Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397280.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_77.0, 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: 1703557
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 66023 characters in sequence are not A, C, G, or T
File 6 of 6
Found at i:1575645 original size:17 final size:18
Alignment explanation
Indices: 1575619--1575662 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
1575609 AATAAAATAA
*
1575619 AAAATCAATAATTAAA-G
1 AAAATGAATAATTAAATG
1575636 AAAATGAAT-ATTAAATG
1 AAAATGAATAATTAAATG
1575653 --AATGAATAAT
1 AAAATGAATAAT
1575663 AATAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.27
Consensus pattern (18 bp):
AAAATGAATAATTAAATG
Found at i:1578226 original size:59 final size:59
Alignment explanation
Indices: 1578135--1578292 Score: 191
Period size: 59 Copynumber: 2.7 Consensus size: 59
1578125 TCTTGGCTTT
* * * *
1578135 AATTAAGAC-TAAAATATTTTATCTTGTCTAAATTGAGATAAATATATTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTATCTTGTCTAAATTAAGACAAACATATTTTCTTGTCTA
*
1578193 GATTAAGACAAAAAATATTTT-TCTTGTCTTAAATTAAGACAAACATATTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTATCTTGTC-TAAATTAAGACAAACATATTTTCTTGTCTA
* * *
1578252 AATTAAGAGC-AAACAT-GTTT-TCTTGTCTAACTTAAGACAAA
1 AATTAAGA-CAAAAAATATTTTATCTTGTCTAAATTAAGACAAA
1578293 AGTGTTAAGG
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
57 13 0.15
58 25 0.28
59 49 0.56
60 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (59 bp):
AATTAAGACAAAAAATATTTTATCTTGTCTAAATTAAGACAAACATATTTTCTTGTCTA
Found at i:1578264 original size:29 final size:28
Alignment explanation
Indices: 1578135--1578292 Score: 183
Period size: 29 Copynumber: 5.4 Consensus size: 28
1578125 TCTTGGCTTT
1578135 AATTAAGACTAAA-ATATTTTATCTTGTCTA
1 AATTAAGAC-AAACATA-TTT-TCTTGTCTA
* * *
1578165 AATTGAGATAAATATATTTTCTTGTCTA
1 AATTAAGACAAACATATTTTCTTGTCTA
* *
1578193 GATTAAGACAAAAAATATTTTTCTTGTCTTA
1 AATTAAGAC-AAACATA-TTTTCTTGTC-TA
1578224 AATTAAGACAAACATATTTTCTTGTCTA
1 AATTAAGACAAACATATTTTCTTGTCTA
*
1578252 AATTAAGAGCAAACATGTTTTCTTGTCTA
1 AATTAAGA-CAAACATATTTTCTTGTCTA
*
1578281 ACTTAAGACAAA
1 AATTAAGACAAA
1578293 AGTGTTAAGG
Statistics
Matches: 113, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
28 29 0.26
29 48 0.42
30 26 0.23
31 10 0.09
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTCTTGTCTA
Found at i:1581101 original size:20 final size:19
Alignment explanation
Indices: 1581067--1581107 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
1581057 ATTTTATTAA
*
1581067 TAAAATAATATTAAAATAT
1 TAAAATAAAATTAAAATAT
1581086 TAAAATTAAAATTAAAATAT
1 TAAAA-TAAAATTAAAATAT
1581106 TA
1 TA
1581108 TTTTATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAATAAAATTAAAATAT
Found at i:1581136 original size:50 final size:50
Alignment explanation
Indices: 1580995--1581138 Score: 270
Period size: 50 Copynumber: 2.9 Consensus size: 50
1580985 GAGAATTTTG
* *
1580995 AATTAAAATATTATTTTATTAATAAAATAATATTAAAATATGAAAATTTA
1 AATTAAAATATTATTTTATTAATAAAATAATATTAAAATATTAAAATTAA
