Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001373.1 Hibiscus syriacus cultivar Beakdansim tig00002685_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: 153372
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3101 original size:24 final size:23
Alignment explanation
Indices: 3073--3126 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
3063 GTATTTAGAA
* *
3073 TTTAAAC-TAATAGTTTTAATTTAT
1 TTTAAACTTAA-ACTTTTAAATT-T
3097 TTTAATACTTAAACTTTTAAATTT
1 TTTAA-ACTTAAACTTTTAAATTT
3121 TTTAAA
1 TTTAAA
3127 ATTATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 11 0.42
25 11 0.42
26 3 0.12
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTAAACTTAAACTTTTAAATTT
Found at i:3362 original size:24 final size:23
Alignment explanation
Indices: 3320--3367 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
3310 TTTAATTTTT
*
3320 TTTAAAATTTATGTATTAAAATAA
1 TTTAAAATTGATGTATT-AAATAA
3344 TTTAAAATTGATAGT-TTAAATAA
1 TTTAAAATTGAT-GTATTAAATAA
3367 T
1 T
3368 AAATGCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 13 0.59
25 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (23 bp):
TTTAAAATTGATGTATTAAATAA
Found at i:6959 original size:18 final size:18
Alignment explanation
Indices: 6936--6970 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6926 GGATATACAA
6936 TGGTCCTTCGAGACATAG
1 TGGTCCTTCGAGACATAG
*
6954 TGGTCCTTCGGGACATA
1 TGGTCCTTCGAGACATA
6971 TACAGTGGTC
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:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (18 bp):
TGGTCCTTCGAGACATAG
Found at i:6980 original size:22 final size:22
Alignment explanation
Indices: 6928--6990 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
6918 GAGTCGAGGG
*
6928 ATATACAATGGTCCTTCGAGAC
1 ATATACAGTGGTCCTTCGAGAC
*
6950 --AT--AGTGGTCCTTCGGGAC
1 ATATACAGTGGTCCTTCGAGAC
*
6968 ATATACAGTGGTCATTCGAGAC
1 ATATACAGTGGTCCTTCGAGAC
6990 A
1 A
6991 AATATTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 14 0.42
20 4 0.12
22 15 0.45
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (22 bp):
ATATACAGTGGTCCTTCGAGAC
Found at i:14067 original size:22 final size:22
Alignment explanation
Indices: 14015--14077 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
14005 GAGTCGAGGG
* *
14015 ATATACAGTCGTCCTTCGGGAC
1 ATATACAGTGGTCATTCGGGAC
*
14037 --AT--AGTGGTCTTTCGGGAC
1 ATATACAGTGGTCATTCGGGAC
*
14055 ATATACAGTGGTCATTCAGGAC
1 ATATACAGTGGTCATTCGGGAC
14077 A
1 A
14078 AATATTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 14 0.42
20 4 0.12
22 15 0.45
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (22 bp):
ATATACAGTGGTCATTCGGGAC
Found at i:19274 original size:22 final size:22
Alignment explanation
Indices: 19246--19292 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
19236 ATGATTATGA
*
19246 CATGATTTCATCTCATATTTTT
1 CATGATTTCATCTCATACTTTT
*
19268 CATGATTTCATCTCATGCTTTT
1 CATGATTTCATCTCATACTTTT
19290 CAT
1 CAT
19293 TCTTTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.51
Consensus pattern (22 bp):
CATGATTTCATCTCATACTTTT
Found at i:20739 original size:20 final size:20
Alignment explanation
Indices: 20711--20751 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20701 TAACAGATTG
*
20711 CCCAAAGGGTACCGATACCC
1 CCCAAAGGGAACCGATACCC
*
20731 CCCAGAGGGAACCGATACCC
1 CCCAAAGGGAACCGATACCC
20751 C
1 C
20752 TATGTAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.41, G:0.22, T:0.07
Consensus pattern (20 bp):
CCCAAAGGGAACCGATACCC
Found at i:25444 original size:23 final size:22
Alignment explanation
Indices: 25412--25472 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
25402 TCTAGTGCTA
* *
25412 GGTATCGATACCCCCTTTGAATG
1 GGTACCGATACCCCC-TTAAATG
* *
25435 GGTACTGATACCCTCCTTAAATT
1 GGTACCGATACCC-CCTTAAATG
25458 GGTACCGATACCCCC
1 GGTACCGATACCCCC
25473 CACGTGAGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 2 0.06
23 28 0.88
24 2 0.06
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (22 bp):
GGTACCGATACCCCCTTAAATG
Found at i:27459 original size:16 final size:16
Alignment explanation
Indices: 27438--27474 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
27428 ATTTTGGATG
27438 TTTGTGAATGCTTGAA
1 TTTGTGAATGCTTGAA
* *
27454 TTTGTGGATGTTTGAA
1 TTTGTGAATGCTTGAA
27470 TTTGT
1 TTTGT
27475 TTTGGATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.27, T:0.51
Consensus pattern (16 bp):
TTTGTGAATGCTTGAA
Found at i:29034 original size:2 final size:2
Alignment explanation
Indices: 29029--29054 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29019 TCTCTCTCTC
29029 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
29055 GAGAGAGAGA
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):
TA
Found at i:30825 original size:22 final size:22
Alignment explanation
Indices: 30799--30849 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
30789 CCAGAATATT
30799 ACTTTAACTATTAAATAATTAC
1 ACTTTAACTATTAAATAATTAC
30821 ACTTTAACTATTAAATAATTAC
1 ACTTTAACTATTAAATAATTAC
30843 ACTTTAA
1 ACTTTAA
30850 TCCTCATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (22 bp):
ACTTTAACTATTAAATAATTAC
Found at i:33867 original size:2 final size:2
Alignment explanation
Indices: 33860--33916 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
33850 CTATTTTTAC
33860 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
*
33902 AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT A
33917 ACATTTTTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41628 original size:11 final size:11
Alignment explanation
Indices: 41612--41636 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41602 GAACTTTTGA
41612 TTCCACGGTGG
1 TTCCACGGTGG
41623 TTCCACGGTGG
1 TTCCACGGTGG
41634 TTC
1 TTC
41637 GGCAGCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.32, T:0.32
Consensus pattern (11 bp):
TTCCACGGTGG
Found at i:42306 original size:3 final size:3
Alignment explanation
