Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009353.1 Hibiscus syriacus cultivar Beakdansim tig00113157_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: 158329
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1634 original size:20 final size:20
Alignment explanation
Indices: 1609--1656 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1599 AAAGCAGTCC
1609 AAAACAAAATAG-G-ACATCTA
1 AAAACAAAATAGAGAAC-T-TA
1629 AAAAC-AAATAGAGAACTTA
1 AAAACAAAATAGAGAACTTA
1648 AAAACAAAA
1 AAAACAAAA
1657 ACCCTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 13 0.52
20 10 0.40
21 2 0.08
ACGTcount: A:0.67, C:0.12, G:0.08, T:0.12
Consensus pattern (20 bp):
AAAACAAAATAGAGAACTTA
Found at i:12125 original size:13 final size:13
Alignment explanation
Indices: 12109--12137 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12099 ATGTATTATG
12109 TATAATATATATA
1 TATAATATATATA
12122 TATAATATATATA
1 TATAATATATATA
12135 TAT
1 TAT
12138 TAAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATATATATA
Found at i:13033 original size:39 final size:39
Alignment explanation
Indices: 12947--13033 Score: 88
Period size: 39 Copynumber: 2.2 Consensus size: 39
12937 TATTAAGTTG
* * *
12947 AAATAA-TTTAATAAATTAAAAATTTAGAAGAGTATAAT
1 AAATAATTTTAATAAATGAAAAATTTAGAACAGTAAAAT
* **
12985 AATAAAATTTTAA-AAATGAAAAATTTAGAACTTTAAAATT
1 AA-ATAATTTTAATAAATGAAAAATTTAGAACAGTAAAA-T
13025 AAATAATTT
1 AAATAATTT
13034 GAGGATTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
38 2 0.05
39 29 0.74
40 8 0.21
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (39 bp):
AAATAATTTTAATAAATGAAAAATTTAGAACAGTAAAAT
Found at i:19962 original size:29 final size:30
Alignment explanation
Indices: 19928--19986 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
19918 TCTTAACTAG
*
19928 ATTTTTAATCTTTT-CTATATGGTCGTTAC
1 ATTTTTAATCTTTTACTATATGATCGTTAC
*
19957 ATTTTTAATCTTTTATTATATGATCGTTAC
1 ATTTTTAATCTTTTACTATATGATCGTTAC
19987 GTGATCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (30 bp):
ATTTTTAATCTTTTACTATATGATCGTTAC
Found at i:22032 original size:22 final size:23
Alignment explanation
Indices: 21989--22034 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
21979 TTACCCTAGT
21989 TTAAATATAGTGATTTTTAAATAA
1 TTAAATATAGTGA-TTTTAAATAA
*
22013 TTAATTATAGTGA-TTTAAATAA
1 TTAAATATAGTGATTTTAAATAA
22035 ATAGTTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (23 bp):
TTAAATATAGTGATTTTAAATAA
Found at i:22042 original size:22 final size:23
Alignment explanation
Indices: 21994--22042 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
21984 CTAGTTTAAA
*
21994 TATAGTGATTTTTAAATAATTAAT
1 TATAGTGA-TTTTAAATAAATAAT
*
22018 TATAGTGA-TTTAAATAAATAGT
1 TATAGTGATTTTAAATAAATAAT
22040 TAT
1 TAT
22043 GTAGTTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
24 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (23 bp):
TATAGTGATTTTAAATAAATAAT
Found at i:25530 original size:21 final size:21
Alignment explanation
Indices: 25506--25562 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
25496 ATTCAACTTT
25506 AATTTAATTTAGATTGTATT-C-
1 AATTTAATTTA-ATT-TATTCCA
*
25527 AATTTAAATTAATTTATTCCA
1 AATTTAATTTAATTTATTCCA
25548 AATTTAAATTTAATT
1 AATTT-AATTTAATT
25563 CAGATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 15 0.48
22 8 0.26
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (21 bp):
AATTTAATTTAATTTATTCCA
Found at i:32632 original size:21 final size:21
Alignment explanation
Indices: 32606--32648 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
32596 TTTTCGGGCT
* *
32606 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
32627 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
32648 A
1 A
32649 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:32756 original size:65 final size:66
Alignment explanation
Indices: 32628--32774 Score: 235
Period size: 65 Copynumber: 2.2 Consensus size: 66
32618 ACCCATTCAA
*
32628 GGGGAACCGATACCCCTTCAACGAATATGATTTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
1 GGGGAACCGATACCCCTTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
32693 G
66 G
* *
32694 GGGGAACCGATACCCC-TCATCGTATATGAAATTCCAGAATGCTAGA-GGGAATCGATACCCCCA
1 GGGGAACCGATACCCCTTCAACGAATATG-AATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
32757 GG
65 GG
*
32759 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
32775 CATGAGAAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
65 44 0.58
66 32 0.42