1581045 AATTAAAATATTATTTTATTAATAAAATAATATTAAAATATTAAAATTAA
1 AATTAAAATATTATTTTATTAATAAAATAATATTAAAATATTAAAATTAA
1581095 AATTAAAATATTATTTTATTAATAAAATAATATTAAAATATTAA
1 AATTAAAATATTATTTTATTAATAAAATAATATTAAAATATTAA
1581139 TATTTTAACT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (50 bp):
AATTAAAATATTATTTTATTAATAAAATAATATTAAAATATTAAAATTAA
Found at i:1592468 original size:25 final size:24
Alignment explanation
Indices: 1592439--1592490 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
1592429 GGTCTATGAT
*
1592439 TATATGTGGC-AAGGCCACAAGTTGA
1 TATATGTGGCTAA-ACCACAAG-TGA
1592464 TATATGTGGCTAAACCACAAGTGA
1 TATATGTGGCTAAACCACAAGTGA
1592488 TAT
1 TAT
1592491 GCACGGTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 17 0.68
26 2 0.08
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (24 bp):
TATATGTGGCTAAACCACAAGTGA
Found at i:1595297 original size:14 final size:14
Alignment explanation
Indices: 1595278--1595304 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1595268 AAATCCATTC
1595278 ACATTGGTAAGGTA
1 ACATTGGTAAGGTA
1595292 ACATTGGTAAGGT
1 ACATTGGTAAGGT
1595305 TATCTCTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (14 bp):
ACATTGGTAAGGTA
Found at i:1595895 original size:20 final size:20
Alignment explanation
Indices: 1595870--1595916 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1595860 TTATTTTAAG
1595870 TTATGTTTTACATGTTTTAT
1 TTATGTTTTACATGTTTTAT
*
1595890 TTATGTTTTGCATGTTTTAT
1 TTATGTTTTACATGTTTTAT
*
1595910 TTGTGTT
1 TTATGTT
1595917 CAAAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.04, G:0.15, T:0.66
Consensus pattern (20 bp):
TTATGTTTTACATGTTTTAT
Found at i:1601496 original size:21 final size:21
Alignment explanation
Indices: 1601470--1601512 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1601460 GATATCAAGA
1601470 ATGCATAGCTCAGAATCCTAC
1 ATGCATAGCTCAGAATCCTAC
1601491 ATGCATAGCTCAGAATCCTAC
1 ATGCATAGCTCAGAATCCTAC
1601512 A
1 A
1601513 CTATTTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (21 bp):
ATGCATAGCTCAGAATCCTAC
Found at i:1606623 original size:11 final size:11
Alignment explanation
Indices: 1606607--1606640 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1606597 AATTAATCTA
1606607 AACTAATGCCT
1 AACTAATGCCT
1606618 AACTAATG-CT
1 AACTAATGCCT
*
1606628 AACTGATGCCT
1 AACTAATGCCT
1606639 AA
1 AA
1606641 AATGTGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (11 bp):
AACTAATGCCT
Found at i:1607677 original size:50 final size:50
Alignment explanation
Indices: 1607602--1607697 Score: 192
Period size: 50 Copynumber: 1.9 Consensus size: 50
1607592 CCTTCTTGAC
1607602 CTCAAGCAAAAATCTAGTTATGAAGGCTACGCAAAATTCATCCCAAACCA
1 CTCAAGCAAAAATCTAGTTATGAAGGCTACGCAAAATTCATCCCAAACCA
1607652 CTCAAGCAAAAATCTAGTTATGAAGGCTACGCAAAATTCATCCCAA
1 CTCAAGCAAAAATCTAGTTATGAAGGCTACGCAAAATTCATCCCAA
1607698 GCCAACATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (50 bp):
CTCAAGCAAAAATCTAGTTATGAAGGCTACGCAAAATTCATCCCAAACCA
Found at i:1617216 original size:56 final size:55
Alignment explanation
Indices: 1617142--1617265 Score: 162
Period size: 56 Copynumber: 2.2 Consensus size: 55
