Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008512.1 Hibiscus syriacus cultivar Beakdansim tig00111372_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: 1759229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1646808 original size:24 final size:25
Alignment explanation
Indices: 1646755--1646810 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
1646745 AACAGAATTC
*
1646755 AAATCAGAACAGAATTCAGGCCATG
1 AAATCAGAACAGAATTCAAGCCATG
* *
1646780 -TATCAGAACAGAATTCAAGTCA-G
1 AAATCAGAACAGAATTCAAGCCATG
1646803 AAATCAGA
1 AAATCAGA
1646811 TAAAATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (25 bp):
AAATCAGAACAGAATTCAAGCCATG
Found at i:1653538 original size:18 final size:18
Alignment explanation
Indices: 1653515--1653562 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
1653505 CAGCTTGGAG
1653515 TGATGAAGATGACTCCAA
1 TGATGAAGATGACTCCAA
1653533 TGATGAAGATGACTCCAA
1 TGATGAAGATGACTCCAA
1653551 TGATGAAGATGA
1 TGATGAAGATGA
1653563 AGTAGCCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (18 bp):
TGATGAAGATGACTCCAA
Found at i:1654067 original size:20 final size:20
Alignment explanation
Indices: 1654042--1654080 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1654032 AATGAGCATT
1654042 GAAACTAAAGTTCAAGGATC
1 GAAACTAAAGTTCAAGGATC
* *
1654062 GAAACTAATGTTTAAGGAT
1 GAAACTAAAGTTCAAGGAT
1654081 TCAAAGCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (20 bp):
GAAACTAAAGTTCAAGGATC
Found at i:1654466 original size:15 final size:16
Alignment explanation
Indices: 1654429--1654467 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1654419 AATTAATATC
1654429 AATTTTTCAAATGCTTT
1 AATTTTTCAAAT-CTTT
*
1654446 ACTTTTTCAAAT-TTT
1 AATTTTTCAAATCTTT
1654461 AATTTTT
1 AATTTTT
1654468 GACCTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.45
17 11 0.55
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (16 bp):
AATTTTTCAAATCTTT
Found at i:1659157 original size:16 final size:16
Alignment explanation
Indices: 1659123--1659163 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1659113 GTTTACTTAA
1659123 GAATGATT-AAATGCT
1 GAATGATTCAAATGCT
1659138 GAATGATTCAAATG-T
1 GAATGATTCAAATGCT
1659153 CGAATGATTCA
1 -GAATGATTCA
1659164 GAGACTCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:1663985 original size:18 final size:19
Alignment explanation
Indices: 1663962--1663997 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1663952 AGACTCAACA
1663962 AAATAAT-ATTTTATAATC
1 AAATAATCATTTTATAATC
1663980 AAATAATCATTTTATAAT
1 AAATAATCATTTTATAAT
1663998 TTTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAATCATTTTATAATC
Found at i:1664936 original size:17 final size:18
Alignment explanation
Indices: 1664916--1664953 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1664906 TTTGATTTAA
1664916 TAAAAT-ATTAATAAATT
1 TAAAATAATTAATAAATT
*
1664933 TAAAATAATTAATAATTT
1 TAAAATAATTAATAAATT
1664951 TAA
1 TAA
1664954 TATTCAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATAATTAATAAATT
Found at i:1665020 original size:395 final size:395
Alignment explanation
Indices: 1664283--1665073 Score: 1494
Period size: 395 Copynumber: 2.0 Consensus size: 395
1664273 CTCACGTTTG
1664283 ATTCACAGGAAAGATTACTACCCGATAATACTCTTTTTACAATAGTAATATTTTTTTTGTTAAAA
1 ATTCACAGGAAAGATTACTACCCGATAATACTCTTTTTACAATAGTAATATTTTTTTTGTTAAAA
*
1664348 TGGTAAGAATTATATTACCTCCAAATTCTTAGGTATTACACAATTTACTTCACTTTGGATAAGAA
66 TGGTAAGAATGATATTACCTCCAAATTCTTAGGTATTACACAATTTACTTCACTTTGGATAAGAA
1664413 TACCTTGAATTAACAAATTCTTTTTATAATGATCATTCTCAATTCTTATTTTTTATGCTTTACTC
131 TACCTTGAATTAACAAATTCTTTTTATAATGATCATTCTCAATTCTTATTTTTTATGCTTTACTC
1664478 AAAACTATAAACATAATAATAATATATAAAGAGTTTGATTTAATAAAATATTAATAAATTTAAAA
196 AAAACTATAAACATAATAATAATATATAAAGAGTTTGATTTAATAAAATATTAATAAATTTAAAA
* *
1664543 TAATTTATAGTTTTAATATTCAATATATTTACTATTTATAATTTTATGGGATGAAAAAAATATTA
261 TAATTAATAATTTTAATATTCAATATATTTACTATTTATAATTTTATGGGATGAAAAAAATATTA
* *
1664608 TTGTAAAAATGTAATTATTTAAAATAATATTTAACTTTTAGTTATTAAAAACGGGTCTTATATAT
326 TTGTAAAAATGTAATTATTTAAAATAACATTTAACTTTTAGTTATTAAAAACGGGTATTATATAT
1664673 TGAAA
391 TGAAA
* *
1664678 ATTCACGGGAAAGATTATTACCCGATAATACTCTTTTTACAATAGTAATA-TTTTTTTGTTAAAA
1 ATTCACAGGAAAGATTACTACCCGATAATACTCTTTTTACAATAGTAATATTTTTTTTGTTAAAA
*
1664742 TGGTGAGAATGATATTACCTCCAAATTCTTAGGTATTACACAATTTACTTCACTTTGGATAAGAA
66 TGGTAAGAATGATATTACCTCCAAATTCTTAGGTATTACACAATTTACTTCACTTTGGATAAGAA
1664807 TACCCTTGAATTAACAAATTCTTTTTATAATGATCATTCTCAATTCTTATTTTTTATGCTTTACT
131 TA-CCTTGAATTAACAAATTCTTTTTATAATGATCATTCTCAATTCTTATTTTTTATGCTTTACT
