Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007864.1 Hibiscus syriacus cultivar Beakdansim tig00110236_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: 1537186
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1473023 original size:50 final size:49
Alignment explanation
Indices: 1472967--1473062 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 49
1472957 CATGAAATTC
1472967 GTTATACTCACGTGACAAATTATAATAAAAAATTATATTTTATAAAAGTT
1 GTTATACTCACGTGACAAATTATAAT-AAAAATTATATTTTATAAAAGTT
* *
1473017 GTTATACTCATGTGACAAATTCTAATAAAAATTATATTTTATAAAA
1 GTTATACTCACGTGACAAATTATAATAAAAATTATATTTTATAAAA
1473063 CTCATTATAC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 20 0.45
50 24 0.55
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (49 bp):
GTTATACTCACGTGACAAATTATAATAAAAATTATATTTTATAAAAGTT
Found at i:1473071 original size:49 final size:50
Alignment explanation
Indices: 1472968--1473072 Score: 158
Period size: 49 Copynumber: 2.1 Consensus size: 50
1472958 ATGAAATTCG
* **
1472968 TTATACTCACGTGACAAATTATAATAAAAAATTATATTTTATAAAAGTTG
1 TTATACTCACGTGACAAATTATAATAAAAAATTATATTTTATAAAACTCA
* *
1473018 TTATACTCATGTGACAAATTCTAAT-AAAAATTATATTTTATAAAACTCA
1 TTATACTCACGTGACAAATTATAATAAAAAATTATATTTTATAAAACTCA
1473067 TTATAC
1 TTATAC
1473073 ATAAGATTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 27 0.54
50 23 0.46
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (50 bp):
TTATACTCACGTGACAAATTATAATAAAAAATTATATTTTATAAAACTCA
Found at i:1481766 original size:19 final size:19
Alignment explanation
Indices: 1481744--1481781 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1481734 AATAAACCAA
*
1481744 ATAAGGTAATATAACATTC
1 ATAAGGTAATACAACATTC
1481763 ATAAGGTAATACAACATTC
1 ATAAGGTAATACAACATTC
1481782 CCGTAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (19 bp):
ATAAGGTAATACAACATTC
Found at i:1482109 original size:31 final size:31
Alignment explanation
Indices: 1482071--1482141 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
1482061 TGATGAATTT
* *
1482071 TTAATTTGACTCATGAACTTTAGATAAAATA
1 TTAATTTGACTCATAAACTTTAGAAAAAATA
* * *
1482102 TTAATTTGA-TCCTAAATTTTATAAAAAATA
1 TTAATTTGACTCATAAACTTTAGAAAAAATA
*
1482132 TTATTTTGAC
1 TTAATTTGAC
1482142 CCTAAACATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (31 bp):
TTAATTTGACTCATAAACTTTAGAAAAAATA
Found at i:1482154 original size:30 final size:30
Alignment explanation
Indices: 1482096--1482169 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
1482086 AACTTTAGAT
* **
1482096 AAAATATTAATTTGATCCTAAATTTTATAA
1 AAAATATTAATTTGACCCTAAACATTATAA
* *
1482126 AAAATATTATTTTGACCCTAAACATTATAT
1 AAAATATTAATTTGACCCTAAACATTATAA
* *
1482156 AACATATCAATTTG
1 AAAATATTAATTTG
1482170 GCCCCTAAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.41
Consensus pattern (30 bp):
AAAATATTAATTTGACCCTAAACATTATAA
Found at i:1482218 original size:26 final size:26
Alignment explanation
Indices: 1482186--1482241 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1482176 AAGTTCTTTC
1482186 CATCGATCGCCACTCACAATTGTCTT
1 CATCGATCGCCACTCACAATTGTCTT
1482212 CATCGATCGCCACTCACAATTGTCTT
1 CATCGATCGCCACTCACAATTGTCTT
1482238 CATC
1 CATC
1482242 AATTAGCACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.23, C:0.36, G:0.11, T:0.30
Consensus pattern (26 bp):
CATCGATCGCCACTCACAATTGTCTT
Found at i:1489539 original size:20 final size:20
Alignment explanation
Indices: 1489516--1489555 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1489506 TTTTTTCTAG
*
1489516 GGGATCGATCCTTTTGAAAA
1 GGGATCGATCCTTTTCAAAA
*
1489536 GGGATCGATTCTTTTCAAAA
1 GGGATCGATCCTTTTCAAAA
1489556 CAAAAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (20 bp):
GGGATCGATCCTTTTCAAAA
Found at i:1495231 original size:159 final size:157
Alignment explanation
Indices: 1495025--1495548 Score: 612
Period size: 159 Copynumber: 3.3 Consensus size: 157
1495015 CATGTAGTTT
* * *
1495025 AAATTTGGTAAAAACAA--ACTTAAAATAAATGGCAAATTGAAGGAATAAAGAGATTATGAAAAG
1 AAATTTGGTAAAAA-AATGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTATGAAAA-
* * * *
1495088 TTAAAGGACTAAATTGAAAAATAAAACATTTTTTTTTATCAAAAAGAGGATTTGAAATTACACAT
64 TTAAAGGACTAAATTGAAAAATAAAA-A--TTTTATTATCAAAAAGAGGAATTGAAAGTACATAT
* * *
1495153 GTATTATACTATGGTTTAGGAGAATGTGGCTC
126 GTATTCTACTATGGTTTAGGAGCATGTGACTC
* *
1495185 AAATTT-G-ATAAAACTGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTATGAAAAAT
1 AAATTTGGTAAAAAAATGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTATG-AAAAT
* * * * * * *
1495248 TGAAGGGCTAAATTGAAAAATAAAAATTTTGTTATAAAAAAGATGAGTTGAAAGTACATGTGTAT
65 TAAAGGACTAAATTGAAAAATAAAAATTTTATTATCAAAAAGAGGAATTGAAAGTACATATGTAT
* *
1495313 TCTATTATGGTTTAGGACCATGTGACTC
130 TCTACTATGGTTTAGGAGCATGTGACTC
* * *
1495341 AAATTTGGTAAAAAAATGACTTAAAATAAATGACGAATTAAAGAAACAAGGAGATTATGGAAAAT
1 AAATTTGGTAAAAAAATGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTAT-GAAAAT
* *
1495406 TTAAGGACTAAATTGAAAAATAAAAA--TTATTATCAAGAAAGAGGAATTGAAAGTATATATGTA
65 TAAAGGACTAAATTGAAAAATAAAAATTTTATTATCAA-AAAGAGGAATTGAAAGTACATATGTA
* * *
1495469 TTCTACAATGTTTTAGGAGCATGTGA-TT
129 TTCTACTATGGTTTAGGAGCATGTGACTC
* * *
1495497 AAAGTTTGGTAAAAAAAATGGACTTAAAATGAAGGAGGAATTGAAGAAATAA
1 AAA-TTTGGT-AAAAAAAT-GACTTAAAATAAATGACGAATTGAAGAAATAA
1495549 TGAAACCAGG
Statistics
Matches: 312, Mismatches: 42, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
156 73 0.23
157 52 0.17
158 86 0.28
159 91 0.29
160 10 0.03
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.29
Consensus pattern (157 bp):
AAATTTGGTAAAAAAATGACTTAAAATAAATGACGAATTGAAGAAATAAAGAGATTATGAAAATT
AAAGGACTAAATTGAAAAATAAAAATTTTATTATCAAAAAGAGGAATTGAAAGTACATATGTATT
CTACTATGGTTTAGGAGCATGTGACTC
Found at i:1497949 original size:20 final size:20
Alignment explanation
Indices: 1497924--1497996 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1497914 GGACTCTATG
1497924 GAGTATCGATACCAAGGGAT
1 GAGTATCGATACCAAGGGAT
***** *
1497944 GAGTATCGATACTCCCTATAG
1 GAGTATCGATAC-CAAGGGAT
*
1497965 GGGTATCGATACCAAGGGAT
1 GAGTATCGATACCAAGGGAT
1497985 GAGTATCGATAC
1 GAGTATCGATAC
1497997 TCCCTATAGG
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 25 0.66
21 13 0.34
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (20 bp):
GAGTATCGATACCAAGGGAT
Found at i:1497972 original size:21 final size:21
Alignment explanation
Indices: 1497946--1498018 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
1497936 CAAGGGATGA
1497946 GTATCGATACTCCCTATAGGG
1 GTATCGATACTCCCTATAGGG
***** * *
1497967 GTATCGATAC-CAAGGGATGA
1 GTATCGATACTCCCTATAGGG
1497987 GTATCGATACTCCCTATAGGG
1 GTATCGATACTCCCTATAGGG
*
1498008 GTATCTATACT
1 GTATCGATACT
1498019 TCCCCTTTTC
Statistics
Matches: 36, Mismatches: 15, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
20 13 0.36
21 23 0.64
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (21 bp):
GTATCGATACTCCCTATAGGG
Found at i:1497983 original size:41 final size:41
Alignment explanation
Indices: 1497926--1498017 Score: 175
Period size: 41 Copynumber: 2.2 Consensus size: 41
1497916 ACTCTATGGA
1497926 GTATCGATACCAAGGGATGAGTATCGATACTCCCTATAGGG
1 GTATCGATACCAAGGGATGAGTATCGATACTCCCTATAGGG
1497967 GTATCGATACCAAGGGATGAGTATCGATACTCCCTATAGGG
1 GTATCGATACCAAGGGATGAGTATCGATACTCCCTATAGGG
*
1498008 GTATCTATAC
1 GTATCGATAC
1498018 TTCCCCTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (41 bp):
GTATCGATACCAAGGGATGAGTATCGATACTCCCTATAGGG
Found at i:1498097 original size:20 final size:21
Alignment explanation
Indices: 1498052--1498101 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1498042 TTAGCACTGG
**
1498052 GGTATCGATACCTTGGGAGAA
1 GGTATCGATACCTTAAGAGAA
*
1498073 -TTATCGATA-CTTAAGAGAA
1 GGTATCGATACCTTAAGAGAA
1498092 GGTATCGATA
1 GGTATCGATA
1498102 TTGTAAGGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (21 bp):
GGTATCGATACCTTAAGAGAA
Found at i:1501819 original size:23 final size:23
Alignment explanation
Indices: 1501792--1501837 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1501782 TCAATGGCCG
1501792 ATGGTCTATGAATCAATAATCTT
1 ATGGTCTATGAATCAATAATCTT
1501815 ATGGTCTATGAATCAATAATCTT
1 ATGGTCTATGAATCAATAATCTT
1501838 CATCGCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (23 bp):
ATGGTCTATGAATCAATAATCTT
Found at i:1502402 original size:35 final size:35
Alignment explanation
Indices: 1502356--1502434 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
1502346 TCTTTCGAGA
*
1502356 GGGGAATACAATACGGAGAATGCTCCATCAATATC
1 GGGGATTACAATACGGAGAATGCTCCATCAATATC
1502391 GGGGATTACAATACGGAGAATGCTCCATCAATATC
1 GGGGATTACAATACGGAGAATGCTCCATCAATATC
1502426 GGGGATTAC
1 GGGGATTAC
1502435 CTCGGGTTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (35 bp):
GGGGATTACAATACGGAGAATGCTCCATCAATATC
Found at i:1505378 original size:22 final size:21
Alignment explanation
Indices: 1505354--1505393 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1505344 GAGAAATTAT