Indices: 42298--42389 Score: 103
Period size: 3 Copynumber: 30.0 Consensus size: 3
42288 ATTTATTAAG
* * *
42298 TAA TAA TAA TATA TAA TAT TAA TAT TAA TAAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * **
42345 TAA TGA TAA TAA TAC TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42390 ATTTAAATGA
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
3 67 0.92
4 6 0.08
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:42676 original size:76 final size:76
Alignment explanation
Indices: 42520--42695 Score: 291
Period size: 76 Copynumber: 2.3 Consensus size: 76
42510 GAAATGTTGA
*
42520 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
42585 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
42597 AAACATCATACACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTG-AAAACATCAAAAAGCTCCCG
42661 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
42673 AAACATCATGCACTGCAGGACTT
1 AAACATCATGCACTGAAGGACTT
42696 TGAAAACATC
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
75 4 0.04
76 53 0.57
77 36 0.39
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:42680 original size:31 final size:31
Alignment explanation
Indices: 42642--42734 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 31
42632 AAGGTTTGAA
42642 AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
1 AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
* * * * *
42673 AAACATC---ATGC-ACTGCAGGAC--TTTGA
1 AAACATCAAAAAGCTCCCGAAGG-CTTTTTGG
42699 AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
1 AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
42730 AAACA
1 AAACA
42735 GCATGCACTG
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
26 11 0.24
27 5 0.11
28 4 0.09
29 4 0.09
30 5 0.11
31 16 0.36
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (31 bp):
AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:42725 original size:57 final size:58
Alignment explanation
Indices: 42636--42752 Score: 209
Period size: 57 Copynumber: 2.0 Consensus size: 58
42626 GACCCGAAGG
*
42636 TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGAC
1 TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGCAGGAC
*
42694 TTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGTAGGAC
1 TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGCAGGAC
42751 TT
1 TT
42753 ACAGATGACC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 53 0.93
58 4 0.07
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (58 bp):
TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGCAGGAC
Found at i:42799 original size:133 final size:133
Alignment explanation
Indices: 42561--42828 Score: 484
Period size: 133 Copynumber: 2.0 Consensus size: 133
42551 CCCGAAGGTT
*
42561 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATACACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATACACTGTAGGACTTACAGAT
42626 GACCCGAAGGTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
66 GACCCGAAGGTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
42691 GAC
131 GAC
*
42694 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATACACTGTAGGACTTACAGAT
* *
42759 GACCCTAAGGCTTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTA
66 GACCCGAAGG-TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCA
42823 GGAC
130 GGAC
42827 TT
1 TT
42829 ACAGATGACC
Statistics
Matches: 130, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
133 126 0.97
134 4 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (133 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATACACTGTAGGACTTACAGAT
GACCCGAAGGTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
GAC
Found at i:43320 original size:76 final size:76
Alignment explanation
Indices: 42693--43293 Score: 1033
Period size: 76 Copynumber: 7.9 Consensus size: 76
42683 CACTGCAGGA
*
42693 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGTAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
42758 TGACCCTAAGG
66 TGACCCTAAGG
42769 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
*
42834 TGACCCGAAGG
66 TGACCCTAAGG
* *
42845 -TTTGAAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
1 CTTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAG
42909 ATGACCCTAAGG
65 ATGACCCTAAGG
*
42921 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTATAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
42986 TGACCCTAAGG
66 TGACCCTAAGG
*
42997 CTTTGAAAACATCAAAAAGCTCCCGAAGGCATTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
*
43062 TGACCCGAAGG
66 TGACCCTAAGG
* * *
43073 TTTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
1 -CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAG
*
43138 ATGACCCGAAGG
65 ATGACCCTAAGG
* * * *
43150 TTTTTGAAAACATTAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
1 -CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAG
43215 ATGACCCTAAGG
65 ATGACCCTAAGG
43227 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
43292 TG
66 TG
43294 TGGGAAATAG
Statistics
Matches: 501, Mismatches: 21, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
75 4 0.01
76 346 0.69
77 151 0.30
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
TGACCCTAAGG
Found at i:43546 original size:185 final size:185
Alignment explanation
Indices: 43234--43608 Score: 714
Period size: 185 Copynumber: 2.0 Consensus size: 185
43224 AGGCTTTGAA
*
43234 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAATGTGGGA
*
43299 AATAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
66 AAGAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
* *
43364 AAAGGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAGTAAC
131 AAAAGATTGAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAGTAAC
43419 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAATGTGGGA
43484 AAGAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
66 AAGAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