1664872 CAAAACTATAAACATAATAATAATATATAAAGAGTTTGATTTAATAAAATATTAATAAATTTAAA
195 CAAAACTATAAACATAATAATAATATATAAAGAGTTTGATTTAATAAAATATTAATAAATTTAAA
1664937 ATAATTAATAATTTTAATATTCAATATATTTACTATTTATAATTTTATGGGATGAAAAAAATATT
260 ATAATTAATAATTTTAATATTCAATATATTTACTATTTATAATTTTATGGGATGAAAAAAATATT
1665002 ATTGTAAAAATGTAATTATTTAAAATAACATTTAACTTTTAGTTATTAAAAACGGGTATTATATA
325 ATTGTAAAAATGTAATTATTTAAAATAACATTTAACTTTTAGTTATTAAAAACGGGTATTATATA
1665067 TTGAAA
390 TTGAAA
1665073 A
1 A
1665074 AAATTATCTT
Statistics
Matches: 387, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
394 79 0.20
395 308 0.80
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (395 bp):
ATTCACAGGAAAGATTACTACCCGATAATACTCTTTTTACAATAGTAATATTTTTTTTGTTAAAA
TGGTAAGAATGATATTACCTCCAAATTCTTAGGTATTACACAATTTACTTCACTTTGGATAAGAA
TACCTTGAATTAACAAATTCTTTTTATAATGATCATTCTCAATTCTTATTTTTTATGCTTTACTC
AAAACTATAAACATAATAATAATATATAAAGAGTTTGATTTAATAAAATATTAATAAATTTAAAA
TAATTAATAATTTTAATATTCAATATATTTACTATTTATAATTTTATGGGATGAAAAAAATATTA
TTGTAAAAATGTAATTATTTAAAATAACATTTAACTTTTAGTTATTAAAAACGGGTATTATATAT
TGAAA
Found at i:1667037 original size:60 final size:61
Alignment explanation
Indices: 1666944--1667060 Score: 227
Period size: 60 Copynumber: 1.9 Consensus size: 61
1666934 CGTTCGATTT
1666944 AATTCATATTTACGTATATTTGCAGCACTTATTATGTTAGGGT-AAAAAAATAAGGTCATG
1 AATTCATATTTACGTATATTTGCAGCACTTATTATGTTAGGGTAAAAAAAATAAGGTCATG
1667004 AATTCATATTTACGTATATTTGCAGCACTTATTATGTTAGGGTAAAAAAAATAAGGT
1 AATTCATATTTACGTATATTTGCAGCACTTATTATGTTAGGGTAAAAAAAATAAGGT
1667061 AATGTGAGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 43 0.77
61 13 0.23
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (61 bp):
AATTCATATTTACGTATATTTGCAGCACTTATTATGTTAGGGTAAAAAAAATAAGGTCATG
Found at i:1670071 original size:18 final size:18
Alignment explanation
Indices: 1670048--1670092 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1670038 TTTTTCAGCA
1670048 TTTTATTTCAATCATTTC
1 TTTTATTTCAATCATTTC
1670066 TTTTATTTCAATCATTTC
1 TTTTATTTCAATCATTTC
1670084 TTTTATTTC
1 TTTTATTTC
1670093 CAACACTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATTTCAATCATTTC
Found at i:1670512 original size:5 final size:5
Alignment explanation
Indices: 1670499--1670539 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
1670489 GCTTTTGCAC
* *
1670499 TTTTA TTTTG TTTTG TTTTA TTTTA TTTTA TTTTA TCTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA
1670540 CGAAAATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1671893 original size:31 final size:30
Alignment explanation
Indices: 1671841--1671901 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
1671831 ATCTTGCCGG
*
1671841 TACTAATTCATTTTTCTCTTTTGTTTGTGT
1 TACTAATTCATTTTTCTCTTTTGCTTGTGT
*
1671871 TACTAACTT-ATTTCTTTTCTTTTGCTTGTGT
1 TACTAA-TTCATTT-TTCTCTTTTGCTTGTGT
1671902 CATTTTTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.13, C:0.15, G:0.10, T:0.62
Consensus pattern (30 bp):
TACTAATTCATTTTTCTCTTTTGCTTGTGT
Found at i:1673908 original size:13 final size:12
Alignment explanation
Indices: 1673892--1673945 Score: 81
Period size: 12 Copynumber: 4.4 Consensus size: 12
1673882 AATAAAAAAC
1673892 AAAAAACAAAGA
1 AAAAAACAAAGA
1673904 AAAAAATCAAAGA
1 AAAAAA-CAAAGA
1673917 AAAAAACAAAGA
1 AAAAAACAAAGA
* *
1673929 GAAAAACGAAGA
1 AAAAAACAAAGA
1673941 AAAAA
1 AAAAA
1673946 GAAGACAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
12 26 0.68
13 12 0.32
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (12 bp):
AAAAAACAAAGA
Found at i:1673908 original size:25 final size:25
Alignment explanation
Indices: 1673871--1673934 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
1673861 CACATCAAAG
1673871 CAAAGAGAGAAAATAAAAAACAAAAAA
1 CAAAGAGA-AAAATAAAAAA-AAAAAA
* * *
1673898 CAAAGAAAAAAATCAAAGAAAAAAA
1 CAAAGAGAAAAATAAAAAAAAAAAA
1673923 CAAAGAGAAAAA
1 CAAAGAGAAAAA
1673935 CGAAGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 17 0.52
26 9 0.27
27 7 0.21
ACGTcount: A:0.78, C:0.08, G:0.11, T:0.03
Consensus pattern (25 bp):
CAAAGAGAAAAATAAAAAAAAAAAA
Found at i:1673944 original size:25 final size:25
Alignment explanation
Indices: 1673892--1673945 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
1673882 AATAAAAAAC
1673892 AAAAAACAAAGAAAAAAATCAAAGA
1 AAAAAACAAAGAAAAAAATCAAAGA
* *
1673917 AAAAAACAAAGAGAAAAA-CGAAGA
1 AAAAAACAAAGAAAAAAATCAAAGA
1673941 AAAAA
1 AAAAA
1673946 GAAGACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (25 bp):
AAAAAACAAAGAAAAAAATCAAAGA