1617132 TTGGGGCTCA
* * *
1617142 TAACCAAAATCCAAAGGTGCTATGAAACCTAACCAAATCCAAATGTGTTACA-GCACC
1 TAACC-AAATCCAAAGGTGCTACGAAACCTAA-CAAATCCAAAGGTGGTA-AGGCACC
* *
1617199 TAACCAAATCCAAAGGTGCTACGACACCTAACAATTCCAAAGGTGGTAAGGCACC
1 TAACCAAATCCAAAGGTGCTACGAAACCTAACAAATCCAAAGGTGGTAAGGCACC
1617254 TAA-CAAATCCAA
1 TAACCAAATCCAA
1617266 TCATCAATTC
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
54 10 0.16
55 22 0.36
56 24 0.39
57 5 0.08
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.18
Consensus pattern (55 bp):
TAACCAAATCCAAAGGTGCTACGAAACCTAACAAATCCAAAGGTGGTAAGGCACC
Found at i:1617241 original size:27 final size:28
Alignment explanation
Indices: 1617142--1617265 Score: 137
Period size: 28 Copynumber: 4.5 Consensus size: 28
1617132 TTGGGGCTCA
* *
1617142 TAACCAAAATCCAAAGGTGCTATGAAACC
1 TAACC-AAATCCAAAGGTGCTACGACACC
* *
1617171 TAACCAAATCCAAATGTGTTAC-AGCACC
1 TAACCAAATCCAAAGGTGCTACGA-CACC
1617199 TAACCAAATCCAAAGGTGCTACGACACC
1 TAACCAAATCCAAAGGTGCTACGACACC
* * * *
1617227 TAA-CAATTCCAAAGGTGGTAAGGCACC
1 TAACCAAATCCAAAGGTGCTACGACACC
1617254 TAA-CAAATCCAA
1 TAACCAAATCCAA
1617266 TCATCAATTC
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
27 32 0.39
28 44 0.54
29 6 0.07
ACGTcount: A:0.42, C:0.27, G:0.14, T:0.18
Consensus pattern (28 bp):
TAACCAAATCCAAAGGTGCTACGACACC
Found at i:1620471 original size:21 final size:22
Alignment explanation
Indices: 1620441--1620484 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1620431 CTCTTGAAGT
1620441 AATTTAAACTAAAACAACATAA
1 AATTTAAACTAAAACAACATAA
* *
1620463 AATTT-AACTAAAATAACTTAA
1 AATTTAAACTAAAACAACATAA
1620484 A
1 A
1620485 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.27
Consensus pattern (22 bp):
AATTTAAACTAAAACAACATAA
Found at i:1626339 original size:20 final size:20
Alignment explanation
Indices: 1626316--1626376 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
1626306 CCGTGTTGGC
1626316 ACTTATAAAATCATGTTAGT
1 ACTTATAAAATCATGTTAGT
* * * *
1626336 ACTTGGTTACATCATGTAAGT
1 ACTT-ATAAAATCATGTTAGT
*
1626357 AC-TATAAAAATTATGTTAGT
1 ACTTAT-AAAATCATGTTAGT
1626377 GCTTGGTTAC
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.50
21 14 0.47
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (20 bp):
ACTTATAAAATCATGTTAGT
Found at i:1626375 original size:41 final size:41
Alignment explanation
Indices: 1626322--1626404 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
1626312 TGGCACTTAT
*
1626322 AAAATCATGTTAGTACTTGGTTACATCATGTAAGTACTATA
1 AAAATCATGTTAGTACTTGGTTACATCATATAAGTACTATA
* * *
1626363 AAAATTATGTTAGTGCTTGGTTACGTCATATAAGTACTATA
1 AAAATCATGTTAGTACTTGGTTACATCATATAAGTACTATA
1626404 A
1 A
1626405 TTATATCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (41 bp):
AAAATCATGTTAGTACTTGGTTACATCATATAAGTACTATA
Found at i:1646282 original size:30 final size:30
Alignment explanation
Indices: 1646203--1646282 Score: 124
Period size: 30 Copynumber: 2.7 Consensus size: 30
1646193 GTATTCAATC
* *
1646203 AAGCCTTTACACTTTTATTCTAAGCCAAAT
1 AAGCCTTTAAACTTTTATTTTAAGCCAAAT
* *
1646233 AAGTCTTTATACTTTTATTTTAAGCCAAAT