43549 AAAAGATTGAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAGTAAC
131 AAAAGATTGAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAGTAAC
43604 AACAT
1 AACAT
43609 GTTGATTGGG
Statistics
Matches: 186, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
185 186 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (185 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAAATGTGGGA
AAGAGTTTACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAG
AAAAGATTGAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAGTAAC
Found at i:44185 original size:22 final size:22
Alignment explanation
Indices: 44160--44232 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
44150 TAAAGCTTTT
* *
44160 ATCTTTGAAAAGTGAATCTATC
1 ATCTTTAAAAAGAGAATCTATC
* * *
44182 ATCTTTAAAAAAAAGAACCTATT
1 ATCTTT-AAAAAGAGAATCTATC
44205 ATCTTTAAAAAGAGAATCTATC
1 ATCTTTAAAAAGAGAATCTATC
44227 ATCTTT
1 ATCTTT
44233 GAAGAGTGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 25 0.60
23 17 0.40
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (22 bp):
ATCTTTAAAAAGAGAATCTATC
Found at i:46942 original size:114 final size:114
Alignment explanation
Indices: 46737--47076 Score: 581
Period size: 114 Copynumber: 3.0 Consensus size: 114
46727 GATCATGCAG
* * * * * *
46737 TTCATCTTTTAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
46802 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
46851 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
46916 ACACTTTCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGTAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
46965 TTTATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
47030 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
47077 CATGGCACTT
Statistics
Matches: 213, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 213 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:49679 original size:2 final size:2
Alignment explanation
Indices: 49672--49701 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49662 ACAACAAAGG
49672 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
49702 TAAAGGATAA
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:54674 original size:11 final size:11
Alignment explanation
Indices: 54658--54682 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54648 GAACTTTTGA
54658 TTCCACGGTGG
1 TTCCACGGTGG
54669 TTCCACGGTGG
1 TTCCACGGTGG
54680 TTC
1 TTC
54683 GGCAGCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.32, T:0.32
Consensus pattern (11 bp):
TTCCACGGTGG
Found at i:55352 original size:3 final size:3
Alignment explanation
Indices: 55344--55429 Score: 100
Period size: 3 Copynumber: 28.0 Consensus size: 3
55334 ATTTATTAAG
* * *
55344 TAA TAA TAA TATA TAA TAT TAA TAT TAA TAAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* **
55391 TAA TAA TAA TAC TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55430 ATTTAAATGA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
3 63 0.91
4 6 0.09
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:55428 original size:15 final size:15
Alignment explanation
Indices: 55339--55435 Score: 72
Period size: 15 Copynumber: 6.3 Consensus size: 15
55329 TAATTATTTA
55339 TTAAGTAATAATAA-T
1 TTAA-TAATAATAATT
* * *
55354 AT-ATAATATTAATA
1 TTAATAATAATAATT
55368 TTAATAAATAATAATGAT
1 TTAAT-AATAATAAT--T
* *
55386 AATAATAATAATAATA
1 -TTAATAATAATAATT
*
55402 CTAATAATAATAATT
1 TTAATAATAATAATT
*
55417 TTAATAATAATAAAT
1 TTAATAATAATAATT
55432 TTAA
1 TTAA
55436 ATGAAAAAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
13 8 0.12
14 2 0.03
15 33 0.52
16 8 0.12
18 9 0.14
19 4 0.06
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (15 bp):
TTAATAATAATAATT
Found at i:55716 original size:76 final size:76
Alignment explanation
Indices: 55560--55735 Score: 291
Period size: 76 Copynumber: 2.3 Consensus size: 76
55550 GAAATGTTGA
*
55560 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCG
55625 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* *
55637 AAACATCATACACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTG-AAAACATCAAAAAGCTCCCG
55701 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
55713 AAACATCATGCACTGCAGGACTT
1 AAACATCATGCACTGAAGGACTT
55736 TGAAAACATC
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
75 4 0.04
76 53 0.57
77 36 0.39
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:55720 original size:31 final size:31
Alignment explanation
Indices: 55682--55774 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 31
55672 AAGGTTTGAA
55682 AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
1 AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
* * * * *
55713 AAACATC---ATGC-ACTGCAGGAC--TTTGA
1 AAACATCAAAAAGCTCCCGAAGG-CTTTTTGG
55739 AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
1 AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
55770 AAACA
1 AAACA
55775 GCATGCACTG
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
26 11 0.24
27 5 0.11
28 4 0.09
29 4 0.09
30 5 0.11
31 16 0.36
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (31 bp):
AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:55765 original size:57 final size:58
Alignment explanation
Indices: 55676--55792 Score: 209
Period size: 57 Copynumber: 2.0 Consensus size: 58
55666 GACCCGAAGG
*
55676 TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGAC
1 TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGCAGGAC
*
55734 TTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGTAGGAC
1 TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGCAGGAC
55791 TT
1 TT
55793 ACAGATGACC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 53 0.93
58 4 0.07
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (58 bp):
TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGCAGGAC
Found at i:55839 original size:133 final size:133