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (66 bp):
GGGGAACCGATACCCCTTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
G
Found at i:33111 original size:29 final size:29
Alignment explanation
Indices: 33077--33148 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
33067 CATATTATGA
* *
33077 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
33106 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
33135 TGCATGACATGAAT
1 TACATGACATGAAT
33149 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:33212 original size:30 final size:30
Alignment explanation
Indices: 33162--33237 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
33152 CAGAAAAGTT
* *
33162 ATATGAGCTATGTGAT-AAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
33192 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
33222 ATATGACTACGTGATA
1 ATATGACTATGTGATA
33238 TGAACTACGG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
29 9 0.21
30 33 0.79
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:33470 original size:13 final size:13
Alignment explanation
Indices: 33452--33514 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
33442 TTATATGGCA
33452 CTACGGTGCAATT
1 CTACGGTGCAATT
33465 CTACGG-GC-A--
1 CTACGGTGCAATT
*
33474 CTTCGGTGCAATT
1 CTACGGTGCAATT
33487 CTACGG-GC-A--
1 CTACGGTGCAATT
*
33496 CTTCGGTGCAATT
1 CTACGGTGCAATT
33509 CTACGG
1 CTACGG
33515 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:33480 original size:22 final size:22
Alignment explanation
Indices: 33448--33528 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
33438 ATCATTATAT
*
33448 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
33470 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
33492 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
33515 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
33529 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:39582 original size:21 final size:21
Alignment explanation
Indices: 39556--39598 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39546 TTTTCGGGCT
* *
39556 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
39577 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
39598 A
1 A
39599 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:39645 original size:17 final size:17
Alignment explanation
Indices: 39623--39656 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39613 AGAATGCTAG
*
39623 AGGGGAATCGATACCCC
1 AGGGGAACCGATACCCC
39640 AGGGGAACCGATACCCC
1 AGGGGAACCGATACCCC
39657 CTCATCGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.29, T:0.09
Consensus pattern (17 bp):
AGGGGAACCGATACCCC
Found at i:39654 original size:63 final size:65
Alignment explanation
Indices: 39577--39724 Score: 219
Period size: 64 Copynumber: 2.3 Consensus size: 65
39567 TACCCATTCA
* *
39577 AGGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATA-CCCC
1 AGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
* *
39640 AGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
*
39705 AGGGGGGAACCGATTCCCCC
1 A--GGGGAACCGATACCCCC
39725 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
63 27 0.36
64 28 0.37
65 5 0.07
67 16 0.21
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (65 bp):
AGGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
Found at i:39713 original size:20 final size:20
Alignment explanation
Indices: 39688--39725 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39678 GAATGCTAGA
*
39688 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
39708 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
39726 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:40061 original size:29 final size:29
Alignment explanation
Indices: 40027--40098 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
40017 CATATTATGA
* *
40027 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
40056 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
40085 TGCATGACATGAAT
1 TACATGACATGAAT
40099 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:40154 original size:30 final size:30
Alignment explanation
Indices: 40112--40188 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
40102 CAGAAAAGTT
* *
40112 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
40143 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
40173 ATATGACTACGTGATA
1 ATATGACTATGTGATA
40189 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:40421 original size:13 final size:13
