Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000357.1 Hibiscus syriacus cultivar Beakdansim tig00000653_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: 87444
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:1429 original size:20 final size:20
Alignment explanation
Indices: 1391--1431 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1381 TTATAATTTT
**
1391 ATATTTTTTAACCTAAATAA
1 ATATTTTTTAAAATAAATAA
*
1411 ATATTTTTTAAAATTAATAA
1 ATATTTTTTAAAATAAATAA
1431 A
1 A
1432 AACAAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTTTTTAAAATAAATAA
Found at i:1814 original size:20 final size:20
Alignment explanation
Indices: 1761--1816 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1751 ATTTCACGAG
* *
1761 TATATATATATTTTTAAAGAA
1 TATATATATA-TATTAAACAA
*
1782 TATGATCTA-ATATTAAACAA
1 TAT-ATATATATATTAAACAA
1802 TATATATATATATTA
1 TATATATATATATTA
1817 TATGGTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.14
20 17 0.59
21 4 0.14
22 4 0.14
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (20 bp):
TATATATATATATTAAACAA
Found at i:14457 original size:7 final size:8
Alignment explanation
Indices: 14450--14500 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 8
14440 ATTTTTTATA
14450 TTTAATAT
1 TTTAATAT
14458 ATTTAATAT
1 -TTTAATAT
14467 TTTAATAAT
1 TTTAAT-AT
*
14476 TATTTATAT
1 T-TTAATAT
14485 TTTAA-AT
1 TTTAATAT
*
14492 TTAAATAT
1 TTTAATAT
14500 T
1 T
14501 CTCTTAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.17
8 12 0.33
9 14 0.39
10 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTAATAT
Found at i:14468 original size:16 final size:17
Alignment explanation
Indices: 14444--14486 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
14434 CATATTATTT
14444 TTTATATTTAAT-A-TA
1 TTTATATTTAATAATTA
14459 TTTAATATTTTAATAATTA
1 TTT-ATA-TTTAATAATTA
14478 TTTATATTT
1 TTTATATTT
14487 TAAATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.12
16 3 0.12
17 9 0.38
18 4 0.17
19 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTATATTTAATAATTA
Found at i:14486 original size:18 final size:16
Alignment explanation
Indices: 14444--14489 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
14434 CATATTATTT
14444 TTTATA-TTTAATATA
1 TTTATATTTTAATATA
14459 TTTAATATTTTAATAATTA
1 TTT-ATATTTTAAT-A-TA
14478 TTTATATTTTAA
1 TTTATATTTTAA
14490 ATTTAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 3 0.11
16 3 0.11
17 6 0.22
18 10 0.37
19 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATATTTTAATATA
Found at i:15193 original size:26 final size:25
Alignment explanation
Indices: 15152--15211 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
15142 CAATTTTCAA
* *
15152 AAAAGTAAAAATAAAAACTGTTTTCT
1 AAAACTAAAAATAAAAA-TATTTTCT
15178 GAAAA-TAAAAATAAAAATATTTTCT
1 -AAAACTAAAAATAAAAATATTTTCT
15203 AAAACTAAA
1 AAAACTAAA
15212 CAAACCCTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 11 0.35
26 12 0.39
27 4 0.13
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (25 bp):
AAAACTAAAAATAAAAATATTTTCT
Found at i:18629 original size:24 final size:24
Alignment explanation
Indices: 18602--18652 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
18592 GTTCGTGAAC
*
18602 GTTCGGTTATGTTCGTTCAGTTAT
1 GTTCAGTTATGTTCGTTCAGTTAT
* *
18626 GTTCATTTATGTTCGTTCATTTAT
1 GTTCAGTTATGTTCGTTCAGTTAT
18650 GTT
1 GTT
18653 TAACCCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCAGTTATGTTCGTTCAGTTAT
Found at i:18643 original size:14 final size:14
Alignment explanation
Indices: 18626--18652 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18616 GTTCAGTTAT
18626 GTTCATTTATGTTC
1 GTTCATTTATGTTC
18640 GTTCATTTATGTT
1 GTTCATTTATGTT
18653 TAACCCAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:23133 original size:11 final size:11
Alignment explanation
Indices: 23111--23144 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
23101 AACACCCCCA
*