Alignment explanation
Indices: 55601--55868 Score: 475
Period size: 133 Copynumber: 2.0 Consensus size: 133
55591 CCCGAAGGTT
*
55601 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATACACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATACACTGTAGGACTTACAGAT
*
55666 GACCCGAAGGTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
66 GACCCGAAGGTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAG
55731 GAC
131 GAC
*
55734 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGTAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATACACTGTAGGACTTACAGAT
* *
55799 GACCCTAAGGCTTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTATA
66 GACCCGAAGG-TTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACA
55863 GGAC
130 GGAC
55867 TT
1 TT
55869 ACAGATGACC
Statistics
Matches: 129, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
133 125 0.97
134 4 0.03
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (133 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATACACTGTAGGACTTACAGAT
GACCCGAAGGTTTGAAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAG
GAC
Found at i:56360 original size:76 final size:76
Alignment explanation
Indices: 55733--56333 Score: 1024
Period size: 76 Copynumber: 7.9 Consensus size: 76
55723 CACTGCAGGA
*
55733 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACAGCATGCACTGTAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
55798 TGACCCTAAGG
66 TGACCCTAAGG
*
55809 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
*
55874 TGACCCGAAGG
66 TGACCCTAAGG
* *
55885 -TTTGAAAAACATCAAAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
1 CTTTG-AAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAG
55949 ATGACCCTAAGG
65 ATGACCCTAAGG
*
55961 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTATAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
56026 TGACCCTAAGG
66 TGACCCTAAGG
56037 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
*
56102 TGACCCGAAGG
66 TGACCCTAAGG
* * * *
56113 TTTTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCGTGCACTGCAGGACTTACAG
1 -CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAG
*
56178 ATGACCCGAAGG
65 ATGACCCTAAGG
* * * *
56190 TTTTTGAAAACATTAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAG
1 -CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAG
56255 ATGACCCTAAGG
65 ATGACCCTAAGG
56267 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
1 CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
56332 TG
66 TG
56334 TGGGAAATAG
Statistics
Matches: 499, Mismatches: 23, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
75 4 0.01
76 345 0.69
77 150 0.30
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
CTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGA
TGACCCTAAGG
Found at i:56627 original size:185 final size:186
Alignment explanation
Indices: 56274--56649 Score: 718
Period size: 185 Copynumber: 2.0 Consensus size: 186
56264 AGGCTTTGAA
56274 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
*
56339 AATAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
66 AAGAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
* *
56404 GAAAGGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAGTAAC
131 GAAAAGATTGAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAGTAAC
56460 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
56525 AAGAGTTTACTAAGT-AAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
66 AAGAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
56589 GAAAAGATTGAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAGTAAC
131 GAAAAGATTGAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAGTAAC
56645 AACAT
1 AACAT
56650 GTTGATTGGG
Statistics
Matches: 187, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
185 108 0.58
186 79 0.42
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Consensus pattern (186 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGA
AAGAGTTTACTAAGTAAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
GAAAAGATTGAATGAGAAACTATGGAAATCATTTTCTCATTATTTTTCAAAGTAAC
Found at i:57228 original size:22 final size:22
Alignment explanation
Indices: 57200--57274 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
57190 AATAAAGCTT
* *
57200 TCATCTTTGAAAAGTGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* *
57222 TCATCTTTAAAAAAAAGAACCTA
1 TCATCTTT-AAAAAGAGAATCTA
*
57245 TTATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
57267 TCATCTTT
1 TCATCTTT
57275 GAAGAGTGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 27 0.61
23 17 0.39
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:59982 original size:114 final size:114
Alignment explanation
Indices: 59777--60116 Score: 581
Period size: 114 Copynumber: 3.0 Consensus size: 114
59767 GATCATGCAG
* * * * * *
59777 TTCATCTTTTAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
59842 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
59891 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
59956 ACACTTTCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGTAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
60005 TTTATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
60070 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
60117 CATGGCACTT
Statistics
Matches: 213, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 213 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:68631 original size:11 final size:11
Alignment explanation
Indices: 68615--68639 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
68605 GAACTTTTGA
68615 TTCCACGGTGG
1 TTCCACGGTGG
68626 TTCCACGGTGG
1 TTCCACGGTGG
68637 TTC
1 TTC
68640 GGCAGCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.32, T:0.32
Consensus pattern (11 bp):
TTCCACGGTGG
Found at i:69309 original size:3 final size:3
Alignment explanation
Indices: 69301--69392 Score: 121