Found at i:1675379 original size:64 final size:64
Alignment explanation
Indices: 1675186--1675485 Score: 265
Period size: 66 Copynumber: 4.7 Consensus size: 64
1675176 ATTTTCTTAA
* * *
1675186 AAACAACGTTTTGTCT-TCCTTGAGACAATTTCTTTTG---AATATATTTGAGTATATTTCTATG
1 AAACAA-GTTTTGTCTCT-TTTGAGACAATTTCTTTTGAAAAAAATATTTGAGTCTATTTCTATG
1675247 G
64 G
* * *
1675248 AAATAAAGTTTTGTCTCTTTTGAGACAGTTTTTCTTTT----AAAATATTTTAGTCTATTTCTAT
1 AAA-CAAGTTTTGTCTCTTTTGAGACA--ATTTCTTTTGAAAAAAATATTTGAGTCTATTTCTAT
1675309 GG
63 GG
** * * *
1675311 AAACAAGTTTTGTCTCTCCTGAGACAATTTCTTTTGAAAAAAATCTTTGAGTCTGTTTATATGG
1 AAACAAGTTTTGTCTCTTTTGAGACAATTTCTTTTGAAAAAAATATTTGAGTCTATTTCTATGG
* * * * * * *
1675375 AAACAAAATTTTGTATCTTTTGATACAGTTTCTTTTGAAGAAAAATATTTGAGTATGTTTCTTTG
1 AAAC-AAGTTTTGTCTCTTTTGAGACAATTTCTTTTGAA-AAAAATATTTGAGTCTATTTCTATG
1675440 G
64 G
* * * *
1675441 AAACAAAATTTTGTCTCTTTTAATACAGTTTCTTTTGAAGAAAAA
1 AAAC-AAGTTTTGTCTCTTTTGAGACAATTTCTTTTGAA-AAAAA
1675486 ACCTTTGAGT
Statistics
Matches: 202, Mismatches: 26, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
60 8 0.04
62 40 0.20
63 28 0.14
64 33 0.16
65 28 0.14
66 65 0.32
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45
Consensus pattern (64 bp):
AAACAAGTTTTGTCTCTTTTGAGACAATTTCTTTTGAAAAAAATATTTGAGTCTATTTCTATGG
Found at i:1675434 original size:66 final size:66
Alignment explanation
Indices: 1675226--1675714 Score: 386
Period size: 66 Copynumber: 7.5 Consensus size: 66
1675216 TCTTTTGAAT
* * *
1675226 ATATTTGAGTATATTTCTATGGAAATAAAGTTTTGTCTCTTTTGAGACAGTTTTTCTTTT-----
1 ATATTTGAGTATGTTTCTATGGAAACAAAATTTTGTCTCTTTTGAGACAG--TTTCTTTTGAAGA
1675286 AAA
64 AAA
* * * * ** *
1675289 ATATTTTAGTCTATTTCTATGGAAAC-AAGTTTTGTCTCTCCTGAGACAATTTCTTTTGAA-AAA
1 ATATTTGAGTATGTTTCTATGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAA
1675352 A
66 A
* * * * *
1675353 ATCTTTGAGTCTGTTTATATGGAAACAAAATTTTGTATCTTTTGATACAGTTTCTTTTGAAGAAA
1 ATATTTGAGTATGTTTCTATGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAA
1675418 A
66 A
* * *
1675419 ATATTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAATACAGTTTCTTTTGAAGAAA
1 ATATTTGAGTATGTTTCTATGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAA
1675484 A
66 A
* * * *
1675485 A-ACCTTTGAGT-CGTTCTCT-T-GAAACAAAA----G--TC-TTGGAGTTC-GTTTCCTTTGGA
1 ATA--TTTGAGTATGTT-TCTATGGAAACAAAATTTTGTCTCTTTTGAG-ACAGTTT-CTTTTG-
*
1675538 ACAAAATTTAAA
60 --AAGA---AAA
* * *
1675550 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGACA
1 ATATTTGAGTATGTTTCTATGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGA-A
1675615 AA
65 AA
* * * * *
1675617 ATTTTTGAGTATGTTTCTATGGAAACAAAATTTTGTCTCTCTTGAAACAATTTCTTTTGAGAAAA
1 ATATTTGAGTATGTTTCTATGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTT--GAAGA
1675682 AAA
64 AAA
* * * *
1675685 ATCTTTCAGTATGTTTCCATTGAAACAAAA
1 ATATTTGAGTATGTTTCTATGGAAACAAAA
1675715 CAACCATATT
Statistics
Matches: 348, Mismatches: 47, Indels: 57
0.77 0.10 0.13
Matches are distributed among these distances:
58 7 0.02
59 8 0.02
60 8 0.02
61 1 0.00
62 23 0.07
63 23 0.07
64 35 0.10
65 46 0.13
66 78 0.22
67 65 0.19
68 29 0.08
69 7 0.02
70 1 0.00
72 8 0.02
73 9 0.03
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (66 bp):
ATATTTGAGTATGTTTCTATGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAA
A
Found at i:1675509 original size:131 final size:131
Alignment explanation
Indices: 1675239--1675714 Score: 385
Period size: 131 Copynumber: 3.6 Consensus size: 131
1675229 TTTGAGTATA
* * * *
1675239 TTTCTATGGAAATAAAGTTTTGTCTCTTTTGAGACAGTTTTTCTTTT-----AAAATATTTTAGT
1 TTTCTATGGAAACAAAATTTTGT-TCTTTTGATACAG--TTTCTTTTGAAAAAAAATATTTGAGT
* * * * ** *
1675299 CTATTTCTATGGAAAC-AAGTTTTGTCTCTCCTGAGACAATTTCTTTTG-A-AAAAAATCTTTGA
63 ATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAAAATCTTTGA
1675361 GTCTG
128 GTC-G
* *
1675366 TTTATATGGAAACAAAATTTTGTATCTTTTGATACAGTTTCTTTTGAAGAAAAATATTTGAGTAT
1 TTTCTATGGAAACAAAATTTTGT-TCTTTTGATACAGTTTCTTTTGAAAAAAAATATTTGAGTAT
* * *
1675431 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTAATACAGTTTCTTTTGAAGAAAAAACCTTTGAGT
65 GTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAAAATCTTTGAGT
1675496 CG
130 CG
* * * *
1675498 TTCTCT-T-GAAACAAAA----G-TC-TTGGAGTTC-GTTTCCTTTGGAACAAAATTTAAAATCT
1 TT-TCTATGGAAACAAAATTTTGTTCTTTTGA-TACAGTTT-CTTTTG---AAAA---AAAATAT
* *
1675554 TTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGACAAAAT
57 TTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAAAAT
* *
1675619 TTTTGAGTATG
122 CTTTGAGT-CG
* * * * *