23111 ACCCGTATCCG
1 ACCCGGATCCG
*
23122 ACCTGGATCCG
1 ACCCGGATCCG
23133 ACCCGGATCCG
1 ACCCGGATCCG
23144 A
1 A
23145 GTCCGAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.21, C:0.41, G:0.24, T:0.15
Consensus pattern (11 bp):
ACCCGGATCCG
Found at i:23965 original size:18 final size:18
Alignment explanation
Indices: 23942--23976 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
23932 ACTGAATATT
23942 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
*
23960 TGTCCCGAAGGACCACT
1 TGTCCCAAAGGACCACT
23977 GATTGTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:24984 original size:2 final size:2
Alignment explanation
Indices: 24977--25018 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
24967 CATGAATTAG
24977 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
25019 TCATATGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28988 original size:24 final size:20
Alignment explanation
Indices: 28933--28990 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 20
28923 AATGAAGGTA
28933 TGCATCGATGCACTCTACAG
1 TGCATCGATGCACTCTACAG
* *
28953 TGTATCGATGCATTCCTTAACATG
1 TGCATCGATGCACT-C-T-ACA-G
28977 TGCATCGATGCACT
1 TGCATCGATGCACT
28991 ACCTGTGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 12 0.40
21 1 0.03
22 1 0.03
23 3 0.10
24 13 0.43
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCACTCTACAG
Found at i:31630 original size:31 final size:31
Alignment explanation
Indices: 31605--31716 Score: 197
Period size: 31 Copynumber: 3.6 Consensus size: 31
31595 TCCATAGATT
* *
31605 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
31636 CCGAAGGACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
31667 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
31698 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
31717 CCTCGACCCT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 77 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:32542 original size:21 final size:21
Alignment explanation
Indices: 32518--32562 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32508 TGTTGTTCGT
* *
32518 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
32539 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
32560 TTG
1 TTG
32563 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:35757 original size:31 final size:31
Alignment explanation
Indices: 35719--35843 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
35709 CCCGAAGGAC
* * *
35719 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
35750 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
35781 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
35812 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
35843 C
1 C
35844 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:36669 original size:21 final size:21
Alignment explanation
Indices: 36645--36689 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
36635 TGTTGTTCGT
* *
36645 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
36666 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
36687 TTG
1 TTG
36690 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:39912 original size:30 final size:30
Alignment explanation
Indices: 39816--39937 Score: 183
Period size: 31 Copynumber: 4.0 Consensus size: 30
39806 CCCGAAGGAC
* *
39816 CAGTCCATA-GATTCCGAAGAACCTAGGTAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAA
*
39846 TCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 -CAGTCCATATGTCCCGAAGAACATAGGT-AA
39878 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
39908 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
39938 ACCCTCGACC
Statistics
Matches: 85, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
30 32 0.38
31 50 0.59
32 3 0.04
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (30 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:39933 original size:61 final size:62