Period size: 3 Copynumber: 30.0 Consensus size: 3
69291 ATTTATTAAG
* *
69301 TAA TAA TAA TATA TAA TAT TAA TAT TAA TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* **
69348 TAA TAA TAA TAA TAC TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
69393 ATTTAAATGA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
3 71 0.92
4 6 0.08
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:72163 original size:18 final size:19
Alignment explanation
Indices: 72140--72185 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
72130 AATTTTGTAC
*
72140 CGATACTCATGG-GAGTAT
1 CGATACTCAGGGAGAGTAT
*
72158 CGATACCCAGGGTAGAGTAT
1 CGATACTCAGGG-AGAGTAT
72178 CGATACTC
1 CGATACTC
72186 CCCATAGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 10 0.43
20 13 0.57
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (19 bp):
CGATACTCAGGGAGAGTAT
Found at i:74328 original size:45 final size:46
Alignment explanation
Indices: 74259--74365 Score: 148
Period size: 45 Copynumber: 2.3 Consensus size: 46
74249 GGTGTACTAA
* * *
74259 GAGTGCATCGATGCATGAAGTGCATTTGATG-TTTCA-AAATAGCC-T
1 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CCTT
74304 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCTT
1 GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCTT
74350 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
74366 GGATAGTTCA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 30 0.54
46 23 0.41
47 3 0.05
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (46 bp):
GAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCTT
Found at i:78037 original size:17 final size:17
Alignment explanation
Indices: 78011--78046 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
78001 AGGTAAGCTC
*
78011 TACAAATGAGTATGCCT
1 TACAAATGAGCATGCCT
*
78028 TACAAGTGAGCATGCCT
1 TACAAATGAGCATGCCT
78045 TA
1 TA
78047 GGTAACACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (17 bp):
TACAAATGAGCATGCCT
Found at i:79128 original size:22 final size:22
Alignment explanation
Indices: 79103--79150 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
79093 TGACAATATT
*
79103 GTAATTTTAGGAAAGTACAAGG
1 GTAATTTTAGAAAAGTACAAGG
79125 GTAATTTTAGAAAAGTACAAGG
1 GTAATTTTAGAAAAGTACAAGG
79147 GTAA
1 GTAA
79151 AATTGGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.25, T:0.27
Consensus pattern (22 bp):
GTAATTTTAGAAAAGTACAAGG
Found at i:80426 original size:2 final size:2
Alignment explanation
Indices: 80419--80457 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
80409 CATTTTACCT
*
80419 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TGA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA T
80458 GAGGAAGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 29 0.88
3 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (2 bp):
TA
Found at i:80846 original size:24 final size:24
Alignment explanation
Indices: 80802--80847 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
80792 GATACATATT
*
80802 TGTACATTCTATGAGGTACATTCG
1 TGTACATTCTATGAGGCACATTCG
*
80826 TGTACATTTTAT-ATGGCACATT
1 TGTACATTCTATGA-GGCACATT
80848 TGGTGCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (24 bp):
TGTACATTCTATGAGGCACATTCG
Found at i:81129 original size:2 final size:2
Alignment explanation
Indices: 81109--81201 Score: 134
Period size: 2 Copynumber: 46.5 Consensus size: 2
81099 TTTACATGTT
* * *
81109 TA TA TA AA TA AA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
81151 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81193 -A TA TGA TA T
1 TA TA T-A TA T
81202 TTACCGTATT
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.01
2 78 0.96
3 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:84547 original size:21 final size:22
Alignment explanation
Indices: 84511--84557 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
84501 GTTTAGGATT
*
84511 TAGGGTTTAAGATTTA-ATTTA
1 TAGGGTTTAAGATTTAGAGTTA
* *
84532 TAGGGTTTAGGGTTTAGAGTTA
1 TAGGGTTTAAGATTTAGAGTTA
84554 TAGG
1 TAGG
84558 ATTTGATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.43
Consensus pattern (22 bp):
TAGGGTTTAAGATTTAGAGTTA
Found at i:85165 original size:2 final size:2
Alignment explanation
Indices: 85158--85226 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
85148 CCAAACAAAG
85158 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
85200 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 A
85227 AAAGTATGCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:86397 original size:2 final size:2
Alignment explanation
Indices: 86390--86420 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
86380 TAAAAATACA
86390 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
86421 ATTTAAAATT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92334 original size:106 final size:106
Alignment explanation
Indices: 92149--93027 Score: 1616
Period size: 106 Copynumber: 8.3 Consensus size: 106
92139 CTGAAATTGG
* * * * *
92149 ATATCTTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
* *
92214 TCCCTTCGTCGTGAAGTTAAACTTTCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
92255 ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
92320 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
92361 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
92425 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
92466 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
92531 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
92572 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
92637 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
92678 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
92743 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
92784 ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
*
92849 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