1675630 TTTCTATGGAAACAAAATTTTGTCTCTCTTGAAACAATTTCTTTTGAGAAAAAAAATCTTTCAGT
1 TTTCTATGGAAACAAAATTTTGT-TCTTTTGATACAGTTTCTTTT--GAAAAAAAATATTTGAGT
*
1675695 ATGTTTCCATT-GAAACAAAA
63 ATGTTT-CTTTGGAAACAAAA
1675715 CAACCATATT
Statistics
Matches: 280, Mismatches: 38, Indels: 54
0.75 0.10 0.15
Matches are distributed among these distances:
124 8 0.03
125 17 0.06
127 33 0.12
128 3 0.01
130 25 0.09
131 111 0.40
132 9 0.03
133 26 0.09
135 26 0.09
136 3 0.01
137 1 0.00
138 4 0.01
139 7 0.03
140 6 0.02
141 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (131 bp):
TTTCTATGGAAACAAAATTTTGTTCTTTTGATACAGTTTCTTTTGAAAAAAAATATTTGAGTATG
TTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAAAAATCTTTGAGTC
G
Found at i:1675577 original size:36 final size:37
Alignment explanation
Indices: 1675510--1675582 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
1675500 CTCTTGAAAC
1675510 AAAAGTCTTGGAGTTCGTTTCCTTTGGAACAAAATTT
1 AAAAGTCTTGGAGTTCGTTTCCTTTGGAACAAAATTT
* *
1675547 AAAA-TCTTTGAGTTTGTTT-CTTTGGAAACAAAATTT
1 AAAAGTCTTGGAGTTCGTTTCCTTTGG-AACAAAATTT
1675583 TGTCTCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 6 0.18
36 23 0.70
37 4 0.12
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (37 bp):
AAAAGTCTTGGAGTTCGTTTCCTTTGGAACAAAATTT
Found at i:1675591 original size:36 final size:36
Alignment explanation
Indices: 1675515--1675661 Score: 94
Period size: 36 Copynumber: 4.2 Consensus size: 36
1675505 GAAACAAAAG
* * ****
1675515 TCTTGGAGTTCGTTTCCTTTGG-AACAAAATTTAAAA
1 TCTTTGAGTTTGTTT-CTTTGGAAACAAAATTTTGTC
1675551 TCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTC
1 TCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTC
*** *
1675587 TCTTTTGAGACAGTTTCTTTTGAAGACAAAA-----T-
1 TC-TTTGAGTTTGTTTCTTTGGAA-ACAAAATTTTGTC
* *
1675619 T-TTTGAGTATGTTTCTATGGAAACAAAATTTTGTC
1 TCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTC
1675654 TCTCTTGA
1 TCT-TTGA
1675662 AACAATTTCT
Statistics
Matches: 85, Mismatches: 15, Indels: 21
0.70 0.12 0.17
Matches are distributed among these distances:
29 6 0.07
30 16 0.19
32 1 0.01
33 1 0.01
34 1 0.01
35 7 0.08
36 26 0.31
37 21 0.25
38 6 0.07
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.44
Consensus pattern (36 bp):
TCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTC
Found at i:1675624 original size:30 final size:29
Alignment explanation
Indices: 1675589--1675650 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
1675579 ATTTTGTCTC
* *
1675589 TTTTGAG-ACAGTTTCTTTTGAAGACAAAAT
1 TTTTGAGTA-AGTTTCTATGGAA-ACAAAAT
*
1675619 TTTTGAGTATGTTTCTATGGAAACAAAAT
1 TTTTGAGTAAGTTTCTATGGAAACAAAAT
1675648 TTT
1 TTT
1675651 GTCTCTCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.36
30 17 0.61
31 1 0.04
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (29 bp):
TTTTGAGTAAGTTTCTATGGAAACAAAAT
Found at i:1675632 original size:67 final size:68
Alignment explanation
Indices: 1675547--1675714 Score: 223
Period size: 67 Copynumber: 2.5 Consensus size: 68
1675537 AACAAAATTT
* * * *
1675547 AAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGA-A
1 AAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAAACAATTTCTTTTGAGA
* *
1675611 GAC
66 AAA
* *
1675614 AAAATTTTTGAGTATGTTTCTATGGAAACAAAATTTTGTCTCTCTTGAAACAATTTCTTTTGAGA
1 AAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAAACAATTTCTTTTGAGA
1675679 AAA
66 AAA
* *
1675682 AAAATCTTTCAGTATGTTTCCATT-GAAACAAAA
1 AAAATCTTTGAGTATGTTT-CTTTGGAAACAAAA
1675715 CAACCATATT
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
67 57 0.66
68 28 0.32
69 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (68 bp):
AAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAAACAATTTCTTTTGAGA
AAA
Found at i:1676080 original size:65 final size:64
Alignment explanation
Indices: 1675890--1676080 Score: 231
Period size: 65 Copynumber: 2.9 Consensus size: 64
1675880 ACAAAACAAA
* *
1675890 CATCTTTGAGATCGTTTCCTTTGAAACGAATTTTGTCTCTTTTGAAATAGTTCTCTTGAAACACC
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAAACAGTTCT-TTGAAACACC
* * * * * * * *
1675955 TATCTTTGAGATCATTT-TCTAGAAATGAATTTTATCTCTTTTCAAACAATTTCTTTTGAAACAC
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAAAC-AGTTC-TTTGAAACAC
1676019 C
64 C
* *
1676020 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACAGCTTCTATGAAA
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAAACAG-TTCTTTGAAA
1676081 GTATCATCTC
Statistics
Matches: 102, Mismatches: 20, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
64 23 0.23
65 51 0.50
66 28 0.27
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.42