Alignment explanation
Indices: 39816--39939 Score: 198
Period size: 61 Copynumber: 2.0 Consensus size: 62
39806 CCCGAAGGAC
* * *
39816 CAGTCCATAGATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATAGATCCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
39878 CAGTCCATATG-TCCCGAAGAACATAGGTAA-CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATA-GATCCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
39939 C
1 C
39940 CCTCGACCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
61 31 0.53
62 26 0.45
63 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (62 bp):
CAGTCCATAGATCCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:40766 original size:20 final size:20
Alignment explanation
Indices: 40743--40785 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
40733 TGTTGTTCGT
* *
40743 TTGAAGGGGTATCGGTTCCC
1 TTGAAGGGGTACCGATTCCC
*
40763 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
40783 TTG
1 TTG
40786 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.21, G:0.30, T:0.33
Consensus pattern (20 bp):
TTGAAGGGGTACCGATTCCC
Found at i:42222 original size:7 final size:7
Alignment explanation
Indices: 42215--42258 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
42205 ATACTACAAA
*
42215 CCCTAAA
1 CCCTAAG
42222 CCCTAAG
1 CCCTAAG
42229 CCCTAAG
1 CCCTAAG
42236 CCCTAAG
1 CCCTAAG
42243 CCCTAAG
1 CCCTAAG
42250 CCCTAAG
1 CCCTAAG
42257 CC
1 CC
42259 TTAAACCCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.30, C:0.45, G:0.11, T:0.14
Consensus pattern (7 bp):
CCCTAAG
Found at i:42232 original size:14 final size:14
Alignment explanation
Indices: 42215--42267 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
42205 ATACTACAAA
42215 CCCTAAACCCTAAG
1 CCCTAAACCCTAAG
*
42229 CCCTAAGCCCTAAG
1 CCCTAAACCCTAAG
*
42243 CCCTAAGCCCTAAG
1 CCCTAAACCCTAAG
*
42257 CCTTAAACCCT
1 CCCTAAACCCT
42268 TAATCTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.30, C:0.43, G:0.09, T:0.17
Consensus pattern (14 bp):
CCCTAAACCCTAAG
Found at i:42239 original size:21 final size:21
Alignment explanation
Indices: 42215--42267 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
42205 ATACTACAAA
42215 CCCTAAACCCTAAGCCCTAAG
1 CCCTAAACCCTAAGCCCTAAG
*
42236 CCCTAAGCCCTAAGCCCTAAG
1 CCCTAAACCCTAAGCCCTAAG
*
42257 CCTTAAACCCT
1 CCCTAAACCCT
42268 TAATCTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.43, G:0.09, T:0.17
Consensus pattern (21 bp):
CCCTAAACCCTAAGCCCTAAG
Found at i:48010 original size:155 final size:156
Alignment explanation
Indices: 47713--48023 Score: 599
Period size: 156 Copynumber: 2.0 Consensus size: 156
47703 TGAATCGACC
47713 ACTCACAAGCTATTACTTTCATTCCAAATCAACAGAAATTAAATTCTTCACGATTAAAATCTGTG
1 ACTCACAAGCTATTACTTTCATTCCAAATCAACAGAAATTAAATTCTTCACGATTAAAATCTGTG
47778 TCGTAGCCGTCTTTCGATTTGGGCCCCGGAATTAGGCTTCGACTTAGGAAAAAATGATTTGGAGT
66 TCGTAGCCGTCTTTCGATTTGGGCCCCGGAATTAGGCTTCGACTTAGGAAAAAATGATTTGGAGT
47843 CGCCACCGACCA-TTTAAAACGAATT
131 CGCCACCGACCATTTTAAAACGAATT
47868 ACTCACAAGCTATTACTTTCATTCCAAATCAACAGAAAATTAAATTCTTCACGATTAAAATCTGT
1 ACTCACAAGCTATTACTTTCATTCCAAATCAACAG-AAATTAAATTCTTCACGATTAAAATCTGT
47933 GTCGTAGCCGTCTTTCGATTTGGGCCCCGGAATTAGGCTTCGACTTAGG-AAAAATGATTTGGAG
65 GTCGTAGCCGTCTTTCGATTTGGGCCCCGGAATTAGGCTTCGACTTAGGAAAAAATGATTTGGAG
47997 TCGCCACCGACCATTTTAAAACGAATT
130 TCGCCACCGACCATTTTAAAACGAATT
48024 TAGGTGGGTC
Statistics
Matches: 154, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
155 63 0.41
156 91 0.59
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (156 bp):
ACTCACAAGCTATTACTTTCATTCCAAATCAACAGAAATTAAATTCTTCACGATTAAAATCTGTG
TCGTAGCCGTCTTTCGATTTGGGCCCCGGAATTAGGCTTCGACTTAGGAAAAAATGATTTGGAGT
CGCCACCGACCATTTTAAAACGAATT
Found at i:48336 original size:13 final size:12
Alignment explanation
Indices: 48280--48368 Score: 53
Period size: 12 Copynumber: 7.2 Consensus size: 12
48270 AATGGATATT
48280 AAATAAATCAAAG
1 AAATAAAT-AAAG
