Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007963.1 Hibiscus syriacus cultivar Beakdansim tig00110392_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: 1627826
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1437262 original size:2 final size:2
Alignment explanation
Indices: 1437255--1437317 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1437245 GTCTATTTTC
1437255 AT 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 AT
1437297 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1437318 CATGGATGGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1438287 original size:14 final size:13
Alignment explanation
Indices: 1438251--1438292 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1438241 ACAAAAGAAA
1438251 AATATATAAATTC
1 AATATATAAATTC
*
1438264 AATGTATAAATAAT-
1 AATATATAAAT--TC
1438278 AATATATAAATTC
1 AATATATAAATTC
1438291 AA
1 AA
1438293 GAAATACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 1 0.04
13 12 0.50
14 10 0.42
15 1 0.04
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (13 bp):
AATATATAAATTC
Found at i:1439069 original size:19 final size:21
Alignment explanation
Indices: 1439031--1439079 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
1439021 TTTTTTAAAA
1439031 TATAATATTATAAATATATTT
1 TATAATATTATAAATATATTT
*
1439052 TATAAT-TTAT-ATTATATTT
1 TATAATATTATAAATATATTT
*
1439071 GAT-ATATTA
1 TATAATATTA
1439080 AATAACATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 2 0.08
19 13 0.52
20 4 0.16
21 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATAATATTATAAATATATTT
Found at i:1451848 original size:2 final size:2
Alignment explanation
Indices: 1451835--1451869 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1451825 AATAAATAGC
*
1451835 AT AT AC 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 A
1451870 GCTTGAAGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1452209 original size:25 final size:25
Alignment explanation
Indices: 1452167--1452225 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
1452157 TATATTTATT
*
1452167 TTTTAACAATGTAACGTTAGATATGA
1 TTTTAA-AACGTAACGTTAGATATGA
*
1452193 TTTTAAAACGTAACGTTCGATATGA
1 TTTTAAAACGTAACGTTAGATATGA
*
1452218 TTTAAAAA
1 TTTTAAAA
1452226 AAAATAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 24 0.80
26 6 0.20
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (25 bp):
TTTTAAAACGTAACGTTAGATATGA
Found at i:1452481 original size:4 final size:4
Alignment explanation
Indices: 1452472--1452501 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1452462 AAATAAGATT
1452472 ATAA ATAA ATAA ATAA ATAA ATAA A-AA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1452502 GACTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:1458956 original size:6 final size:6
Alignment explanation
Indices: 1458945--1458971 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1458935 GCTAATCCCT
1458945 TCCTTC TCCTTC TCCTTC TCCTTC TCC
1 TCCTTC TCCTTC TCCTTC TCCTTC TCC
1458972 ATGGCTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCTTC
Found at i:1461058 original size:2 final size:2
Alignment explanation
Indices: 1461051--1461094 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
1461041 CTTTCAAACA
* * * *
1461051 AT AT AT AT AT AT AT TT AT AT AT AT GT AT AT AT AT GT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1461093 AT
1 AT
1461095 GTGTATGTGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1461089 original size:12 final size:12
Alignment explanation
Indices: 1461052--1461094 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
1461042 TTTCAAACAA
*
1461052 TATATATATATA
1 TATATATATATG
*
1461064 TTTATATATATG
1 TATATATATATG
*
1461076 TATATATATGTG
1 TATATATATATG
1461088 TATATAT
1 TATATAT
1461095 GTGTATGTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (12 bp):
TATATATATATG
Found at i:1461100 original size:10 final size:10
Alignment explanation
Indices: 1461051--1461096 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
1461041 CTTTCAAACA
*
1461051 ATATATATAT
1 ATATGTATAT
*
1461061 ATATTTATAT
1 ATATGTATAT
1461071 ATATGTATAT
1 ATATGTATAT
*
1461081 ATATGTGTAT
1 ATATGTATAT
1461091 ATATGT
1 ATATGT
1461097 GTATGTGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (10 bp):
ATATGTATAT
Found at i:1466646 original size:13 final size:14
Alignment explanation
Indices: 1466628--1466656 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1466618 AAAATTTTAT
1466628 TTTTAAAAATA-AA
1 TTTTAAAAATATAA
1466641 TTTTAAAAATATAA
1 TTTTAAAAATATAA
1466655 TT
1 TT
1466657 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTTAAAAATATAA
Found at i:1468934 original size:15 final size:15
Alignment explanation
Indices: 1468914--1468951 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1468904 AATGGTGATG
1468914 AAGATGCTGATATTC
1 AAGATGCTGATATTC
1468929 AAGATGCTGATATTC
1 AAGATGCTGATATTC
1468944 AAGATGCT
1 AAGATGCT
1468952 CTAGCCACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (15 bp):
AAGATGCTGATATTC
Found at i:1472558 original size:22 final size:23
Alignment explanation
Indices: 1472521--1472585 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1472511 TTAGTGCAGA
* *
1472521 GGGAATCGATACCCCCCTTGAAG
1 GGGAATCGATTCCCCCTTTGAAG
*
1472544 GGGAATCGATTCCCCCTTTGAAT
1 GGGAATCGATTCCCCCTTTGAAG
* * *
1472567 GGGAACCTATTCCCTCTTT
1 GGGAATCGATTCCCCCTTT
1472586 TAGGGAATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (23 bp):
GGGAATCGATTCCCCCTTTGAAG
Found at i:1475046 original size:19 final size:19
Alignment explanation
Indices: 1475022--1475082 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
1475012 AAACCGAAAC
1475022 CGGTTTTTTCGGTTCGGTT
1 CGGTTTTTTCGGTTCGGTT
*
1475041 CGGTTTTTT---TACCGGTT
1 CGGTTTTTTCGGT-TCGGTT
*
1475058 CGGGTTTTTCGGTTCGGTT
1 CGGTTTTTTCGGTTCGGTT
1475077 CGGTTT
1 CGGTTT
1475083 ATCAGTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.38
19 19 0.56
20 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.31, T:0.51
Consensus pattern (19 bp):
CGGTTTTTTCGGTTCGGTT
Found at i:1481097 original size:6 final size:6
Alignment explanation
Indices: 1481086--1481110 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1481076 TCACCAAGAG
1481086 AATTGC AATTGC AATTGC AATTGC A
1 AATTGC AATTGC AATTGC AATTGC A
1481111 TGCATGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (6 bp):
AATTGC
Found at i:1487415 original size:30 final size:30
Alignment explanation
Indices: 1487381--1487447 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
1487371 TATTTAATAA
* *
1487381 AAATAATAATCTAATTATATATATATATAT
1 AAATAATAATATAATTATATATAAATATAT
* * * *
1487411 AAATATTATTATAATTATTTCTAAATATAT