1505354 TTTTAAAATAT-AAAAATGATG
1 TTTTAAAAT-TGAAAAATGATG
1505375 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
1505394 AAACAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATG
Found at i:1507803 original size:64 final size:63
Alignment explanation
Indices: 1507735--1507943 Score: 235
Period size: 65 Copynumber: 3.2 Consensus size: 63
1507725 TTGCACCAAG
*
1507735 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGG-T
* * *
1507799 TGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG-
1 TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATATCCTGAGTGCATCGATGCATGGT
* * * * *
1507862 AGAATGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAAT-TCACT-AATGCATCGATGCAT
1 TG--TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATATC-CTGAGTGCATCGATGCAT
1507925 GGT
61 GGT
*
1507928 TGATGCATCGGTGCAT
1 TG-TGCATCGATGCAT
1507944 CACCTCAAAT
Statistics
Matches: 125, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 34 0.27
65 85 0.68
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (63 bp):
TGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATCCTGAGTGCATCGATGCATGGT
Found at i:1507885 original size:17 final size:19
Alignment explanation
Indices: 1507847--1507893 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1507837 ATATTCAGAG
1507847 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1507866 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
1507883 TGCATTCGATG
1 TGCA-TCGATG
1507894 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1516302 original size:63 final size:64
Alignment explanation
Indices: 1516250--1516410 Score: 227
Period size: 63 Copynumber: 2.5 Consensus size: 64
1516240 CGGTGCACCA
*
1516250 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATA-GCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCAGAGTGCATCGATGCATGG
** * *
1516313 CTTGTGCATCGATGCAT-CAATGCATTCGATGTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCAGAGTGCATCGATGCATGG
** * *
1516376 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
1516411 CAATTAATTC
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
62 23 0.27
63 46 0.54
64 16 0.19
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATATGCAGAGTGCATCGATGCATGG
Found at i:1516399 original size:17 final size:19
Alignment explanation
Indices: 1516361--1516407 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1516351 ATATTCAGAG
1516361 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1516380 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
1516397 TGCATTCGATG
1 TGCA-TCGATG
1516408 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1517682 original size:16 final size:15
Alignment explanation
Indices: 1517627--1517679 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1517617 TTTTAAAAAA
*
1517627 ATAATAATATAATAAT
1 ATAATAA-AAAATAAT
*
1517643 AATGAATAAAAAATGAAA
1 -AT-AATAAAAAAT-AAT
1517661 ATAATAAAAAATAAT
1 ATAATAAAAAATAAT
1517676 ATAA
1 ATAA
1517680 ATATATAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.19
16 10 0.32
17 8 0.26
18 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
ATAATAAAAAATAAT
Found at i:1517907 original size:18 final size:17
Alignment explanation
Indices: 1517884--1517936 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 17
1517874 ATATATATAT
1517884 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1517902 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1517919 ATATATAATAAATAAATG
1 ATA-ATAAT-AATAAATG
1517937 GACTAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 7 0.23
18 16 0.52
19 8 0.26
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1518309 original size:37 final size:36
Alignment explanation
Indices: 1518259--1518361 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 36
1518249 GTGCTTGTGG
* * *
1518259 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATC-TAGTAGAACTCT
* * * *
1518296 ATCCTATTTTTAGGAGTTTGAATCCTAGAAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAAT-CTAGTAGAACTCT
1518333 ATCCTA-TTTTAGGAGTTTGAATCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCTAGTAG
1518362 GACGAAAATG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
35 5 0.09
36 16 0.29
37 34 0.61
38 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCTAGTAGAACTCT
Found at i:1520349 original size:23 final size:21
Alignment explanation
Indices: 1520297--1520358 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