1 AAGCCTTTAAACTTTTATTTTAAGCCAAAT
1646263 AAGCCTTTAAACTTTTATTT
1 AAGCCTTTAAACTTTTATTT
1646283 GGAGTTAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (30 bp):
AAGCCTTTAAACTTTTATTTTAAGCCAAAT
Found at i:1646301 original size:30 final size:30
Alignment explanation
Indices: 1646207--1646301 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
1646197 TCAATCAAGC
*
1646207 CTTTACACTTTTATTCT-AAGCCAAATAAGT
1 CTTTAAACTTTTATT-TGAAGCCAAATAAGT
* * *
1646237 CTTTATACTTTTATTTTAAGCCAAATAAGC
1 CTTTAAACTTTTATTTGAAGCCAAATAAGT
* **
1646267 CTTTAAACTTTTATTTGGAGTTAAATAAGT
1 CTTTAAACTTTTATTTGAAGCCAAATAAGT
1646297 CTTTA
1 CTTTA
1646302 TGAGTAATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 1 0.02
30 55 0.98
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (30 bp):
CTTTAAACTTTTATTTGAAGCCAAATAAGT
Found at i:1649029 original size:28 final size:26
Alignment explanation
Indices: 1648997--1649084 Score: 69
Period size: 28 Copynumber: 3.4 Consensus size: 26
1648987 TTTTTAAAAA
1648997 TTATAATATTAAAACT-TATAAACTTCAT
1 TTATAATATTAAAA-TATATAAA-TT-AT
1649025 TTATAAT-TATAAAATATATAAATTAT
1 TTATAATAT-TAAAATATATAAATTAT
* **
1649051 GTATAA-ATT-AAATATATGTA-TAT
1 TTATAATATTAAAATATATAAATTAT
*
1649074 ATATAATATTA
1 TTATAATATTA
1649085 CTTTATTATA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
23 8 0.16
24 12 0.24
25 1 0.02
26 8 0.16
27 4 0.08
28 18 0.35
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.44
Consensus pattern (26 bp):
TTATAATATTAAAATATATAAATTAT
Found at i:1649081 original size:17 final size:17
Alignment explanation
Indices: 1649038--1649082 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1649028 TAATTATAAA
1649038 ATATATA-AAT-TATGT
1 ATATATATAATATATGT
*
1649053 ATAAAT-TAAATATATGT
1 ATATATAT-AATATATGT
1649070 ATATATATAATAT
1 ATATATATAATAT
1649083 TACTTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 5 0.21
16 3 0.12
17 15 0.62
18 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
ATATATATAATATATGT
Found at i:1649400 original size:215 final size:216
Alignment explanation
Indices: 1649047--1649508 Score: 553
Period size: 215 Copynumber: 2.1 Consensus size: 216
1649037 AATATATAAA
* * * * *
1649047 TTATGTATAAATTAAATATATGTATATATATAATATTACTTTATTATATATATGAAATTCATGAT
1 TTATGTATAAATTAAATATACGTATATATATAATATAACTTTATTATATATATAAAATTAATGAC
* *
1649112 ATAACTCATATGTTATAATATTTTAATTTTTTTATCCAATTTTTTTATAAATAATAACTAATTAT
66 ATAACTCATATGTTATAATATTTTAA--TTATTA--CAATTTTTGTATAAATAATAACTAATTAT
* *
1649177 AAATAATATGTTATAAAAATTAAGACCATAACTAA-AAAATTATTAAGCGTAATCATATAAATAA
127 AAATAATATGTTATAAAAACTAAGACCATAACTAATAAAATTATTAAGCATAATCATATAAATAA
* *
1649241 AGCCTATTATAAGTTACAGTAATGC
192 AACCTATCATAAGTTACAGTAATGC
*
1649266 TTATGTATAAATTAAATATACGTATATGTATAACATATAACTTTATTATGTATATATAAAATTAA
1 TTATGTATAAATTAAATATACGTATATATAT-A-ATATAACTTTATTA--TATATATAAAATTAA
** * *
1649331 TGACATAGTTTATATGTTATAATGTTTT-A-TATTA-AA-TTTTGTATAAATAATAACTAATTAT
62 TGACATAACTCATATGTTATAATATTTTAATTATTACAATTTTTGTATAAATAATAACTAATTAT
*** ** * *
1649392 AAATAATATGTTATAAAAACTAAGGTGATAACTAATAAGTTTATTGAGTATAATCATATAAATAA