1 AAATAATAATATAATTATATATAAATATAT
1487441 AAGATAA
1 AA-ATAA
1487448 AATTTTATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (30 bp):
AAATAATAATATAATTATATATAAATATAT
Found at i:1488337 original size:16 final size:16
Alignment explanation
Indices: 1488316--1488354 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1488306 TGTGCAAATC
1488316 CGGGTATCCAAATTTT
1 CGGGTATCCAAATTTT
**
1488332 CGGGTA-CCCGATTTT
1 CGGGTATCCAAATTTT
1488347 CGGGTATC
1 CGGGTATC
1488355 TAGAATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (16 bp):
CGGGTATCCAAATTTT
Found at i:1488426 original size:15 final size:15
Alignment explanation
Indices: 1488406--1488462 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
1488396 CCGGATATTA
1488406 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
1488421 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
1488437 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
1488453 CGGGTACCCG
1 CGGGTACCCG
1488463 ATACCCGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 21 0.58
16 4 0.11
17 11 0.31
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:1488430 original size:32 final size:32
Alignment explanation
Indices: 1488394--1488462 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
1488384 CCGTGTCCCG
1488394 ACCCGGATATTACGGGTACCCGGTAATCGGGT
1 ACCCGGATATTACGGGTACCCGGTAATCGGGT
* *
1488426 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATATTACGGGTACCCGGTAATCGGGT
1488458 ACCCG
1 ACCCG
1488463 ATACCCGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.22
Consensus pattern (32 bp):
ACCCGGATATTACGGGTACCCGGTAATCGGGT
Found at i:1492553 original size:31 final size:31
Alignment explanation
Indices: 1492487--1492576 Score: 128
Period size: 31 Copynumber: 2.8 Consensus size: 31
1492477 GAAGGACCTA
*
1492487 TCCATATGTTCCGAAGAACATAGGTAATACTG
1 TCCATATGTCCCGAAG-ACATAGGTAATACTG
1492519 TCCATATGTCCCGAATGACATAGGTAA-ACTG
1 TCCATATGTCCCGAA-GACATAGGTAATACTG
*
1492550 TCCATATGTCTCGAAAGACATAGGTAA
1 TCCATATGTCCCG-AAGACATAGGTAA
1492577 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 27 0.50
32 26 0.48
33 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
TCCATATGTCCCGAAGACATAGGTAATACTG
Found at i:1492709 original size:21 final size:21
Alignment explanation
Indices: 1492650--1492709 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
1492640 TTTTATCTTT
*
1492650 TCACATATTCATATAAACATA
1 TCACATATTCATATAAGCATA
* * *
1492671 TAACATATTCATAGAAGCCTA
1 TCACATATTCATATAAGCATA
1492692 TCACATATTCATATAAGC
1 TCACATATTCATATAAGC
1492710 TCATAGCTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
TCACATATTCATATAAGCATA
Found at i:1497858 original size:64 final size:63
Alignment explanation
Indices: 1497777--1497993 Score: 222
Period size: 64 Copynumber: 3.4 Consensus size: 63
1497767 TTGAAGGTGT
* * **
1497777 ATCGTTGCATAGGTAGTGCATCGAT-ATACTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATCAT-C-CCATTAATAAT-AAAACATCGAATGCAATTCATG
1497840 C
63 C
* **
1497841 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGAT-CATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* * ** * * * *
1497905 ATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACAACATCGAATACATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGAT-CATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* *
1497969 AACGATGCATCAGTAGTGCATCGAT
1 ATCGATGCATAAGTAGTGCATCGAT
1497994 GCATACCTTC
Statistics
Matches: 130, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
64 124 0.95
65 4 0.03
66 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAAGTAGTGCATCGATCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:1497994 original size:64 final size:64
Alignment explanation
Indices: 1497819--1497997 Score: 243
Period size: 64 Copynumber: 2.8 Consensus size: 64
1497809 TTTAAAATAA
**
1497819 AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATG
1 AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATG
** * *
1497883 AAACATCGAATGCAATTGGTGCATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAAT-
1 AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATG
* * * * *
1497946 ACAACATCGAATACATTTTATGCAACGATGCATCAGTAGTGCATCGATGCAT
1 A-AACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCAT
1497998 ACCTTCATTA
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 1 0.01
64 100 0.99
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
AAACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATG
Found at i:1498692 original size:31 final size:31
Alignment explanation
Indices: 1498654--1498809 Score: 278
Period size: 31 Copynumber: 5.0 Consensus size: 31
1498644 AGGGTCGAGG
1498654 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1498685 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1498716 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1498747 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1498778 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1498809 G
1 G
1498810 GTCCTTCGGG
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 121 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1501538 original size:30 final size:31
Alignment explanation
Indices: 1501499--1501565 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
1501489 GAATGACCTA
* * * *
1501499 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGAAAACTG
*
1501529 TCCATAGGTCCCAAAGAACCTAGGAAAACTG
1 TCCATAGGTCACAAAGAACCTAGGAAAACTG
1501560 TCCATA
1 TCCATA
1501566 TGTTCCTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGAAAACTG
Found at i:1501562 original size:31 final size:30
Alignment explanation
Indices: 1501511--1501608 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 30
1501501 CAGAGGTCAT
* * *
1501511 AAAGAACCTCGGCAACTGTCCATAGGTCCC
1 AAAGAACCTAGGAAACTGTCCATATGTCCC
*
1501541 AAAGAACCTAGGAAAACTGTCCATATGTTCC
1 AAAGAACCTAGG-AAACTGTCCATATGTCCC
** * *
1501572 TTAGAACATAGGTATACTGTCCATATGTCCC
1 AAAGAACCTAGG-AAACTGTCCATATGTCCC
1501603 GAAAGA
1 -AAAGA
1501609 CATAGGTAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
30 11 0.20
31 40 0.74
32 3 0.06
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (30 bp):
AAAGAACCTAGGAAACTGTCCATATGTCCC
Found at i:1501630 original size:32 final size:32
Alignment explanation
Indices: 1501525--1501649 Score: 123
Period size: 31 Copynumber: 4.0 Consensus size: 32
1501515 AACCTCGGCA
* * * *
1501525 ACTGTCCATAGGTCCCAAAGAACCTAGG-AAA
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAT
* **
1501556 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAT
1501587 ACTGTCCATATGTCCCGAA-AGACATAGGTAATT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGTAA-T
* *