92890 ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
92955 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
92996 ATATCATTCGTTGTGAAGTTGAAATTGGCTCT
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
93028 AAAGGCTGTA
Statistics
Matches: 754, Mismatches: 18, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
105 103 0.14
106 651 0.86
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
Found at i:106467 original size:12 final size:12
Alignment explanation
Indices: 106450--106477 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
106440 GCCATTAATA
106450 AATTAAATTTAT
1 AATTAAATTTAT
106462 AATTAAATTTAT
1 AATTAAATTTAT
106474 AATT
1 AATT
106478 TATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAAATTTAT
Found at i:106744 original size:48 final size:50
Alignment explanation
Indices: 106683--106808 Score: 132
Period size: 48 Copynumber: 2.6 Consensus size: 50
106673 ATGTACATAA
*
106683 TTACATCAATGTAAGTATGTGTTAAGTGCTACA-CTTTT-TTTTATTCAC
1 TTACACCAATGTAAGTATGTGTTAAGTGCTACATCTTTTATTTTATTCAC
* * * * * *
106731 TTACACCATTGTAAGTGTGTATTAAGTGTTATATTTTTTTATTTTATTCAC
1 TTACACCAATGTAAGTATGTGTTAAGTGCTACA-TCTTTTATTTTATTCAC
** *
106782 TTACACCGGTGT-TGTATGTGTTAAGTG
1 TTACACCAATGTAAGTATGTGTTAAGTG
106809 TTACTGTCGA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 27 0.43
50 16 0.25
51 20 0.32
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.48
Consensus pattern (50 bp):
TTACACCAATGTAAGTATGTGTTAAGTGCTACATCTTTTATTTTATTCAC
Found at i:106990 original size:15 final size:16
Alignment explanation
Indices: 106970--107002 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
106960 TACCTTTTAA
106970 AATAA-TTTAAAAAAT
1 AATAATTTTAAAAAAT
*
106985 AATAATTTTAAAAGAT
1 AATAATTTTAAAAAAT
107001 AA
1 AA
107003 AAAAATGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AATAATTTTAAAAAAT
Found at i:109017 original size:3 final size:3
Alignment explanation
Indices: 109004--109053 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
108994 AAACAAAAAT
*
109004 ATA ATA A-A ATA AT- ATA A-A ATA ATA ATA ATA ATTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
109047 ATA ATA A
1 ATA ATA A
109054 AATTAGCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:109019 original size:13 final size:15
Alignment explanation
Indices: 109004--109053 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 15
108994 AAACAAAAAT
109004 ATAATAA-AATAAT-
1 ATAATAATAATAATA
109017 ATAA-AATAATAATA
1 ATAATAATAATAATA
*
109031 ATAATTAATATTAATA
1 ATAA-TAATAATAATA
109047 ATAATAA
1 ATAATAA
109054 AATTAGCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 2 0.06
13 10 0.31
14 4 0.12
15 3 0.09
16 13 0.41
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAATAATAATAATA
Found at i:112358 original size:13 final size:14
Alignment explanation
Indices: 112340--112370 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
112330 AATTTTGGAA
112340 AAAAGG-AAATTTG
1 AAAAGGAAAATTTG
112353 AAAAGGAAAATTTG
1 AAAAGGAAAATTTG
112367 AAAA
1 AAAA
112371 ATTATGGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.19
Consensus pattern (14 bp):
AAAAGGAAAATTTG
Found at i:112441 original size:27 final size:28
Alignment explanation
Indices: 112409--112508 Score: 96
Period size: 29 Copynumber: 3.6 Consensus size: 28
112399 CGGGGAAAAA
* *
112409 GAAATTTTACACAA-TAATTCTGAAACAT
1 GAAATTTTA-AAAATTAATTCTGAAACAG
*
112437 G-AATTTTAAAAATTAATTCTTAAACAG
1 GAAATTTTAAAAATTAATTCTGAAACAG
* * ** *
112464 GAAATTTTAAAAGCTAAATTCCAAAATAG
1 GAAATTTTAAAA-ATTAATTCTGAAACAG
112493 GAAATTTTAAAAATTA
1 GAAATTTTAAAAATTA
112509 TTTTTTACTG
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
26 3 0.05
27 20 0.34
28 13 0.22
29 23 0.39
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (28 bp):
GAAATTTTAAAAATTAATTCTGAAACAG
Found at i:112647 original size:27 final size:27
Alignment explanation
Indices: 112591--112681 Score: 114
Period size: 28 Copynumber: 3.3 Consensus size: 27
112581 AACTGAATAA
* *
112591 AAAAATTAATTCCGAAACATGAATTCTT
1 AAAAATTAATTACGAAACA-GGATTCTT
112619 AAAAATTAACTT-CGAAACAGGCATT-TT
1 AAAAATTAA-TTACGAAACAGG-ATTCTT
112646 AAAAATTAATTACGAAACAGGATATCTT
1 AAAAATTAATTACGAAACAGGAT-TCTT
112674 AAAAATTA
1 AAAAATTA
112682 TTTCCGAAGT
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
26 4 0.07
27 22 0.39
28 29 0.51
29 2 0.04
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (27 bp):
AAAAATTAATTACGAAACAGGATTCTT
Found at i:115447 original size:24 final size:24
Alignment explanation
Indices: 115420--115479 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
115410 TTTCACTTAA
*
115420 TGGAGCAGGCGTTGCACGCATTGT
1 TGGAGCATGCGTTGCACGCATTGT
* * *
115444 TGGAGCATGTGTTGTATGCATTGT
1 TGGAGCATGCGTTGCACGCATTGT
115468 TGGAGCATGCGT
1 TGGAGCATGCGT
115480 CGTTGGAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.17, C:0.15, G:0.37, T:0.32
Consensus pattern (24 bp):
TGGAGCATGCGTTGCACGCATTGT
Found at i:117930 original size:16 final size:14
Alignment explanation
Indices: 117894--117922 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
117884 CTATCAATAT
117894 TCTTATAATTTATA
1 TCTTATAATTTATA
117908 TCTTATAA-TTATA
1 TCTTATAATTTATA
117921 TC
1 TC
117923 CTCTTATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTTATAATTTATA
Found at i:120049 original size:31 final size:31
Alignment explanation
Indices: 120011--120135 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
120001 CCCGAAGGAC
* *
120011 CAGTCCATA-GATTCCGAAGAACATAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
120042 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
120073 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
120104 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
120135 C
1 C
120136 CCTCGACCCT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:120963 original size:21 final size:21
Alignment explanation
Indices: 120939--120983 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