Consensus pattern (64 bp):
CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAAACAGTTCTTTGAAACACC
Found at i:1676089 original size:65 final size:63
Alignment explanation
Indices: 1675890--1676111 Score: 223
Period size: 65 Copynumber: 3.4 Consensus size: 63
1675880 ACAAAACAAA
* *
1675890 CATCTTTGAGATCGTTTCCTTTGAAACGAATTTTGTCTCTTTTGAAATAGTTCTCTTGAAACAC
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAAACAGTTCT-TTGAAACAC
* * * * * * *
1675954 CTATCTTTGAGATCATTT-TCTAGAAATGAATTTTATCTCTTTTCAAACAATTTCTTTTGAAACA
1 C-ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAAAC-AGTTC-TTTGAAACA
1676018 CC
63 -C
* * * *
1676020 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAGACAGCTTCTATGAAAGTAT
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAAACAG-TTCTTTGAAA-CAC
* *
1676085 CATCTCTGAG-TCAGTTTCTCTTGAAAC
1 CATCTTTGAGATC-GTTTCCCTTGAAAC
1676112 CATTATCCGT
Statistics
Matches: 128, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
64 26 0.20
65 71 0.55
66 31 0.24
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (63 bp):
CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTTTTGAAACAGTTCTTTGAAACAC
Found at i:1676379 original size:136 final size:135
Alignment explanation
Indices: 1676157--1676459 Score: 423
Period size: 136 Copynumber: 2.2 Consensus size: 135
1676147 GTATGAGCTA
* * * * *
1676157 TGTCATCC-CCTGACCAGACCTTCTCATAACGTAGGAGCCGTGTCACGCTTAGATAGCCAGACTT
1 TGTCATCCACC-GACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGA-TT
*
1676221 CCTCATCATATAGGAACTGTGTTATCACTATATCCCTAAAGATAACCAGTCGTCCTCATCACGTA
64 CCTCATCATATAGGAACCGTGTTATCACTATATCCCTAAAGATAACCAGTCGTCCTCATCACGTA
*
1676286 AAAACTG
129 AAAACCG
* *
1676293 TGTCATCTACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAG-TT-G
1 TGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGATTCC
* * *
1676356 TCTTCATAGCGTATGAACCGTGTTATCACTATATCCCTAAAGATAACCAGTTGTCCTCATCACGT
66 TCATCATA---TAGGAACCGTGTTATCACTATATCCCTAAAGATAACCAGTCGTCCTCATCACGT
*
1676421 AGAAACCG
128 AAAAACCG
1676429 TGTCATCCACCGACCAGACCTCCTCATCACG
1 TGTCATCCACCGACCAGACCTCCTCATCACG
1676460 CTTAGATAGC
Statistics
Matches: 149, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
133 7 0.05
134 2 0.01
136 138 0.93
137 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (135 bp):
TGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGATTCC
TCATCATATAGGAACCGTGTTATCACTATATCCCTAAAGATAACCAGTCGTCCTCATCACGTAAA
AACCG
Found at i:1678294 original size:16 final size:16
Alignment explanation
Indices: 1678269--1678321 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1678259 TTTTATTTTA
1678269 TTTA-TTTTCTAGCAC
1 TTTATTTTTCTAGCAC
*
1678284 TTTATTTTTCTA-CTC
1 TTTATTTTTCTAGCAC
*
1678299 TTTAATTTTTC-AGCAT
1 TTT-ATTTTTCTAGCAC
1678315 TTTATTT
1 TTTATTT
1678322 CAATCATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 14 0.44
16 18 0.56
ACGTcount: A:0.19, C:0.15, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTATTTTTCTAGCAC
Found at i:1681727 original size:119 final size:119
Alignment explanation
Indices: 1681506--1681728 Score: 288
Period size: 119 Copynumber: 1.9 Consensus size: 119
1681496 TAAAAATGGT
* * *
1681506 CTTCTTTTGAAAGCTAAAATAGACTTGGAATATCAAAATGAAATTTTGAAAAAGGAGTTAGAGCT
1 CTTCTTTAGAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATATTGAAAAAGGAGTTAGAGCT
* *
1681571 TTAAAAAATGAAATCTGAAAAAATTTGAAAAATAAATTTTTCGAATTAAACAAA
66 CTAAAAAATGAAATCTGAAAAAATTTGAAAAAAAAATTTTTCGAATTAAACAAA
* * * * * *
1681625 CTTCTTCTAGAAA-CTAAAATGGATTTTGAAAATCAAAATGAAATATTGAAGAAGGATTTAGATC
1 CTTCTT-TAGAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATATTGAAAAAGGAGTTAGAGC
* **
1681689 TCTAAAAAATGAAATTTG-AAAGCTTTGAAAAAGAAAATTT
65 TCTAAAAAATGAAATCTGAAAAAATTTGAAAAA-AAAATTT
1681729 CAATTTAAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
118 12 0.14
119 71 0.81
120 5 0.06
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (119 bp):
CTTCTTTAGAAAGCTAAAATAGACTTGGAAAATCAAAATGAAATATTGAAAAAGGAGTTAGAGCT
CTAAAAAATGAAATCTGAAAAAATTTGAAAAAAAAATTTTTCGAATTAAACAAA
Found at i:1686152 original size:21 final size:22
Alignment explanation
Indices: 1686123--1686188 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 22
1686113 TAAAAAAATG
*
1686123 TTTTGATTTTAAA-ATTGTTG-T
1 TTTTTATTTTAAATA-TGTTGTT
*
1686144 TTTTTA-TTTAATTATGTTGTT
1 TTTTTATTTTAAATATGTTGTT
*
1686165 TTTTTA-TTTAATTATGTTGTT
1 TTTTTATTTTAAATATGTTGTT
1686186 TTT
1 TTT
1686189 CTGAAACTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.24
21 31 0.76