1501620 A-TGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTCCCGAAGAACATAGGTAA
1501650 ACCCTCGACT
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.01
31 48 0.62
32 26 0.33
33 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (32 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:1501630 original size:63 final size:62
Alignment explanation
Indices: 1501525--1501648 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 62
1501515 AACCTCGGCA
* *
1501525 ACTGTCCATAGGTCCCAAAGAACCTAGGAAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTCCCAAAGAACATAGGAAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
1501587 ACTGTCCATATGTCCCGAAAG-ACATAGGTAATTA-TGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGGTCCC-AAAGAACATAGG-AA-AACTGTCCATATGTTCCGTAGAACATAGGTA
1501649 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
62 21 0.38
63 33 0.60
64 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCAAAGAACATAGGAAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:1502455 original size:160 final size:160
Alignment explanation
Indices: 1502191--1502510 Score: 631
Period size: 160 Copynumber: 2.0 Consensus size: 160
1502181 CCATCACTGG
1502191 CTCATCGCAAGCCAATGTTTGTTCAATAGCATAAGTACAATTAAATTGCACTCACCTTAGCCTTG
1 CTCATCGCAAGCCAATGTTTGTTCAATAGCATAAGTACAATTAAATTGCACTCACCTTAGCCTTG
*
1502256 CTTTGATTCGATCCTAATTCTTTGATTGTTCCGGAACTTGTTTAGGCTCAATATCTACATAAACA
66 CTTTGATTCGATCCTAATTCTTTAATTGTTCCGGAACTTGTTTAGGCTCAATATCTACATAAACA
1502321 TACTTTTCAAGACGATTATCAGAAGCCTAA
131 TACTTTTCAAGACGATTATCAGAAGCCTAA
1502351 CTCATCGCAAGCCAATGTTTGTTCAATAGCATAAGTACAATTAAATTGCACTCACCTTAGCCTTG
1 CTCATCGCAAGCCAATGTTTGTTCAATAGCATAAGTACAATTAAATTGCACTCACCTTAGCCTTG
1502416 CTTTGATTCGATCCTAATTCTTTAATTGTTCCGGAACTTGTTTAGGCTCAATATCTACATAAACA
66 CTTTGATTCGATCCTAATTCTTTAATTGTTCCGGAACTTGTTTAGGCTCAATATCTACATAAACA
1502481 TACTTTTCAAGACGATTATCAGAAGCCTAA
131 TACTTTTCAAGACGATTATCAGAAGCCTAA
1502511 ACCTTATAAC
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 159 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.34
Consensus pattern (160 bp):
CTCATCGCAAGCCAATGTTTGTTCAATAGCATAAGTACAATTAAATTGCACTCACCTTAGCCTTG
CTTTGATTCGATCCTAATTCTTTAATTGTTCCGGAACTTGTTTAGGCTCAATATCTACATAAACA
TACTTTTCAAGACGATTATCAGAAGCCTAA
Found at i:1503499 original size:45 final size:45
Alignment explanation
Indices: 1503435--1503587 Score: 263
Period size: 45 Copynumber: 3.4 Consensus size: 45
1503425 GGATGTTACA
*
1503435 AAGTATATTGGTAAAATAAGCTTACGAGATTATGGAATAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGT
*
1503480 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGTT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGT
1503525 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGTG-ATAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATG-GAATAAATGGT
*
1503570 AAGTATAATGGTAAAATA
1 AAGTATATTGGTAAAATA
1503588 TTGGATATGT
Statistics
Matches: 103, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 102 0.99
46 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (45 bp):
AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGT
Found at i:1504661 original size:36 final size:36
Alignment explanation
Indices: 1504615--1504754 Score: 214
Period size: 36 Copynumber: 3.9 Consensus size: 36
1504605 CTTAATATTC
1504615 AATAAG-AAAATATCCAAATTTCTTATGAAAACTTT
1 AATAAGAAAAATATCCAAATTTCTTATGAAAACTTT
*
1504650 AATAAGGAAAATATCCAAATTTCTTATGAAAACTTT
1 AATAAGAAAAATATCCAAATTTCTTATGAAAACTTT
*
1504686 AATAAGAAAAATA-CTCAAATTTCTTATGAAACCTTT
1 AATAAGAAAAATATC-CAAATTTCTTATGAAAACTTT
*
1504722 AATAAGAAAAAATACCCAAATTTCTTAT-AAAAC
1 AATAAG-AAAAATATCCAAATTTCTTATGAAAAC
1504755 CTAAATTGAT
Statistics
Matches: 98, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
35 7 0.07
36 71 0.72
37 19 0.19
38 1 0.01
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (36 bp):
AATAAGAAAAATATCCAAATTTCTTATGAAAACTTT
Found at i:1507541 original size:2 final size:2
Alignment explanation
Indices: 1507534--1507559 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1507524 CAGAGTAGTA
1507534 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
1507560 CTTAACTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1515124 original size:32 final size:32
Alignment explanation
Indices: 1515083--1515144 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1515073 GCATAATCTA
* *
1515083 CCTCTGTGTATGCTTCCAAAGTCGAGTTCCTC
1 CCTCCGTGTATGCTTCCAAAGTCAAGTTCCTC
*
1515115 CCTCCGTGTATGCTTCCAGAGTCAAGTTCC
1 CCTCCGTGTATGCTTCCAAAGTCAAGTTCC
1515145 CCTCTCTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.16, C:0.32, G:0.19, T:0.32
Consensus pattern (32 bp):
CCTCCGTGTATGCTTCCAAAGTCAAGTTCCTC
Found at i:1521110 original size:14 final size:14
Alignment explanation
Indices: 1521087--1521122 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1521077 ATAGCCGATA
*
1521087 AATAGAACATATAT
1 AATAGTACATATAT
1521101 AATAGTACATATAT
1 AATAGTACATATAT
1521115 AATAGTAC
1 AATAGTAC
1521123 TTATTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (14 bp):
AATAGTACATATAT
Found at i:1523693 original size:21 final size:21
Alignment explanation
Indices: 1523663--1523808 Score: 115
Period size: 21 Copynumber: 7.0 Consensus size: 21
1523653 GATTTACATA
*
1523663 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
1523684 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
1523707 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
1523726 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
1523749 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
1523768 TTCGCGTTGCAATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
1523791 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
1523809 AATCGCAATG
Statistics
Matches: 99, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
19 24 0.24
21 49 0.49
23 26 0.26
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:1523716 original size:42 final size:42
Alignment explanation
Indices: 1523669--1523808 Score: 244
Period size: 42 Copynumber: 3.3 Consensus size: 42
1523659 CATATTCGCA
*
1523669 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
1523711 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
1523753 TTGCGATAGTCGAAGTTCGCGTTGCAATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1523795 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1523809 AATCGCAATG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 94 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:1523926 original size:5 final size:6
Alignment explanation
Indices: 1523894--1523933 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
1523884 GACACGTATT