120929 TGTTGTTCGT
* *
120939 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
120960 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
120981 TTG
1 TTG
120984 CCCAAAAATC
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:132804 original size:22 final size:22
Alignment explanation
Indices: 132776--132839 Score: 119
Period size: 22 Copynumber: 2.9 Consensus size: 22
132766 TCGAGGGTTA
*
132776 CATAGGTCATTCGGGACATATG
1 CATAGGTCCTTCGGGACATATG
132798 CATAGGTCCTTCGGGACATATG
1 CATAGGTCCTTCGGGACATATG
132820 CATAGGTCCTTCGGGACATA
1 CATAGGTCCTTCGGGACATA
132840 GATTTTACAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (22 bp):
CATAGGTCCTTCGGGACATATG
Found at i:137928 original size:81 final size:81
Alignment explanation
Indices: 137775--137935 Score: 184
Period size: 81 Copynumber: 2.0 Consensus size: 81
137765 AAAAATTCCT
** * * *
137775 TTATTCTCTTACTCAAGAGTGTTTAACGTTCGTCTAACTAGCATAATTGACAATTTTTTTTCCAA
1 TTATTCTCTTACTCAAGAGTACTTAACGTTCATCTAACTAGCATAATTGACAATTTTCTGTCCAA
*
137840 ATGCACAGCTAGGCCA
66 ATACACAGCTAGGCCA
* *
137856 TTATTCTTTTACTCAACG-GTACTTAACCGTTCATCTAACTGGCATAATTGACACA-TTTCTGT-
1 TTATTCTCTTACTCAA-GAGTACTTAA-CGTTCATCTAACTAGCATAATTGACA-ATTTTCTGTC
* *
137918 CATATACACAGTTAGGCC
63 CAAATACACAGCTAGGCC
137936 TCAAGATCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
81 36 0.54
82 30 0.45
83 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (81 bp):
TTATTCTCTTACTCAAGAGTACTTAACGTTCATCTAACTAGCATAATTGACAATTTTCTGTCCAA
ATACACAGCTAGGCCA
Found at i:138518 original size:45 final size:45
Alignment explanation
Indices: 138453--138768 Score: 321
Period size: 45 Copynumber: 7.0 Consensus size: 45
138443 CACTTTAAAT
* * * * * *
138453 TATAACAT-CTTTTCTATTGATAATGCATCCATTTGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* *
138497 TATAGAATACTTTTTTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * * *
138542 CATAGTATA-TCGTTATGTTGATAATGTACCCATAAACATTTCAAC
1 TATAGCATACT-TTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * * * * *
138587 TCTAGCATGCTCTTCTGCTGATAATGCACCCATTTGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * * * * *
138632 TCTAGCATACATTTATGTTGATAATGCATCAATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
** *
138677 CCTAGCATACTTTTCTGTTGATAATGTATCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* *
138722 CATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
138767 TA
1 TA
138769 CGATATCTTT
Statistics
Matches: 227, Mismatches: 42, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
44 7 0.03
45 219 0.96
46 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (45 bp):
TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
Found at i:138653 original size:135 final size:135
Alignment explanation
Indices: 138470--138768 Score: 368
Period size: 135 Copynumber: 2.2 Consensus size: 135
138460 TCTTTTCTAT
* * * * *
138470 TGATAATGCATCCATTTGCATTTCAACTATAGAATACTTTTTTGTTGATAATGTACCCATATACA
1 TGATAATGCACCCATTTGCATTTCAACTATAGAATACATTTATGTTGATAATGCACCAATATACA
* *
138535 TTTCAACCATAGTATA-TCGTTATGTTGATAATGTACCCATAAACATTTCAACTC-TAGCATGCT
66 TTTCAACCATAGCATACT-GTTATGTTGATAATGTACCCATAAACATTTCAAC-CATAGCATACT
138598 CTTCTGC
129 CTTCTGC
* * * *
138605 TGATAATGCACCCATTTGCATTTCAACTCTAGCATACATTTATGTTGATAATGCATCAATATGCA
1 TGATAATGCACCCATTTGCATTTCAACTATAGAATACATTTATGTTGATAATGCACCAATATACA
* * * * * * *
138670 TTTCAACCCTAGCATACTTTTCTGTTGATAATGTATCCATATACATTTCAACCATAGTATACTTT
66 TTTCAACCATAGCATACTGTTATGTTGATAATGTACCCATAAACATTTCAACCATAGCATACTCT
*
138735 TCTGT
131 TCTGC
* * *
138740 TGATAATGTACCCATATACATTTCAACTA
1 TGATAATGCACCCATTTGCATTTCAACTA
138769 CGATATCTTT
Statistics
Matches: 139, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
134 1 0.01
135 137 0.99
136 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.38
Consensus pattern (135 bp):
TGATAATGCACCCATTTGCATTTCAACTATAGAATACATTTATGTTGATAATGCACCAATATACA
TTTCAACCATAGCATACTGTTATGTTGATAATGTACCCATAAACATTTCAACCATAGCATACTCT
TCTGC
Found at i:138791 original size:45 final size:44
Alignment explanation
Indices: 138488--138805 Score: 135
Period size: 45 Copynumber: 7.1 Consensus size: 44
138478 CATCCATTTG
* * * ***
138488 CATTTCAACTATAGAATACTTTTTTGTTGATAATGTACCCATATA
1 CATTTCAACCATAGTATACTTTTCTGCCAATAATGTA-CCATATA
* * *** *
138533 CATTTCAACCATAGTATA-TCGTTATGTTGATAATGTACCCATAAA
1 CATTTCAACCATAGTATACT-TTTCTGCCAATAATGTA-CCATATA
* * * ** * * *
138578 CATTTCAACTC-TAGCATGCTCTTCTGCTGATAATGCACCCATTTG
1 CATTTCAAC-CATAGTATACTTTTCTGCCAATAATGTA-CCATATA
* * * *** * * *
138623 CATTTCAACTC-TAGCATACATTTATGTTGATAATGCATCAATATG
1 CATTTCAAC-CATAGTATACTTTTCTGCCAATAATGTA-CCATATA
* * ***
138668 CATTTCAACCCTAGCATACTTTTCTGTTGATAATGTATCCATATA
1 CATTTCAACCATAGTATACTTTTCTGCCAATAATGTA-CCATATA
***
138713 CATTTCAACCATAGTATACTTTTCTGTTGATAATGTACCCATATA
1 CATTTCAACCATAGTATACTTTTCTGCCAATAATGTA-CCATATA
* *
138758 CATTTCAA-C-TACG-ATATCTTTTCATGCCAATAATGCACCATATG
1 CATTTCAACCATA-GTATA-CTTTTC-TGCCAATAATGTACCATATA
138802 CATT
1 CATT
138806 AGTATTTTTC
Statistics
Matches: 231, Mismatches: 35, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
43 5 0.02
44 20 0.09
45 204 0.88
46 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (44 bp):
CATTTCAACCATAGTATACTTTTCTGCCAATAATGTACCATATA
Found at i:138791 original size:90 final size:89
Alignment explanation
Indices: 138469--138805 Score: 283
Period size: 90 Copynumber: 3.8 Consensus size: 89
138459 ATCTTTTCTA
* * * * * * * *
138469 TTGATAATGCATCCATTTGCATTTCAACTATAGA-ATACTTTTTTGTTGATAATGTACCCATATA
1 TTGATAATGTACCCATATACATTTCAACTA-CGATAT-CTTTTCTGCTGATAATGCACCCATATA
*
138533 CATTTCAACCATAGTATA-TCGTTATG
64 CATTTCAACCATAGTATACT-TTTATG
* * * * * *
138559 TTGATAATGTACCCATAAACATTTCAACT-CTAGCATGCTCTTCTGCTGATAATGCACCCATTTG
1 TTGATAATGTACCCATATACATTTCAACTACGA-TAT-CTTTTCTGCTGATAATGCACCCATATA
* *
138623 CATTTCAACTC-TAGCATACATTTATG
64 CATTTCAAC-CATAGTATACTTTTATG