1520287 TTTTGGTGCA
*
1520297 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
1520317 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
1520338 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
1520359 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:1520384 original size:20 final size:20
Alignment explanation
Indices: 1520299--1520384 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
1520289 TTGGTGCAGA
* *
1520299 GGGAATCGA-TCCCCCCTTG
1 GGGAACCGATTCCCCCCTAG
*
1520318 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCC-CT--AG
*
1520342 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCC-TAG
* *
1520363 GGGAATCGATACCCCCCTAG
1 GGGAACCGATTCCCCCCTAG
1520383 GG
1 GG
1520385 TTCTGGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.23
21 23 0.43
22 1 0.02
23 16 0.30
24 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCCCTAG
Found at i:1525287 original size:40 final size:40
Alignment explanation
Indices: 1525236--1525320 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
1525226 CCAGTAGGTT
* * *
1525236 GGTGGCTAACTTGTACACATTAGAAAATTCATCTTTGGTA
1 GGTGGCCAACTTGTACACATTAGAAAATTCAACTTTAGTA
* *
1525276 GGTGGCCAACTTGTATACATTGGAAAATTCAACTTTAGTA
1 GGTGGCCAACTTGTACACATTAGAAAATTCAACTTTAGTA
1525316 GGTGG
1 GGTGG
1525321 TCAAACTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (40 bp):
GGTGGCCAACTTGTACACATTAGAAAATTCAACTTTAGTA
Found at i:1526644 original size:28 final size:27
Alignment explanation
Indices: 1526595--1526707 Score: 104
Period size: 27 Copynumber: 4.0 Consensus size: 27
1526585 AAAAGGTAAA
*
1526595 ATAAAAAAAATTATATTGTTTAAGTTAAG
1 ATAAGAAAAA-TATATT-TTTAAGTTAAG
*
1526624 ATAAGTCAAAAATATA-TTTTAAGTTAAA
1 ATAAG--AAAAATATATTTTTAAGTTAAG
*
1526652 ATAAGAATAATATATTTTTAAGTTAAG
1 ATAAGAAAAATATATTTTTAAGTTAAG
*
1526679 A-AAAATAAAATATATCTTTTGATAGTTAA
1 ATAAGA-AAAATATAT-TTTT-A-AGTTAA
1526708 TATATGAATT
Statistics
Matches: 71, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
26 11 0.15
27 20 0.28
28 19 0.27
29 6 0.08
30 10 0.14
31 5 0.07
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (27 bp):
ATAAGAAAAATATATTTTTAAGTTAAG
Found at i:1532515 original size:51 final size:52
Alignment explanation
Indices: 1532435--1532540 Score: 205
Period size: 51 Copynumber: 2.1 Consensus size: 52
1532425 CATGTACAAA
1532435 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
1 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
1532487 TATGAATGAATTAG-TGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
1 TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
1532538 TAT
1 TAT
1532541 CCTCATGTGC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 40 0.74
52 14 0.26
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42
Consensus pattern (52 bp):
TATGAATGAATTAGTTGTGAATCGCATGGCATTTTTGTTATGAGATGTATGT
Found at i:1534581 original size:20 final size:21
Alignment explanation
Indices: 1534539--1534582 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1534529 GATTTCTGGG
*
1534539 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
1534560 CAAGGGGAA-CGATACCCCTT
1 CAAGGGGAATCGATACCCATT
1534580 CAA
1 CAA
1534583 ACGACGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:1535425 original size:31 final size:31
Alignment explanation
Indices: 1535387--1535542 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
1535377 AGGGTCGAGG
*
1535387 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1535418 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1535449 GATTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1535480 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1535511 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1535542 G
1 G
1535543 GTCCTTCGGG
Statistics
Matches: 112, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
31 111 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1535541 original size:62 final size:62
Alignment explanation
Indices: 1535389--1535542 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
1535379 GGTCGAGGGT
*
1535389 TTACCTATGTTCTTCTGG-ACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
1535451 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
*
1535513 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
1535543 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 2 0.02
62 83 0.97
63 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Done.