1523894 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG A-CACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1523934 GACGGACGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 1 0.03
5 11 0.33
6 21 0.64
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1524628 original size:21 final size:21
Alignment explanation
Indices: 1524561--1524634 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
1524551 TTTGGAATAA
* * *
1524561 ATCGCAACGCAAACTTCGACT
1 ATCGCAATGCGAACTTAGACT
*
1524582 ATCGCAATGCGAA--TATGTA-A
1 ATCGCAATGCGAACTTA-G-ACT
1524602 ATCGCAATGCGAACTTAGACT
1 ATCGCAATGCGAACTTAGACT
*
1524623 ATCGCATTGCGA
1 ATCGCAATGCGA
1524635 TTTACATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 1 0.02
20 15 0.36
21 24 0.57
22 2 0.05
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTAGACT
Found at i:1524696 original size:21 final size:21
Alignment explanation
Indices: 1524643--1524688 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1524633 GATTTACATA
1524643 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
1524664 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
1524685 TTCG
1 TTCG
1524689 TGTTGCGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1526490 original size:18 final size:16
Alignment explanation
Indices: 1526467--1526516 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 16
1526457 AATTTAGGTT
1526467 TAAAATTTTATTTTAA
1 TAAAATTTTATTTTAA
**
1526483 TATTAAATTTTAAATTAA
1 TA--AAATTTTATTTTAA
*
1526501 TAAAATTATATTTTAA
1 TAAAATTTTATTTTAA
1526517 ATATATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAATTTTATTTTAA
Found at i:1530490 original size:19 final size:18
Alignment explanation
Indices: 1530468--1530525 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
1530458 AAAAAAGAAA
1530468 TTTATGATTAAAATTATAT
1 TTTAT-ATTAAAATTATAT
*
1530487 TTTAATATTAAAATTTTAT
1 TTT-ATATTAAAATTATAT
*
1530506 ATTA-A-TAAAATTATAT
1 TTTATATTAAAATTATAT
1530522 TTTA
1 TTTA
1530526 AATATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 13 0.38
17 1 0.03
18 1 0.03
19 17 0.50
20 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTATATTAAAATTATAT
Found at i:1530526 original size:16 final size:17
Alignment explanation
Indices: 1530474--1530526 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1530464 GAAATTTATG
1530474 ATTAAAATTATATTTTAA
1 ATTAAAATTATATTTT-A
* *
1530492 TATTAAAATTTTATATTA
1 -ATTAAAATTATATTTTA
1530510 A-TAAAATTATATTTTA
1 ATTAAAATTATATTTTA
1530526 A
1 A
1530527 ATATATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 14 0.47
17 1 0.03
18 1 0.03
19 14 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAAAATTATATTTTA
Found at i:1530725 original size:21 final size:20
Alignment explanation
Indices: 1530639--1530796 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1530629 AAATGACCAA
**
1530639 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1530658 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1530678 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1530698 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1530719 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1530740 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1530760 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1530781 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1530797 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1530787 original size:20 final size:20
Alignment explanation
Indices: 1530763--1531012 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
1530753 CGATTTTCCA
** *
1530763 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
1530783 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
1530803 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
1530823 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
1530843 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
1530863 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1530883 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1530903 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1530923 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1530943 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1530963 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1530983 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
1531003 AAATCACAAC
1 AAATCGCAAC
1531013 ACTGAAATTT
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:1531732 original size:24 final size:24
Alignment explanation
Indices: 1531693--1531739 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1531683 AAATTTGGTC
1531693 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1531717 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1531740 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1531930 original size:12 final size:12
Alignment explanation
Indices: 1531913--1531937 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1531903 ATATAATCCT
1531913 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1531925 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1531937 G
1 G
1531938 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1534313 original size:19 final size:19
Alignment explanation
Indices: 1534273--1534370 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1534263 GATTCTCTCG
1534273 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1534293 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1534312 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1534326 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1534345 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1534364 TTGCGAT
1 TTGCGAT
1534371 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1534367 original size:52 final size:53
Alignment explanation
Indices: 1534254--1534370 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1534244 GAAATGAAAA
1534254 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1534307 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1534359 TCGCATTGCGAT
1 TCGCATTGCGAT
1534371 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1534466 original size:14 final size:14
Alignment explanation
Indices: 1534447--1534501 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1534437 CGGAAATGAA
1534447 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1534461 AATCGCAATGAGAAATG
1 AATCGCAACGAG--A-G
1534478 AAAATCGCAACGAGAG
1 --AATCGCAACGAGAG
1534494 AATCGCAA
1 AATCGCAA
1534502 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 19 0.56
16 2 0.06
17 2 0.06
19 11 0.32
ACGTcount: A:0.47, C:0.18, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1534481 original size:33 final size:33