Alignment explanation
Indices: 40403--40465 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
40393 TTATATGGCA
40403 CTACGGTGCAATT
1 CTACGGTGCAATT
40416 CTACGG-GC-A--
1 CTACGGTGCAATT
*
40425 CTTCGGTGCAATT
1 CTACGGTGCAATT
40438 CTACGG-GC-A--
1 CTACGGTGCAATT
*
40447 CTTCGGTGCAATT
1 CTACGGTGCAATT
40460 CTACGG
1 CTACGG
40466 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:40431 original size:22 final size:22
Alignment explanation
Indices: 40399--40479 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
40389 ATCATTATAT
*
40399 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
40421 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
40443 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
40466 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
40480 TTTATATGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:42132 original size:29 final size:29
Alignment explanation
Indices: 42090--42148 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42080 ATTTTCACCT
42090 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
42119 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
42148 A
1 A
42149 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:46820 original size:29 final size:29
Alignment explanation
Indices: 46778--46836 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
46768 ATTTTCACCT
46778 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
46807 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
46836 A
1 A
46837 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:55409 original size:147 final size:144
Alignment explanation
Indices: 55102--55393 Score: 530
Period size: 147 Copynumber: 2.0 Consensus size: 144
55092 CATAAGGGCA
*
55102 GTGAAATCATTTTTTTAATGAGAAGAATATAATACTGATTCAGTTCCATGTTAAACAATGATTTG
1 GTGAAATCATCTTTTTAATGAGAAGAATATAATACTGATTCAGTTCCATGTTAAACAATGATTTG
55167 GCTGGTTGCACGTGGCATTCTATTTTCATATTGTCATATGTTAAGCACTGGTCTTAAAAAAATGT
66 GCTGGTTGCACGTGGCATTCTATTTTCATATTGTCATATGTTAAGCACTGGTCTTAAAAAAATGT
55232 TAAGCGTCCCTCTT
131 TAAGCGTCCCTCTT
*
55246 GGTGAAATCATTTTTTTAATGATGAAGAATATTAATACTGATTCAGTTCCATGTTAAACAATGAT
1 -GTGAAATCATCTTTTTAATGA-GAAGAATA-TAATACTGATTCAGTTCCATGTTAAACAATGAT
55311 TTGGCTGGTTGCACGTGGCATTCTATTTTCATATTGTCATATTGTTAAGCACTGGTCTTAAAAAA
63 TTGGCTGGTTGCACGTGGCATTCTATTTTCATATTGTCATA-TGTTAAGCACTGGTCTTAAAAAA
55376 ATGTTAAGCGTCCCTCTT
127 ATGTTAAGCGTCCCTCTT
55394 TGATTTTATG
Statistics
Matches: 144, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
145 21 0.15
146 8 0.06
147 74 0.51
148 41 0.28
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (144 bp):
GTGAAATCATCTTTTTAATGAGAAGAATATAATACTGATTCAGTTCCATGTTAAACAATGATTTG
GCTGGTTGCACGTGGCATTCTATTTTCATATTGTCATATGTTAAGCACTGGTCTTAAAAAAATGT
TAAGCGTCCCTCTT
Found at i:59864 original size:2 final size:2
Alignment explanation
Indices: 59857--59886 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59847 AAACTTAATC
59857 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
59887 GTGTGTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66628 original size:12 final size:12
Alignment explanation
Indices: 66611--66641 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
66601 CTACTTAGAT
66611 GGGATGAGAAAG
1 GGGATGAGAAAG
66623 GGGATGAGAAAG
1 GGGATGAGAAAG
66635 GGGATGA
1 GGGATGA
66642 AAGAGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.52, T:0.10
Consensus pattern (12 bp):
GGGATGAGAAAG
Found at i:72095 original size:2 final size:2
Alignment explanation
Indices: 72082--72308 Score: 51
Period size: 2 Copynumber: 121.5 Consensus size: 2
72072 TGTCCGATAG
*
72082 TA TA TA TT TA TA TA T- TA T- TA TA T- TA TA TA GTA GTA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA
* * *
72122 TA T- TA TA T- TC CA TA T- TA TA TA TA T- TA TA GTA GTA T- TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA
* * *
72161 TA TA CTA TA TA T- TA TA TG T- TA TA TA GCA TA TA CA T- TA TA -A
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
72201 AA TA TA TA T- TA CT- TA T- TA TA TA TA T- TA CA TA GTA CA TA T-
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
72240 TA AA GTA TA T- TA T- TA TA CT- TA TA T- TA TA TA TA TA GTA TA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA
72279 T- TA TA T- TA -A TA T- TA TA GTA T- TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T
72309 TAGTTATAGT
Statistics
Matches: 168, Mismatches: 19, Indels: 76
0.64 0.07 0.29
Matches are distributed among these distances:
