 5 0.12
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (28 bp):
ATTGTTCGAGTTCTAGTCCCTGAAGAAA
Found at i:791296 original size:360 final size:360
Alignment explanation
Indices: 790814--791616 Score: 1379
Period size: 360 Copynumber: 2.2 Consensus size: 360
790804 CGATCGTTGG
790814 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGA-CCGTAGGAAGATTA-TGTTCG
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
* *
790877 AGTTCTAGTCCCTGAAGAAAATTGGGCATTCTCGTAGGAAGATTATTGTTCAAGTTCTAGTCCCT
66 AGTTCTAATCCCTGAAGAAAATTGGGCAGTCTCGTAGGAAGATTATTGTTCAAGTTCTAGTCCCT
790942 GAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCGAGTTCTAGTCCTTGAAG-AAAATTGG
131 GAAGAAAATTGGGCAGA-CCGTAGGAAGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAAATTGG
* *
791006 GCAGACCCGTAGGAAGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGG
195 GCAGACCCGTAGGAAGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCAGTAGG
791071 AAGAAATATTGTTCGAGTTCTAGT-CCTGAAGAAAATTGGGCAGTCTCGTAGGAAG-ATTGTTCG
260 AAG-AATATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGAAGTATTGTTCG
791134 AGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
324 AGTTCTAGT-CCTGAAGAAAATTGGACAGA-CCGTAGGA
791173 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
*
791238 AGTTCTAATCCCTGAAGAAAATTGGGC-GTCTCGTAGGAAGATTATTGTTCGAGTTCTAGTCCCT
66 AGTTCTAATCCCTGAAGAAAATTGGGCAGTCTCGTAGGAAGATTATTGTTCAAGTTCTAGTCCCT
*
791302 GAAGAAAATTGGGCAGACCGTAGGAAGATTATTGTTCGAGTTCTAGTCCTTGATGAAAAATTGGG
131 GAAGAAAATTGGGCAGACCGTAGGAAGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAAATTGGG
* *
791367 CAGACCCGTAGGAAGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTAGTAGGA
196 CAGACCCGTAGGAAGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCAGTAGGA
*
791432 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGAAGATTATTGTTCG
261 AGAATATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGAAG--TATTGTTCG
791497 AGTTCTAGTCCTGAAGAAAATTGGACAGACCGTAGGA
324 AGTTCTAGTCCTGAAGAAAATTGGACAGACCGTAGGA
* * *
791534 AGATTA-TGTTCGAGTTCTAGTCCCTGAAG-AAATTGGGCAGTCTCGTAGGAAGATTATCGTTCG
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
*
791597 AGTTCTACTCCCTGAAGAAA
66 AGTTCTAATCCCTGAAGAAA
791617 TAGAGAGCGA
Statistics
Matches: 424, Mismatches: 13, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
359 149 0.35
360 192 0.45
361 46 0.11
362 20 0.05
363 17 0.04
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (360 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGAAGATTATTGTTCG
AGTTCTAATCCCTGAAGAAAATTGGGCAGTCTCGTAGGAAGATTATTGTTCAAGTTCTAGTCCCT
GAAGAAAATTGGGCAGACCGTAGGAAGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAAATTGGG
CAGACCCGTAGGAAGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCAGTAGGA
AGAATATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGAAGTATTGTTCGAG
TTCTAGTCCTGAAGAAAATTGGACAGACCGTAGGA
Found at i:791426 original size:26 final size:26
Alignment explanation
Indices: 791396--791476 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 26
791386 TTTTTCGAGT
791396 TCTAGTCCCTGAAGAAAATTGGACAG
1 TCTAGTCCCTGAAGAAAATTGGACAG
** ** **
791422 TCTAGT--AGGAAGATTATTGTTCGAG
1 TCTAGTCCCTGAAGAAAATTGGAC-AG
*
791447 TTCTAGTCCCTGAAGAAAATTGGGCAG
1 -TCTAGTCCCTGAAGAAAATTGGACAG
791474 TCT
1 TCT
791477 CGTAGGAAGA
Statistics
Matches: 39, Mismatches: 12, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
24 10 0.26
25 2 0.05
26 15 0.38
27 2 0.05
28 10 0.26
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (26 bp):
TCTAGTCCCTGAAGAAAATTGGACAG
Done.