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.70
Consensus pattern (22 bp):
TTTTTATTTTAAATATGTTGTT
Found at i:1686153 original size:20 final size:20
Alignment explanation
Indices: 1686138--1686188 Score: 93
Period size: 21 Copynumber: 2.5 Consensus size: 20
1686128 ATTTTAAAAT
1686138 TGTTGTTTTTTATTTAATTA
1 TGTTGTTTTTTATTTAATTA
1686158 TGTTGTTTTTTTATTTAATTA
1 TGTTG-TTTTTTATTTAATTA
1686179 TGTTGTTTTT
1 TGTTGTTTTT
1686189 CTGAAACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.73
Consensus pattern (20 bp):
TGTTGTTTTTTATTTAATTA
Found at i:1693971 original size:20 final size:20
Alignment explanation
Indices: 1693948--1694002 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1693938 TTCCTTTAGG
*
1693948 GGGTATCTATACCCTTCTTA
1 GGGTATCGATACCCTTCTTA
*
1693968 GGGTATCGGTACCCTTCTTA
1 GGGTATCGATACCCTTCTTA
*
1693988 GGGTATCGGTACCCT
1 GGGTATCGATACCCT
1694003 CATTGCATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (20 bp):
GGGTATCGATACCCTTCTTA
Found at i:1697567 original size:20 final size:20
Alignment explanation
Indices: 1697534--1697587 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1697524 ATGTGAAATT
*
1697534 TGTCCCGAAAGACCTATATA
1 TGTCCCGAAGGACCTATATA
* * *
1697554 TGTTCCGAAGGACCTCTGTA
1 TGTCCCGAAGGACCTATATA
1697574 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
1697588 ACTATCTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATATA
Found at i:1697623 original size:32 final size:32
Alignment explanation
Indices: 1697587--1697715 Score: 140
Period size: 32 Copynumber: 4.0 Consensus size: 32
1697577 CCCGAAGGAC
* *
1697587 CACTATCTATATGT-TATGAAGAACATAGGTAA
1 CACTATCCATATGTCT-CGAAGAACATAGGTAA
*
1697619 CACTATCCATATGTCTCGAAGGACATAGGTAA
1 CACTATCCATATGTCTCGAAGAACATAGGTAA
* *
1697651 TC-CTATGCATATGTCCCGAAGGAA-ATAGGTAA
1 -CACTATCCATATGTCTCGAA-GAACATAGGTAA
*
1697683 CACTGTCCATATGTCTCGAA-AGACATAGGTAA
1 CACTATCCATATGTCTCGAAGA-ACATAGGTAA
1697715 C
1 C
1697716 CTCGACTCTT
Statistics
Matches: 82, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
30 1 0.01
31 2 0.02
32 75 0.91
33 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (32 bp):
CACTATCCATATGTCTCGAAGAACATAGGTAA
Found at i:1701414 original size:13 final size:13
Alignment explanation
Indices: 1701392--1701425 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1701382 AGGGGGAGTA
*
1701392 ATTTTCAAAATTG
1 ATTTTCAAAAATG
1701405 A-TTTCAAAAATG
1 ATTTTCAAAAATG
1701417 ATTTTCAAA
1 ATTTTCAAA
1701426 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:1703780 original size:11 final size:11
Alignment explanation
Indices: 1703764--1703788 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1703754 TAACCAAGTC
1703764 ATCCTAGTATG
1 ATCCTAGTATG
1703775 ATCCTAGTATG
1 ATCCTAGTATG
1703786 ATC
1 ATC
1703789 ATCAACAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (11 bp):
ATCCTAGTATG
Found at i:1705722 original size:2 final size:2
Alignment explanation
Indices: 1705715--1705753 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1705705 TGTATACAAA
1705715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1705754 GTATTAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1710752 original size:20 final size:20
Alignment explanation
Indices: 1710716--1710753 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1710706 ATCCTATTCC
**
1710716 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1710736 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1710754 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1712518 original size:18 final size:19
Alignment explanation
Indices: 1712474--1712519 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
1712464 ATGCTTCGTT
1712474 CTTTTTTTGTATATTTTAA
1 CTTTTTTTGTATATTTTAA
*
1712493 -TTTATTTTTTA-ATTTTATA
1 CTTT-TTTTGTATATTTTA-A
1712512 CTTTTTTT
1 CTTTTTTT
1712520 ATGACCATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 9 0.39
19 11 0.48
20 3 0.13
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (19 bp):
CTTTTTTTGTATATTTTAA
Found at i:1714463 original size:30 final size:30
Alignment explanation
Indices: 1714428--1714491 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1714418 CAATACAGTC
* * *
1714428 CCCCAATATTTAGTCTGTTTGTAATATGGT
1 CCCCAACATTTAGTCTATTTGCAATATGGT
*
1714458 CCCCAACATTTAGTTTATTTGCAATATGGT
1 CCCCAACATTTAGTCTATTTGCAATATGGT
1714488 CCCC
1 CCCC
1714492 CAAGTAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.39
Consensus pattern (30 bp):
CCCCAACATTTAGTCTATTTGCAATATGGT
Found at i:1725073 original size:30 final size:30