1 28 0.17
2 118 0.70
3 22 0.13
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72107 original size:5 final size:5
Alignment explanation
Indices: 72084--72335 Score: 81
Period size: 5 Copynumber: 50.6 Consensus size: 5
72074 TCCGATAGTA
*
72084 TATAT T-TAT ATATTAT TATAT TATA- TAGTAG TAT-T ATATAT TATAT
1 TATAT TATAT -TA-TAT TATAT TATAT TA-TAT TATAT -TATAT TATAT
* *
72130 TCCATAT TATA- TATAT TATAG TAGTAT TAT-G TATACT ATATAT TATAT
1 T--ATAT TATAT TATAT TATAT TA-TAT TATAT TATA-T -TATAT TATAT
* * * * *
72178 GT-TA- TATAG CATA- TACAT TATAA AATA- TATAT TACTTAT TATA-
1 -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA--TAT TATAT
* * * *
72221 TATAT TACA- TAGTA- CATAT TAAAG TATA- T-TAT TATACT TATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATA-T TATAT TATAT
* * *
72269 ATATAG TATAT TATAT TAATAT TATA- -GTAT TATAT TATAT TA-GT TATAGT
1 -TATAT TATAT TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT TATA-T
*
72319 TATAT TCTAT T-TAT TAT
1 TATAT TATAT TATAT TAT
72336 TATACTAATA
Statistics
Matches: 187, Mismatches: 26, Indels: 68
0.67 0.09 0.24
Matches are distributed among these distances:
3 5 0.03
4 36 0.19
5 99 0.53
6 30 0.16
7 17 0.09
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (5 bp):
TATAT
Found at i:72110 original size:7 final size:7
Alignment explanation
Indices: 72082--72303 Score: 86
Period size: 7 Copynumber: 30.7 Consensus size: 7
72072 TGTCCGATAG
72082 TATATATT
1 TATATA-T
72090 TATATAT
1 TATATAT
72097 TATTATAT
1 TA-TATAT
*
72105 TATATAG
1 TATATAT
*
72112 TA-GTAT
1 TATATAT
72118 TATATAT
1 TATATAT
72125 TATAT-T
1 TATATAT
*
72131 CCATAT-T
1 -TATATAT
72138 ATATATAT
1 -TATATAT
*
72146 TATAGTAG
1 TATA-TAT
72154 TAT-TA-
1 TATATAT
* *
72159 TGTATAC
1 TATATAT
72166 TATATAT
1 TATATAT
*
72173 TATATGT
1 TATATAT
*
72180 TATATAGCA
1 TATATA--T
*
72189 TATACAT
1 TATATAT
* *
72196 TATAAAA
1 TATATAT
72203 TATATAT
1 TATATAT
72210 TACT-TATT
1 TA-TATA-T
72218 ATATATAT
1 -TATATAT
* *
72226 TACATAG
1 TATATAT
*
72233 TACATAT
1 TATATAT
72240 TAAAGTATAT
1 T--A-TATAT
*
72250 TATTATAC
1 TA-TATAT
72258 T-TATAT
1 TATATAT
72264 TATATA-
1 TATATAT
72270 TATAGTA-
1 TATA-TAT
72277 TATTATAT
1 TA-TATAT
72285 TA-ATAT
1 TATATAT
72291 TATAGTAT
1 TATA-TAT
72299 TATAT
1 TATAT
72304 TATATTAGTT
Statistics
Matches: 165, Mismatches: 27, Indels: 45
0.70 0.11 0.19
Matches are distributed among these distances:
5 2 0.01
6 24 0.15
7 84 0.51
8 40 0.24
9 10 0.06
10 5 0.03
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (7 bp):
TATATAT
Found at i:72123 original size:36 final size:36
Alignment explanation
Indices: 72082--72186 Score: 108
Period size: 39 Copynumber: 2.8 Consensus size: 36
72072 TGTCCGATAG
72082 TATATATTTATATATTATTATATTATATAGTAGTAT
1 TATATATTTATATATTATTATATTATATAGTAGTAT
72118 TATATA-TTATAT-TCCATATTATATATATTATAGTAGTAT
1 TATATATTTATATAT---TATTATAT-TA-TATAGTAGTAT
* * *
72157 TATGTATACTATATATTA-TATGTTATATAG
1 TATATAT-TTATATATTATTATATTATATAG
72187 CATATACATT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
34 1 0.02
35 6 0.10
36 11 0.19
37 10 0.17
38 6 0.10
39 18 0.31
41 5 0.09
42 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (36 bp):
TATATATTTATATATTATTATATTATATAGTAGTAT
Found at i:72266 original size:11 final size:10
Alignment explanation
Indices: 72250--72335 Score: 72
Period size: 11 Copynumber: 8.6 Consensus size: 10
72240 TAAAGTATAT
72250 TATTATACTTA
1 TATTATA-TTA
72261 TATTATATATA
1 TATTATAT-TA
*
72272 TAGTATATTA
1 TATTATATTA
72282 TATTAATATTA
1 TATT-ATATTA
*
72293 TA--GTATTA
1 TATTATATTA
72301 TATTATATTA
1 TATTATATTA
*
72311 -GTTATAGTTA
1 TATTATA-TTA
*
72321 TATTCTATT-
1 TATTATATTA
72330 TATTAT
1 TATTAT
72336 TATACTAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
8 7 0.11
9 10 0.16
10 16 0.26
11 28 0.46
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (10 bp):
TATTATATTA
Found at i:72280 original size:16 final size:15
Alignment explanation
Indices: 72084--72349 Score: 92
Period size: 14 Copynumber: 17.2 Consensus size: 15
72074 TCCGATAGTA
*
72084 TATATTTATATATTAT
1 TATATATATATA-TAT
72100 TATATTATATAGTAGTAT
1 TATA-TATATA-TA-TAT
72118 TATATATTATATTCCATAT
1 TATATA-TATA-T--ATAT
*
72137 TATATATAT-TATAG
1 TATATATATATATAT
* *
72151 TAGTAT-TATGTATAC
1 TA-TATATATATATAT
*
72166 TATATAT-TATATGT
1 TATATATATATATAT
* *
72180 TATATAGCATATACAT
1 TATATA-TATATATAT
*
72196 TATA-AAATATATAT
1 TATATATATATATAT
72210 TACT-TATTATATATAT
1 TA-TATA-TATATATAT
* * *