* * * * * * *
138649 TTGATAATGCATCAATATGCATTTCAACCCTA-GCATA-CTTTTCTGTTGATAATGTATCCATAT
1 TTGATAATGTACCCATATACATTTCAA--CTACG-ATATCTTTTCTGCTGATAATGCACCCATAT
*
138712 ACATTTCAACCATAGTATACTTTTCTG
63 ACATTTCAACCATAGTATACTTTTATG
** *
138739 TTGATAATGTACCCATATACATTTCAACTACGATATCTTTTCATGCCAATAATGCA-CCATATGC
1 TTGATAATGTACCCATATACATTTCAACTACGATATCTTTTC-TGCTGATAATGCACCCATATAC
138803 ATT
65 ATT
138806 AGTATTTTTC
Statistics
Matches: 193, Mismatches: 42, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
88 7 0.04
89 18 0.09
90 163 0.84
91 1 0.01
92 3 0.02
93 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (89 bp):
TTGATAATGTACCCATATACATTTCAACTACGATATCTTTTCTGCTGATAATGCACCCATATACA
TTTCAACCATAGTATACTTTTATG
Found at i:138791 original size:135 final size:133
Alignment explanation
Indices: 138557--138805 Score: 297
Period size: 135 Copynumber: 1.8 Consensus size: 133
138547 TATATCGTTA
* *
138557 TGTTGATAATGTACCCATAAACATTTCAACTCTAGCATGCTCTTCTGCTGATAATGCACCCATTT
1 TGTTGATAATGTACCCATAAACATTTCAACTCTAGCATACTCTTCTGCTGATAATGCACCCATAT
* ***
138622 GCATTTCAACTCTAGCATACATTTATGTTGATAATGCATCAATATGCATTTCAACCCTAGCATAC
66 ACATTTCAACTC-AGCATACATTTATGCCAATAATGCA-CAATATGCATTTCAACCCTAGCATAC
138687 TTTTC
129 TTTTC
* * * * * *
138692 TGTTGATAATGTATCCATATACATTTCAAC-CATAGTATACTTTTCTGTTGATAATGTACCCATA
1 TGTTGATAATGTACCCATAAACATTTCAACTC-TAGCATACTCTTCTGCTGATAATGCACCCATA
* *
138756 TACATTTCAACT-A-CGATATCTTTTCATGCCAATAATGCACCATATGCATT
65 TACATTTCAACTCAGC-ATA-CATTT-ATGCCAATAATGCACAATATGCATT
138806 AGTATTTTTC
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
132 1 0.01
133 4 0.04
134 15 0.16
135 76 0.79
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.37
Consensus pattern (133 bp):
TGTTGATAATGTACCCATAAACATTTCAACTCTAGCATACTCTTCTGCTGATAATGCACCCATAT
ACATTTCAACTCAGCATACATTTATGCCAATAATGCACAATATGCATTTCAACCCTAGCATACTT
TTC
Found at i:144028 original size:45 final size:45
Alignment explanation
Indices: 143965--144318 Score: 383
Period size: 45 Copynumber: 7.9 Consensus size: 45
143955 CACTTTACAT
* **
143965 TATAACAT-CTTTTCTGTTGATAATGCACCCATATGGATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
** *
144009 TATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* *
144054 CATAGTATA-TTATTCTGTTGATAATGCACCCATATACATTTCAAC
1 TATAGCATACTT-TTCTGTTGATAATGCACCCATATACATTTCAAC
* * * *
144099 TCTAGCATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* * *
144144 TCTAGCATACATTTCTGTTGATAATGCACCCATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* * *
144189 TCTAGCATACTTTTCTATTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* * * * * *
144234 TATAGTATACATTTT-TGTTGATAATGTACTCATATAAATTACAAT
1 TATAGCATAC-TTTTCTGTTGATAATGCACCCATATACATTTCAAC
** * * * *
144279 TACGGCAT-CCTTTCATGCTAATAATGCACCCATATGCATT
1 TATAGCATACTTTTC-TGTTGATAATGCACCCATATACATT
144319 AGTATTTTCA
Statistics
Matches: 267, Mismatches: 37, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
43 3 0.01
44 10 0.04
45 249 0.93
46 5 0.02
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (45 bp):
TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
Found at i:144878 original size:96 final size:95
Alignment explanation
Indices: 144747--144939 Score: 255
Period size: 96 Copynumber: 2.0 Consensus size: 95
144737 ACCGATACTT
* * * *
144747 CTATACTACGGTACCAATACCCCCTTTAGGTATCGATACCAAAAATAGGTTCGATGTT-GCATGG
1 CTATACTACGATACCAATACCCCCTATAGGTATCGATACCAAAAATAGATTCGATGTTAGCA-AG
* * *
144811 TATCGATACCCTTACCGTAGGTATCAATACCA
65 TATCGATACCATCACCAT-GGTATCAATACCA
* * *
144843 CTATACTATGATACCAATA-CCCCTATATGGTATCGATACCAAAATTAGATTCGATGTTATCAAG
1 CTATACTACGATACCAATACCCCCTATA-GGTATCGATACCAAAAATAGATTCGATGTTAGCAAG
144907 TATCGATACCATCACCATGGTATCAATACCA
65 TATCGATACCATCACCATGGTATCAATACCA
144938 CT
1 CT
144940 TCATTAGGTA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
95 22 0.26
96 61 0.72
97 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (95 bp):
CTATACTACGATACCAATACCCCCTATAGGTATCGATACCAAAAATAGATTCGATGTTAGCAAGT
ATCGATACCATCACCATGGTATCAATACCA
Found at i:150085 original size:45 final size:45
Alignment explanation
Indices: 149868--150124 Score: 336
Period size: 45 Copynumber: 5.7 Consensus size: 45
149858 AATTTAACAT
* * *
149868 CTTTTCTGTTGATAATACACCCATATGCATTTCAAATATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * *
149913 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAATATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * **
149958 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTCTAACATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
150003 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * *
150048 CTTTTTTGTTGATAATGCACCCATATGCATTTCAACTCTGGCAT-
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* ***
150092 CCTTTCATGCCAATAATGCACCCATATGCATTT
1 CTTTTC-TGTTGATAATGCACCCATATGCATTT
150125 TTCTATTATG
Statistics
Matches: 192, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 4 0.02
45 188 0.98
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:150189 original size:79 final size:79
Alignment explanation
Indices: 150058--150291 Score: 342
Period size: 79 Copynumber: 3.0 Consensus size: 79
150048 CTTTTTTGTT
* * * * ** *
150058 GATAATGCACCCATATGCATTTCAACTCTGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
* *
150123 TTTTCTATTATGCC
66 TATTCTTTTATGCC
* *
150137 GATAATGTACCTATATACATATCATCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
150202 TATTCTTTTATGCC
66 TATTCTTTTATGCC
* **
150216 GATAATGTACCCATATACATATCAGCTAAAGCATAATTTCATGCCACTAATGCACCCATATGCAT
1 GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
150281 TATTCTTTTAT
66 TATTCTTTTAT
150292 TCATTAGTTT
Statistics
Matches: 140, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 140 1.00
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (79 bp):
GATAATGTACCCATATACATATCAGCTAAGGCATCCTTTCATGCCACTAATGCACCCATATGCAT
TATTCTTTTATGCC
Done.