*
48293 AAA-AACATAAAA
1 AAATAA-ATAAAG
*
48305 AAAAAAATAGAA-
1 AAATAAATA-AAG
*
48317 TAATAAATCAAAG
1 AAATAAAT-AAAG
48330 AAATAAAATATAGAG
1 AAAT-AAATA-A-AG
48345 AAATAAAT-AA-
1 AAATAAATAAAG
48355 AAATAAAT-AAG
1 AAATAAATAAAG
48366 AAA
1 AAA
48369 AAGTCTTTTG
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
10 10 0.16
11 4 0.06
12 20 0.32
13 14 0.22
14 9 0.14
15 6 0.10
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (12 bp):
AAATAAATAAAG
Found at i:49533 original size:3 final size:3
Alignment explanation
Indices: 49525--49561 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
49515 AAAAATATTA
49525 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
49562 TATGTATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:49630 original size:17 final size:18
Alignment explanation
Indices: 49608--49652 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
49598 TATATACTAG
49608 TATATATAAC-TATAATA
1 TATATATAACATATAATA
*
49625 TATATATGAACATATAGTA
1 TATATAT-AACATATAATA
49644 TACTATATA
1 TA-TATATA
49653 GTATAAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 3 0.12
19 9 0.38
20 5 0.21
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (18 bp):
TATATATAACATATAATA
Found at i:49639 original size:25 final size:25
Alignment explanation
Indices: 49611--49664 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
49601 ATACTAGTAT
*
49611 ATATAACTATAATATATA-TATGAAC
1 ATAT-ACTATAATATATAGTATAAAC
* *
49636 ATATAGTATACTATATAGTATAAAC
1 ATATACTATAATATATAGTATAAAC
49661 ATAT
1 ATAT
49665 GCACTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (25 bp):
ATATACTATAATATATAGTATAAAC
Found at i:49650 original size:24 final size:25
Alignment explanation
Indices: 49618--49664 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
49608 TATATATAAC
*
49618 TATAATATATA-TATGAACATATAG
1 TATAATATATAGTATAAACATATAG
*
49642 TATACTATATAGTATAAACATAT
1 TATAATATATAGTATAAACATAT
49665 GCACTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (25 bp):
TATAATATATAGTATAAACATATAG
Found at i:50392 original size:83 final size:84
Alignment explanation
Indices: 50265--50855 Score: 301
Period size: 85 Copynumber: 7.1 Consensus size: 84
50255 AGCTGAATGG
* * * * *
50265 AATCGAACTCGACA-AT-TTTATTGACAGATAGCCCTTCTTGCCTTGGGATATGCTGTAAATAAT
1 AATCGAACTCGA-AGGTATTTATTGACAGATAACCCTTCTAGCCTTGAGATATGCTGCAAATAAT
50328 GTG-CCTA-AGAGCTGAGCGT
65 GTGCCCTAGA-AGCTGAGCGT
* * * *
50347 AGTCGAACTCGAAGGTATTTATTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATG
1 AATCGAACTCGAAGGTATTTATTGACAGATAACCCTTCTAGCCTTGAGATATGCTGCAAATAATG
* *
50412 TGCCCTCGAAGCTGAGTGT
66 TGCCCTAGAAGCTGAGCGT
* * * * * * * * ** * *
50431 AATCGAACTCG-A-G-AGTCT-TTGGCAAATAGCCCTTCTCGACTTAAGCTATTTTGCAATTGAT
1 AATCGAACTCGAAGGTA-TTTATTGACAGATAACCCTTCTAGCCTTGAGATATGCTGCAAATAAT
* *
50492 GTG-CCTCGGAGCTGAGCGT
65 GTGCCCTAGAAGCTGAGCGT
* * * * * * * * * * *
50511 AGTCAAACCCAAAGGTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTATTT-ATTGACAGATAACCCTTCTAGCCTTGAGATATGCTGCAAATAAT
* **
50576 GTGCCCTCGAAGCTGAATGT
65 GTGCCCTAGAAGCTGAGCGT
* * * * * * * * * * * * *
50596 AATCAAACTTG-AGG-GTCT-CTGACAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATA
1 AATCGAACTCGAAGGTATTTATTGACAGATAACCCTTCTAGCCTTGAGATATGCTGCAAATAATG
* *
50658 TG-CCTTGGAGCTGAGCGT
66 TGCCCTAGAAGCTGAGCGT
** * * * * * * ** * * * *
50676 TGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCCTCTCGATTTAAGTTATGCTGCAAATGAC
1 AATCGAACTCGAAGGTATTT-ATTGACAGATAACCCTTCTAGCCTTGAGATATGCTGCAAATAAT
* *
50741 GTGCCCTCGAAGCTGAGTGT
65 GTGCCCTAGAAGCTGAGCGT
* * * * * * * *
50761 AATCGAACTCAAAGGTCTTT-TGGTCACAGATAACCCTTCTAGCCTTGAGTTCTACTGTAAATGA
1 AATCGAACTCGAAGGTATTTAT--TGACAGATAACCCTTCTAGCCTTGAGATATGCTGCAAATAA
* *
50825 TGTGCCCTCGAAGCTGAGTGT
64 TGTGCCCTAGAAGCTGAGCGT
50846 AATCGAACTC
1 AATCGAACTC
50856 AGGGGTCTTT
Statistics
Matches: 404, Mismatches: 87, Indels: 33
0.77 0.17 0.06