Alignment explanation
Indices: 1725013--1725101 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
1725003 AATGGATTTA
* * * *
1725013 TTTAGTGATCAAATTATATATTTGGTAAAG
1 TTTAGTGACCAAAGTATAAATTTGGAAAAG
1725043 TTTAGTGACCAAAGTATAAACTTT-GAAAAG
1 TTTAGTGACCAAAGTATAAA-TTTGGAAAAG
* * *
1725073 TTTAAG-GACCAAAATGTAATTTTGGAAAA
1 TTT-AGTGACCAAAGTATAAATTTGGAAAA
1725102 ATTACAAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 3 0.06
30 41 0.84
31 5 0.10
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAATTTGGAAAAG
Found at i:1725214 original size:25 final size:25
Alignment explanation
Indices: 1725180--1725227 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1725170 ATACTTTATG
1725180 TTTAATTTCAGGTTTAAGTTGAAAT
1 TTTAATTTCAGGTTTAAGTTGAAAT
*
1725205 TTTAATTTCAGGTTTAATTTGAA
1 TTTAATTTCAGGTTTAAGTTGAA
1725228 TTGTTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (25 bp):
TTTAATTTCAGGTTTAAGTTGAAAT
Found at i:1732367 original size:30 final size:30
Alignment explanation
Indices: 1732307--1732395 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
1732297 AATGGATTTA
* * *
1732307 TTTAGTGATCAAAGTATACATTTGGTAAAG
1 TTTAGTGACCAAAGTATAAATTTGGAAAAG
1732337 TTTAGTGACCAAAGTATAAACTTT-GAAAAG
1 TTTAGTGACCAAAGTATAAA-TTTGGAAAAG
* * * *
1732367 TTCAAG-GACCAAAATGTAATTTTGGAAAA
1 TT-TAGTGACCAAAGTATAAATTTGGAAAA
1732396 ATTAAAAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 3 0.06
30 41 0.84
31 5 0.10
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAATTTGGAAAAG
Found at i:1736243 original size:129 final size:130
Alignment explanation
Indices: 1736090--1736411 Score: 468
Period size: 129 Copynumber: 2.5 Consensus size: 130
1736080 TTGTTTTTAT
*
1736090 GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATGAGATG
1 GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATG
* * * **
1736155 ACATTTATTCTCGATTGGAAATAATTGGATATTATCGTT-TTCTC-AGATTAATATTTAATTGTA
66 ACATTTATTCTCAATCGGAAATAATTGGATATTATCGTTCCTCTCGA-ATTAATATCGAATTGTA
1736218 G
130 G
* * *
1736219 GATGAAATAATAATATCTCTTCATTTCGATTGGAGTAATAAATGACTGTTTTAAGGCATGAGATG
1 GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATG
* *
1736284 TCATTTATTCTCAATCGGAAATAATTGGATATTATCGTTCCTCTCGAATTAATATCGAATTTTAG
66 ACATTTATTCTCAATCGGAAATAATTGGATATTATCGTTCCTCTCGAATTAATATCGAATTGTAG
* * * * * *
1736349 AAGGAAATAGTAATATTTCTTTATTTTGATTGGAGTAAGAAATGACTGCTTTAAGGCATGAGA
1 GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGA
1736412 GGTTGTTTCT
Statistics
Matches: 172, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
129 97 0.56
130 74 0.43
131 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (130 bp):
GATGAAATAGTAATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGATG
ACATTTATTCTCAATCGGAAATAATTGGATATTATCGTTCCTCTCGAATTAATATCGAATTGTAG
Found at i:1738188 original size:44 final size:43
Alignment explanation
Indices: 1738102--1738205 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 43
1738092 GAGATATGAT
* * * * *
1738102 TTAAATTGTTATTTATTTTTAAAGAGTTTTAAATAAGTAATAA
1 TTAAATTATTATTTAATTTAAAAAAATTTTAAATAAGTAATAA
1738145 TTAAATTATTATTTAATTTAAAATAAATTTTAAATTAA-TAATAA
1 TTAAATTATTATTTAATTTAAAA-AAATTTTAAA-TAAGTAATAA
* *
1738189 TTTAATTAGTTAATTAA
1 TTAAATTA-TTATTTAA
1738206 ATGGTGGATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
43 20 0.39
44 21 0.41
45 10 0.20
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (43 bp):
TTAAATTATTATTTAATTTAAAAAAATTTTAAATAAGTAATAA
Found at i:1740871 original size:20 final size:22
Alignment explanation
Indices: 1740836--1740877 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1740826 TGTATCTACT
1740836 AATTATGATAAATTAA-AAATA
1 AATTATGATAAATTAATAAATA
*
1740857 AATTAT-ATCAATTAATAAATA
1 AATTATGATAAATTAATAAATA
1740878 CTCTTACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AATTATGATAAATTAATAAATA
Found at i:1741567 original size:21 final size:20
Alignment explanation
Indices: 1741541--1741580 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1741531 TGTGTGTGTG
1741541 TATATAAGATAAAGATATAAT
1 TATATAAGATAAA-ATATAAT
*
1741562 TATATAAGATATAATATAA
1 TATATAAGATAAAATATAA
1741581 AAAATAGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (20 bp):
TATATAAGATAAAATATAAT
Found at i:1745310 original size:60 final size:60
Alignment explanation
Indices: 1745195--1745310 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
1745185 AAATTATTTT
* * * * * *
1745195 TATTCTAAATTAATTCCTAAACTTTTAAATATTGTAATTTCATCCTTAGACTATTACTAG
1 TATTCTAAATTAAGTCCTAAACTTTTAAATACTGTAAGTTCATCCCTAAAATATTACTAG