Alignment explanation
Indices: 1534429--1534520 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
1534419 CCATTACATT
*
1534429 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATG-AGAAATGAAAATCGCAACGAGAGAA
1534463 TCGCAATGAGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGAGAAATGAAAATCGCAACGAGAGAA
*
1534496 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGAGAAATGAAAATCGCAA
1534521 TGCGAAATGA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 48 0.86
34 8 0.14
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGAGAAATGAAAATCGCAACGAGAGAA
Found at i:1534576 original size:19 final size:19
Alignment explanation
Indices: 1534429--1534577 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
1534419 CCATTACATT
1534429 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
1534449 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
1534463 TCGCAATGAGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
1534482 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
1534496 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
1534515 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
1534534 TCGCAA--CG--A-GATAA
1 TCGCAATGCGAAATGAAAA
*
1534548 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
1534567 TCGCATTGCGA
1 TCGCAATGCGA
1534578 TTATCCCATT
Statistics
Matches: 104, Mismatches: 10, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
14 30 0.29
15 3 0.03
16 5 0.05
17 4 0.04
18 4 0.04
19 52 0.50
20 6 0.06
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:1534577 original size:52 final size:52
Alignment explanation
Indices: 1534461--1534577 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
1534451 GCAACGAGAG
*
1534461 AATCGCAATGAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
1534513 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
1534565 AATCGCATTGCGA
1 AATCGCAATGCGA
1534578 TTATCCCATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1534627 original size:19 final size:19
Alignment explanation
Indices: 1534584--1534683 Score: 138
Period size: 19 Copynumber: 5.5 Consensus size: 19
1534574 GCGATTATCC
1534584 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
*
1534604 CATTGCGATTTTCATTTTG
1 CATTGCGATTTTCATTTCG
*
1534623 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
1534639 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1534656 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1534675 CATTGCGAT
1 CATTGCGAT
1534684 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
14 6 0.08
16 6 0.08
17 7 0.10
19 35 0.49
20 17 0.24
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:1534680 original size:52 final size:53
Alignment explanation
Indices: 1534567--1534683 Score: 191
Period size: 53 Copynumber: 2.2 Consensus size: 53
1534557 GAAATTAAAA
1534567 TCGCATTGCGATTATCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTATCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* * * *
1534620 TTGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTATCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1534672 TCGCATTGCGAT
1 TCGCATTGCGAT
1534684 AGTCAATTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
52 29 0.49
53 30 0.51
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTATCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1534809 original size:14 final size:14
Alignment explanation
Indices: 1534790--1534825 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1534780 CATCAATTAC
1534790 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1534804 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1534818 AC-AATCAA
1 ACAAATCAA
1534826 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1536777 original size:33 final size:33
Alignment explanation
Indices: 1536740--1536832 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
1536730 GCGAAACCAA
1536740 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1536773 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1536806 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1536833 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1536778 original size:14 final size:14
Alignment explanation
Indices: 1536759--1536815 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
1536749 GCGAAATGAA
1536759 AATCGCAACGAAAG
1 AATCGCAACGAAAG
1536773 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1536790 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1536806 AATCGCAACG
1 AATCGCAACG
1536816 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1536797 original size:19 final size:19
Alignment explanation
Indices: 1536703--1536837 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
1536693 TAGTTTACTT
* *
1536703 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1536723 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1536742 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1536761 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1536775 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1536794 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1536808 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1536827 TCGCAATGCGA
1 TCGCAACGCGA
1536838 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 6, Indels: 21
0.79 0.05 0.17
Matches are distributed among these distances:
14 16 0.16
16 12 0.12
17 12 0.12
19 47 0.47
20 12 0.12
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1536829 original size:52 final size:54
Alignment explanation
Indices: 1536703--1536837 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 54
1536693 TAGTTTACTT
* *
1536703 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAATGCGAAACCAAAATCGCAAC-CGAAATG-AAA
**
1536761 TCGCAA-CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
1536808 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAATGCGA
1536838 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
47 8 0.12
49 6 0.09
50 6 0.09
52 37 0.54
56 5 0.07
58 6 0.09
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:1536855 original size:19 final size:19
Alignment explanation
Indices: 1536833--1536961 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1536823 AAAATCGCAA
1536833 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1536852 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1536866 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1536885 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1536899 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1536918 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1536937 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1536957 TGCGA
1 TGCGA