Matches are distributed among these distances:
80 41 0.10
81 83 0.21
82 20 0.05
83 47 0.12
84 102 0.25
85 111 0.27
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (84 bp):
AATCGAACTCGAAGGTATTTATTGACAGATAACCCTTCTAGCCTTGAGATATGCTGCAAATAATG
TGCCCTAGAAGCTGAGCGT
Found at i:50556 original size:84 final size:85
Alignment explanation
Indices: 50337--50855 Score: 488
Period size: 85 Copynumber: 6.2 Consensus size: 85
50327 TGTGCCTAAG
* * * * * *
50337 AGCTGAGCGTAGTCGAACTCGAAGGTATTT-ATTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAATCAAACTCGAAGGTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGC
50401 TGCAAATGATGTGCCCTCGA
66 TGCAAATGATGTGCCCTCGA
* * * * * *
50421 AGCTGAGTGTAATCGAACTCG-AGAGTC--T--TTGGCAAATAGCCCTTCTCGACTTAAGCTATT
1 AGCTGAGCGTAATCAAACTCGAAG-GTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
50481 TTGCAATTGATGTG-CCTCGG
65 CTGCAAATGATGTGCCCTCGA
* * *
50501 AGCTGAGCGTAGTCAAACCCAAAGGTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGC
1 AGCTGAGCGTAATCAAACTCGAAGGTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGC
50566 TGCAAATGATGTGCCCTCGA
66 TGCAAATGATGTGCCCTCGA
** * * * * * *
50586 AGCTGAATGTAATCAAACTTGAGGGTCTCTGA----CAGATAGCCCTTCTCGACTTAAGCTATGT
1 AGCTGAGCGTAATCAAACTCGAAGGTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* * *
50647 TGCAAATGATATG-CCTTGG
66 TGCAAATGATGTGCCCTCGA
** * * *
50666 AGCTGAGCGTTGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCCTCTCGATTTAAGTTATGC
1 AGCTGAGCGTAATCAAACTCGAAGGTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGC
*
50731 TGCAAATGACGTGCCCTCGA
66 TGCAAATGATGTGCCCTCGA
* * * * ** * * * * *
50751 AGCTGAGTGTAATCGAACTCAAAGGTCTTTTG-GTCACAGATAACCCTTCTAGCCTTGAGTTCTA
1 AGCTGAGCGTAATCAAACTCGAAGGTC-TTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
50815 CTGTAAATGATGTGCCCTCGA
65 CTGCAAATGATGTGCCCTCGA
* *
50836 AGCTGAGTGTAATCGAACTC
1 AGCTGAGCGTAATCAAACTC
50856 AGGGGTCTTT
Statistics
Matches: 349, Mismatches: 73, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
80 52 0.15
81 77 0.22
82 2 0.01
83 2 0.01
84 96 0.28
85 116 0.33
86 4 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (85 bp):
AGCTGAGCGTAATCAAACTCGAAGGTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGTTATGC
TGCAAATGATGTGCCCTCGA
Found at i:50572 original size:165 final size:165
Alignment explanation
Indices: 50321--50770 Score: 659
Period size: 165 Copynumber: 2.7 Consensus size: 165
50311 GATATGCTGT
* * * *
50321 AAATAATGTGCCTAAGAGCTGAGCGTAGTCGAACTCGAAGGTATTT-ATTGGCAGATAACCCTTC
1 AAATGATGTGCCTAGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGATTGGCAGATAACCCTTC
* * * *
50385 TAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTT
66 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTC
* *
50450 TGGCAAATAGCCCTTCTCGACTTAAGCTATTTTGC
131 TGACAAATAGCCCTTCTCGACTTAAGCTATGTTGC
* * * *
50485 AATTGATGTGCCTCGGAGCTGAGCGTAGTCAAACCCAAAGGTCTTTGATTGGCAGATAACCCTTC
1 AAATGATGTGCCTAGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGATTGGCAGATAACCCTTC
* * * *
50550 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAATGTAATCAAACTTGAGGGTCTC
66 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTC
*
50615 TGACAGATAGCCCTTCTCGACTTAAGCTATGTTGC
131 TGACAAATAGCCCTTCTCGACTTAAGCTATGTTGC
* * * * *
50650 AAATGATATGCCTTGGAGCTGAGCGTTGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCCTC
1 AAATGATGTGCCTAGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGATTGGCAGATAACCCTTC
* *
50715 TCGATTTAAGTTATGCTGCAAATGACGTGCCCTCGAAGCTGAGTGTAATCGAACTC
66 TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
50771 AAAGGTCTTT
Statistics
Matches: 253, Mismatches: 32, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
164 38 0.15
165 215 0.85
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (165 bp):
AAATGATGTGCCTAGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGATTGGCAGATAACCCTTC
TCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGAGTCTC
TGACAAATAGCCCTTCTCGACTTAAGCTATGTTGC
Found at i:51129 original size:106 final size:106
Alignment explanation
Indices: 50994--51192 Score: 335
Period size: 106 Copynumber: 1.9 Consensus size: 106
50984 GCATTATTCC
* * * *
50994 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGGGAATTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTATTTATTGACAA
51059 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
51100 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTATTTATTGACAA
*
51165 CCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 CCAGCGATCCCTTCGTCGTGAAGTTGAA
51193 GTTGTTAAAT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 86 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTATTTATTGACAA
CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:51223 original size:88 final size:88
Alignment explanation
Indices: 51116--51280 Score: 312
Period size: 88 Copynumber: 1.9 Consensus size: 88
51106 AATATCCTTC
51116 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCCTTCGT
1 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCCTTCGT
51181 CGTGAAGTTGAAGTTGTTAAATT
66 CGTGAAGTTGAAGTTGTTAAATT
* *
51204 GTTGTTAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGT
1 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCCTTCGT
51269 CGTGAAGTTGAA
66 CGTGAAGTTGAA
51281 CATGCGTTGT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (88 bp):
GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCCTTCGT
CGTGAAGTTGAAGTTGTTAAATT
Found at i:51389 original size:106 final size:106
Alignment explanation
Indices: 51210--52103 Score: 1477
Period size: 106 Copynumber: 8.4 Consensus size: 106
51200 AATTGTTGTT
51210 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
*
51275 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
66 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
*
51316 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
51381 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
66 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * *
51422 AAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
*
51487 GTTGAACATGCGTTGTCTGGAGTACAATATCCTTCGCTGTG
66 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* *
51528 AAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
51593 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
66 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * * * *
51634 CAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
51699 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
66 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
51740 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
51805 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
66 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * * *
51846 AAGTTGAAATTGGCTCTGATATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
1 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
51911 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
66 GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* * * *
51952 AAGTTGAAATTGGCTCTAGAAGTGGA-AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGA
1 AAGTTGAAATTGGCTCT-GAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGA
* * * *
52016 AGTTGAACTTGCGTTGTCTGGAGTCCAATTTTCTTCGCTGCG
65 AGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
* *
52058 AAGTTGAAATAGACTCCGAATGAAATTG-GAAAGTTGTTTGTTGACA
1 AAGTTGAAATTGGCT-C---TGAAATTGAG-AAGTTGTTTGTTGACA
52104 GACAACTTTT
Statistics
Matches: 742, Mismatches: 39, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
106 717 0.97
107 5 0.01
109 5 0.01
110 15 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
GTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTG
Found at i:56017 original size:37 final size:37
Alignment explanation
Indices: 55973--56053 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
55963 AATGGATATT