*
1745255 TATTCTAAATT-AGTCCTCAAATTTTTAAATACT-TAAGTTCTATCCCTAAAATATTA
1 TATTCTAAATTAAGTCCT-AAACTTTTAAATACTGTAAGTTC-ATCCCTAAAATATTA
1745311 TCTTCATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 11 0.23
60 36 0.77
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (60 bp):
TATTCTAAATTAAGTCCTAAACTTTTAAATACTGTAAGTTCATCCCTAAAATATTACTAG
Found at i:1753164 original size:33 final size:34
Alignment explanation
Indices: 1753109--1753177 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 34
1753099 AAAGATGGAC
*
1753109 TTCGTTGCAAATTTTCTTCTTTCTTTGGGCTCCG
1 TTCGTTGCAAATTTTCTGCTTTCTTTGGGCTCCG
1753143 TTCGTTGCAAA-TTTCTGCTTTCTTTGGGCTCCG
1 TTCGTTGCAAATTTTCTGCTTTCTTTGGGCTCCG
1753176 TT
1 TT
1753178 TTCATTTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.09, C:0.23, G:0.19, T:0.49
Consensus pattern (34 bp):
TTCGTTGCAAATTTTCTGCTTTCTTTGGGCTCCG
Found at i:1753406 original size:23 final size:23
Alignment explanation
Indices: 1753380--1753429 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1753370 ATCAAGTACA
1753380 ATAACATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
1753403 ATAATGTAATAGGTAGCGGTTAT
1 ATAACATAATAGGTAGCGCTTAT
1753426 ATAA
1 ATAA
1753430 TAAAATAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1753430 original size:23 final size:23
Alignment explanation
Indices: 1753386--1753430 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1753376 TACAATAACA
1753386 TAATAGGTAGCGCTTATATAATG
1 TAATAGGTAGCGCTTATATAATG
*
1753409 TAATAGGTAGCGGTTATATAAT
1 TAATAGGTAGCGCTTATATAAT
1753431 AAAATAAACA
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:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (23 bp):
TAATAGGTAGCGCTTATATAATG
Found at i:1753436 original size:23 final size:23
Alignment explanation
Indices: 1753387--1753436 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1753377 ACAATAACAT
**
1753387 AATAGGTAGCGCTTATATAATGT
1 AATAGGTAGCGCTTATATAATAA
*
1753410 AATAGGTAGCGGTTATATAATAA
1 AATAGGTAGCGCTTATATAATAA
1753433 AATA
1 AATA
1753437 AACATTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (23 bp):
AATAGGTAGCGCTTATATAATAA
Found at i:1753971 original size:199 final size:198
Alignment explanation
Indices: 1753496--1754157 Score: 858
Period size: 199 Copynumber: 3.3 Consensus size: 198
1753486 TTATATTAAC
* * *
1753496 CTATTTTCTAACT-AAACCGGTATATTTATACTGGTAACATTGCAAATTTACCTATTACATTATA
1 CTATTTTCTCA-TAAAACCGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATA
*
1753560 ATTATCGGTTTCGATGTTTTTGGGATCGATACAATTTT-A-AATGTATCGACACTTTATGTGTGC
65 ATTATCGGTTTCGATGTTTTTGGGATCGATAC--TTTTAATAATGTATCGACACTTTATGCGTGC
* * * * * *
1753623 ACCTCGTTGGGCATTCTTTCTGGAAAAAAAAATATCGACACAAACTTAAAAAGTGTCGATACATT
128 ACCTCGTTTGGCATTCATTCTGG-ACAAATAGTATCGACACAAATTTAAAAAGTGTCGATACATT
* *
1753688 GTGTAGA
192 ATGTTGA
* * * *
1753695 CTATTTTCTCATAAAACC-GTATATTTCTA-TCGGGTGCATTGTAAATTTACCTATTACATTGTA
1 CTATTTTCTCATAAAACCGGTATATTTATACT-GGTTACATTGTAAATTTACCTATTACATTATA
*
1753758 ATTATCGGTTTCGATGTTTTTAGGATCGATACTTTTAATAACTGTATCGACACTTTATGCGTGCA
65 ATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAA-TGTATCGACACTTTATGCGTGCA
* * * *
1753823 CAC-CGTTTGACACTCATTATGGACAAATTGTATCGACACAAATTTAAAAAGTGTCGATACATTA
129 C-CTCGTTTGGCATTCATTCTGGACAAATAGTATCGACACAAATTTAAAAAGTGTCGATACATTA
1753887 TGTTGA
193 TGTTGA
* * *
1753893 CATATTCTCTCATAAAACCGGTATATTTATACTGATTACATTATAAATTTA-CTATTACATTATA
1 C-TATTTTCTCATAAAACCGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATA
*
1753957 ATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGATACTTTATGCGTGCA
65 ATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAAT-AATGTATCGACACTTTATGCGTGCA
** *
1754022 CCTCGTTTGGGCATTCATTCTGGAC-AATAAGTATCGACACAAATTCCACAAGTGTCGATACATT
129 CCTCGTTT-GGCATTCATTCTGGACAAAT-AGTATCGACACAAATTTAAAAAGTGTCGATACATT
1754086 ATGTTGA
192 ATGTTGA
* * * *
1754093 CCTATTTTCTAAT-TAACCGGTATATTTATAC-GGTTACATTGTTAATTTACATATTACATTATA
1 -CTATTTTCTCATAAAACCGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATA
1754156 AT
65 AT
1754158 CGATATTTTT
Statistics
Matches: 404, Mismatches: 44, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
196 4 0.01
197 2 0.00
198 129 0.32
199 180 0.45
200 87 0.22
201 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (198 bp):
CTATTTTCTCATAAAACCGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAA
TTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAATGTATCGACACTTTATGCGTGCACC
TCGTTTGGCATTCATTCTGGACAAATAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGT
TGA
Done.