1536962 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1536875 original size:33 final size:33
Alignment explanation
Indices: 1536833--1536924 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1536823 AAAATCGCAA
1536833 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1536866 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1536899 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1536925 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1537164 original size:93 final size:93
Alignment explanation
Indices: 1537005--1537477 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
1536995 TTGAATGGAT
1537005 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1537070 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1537098 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1537163 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1537191 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1537255 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1537283 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1537348 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1537376 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1537441 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1537469 AAATTTACT
1 AAATTTACT
1537478 AAGCAATCTA
Statistics
Matches: 376, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.24
93 285 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1537318 original size:185 final size:186
Alignment explanation
Indices: 1537005--1537477 Score: 921
Period size: 185 Copynumber: 2.5 Consensus size: 186
1536995 TTGAATGGAT
1537005 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1537070 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1537135 TACTATTTCACAGTGTTATAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1537191 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1537255 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1537320 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1537376 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1537441 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1537478 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
185 184 0.65
186 100 0.35
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1539195 original size:14 final size:14
Alignment explanation
Indices: 1539176--1539265 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1539166 TTGAAATGAA
1539176 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1539190 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1539207 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1539223 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1539242 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1539256 AATCGCAACG
1 AATCGCAACG
1539266 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1539213 original size:33 final size:33
Alignment explanation
Indices: 1539168--1539282 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1539158 TCTTTTGGTT
1539168 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1539201 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1539234 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1539267 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1539283 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1539214 original size:19 final size:18
Alignment explanation
Indices: 1539175--1539287 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1539165 GTTGAAATGA
1539175 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1539190 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1539207 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1539223 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1539240 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1539256 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1539273 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1539288 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1539318 original size:14 final size:14
Alignment explanation
Indices: 1539299--1539352 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1539289 TTTGGTTTCG
1539299 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1539313 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1539332 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1539346 CGTTGCG
1 CGTTGCG
1539353 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1539331 original size:33 final size:33
Alignment explanation
Indices: 1539283--1539363 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1539273 AAAATCGCAA
**
1539283 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1539316 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1539349 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
1539364 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.23, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1539399 original size:41 final size:41
Alignment explanation
Indices: 1539339--1539416 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1539329 TCGCGTTGCG
* *
1539339 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1539380 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1539417 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1539415 original size:21 final size:21
Alignment explanation
Indices: 1539340--1539415 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1539330 CGCGTTGCGA
*
1539340 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1539361 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1539381 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1539402 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1539416 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1539540 original size:18 final size:18
Alignment explanation
Indices: 1539517--1539566 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
1539507 CGAGAGAATA
1539517 GCAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
*
1539535 GCAA--CGACA-G-AATC
1 GCAACGCGAAATGAAATC
*
1539549 GTAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
1539567 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 8 0.32
17 1 0.04
18 8 0.32
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:1539541 original size:32 final size:32
Alignment explanation
Indices: 1539498--1539566 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
1539488 ACTAACTTGA
* *
1539498 AAATCGGAACGAGAGAATAGCAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
* *
1539530 AAATCGCAACGACAGAATCGTAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
1539562 AAATC
1 AAATC