*
55973 AAATAAATCAAAGAAA-AACATA-AAAAAATAAATAGA
1 AAATAAATCAAAGAAATAAAATATAAAAAATAAATA-A
*
56009 ATAATAAATCAAAGAAATAAAATATAAGAAATAAATAA
1 A-AATAAATCAAAGAAATAAAATATAAAAAATAAATAA
56047 AAATAAA
1 AAATAAA
56054 ATAAGAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 1 0.03
37 21 0.52
38 7 0.17
39 11 0.28
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.17
Consensus pattern (37 bp):
AAATAAATCAAAGAAATAAAATATAAAAAATAAATAA
Found at i:57304 original size:25 final size:26
Alignment explanation
Indices: 57252--57319 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
57242 GGGGCCTGAA
*
57252 AAAATATTAAATAATA-AT-TATTAT
1 AAAATAATAAATAATATATGTATTAT
57276 --AATAAT-AATAATATATGTATTAT
1 AAAATAATAAATAATATATGTATTAT
*
57299 AAAAT-ATAAATAAAATATGTA
1 AAAATAATAAATAATATATGTA
57320 ATGTATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 7 0.19
22 7 0.19
23 6 0.16
24 2 0.05
25 15 0.41
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (26 bp):
AAAATAATAAATAATATATGTATTAT
Found at i:57346 original size:18 final size:18
Alignment explanation
Indices: 57318--57364 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
57308 ATAAAATATG
*
57318 TAATGTATATATACTACA
1 TAATATATATATACTACA
* *
57336 TAGTATATATA-ACTATA
1 TAATATATATATACTACA
57353 TAATA-ATATATA
1 TAATATATATATA
57365 TGAACATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 5 0.21
17 10 0.42
18 9 0.38
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (18 bp):
TAATATATATATACTACA
Found at i:61406 original size:33 final size:33
Alignment explanation
Indices: 61369--61434 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
61359 TCCTTAGATT
* *
61369 TCCTCGCA-TAGCTCGCTCGACTGCCCTCGAATG
1 TCCTCGCAGT-GCTCGCTCGAATGACCTCGAATG
61402 TCCTCGCAGTGCTCGCTCGAATGACCTCGAATG
1 TCCTCGCAGTGCTCGCTCGAATGACCTCGAATG
61435 CTCTCGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.17, C:0.36, G:0.23, T:0.24
Consensus pattern (33 bp):
TCCTCGCAGTGCTCGCTCGAATGACCTCGAATG
Found at i:67636 original size:39 final size:39
Alignment explanation
Indices: 67593--67675 Score: 157
Period size: 39 Copynumber: 2.1 Consensus size: 39
67583 GATACTTAAA
67593 GCACAAATTGCATAATAGATGTATACAATGCAAGCAGAG
1 GCACAAATTGCATAATAGATGTATACAATGCAAGCAGAG
*
67632 GCACAAATTGCATAATAGATGTATACAATGCAAGCGGAG
1 GCACAAATTGCATAATAGATGTATACAATGCAAGCAGAG
67671 GCACA
1 GCACA
67676 TAAACACAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (39 bp):
GCACAAATTGCATAATAGATGTATACAATGCAAGCAGAG
Found at i:78573 original size:3 final size:3
Alignment explanation
Indices: 78552--78646 Score: 75
Period size: 3 Copynumber: 32.0 Consensus size: 3
78542 TTTGCCCGTT
* * * * * * *
78552 TTA TTT TTA TTA TTT TTA TTA TTA TAA TTG TTG TAA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
78600 TTG TTA TAA TTA TTA TTA TAA TTA TTA CTA TTA TTA -TA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
78647 ATAAATATTA
Statistics
Matches: 69, Mismatches: 22, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:78591 original size:21 final size:21
Alignment explanation
Indices: 78567--78636 Score: 106
Period size: 21 Copynumber: 3.3 Consensus size: 21
78557 TTTATTATTT
*
78567 TTATTATTATAATTGTTGTAA
1 TTATTATTATAATTGTTATAA
78588 TTATTATTATAATTGTTATAA
1 TTATTATTATAATTGTTATAA
*
78609 TTATTATTATAATTATTACT-A
1 TTATTATTATAATTGTTA-TAA
78630 TTATTAT
1 TTATTAT
78637 ATTTTTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 45 0.98
22 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (21 bp):
TTATTATTATAATTGTTATAA
Found at i:80416 original size:22 final size:22
Alignment explanation
Indices: 80369--80418 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
80359 AATTCCTTTT
* *
80369 ATTTTAGCCATTATTAAATGCT
1 ATTTTAGCCATTATTAAATACA
* *
80391 ATTTTAGTCATTATTTAATACA
1 ATTTTAGCCATTATTAAATACA
80413 ATTTTA
1 ATTTTA
80419 TTCTATTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (22 bp):