72226 TACATA-GTACATAT
1 TATATATATATATAT
*
72240 TAAAGTATATTATTATACT
1 TATA-TATA-TA-TATA-T
*
72259 TATATTATATATATAG
1 TATA-TATATATATAT
*
72275 TATAT-TATAT-TAA
1 TATATATATATATAT
72288 TAT-TATAGTATTATAT
1 TATATATA-TA-TATAT
72304 TATAT-TAGT-TATAGT
1 TATATATA-TATATA-T
* *
72319 TATAT-TCTATTTAT
1 TATATATATATATAT
72333 TAT-TATACTA-ATAT
1 TATATATA-TATATAT
72347 TAT
1 TAT
72350 TTTTTCAATT
Statistics
Matches: 193, Mismatches: 29, Indels: 58
0.69 0.10 0.21
Matches are distributed among these distances:
12 1 0.01
13 8 0.04
14 62 0.32
15 29 0.15
16 39 0.20
17 14 0.07
18 22 0.11
19 17 0.09
20 1 0.01
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:72835 original size:32 final size:32
Alignment explanation
Indices: 72770--72849 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
72760 CAACCAAGCA
72770 AACAAAGCAAAAACAAGCAATCGAAACAACAAG
1 AACAAAGCAAAAA-AAGCAATCGAAACAACAAG
* * *
72803 AACAAAGCAGAAAAAA-CATTCGAAATAGCAAG
1 AACAAAGCA-AAAAAAGCAATCGAAACAACAAG
*
72835 AA-AAATCACAAAAAA
1 AACAAAGCA-AAAAAA
72850 TATCAAGGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 11 0.27
32 15 0.37
33 11 0.27
34 4 0.10
ACGTcount: A:0.65, C:0.17, G:0.11, T:0.06
Consensus pattern (32 bp):
AACAAAGCAAAAAAAGCAATCGAAACAACAAG
Found at i:74163 original size:21 final size:22
Alignment explanation
Indices: 74120--74165 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
74110 TGTATAATTA
*
74120 TAAATTAGTTAAAATTTAAAGG
1 TAAATTAGTTAAAATTAAAAGG
*
74142 TAAATTATTTAAAA-TAAAAGG
1 TAAATTAGTTAAAATTAAAAGG
74163 TAA
1 TAA
74166 CTATATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (22 bp):
TAAATTAGTTAAAATTAAAAGG
Found at i:88786 original size:23 final size:25
Alignment explanation
Indices: 88746--88791 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
88736 TGTGACATGA
88746 TTTTTCTCTACTCTTGTAGCACGCG
1 TTTTTCTCTACTCTTGTAGCACGCG
88771 TTTTTCT-T-CTCTTGTAGCACG
1 TTTTTCTCTACTCTTGTAGCACG
88792 ATCCTCATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 1 0.05
25 7 0.33
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (25 bp):
TTTTTCTCTACTCTTGTAGCACGCG
Found at i:98680 original size:27 final size:26
Alignment explanation
Indices: 98650--98701 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
98640 ATAACAAATA
98650 TTAAAT-ATATTTAAACTTAATATTTTT
1 TTAAATGA-ATTTAAACTTAA-ATTTTT
*
98677 TTAATTGAATTTAAACTTAAATTTT
1 TTAAATGAATTTAAACTTAAATTTT
98702 CGTATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 17 0.74
28 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (26 bp):
TTAAATGAATTTAAACTTAAATTTTT
Found at i:103993 original size:24 final size:20
Alignment explanation
Indices: 103966--104023 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
103956 GCATGGGTAG
103966 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG---AAGAA
* *
103990 TGCATTGATGCACTGCAGAA
1 TGCATCGATGCACTGAAGAA
104010 TGCATCGATGCACT
1 TGCATCGATGCACT
104024 TCAAAGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 17 0.55
23 2 0.06
24 12 0.39
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGAAGAA
Found at i:104011 original size:20 final size:20
Alignment explanation
Indices: 103986--104023 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
103976 CACATGTTAA
*
103986 AGAATGCATTGATGCACTGC
1 AGAATGCATCGATGCACTGC
104006 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
104024 TCAAAGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGC
Found at i:108358 original size:63 final size:63
Alignment explanation
Indices: 108285--108406 Score: 226
Period size: 63 Copynumber: 1.9 Consensus size: 63
108275 CTTCATCCAT
* *
108285 TACCGATACTTCAAGAATAAAACAGTGATATTTGGTAAAGGGGTATTGATACTGGTTGAGAAG
1 TACCGATACTTCAAGAACAAAACAATGATATTTGGTAAAGGGGTATTGATACTGGTTGAGAAG
108348 TACCGATACTTCAAGAACAAAACAATGATATTTGGTAAAGGGGTATTGATACTGGTTGA
1 TACCGATACTTCAAGAACAAAACAATGATATTTGGTAAAGGGGTATTGATACTGGTTGA
108407 ACAATATTGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (63 bp):
TACCGATACTTCAAGAACAAAACAATGATATTTGGTAAAGGGGTATTGATACTGGTTGAGAAG
Found at i:108514 original size:35 final size:35
Alignment explanation
Indices: 108475--108553 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
108465 GGAAGGTATA
108475 ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
1 ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
108510 ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
1 ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
108545 ATCGATACC