1539567 TAAGTGAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATG
Found at i:1539798 original size:22 final size:22
Alignment explanation
Indices: 1539746--1539800 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1539736 TGGTTGTGAG
**
1539746 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1539768 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1539790 GGATTTCTTCG
1 GGATTTCTTCG
1539801 CCGTAAAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1539971 original size:20 final size:20
Alignment explanation
Indices: 1539946--1540139 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
1539936 CTTTAAATAT
1539946 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1539966 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1539988 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1540007 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
1540027 CACATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1540047 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1540067 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1540087 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1540107 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1540127 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1540140 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1540133 original size:60 final size:60
Alignment explanation
Indices: 1539946--1540139 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1539936 CTTTAAATAT
**
1539946 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * * *** *
1540007 CGCGTTGCGATATACGGATACACATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1540067 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1540127 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1540140 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 83 0.75
61 27 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1540156 original size:21 final size:21
Alignment explanation
Indices: 1540126--1540208 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1540116 ATTTTCATAT
*
1540126 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1540147 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1540168 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1540189 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1540209 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1540199 original size:42 final size:43
Alignment explanation
Indices: 1540106--1540204 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1540096 ATTTATGTGT
* *
1540106 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1540147 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1540189 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1540205 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1540759 original size:26 final size:26
Alignment explanation
Indices: 1540712--1540761 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1540702 GTTTTATTAT
**
1540712 CAAAACCGATAAAACGCCTAATATAA
1 CAAAACCGATAAAACGAATAATATAA
1540738 CAAAACCGATAGAAAC-AATAATAT
1 CAAAACCGATA-AAACGAATAATAT
1540762 TTATGATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (26 bp):
CAAAACCGATAAAACGAATAATATAA
Found at i:1542618 original size:4 final size:4
Alignment explanation
Indices: 1542609--1542633 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1542599 TCACTGGTTC
1542609 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
1542634 AAACTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:1546833 original size:38 final size:38
Alignment explanation
Indices: 1546782--1546861 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
1546772 CTGTTCACCT
* *
1546782 TATCCATTTTAGTTTTCTATTTTTGCAGCATCCATGCA
1 TATCCAATTTAGTTTTCTATTTTTACAGCATCCATGCA
1546820 TATCCAATTTAGTTTTCTATTTTTACAGCATCCATGCA
1 TATCCAATTTAGTTTTCTATTTTTACAGCATCCATGCA
1546858 TATC
1 TATC
1546862 AATGCTTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.46
Consensus pattern (38 bp):
TATCCAATTTAGTTTTCTATTTTTACAGCATCCATGCA
Found at i:1551868 original size:27 final size:27
Alignment explanation
Indices: 1551826--1551893 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1551816 CTGTAGGAAT
1551826 TATAGAG--ATGATTTGTTACAATTCC
1 TATAGAGATATGATTTGTTACAATTCC
*
1551851 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACAATTCC
1551878 TATAGAGATATGATTT
1 TATAGAGATATGATTT
1551894 TGTAAATAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 7 0.17
27 33 0.82
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACAATTCC
Found at i:1555615 original size:27 final size:27
Alignment explanation
Indices: 1555573--1555640 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1555563 GTGTAGGAAT
1555573 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1555598 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1555625 TATAGAGATATGATTT
1 TATAGAGATATGATTT
1555641 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1560310 original size:15 final size:16
Alignment explanation
Indices: 1560290--1560321 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1560280 TGACTGCAAG
1560290 ATGAAA-AGGTAAAAA
1 ATGAAAGAGGTAAAAA
1560305 ATGAAAGAGGTAAAAA
1 ATGAAAGAGGTAAAAA
1560321 A
1 A
1560322 CTGTTGCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (16 bp):
ATGAAAGAGGTAAAAA
Found at i:1566827 original size:31 final size:31
Alignment explanation
Indices: 1566792--1566856 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1566782 CAATACAATA
*
1566792 CCCCAACATTTAGTCTATTTGTAAAATGGTC
1 CCCCAACATTTAGTCTATTTGCAAAATGGTC
*
1566823 CCCCAACATTTAGTCTATTTGCAATATGGTC
1 CCCCAACATTTAGTCTATTTGCAAAATGGTC
1566854 CCC
1 CCC
1566857 GACTGTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (31 bp):
CCCCAACATTTAGTCTATTTGCAAAATGGTC
Found at i:1568117 original size:31 final size:30
Alignment explanation
Indices: 1568044--1568102 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
1568034 AATGGTCGAG
1568044 GACCATATTGCAAACAGACTAAATGTTGGA
1 GACCATATTGCAAACAGACTAAATGTTGGA
1568074 GACCATATTGCAAACAGACTAAATGTTGG
1 GACCATATTGCAAACAGACTAAATGTTGG
1568103 GGGACTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (30 bp):
GACCATATTGCAAACAGACTAAATGTTGGA
Found at i:1569317 original size:31 final size:31
Alignment explanation
Indices: 1569282--1569356 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
1569272 AATGGTCGAG
1569282 GACCATATTGCAAACAGACTAAATGTTGGGA
1 GACCATATTGCAAACAGACTAAATGTTGGGA
*
1569313 GACCATATTGCAAACAGACTAAATGTTGGGG
1 GACCATATTGCAAACAGACTAAATGTTGGGA
**
1569344 GACTGTATTGCAA
1 GACCATATTGCAA
1569357 TTTTTAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
GACCATATTGCAAACAGACTAAATGTTGGGA