127 AAATAATATGTTATAAAAACTAAGACCATAACTAATAAAATTATTAAGCATAATCATATAAATAA
** **
1649457 AATTTATCATAAGTTATGGTAATGC
192 AACCTATCATAAGTTACAGTAATGC
1649482 TTATGTAT-AATTAAATATA--TATATATA
1 TTATGTATAAATTAAATATACGTATATATA
1649509 ATATTTACAC
Statistics
Matches: 210, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
213 7 0.03
215 66 0.31
216 53 0.25
219 33 0.16
220 1 0.00
221 13 0.06
222 1 0.00
223 36 0.17
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (216 bp):
TTATGTATAAATTAAATATACGTATATATATAATATAACTTTATTATATATATAAAATTAATGAC
ATAACTCATATGTTATAATATTTTAATTATTACAATTTTTGTATAAATAATAACTAATTATAAAT
AATATGTTATAAAAACTAAGACCATAACTAATAAAATTATTAAGCATAATCATATAAATAAAACC
TATCATAAGTTACAGTAATGC
Found at i:1649841 original size:16 final size:15
Alignment explanation
Indices: 1649805--1649845 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1649795 ATTCTTCTTA
* *
1649805 ATATATATAAAAAAT
1 ATATATATATAAATT
1649820 AT-TATATAT-AATT
1 ATATATATATAAATT
1649833 ATATATATATAAA
1 ATATATATATAAA
1649846 ATTAGTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.23
14 13 0.59
15 4 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATATATATAAATT
Found at i:1649848 original size:16 final size:16
Alignment explanation
Indices: 1649805--1649849 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1649795 ATTCTTCTTA
*
1649805 ATATATATAAAA-AAT
1 ATATATATAAAATTAT
*
1649820 AT-TATATATAATTAT
1 ATATATATAAAATTAT
1649835 ATATATATAAAATTA
1 ATATATATAAAATTA
1649850 GTTCGGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 8 0.32
15 6 0.24
16 11 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATAAAATTAT
Found at i:1656108 original size:15 final size:15
Alignment explanation
Indices: 1656088--1656145 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
1656078 TATAGCCAAT
*
1656088 TTCCCTCCAAAAGAG
1 TTCCCTCCAAAAAAG
*
1656103 TTCCCTCTAAAAAAAG
1 TTCCCTC-CAAAAAAG
* *
1656119 TTCCCTCCAAAATAT
1 TTCCCTCCAAAAAAG
1656134 TTCCCTCCAAAA
1 TTCCCTCCAAAA
1656146 CATTTAGGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 24 0.65
16 13 0.35
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26
Consensus pattern (15 bp):
TTCCCTCCAAAAAAG
Found at i:1656150 original size:15 final size:15
Alignment explanation
Indices: 1656085--1656150 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
1656075 ATTTATAGCC
1656085 AATTTCCCTCCAAAA
1 AATTTCCCTCCAAAA
* * *
1656100 GAGTTCCCTCTAAAAA
1 AATTTCCCTC-CAAAA
*
1656116 AAGTTCCCTCCAAAA
1 AATTTCCCTCCAAAA
*
1656131 TATTTCCCTCCAAAA
1 AATTTCCCTCCAAAA
*
1656146 CATTT
1 AATTT
1656151 AGGAGGGAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
15 29 0.69
16 13 0.31
ACGTcount: A:0.36, C:0.30, G:0.05, T:0.29
Consensus pattern (15 bp):
AATTTCCCTCCAAAA
Found at i:1691278 original size:17 final size:17
Alignment explanation
Indices: 1691258--1691290 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1691248 ATAATAATAA
1691258 AATAAG-AGTTATTATTC
1 AATAAGAAGTT-TTATTC
1691275 AATAAGAAGTTTTATT
1 AATAAGAAGTTTTATT
1691291 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (17 bp):
AATAAGAAGTTTTATTC
Done.