1 ATCGATACC
108554 CATTTTTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (35 bp):
ATCGATACCAAGAGTACCGATATCATAAGGTCAGT
Found at i:108515 original size:20 final size:20
Alignment explanation
Indices: 108487--108551 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
108477 CGATACCAAG
108487 AGTACCGATATCATAAGGTC
1 AGTACCGATATCATAAGGTC
* *
108507 AGTATCGATA-C-CAA-G--
1 AGTACCGATATCATAAGGTC
108522 AGTACCGATATCATAAGGTC
1 AGTACCGATATCATAAGGTC
*
108542 AGTATCGATA
1 AGTACCGATA
108552 CCCATTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
15 9 0.26
16 1 0.03
17 3 0.09
18 3 0.09
19 1 0.03
20 18 0.51
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (20 bp):
AGTACCGATATCATAAGGTC
Found at i:109453 original size:31 final size:31
Alignment explanation
Indices: 109412--109505 Score: 143
Period size: 31 Copynumber: 3.0 Consensus size: 31
109402 AAGAGTCGAG
* *
109412 GGTTACCTATGTCCTTCGAGACATATGGATA
1 GGTTACCTATGTTCTTCGGGACATATGGATA
* * *
109443 GGTTATCTATGTTCTTCGGGACATATAGACA
1 GGTTACCTATGTTCTTCGGGACATATGGATA
109474 GGTTACCTATGTTCTTCGGGACATATGGATA
1 GGTTACCTATGTTCTTCGGGACATATGGATA
109505 G
1 G
109506 TGGTCATTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (31 bp):
GGTTACCTATGTTCTTCGGGACATATGGATA
Found at i:115423 original size:20 final size:19
Alignment explanation
Indices: 115400--115454 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
115390 AAGCTGTTCG
115400 AAAAAGAAAAAAAAGAGAAA
1 AAAAAGAAAAAAAAGA-AAA
* **
115420 AAAAAGACATGAAAGAAAA
1 AAAAAGAAAAAAAAGAAAA
115439 AAAATAGAAAACAAAA
1 AAAA-AGAAAA-AAAA
115455 CAATAAAGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 7 0.26
20 17 0.63
21 3 0.11
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAAAAAGAAAA
Found at i:117021 original size:2 final size:2
Alignment explanation
Indices: 117014--117048 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
117004 TCCTAAAACC
* *
117014 TA TA TA TA TA TA TA TA TA TA TA TA TG TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
117049 TCGAGGAATG
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:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:118626 original size:27 final size:25
Alignment explanation
Indices: 118578--118627 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
118568 TTGTCATAAC
* *
118578 TATTTTTTTTTTTAAAATAATTAAA
1 TATTTTTTTTTTAAAAACAATTAAA
118603 TATTATTTTTTTTAAAACACAATTA
1 TATT-TTTTTTTTAAAA-ACAATTA
118628 TGACTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 11 0.52
27 6 0.29
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTTTTTTTTAAAAACAATTAAA
Found at i:121251 original size:25 final size:25
Alignment explanation
Indices: 121128--121245 Score: 204
Period size: 25 Copynumber: 4.8 Consensus size: 25
121118 AGTTAGGGGA
121128 TTAGGG-TTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
121152 TTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
121177 TTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
*
121202 TTAGGGTTTGAAACCCT-AATCTGAT
1 TTAGGGTTTGAAACCCTAAAT-TGTT
121227 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
121246 TCTGATGGGT
Statistics
Matches: 90, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
24 9 0.10
25 80 0.89
26 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAATTGTT
Found at i:121328 original size:16 final size:17
Alignment explanation
Indices: 121309--121353 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
121299 AAAAAAGATG
*
121309 TAATATGTAA-AATTAA
1 TAATATATAATAATTAA
121325 TAATA-ATAATAATTAA
1 TAATATATAATAATTAA
*
121341 TAATATAAAATAA
1 TAATATATAATAA
121354 AATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 16 0.64
17 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATATAATAATTAA
Found at i:121330 original size:3 final size:3
Alignment explanation
Indices: 121322--121371 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
121312 TATGTAAAAT
121322 TAA TAA TAA TAA TAA TTAA TAA T-A TAA -AA TAA -AA TAA -AA -AA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
121363 TAA TAA TAA
1 TAA TAA TAA
121372 AAAAATATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 10 0.24
3 29 0.69
4 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:121333 original size:6 final size:6
Alignment explanation
Indices: 121322--121371 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 6
121312 TATGTAAAAT
121322 TAATAA TAATAA TAATTAA TAAT-A TAA-AA TAA-AA TAA-AA -AATAA