Found at i:1571857 original size:19 final size:18
Alignment explanation
Indices: 1571814--1571865 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1571804 TGGTTTATGA
1571814 TTATATTTTTA-A-AATT
1 TTATATTTTTATATAATT
*
1571830 TTAAAATTTTTATATAATT
1 TT-ATATTTTTATATAATT
1571849 TATATATTTTTAT-TAAT
1 T-TATATTTTTATATAAT
1571866 ACCTATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 2 0.07
17 8 0.27
18 5 0.17
19 14 0.47
20 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTTTTATATAATT
Found at i:1586760 original size:17 final size:16
Alignment explanation
Indices: 1586725--1586772 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
1586715 TGCAAAAAAA
* *
1586725 TAAATAAGTAAAATAT
1 TAAATAAATTAAATAT
*
1586741 TAAATAATTTAAATACT
1 TAAATAAATTAAATA-T
1586758 TAAATAAATTAAATA
1 TAAATAAATTAAATA
1586773 AAAAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAATAAATTAAATAT
Found at i:1587286 original size:17 final size:17
Alignment explanation
Indices: 1587253--1587302 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1587243 TTTTAAGAGG
1587253 ATAAAAA-TT-AATTATT
1 ATAAAAATTTAAATTA-T
1587269 AATAAAAATATTAAATTAT
1 -ATAAAAAT-TTAAATTAT
*
1587288 ATCAAAATTTAAATT
1 ATAAAAATTTAAATT
1587303 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 14 0.48
18 7 0.24
19 3 0.10
20 5 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAAATTTAAATTAT
Found at i:1597485 original size:18 final size:18
Alignment explanation
Indices: 1597450--1597485 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1597440 AAAATGGGTA
* *
1597450 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
1597468 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
1597486 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:1599554 original size:36 final size:36
Alignment explanation
Indices: 1599505--1599781 Score: 491
Period size: 36 Copynumber: 7.7 Consensus size: 36
1599495 CAAAAGTTTG
* * *
1599505 TTCCGATTCAAGTCAAACGGAGGGAAGCATCTGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
* *
1599541 TTCCGATTTAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
* *
1599577 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGTAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1599613 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1599649 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1599685 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1599721 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1599757 TTCCGATTCAAGTCGAACGGAAGGA
1 TTCCGATTCAAGTCGAACGGAAGGA
1599782 TGTGTCTTAC
Statistics
Matches: 234, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 234 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
Found at i:1609590 original size:16 final size:18
Alignment explanation
Indices: 1609555--1609602 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
1609545 TAACAATATT
*
1609555 TATATTTCTTTATTTGTA
1 TATATTTCATTATTTGTA
1609573 TATATTTCATT-TTT-TA
1 TATATTTCATTATTTGTA
*
1609589 TATATGTCA-TATTT
1 TATATTTCATTATTT
1609603 ATTAATCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 13 0.48
17 3 0.11
18 10 0.37
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (18 bp):
TATATTTCATTATTTGTA
Found at i:1612422 original size:20 final size:20
Alignment explanation
Indices: 1612388--1612441 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1612378 GTAAAGAAAA
1612388 TTACAA-TTA-AACTAATAC
1 TTACAAGTTACAACTAATAC
1612406 TTACAAGTTACAACTAATAC
1 TTACAAGTTACAACTAATAC
*
1612426 TAACAAGTTACAACTA
1 TTACAAGTTACAACTA
1612442 TAAAATAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
18 6 0.18
19 3 0.09
20 24 0.73
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.30
Consensus pattern (20 bp):
TTACAAGTTACAACTAATAC
Found at i:1612522 original size:8 final size:8
Alignment explanation
Indices: 1612509--1612547 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
1612499 TTATGACTTT
1612509 AAAATTAC
1 AAAATTAC
1612517 AAAATTAC
1 AAAATTAC
1612525 AAAATTA-
1 AAAATTAC
1612532 ATAAATTAC
1 A-AAATTAC
1612541 AAAATTA
1 AAAATTA
1612548 ATAAATTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 27 0.93
9 1 0.03
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATTAC
Found at i:1612563 original size:24 final size:24
Alignment explanation
Indices: 1612510--1612555 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1612500 TATGACTTTA
1612510 AAATTACAAAATTACAAAATTAAT
1 AAATTACAAAATTACAAAATTAAT
1612534 AAATTACAAAATTA-ATAAATTA
1 AAATTACAAAATTACA-AAATTA
1612556 TGATATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATTACAAAATTACAAAATTAAT
Found at i:1612568 original size:16 final size:16
Alignment explanation
Indices: 1612509--1612555 Score: 78
Period size: 16 Copynumber: 2.9 Consensus size: 16
1612499 TTATGACTTT
1612509 AAAATTACA-AAATTAC
1 AAAATTA-ATAAATTAC
1612525 AAAATTAATAAATTAC
1 AAAATTAATAAATTAC
1612541 AAAATTAATAAATTA
1 AAAATTAATAAATTA
1612556 TGATATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 1 0.03
16 29 0.97
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTAATAAATTAC
Found at i:1616847 original size:23 final size:23
Alignment explanation
Indices: 1616821--1616864 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1616811 ATATGATTTT
*
1616821 TTATTAAAATTGCATATTTCCCG
1 TTATTAAAATTGCATACTTCCCG
**
1616844 TTATTTGAATTGCATACTTCC
1 TTATTAAAATTGCATACTTCC
1616865 AGTTTGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (23 bp):
TTATTAAAATTGCATACTTCCCG
Found at i:1627580 original size:29 final size:29
Alignment explanation
Indices: 1627547--1627634 Score: 158
Period size: 29 Copynumber: 3.0 Consensus size: 29
1627537 CTCGAATGAC
1627547 CTATCCAGAGGTCATAAAGATCCTCGGTA
1 CTATCCAGAGGTCATAAAGATCCTCGGTA
1627576 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-A
*
1627606 CTATCCAGAGATCATAAAGATCCTCGGTA
1 CTATCCAGAGGTCATAAAGATCCTCGGTA
1627635 AACTGTTCAT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 29 0.51
30 28 0.49
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (29 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTA
Found at i:1627611 original size:30 final size:30
Alignment explanation
Indices: 1627547--1627635 Score: 162
Period size: 30 Copynumber: 3.0 Consensus size: 30
1627537 CTCGAATGAC
1627547 CTATCCAGAGGTCATAAAGATCCTCGGT-A
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1627576 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1627606 CTATCCAGAGATCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1627636 ACTGTTCATA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
29 28 0.48
30 30 0.52
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Done.