ATTTTAGCCATTATTAAATACA
Found at i:80646 original size:22 final size:20
Alignment explanation
Indices: 80608--80681 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
80598 TTTCTGATAT
80608 TTTTAATAAATAAATATTTTA
1 TTTT-ATAAATAAATATTTTA
* *
80629 CTTTTATAAATTATATATATTA
1 -TTTTATAAA-TAAATATTTTA
*
80651 TTTTTTAAATAAATATTTTA
1 TTTTATAAATAAATATTTTA
80671 TTTTTATAAAT
1 -TTTTATAAAT
80682 TATATATATA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 9 0.20
21 22 0.50
22 13 0.30
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATAAATAAATATTTTA
Found at i:80662 original size:42 final size:44
Alignment explanation
Indices: 80604--80695 Score: 152
Period size: 42 Copynumber: 2.1 Consensus size: 44
80594 CCATTTTCTG
80604 ATATTTTTAATAAATAAATATTTTACTTTTATAAATTATATATAT
1 ATATTTTT-ATAAATAAATATTTTACTTTTATAAATTATATATAT
*
80649 -TATTTTT-TAAATAAATATTTTATTTTTATAAATTATATATAT
1 ATATTTTTATAAATAAATATTTTACTTTTATAAATTATATATAT
80691 ATATT
1 ATATT
80696 ATATTTTATT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
42 34 0.76
43 4 0.09
44 7 0.16
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (44 bp):
ATATTTTTATAAATAAATATTTTACTTTTATAAATTATATATAT
Found at i:80686 original size:20 final size:21
Alignment explanation
Indices: 80605--80681 Score: 102
Period size: 22 Copynumber: 3.6 Consensus size: 21
80595 CATTTTCTGA
80605 TATTTTTAATAAATAAATATTT
1 TATTTTT-ATAAATAAATATTT
* * *
80627 TACTTTTATAAATTATATATAT
1 TATTTTTATAAA-TAAATATTT
80649 TATTTTT-TAAATAAATATTT
1 TATTTTTATAAATAAATATTT
80669 TATTTTTATAAAT
1 TATTTTTATAAAT
80682 TATATATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
20 14 0.30
21 14 0.30
22 19 0.40
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTTTATAAATAAATATTT
Found at i:80697 original size:20 final size:20
Alignment explanation
Indices: 80630--80698 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
80620 AATATTTTAC
80630 TTTTATAAATTATATATATTA
1 TTTTATAAATTATATATA-TA
* * *
80651 TTTTTTAAA-TAAATATTTTA
1 TTTTATAAATTATATA-TATA
80671 TTTTTATAAATTATATATATA
1 -TTTTATAAATTATATATATA
*
80692 TATTATA
1 TTTTATA
80699 TTTTATTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
20 13 0.34
21 20 0.53
22 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTATAAATTATATATATA
Found at i:80704 original size:20 final size:19
Alignment explanation
Indices: 80687--80728 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
80677 TAAATTATAT
80687 ATATATATTATATTTTATTA
1 ATATATATT-TATTTTATTA
*
80707 ATATTTATTTATTTT-TTA
1 ATATATATTTATTTTATTA
80725 ATAT
1 ATAT
80729 TAAGAAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 6 0.29
20 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATATATATTTATTTTATTA
Found at i:80725 original size:18 final size:20
Alignment explanation
Indices: 80687--80729 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
80677 TAAATTATAT
*
80687 ATATATATTATATTTTATTA
1 ATATTTATTATATTTTATTA
80707 ATATTTATT-TATTTT-TTA
1 ATATTTATTATATTTTATTA
80725 ATATT
1 ATATT
80730 AAGAAATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATTTATTATATTTTATTA
Found at i:81358 original size:28 final size:26
Alignment explanation
Indices: 81327--81384 Score: 62
Period size: 28 Copynumber: 2.2 Consensus size: 26
81317 TAATTTTTTC
*
81327 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA--TATTA
** *
81355 TTTTCTTAATATTTATATGTATATTA
1 TTTTCAAAATATTTATATATATATTA
81381 TTTT
1 TTTT
81385 ATTAATGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 9 0.35
28 17 0.65
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTCAAAATATTTATATATATATTA
Found at i:82991 original size:12 final size:13
Alignment explanation
Indices: 82974--83002 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
82964 ACATTCACAT
82974 ATTTACA-TTTGC
1 ATTTACATTTTGC
82986 ATTTACATTTTGC
1 ATTTACATTTTGC
82999 ATTT
1 ATTT
83003 TTTTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Done.