1 TAATAA TAATAA TAA-TAA TAATAA TAATAA TAATAA TAATAA TAATAA
121366 TAATAA
1 TAATAA
121372 AAAAATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 2 0.05
5 17 0.43
6 15 0.38
7 6 0.15
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
TAATAA
Found at i:121356 original size:35 final size:33
Alignment explanation
Indices: 121316--121383 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 33
121306 ATGTAATATG
* * *
121316 TAAAATTAATAATAATAATAATTAATAATATAAAA
1 TAAAATAAAAAATAATAATAA--AAAAATATAAAA
121351 TAAAATAAAAAATAATAATAAAAAAATATAAAA
1 TAAAATAAAAAATAATAATAAAAAAATATAAAA
121384 GACCCGGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 11 0.37
35 19 0.63
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (33 bp):
TAAAATAAAAAATAATAATAAAAAAATATAAAA
Found at i:121357 original size:25 final size:26
Alignment explanation
Indices: 121323--121375 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
121313 ATGTAAAATT
* * *
121323 AATAATAATAATAATTAATAATATAA
1 AATAATAATAAAAAATAATAATAAAA
121349 AATAA-AATAAAAAATAATAATAAAA
1 AATAATAATAAAAAATAATAATAAAA
121374 AA
1 AA
121376 ATATAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (26 bp):
AATAATAATAAAAAATAATAATAAAA
Found at i:121364 original size:22 final size:23
Alignment explanation
Indices: 121339--121383 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
121329 AATAATAATT
121339 AATAAT-ATAAAATAAA-ATAAAA
1 AATAATAATAAAA-AAATATAAAA
121361 AATAATAATAAAAAAATATAAAA
1 AATAATAATAAAAAAATATAAAA
121384 GACCCGGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (23 bp):
AATAATAATAAAAAAATATAAAA
Found at i:121381 original size:13 final size:14
Alignment explanation
Indices: 121324--121374 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 14
121314 TGTAAAATTA
*
121324 ATAATAATAATAAT
1 ATAATAATAAAAAT
*
121338 -TAATAATATAAA-
1 ATAATAATAAAAAT
121350 ATAA-AATAAAAA-
1 ATAATAATAAAAAT
121362 ATAATAATAAAAA
1 ATAATAATAAAAA
121375 AATATAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 11 0.34
13 21 0.66
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAATAATAAAAAT
Found at i:122889 original size:10 final size:11
Alignment explanation
Indices: 122873--122901 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
122863 CATATTTTCA
122873 TTTTTTTCCTC
1 TTTTTTTCCTC
122884 TTTTTTTCCTC
1 TTTTTTTCCTC
122895 TTTTTTT
1 TTTTTTT
122902 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTCCTC
Found at i:133475 original size:9 final size:9
Alignment explanation
Indices: 133463--133488 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
133453 GGGAAAAAAT
133463 AAAAATAAA
1 AAAAATAAA
133472 AAAAATAAA
1 AAAAATAAA
133481 AAAAATAA
1 AAAAATAA
133489 CACCCAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:136370 original size:25 final size:25
Alignment explanation
Indices: 136247--136364 Score: 204
Period size: 25 Copynumber: 4.8 Consensus size: 25
136237 AGTTAGGGGA
136247 TTAGGG-TTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
136271 TTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
136296 TTAGGGTTTGAAACCCTAAATTGTT
1 TTAGGGTTTGAAACCCTAAATTGTT
*
136321 TTAGGGTTTGAAACCCT-AATCTGAT
1 TTAGGGTTTGAAACCCTAAAT-TGTT
136346 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
136365 TCTGATGGGT
Statistics
Matches: 90, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
24 9 0.10
25 80 0.89
26 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAATTGTT
Found at i:136447 original size:16 final size:16
Alignment explanation
Indices: 136438--136485 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
136428 TAATATGTAA
136438 AATTAATAATAATAAT
1 AATTAATAATAATAAT
136454 AATTAATAA-AATAA-
1 AATTAATAATAATAAT
* *
136468 AATAAAAAATAATAAT
1 AATTAATAATAATAAT
136484 AA
1 AA
136486 AAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 7 0.25
15 10 0.36
16 11 0.39
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTAATAATAATAAT
Found at i:136449 original size:3 final size:3
Alignment explanation
Indices: 136441--136485 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
136431 TATGTAAAAT
136441 TAA TAA TAA TAA TAA TTAA TAA -AA TAA -AA TAA -AA -AA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
136483 TAA
1 TAA
136486 AAAAAATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.21
3 27 0.71
4 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:136452 original size:6 final size:6
Alignment explanation
Indices: 136441--136485 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 6
136431 TATGTAAAAT
136441 TAATAA TAATAA TAATTAA TAA-AA TAA-AA TAA-AA -AATAA TAATAA
1 TAATAA TAATAA TAA-TAA TAATAA TAATAA TAATAA TAATAA TAATAA
136486 AAAAAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 2 0.06
5 14 0.39
6 14 0.39
7 6 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
TAATAA
Found at i:136483 original size:23 final size:23
Alignment explanation
Indices: 136442--136498 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 23
136432 ATGTAAAATT
136442 AATAATAATAATAATTAATAAAATAA
1 AATAA-AA-AATAATTAATAAAA-AA
136468 AATAAAAAATAA-TAATAAAAAA
1 AATAAAAAATAATTAATAAAAAA
*
136490 AATATAAAA
1 AATAAAAAA
136499 GACCCGGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 10 0.33
23 8 0.27
24 5 0.17
25 2 0.07
26 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (23 bp):
AATAAAAAATAATTAATAAAAAA
Found at i:136488 original size:12 final size:12
Alignment explanation
Indices: 136435--136498 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
136425 ATGTAATATG
*
136435 TAAAATTAATAA
1 TAAAAATAATAA
*
136447 TAATAATAATTAA
1 TAAAAATAA-TAA
136460 T-AAAATAA-AA
1 TAAAAATAATAA
136470 TAAAAAATAATAA
1 T-AAAAATAATAA
*
136483 TAAAAAAAAT-A
1 TAAAAATAATAA
136494 TAAAA
1 TAAAA
136499 GACCCGGACA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 3 0.07
11 6 0.14
12 28 0.64
13 7 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAAATAATAA
Found at i:137619 original size:2 final size:2
Alignment explanation
Indices: 137612--137642 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
137602 ATGTTCCCTC
137612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
137643 TGGCTAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:138668 original size:21 final size:20
Alignment explanation
Indices: 138631--138669 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
138621 TAAATGTTAC
**
138631 TTTTGTTATTTCTCTTTTGA
1 TTTTGTTATTTAACTTTTGA
138651 TTTTGTTCATTTAACTTTT
1 TTTTGTT-ATTTAACTTTT
138670 AATTATTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.13, C:0.10, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTTGTTATTTAACTTTTGA
Found at i:144717 original size:24 final size:23
Alignment explanation
Indices: 144663--144719 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
144653 TCTACAAAAT
* **
144663 ATATGATTGGACCAATCTTATTT
1 ATATAATTGGACCAATCTTATAA
*
144686 TTAGTAATTGGACCAATCTTATCAA
1 ATA-TAATTGGACCAATCTTAT-AA
144711 ATATAATTG
1 ATATAATTG
144720 TTCTGTGGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 2 0.07
24 23 0.85
25 2 0.07
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (23 bp):
ATATAATTGGACCAATCTTATAA
Found at i:147903 original size:3 final size:3
Alignment explanation
Indices: 147895--147920 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
147885 TGTCCGAGTT
147895 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
147921 TTAACAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:149670 original size:22 final size:21
Alignment explanation
Indices: 149645--149693 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
149635 TATTAAATAA
* *
149645 ATATTATCCATGTTTGTTGTAT
1 ATATTATACATG-TTGTTATAT
*
149667 ATATATATATATGTTGTTATAT
1 ATAT-TATACATGTTGTTATAT
149689 ATATT
1 ATATT
149694 TTTAATTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 16 0.70
23 6 0.26
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (21 bp):
ATATTATACATGTTGTTATAT
Found at i:149873 original size:26 final size:27
Alignment explanation
Indices: 149841--149899 Score: 111
Period size: 26 Copynumber: 2.2 Consensus size: 27
149831 GAATATGAAC
149841 TTAAAAGCACGAGCCTTTATGAATTTA
1 TTAAAAGCACGAGCCTTTATGAATTTA
149868 -TAAAAGCACGAGCCTTTATGAATTTA
1 TTAAAAGCACGAGCCTTTATGAATTTA
149894 TTAAAA
1 TTAAAA
149900 TCATAGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 26 0.84
27 5 0.16
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (27 bp):
TTAAAAGCACGAGCCTTTATGAATTTA
Found at i:151616 original size:16 final size:16
Alignment explanation
Indices: 151596--151647 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
151586 GAAATATAAG
151596 ACTTAATAAATTTTAA
1 ACTTAATAAATTTTAA
* *
151612 CCTTATTAATATCTTTAA
1 ACTTAATAA-AT-TTTAA
* *
151630 ACTCAATTAATTTTAA
1 ACTTAATAAATTTTAA
151646 AC
1 AC
151648 CCAAATAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 14 0.50
17 4 0.14
18 10 0.36
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.44
Consensus pattern (16 bp):
ACTTAATAAATTTTAA
Done.